Multiple sequence alignment - TraesCS5D01G167200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G167200 chr5D 100.000 9249 0 0 1 9249 260681474 260672226 0.000000e+00 17080.0
1 TraesCS5D01G167200 chr5D 84.785 1814 156 31 3173 4938 458662697 458664438 0.000000e+00 1711.0
2 TraesCS5D01G167200 chr5D 88.358 1005 77 20 4065 5042 243875255 243876246 0.000000e+00 1171.0
3 TraesCS5D01G167200 chr5D 86.431 678 62 11 3172 3847 445301423 445300774 0.000000e+00 715.0
4 TraesCS5D01G167200 chr5D 87.716 578 39 11 3220 3796 243874715 243875261 0.000000e+00 645.0
5 TraesCS5D01G167200 chr5D 78.657 998 97 57 4091 5037 57649530 57650462 2.920000e-154 556.0
6 TraesCS5D01G167200 chr5B 96.176 1595 30 5 1607 3172 293658662 293660254 0.000000e+00 2579.0
7 TraesCS5D01G167200 chr5B 94.637 1324 38 10 6435 7737 293663086 293664397 0.000000e+00 2021.0
8 TraesCS5D01G167200 chr5B 86.131 1543 142 22 3520 5027 40993964 40995469 0.000000e+00 1598.0
9 TraesCS5D01G167200 chr5B 95.844 770 14 5 841 1610 293657858 293658609 0.000000e+00 1229.0
10 TraesCS5D01G167200 chr5B 96.021 754 17 7 7750 8490 293664380 293665133 0.000000e+00 1214.0
11 TraesCS5D01G167200 chr5B 95.230 566 15 4 5885 6439 293660725 293661289 0.000000e+00 885.0
12 TraesCS5D01G167200 chr5B 98.330 479 8 0 5034 5512 293660252 293660730 0.000000e+00 841.0
13 TraesCS5D01G167200 chr5B 94.595 444 11 4 8812 9249 293665537 293665973 0.000000e+00 675.0
14 TraesCS5D01G167200 chr5B 97.523 323 7 1 8505 8827 293665199 293665520 1.360000e-152 551.0
15 TraesCS5D01G167200 chr5B 76.908 524 93 21 8557 9058 221703787 221703270 1.180000e-68 272.0
16 TraesCS5D01G167200 chr5B 100.000 50 0 0 6482 6531 202220711 202220662 9.890000e-15 93.5
17 TraesCS5D01G167200 chr7D 89.913 1844 107 28 3212 5034 251378012 251376227 0.000000e+00 2302.0
18 TraesCS5D01G167200 chr7D 82.054 1850 203 50 3215 5036 587916845 587915097 0.000000e+00 1458.0
19 TraesCS5D01G167200 chr7D 87.469 806 60 10 4249 5036 106390774 106391556 0.000000e+00 891.0
20 TraesCS5D01G167200 chr7D 88.432 657 70 6 159 812 82608417 82607764 0.000000e+00 787.0
21 TraesCS5D01G167200 chr7D 87.356 522 43 15 4463 4966 634074401 634074917 2.240000e-160 577.0
22 TraesCS5D01G167200 chr7D 93.388 121 7 1 6826 6946 475155279 475155398 2.650000e-40 178.0
23 TraesCS5D01G167200 chr7D 92.623 122 7 2 6826 6946 329100434 329100554 3.430000e-39 174.0
24 TraesCS5D01G167200 chr7D 91.803 122 9 1 6826 6947 6755679 6755559 1.600000e-37 169.0
25 TraesCS5D01G167200 chr2D 88.138 1880 130 33 3170 5036 39407536 39409335 0.000000e+00 2150.0
26 TraesCS5D01G167200 chr2D 83.486 1859 204 56 3229 5037 630678962 630677157 0.000000e+00 1637.0
27 TraesCS5D01G167200 chr2D 88.983 590 64 1 226 815 650950490 650949902 0.000000e+00 728.0
28 TraesCS5D01G167200 chr2D 80.952 609 93 10 8552 9141 364788340 364788944 2.350000e-125 460.0
29 TraesCS5D01G167200 chr2D 80.624 609 94 11 8552 9141 364660702 364661305 5.090000e-122 449.0
30 TraesCS5D01G167200 chr2D 86.869 396 43 8 5510 5900 7649364 7648973 1.430000e-117 435.0
31 TraesCS5D01G167200 chr2D 100.000 49 0 0 6480 6528 91206361 91206409 3.560000e-14 91.6
32 TraesCS5D01G167200 chr5A 94.437 1402 34 8 5885 7273 345350785 345349415 0.000000e+00 2117.0
33 TraesCS5D01G167200 chr5A 83.647 1596 161 59 3350 4886 286004845 286003291 0.000000e+00 1410.0
34 TraesCS5D01G167200 chr5A 95.986 872 20 5 2315 3172 345352489 345351619 0.000000e+00 1402.0
35 TraesCS5D01G167200 chr5A 87.015 1186 108 22 3883 5041 591431253 591432419 0.000000e+00 1295.0
36 TraesCS5D01G167200 chr5A 97.376 724 18 1 1607 2330 345353229 345352507 0.000000e+00 1230.0
37 TraesCS5D01G167200 chr5A 98.000 700 14 0 7750 8449 345348591 345347892 0.000000e+00 1216.0
38 TraesCS5D01G167200 chr5A 94.067 691 15 4 930 1613 345353950 345353279 0.000000e+00 1026.0
39 TraesCS5D01G167200 chr5A 96.178 471 8 3 7273 7737 345349040 345348574 0.000000e+00 761.0
40 TraesCS5D01G167200 chr5A 94.628 484 15 3 8540 9023 345347794 345347322 0.000000e+00 739.0
41 TraesCS5D01G167200 chr5A 85.783 626 53 14 4436 5034 414714964 414714348 1.690000e-176 630.0
42 TraesCS5D01G167200 chr5A 93.750 320 6 1 5193 5512 345351085 345350780 1.410000e-127 468.0
43 TraesCS5D01G167200 chr5A 96.257 187 7 0 9063 9249 345347322 345347136 3.240000e-79 307.0
44 TraesCS5D01G167200 chr5A 96.933 163 5 0 5034 5196 345351621 345351459 3.290000e-69 274.0
45 TraesCS5D01G167200 chr5A 77.551 196 39 5 7017 7209 362403332 362403525 7.590000e-21 113.0
46 TraesCS5D01G167200 chr1D 85.722 1912 130 60 3170 5037 458348188 458350000 0.000000e+00 1886.0
47 TraesCS5D01G167200 chr1D 86.534 1411 130 38 3662 5034 432034279 432032891 0.000000e+00 1498.0
48 TraesCS5D01G167200 chr1D 88.432 657 71 5 159 814 487022552 487023204 0.000000e+00 787.0
49 TraesCS5D01G167200 chr1D 86.850 654 82 4 159 810 106292456 106293107 0.000000e+00 728.0
50 TraesCS5D01G167200 chr1D 88.918 379 38 4 5512 5890 482241916 482241542 1.820000e-126 464.0
51 TraesCS5D01G167200 chr1D 87.565 386 34 11 5506 5890 10851652 10852024 1.430000e-117 435.0
52 TraesCS5D01G167200 chr1D 98.113 53 1 0 6479 6531 326476769 326476821 9.890000e-15 93.5
53 TraesCS5D01G167200 chr1D 100.000 49 0 0 6483 6531 69108753 69108705 3.560000e-14 91.6
54 TraesCS5D01G167200 chr1D 98.000 50 1 0 6479 6528 269365935 269365984 4.600000e-13 87.9
55 TraesCS5D01G167200 chr3A 85.167 1881 152 38 3170 5003 262519631 262521431 0.000000e+00 1810.0
56 TraesCS5D01G167200 chr6D 81.808 1814 232 55 3212 4983 285245460 285243703 0.000000e+00 1432.0
57 TraesCS5D01G167200 chr6D 87.371 388 33 8 5511 5891 82697430 82697052 1.850000e-116 431.0
58 TraesCS5D01G167200 chr6D 88.298 94 11 0 6583 6676 356733600 356733507 7.590000e-21 113.0
59 TraesCS5D01G167200 chr6D 100.000 49 0 0 6483 6531 249987209 249987161 3.560000e-14 91.6
60 TraesCS5D01G167200 chr6D 100.000 49 0 0 6483 6531 267532818 267532866 3.560000e-14 91.6
61 TraesCS5D01G167200 chr6D 100.000 49 0 0 6483 6531 269703810 269703858 3.560000e-14 91.6
62 TraesCS5D01G167200 chr6D 96.226 53 2 0 6479 6531 106030368 106030316 4.600000e-13 87.9
63 TraesCS5D01G167200 chr6D 90.909 66 4 2 6463 6528 126434196 126434259 4.600000e-13 87.9
64 TraesCS5D01G167200 chr6D 97.959 49 1 0 6483 6531 35699552 35699504 1.650000e-12 86.1
65 TraesCS5D01G167200 chr6D 97.959 49 1 0 6483 6531 39376959 39376911 1.650000e-12 86.1
66 TraesCS5D01G167200 chr6D 100.000 46 0 0 6483 6528 48673939 48673984 1.650000e-12 86.1
67 TraesCS5D01G167200 chr6D 100.000 46 0 0 6483 6528 50114933 50114978 1.650000e-12 86.1
68 TraesCS5D01G167200 chr6D 100.000 43 0 0 6483 6525 449230321 449230279 7.700000e-11 80.5
69 TraesCS5D01G167200 chr3D 82.578 1699 191 65 3382 5034 548819917 548818278 0.000000e+00 1400.0
70 TraesCS5D01G167200 chr3D 89.944 358 26 6 5511 5867 570108430 570108082 3.940000e-123 453.0
71 TraesCS5D01G167200 chr3D 93.333 120 7 1 6829 6947 475553675 475553556 9.550000e-40 176.0
72 TraesCS5D01G167200 chr2A 85.813 1297 140 14 3756 5034 43055186 43053916 0.000000e+00 1336.0
73 TraesCS5D01G167200 chr2A 89.691 388 31 6 5508 5892 1220696 1221077 3.880000e-133 486.0
74 TraesCS5D01G167200 chr2A 93.277 119 8 0 6829 6947 564613553 564613435 9.550000e-40 176.0
75 TraesCS5D01G167200 chr2A 92.437 119 9 0 6829 6947 528139699 528139581 4.440000e-38 171.0
76 TraesCS5D01G167200 chr7A 87.074 1145 103 26 3914 5036 457573642 457572521 0.000000e+00 1253.0
77 TraesCS5D01G167200 chr7A 86.056 710 67 14 3216 3924 457598924 457598246 0.000000e+00 734.0
78 TraesCS5D01G167200 chr7A 85.981 428 25 17 4635 5037 463015521 463015104 8.580000e-115 425.0
79 TraesCS5D01G167200 chr7A 100.000 50 0 0 6479 6528 17902476 17902525 9.890000e-15 93.5
80 TraesCS5D01G167200 chr7A 88.889 72 7 1 6460 6531 516977423 516977353 4.600000e-13 87.9
81 TraesCS5D01G167200 chr7B 83.071 1400 158 42 3699 5041 720343270 720341893 0.000000e+00 1199.0
82 TraesCS5D01G167200 chr7B 82.260 823 92 32 4250 5036 19278033 19277229 0.000000e+00 662.0
83 TraesCS5D01G167200 chr7B 87.918 389 41 5 5507 5892 742443209 742443594 3.940000e-123 453.0
84 TraesCS5D01G167200 chr7B 89.855 69 4 3 6461 6528 24405959 24406025 1.650000e-12 86.1
85 TraesCS5D01G167200 chr7B 90.769 65 5 1 6464 6528 266735199 266735262 1.650000e-12 86.1
86 TraesCS5D01G167200 chr7B 90.909 44 1 3 6751 6793 65349471 65349430 1.000000e-03 56.5
87 TraesCS5D01G167200 chr7B 100.000 28 0 0 6751 6778 449503495 449503468 1.700000e-02 52.8
88 TraesCS5D01G167200 chr4B 82.965 1221 142 26 3216 4434 402098000 402096844 0.000000e+00 1042.0
89 TraesCS5D01G167200 chr4B 88.218 662 69 5 159 814 526721337 526721995 0.000000e+00 782.0
90 TraesCS5D01G167200 chr4B 73.140 726 151 30 8552 9249 341003313 341002604 4.350000e-53 220.0
91 TraesCS5D01G167200 chr4B 74.528 530 105 17 8552 9057 341072657 341072134 4.380000e-48 204.0
92 TraesCS5D01G167200 chr1B 88.737 657 71 3 159 814 678204962 678205616 0.000000e+00 800.0
93 TraesCS5D01G167200 chr1B 90.769 65 4 2 6464 6528 155524956 155525018 1.650000e-12 86.1
94 TraesCS5D01G167200 chr4D 87.902 653 74 3 159 811 447333541 447334188 0.000000e+00 763.0
95 TraesCS5D01G167200 chr4D 84.853 647 96 2 169 815 18398778 18398134 0.000000e+00 651.0
96 TraesCS5D01G167200 chr4D 100.000 49 0 0 6483 6531 10263543 10263591 3.560000e-14 91.6
97 TraesCS5D01G167200 chr4D 87.838 74 8 1 6458 6531 173574988 173574916 1.650000e-12 86.1
98 TraesCS5D01G167200 chr6A 86.524 653 84 4 161 812 602618801 602619450 0.000000e+00 715.0
99 TraesCS5D01G167200 chr6A 91.736 121 8 2 6826 6946 56069164 56069282 5.740000e-37 167.0
100 TraesCS5D01G167200 chr6A 94.737 57 3 0 6474 6530 613804885 613804941 1.280000e-13 89.8
101 TraesCS5D01G167200 chr2B 81.250 608 92 9 8552 9141 432853283 432853886 1.090000e-128 472.0
102 TraesCS5D01G167200 chr2B 75.401 561 96 16 8552 9092 234497249 234496711 5.580000e-57 233.0
103 TraesCS5D01G167200 chr2B 87.248 149 18 1 1 149 596806241 596806388 1.600000e-37 169.0
104 TraesCS5D01G167200 chr2B 82.119 151 23 4 1 149 273801581 273801433 9.750000e-25 126.0
105 TraesCS5D01G167200 chr2B 86.420 81 7 4 6449 6528 663362342 663362419 1.650000e-12 86.1
106 TraesCS5D01G167200 chr2B 100.000 30 0 0 6747 6776 468443617 468443588 1.000000e-03 56.5
107 TraesCS5D01G167200 chrUn 88.325 394 28 8 4656 5036 2383243 2383631 3.040000e-124 457.0
108 TraesCS5D01G167200 chrUn 100.000 49 0 0 6483 6531 235689547 235689595 3.560000e-14 91.6
109 TraesCS5D01G167200 chrUn 100.000 49 0 0 6483 6531 248749765 248749813 3.560000e-14 91.6
110 TraesCS5D01G167200 chr6B 87.927 381 37 7 5511 5890 671139872 671139500 3.070000e-119 440.0
111 TraesCS5D01G167200 chr6B 87.179 78 7 3 6455 6531 432486746 432486671 1.650000e-12 86.1
112 TraesCS5D01G167200 chr1A 87.696 382 39 8 5511 5890 352851895 352851520 1.100000e-118 438.0
113 TraesCS5D01G167200 chr3B 93.277 119 7 1 6829 6947 824292012 824291895 3.430000e-39 174.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G167200 chr5D 260672226 260681474 9248 True 17080.000 17080 100.0000 1 9249 1 chr5D.!!$R1 9248
1 TraesCS5D01G167200 chr5D 458662697 458664438 1741 False 1711.000 1711 84.7850 3173 4938 1 chr5D.!!$F2 1765
2 TraesCS5D01G167200 chr5D 243874715 243876246 1531 False 908.000 1171 88.0370 3220 5042 2 chr5D.!!$F3 1822
3 TraesCS5D01G167200 chr5D 445300774 445301423 649 True 715.000 715 86.4310 3172 3847 1 chr5D.!!$R2 675
4 TraesCS5D01G167200 chr5D 57649530 57650462 932 False 556.000 556 78.6570 4091 5037 1 chr5D.!!$F1 946
5 TraesCS5D01G167200 chr5B 40993964 40995469 1505 False 1598.000 1598 86.1310 3520 5027 1 chr5B.!!$F1 1507
6 TraesCS5D01G167200 chr5B 293657858 293665973 8115 False 1249.375 2579 96.0445 841 9249 8 chr5B.!!$F2 8408
7 TraesCS5D01G167200 chr5B 221703270 221703787 517 True 272.000 272 76.9080 8557 9058 1 chr5B.!!$R2 501
8 TraesCS5D01G167200 chr7D 251376227 251378012 1785 True 2302.000 2302 89.9130 3212 5034 1 chr7D.!!$R3 1822
9 TraesCS5D01G167200 chr7D 587915097 587916845 1748 True 1458.000 1458 82.0540 3215 5036 1 chr7D.!!$R4 1821
10 TraesCS5D01G167200 chr7D 106390774 106391556 782 False 891.000 891 87.4690 4249 5036 1 chr7D.!!$F1 787
11 TraesCS5D01G167200 chr7D 82607764 82608417 653 True 787.000 787 88.4320 159 812 1 chr7D.!!$R2 653
12 TraesCS5D01G167200 chr7D 634074401 634074917 516 False 577.000 577 87.3560 4463 4966 1 chr7D.!!$F4 503
13 TraesCS5D01G167200 chr2D 39407536 39409335 1799 False 2150.000 2150 88.1380 3170 5036 1 chr2D.!!$F1 1866
14 TraesCS5D01G167200 chr2D 630677157 630678962 1805 True 1637.000 1637 83.4860 3229 5037 1 chr2D.!!$R2 1808
15 TraesCS5D01G167200 chr2D 650949902 650950490 588 True 728.000 728 88.9830 226 815 1 chr2D.!!$R3 589
16 TraesCS5D01G167200 chr2D 364788340 364788944 604 False 460.000 460 80.9520 8552 9141 1 chr2D.!!$F4 589
17 TraesCS5D01G167200 chr2D 364660702 364661305 603 False 449.000 449 80.6240 8552 9141 1 chr2D.!!$F3 589
18 TraesCS5D01G167200 chr5A 286003291 286004845 1554 True 1410.000 1410 83.6470 3350 4886 1 chr5A.!!$R1 1536
19 TraesCS5D01G167200 chr5A 591431253 591432419 1166 False 1295.000 1295 87.0150 3883 5041 1 chr5A.!!$F2 1158
20 TraesCS5D01G167200 chr5A 345347136 345353950 6814 True 954.000 2117 95.7612 930 9249 10 chr5A.!!$R3 8319
21 TraesCS5D01G167200 chr5A 414714348 414714964 616 True 630.000 630 85.7830 4436 5034 1 chr5A.!!$R2 598
22 TraesCS5D01G167200 chr1D 458348188 458350000 1812 False 1886.000 1886 85.7220 3170 5037 1 chr1D.!!$F5 1867
23 TraesCS5D01G167200 chr1D 432032891 432034279 1388 True 1498.000 1498 86.5340 3662 5034 1 chr1D.!!$R2 1372
24 TraesCS5D01G167200 chr1D 487022552 487023204 652 False 787.000 787 88.4320 159 814 1 chr1D.!!$F6 655
25 TraesCS5D01G167200 chr1D 106292456 106293107 651 False 728.000 728 86.8500 159 810 1 chr1D.!!$F2 651
26 TraesCS5D01G167200 chr3A 262519631 262521431 1800 False 1810.000 1810 85.1670 3170 5003 1 chr3A.!!$F1 1833
27 TraesCS5D01G167200 chr6D 285243703 285245460 1757 True 1432.000 1432 81.8080 3212 4983 1 chr6D.!!$R6 1771
28 TraesCS5D01G167200 chr3D 548818278 548819917 1639 True 1400.000 1400 82.5780 3382 5034 1 chr3D.!!$R2 1652
29 TraesCS5D01G167200 chr2A 43053916 43055186 1270 True 1336.000 1336 85.8130 3756 5034 1 chr2A.!!$R1 1278
30 TraesCS5D01G167200 chr7A 457572521 457573642 1121 True 1253.000 1253 87.0740 3914 5036 1 chr7A.!!$R1 1122
31 TraesCS5D01G167200 chr7A 457598246 457598924 678 True 734.000 734 86.0560 3216 3924 1 chr7A.!!$R2 708
32 TraesCS5D01G167200 chr7B 720341893 720343270 1377 True 1199.000 1199 83.0710 3699 5041 1 chr7B.!!$R4 1342
33 TraesCS5D01G167200 chr7B 19277229 19278033 804 True 662.000 662 82.2600 4250 5036 1 chr7B.!!$R1 786
34 TraesCS5D01G167200 chr4B 402096844 402098000 1156 True 1042.000 1042 82.9650 3216 4434 1 chr4B.!!$R3 1218
35 TraesCS5D01G167200 chr4B 526721337 526721995 658 False 782.000 782 88.2180 159 814 1 chr4B.!!$F1 655
36 TraesCS5D01G167200 chr4B 341002604 341003313 709 True 220.000 220 73.1400 8552 9249 1 chr4B.!!$R1 697
37 TraesCS5D01G167200 chr4B 341072134 341072657 523 True 204.000 204 74.5280 8552 9057 1 chr4B.!!$R2 505
38 TraesCS5D01G167200 chr1B 678204962 678205616 654 False 800.000 800 88.7370 159 814 1 chr1B.!!$F2 655
39 TraesCS5D01G167200 chr4D 447333541 447334188 647 False 763.000 763 87.9020 159 811 1 chr4D.!!$F2 652
40 TraesCS5D01G167200 chr4D 18398134 18398778 644 True 651.000 651 84.8530 169 815 1 chr4D.!!$R1 646
41 TraesCS5D01G167200 chr6A 602618801 602619450 649 False 715.000 715 86.5240 161 812 1 chr6A.!!$F2 651
42 TraesCS5D01G167200 chr2B 432853283 432853886 603 False 472.000 472 81.2500 8552 9141 1 chr2B.!!$F1 589
43 TraesCS5D01G167200 chr2B 234496711 234497249 538 True 233.000 233 75.4010 8552 9092 1 chr2B.!!$R1 540

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
93 94 0.035317 AGTCAATGCGAAGAGTGGCA 59.965 50.0 0.00 0.00 43.14 4.92 F
198 199 0.322546 CGGCTAGGGTTTTTGCCTCT 60.323 55.0 0.00 0.00 42.90 3.69 F
432 435 0.392706 TAGTATCGTCGGAGGGCGTA 59.607 55.0 0.00 0.00 0.00 4.42 F
856 864 0.725784 CAACGATTGGCACACGCTTC 60.726 55.0 11.44 0.00 39.29 3.86 F
2268 2339 0.029834 AGTTTGAAGCACAGCGCAAG 59.970 50.0 11.47 3.78 46.13 4.01 F
2798 2932 0.669318 CGAGCCTGCCAAAGTCGTAA 60.669 55.0 0.00 0.00 0.00 3.18 F
3654 3848 0.032615 TCCCTCTCTCTCTCCAAGCC 60.033 60.0 0.00 0.00 0.00 4.35 F
3656 3850 0.325110 CCTCTCTCTCTCCAAGCCCA 60.325 60.0 0.00 0.00 0.00 5.36 F
5540 6374 0.529773 TAAGCTATGCGTGAAGGGCG 60.530 55.0 0.00 0.00 0.00 6.13 F
5711 6545 0.034896 AAGTGGCACTCGTTGGTAGG 59.965 55.0 22.31 0.00 0.00 3.18 F
6298 7143 0.035881 ACACATGTGGTCTCAGCAGG 59.964 55.0 28.64 0.23 34.19 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1441 3.494924 CCAACAGAATCCGCATATCCTCA 60.495 47.826 0.00 0.00 0.00 3.86 R
2055 2126 4.504461 CGTACAAGTTGATAGTCATCCTGC 59.496 45.833 10.54 0.00 0.00 4.85 R
2243 2314 1.866880 GCTGTGCTTCAAACTTGCCAG 60.867 52.381 0.00 0.00 0.00 4.85 R
2515 2619 0.317938 GCGTACCTACATGCGGAGAG 60.318 60.000 8.51 1.08 0.00 3.20 R
3639 3833 0.975040 GCTGGGCTTGGAGAGAGAGA 60.975 60.000 0.00 0.00 0.00 3.10 R
3663 3857 1.306482 TGGGCTTGGGGAGAGAGAG 60.306 63.158 0.00 0.00 0.00 3.20 R
5573 6407 0.400213 AGATTTCTCACCACGGCCAA 59.600 50.000 2.24 0.00 0.00 4.52 R
5574 6408 0.400213 AAGATTTCTCACCACGGCCA 59.600 50.000 2.24 0.00 0.00 5.36 R
6600 9249 0.038618 CGTGTGACCGATTGTCCTCA 60.039 55.000 0.00 0.00 43.78 3.86 R
6946 9610 0.916358 CAGTCCCTCCCCAATCAGGT 60.916 60.000 0.00 0.00 34.66 4.00 R
8267 11318 1.199327 CAGTCTGCTGGAATGCACTTG 59.801 52.381 0.00 0.00 39.01 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.709987 CTTTTCCAGTGCTTGTGAAAGG 58.290 45.455 0.00 0.00 31.85 3.11
22 23 2.727123 TTCCAGTGCTTGTGAAAGGA 57.273 45.000 0.00 0.00 0.00 3.36
23 24 2.727123 TCCAGTGCTTGTGAAAGGAA 57.273 45.000 0.00 0.00 0.00 3.36
24 25 3.011566 TCCAGTGCTTGTGAAAGGAAA 57.988 42.857 0.00 0.00 0.00 3.13
25 26 3.360867 TCCAGTGCTTGTGAAAGGAAAA 58.639 40.909 0.00 0.00 0.00 2.29
26 27 3.766591 TCCAGTGCTTGTGAAAGGAAAAA 59.233 39.130 0.00 0.00 0.00 1.94
27 28 4.114794 CCAGTGCTTGTGAAAGGAAAAAG 58.885 43.478 0.00 0.00 0.00 2.27
28 29 4.142182 CCAGTGCTTGTGAAAGGAAAAAGA 60.142 41.667 0.00 0.00 0.00 2.52
29 30 5.410067 CAGTGCTTGTGAAAGGAAAAAGAA 58.590 37.500 0.00 0.00 0.00 2.52
30 31 5.868801 CAGTGCTTGTGAAAGGAAAAAGAAA 59.131 36.000 0.00 0.00 0.00 2.52
31 32 6.368516 CAGTGCTTGTGAAAGGAAAAAGAAAA 59.631 34.615 0.00 0.00 0.00 2.29
32 33 6.934083 AGTGCTTGTGAAAGGAAAAAGAAAAA 59.066 30.769 0.00 0.00 0.00 1.94
60 61 5.921962 ATCAATAAAAGGAAGGAAGTGGC 57.078 39.130 0.00 0.00 0.00 5.01
61 62 4.735369 TCAATAAAAGGAAGGAAGTGGCA 58.265 39.130 0.00 0.00 0.00 4.92
62 63 5.332743 TCAATAAAAGGAAGGAAGTGGCAT 58.667 37.500 0.00 0.00 0.00 4.40
63 64 5.185635 TCAATAAAAGGAAGGAAGTGGCATG 59.814 40.000 0.00 0.00 0.00 4.06
64 65 1.260544 AAAGGAAGGAAGTGGCATGC 58.739 50.000 9.90 9.90 0.00 4.06
65 66 0.407139 AAGGAAGGAAGTGGCATGCT 59.593 50.000 18.92 0.00 0.00 3.79
66 67 1.289160 AGGAAGGAAGTGGCATGCTA 58.711 50.000 18.92 9.16 0.00 3.49
67 68 1.635487 AGGAAGGAAGTGGCATGCTAA 59.365 47.619 18.92 3.29 0.00 3.09
68 69 2.243221 AGGAAGGAAGTGGCATGCTAAT 59.757 45.455 18.92 8.20 0.00 1.73
69 70 2.620585 GGAAGGAAGTGGCATGCTAATC 59.379 50.000 18.92 13.11 0.00 1.75
70 71 3.282021 GAAGGAAGTGGCATGCTAATCA 58.718 45.455 18.92 3.67 0.00 2.57
71 72 3.370840 AGGAAGTGGCATGCTAATCAA 57.629 42.857 18.92 0.00 0.00 2.57
72 73 3.700538 AGGAAGTGGCATGCTAATCAAA 58.299 40.909 18.92 0.00 0.00 2.69
73 74 3.698040 AGGAAGTGGCATGCTAATCAAAG 59.302 43.478 18.92 0.00 0.00 2.77
74 75 3.696051 GGAAGTGGCATGCTAATCAAAGA 59.304 43.478 18.92 0.00 0.00 2.52
75 76 4.201990 GGAAGTGGCATGCTAATCAAAGAG 60.202 45.833 18.92 0.00 0.00 2.85
76 77 3.960571 AGTGGCATGCTAATCAAAGAGT 58.039 40.909 18.92 0.00 0.00 3.24
77 78 3.944015 AGTGGCATGCTAATCAAAGAGTC 59.056 43.478 18.92 0.00 0.00 3.36
78 79 3.691118 GTGGCATGCTAATCAAAGAGTCA 59.309 43.478 18.92 0.00 0.00 3.41
79 80 4.156556 GTGGCATGCTAATCAAAGAGTCAA 59.843 41.667 18.92 0.00 0.00 3.18
80 81 4.951715 TGGCATGCTAATCAAAGAGTCAAT 59.048 37.500 18.92 0.00 0.00 2.57
81 82 5.163591 TGGCATGCTAATCAAAGAGTCAATG 60.164 40.000 18.92 0.00 0.00 2.82
82 83 4.738740 GCATGCTAATCAAAGAGTCAATGC 59.261 41.667 11.37 0.00 0.00 3.56
83 84 4.604843 TGCTAATCAAAGAGTCAATGCG 57.395 40.909 0.00 0.00 0.00 4.73
84 85 4.252878 TGCTAATCAAAGAGTCAATGCGA 58.747 39.130 0.00 0.00 0.00 5.10
85 86 4.694982 TGCTAATCAAAGAGTCAATGCGAA 59.305 37.500 0.00 0.00 0.00 4.70
86 87 5.163824 TGCTAATCAAAGAGTCAATGCGAAG 60.164 40.000 0.00 0.00 0.00 3.79
87 88 5.063944 GCTAATCAAAGAGTCAATGCGAAGA 59.936 40.000 0.00 0.00 0.00 2.87
88 89 5.542616 AATCAAAGAGTCAATGCGAAGAG 57.457 39.130 0.00 0.00 0.00 2.85
89 90 3.995199 TCAAAGAGTCAATGCGAAGAGT 58.005 40.909 0.00 0.00 0.00 3.24
90 91 3.742882 TCAAAGAGTCAATGCGAAGAGTG 59.257 43.478 0.00 0.00 0.00 3.51
91 92 2.376808 AGAGTCAATGCGAAGAGTGG 57.623 50.000 0.00 0.00 0.00 4.00
92 93 0.723981 GAGTCAATGCGAAGAGTGGC 59.276 55.000 0.00 0.00 0.00 5.01
93 94 0.035317 AGTCAATGCGAAGAGTGGCA 59.965 50.000 0.00 0.00 43.14 4.92
94 95 0.874390 GTCAATGCGAAGAGTGGCAA 59.126 50.000 0.00 0.00 42.19 4.52
95 96 1.470098 GTCAATGCGAAGAGTGGCAAT 59.530 47.619 0.00 0.00 42.19 3.56
96 97 2.095059 GTCAATGCGAAGAGTGGCAATT 60.095 45.455 0.00 0.00 42.19 2.32
97 98 2.557924 TCAATGCGAAGAGTGGCAATTT 59.442 40.909 0.00 0.00 42.19 1.82
98 99 3.005684 TCAATGCGAAGAGTGGCAATTTT 59.994 39.130 0.00 0.00 42.19 1.82
99 100 4.217334 TCAATGCGAAGAGTGGCAATTTTA 59.783 37.500 0.00 0.00 42.19 1.52
100 101 3.552604 TGCGAAGAGTGGCAATTTTAC 57.447 42.857 0.00 0.00 35.30 2.01
101 102 2.095969 TGCGAAGAGTGGCAATTTTACG 60.096 45.455 0.00 0.00 35.30 3.18
102 103 2.158841 GCGAAGAGTGGCAATTTTACGA 59.841 45.455 11.75 0.00 0.00 3.43
103 104 3.364565 GCGAAGAGTGGCAATTTTACGAA 60.365 43.478 11.75 0.00 0.00 3.85
104 105 4.394795 CGAAGAGTGGCAATTTTACGAAG 58.605 43.478 0.00 0.00 0.00 3.79
105 106 3.831715 AGAGTGGCAATTTTACGAAGC 57.168 42.857 0.00 0.00 0.00 3.86
106 107 2.488153 AGAGTGGCAATTTTACGAAGCC 59.512 45.455 0.00 0.00 45.41 4.35
111 112 4.110036 GGCAATTTTACGAAGCCAATCT 57.890 40.909 0.00 0.00 44.59 2.40
112 113 4.494484 GGCAATTTTACGAAGCCAATCTT 58.506 39.130 0.00 0.00 44.59 2.40
113 114 5.646606 GGCAATTTTACGAAGCCAATCTTA 58.353 37.500 0.00 0.00 44.59 2.10
114 115 6.096695 GGCAATTTTACGAAGCCAATCTTAA 58.903 36.000 0.00 0.00 44.59 1.85
115 116 6.588373 GGCAATTTTACGAAGCCAATCTTAAA 59.412 34.615 0.00 0.00 44.59 1.52
116 117 7.117092 GGCAATTTTACGAAGCCAATCTTAAAA 59.883 33.333 0.00 7.92 44.59 1.52
117 118 8.162245 GCAATTTTACGAAGCCAATCTTAAAAG 58.838 33.333 0.00 0.00 36.84 2.27
118 119 9.191995 CAATTTTACGAAGCCAATCTTAAAAGT 57.808 29.630 0.00 6.52 36.84 2.66
119 120 8.742554 ATTTTACGAAGCCAATCTTAAAAGTG 57.257 30.769 0.00 0.00 36.84 3.16
120 121 4.766404 ACGAAGCCAATCTTAAAAGTGG 57.234 40.909 0.00 0.00 34.56 4.00
128 129 6.956299 CCAATCTTAAAAGTGGCAATTCTG 57.044 37.500 0.00 0.00 0.00 3.02
129 130 6.690530 CCAATCTTAAAAGTGGCAATTCTGA 58.309 36.000 0.00 0.00 0.00 3.27
130 131 6.810182 CCAATCTTAAAAGTGGCAATTCTGAG 59.190 38.462 0.00 0.00 0.00 3.35
131 132 7.309377 CCAATCTTAAAAGTGGCAATTCTGAGA 60.309 37.037 0.00 0.00 0.00 3.27
132 133 7.765695 ATCTTAAAAGTGGCAATTCTGAGAA 57.234 32.000 0.00 0.00 0.00 2.87
133 134 7.206981 TCTTAAAAGTGGCAATTCTGAGAAG 57.793 36.000 0.00 1.25 0.00 2.85
134 135 3.930634 AAAGTGGCAATTCTGAGAAGC 57.069 42.857 0.00 0.00 0.00 3.86
135 136 1.831580 AGTGGCAATTCTGAGAAGCC 58.168 50.000 16.13 16.13 45.41 4.35
138 139 0.449388 GGCAATTCTGAGAAGCCACG 59.551 55.000 17.59 0.00 44.59 4.94
139 140 1.160137 GCAATTCTGAGAAGCCACGT 58.840 50.000 0.00 0.00 0.00 4.49
140 141 2.346803 GCAATTCTGAGAAGCCACGTA 58.653 47.619 0.00 0.00 0.00 3.57
141 142 2.939103 GCAATTCTGAGAAGCCACGTAT 59.061 45.455 0.00 0.00 0.00 3.06
142 143 3.375299 GCAATTCTGAGAAGCCACGTATT 59.625 43.478 0.00 0.00 0.00 1.89
143 144 4.728882 GCAATTCTGAGAAGCCACGTATTG 60.729 45.833 0.00 0.00 0.00 1.90
144 145 3.678056 TTCTGAGAAGCCACGTATTGT 57.322 42.857 0.00 0.00 0.00 2.71
145 146 4.794278 TTCTGAGAAGCCACGTATTGTA 57.206 40.909 0.00 0.00 0.00 2.41
146 147 4.794278 TCTGAGAAGCCACGTATTGTAA 57.206 40.909 0.00 0.00 0.00 2.41
147 148 4.744570 TCTGAGAAGCCACGTATTGTAAG 58.255 43.478 0.00 0.00 0.00 2.34
148 149 4.219944 TCTGAGAAGCCACGTATTGTAAGT 59.780 41.667 0.00 0.00 0.00 2.24
149 150 4.890088 TGAGAAGCCACGTATTGTAAGTT 58.110 39.130 0.00 0.00 0.00 2.66
150 151 5.302360 TGAGAAGCCACGTATTGTAAGTTT 58.698 37.500 0.00 0.00 0.00 2.66
151 152 5.761234 TGAGAAGCCACGTATTGTAAGTTTT 59.239 36.000 0.00 0.00 0.00 2.43
152 153 6.261381 TGAGAAGCCACGTATTGTAAGTTTTT 59.739 34.615 0.00 0.00 0.00 1.94
191 192 2.594131 AGAAAAAGCGGCTAGGGTTTT 58.406 42.857 1.35 6.37 46.22 2.43
198 199 0.322546 CGGCTAGGGTTTTTGCCTCT 60.323 55.000 0.00 0.00 42.90 3.69
199 200 1.065709 CGGCTAGGGTTTTTGCCTCTA 60.066 52.381 0.00 0.00 42.90 2.43
230 231 2.675423 CCGACCTCCCACGTCTCA 60.675 66.667 0.00 0.00 0.00 3.27
294 296 1.227973 GGCGGGAGGGCTCTATTTG 60.228 63.158 0.00 0.00 38.40 2.32
301 303 3.008485 GGGAGGGCTCTATTTGTAGATGG 59.992 52.174 0.00 0.00 0.00 3.51
330 332 5.477291 TCAAGTTTTGTTAGGGTTTGTGTCA 59.523 36.000 0.00 0.00 0.00 3.58
355 357 1.070108 CAAGAAGACGAGACGACGACA 60.070 52.381 0.00 0.00 37.03 4.35
356 358 1.224075 AGAAGACGAGACGACGACAA 58.776 50.000 0.00 0.00 37.03 3.18
383 385 7.502060 TCTTGAAGATGGAATAAGGTTCTCT 57.498 36.000 0.00 0.00 0.00 3.10
404 406 2.901042 CCTAGCCCCCGTCTCAAC 59.099 66.667 0.00 0.00 0.00 3.18
432 435 0.392706 TAGTATCGTCGGAGGGCGTA 59.607 55.000 0.00 0.00 0.00 4.42
451 454 2.997897 GGAGGTGTGTCTCCGGCT 60.998 66.667 0.00 0.00 43.19 5.52
459 462 1.378646 TGTCTCCGGCTGATCTCGT 60.379 57.895 0.00 0.00 0.00 4.18
493 496 1.496857 TGGTTGTCTTTGGTGGATCCA 59.503 47.619 11.44 11.44 45.60 3.41
516 524 4.081862 ACTCGAATCCGGTCTTTGTTCATA 60.082 41.667 0.00 0.00 36.24 2.15
551 559 4.714802 TGGATCCTTCCGATCTAAACTTCA 59.285 41.667 14.23 0.00 45.90 3.02
629 637 3.204526 CGACTTCCCGACTGTCTACTAT 58.795 50.000 6.21 0.00 0.00 2.12
643 651 6.014499 ACTGTCTACTATAACAAGTTGTGCCT 60.014 38.462 9.79 0.00 0.00 4.75
645 653 6.014925 TGTCTACTATAACAAGTTGTGCCTGA 60.015 38.462 9.79 0.00 0.00 3.86
729 737 1.338200 CGCTAGGTGGCCTATGAATCC 60.338 57.143 3.32 0.00 35.36 3.01
741 749 7.174253 GTGGCCTATGAATCCGAATGTAATTTA 59.826 37.037 3.32 0.00 36.07 1.40
787 795 9.889128 TGTACTGTCATGATTGAAGATGAATAA 57.111 29.630 0.00 0.00 32.48 1.40
803 811 8.059798 AGATGAATAAATCCACAGTTTTCCAG 57.940 34.615 0.00 0.00 0.00 3.86
833 841 7.486407 AAAAGTGGCAAATATCCAATTCTCT 57.514 32.000 0.00 0.00 40.52 3.10
834 842 6.705863 AAGTGGCAAATATCCAATTCTCTC 57.294 37.500 0.00 0.00 37.32 3.20
835 843 5.136105 AGTGGCAAATATCCAATTCTCTCC 58.864 41.667 0.00 0.00 35.01 3.71
836 844 4.279420 GTGGCAAATATCCAATTCTCTCCC 59.721 45.833 0.00 0.00 35.01 4.30
837 845 3.829026 GGCAAATATCCAATTCTCTCCCC 59.171 47.826 0.00 0.00 0.00 4.81
838 846 4.473444 GCAAATATCCAATTCTCTCCCCA 58.527 43.478 0.00 0.00 0.00 4.96
839 847 4.895297 GCAAATATCCAATTCTCTCCCCAA 59.105 41.667 0.00 0.00 0.00 4.12
856 864 0.725784 CAACGATTGGCACACGCTTC 60.726 55.000 11.44 0.00 39.29 3.86
884 892 3.228453 TGTCCTCACGGTTTCTTCTAGT 58.772 45.455 0.00 0.00 0.00 2.57
977 985 3.649277 CTTGAGGCAGGGACGTCCG 62.649 68.421 27.68 16.32 41.52 4.79
1349 1364 4.380531 GCTTATGCTAGACTTGGTATGCA 58.619 43.478 0.00 0.00 36.03 3.96
1351 1366 5.471456 GCTTATGCTAGACTTGGTATGCATT 59.529 40.000 3.54 0.00 40.82 3.56
1426 1441 1.160137 GATGTGCGAGGAAAAGCTGT 58.840 50.000 0.00 0.00 0.00 4.40
1919 1990 7.223387 GCTGAATTTGGTATGATGGTCATTTTC 59.777 37.037 0.00 0.00 38.26 2.29
2020 2091 8.186163 GGGCGCTATTTTAGTTTGTATTTACTT 58.814 33.333 7.64 0.00 0.00 2.24
2086 2157 0.753867 TCAACTTGTACGGGACTGCA 59.246 50.000 0.00 0.00 0.00 4.41
2208 2279 3.487207 CACGTGTCTTATCATGGATGACG 59.513 47.826 7.58 0.00 40.03 4.35
2243 2314 3.255149 TCGGGTCTAGACACTCTTTTCAC 59.745 47.826 22.47 2.02 31.07 3.18
2268 2339 0.029834 AGTTTGAAGCACAGCGCAAG 59.970 50.000 11.47 3.78 46.13 4.01
2501 2605 3.509575 GCTGGGTGGTGATGTGAATTTAA 59.490 43.478 0.00 0.00 0.00 1.52
2614 2740 4.655762 TGTGCTATCCAGTACTTAGCAG 57.344 45.455 22.32 7.30 46.44 4.24
2649 2775 7.333423 AGTGCTGATTCGTGCTAGTTAAAATAA 59.667 33.333 0.00 0.00 0.00 1.40
2798 2932 0.669318 CGAGCCTGCCAAAGTCGTAA 60.669 55.000 0.00 0.00 0.00 3.18
2838 2972 5.510671 TCTGCAACTTTCTCAACGAATTTC 58.489 37.500 0.00 0.00 0.00 2.17
2919 3053 4.410400 GGTCACCCTTCCCAGCCG 62.410 72.222 0.00 0.00 0.00 5.52
3046 3182 5.671493 TCTAAGGAAGCCTTAAGTATGTGC 58.329 41.667 7.29 0.00 44.32 4.57
3048 3184 5.693769 AAGGAAGCCTTAAGTATGTGCTA 57.306 39.130 0.97 0.00 42.74 3.49
3562 3735 3.304057 GGCAGCTATAAAATCAACGCCTC 60.304 47.826 0.00 0.00 34.17 4.70
3640 3834 3.967335 CGCCGACGATCCTCCCTC 61.967 72.222 0.00 0.00 43.93 4.30
3643 3837 1.149627 CCGACGATCCTCCCTCTCT 59.850 63.158 0.00 0.00 0.00 3.10
3646 3840 1.876416 CGACGATCCTCCCTCTCTCTC 60.876 61.905 0.00 0.00 0.00 3.20
3647 3841 1.420138 GACGATCCTCCCTCTCTCTCT 59.580 57.143 0.00 0.00 0.00 3.10
3648 3842 1.420138 ACGATCCTCCCTCTCTCTCTC 59.580 57.143 0.00 0.00 0.00 3.20
3649 3843 1.271379 CGATCCTCCCTCTCTCTCTCC 60.271 61.905 0.00 0.00 0.00 3.71
3650 3844 1.780309 GATCCTCCCTCTCTCTCTCCA 59.220 57.143 0.00 0.00 0.00 3.86
3651 3845 1.687492 TCCTCCCTCTCTCTCTCCAA 58.313 55.000 0.00 0.00 0.00 3.53
3652 3846 1.568597 TCCTCCCTCTCTCTCTCCAAG 59.431 57.143 0.00 0.00 0.00 3.61
3653 3847 1.402787 CTCCCTCTCTCTCTCCAAGC 58.597 60.000 0.00 0.00 0.00 4.01
3654 3848 0.032615 TCCCTCTCTCTCTCCAAGCC 60.033 60.000 0.00 0.00 0.00 4.35
3655 3849 1.048160 CCCTCTCTCTCTCCAAGCCC 61.048 65.000 0.00 0.00 0.00 5.19
3656 3850 0.325110 CCTCTCTCTCTCCAAGCCCA 60.325 60.000 0.00 0.00 0.00 5.36
3657 3851 1.113788 CTCTCTCTCTCCAAGCCCAG 58.886 60.000 0.00 0.00 0.00 4.45
3658 3852 0.975040 TCTCTCTCTCCAAGCCCAGC 60.975 60.000 0.00 0.00 0.00 4.85
3659 3853 1.970352 CTCTCTCTCCAAGCCCAGCC 61.970 65.000 0.00 0.00 0.00 4.85
3660 3854 3.382803 CTCTCTCCAAGCCCAGCCG 62.383 68.421 0.00 0.00 0.00 5.52
3766 3965 4.672251 GGGTGAGAGCCGTACCTA 57.328 61.111 0.00 0.00 34.87 3.08
4542 4821 3.799755 GTGGGCGCGCGAAGATTT 61.800 61.111 37.18 0.00 0.00 2.17
4728 5077 0.677414 AGGAGAAGGACGACGAGGAC 60.677 60.000 0.00 0.00 0.00 3.85
4845 5243 3.252215 CCATGTTTGTCGAACTTTAGCCA 59.748 43.478 4.58 0.00 39.08 4.75
5056 5513 1.404391 CTGCCTGATTGACCAAGCATC 59.596 52.381 0.95 0.00 36.03 3.91
5084 5541 4.072131 ACCAGTCAAATAGCATGAACGTT 58.928 39.130 0.00 0.00 0.00 3.99
5366 6200 5.185828 TCTGAGCTGAATAACAAGTGCTAGA 59.814 40.000 0.00 0.00 29.72 2.43
5460 6294 8.962679 TGTTCTTAAACATGTACCTTTGACTTT 58.037 29.630 0.00 0.00 40.45 2.66
5512 6346 5.974108 TGCGAGGCTTAGTAAGAACTAATT 58.026 37.500 14.27 0.00 45.03 1.40
5513 6347 7.104043 TGCGAGGCTTAGTAAGAACTAATTA 57.896 36.000 14.27 0.00 45.03 1.40
5514 6348 7.549839 TGCGAGGCTTAGTAAGAACTAATTAA 58.450 34.615 14.27 0.00 45.03 1.40
5515 6349 8.036575 TGCGAGGCTTAGTAAGAACTAATTAAA 58.963 33.333 14.27 0.00 45.03 1.52
5516 6350 8.326713 GCGAGGCTTAGTAAGAACTAATTAAAC 58.673 37.037 14.27 0.00 45.03 2.01
5517 6351 8.815189 CGAGGCTTAGTAAGAACTAATTAAACC 58.185 37.037 14.27 0.91 45.03 3.27
5518 6352 9.107177 GAGGCTTAGTAAGAACTAATTAAACCC 57.893 37.037 14.27 0.72 45.03 4.11
5519 6353 8.608598 AGGCTTAGTAAGAACTAATTAAACCCA 58.391 33.333 14.27 0.00 45.03 4.51
5520 6354 9.404848 GGCTTAGTAAGAACTAATTAAACCCAT 57.595 33.333 14.27 0.00 45.03 4.00
5530 6364 9.678941 GAACTAATTAAACCCATTAAGCTATGC 57.321 33.333 0.00 0.00 36.94 3.14
5531 6365 7.871853 ACTAATTAAACCCATTAAGCTATGCG 58.128 34.615 0.00 0.00 36.94 4.73
5532 6366 6.709018 AATTAAACCCATTAAGCTATGCGT 57.291 33.333 0.00 0.00 36.94 5.24
5533 6367 5.493133 TTAAACCCATTAAGCTATGCGTG 57.507 39.130 0.00 0.00 0.00 5.34
5534 6368 3.275617 AACCCATTAAGCTATGCGTGA 57.724 42.857 0.00 0.00 0.00 4.35
5535 6369 3.275617 ACCCATTAAGCTATGCGTGAA 57.724 42.857 0.00 0.00 0.00 3.18
5536 6370 3.206150 ACCCATTAAGCTATGCGTGAAG 58.794 45.455 0.00 0.00 0.00 3.02
5537 6371 2.549754 CCCATTAAGCTATGCGTGAAGG 59.450 50.000 0.00 0.00 0.00 3.46
5538 6372 2.549754 CCATTAAGCTATGCGTGAAGGG 59.450 50.000 0.00 0.00 0.00 3.95
5539 6373 1.663695 TTAAGCTATGCGTGAAGGGC 58.336 50.000 0.00 0.00 0.00 5.19
5540 6374 0.529773 TAAGCTATGCGTGAAGGGCG 60.530 55.000 0.00 0.00 0.00 6.13
5541 6375 3.272334 GCTATGCGTGAAGGGCGG 61.272 66.667 0.00 0.00 0.00 6.13
5542 6376 3.272334 CTATGCGTGAAGGGCGGC 61.272 66.667 0.00 0.00 0.00 6.53
5543 6377 4.849310 TATGCGTGAAGGGCGGCC 62.849 66.667 22.67 22.67 0.00 6.13
5548 6382 4.966787 GTGAAGGGCGGCCAACCA 62.967 66.667 31.59 20.58 34.57 3.67
5549 6383 4.659172 TGAAGGGCGGCCAACCAG 62.659 66.667 31.59 0.00 34.57 4.00
5553 6387 4.506255 GGGCGGCCAACCAGCTAT 62.506 66.667 25.33 0.00 36.24 2.97
5554 6388 3.211963 GGCGGCCAACCAGCTATG 61.212 66.667 15.62 0.00 36.24 2.23
5555 6389 3.892581 GCGGCCAACCAGCTATGC 61.893 66.667 2.24 0.00 34.11 3.14
5556 6390 3.211963 CGGCCAACCAGCTATGCC 61.212 66.667 2.24 0.00 38.74 4.40
5557 6391 2.044053 GGCCAACCAGCTATGCCA 60.044 61.111 0.00 0.00 41.76 4.92
5558 6392 2.418083 GGCCAACCAGCTATGCCAC 61.418 63.158 0.00 0.00 41.76 5.01
5559 6393 2.764314 GCCAACCAGCTATGCCACG 61.764 63.158 0.00 0.00 0.00 4.94
5560 6394 1.377202 CCAACCAGCTATGCCACGT 60.377 57.895 0.00 0.00 0.00 4.49
5561 6395 1.647545 CCAACCAGCTATGCCACGTG 61.648 60.000 9.08 9.08 0.00 4.49
5562 6396 1.377202 AACCAGCTATGCCACGTGG 60.377 57.895 30.66 30.66 38.53 4.94
5581 6415 4.347453 GCAAGCTGGTTGGCCGTG 62.347 66.667 19.87 0.00 36.56 4.94
5582 6416 3.673484 CAAGCTGGTTGGCCGTGG 61.673 66.667 11.59 0.00 37.67 4.94
5583 6417 4.204028 AAGCTGGTTGGCCGTGGT 62.204 61.111 0.00 0.00 37.67 4.16
5584 6418 4.954970 AGCTGGTTGGCCGTGGTG 62.955 66.667 0.00 0.00 37.67 4.17
5585 6419 4.947147 GCTGGTTGGCCGTGGTGA 62.947 66.667 0.00 0.00 37.67 4.02
5586 6420 2.669569 CTGGTTGGCCGTGGTGAG 60.670 66.667 0.00 0.00 37.67 3.51
5587 6421 3.164977 TGGTTGGCCGTGGTGAGA 61.165 61.111 0.00 0.00 37.67 3.27
5588 6422 2.112297 GGTTGGCCGTGGTGAGAA 59.888 61.111 0.00 0.00 0.00 2.87
5589 6423 1.527380 GGTTGGCCGTGGTGAGAAA 60.527 57.895 0.00 0.00 0.00 2.52
5590 6424 0.893727 GGTTGGCCGTGGTGAGAAAT 60.894 55.000 0.00 0.00 0.00 2.17
5591 6425 0.521735 GTTGGCCGTGGTGAGAAATC 59.478 55.000 0.00 0.00 0.00 2.17
5592 6426 0.400213 TTGGCCGTGGTGAGAAATCT 59.600 50.000 0.00 0.00 0.00 2.40
5593 6427 0.400213 TGGCCGTGGTGAGAAATCTT 59.600 50.000 0.00 0.00 0.00 2.40
5594 6428 1.202879 TGGCCGTGGTGAGAAATCTTT 60.203 47.619 0.00 0.00 0.00 2.52
5595 6429 1.886542 GGCCGTGGTGAGAAATCTTTT 59.113 47.619 0.00 0.00 0.00 2.27
5596 6430 2.095212 GGCCGTGGTGAGAAATCTTTTC 60.095 50.000 0.00 0.00 0.00 2.29
5597 6431 2.412847 GCCGTGGTGAGAAATCTTTTCG 60.413 50.000 0.00 0.00 0.00 3.46
5598 6432 3.064207 CCGTGGTGAGAAATCTTTTCGA 58.936 45.455 0.00 0.00 0.00 3.71
5599 6433 3.496884 CCGTGGTGAGAAATCTTTTCGAA 59.503 43.478 0.00 0.00 0.00 3.71
5600 6434 4.154195 CCGTGGTGAGAAATCTTTTCGAAT 59.846 41.667 0.00 0.00 0.00 3.34
5601 6435 5.334879 CCGTGGTGAGAAATCTTTTCGAATT 60.335 40.000 0.00 0.00 0.00 2.17
5602 6436 6.142817 CGTGGTGAGAAATCTTTTCGAATTT 58.857 36.000 0.00 0.00 0.00 1.82
5603 6437 6.636850 CGTGGTGAGAAATCTTTTCGAATTTT 59.363 34.615 0.00 0.00 0.00 1.82
5604 6438 7.167468 CGTGGTGAGAAATCTTTTCGAATTTTT 59.833 33.333 0.00 0.00 0.00 1.94
5661 6495 4.569719 TTTTTAGATGGAGGTGAGGACC 57.430 45.455 0.00 0.00 43.52 4.46
5673 6507 4.302559 GGTGAGGACCTCTGGTATTTTT 57.697 45.455 22.14 0.00 39.47 1.94
5695 6529 6.926630 TTTAAATGGAGGGTTATGCAAAGT 57.073 33.333 0.00 0.00 0.00 2.66
5696 6530 4.806640 AAATGGAGGGTTATGCAAAGTG 57.193 40.909 0.00 0.00 0.00 3.16
5697 6531 2.214376 TGGAGGGTTATGCAAAGTGG 57.786 50.000 0.00 0.00 0.00 4.00
5698 6532 0.817654 GGAGGGTTATGCAAAGTGGC 59.182 55.000 0.00 0.00 0.00 5.01
5705 6539 4.234019 TGCAAAGTGGCACTCGTT 57.766 50.000 22.31 9.86 39.25 3.85
5706 6540 1.726865 TGCAAAGTGGCACTCGTTG 59.273 52.632 22.31 22.13 42.38 4.10
5707 6541 1.008538 GCAAAGTGGCACTCGTTGG 60.009 57.895 25.45 10.26 40.51 3.77
5708 6542 1.724582 GCAAAGTGGCACTCGTTGGT 61.725 55.000 25.45 7.67 40.51 3.67
5709 6543 1.588674 CAAAGTGGCACTCGTTGGTA 58.411 50.000 22.31 0.00 37.58 3.25
5710 6544 1.531149 CAAAGTGGCACTCGTTGGTAG 59.469 52.381 22.31 1.23 37.58 3.18
5711 6545 0.034896 AAGTGGCACTCGTTGGTAGG 59.965 55.000 22.31 0.00 0.00 3.18
5712 6546 2.033194 GTGGCACTCGTTGGTAGGC 61.033 63.158 11.13 0.00 0.00 3.93
5713 6547 2.214216 TGGCACTCGTTGGTAGGCT 61.214 57.895 0.00 0.00 0.00 4.58
5714 6548 1.741770 GGCACTCGTTGGTAGGCTG 60.742 63.158 0.00 0.00 0.00 4.85
5715 6549 2.391389 GCACTCGTTGGTAGGCTGC 61.391 63.158 0.00 0.00 0.00 5.25
5716 6550 2.094659 CACTCGTTGGTAGGCTGCG 61.095 63.158 0.00 0.00 0.00 5.18
5717 6551 2.509336 CTCGTTGGTAGGCTGCGG 60.509 66.667 0.00 0.00 0.00 5.69
5718 6552 3.296709 CTCGTTGGTAGGCTGCGGT 62.297 63.158 0.00 0.00 0.00 5.68
5719 6553 3.118454 CGTTGGTAGGCTGCGGTG 61.118 66.667 0.00 0.00 0.00 4.94
5720 6554 2.746277 GTTGGTAGGCTGCGGTGG 60.746 66.667 0.00 0.00 0.00 4.61
5721 6555 3.246112 TTGGTAGGCTGCGGTGGT 61.246 61.111 0.00 0.00 0.00 4.16
5722 6556 1.914263 TTGGTAGGCTGCGGTGGTA 60.914 57.895 0.00 0.00 0.00 3.25
5723 6557 1.481901 TTGGTAGGCTGCGGTGGTAA 61.482 55.000 0.00 0.00 0.00 2.85
5724 6558 1.268992 TGGTAGGCTGCGGTGGTAAT 61.269 55.000 0.00 0.00 0.00 1.89
5725 6559 0.107361 GGTAGGCTGCGGTGGTAATT 60.107 55.000 0.00 0.00 0.00 1.40
5726 6560 1.680860 GGTAGGCTGCGGTGGTAATTT 60.681 52.381 0.00 0.00 0.00 1.82
5727 6561 1.669265 GTAGGCTGCGGTGGTAATTTC 59.331 52.381 0.00 0.00 0.00 2.17
5728 6562 0.328258 AGGCTGCGGTGGTAATTTCT 59.672 50.000 0.00 0.00 0.00 2.52
5729 6563 1.173913 GGCTGCGGTGGTAATTTCTT 58.826 50.000 0.00 0.00 0.00 2.52
5730 6564 1.544246 GGCTGCGGTGGTAATTTCTTT 59.456 47.619 0.00 0.00 0.00 2.52
5731 6565 2.415491 GGCTGCGGTGGTAATTTCTTTC 60.415 50.000 0.00 0.00 0.00 2.62
5732 6566 2.488153 GCTGCGGTGGTAATTTCTTTCT 59.512 45.455 0.00 0.00 0.00 2.52
5733 6567 3.057526 GCTGCGGTGGTAATTTCTTTCTT 60.058 43.478 0.00 0.00 0.00 2.52
5734 6568 4.558697 GCTGCGGTGGTAATTTCTTTCTTT 60.559 41.667 0.00 0.00 0.00 2.52
5735 6569 5.523438 TGCGGTGGTAATTTCTTTCTTTT 57.477 34.783 0.00 0.00 0.00 2.27
5736 6570 5.908341 TGCGGTGGTAATTTCTTTCTTTTT 58.092 33.333 0.00 0.00 0.00 1.94
5806 6640 3.826637 TTTTTAGACGGAGGCGAGG 57.173 52.632 0.00 0.00 0.00 4.63
5807 6641 1.259609 TTTTTAGACGGAGGCGAGGA 58.740 50.000 0.00 0.00 0.00 3.71
5808 6642 0.529378 TTTTAGACGGAGGCGAGGAC 59.471 55.000 0.00 0.00 0.00 3.85
5809 6643 0.323178 TTTAGACGGAGGCGAGGACT 60.323 55.000 0.00 0.00 0.00 3.85
5810 6644 0.747283 TTAGACGGAGGCGAGGACTC 60.747 60.000 0.00 0.00 36.87 3.36
5811 6645 1.624479 TAGACGGAGGCGAGGACTCT 61.624 60.000 0.00 0.00 37.91 3.24
5812 6646 1.153208 GACGGAGGCGAGGACTCTA 60.153 63.158 0.00 0.00 37.91 2.43
5813 6647 1.438562 GACGGAGGCGAGGACTCTAC 61.439 65.000 0.00 0.00 37.91 2.59
5814 6648 1.451567 CGGAGGCGAGGACTCTACA 60.452 63.158 0.00 0.00 37.91 2.74
5815 6649 0.820074 CGGAGGCGAGGACTCTACAT 60.820 60.000 0.00 0.00 37.91 2.29
5816 6650 1.542767 CGGAGGCGAGGACTCTACATA 60.543 57.143 0.00 0.00 37.91 2.29
5817 6651 2.797786 GGAGGCGAGGACTCTACATAT 58.202 52.381 0.00 0.00 37.91 1.78
5818 6652 3.158676 GGAGGCGAGGACTCTACATATT 58.841 50.000 0.00 0.00 37.91 1.28
5819 6653 3.574826 GGAGGCGAGGACTCTACATATTT 59.425 47.826 0.00 0.00 37.91 1.40
5820 6654 4.039366 GGAGGCGAGGACTCTACATATTTT 59.961 45.833 0.00 0.00 37.91 1.82
5821 6655 5.453480 GGAGGCGAGGACTCTACATATTTTT 60.453 44.000 0.00 0.00 37.91 1.94
5822 6656 5.602628 AGGCGAGGACTCTACATATTTTTC 58.397 41.667 0.00 0.00 0.00 2.29
5823 6657 5.364157 AGGCGAGGACTCTACATATTTTTCT 59.636 40.000 0.00 0.00 0.00 2.52
5824 6658 6.049790 GGCGAGGACTCTACATATTTTTCTT 58.950 40.000 0.00 0.00 0.00 2.52
5825 6659 6.539103 GGCGAGGACTCTACATATTTTTCTTT 59.461 38.462 0.00 0.00 0.00 2.52
5826 6660 7.709613 GGCGAGGACTCTACATATTTTTCTTTA 59.290 37.037 0.00 0.00 0.00 1.85
5827 6661 9.095065 GCGAGGACTCTACATATTTTTCTTTAA 57.905 33.333 0.00 0.00 0.00 1.52
5842 6676 8.498054 TTTTTCTTTAAATGGAAATGTGCACA 57.502 26.923 24.08 24.08 32.54 4.57
5843 6677 7.475771 TTTCTTTAAATGGAAATGTGCACAC 57.524 32.000 24.37 10.18 0.00 3.82
5844 6678 6.154203 TCTTTAAATGGAAATGTGCACACA 57.846 33.333 24.37 16.19 46.44 3.72
5845 6679 6.215121 TCTTTAAATGGAAATGTGCACACAG 58.785 36.000 24.37 2.77 45.48 3.66
5846 6680 2.443887 AATGGAAATGTGCACACAGC 57.556 45.000 24.37 13.66 45.48 4.40
5847 6681 1.624336 ATGGAAATGTGCACACAGCT 58.376 45.000 24.37 2.54 45.48 4.24
5848 6682 1.401761 TGGAAATGTGCACACAGCTT 58.598 45.000 24.37 13.09 45.48 3.74
5849 6683 1.337703 TGGAAATGTGCACACAGCTTC 59.662 47.619 24.37 20.19 45.48 3.86
5850 6684 1.336240 GGAAATGTGCACACAGCTTCC 60.336 52.381 24.37 24.49 45.48 3.46
5851 6685 1.610522 GAAATGTGCACACAGCTTCCT 59.389 47.619 24.37 0.00 45.48 3.36
5852 6686 1.242076 AATGTGCACACAGCTTCCTC 58.758 50.000 24.37 0.00 45.48 3.71
5853 6687 0.399454 ATGTGCACACAGCTTCCTCT 59.601 50.000 24.37 0.00 45.48 3.69
5854 6688 0.181114 TGTGCACACAGCTTCCTCTT 59.819 50.000 17.42 0.00 45.94 2.85
5855 6689 1.416030 TGTGCACACAGCTTCCTCTTA 59.584 47.619 17.42 0.00 45.94 2.10
5856 6690 2.158827 TGTGCACACAGCTTCCTCTTAA 60.159 45.455 17.42 0.00 45.94 1.85
5857 6691 2.481952 GTGCACACAGCTTCCTCTTAAG 59.518 50.000 13.17 0.00 45.94 1.85
5862 6696 4.617875 GCTTCCTCTTAAGCGGCA 57.382 55.556 6.62 0.00 42.21 5.69
5863 6697 2.090693 GCTTCCTCTTAAGCGGCAC 58.909 57.895 6.62 0.00 42.21 5.01
5864 6698 1.369839 GCTTCCTCTTAAGCGGCACC 61.370 60.000 6.62 0.00 42.21 5.01
5865 6699 0.036388 CTTCCTCTTAAGCGGCACCA 60.036 55.000 6.62 0.00 0.00 4.17
5866 6700 0.321298 TTCCTCTTAAGCGGCACCAC 60.321 55.000 6.62 0.00 0.00 4.16
5867 6701 1.003839 CCTCTTAAGCGGCACCACA 60.004 57.895 1.45 0.00 0.00 4.17
5868 6702 1.021390 CCTCTTAAGCGGCACCACAG 61.021 60.000 1.45 0.00 0.00 3.66
5869 6703 1.003839 TCTTAAGCGGCACCACAGG 60.004 57.895 1.45 0.00 0.00 4.00
5870 6704 2.033448 TTAAGCGGCACCACAGGG 59.967 61.111 1.45 0.00 41.29 4.45
5888 6722 3.166434 TGGTGCCCCAACCACTAG 58.834 61.111 0.00 0.00 45.43 2.57
5889 6723 1.772567 TGGTGCCCCAACCACTAGT 60.773 57.895 0.00 0.00 45.43 2.57
6298 7143 0.035881 ACACATGTGGTCTCAGCAGG 59.964 55.000 28.64 0.23 34.19 4.85
6778 9427 1.670949 ATTGCCCGTGTGTTGCAACA 61.671 50.000 27.96 27.96 46.60 3.33
7195 9859 8.021396 GTGGAAACCAAGATTAAGAACACATAC 58.979 37.037 0.00 0.00 34.18 2.39
7238 9902 0.464916 TAGGCTGTGATGGCATGCTG 60.465 55.000 18.92 2.97 34.73 4.41
7359 10410 4.626287 GCAACCTCATCTCCCAAATACTGA 60.626 45.833 0.00 0.00 0.00 3.41
7361 10412 3.456277 ACCTCATCTCCCAAATACTGACC 59.544 47.826 0.00 0.00 0.00 4.02
7412 10463 1.738908 CATCACCACATCATGAACGCA 59.261 47.619 0.00 0.00 0.00 5.24
7413 10464 1.889545 TCACCACATCATGAACGCAA 58.110 45.000 0.00 0.00 0.00 4.85
7718 10769 4.595781 ACCCTGTTTTATCTGTCTACCACA 59.404 41.667 0.00 0.00 0.00 4.17
7719 10770 5.072600 ACCCTGTTTTATCTGTCTACCACAA 59.927 40.000 0.00 0.00 33.31 3.33
7720 10771 6.180472 CCCTGTTTTATCTGTCTACCACAAT 58.820 40.000 0.00 0.00 33.31 2.71
7721 10772 6.316390 CCCTGTTTTATCTGTCTACCACAATC 59.684 42.308 0.00 0.00 33.31 2.67
7722 10773 7.106239 CCTGTTTTATCTGTCTACCACAATCT 58.894 38.462 0.00 0.00 33.31 2.40
7723 10774 7.278868 CCTGTTTTATCTGTCTACCACAATCTC 59.721 40.741 0.00 0.00 33.31 2.75
7724 10775 7.907389 TGTTTTATCTGTCTACCACAATCTCT 58.093 34.615 0.00 0.00 33.31 3.10
7725 10776 8.375506 TGTTTTATCTGTCTACCACAATCTCTT 58.624 33.333 0.00 0.00 33.31 2.85
7726 10777 8.874816 GTTTTATCTGTCTACCACAATCTCTTC 58.125 37.037 0.00 0.00 33.31 2.87
7727 10778 7.962995 TTATCTGTCTACCACAATCTCTTCT 57.037 36.000 0.00 0.00 33.31 2.85
7728 10779 5.906113 TCTGTCTACCACAATCTCTTCTC 57.094 43.478 0.00 0.00 33.31 2.87
7729 10780 4.707448 TCTGTCTACCACAATCTCTTCTCC 59.293 45.833 0.00 0.00 33.31 3.71
7730 10781 4.416516 TGTCTACCACAATCTCTTCTCCA 58.583 43.478 0.00 0.00 29.30 3.86
7731 10782 5.026121 TGTCTACCACAATCTCTTCTCCAT 58.974 41.667 0.00 0.00 29.30 3.41
7732 10783 5.485353 TGTCTACCACAATCTCTTCTCCATT 59.515 40.000 0.00 0.00 29.30 3.16
7733 10784 6.013379 TGTCTACCACAATCTCTTCTCCATTT 60.013 38.462 0.00 0.00 29.30 2.32
7734 10785 6.314896 GTCTACCACAATCTCTTCTCCATTTG 59.685 42.308 0.00 0.00 0.00 2.32
7735 10786 4.990526 ACCACAATCTCTTCTCCATTTGT 58.009 39.130 0.00 0.00 0.00 2.83
7736 10787 5.388654 ACCACAATCTCTTCTCCATTTGTT 58.611 37.500 0.00 0.00 0.00 2.83
7737 10788 5.835280 ACCACAATCTCTTCTCCATTTGTTT 59.165 36.000 0.00 0.00 0.00 2.83
7738 10789 6.324770 ACCACAATCTCTTCTCCATTTGTTTT 59.675 34.615 0.00 0.00 0.00 2.43
7739 10790 7.147672 ACCACAATCTCTTCTCCATTTGTTTTT 60.148 33.333 0.00 0.00 0.00 1.94
8034 11085 1.402456 CCATGAAAGCAGCAGTGAAGC 60.402 52.381 0.00 0.00 0.00 3.86
8267 11318 9.294030 GATTGTAATGATTTTGACTCAACATCC 57.706 33.333 13.15 1.93 31.77 3.51
8362 11426 2.045524 TCTGGAAAGGCATGGCAAAAA 58.954 42.857 22.64 1.87 0.00 1.94
8439 11503 1.226746 GTTCGGTTGACAGGGAAGTG 58.773 55.000 0.00 0.00 0.00 3.16
8490 11555 9.990360 GGATTAAATCCCTAACAAAGTCAAAAA 57.010 29.630 0.00 0.00 43.88 1.94
8495 11560 6.709018 TCCCTAACAAAGTCAAAAAGAAGG 57.291 37.500 0.00 0.00 0.00 3.46
8497 11562 5.069119 CCCTAACAAAGTCAAAAAGAAGGCT 59.931 40.000 0.00 0.00 0.00 4.58
8500 11565 9.010029 CCTAACAAAGTCAAAAAGAAGGCTATA 57.990 33.333 0.00 0.00 0.00 1.31
8503 11568 6.490040 ACAAAGTCAAAAAGAAGGCTATAGCA 59.510 34.615 25.53 0.00 44.36 3.49
8604 11719 6.432162 AATGATGACATTACTGCAAGTCTTGT 59.568 34.615 14.03 0.00 40.39 3.16
8650 11771 2.204461 TGCTTTGGCACTGCAGCAT 61.204 52.632 15.27 0.00 44.28 3.79
8983 12148 2.232452 TGTAGAGCAGCAGGAAGAACTC 59.768 50.000 0.00 0.00 0.00 3.01
9149 12314 4.579340 TGGTGCATTGTTTGAAAATTGCAT 59.421 33.333 11.92 0.00 33.54 3.96
9199 12370 2.369860 TGGCTCAGACAGTCTGTTTGAT 59.630 45.455 26.65 1.64 44.58 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.381272 TCCTTTCACAAGCACTGGAAAAG 59.619 43.478 0.00 0.00 33.60 2.27
3 4 2.727123 TCCTTTCACAAGCACTGGAA 57.273 45.000 0.00 0.00 0.00 3.53
6 7 4.997565 TCTTTTTCCTTTCACAAGCACTG 58.002 39.130 0.00 0.00 0.00 3.66
8 9 6.720012 TTTTCTTTTTCCTTTCACAAGCAC 57.280 33.333 0.00 0.00 0.00 4.40
34 35 8.311109 GCCACTTCCTTCCTTTTATTGATTTTA 58.689 33.333 0.00 0.00 0.00 1.52
35 36 7.161404 GCCACTTCCTTCCTTTTATTGATTTT 58.839 34.615 0.00 0.00 0.00 1.82
36 37 6.269769 TGCCACTTCCTTCCTTTTATTGATTT 59.730 34.615 0.00 0.00 0.00 2.17
37 38 5.779771 TGCCACTTCCTTCCTTTTATTGATT 59.220 36.000 0.00 0.00 0.00 2.57
38 39 5.332743 TGCCACTTCCTTCCTTTTATTGAT 58.667 37.500 0.00 0.00 0.00 2.57
39 40 4.735369 TGCCACTTCCTTCCTTTTATTGA 58.265 39.130 0.00 0.00 0.00 2.57
40 41 5.413499 CATGCCACTTCCTTCCTTTTATTG 58.587 41.667 0.00 0.00 0.00 1.90
41 42 4.081476 GCATGCCACTTCCTTCCTTTTATT 60.081 41.667 6.36 0.00 0.00 1.40
42 43 3.448660 GCATGCCACTTCCTTCCTTTTAT 59.551 43.478 6.36 0.00 0.00 1.40
43 44 2.825532 GCATGCCACTTCCTTCCTTTTA 59.174 45.455 6.36 0.00 0.00 1.52
44 45 1.620323 GCATGCCACTTCCTTCCTTTT 59.380 47.619 6.36 0.00 0.00 2.27
45 46 1.203100 AGCATGCCACTTCCTTCCTTT 60.203 47.619 15.66 0.00 0.00 3.11
46 47 0.407139 AGCATGCCACTTCCTTCCTT 59.593 50.000 15.66 0.00 0.00 3.36
47 48 1.289160 TAGCATGCCACTTCCTTCCT 58.711 50.000 15.66 0.00 0.00 3.36
48 49 2.128771 TTAGCATGCCACTTCCTTCC 57.871 50.000 15.66 0.00 0.00 3.46
49 50 3.282021 TGATTAGCATGCCACTTCCTTC 58.718 45.455 15.66 1.32 0.00 3.46
50 51 3.370840 TGATTAGCATGCCACTTCCTT 57.629 42.857 15.66 0.00 0.00 3.36
51 52 3.370840 TTGATTAGCATGCCACTTCCT 57.629 42.857 15.66 0.00 0.00 3.36
52 53 3.696051 TCTTTGATTAGCATGCCACTTCC 59.304 43.478 15.66 0.00 0.00 3.46
53 54 4.397417 ACTCTTTGATTAGCATGCCACTTC 59.603 41.667 15.66 7.31 0.00 3.01
54 55 4.338879 ACTCTTTGATTAGCATGCCACTT 58.661 39.130 15.66 0.00 0.00 3.16
55 56 3.944015 GACTCTTTGATTAGCATGCCACT 59.056 43.478 15.66 0.00 0.00 4.00
56 57 3.691118 TGACTCTTTGATTAGCATGCCAC 59.309 43.478 15.66 4.07 0.00 5.01
57 58 3.954200 TGACTCTTTGATTAGCATGCCA 58.046 40.909 15.66 0.00 0.00 4.92
58 59 4.970662 TTGACTCTTTGATTAGCATGCC 57.029 40.909 15.66 0.00 0.00 4.40
59 60 4.738740 GCATTGACTCTTTGATTAGCATGC 59.261 41.667 10.51 10.51 0.00 4.06
60 61 4.968181 CGCATTGACTCTTTGATTAGCATG 59.032 41.667 0.00 0.00 0.00 4.06
61 62 4.877823 TCGCATTGACTCTTTGATTAGCAT 59.122 37.500 0.00 0.00 0.00 3.79
62 63 4.252878 TCGCATTGACTCTTTGATTAGCA 58.747 39.130 0.00 0.00 0.00 3.49
63 64 4.864916 TCGCATTGACTCTTTGATTAGC 57.135 40.909 0.00 0.00 0.00 3.09
64 65 6.312426 ACTCTTCGCATTGACTCTTTGATTAG 59.688 38.462 0.00 0.00 0.00 1.73
65 66 6.091305 CACTCTTCGCATTGACTCTTTGATTA 59.909 38.462 0.00 0.00 0.00 1.75
66 67 4.999950 ACTCTTCGCATTGACTCTTTGATT 59.000 37.500 0.00 0.00 0.00 2.57
67 68 4.391216 CACTCTTCGCATTGACTCTTTGAT 59.609 41.667 0.00 0.00 0.00 2.57
68 69 3.742882 CACTCTTCGCATTGACTCTTTGA 59.257 43.478 0.00 0.00 0.00 2.69
69 70 3.120408 CCACTCTTCGCATTGACTCTTTG 60.120 47.826 0.00 0.00 0.00 2.77
70 71 3.070018 CCACTCTTCGCATTGACTCTTT 58.930 45.455 0.00 0.00 0.00 2.52
71 72 2.693069 CCACTCTTCGCATTGACTCTT 58.307 47.619 0.00 0.00 0.00 2.85
72 73 1.674221 GCCACTCTTCGCATTGACTCT 60.674 52.381 0.00 0.00 0.00 3.24
73 74 0.723981 GCCACTCTTCGCATTGACTC 59.276 55.000 0.00 0.00 0.00 3.36
74 75 0.035317 TGCCACTCTTCGCATTGACT 59.965 50.000 0.00 0.00 0.00 3.41
75 76 0.874390 TTGCCACTCTTCGCATTGAC 59.126 50.000 0.00 0.00 34.35 3.18
76 77 1.825090 ATTGCCACTCTTCGCATTGA 58.175 45.000 0.00 0.00 34.35 2.57
77 78 2.642139 AATTGCCACTCTTCGCATTG 57.358 45.000 0.00 0.00 34.35 2.82
78 79 3.665745 AAAATTGCCACTCTTCGCATT 57.334 38.095 0.00 0.00 34.35 3.56
79 80 3.426159 CGTAAAATTGCCACTCTTCGCAT 60.426 43.478 0.00 0.00 34.35 4.73
80 81 2.095969 CGTAAAATTGCCACTCTTCGCA 60.096 45.455 0.00 0.00 0.00 5.10
81 82 2.158841 TCGTAAAATTGCCACTCTTCGC 59.841 45.455 0.00 0.00 0.00 4.70
82 83 4.394795 CTTCGTAAAATTGCCACTCTTCG 58.605 43.478 0.00 0.00 0.00 3.79
83 84 4.159120 GCTTCGTAAAATTGCCACTCTTC 58.841 43.478 0.00 0.00 0.00 2.87
84 85 3.057526 GGCTTCGTAAAATTGCCACTCTT 60.058 43.478 0.00 0.00 42.79 2.85
85 86 2.488153 GGCTTCGTAAAATTGCCACTCT 59.512 45.455 0.00 0.00 42.79 3.24
86 87 2.863739 GGCTTCGTAAAATTGCCACTC 58.136 47.619 0.00 0.00 42.79 3.51
90 91 4.110036 AGATTGGCTTCGTAAAATTGCC 57.890 40.909 0.00 0.00 43.49 4.52
91 92 7.575332 TTTAAGATTGGCTTCGTAAAATTGC 57.425 32.000 6.65 0.00 38.05 3.56
92 93 9.191995 ACTTTTAAGATTGGCTTCGTAAAATTG 57.808 29.630 15.83 11.07 38.20 2.32
93 94 9.191995 CACTTTTAAGATTGGCTTCGTAAAATT 57.808 29.630 15.83 11.10 38.20 1.82
94 95 7.812669 CCACTTTTAAGATTGGCTTCGTAAAAT 59.187 33.333 15.83 8.64 38.20 1.82
95 96 7.142680 CCACTTTTAAGATTGGCTTCGTAAAA 58.857 34.615 15.17 15.17 37.28 1.52
96 97 6.674066 CCACTTTTAAGATTGGCTTCGTAAA 58.326 36.000 0.00 5.54 38.05 2.01
97 98 6.249035 CCACTTTTAAGATTGGCTTCGTAA 57.751 37.500 0.00 0.00 38.05 3.18
98 99 5.873179 CCACTTTTAAGATTGGCTTCGTA 57.127 39.130 0.00 0.00 38.05 3.43
99 100 4.766404 CCACTTTTAAGATTGGCTTCGT 57.234 40.909 0.00 0.00 38.05 3.85
105 106 6.690530 TCAGAATTGCCACTTTTAAGATTGG 58.309 36.000 0.00 0.00 0.00 3.16
106 107 7.596494 TCTCAGAATTGCCACTTTTAAGATTG 58.404 34.615 0.00 0.00 0.00 2.67
107 108 7.765695 TCTCAGAATTGCCACTTTTAAGATT 57.234 32.000 0.00 0.00 0.00 2.40
108 109 7.576477 GCTTCTCAGAATTGCCACTTTTAAGAT 60.576 37.037 0.00 0.00 0.00 2.40
109 110 6.294176 GCTTCTCAGAATTGCCACTTTTAAGA 60.294 38.462 0.00 0.00 0.00 2.10
110 111 5.860716 GCTTCTCAGAATTGCCACTTTTAAG 59.139 40.000 0.00 0.00 0.00 1.85
111 112 5.278957 GGCTTCTCAGAATTGCCACTTTTAA 60.279 40.000 11.92 0.00 42.79 1.52
112 113 4.218417 GGCTTCTCAGAATTGCCACTTTTA 59.782 41.667 11.92 0.00 42.79 1.52
113 114 3.006217 GGCTTCTCAGAATTGCCACTTTT 59.994 43.478 11.92 0.00 42.79 2.27
114 115 2.560105 GGCTTCTCAGAATTGCCACTTT 59.440 45.455 11.92 0.00 42.79 2.66
115 116 2.165998 GGCTTCTCAGAATTGCCACTT 58.834 47.619 11.92 0.00 42.79 3.16
116 117 1.831580 GGCTTCTCAGAATTGCCACT 58.168 50.000 11.92 0.00 42.79 4.00
119 120 0.449388 CGTGGCTTCTCAGAATTGCC 59.551 55.000 10.22 10.22 43.49 4.52
120 121 1.160137 ACGTGGCTTCTCAGAATTGC 58.840 50.000 0.00 0.00 0.00 3.56
121 122 4.393062 ACAATACGTGGCTTCTCAGAATTG 59.607 41.667 0.00 0.00 0.00 2.32
122 123 4.579869 ACAATACGTGGCTTCTCAGAATT 58.420 39.130 0.00 0.00 0.00 2.17
123 124 4.207891 ACAATACGTGGCTTCTCAGAAT 57.792 40.909 0.00 0.00 0.00 2.40
124 125 3.678056 ACAATACGTGGCTTCTCAGAA 57.322 42.857 0.00 0.00 0.00 3.02
125 126 4.219944 ACTTACAATACGTGGCTTCTCAGA 59.780 41.667 0.00 0.00 0.00 3.27
126 127 4.495422 ACTTACAATACGTGGCTTCTCAG 58.505 43.478 0.00 0.00 0.00 3.35
127 128 4.530710 ACTTACAATACGTGGCTTCTCA 57.469 40.909 0.00 0.00 0.00 3.27
128 129 5.857822 AAACTTACAATACGTGGCTTCTC 57.142 39.130 0.00 0.00 0.00 2.87
129 130 6.628919 AAAAACTTACAATACGTGGCTTCT 57.371 33.333 0.00 0.00 0.00 2.85
149 150 2.986019 TGGAGGAGGGACATCAGAAAAA 59.014 45.455 0.00 0.00 0.00 1.94
150 151 2.631384 TGGAGGAGGGACATCAGAAAA 58.369 47.619 0.00 0.00 0.00 2.29
151 152 2.342406 TGGAGGAGGGACATCAGAAA 57.658 50.000 0.00 0.00 0.00 2.52
152 153 2.191400 CTTGGAGGAGGGACATCAGAA 58.809 52.381 0.00 0.00 0.00 3.02
153 154 1.362584 TCTTGGAGGAGGGACATCAGA 59.637 52.381 0.00 0.00 0.00 3.27
154 155 1.871418 TCTTGGAGGAGGGACATCAG 58.129 55.000 0.00 0.00 0.00 2.90
155 156 2.342406 TTCTTGGAGGAGGGACATCA 57.658 50.000 0.00 0.00 0.00 3.07
156 157 3.721087 TTTTCTTGGAGGAGGGACATC 57.279 47.619 0.00 0.00 0.00 3.06
157 158 3.815757 GCTTTTTCTTGGAGGAGGGACAT 60.816 47.826 0.00 0.00 0.00 3.06
212 213 2.675772 GAGACGTGGGAGGTCGGT 60.676 66.667 0.00 0.00 37.99 4.69
217 218 4.919653 CACATGAGACGTGGGAGG 57.080 61.111 0.00 0.00 0.00 4.30
290 292 8.695456 ACAAAACTTGAAGAACCATCTACAAAT 58.305 29.630 0.00 0.00 33.77 2.32
294 296 8.290325 CCTAACAAAACTTGAAGAACCATCTAC 58.710 37.037 0.00 0.00 33.77 2.59
301 303 7.062956 CACAAACCCTAACAAAACTTGAAGAAC 59.937 37.037 0.00 0.00 0.00 3.01
330 332 1.813178 TCGTCTCGTCTTCTTGAGCAT 59.187 47.619 0.00 0.00 32.20 3.79
355 357 8.166726 AGAACCTTATTCCATCTTCAAGAAGTT 58.833 33.333 9.44 0.00 39.38 2.66
356 358 7.694093 AGAACCTTATTCCATCTTCAAGAAGT 58.306 34.615 9.44 0.00 39.38 3.01
400 402 3.076621 ACGATACTAGACACACCGTTGA 58.923 45.455 0.00 0.00 0.00 3.18
404 406 1.004185 CCGACGATACTAGACACACCG 60.004 57.143 0.00 0.00 0.00 4.94
451 454 2.159240 CCGACCAAATCTCACGAGATCA 60.159 50.000 9.92 0.00 46.75 2.92
459 462 1.142060 ACAACCACCGACCAAATCTCA 59.858 47.619 0.00 0.00 0.00 3.27
493 496 2.036733 TGAACAAAGACCGGATTCGAGT 59.963 45.455 9.46 0.00 39.00 4.18
498 501 5.745227 AGACATATGAACAAAGACCGGATT 58.255 37.500 9.46 0.00 0.00 3.01
516 524 3.054065 GGAAGGATCCAACCTGAAGACAT 60.054 47.826 15.82 0.00 45.79 3.06
551 559 4.388499 AACCGCCGCCGATGAAGT 62.388 61.111 0.00 0.00 36.29 3.01
629 637 2.805295 CGGAGTCAGGCACAACTTGTTA 60.805 50.000 0.00 0.00 0.00 2.41
643 651 1.677966 CCCTTCCTCGTCGGAGTCA 60.678 63.158 0.00 0.00 44.28 3.41
645 653 2.362632 CCCCTTCCTCGTCGGAGT 60.363 66.667 0.00 0.00 44.28 3.85
682 690 4.749310 AGCACTGAAGCGAGCCGG 62.749 66.667 0.00 0.00 40.15 6.13
815 823 3.829026 GGGGAGAGAATTGGATATTTGCC 59.171 47.826 0.00 0.00 0.00 4.52
816 824 4.473444 TGGGGAGAGAATTGGATATTTGC 58.527 43.478 0.00 0.00 0.00 3.68
817 825 5.009010 CGTTGGGGAGAGAATTGGATATTTG 59.991 44.000 0.00 0.00 0.00 2.32
818 826 5.104109 TCGTTGGGGAGAGAATTGGATATTT 60.104 40.000 0.00 0.00 0.00 1.40
819 827 4.412199 TCGTTGGGGAGAGAATTGGATATT 59.588 41.667 0.00 0.00 0.00 1.28
820 828 3.973973 TCGTTGGGGAGAGAATTGGATAT 59.026 43.478 0.00 0.00 0.00 1.63
821 829 3.380393 TCGTTGGGGAGAGAATTGGATA 58.620 45.455 0.00 0.00 0.00 2.59
822 830 2.196595 TCGTTGGGGAGAGAATTGGAT 58.803 47.619 0.00 0.00 0.00 3.41
823 831 1.651737 TCGTTGGGGAGAGAATTGGA 58.348 50.000 0.00 0.00 0.00 3.53
824 832 2.684881 CAATCGTTGGGGAGAGAATTGG 59.315 50.000 0.00 0.00 0.00 3.16
837 845 0.725784 GAAGCGTGTGCCAATCGTTG 60.726 55.000 0.00 0.00 44.31 4.10
838 846 1.574428 GAAGCGTGTGCCAATCGTT 59.426 52.632 0.00 0.00 44.31 3.85
839 847 2.667318 CGAAGCGTGTGCCAATCGT 61.667 57.895 0.00 0.00 44.31 3.73
884 892 1.434188 TCCTCTGCTTGACTTTGGGA 58.566 50.000 0.00 0.00 0.00 4.37
986 994 3.790437 ACATGCCTCCTGCCTCCG 61.790 66.667 0.00 0.00 40.16 4.63
987 995 2.124403 CACATGCCTCCTGCCTCC 60.124 66.667 0.00 0.00 40.16 4.30
988 996 2.124403 CCACATGCCTCCTGCCTC 60.124 66.667 0.00 0.00 40.16 4.70
989 997 3.736224 CCCACATGCCTCCTGCCT 61.736 66.667 0.00 0.00 40.16 4.75
1330 1345 7.880160 AAAAATGCATACCAAGTCTAGCATA 57.120 32.000 0.00 0.00 41.37 3.14
1426 1441 3.494924 CCAACAGAATCCGCATATCCTCA 60.495 47.826 0.00 0.00 0.00 3.86
1898 1969 5.360714 AGCGAAAATGACCATCATACCAAAT 59.639 36.000 0.00 0.00 35.76 2.32
2020 2091 8.885494 AAAAGCATTAAGTTTTCAGCAACATA 57.115 26.923 0.00 0.00 29.74 2.29
2055 2126 4.504461 CGTACAAGTTGATAGTCATCCTGC 59.496 45.833 10.54 0.00 0.00 4.85
2086 2157 8.807118 ACTCGAGTCATATATTTGTCCACATAT 58.193 33.333 13.58 0.00 0.00 1.78
2243 2314 1.866880 GCTGTGCTTCAAACTTGCCAG 60.867 52.381 0.00 0.00 0.00 4.85
2268 2339 7.540474 TGAGTATAGTGTCTCCCAATATTCC 57.460 40.000 0.00 0.00 35.95 3.01
2501 2605 2.292267 CGGAGAGCTGTGCCATTTAAT 58.708 47.619 0.00 0.00 0.00 1.40
2515 2619 0.317938 GCGTACCTACATGCGGAGAG 60.318 60.000 8.51 1.08 0.00 3.20
2521 2625 2.618053 ACAAAGAGCGTACCTACATGC 58.382 47.619 0.00 0.00 0.00 4.06
2614 2740 3.725740 CACGAATCAGCACTTTTTGTCAC 59.274 43.478 0.00 0.00 0.00 3.67
2649 2775 3.084039 CCCGCATATATTTGTCCATGCT 58.916 45.455 4.77 0.00 41.25 3.79
2798 2932 3.376859 TGCAGAAGTGAACAATTGAACGT 59.623 39.130 13.59 5.70 0.00 3.99
3046 3182 6.390721 CACGTGATAGGGACAATAGGAATAG 58.609 44.000 10.90 0.00 0.00 1.73
3048 3184 4.040461 CCACGTGATAGGGACAATAGGAAT 59.960 45.833 19.30 0.00 0.00 3.01
3175 3312 4.593864 GGGACGCGGCTGGAGATC 62.594 72.222 13.91 0.00 0.00 2.75
3525 3698 4.807039 GCCCGGCGTCGTGTGTAT 62.807 66.667 9.28 0.00 33.95 2.29
3543 3716 3.477530 GGGAGGCGTTGATTTTATAGCT 58.522 45.455 0.00 0.00 0.00 3.32
3639 3833 0.975040 GCTGGGCTTGGAGAGAGAGA 60.975 60.000 0.00 0.00 0.00 3.10
3640 3834 1.521616 GCTGGGCTTGGAGAGAGAG 59.478 63.158 0.00 0.00 0.00 3.20
3643 3837 3.393970 CGGCTGGGCTTGGAGAGA 61.394 66.667 0.00 0.00 0.00 3.10
3654 3848 3.535962 GAGAGAGAGGGCGGCTGG 61.536 72.222 9.56 0.00 0.00 4.85
3655 3849 3.535962 GGAGAGAGAGGGCGGCTG 61.536 72.222 9.56 0.00 0.00 4.85
3656 3850 4.851214 GGGAGAGAGAGGGCGGCT 62.851 72.222 9.56 0.00 0.00 5.52
3658 3852 3.984186 TTGGGGAGAGAGAGGGCGG 62.984 68.421 0.00 0.00 0.00 6.13
3659 3853 2.364317 TTGGGGAGAGAGAGGGCG 60.364 66.667 0.00 0.00 0.00 6.13
3660 3854 2.741055 GCTTGGGGAGAGAGAGGGC 61.741 68.421 0.00 0.00 0.00 5.19
3661 3855 2.069430 GGCTTGGGGAGAGAGAGGG 61.069 68.421 0.00 0.00 0.00 4.30
3662 3856 2.069430 GGGCTTGGGGAGAGAGAGG 61.069 68.421 0.00 0.00 0.00 3.69
3663 3857 1.306482 TGGGCTTGGGGAGAGAGAG 60.306 63.158 0.00 0.00 0.00 3.20
3664 3858 1.306482 CTGGGCTTGGGGAGAGAGA 60.306 63.158 0.00 0.00 0.00 3.10
3665 3859 1.306482 TCTGGGCTTGGGGAGAGAG 60.306 63.158 0.00 0.00 0.00 3.20
3666 3860 1.613630 GTCTGGGCTTGGGGAGAGA 60.614 63.158 0.00 0.00 0.00 3.10
4104 4313 2.232298 CTCGAGGTGCTGGAGAACCC 62.232 65.000 3.91 0.00 45.33 4.11
4845 5243 1.000717 CGGCAAACGGGACAAAGATTT 60.001 47.619 0.00 0.00 39.42 2.17
5056 5513 2.422597 TGCTATTTGACTGGTCCAACG 58.577 47.619 0.00 0.00 0.00 4.10
5084 5541 4.819630 GTCCAAACATAGTCCAACTCAACA 59.180 41.667 0.00 0.00 0.00 3.33
5366 6200 9.066892 TCAATGCAAGTCAAATTCTTACTAAGT 57.933 29.630 0.00 0.00 0.00 2.24
5460 6294 7.394077 TGTTATTCAGCTCAAAATTCTCCATCA 59.606 33.333 0.00 0.00 0.00 3.07
5516 6350 2.549754 CCTTCACGCATAGCTTAATGGG 59.450 50.000 11.00 11.00 43.43 4.00
5517 6351 2.549754 CCCTTCACGCATAGCTTAATGG 59.450 50.000 0.00 0.00 0.00 3.16
5518 6352 2.031682 GCCCTTCACGCATAGCTTAATG 60.032 50.000 0.00 0.00 0.00 1.90
5519 6353 2.222027 GCCCTTCACGCATAGCTTAAT 58.778 47.619 0.00 0.00 0.00 1.40
5520 6354 1.663695 GCCCTTCACGCATAGCTTAA 58.336 50.000 0.00 0.00 0.00 1.85
5521 6355 0.529773 CGCCCTTCACGCATAGCTTA 60.530 55.000 0.00 0.00 0.00 3.09
5522 6356 1.815421 CGCCCTTCACGCATAGCTT 60.815 57.895 0.00 0.00 0.00 3.74
5523 6357 2.202932 CGCCCTTCACGCATAGCT 60.203 61.111 0.00 0.00 0.00 3.32
5524 6358 3.272334 CCGCCCTTCACGCATAGC 61.272 66.667 0.00 0.00 0.00 2.97
5525 6359 3.272334 GCCGCCCTTCACGCATAG 61.272 66.667 0.00 0.00 0.00 2.23
5526 6360 4.849310 GGCCGCCCTTCACGCATA 62.849 66.667 0.00 0.00 0.00 3.14
5531 6365 4.966787 TGGTTGGCCGCCCTTCAC 62.967 66.667 7.03 0.00 37.67 3.18
5532 6366 4.659172 CTGGTTGGCCGCCCTTCA 62.659 66.667 7.03 1.26 37.67 3.02
5536 6370 4.506255 ATAGCTGGTTGGCCGCCC 62.506 66.667 7.03 8.51 37.67 6.13
5537 6371 3.211963 CATAGCTGGTTGGCCGCC 61.212 66.667 1.04 1.04 37.67 6.13
5538 6372 3.892581 GCATAGCTGGTTGGCCGC 61.893 66.667 0.00 0.00 37.67 6.53
5539 6373 3.211963 GGCATAGCTGGTTGGCCG 61.212 66.667 0.00 0.00 37.67 6.13
5540 6374 2.044053 TGGCATAGCTGGTTGGCC 60.044 61.111 14.30 12.70 44.82 5.36
5541 6375 2.764314 CGTGGCATAGCTGGTTGGC 61.764 63.158 0.00 4.54 38.77 4.52
5542 6376 1.377202 ACGTGGCATAGCTGGTTGG 60.377 57.895 0.00 0.00 0.00 3.77
5543 6377 1.647545 CCACGTGGCATAGCTGGTTG 61.648 60.000 24.02 0.00 0.00 3.77
5544 6378 1.377202 CCACGTGGCATAGCTGGTT 60.377 57.895 24.02 0.00 0.00 3.67
5545 6379 2.268920 CCACGTGGCATAGCTGGT 59.731 61.111 24.02 0.00 0.00 4.00
5558 6392 4.688419 CAACCAGCTTGCGCCACG 62.688 66.667 4.18 0.00 36.60 4.94
5559 6393 4.347453 CCAACCAGCTTGCGCCAC 62.347 66.667 4.18 0.00 36.60 5.01
5564 6398 4.347453 CACGGCCAACCAGCTTGC 62.347 66.667 2.24 0.00 34.57 4.01
5565 6399 3.673484 CCACGGCCAACCAGCTTG 61.673 66.667 2.24 0.00 34.57 4.01
5566 6400 4.204028 ACCACGGCCAACCAGCTT 62.204 61.111 2.24 0.00 34.57 3.74
5567 6401 4.954970 CACCACGGCCAACCAGCT 62.955 66.667 2.24 0.00 34.57 4.24
5568 6402 4.947147 TCACCACGGCCAACCAGC 62.947 66.667 2.24 0.00 34.57 4.85
5569 6403 2.669569 CTCACCACGGCCAACCAG 60.670 66.667 2.24 0.00 34.57 4.00
5570 6404 2.272230 TTTCTCACCACGGCCAACCA 62.272 55.000 2.24 0.00 34.57 3.67
5571 6405 0.893727 ATTTCTCACCACGGCCAACC 60.894 55.000 2.24 0.00 0.00 3.77
5572 6406 0.521735 GATTTCTCACCACGGCCAAC 59.478 55.000 2.24 0.00 0.00 3.77
5573 6407 0.400213 AGATTTCTCACCACGGCCAA 59.600 50.000 2.24 0.00 0.00 4.52
5574 6408 0.400213 AAGATTTCTCACCACGGCCA 59.600 50.000 2.24 0.00 0.00 5.36
5575 6409 1.534729 AAAGATTTCTCACCACGGCC 58.465 50.000 0.00 0.00 0.00 6.13
5576 6410 2.412847 CGAAAAGATTTCTCACCACGGC 60.413 50.000 1.82 0.00 0.00 5.68
5577 6411 3.064207 TCGAAAAGATTTCTCACCACGG 58.936 45.455 1.82 0.00 0.00 4.94
5578 6412 4.725556 TTCGAAAAGATTTCTCACCACG 57.274 40.909 0.00 0.00 0.00 4.94
5579 6413 7.930513 AAAATTCGAAAAGATTTCTCACCAC 57.069 32.000 0.00 0.00 0.00 4.16
5640 6474 4.569719 GGTCCTCACCTCCATCTAAAAA 57.430 45.455 0.00 0.00 40.00 1.94
5652 6486 4.302559 AAAAATACCAGAGGTCCTCACC 57.697 45.455 21.26 0.00 44.19 4.02
5670 6504 7.659390 CACTTTGCATAACCCTCCATTTAAAAA 59.341 33.333 0.00 0.00 0.00 1.94
5671 6505 7.158021 CACTTTGCATAACCCTCCATTTAAAA 58.842 34.615 0.00 0.00 0.00 1.52
5672 6506 6.295575 CCACTTTGCATAACCCTCCATTTAAA 60.296 38.462 0.00 0.00 0.00 1.52
5673 6507 5.186797 CCACTTTGCATAACCCTCCATTTAA 59.813 40.000 0.00 0.00 0.00 1.52
5674 6508 4.709397 CCACTTTGCATAACCCTCCATTTA 59.291 41.667 0.00 0.00 0.00 1.40
5675 6509 3.515104 CCACTTTGCATAACCCTCCATTT 59.485 43.478 0.00 0.00 0.00 2.32
5676 6510 3.099141 CCACTTTGCATAACCCTCCATT 58.901 45.455 0.00 0.00 0.00 3.16
5677 6511 2.738743 CCACTTTGCATAACCCTCCAT 58.261 47.619 0.00 0.00 0.00 3.41
5678 6512 1.890573 GCCACTTTGCATAACCCTCCA 60.891 52.381 0.00 0.00 0.00 3.86
5679 6513 0.817654 GCCACTTTGCATAACCCTCC 59.182 55.000 0.00 0.00 0.00 4.30
5680 6514 1.202348 GTGCCACTTTGCATAACCCTC 59.798 52.381 0.00 0.00 44.30 4.30
5681 6515 1.203050 AGTGCCACTTTGCATAACCCT 60.203 47.619 0.00 0.00 44.30 4.34
5682 6516 1.202348 GAGTGCCACTTTGCATAACCC 59.798 52.381 0.00 0.00 44.30 4.11
5683 6517 1.135689 CGAGTGCCACTTTGCATAACC 60.136 52.381 0.00 0.00 44.30 2.85
5684 6518 1.535462 ACGAGTGCCACTTTGCATAAC 59.465 47.619 0.00 0.00 44.30 1.89
5685 6519 1.890876 ACGAGTGCCACTTTGCATAA 58.109 45.000 0.00 0.00 44.30 1.90
5686 6520 1.535028 CAACGAGTGCCACTTTGCATA 59.465 47.619 0.00 0.00 44.30 3.14
5687 6521 0.311790 CAACGAGTGCCACTTTGCAT 59.688 50.000 0.00 0.00 44.30 3.96
5688 6522 1.723608 CCAACGAGTGCCACTTTGCA 61.724 55.000 0.00 0.00 39.37 4.08
5689 6523 1.008538 CCAACGAGTGCCACTTTGC 60.009 57.895 0.00 0.00 0.00 3.68
5690 6524 1.531149 CTACCAACGAGTGCCACTTTG 59.469 52.381 0.00 0.07 0.00 2.77
5691 6525 1.542547 CCTACCAACGAGTGCCACTTT 60.543 52.381 0.00 0.00 0.00 2.66
5692 6526 0.034896 CCTACCAACGAGTGCCACTT 59.965 55.000 0.00 0.00 0.00 3.16
5693 6527 1.671742 CCTACCAACGAGTGCCACT 59.328 57.895 0.00 0.00 0.00 4.00
5694 6528 2.033194 GCCTACCAACGAGTGCCAC 61.033 63.158 0.00 0.00 0.00 5.01
5695 6529 2.214216 AGCCTACCAACGAGTGCCA 61.214 57.895 0.00 0.00 0.00 4.92
5696 6530 1.741770 CAGCCTACCAACGAGTGCC 60.742 63.158 0.00 0.00 0.00 5.01
5697 6531 2.391389 GCAGCCTACCAACGAGTGC 61.391 63.158 0.00 0.00 0.00 4.40
5698 6532 2.094659 CGCAGCCTACCAACGAGTG 61.095 63.158 0.00 0.00 0.00 3.51
5699 6533 2.261671 CGCAGCCTACCAACGAGT 59.738 61.111 0.00 0.00 0.00 4.18
5700 6534 2.509336 CCGCAGCCTACCAACGAG 60.509 66.667 0.00 0.00 0.00 4.18
5701 6535 3.307906 ACCGCAGCCTACCAACGA 61.308 61.111 0.00 0.00 0.00 3.85
5702 6536 3.118454 CACCGCAGCCTACCAACG 61.118 66.667 0.00 0.00 0.00 4.10
5703 6537 2.175035 TACCACCGCAGCCTACCAAC 62.175 60.000 0.00 0.00 0.00 3.77
5704 6538 1.481901 TTACCACCGCAGCCTACCAA 61.482 55.000 0.00 0.00 0.00 3.67
5705 6539 1.268992 ATTACCACCGCAGCCTACCA 61.269 55.000 0.00 0.00 0.00 3.25
5706 6540 0.107361 AATTACCACCGCAGCCTACC 60.107 55.000 0.00 0.00 0.00 3.18
5707 6541 1.669265 GAAATTACCACCGCAGCCTAC 59.331 52.381 0.00 0.00 0.00 3.18
5708 6542 1.557832 AGAAATTACCACCGCAGCCTA 59.442 47.619 0.00 0.00 0.00 3.93
5709 6543 0.328258 AGAAATTACCACCGCAGCCT 59.672 50.000 0.00 0.00 0.00 4.58
5710 6544 1.173913 AAGAAATTACCACCGCAGCC 58.826 50.000 0.00 0.00 0.00 4.85
5711 6545 2.488153 AGAAAGAAATTACCACCGCAGC 59.512 45.455 0.00 0.00 0.00 5.25
5712 6546 4.766404 AAGAAAGAAATTACCACCGCAG 57.234 40.909 0.00 0.00 0.00 5.18
5713 6547 5.523438 AAAAGAAAGAAATTACCACCGCA 57.477 34.783 0.00 0.00 0.00 5.69
5788 6622 1.067354 GTCCTCGCCTCCGTCTAAAAA 60.067 52.381 0.00 0.00 35.54 1.94
5789 6623 0.529378 GTCCTCGCCTCCGTCTAAAA 59.471 55.000 0.00 0.00 35.54 1.52
5790 6624 0.323178 AGTCCTCGCCTCCGTCTAAA 60.323 55.000 0.00 0.00 35.54 1.85
5791 6625 0.747283 GAGTCCTCGCCTCCGTCTAA 60.747 60.000 0.00 0.00 35.54 2.10
5792 6626 1.153208 GAGTCCTCGCCTCCGTCTA 60.153 63.158 0.00 0.00 35.54 2.59
5793 6627 1.624479 TAGAGTCCTCGCCTCCGTCT 61.624 60.000 0.00 0.00 35.54 4.18
5794 6628 1.153208 TAGAGTCCTCGCCTCCGTC 60.153 63.158 0.00 0.00 35.54 4.79
5795 6629 1.451747 GTAGAGTCCTCGCCTCCGT 60.452 63.158 0.00 0.00 35.54 4.69
5796 6630 0.820074 ATGTAGAGTCCTCGCCTCCG 60.820 60.000 0.00 0.00 34.09 4.63
5797 6631 2.273538 TATGTAGAGTCCTCGCCTCC 57.726 55.000 0.00 0.00 34.09 4.30
5798 6632 4.857509 AAATATGTAGAGTCCTCGCCTC 57.142 45.455 0.00 0.00 34.09 4.70
5799 6633 5.364157 AGAAAAATATGTAGAGTCCTCGCCT 59.636 40.000 0.00 0.00 34.09 5.52
5800 6634 5.602628 AGAAAAATATGTAGAGTCCTCGCC 58.397 41.667 0.00 0.00 34.09 5.54
5801 6635 7.541122 AAAGAAAAATATGTAGAGTCCTCGC 57.459 36.000 0.00 0.00 34.09 5.03
5816 6650 9.118300 TGTGCACATTTCCATTTAAAGAAAAAT 57.882 25.926 17.42 3.67 35.72 1.82
5817 6651 8.394121 GTGTGCACATTTCCATTTAAAGAAAAA 58.606 29.630 24.69 1.79 35.72 1.94
5818 6652 7.550551 TGTGTGCACATTTCCATTTAAAGAAAA 59.449 29.630 24.69 2.08 35.72 2.29
5819 6653 7.044181 TGTGTGCACATTTCCATTTAAAGAAA 58.956 30.769 24.69 5.41 36.21 2.52
5820 6654 6.577103 TGTGTGCACATTTCCATTTAAAGAA 58.423 32.000 24.69 0.00 36.21 2.52
5821 6655 6.154203 TGTGTGCACATTTCCATTTAAAGA 57.846 33.333 24.69 0.00 36.21 2.52
5822 6656 5.107375 GCTGTGTGCACATTTCCATTTAAAG 60.107 40.000 24.69 0.78 41.01 1.85
5823 6657 4.749099 GCTGTGTGCACATTTCCATTTAAA 59.251 37.500 24.69 0.00 41.01 1.52
5824 6658 4.039004 AGCTGTGTGCACATTTCCATTTAA 59.961 37.500 24.69 0.00 45.94 1.52
5825 6659 3.573538 AGCTGTGTGCACATTTCCATTTA 59.426 39.130 24.69 0.00 45.94 1.40
5826 6660 2.366266 AGCTGTGTGCACATTTCCATTT 59.634 40.909 24.69 4.47 45.94 2.32
5827 6661 1.965643 AGCTGTGTGCACATTTCCATT 59.034 42.857 24.69 4.82 45.94 3.16
5828 6662 1.624336 AGCTGTGTGCACATTTCCAT 58.376 45.000 24.69 4.61 45.94 3.41
5829 6663 1.337703 GAAGCTGTGTGCACATTTCCA 59.662 47.619 24.69 15.02 45.94 3.53
5830 6664 1.336240 GGAAGCTGTGTGCACATTTCC 60.336 52.381 24.69 25.36 45.94 3.13
5831 6665 1.610522 AGGAAGCTGTGTGCACATTTC 59.389 47.619 24.69 21.31 45.94 2.17
5832 6666 1.610522 GAGGAAGCTGTGTGCACATTT 59.389 47.619 24.69 14.81 45.94 2.32
5833 6667 1.202855 AGAGGAAGCTGTGTGCACATT 60.203 47.619 24.69 13.31 45.94 2.71
5834 6668 0.399454 AGAGGAAGCTGTGTGCACAT 59.601 50.000 24.69 6.14 45.94 3.21
5835 6669 0.181114 AAGAGGAAGCTGTGTGCACA 59.819 50.000 17.42 17.42 45.94 4.57
5836 6670 2.169832 TAAGAGGAAGCTGTGTGCAC 57.830 50.000 10.75 10.75 45.94 4.57
5837 6671 2.771089 CTTAAGAGGAAGCTGTGTGCA 58.229 47.619 0.00 0.00 45.94 4.57
5838 6672 1.466558 GCTTAAGAGGAAGCTGTGTGC 59.533 52.381 6.67 0.00 46.85 4.57
5845 6679 1.369839 GGTGCCGCTTAAGAGGAAGC 61.370 60.000 27.37 22.78 46.90 3.86
5846 6680 0.036388 TGGTGCCGCTTAAGAGGAAG 60.036 55.000 27.37 3.15 37.14 3.46
5847 6681 0.321298 GTGGTGCCGCTTAAGAGGAA 60.321 55.000 27.37 15.91 37.14 3.36
5848 6682 1.295423 GTGGTGCCGCTTAAGAGGA 59.705 57.895 27.37 10.76 37.14 3.71
5849 6683 1.003839 TGTGGTGCCGCTTAAGAGG 60.004 57.895 19.99 19.99 38.10 3.69
5850 6684 1.021390 CCTGTGGTGCCGCTTAAGAG 61.021 60.000 6.67 2.25 0.00 2.85
5851 6685 1.003839 CCTGTGGTGCCGCTTAAGA 60.004 57.895 6.67 0.00 0.00 2.10
5852 6686 2.040544 CCCTGTGGTGCCGCTTAAG 61.041 63.158 0.00 0.00 0.00 1.85
5853 6687 2.033448 CCCTGTGGTGCCGCTTAA 59.967 61.111 3.31 0.00 0.00 1.85
5854 6688 3.246112 ACCCTGTGGTGCCGCTTA 61.246 61.111 3.31 0.00 45.58 3.09
5873 6707 1.557832 TCATACTAGTGGTTGGGGCAC 59.442 52.381 5.39 0.00 0.00 5.01
5874 6708 1.959710 TCATACTAGTGGTTGGGGCA 58.040 50.000 5.39 0.00 0.00 5.36
5875 6709 3.118038 TGAATCATACTAGTGGTTGGGGC 60.118 47.826 5.39 0.00 0.00 5.80
5876 6710 4.771114 TGAATCATACTAGTGGTTGGGG 57.229 45.455 5.39 0.00 0.00 4.96
5877 6711 6.881065 CCATATGAATCATACTAGTGGTTGGG 59.119 42.308 5.39 0.00 0.00 4.12
5878 6712 7.453393 ACCATATGAATCATACTAGTGGTTGG 58.547 38.462 16.44 13.98 34.36 3.77
5881 6715 8.260818 GCATACCATATGAATCATACTAGTGGT 58.739 37.037 22.39 22.39 38.61 4.16
5882 6716 8.481314 AGCATACCATATGAATCATACTAGTGG 58.519 37.037 15.41 15.41 32.28 4.00
6418 7266 4.142381 ACGGACCTAATTAACTACACGGAC 60.142 45.833 0.00 0.00 0.00 4.79
6422 7270 7.838771 ATTGAACGGACCTAATTAACTACAC 57.161 36.000 0.00 0.00 0.00 2.90
6600 9249 0.038618 CGTGTGACCGATTGTCCTCA 60.039 55.000 0.00 0.00 43.78 3.86
6778 9427 7.284489 ACAACCAAACTTAATATGTGTGACACT 59.716 33.333 17.47 5.18 35.11 3.55
6946 9610 0.916358 CAGTCCCTCCCCAATCAGGT 60.916 60.000 0.00 0.00 34.66 4.00
7359 10410 3.445096 GCCTATTGTTTGCAGAGATTGGT 59.555 43.478 0.00 0.00 0.00 3.67
7361 10412 4.418392 GTGCCTATTGTTTGCAGAGATTG 58.582 43.478 0.00 0.00 35.33 2.67
7745 10796 7.281774 TGCATAACAAATGGAGAAGAGATTCTC 59.718 37.037 5.49 5.49 45.05 2.87
7746 10797 7.114754 TGCATAACAAATGGAGAAGAGATTCT 58.885 34.615 0.00 0.00 0.00 2.40
7747 10798 7.325660 TGCATAACAAATGGAGAAGAGATTC 57.674 36.000 0.00 0.00 0.00 2.52
7748 10799 6.320672 CCTGCATAACAAATGGAGAAGAGATT 59.679 38.462 7.93 0.00 39.43 2.40
8034 11085 1.868498 TGAACAACTCGGGTTTTAGCG 59.132 47.619 0.00 0.00 32.73 4.26
8216 11267 1.843753 GCGGCGTATACATTTTGTTGC 59.156 47.619 9.37 0.00 0.00 4.17
8267 11318 1.199327 CAGTCTGCTGGAATGCACTTG 59.801 52.381 0.00 0.00 39.01 3.16
8374 11438 3.057174 TCGCGGCAACTAAAATTTCCATT 60.057 39.130 6.13 0.00 0.00 3.16
8439 11503 5.372373 CTCAATCTCTGGTAAATCCCCTTC 58.628 45.833 0.00 0.00 34.77 3.46
8482 11547 5.560724 TGTGCTATAGCCTTCTTTTTGACT 58.439 37.500 21.84 0.00 41.18 3.41
8483 11548 5.880054 TGTGCTATAGCCTTCTTTTTGAC 57.120 39.130 21.84 9.54 41.18 3.18
8484 11549 7.609918 TGTTATGTGCTATAGCCTTCTTTTTGA 59.390 33.333 21.84 0.00 41.18 2.69
8485 11550 7.761409 TGTTATGTGCTATAGCCTTCTTTTTG 58.239 34.615 21.84 0.00 41.18 2.44
8489 11554 6.595682 ACATGTTATGTGCTATAGCCTTCTT 58.404 36.000 21.84 12.15 43.01 2.52
8490 11555 6.179906 ACATGTTATGTGCTATAGCCTTCT 57.820 37.500 21.84 6.82 43.01 2.85
8491 11556 5.991606 TGACATGTTATGTGCTATAGCCTTC 59.008 40.000 21.84 12.44 45.03 3.46
8492 11557 5.928976 TGACATGTTATGTGCTATAGCCTT 58.071 37.500 21.84 12.96 45.03 4.35
8493 11558 5.551305 TGACATGTTATGTGCTATAGCCT 57.449 39.130 21.84 9.23 45.03 4.58
8494 11559 6.652481 AGATTGACATGTTATGTGCTATAGCC 59.348 38.462 21.84 13.33 45.03 3.93
8495 11560 7.664082 AGATTGACATGTTATGTGCTATAGC 57.336 36.000 18.18 18.18 45.03 2.97
8497 11562 7.498570 TGCAAGATTGACATGTTATGTGCTATA 59.501 33.333 18.16 5.78 45.03 1.31
8500 11565 4.460034 TGCAAGATTGACATGTTATGTGCT 59.540 37.500 18.16 5.47 45.03 4.40
8501 11566 4.735985 TGCAAGATTGACATGTTATGTGC 58.264 39.130 0.00 9.36 45.03 4.57
8604 11719 0.324738 TGGTTGTTGTTTCTGGGCCA 60.325 50.000 5.85 5.85 0.00 5.36
8650 11771 3.131933 GCTAGACAGCTTCTGGATCTTCA 59.868 47.826 11.55 0.00 44.93 3.02
8983 12148 1.336877 TCGCATTCTTGACGACTTCG 58.663 50.000 0.00 0.00 46.33 3.79
9149 12314 4.365514 AACCAACCATGTGACATAGTCA 57.634 40.909 0.00 0.00 40.50 3.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.