Multiple sequence alignment - TraesCS2A01G570200

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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 TraesCS2A01G570200 chr2A 100.000 5888 0 0 1 5888 767793266 767787379 0.000000e+00 10874.0
1 TraesCS2A01G570200 chr2A 97.441 977 22 1 4024 5000 767571684 767572657 0.000000e+00 1663.0
2 TraesCS2A01G570200 chr2A 89.986 719 56 10 1594 2305 767570737 767571446 0.000000e+00 915.0
3 TraesCS2A01G570200 chr2A 95.802 262 9 1 5069 5330 746759130 746759389 7.050000e-114 422.0
4 TraesCS2A01G570200 chr2A 97.738 221 2 3 2197 2416 767790959 767790741 1.550000e-100 377.0
5 TraesCS2A01G570200 chr2A 97.738 221 2 3 2308 2526 767791070 767790851 1.550000e-100 377.0
6 TraesCS2A01G570200 chr2A 79.342 547 93 9 1036 1572 767569934 767570470 3.350000e-97 366.0
7 TraesCS2A01G570200 chr2A 77.778 612 107 24 4094 4692 767562352 767562947 3.380000e-92 350.0
8 TraesCS2A01G570200 chr2A 81.081 444 54 14 1642 2070 767560505 767560933 1.580000e-85 327.0
9 TraesCS2A01G570200 chr2A 79.560 455 71 13 1642 2085 767485747 767485304 7.410000e-79 305.0
10 TraesCS2A01G570200 chr2A 79.147 422 60 16 1642 2048 766714969 766715377 3.500000e-67 267.0
11 TraesCS2A01G570200 chr2A 95.035 141 6 1 3891 4031 630094756 630094617 2.760000e-53 220.0
12 TraesCS2A01G570200 chr2A 90.260 154 15 0 2420 2573 767571342 767571495 1.000000e-47 202.0
13 TraesCS2A01G570200 chr2A 99.099 111 0 1 2197 2307 767790850 767790741 1.290000e-46 198.0
14 TraesCS2A01G570200 chr2A 99.099 111 0 1 2417 2526 767791070 767790960 1.290000e-46 198.0
15 TraesCS2A01G570200 chr2A 88.571 105 11 1 2311 2414 767571342 767571446 6.190000e-25 126.0
16 TraesCS2A01G570200 chr2A 92.135 89 7 0 5329 5417 767572720 767572808 6.190000e-25 126.0
17 TraesCS2A01G570200 chr2A 97.015 67 2 0 973 1039 767781554 767781620 4.820000e-21 113.0
18 TraesCS2A01G570200 chr2A 82.692 104 8 8 4956 5055 767567190 767567093 3.780000e-12 84.2
19 TraesCS2A01G570200 chr2A 93.617 47 2 1 3851 3897 767562246 767562291 1.060000e-07 69.4
20 TraesCS2A01G570200 chr2A 88.889 54 5 1 3851 3904 767480576 767480524 1.370000e-06 65.8
21 TraesCS2A01G570200 chrUn 97.422 1901 23 4 973 2857 31531133 31529243 0.000000e+00 3216.0
22 TraesCS2A01G570200 chrUn 98.324 1193 19 1 2855 4047 31529094 31527903 0.000000e+00 2091.0
23 TraesCS2A01G570200 chrUn 96.964 1153 17 8 3918 5070 31527901 31526767 0.000000e+00 1919.0
24 TraesCS2A01G570200 chrUn 92.873 926 50 12 5 922 31532205 31531288 0.000000e+00 1330.0
25 TraesCS2A01G570200 chrUn 95.113 573 14 9 5328 5888 31526769 31526199 0.000000e+00 891.0
26 TraesCS2A01G570200 chrUn 87.733 750 82 8 4146 4886 31552345 31553093 0.000000e+00 867.0
27 TraesCS2A01G570200 chrUn 97.706 218 3 2 2310 2526 31529896 31529680 2.000000e-99 374.0
28 TraesCS2A01G570200 chrUn 97.285 221 3 3 2197 2416 31529788 31529570 7.210000e-99 372.0
29 TraesCS2A01G570200 chrUn 98.198 111 1 1 2197 2307 31529679 31529570 6.020000e-45 193.0
30 TraesCS2A01G570200 chrUn 98.165 109 0 2 2419 2526 31529896 31529789 7.790000e-44 189.0
31 TraesCS2A01G570200 chrUn 90.476 84 8 0 5333 5416 31520373 31520456 1.730000e-20 111.0
32 TraesCS2A01G570200 chrUn 82.313 147 6 11 910 1037 31517911 31518056 6.240000e-20 110.0
33 TraesCS2A01G570200 chrUn 98.182 55 0 1 907 960 31531250 31531196 1.750000e-15 95.3
34 TraesCS2A01G570200 chrUn 83.168 101 12 5 4956 5055 31520206 31520302 2.920000e-13 87.9
35 TraesCS2A01G570200 chr2B 98.260 977 17 0 4024 5000 799251756 799250780 0.000000e+00 1711.0
36 TraesCS2A01G570200 chr2B 90.000 710 61 7 1599 2305 799252687 799251985 0.000000e+00 909.0
37 TraesCS2A01G570200 chr2B 78.676 544 102 9 1036 1572 799253441 799252905 3.380000e-92 350.0
38 TraesCS2A01G570200 chr2B 90.556 180 16 1 3680 3859 342244564 342244386 2.740000e-58 237.0
39 TraesCS2A01G570200 chr2B 88.372 129 9 2 3536 3659 799251949 799251822 3.680000e-32 150.0
40 TraesCS2A01G570200 chr2B 78.346 254 38 15 228 471 494906714 494906468 1.320000e-31 148.0
41 TraesCS2A01G570200 chr2B 78.495 186 33 6 271 456 482132816 482132994 1.340000e-21 115.0
42 TraesCS2A01G570200 chr2B 90.741 54 4 1 3851 3904 799285393 799285341 2.940000e-08 71.3
43 TraesCS2A01G570200 chr2D 97.748 977 21 1 4024 5000 642444914 642445889 0.000000e+00 1681.0
44 TraesCS2A01G570200 chr2D 87.967 723 58 13 1590 2307 642500452 642501150 0.000000e+00 826.0
45 TraesCS2A01G570200 chr2D 86.769 718 81 11 4343 5055 642501943 642502651 0.000000e+00 787.0
46 TraesCS2A01G570200 chr2D 84.551 479 67 6 4415 4886 642954000 642954478 8.930000e-128 468.0
47 TraesCS2A01G570200 chr2D 88.718 390 29 9 1594 1979 642443803 642444181 4.160000e-126 462.0
48 TraesCS2A01G570200 chr2D 87.345 403 27 6 4026 4425 642941655 642942036 1.950000e-119 440.0
49 TraesCS2A01G570200 chr2D 85.604 389 38 13 1590 1978 642940642 642941012 5.530000e-105 392.0
50 TraesCS2A01G570200 chr2D 90.847 295 22 3 2015 2305 642444178 642444471 1.990000e-104 390.0
51 TraesCS2A01G570200 chr2D 79.336 542 102 5 1036 1572 642443000 642443536 7.210000e-99 372.0
52 TraesCS2A01G570200 chr2D 78.431 612 101 13 973 1572 642499594 642500186 2.590000e-98 370.0
53 TraesCS2A01G570200 chr2D 88.129 278 16 9 4024 4296 642501674 642501939 1.230000e-81 315.0
54 TraesCS2A01G570200 chr2D 84.615 325 36 9 1977 2300 642941106 642941417 1.590000e-80 311.0
55 TraesCS2A01G570200 chr2D 89.172 157 14 2 2419 2573 642444365 642444520 6.020000e-45 193.0
56 TraesCS2A01G570200 chr2D 88.820 161 11 3 3536 3691 642444507 642444665 2.170000e-44 191.0
57 TraesCS2A01G570200 chr2D 86.420 162 13 4 3536 3691 642501184 642501342 1.010000e-37 169.0
58 TraesCS2A01G570200 chr2D 87.591 137 17 0 1253 1389 642933315 642933451 6.110000e-35 159.0
59 TraesCS2A01G570200 chr2D 82.184 174 13 5 3536 3691 642941436 642941609 3.700000e-27 134.0
60 TraesCS2A01G570200 chr2D 87.963 108 9 3 2310 2414 642444365 642444471 2.230000e-24 124.0
61 TraesCS2A01G570200 chr2D 90.476 84 8 0 5333 5416 642440123 642440040 1.730000e-20 111.0
62 TraesCS2A01G570200 chr2D 90.476 84 8 0 5333 5416 642873264 642873347 1.730000e-20 111.0
63 TraesCS2A01G570200 chr2D 83.471 121 16 4 2416 2536 642941317 642941433 6.240000e-20 110.0
64 TraesCS2A01G570200 chr2D 98.276 58 1 0 980 1037 642870902 642870959 1.040000e-17 102.0
65 TraesCS2A01G570200 chr2D 83.495 103 15 2 2307 2409 642941317 642941417 1.750000e-15 95.3
66 TraesCS2A01G570200 chr2D 83.495 103 11 6 4956 5055 642440293 642440194 2.260000e-14 91.6
67 TraesCS2A01G570200 chr2D 97.778 45 1 0 4956 5000 642476988 642476944 1.760000e-10 78.7
68 TraesCS2A01G570200 chr2D 87.879 66 8 0 5332 5397 642502721 642502786 1.760000e-10 78.7
69 TraesCS2A01G570200 chr2D 95.745 47 1 1 3851 3897 642941606 642941651 2.280000e-09 75.0
70 TraesCS2A01G570200 chr3A 91.304 437 35 2 5454 5888 13531866 13532301 1.410000e-165 593.0
71 TraesCS2A01G570200 chr3A 91.908 173 13 1 3684 3855 20953888 20953716 2.120000e-59 241.0
72 TraesCS2A01G570200 chr3A 90.857 175 15 1 3680 3854 1759691 1759864 3.550000e-57 233.0
73 TraesCS2A01G570200 chr3A 90.857 175 14 2 3681 3854 555696184 555696011 3.550000e-57 233.0
74 TraesCS2A01G570200 chr6B 93.909 394 20 3 5498 5888 20082510 20082902 5.080000e-165 592.0
75 TraesCS2A01G570200 chr6B 91.349 393 26 3 5498 5888 20028450 20028836 1.120000e-146 531.0
76 TraesCS2A01G570200 chr6B 76.204 353 68 10 5530 5877 543846933 543846592 7.840000e-39 172.0
77 TraesCS2A01G570200 chr7A 96.992 266 7 1 5068 5333 679063945 679064209 4.190000e-121 446.0
78 TraesCS2A01G570200 chr7A 96.981 265 7 1 5067 5331 566529874 566530137 1.510000e-120 444.0
79 TraesCS2A01G570200 chr7A 95.802 262 10 1 5069 5330 80195814 80195554 7.050000e-114 422.0
80 TraesCS2A01G570200 chr7A 94.796 269 12 2 5068 5336 232743804 232744070 9.130000e-113 418.0
81 TraesCS2A01G570200 chr7A 94.767 172 9 0 3690 3861 115807523 115807694 9.730000e-68 268.0
82 TraesCS2A01G570200 chr7A 91.525 177 13 2 3679 3854 699175595 699175770 5.900000e-60 243.0
83 TraesCS2A01G570200 chr7A 90.608 181 13 2 3679 3859 32960051 32960227 2.740000e-58 237.0
84 TraesCS2A01G570200 chr7A 90.608 181 13 2 3679 3859 115779393 115779569 2.740000e-58 237.0
85 TraesCS2A01G570200 chr5A 95.926 270 8 2 5067 5334 546242004 546241736 9.060000e-118 435.0
86 TraesCS2A01G570200 chr5A 96.212 264 7 2 5069 5330 598682815 598683077 4.220000e-116 429.0
87 TraesCS2A01G570200 chr5A 94.245 278 13 2 5055 5330 385384152 385383876 7.050000e-114 422.0
88 TraesCS2A01G570200 chr5A 94.203 276 10 4 5069 5344 556734461 556734730 3.280000e-112 416.0
89 TraesCS2A01G570200 chr5A 77.403 385 53 19 172 547 509123108 509122749 1.290000e-46 198.0
90 TraesCS2A01G570200 chr4A 88.664 247 22 2 5454 5697 514067646 514067403 4.460000e-76 296.0
91 TraesCS2A01G570200 chr4A 81.152 191 31 4 263 452 340538330 340538516 1.320000e-31 148.0
92 TraesCS2A01G570200 chr1D 96.407 167 6 0 3689 3855 81276520 81276354 5.810000e-70 276.0
93 TraesCS2A01G570200 chr1D 94.798 173 9 0 3689 3861 331539430 331539258 2.700000e-68 270.0
94 TraesCS2A01G570200 chr4D 95.322 171 7 1 3690 3860 93338042 93338211 2.700000e-68 270.0
95 TraesCS2A01G570200 chr4D 76.036 338 72 7 5502 5833 304312067 304312401 3.650000e-37 167.0
96 TraesCS2A01G570200 chr4D 77.941 272 46 13 5611 5877 53480516 53480778 2.200000e-34 158.0
97 TraesCS2A01G570200 chr3D 94.767 172 9 0 3684 3855 355892347 355892518 9.730000e-68 268.0
98 TraesCS2A01G570200 chr3D 93.662 142 9 0 3895 4036 358792639 358792498 4.620000e-51 213.0
99 TraesCS2A01G570200 chr3D 91.892 37 3 0 686 722 462829788 462829824 1.100000e-02 52.8
100 TraesCS2A01G570200 chr3B 94.767 172 9 0 3690 3861 655849421 655849592 9.730000e-68 268.0
101 TraesCS2A01G570200 chr3B 93.855 179 10 1 3690 3867 673063301 673063479 9.730000e-68 268.0
102 TraesCS2A01G570200 chr3B 97.674 129 3 0 3897 4025 383716619 383716491 7.680000e-54 222.0
103 TraesCS2A01G570200 chr3B 83.766 154 20 5 3898 4048 76508378 76508227 2.210000e-29 141.0
104 TraesCS2A01G570200 chr3B 83.969 131 17 4 3898 4026 411123586 411123714 8.010000e-24 122.0
105 TraesCS2A01G570200 chr5B 93.750 176 11 0 3680 3855 486081483 486081658 1.260000e-66 265.0
106 TraesCS2A01G570200 chr5B 94.928 138 6 1 3899 4036 640272867 640272731 1.290000e-51 215.0
107 TraesCS2A01G570200 chr7B 90.625 192 16 2 3690 3881 675384808 675384619 2.720000e-63 254.0
108 TraesCS2A01G570200 chr7B 97.656 128 3 0 3899 4026 461475566 461475693 2.760000e-53 220.0
109 TraesCS2A01G570200 chr7B 95.620 137 5 1 3897 4032 678632356 678632492 9.930000e-53 219.0
110 TraesCS2A01G570200 chr7B 76.078 464 81 26 5 452 335802773 335802324 1.290000e-51 215.0
111 TraesCS2A01G570200 chr7D 77.754 463 67 26 5 452 191109630 191109189 9.800000e-63 252.0
112 TraesCS2A01G570200 chr4B 90.000 160 11 5 3884 4039 14529630 14529788 1.000000e-47 202.0


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 TraesCS2A01G570200 chr2A 767787379 767793266 5887 True 2404.800000 10874 98.734800 1 5888 5 chr2A.!!$R5 5887
1 TraesCS2A01G570200 chr2A 767569934 767572808 2874 False 566.333333 1663 89.622500 1036 5417 6 chr2A.!!$F5 4381
2 TraesCS2A01G570200 chr2A 767560505 767562947 2442 False 248.800000 350 84.158667 1642 4692 3 chr2A.!!$F4 3050
3 TraesCS2A01G570200 chrUn 31526199 31532205 6006 True 1067.030000 3216 97.023200 5 5888 10 chrUn.!!$R1 5883
4 TraesCS2A01G570200 chrUn 31552345 31553093 748 False 867.000000 867 87.733000 4146 4886 1 chrUn.!!$F1 740
5 TraesCS2A01G570200 chr2B 799250780 799253441 2661 True 780.000000 1711 88.827000 1036 5000 4 chr2B.!!$R4 3964
6 TraesCS2A01G570200 chr2D 642443000 642445889 2889 False 487.571429 1681 88.943429 1036 5000 7 chr2D.!!$F3 3964
7 TraesCS2A01G570200 chr2D 642499594 642502786 3192 False 424.283333 826 85.932500 973 5397 6 chr2D.!!$F4 4424
8 TraesCS2A01G570200 chr2D 642940642 642942036 1394 False 222.471429 440 86.065571 1590 4425 7 chr2D.!!$F6 2835

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
71 72 0.255890 AATGCAGCCAGGGTTACGAT 59.744 50.000 0.00 0.0 0.00 3.73 F
366 370 0.672342 ACACTCTTAGCCGAACGTGT 59.328 50.000 0.00 0.0 0.00 4.49 F
523 527 0.815615 GCTCCGGGTGCTTTGATAGG 60.816 60.000 13.59 0.0 0.00 2.57 F
870 876 1.194218 TTCATGTCTCGGCTCCATCA 58.806 50.000 0.00 0.0 0.00 3.07 F
1275 1388 1.285078 AGTTTGCCCTATCTGGTTCCC 59.715 52.381 0.00 0.0 0.00 3.97 F
2394 3756 1.133513 TGTTCAATTGGGTGTCTGGCT 60.134 47.619 5.42 0.0 0.00 4.75 F
3204 4829 1.003545 CTGCAACTCTTGTGTCGTTGG 60.004 52.381 0.00 0.0 38.67 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1027 1140 1.213296 TCCTTATTCTCCCTGCCCAC 58.787 55.000 0.00 0.0 0.00 4.61 R
1718 2085 1.560923 GAGTGGATTCGATGACACGG 58.439 55.000 7.83 0.0 38.78 4.94 R
2374 3736 1.133513 AGCCAGACACCCAATTGAACA 60.134 47.619 7.12 0.0 0.00 3.18 R
2377 3739 1.425066 AGAAGCCAGACACCCAATTGA 59.575 47.619 7.12 0.0 0.00 2.57 R
3204 4829 0.912486 AGTAGTTCCCATCCCAGCAC 59.088 55.000 0.00 0.0 0.00 4.40 R
3843 5488 1.032794 TCTGCATGCTACTACCTCCG 58.967 55.000 20.33 0.0 0.00 4.63 R
5005 7303 1.313772 CACAAACGGTTGGGACATCA 58.686 50.000 19.08 0.0 40.98 3.07 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
30 31 3.370061 GGTCTATAACACAAGCCGAACAC 59.630 47.826 0.00 0.00 0.00 3.32
71 72 0.255890 AATGCAGCCAGGGTTACGAT 59.744 50.000 0.00 0.00 0.00 3.73
73 74 1.220749 GCAGCCAGGGTTACGATCA 59.779 57.895 0.00 0.00 0.00 2.92
102 103 2.520458 CAGTGGTTCCCTTGCCCA 59.480 61.111 0.00 0.00 0.00 5.36
143 146 1.010574 TTTTTGCGTCGTTGGCTCG 60.011 52.632 0.00 0.00 0.00 5.03
152 155 2.770532 GTCGTTGGCTCGCTTATTTTC 58.229 47.619 0.00 0.00 0.00 2.29
245 248 4.783242 TGCTATTTTCACTTCTTTCGTGC 58.217 39.130 0.00 0.00 32.54 5.34
246 249 4.515191 TGCTATTTTCACTTCTTTCGTGCT 59.485 37.500 0.00 0.00 32.54 4.40
251 254 3.385193 TCACTTCTTTCGTGCTGATGA 57.615 42.857 0.00 0.00 32.54 2.92
260 263 2.340337 TCGTGCTGATGACTTCATGTG 58.660 47.619 0.00 0.00 36.57 3.21
281 284 3.066621 TGTTTGTGACTGCTAGCTTTTGG 59.933 43.478 17.23 3.74 0.00 3.28
307 310 5.091552 TCTCCCACATGAGGTACTTAACTT 58.908 41.667 8.47 0.00 41.55 2.66
317 320 3.955701 AGGTACTTAACTTGGGTGACCCA 60.956 47.826 21.79 21.79 46.76 4.51
336 340 3.388308 CCAGAGATAACAATCGCAGAGG 58.612 50.000 0.00 0.00 43.63 3.69
362 366 3.120060 TCTCGTTACACTCTTAGCCGAAC 60.120 47.826 0.00 0.00 0.00 3.95
366 370 0.672342 ACACTCTTAGCCGAACGTGT 59.328 50.000 0.00 0.00 0.00 4.49
373 377 1.937278 TAGCCGAACGTGTGAAAACA 58.063 45.000 0.00 0.00 0.00 2.83
466 470 6.147164 TGTTATGGCTTAAGACGACTTTGAAG 59.853 38.462 6.67 5.70 37.53 3.02
470 474 3.432592 GCTTAAGACGACTTTGAAGGGTC 59.567 47.826 6.67 8.33 37.53 4.46
476 480 1.509703 GACTTTGAAGGGTCGGTGTC 58.490 55.000 0.00 0.00 0.00 3.67
523 527 0.815615 GCTCCGGGTGCTTTGATAGG 60.816 60.000 13.59 0.00 0.00 2.57
549 553 1.764571 AAGTTGTGGCCGAGGTGCTA 61.765 55.000 0.00 0.00 0.00 3.49
750 756 6.764308 AGATGCATCAAAATATATTCCCGG 57.236 37.500 27.81 0.00 0.00 5.73
753 759 5.136828 TGCATCAAAATATATTCCCGGTGT 58.863 37.500 0.00 0.00 0.00 4.16
833 839 9.083422 AGGGAAAAGGAATAAGAAAAAGAGAAG 57.917 33.333 0.00 0.00 0.00 2.85
864 870 4.647424 TTTTGTTTTTCATGTCTCGGCT 57.353 36.364 0.00 0.00 0.00 5.52
865 871 3.896648 TTGTTTTTCATGTCTCGGCTC 57.103 42.857 0.00 0.00 0.00 4.70
866 872 2.151202 TGTTTTTCATGTCTCGGCTCC 58.849 47.619 0.00 0.00 0.00 4.70
867 873 2.151202 GTTTTTCATGTCTCGGCTCCA 58.849 47.619 0.00 0.00 0.00 3.86
868 874 2.749621 GTTTTTCATGTCTCGGCTCCAT 59.250 45.455 0.00 0.00 0.00 3.41
869 875 2.315925 TTTCATGTCTCGGCTCCATC 57.684 50.000 0.00 0.00 0.00 3.51
870 876 1.194218 TTCATGTCTCGGCTCCATCA 58.806 50.000 0.00 0.00 0.00 3.07
1027 1140 4.933064 GCGGGCAGATCTCGTCCG 62.933 72.222 24.74 24.74 43.13 4.79
1156 1269 1.979155 GTTGCTGGGAAGAAGGCCC 60.979 63.158 0.00 0.00 46.22 5.80
1275 1388 1.285078 AGTTTGCCCTATCTGGTTCCC 59.715 52.381 0.00 0.00 0.00 3.97
1609 1745 5.065914 TCAGCTTTGCTTCTTCTTGTACAT 58.934 37.500 0.00 0.00 36.40 2.29
1640 2005 5.952347 ATTCTAGTCCCTTGAATAACGGT 57.048 39.130 0.15 0.00 35.07 4.83
1703 2070 4.678309 GCCACACTGTCTCCTATGTACTTC 60.678 50.000 0.00 0.00 0.00 3.01
1718 2085 2.280797 TTCACGCACTCTGCACCC 60.281 61.111 0.00 0.00 45.36 4.61
1921 2288 6.054860 AGTCACTGAAAAGGTATGTATGCT 57.945 37.500 0.00 0.00 0.00 3.79
1922 2289 7.182817 AGTCACTGAAAAGGTATGTATGCTA 57.817 36.000 0.00 0.00 0.00 3.49
1923 2290 7.796054 AGTCACTGAAAAGGTATGTATGCTAT 58.204 34.615 0.00 0.00 0.00 2.97
1924 2291 7.712639 AGTCACTGAAAAGGTATGTATGCTATG 59.287 37.037 0.00 0.00 0.00 2.23
1925 2292 6.483307 TCACTGAAAAGGTATGTATGCTATGC 59.517 38.462 0.00 0.00 0.00 3.14
2312 3674 4.979943 TTTTTCAGTCAATGAGCACACA 57.020 36.364 0.00 0.00 39.68 3.72
2313 3675 5.518848 TTTTTCAGTCAATGAGCACACAT 57.481 34.783 0.00 0.00 39.68 3.21
2314 3676 4.754372 TTTCAGTCAATGAGCACACATC 57.246 40.909 0.00 0.00 39.68 3.06
2315 3677 3.690475 TCAGTCAATGAGCACACATCT 57.310 42.857 0.00 0.00 32.77 2.90
2316 3678 4.806640 TCAGTCAATGAGCACACATCTA 57.193 40.909 0.00 0.00 32.77 1.98
2317 3679 5.349061 TCAGTCAATGAGCACACATCTAT 57.651 39.130 0.00 0.00 32.77 1.98
2318 3680 5.114081 TCAGTCAATGAGCACACATCTATG 58.886 41.667 0.00 0.00 32.77 2.23
2319 3681 4.874396 CAGTCAATGAGCACACATCTATGT 59.126 41.667 0.00 0.00 42.84 2.29
2320 3682 7.343068 TCAGTCAATGAGCACACATCTATGTG 61.343 42.308 19.08 19.08 46.63 3.21
2333 3695 6.534475 ACATCTATGTGGATGCAAACAATT 57.466 33.333 6.31 0.00 44.81 2.32
2334 3696 7.643569 ACATCTATGTGGATGCAAACAATTA 57.356 32.000 6.31 0.00 44.81 1.40
2335 3697 8.241497 ACATCTATGTGGATGCAAACAATTAT 57.759 30.769 6.31 0.00 44.81 1.28
2336 3698 9.353431 ACATCTATGTGGATGCAAACAATTATA 57.647 29.630 6.31 0.00 44.81 0.98
2358 3720 9.634021 TTATATATTTGATGCCTTTGTACCACA 57.366 29.630 0.00 0.00 0.00 4.17
2359 3721 6.849085 ATATTTGATGCCTTTGTACCACAA 57.151 33.333 0.00 0.00 36.11 3.33
2360 3722 5.743636 ATTTGATGCCTTTGTACCACAAT 57.256 34.783 0.00 0.00 38.00 2.71
2361 3723 4.517952 TTGATGCCTTTGTACCACAATG 57.482 40.909 0.00 0.00 38.00 2.82
2362 3724 3.760738 TGATGCCTTTGTACCACAATGA 58.239 40.909 6.52 0.00 38.00 2.57
2363 3725 4.343231 TGATGCCTTTGTACCACAATGAT 58.657 39.130 6.52 0.00 38.00 2.45
2364 3726 4.158209 TGATGCCTTTGTACCACAATGATG 59.842 41.667 6.52 0.00 38.00 3.07
2365 3727 2.230992 TGCCTTTGTACCACAATGATGC 59.769 45.455 6.52 3.90 38.00 3.91
2366 3728 2.230992 GCCTTTGTACCACAATGATGCA 59.769 45.455 0.00 0.00 38.00 3.96
2367 3729 3.305950 GCCTTTGTACCACAATGATGCAA 60.306 43.478 0.00 0.00 38.00 4.08
2368 3730 4.236935 CCTTTGTACCACAATGATGCAAC 58.763 43.478 0.00 0.00 38.00 4.17
2369 3731 4.022068 CCTTTGTACCACAATGATGCAACT 60.022 41.667 0.00 0.00 38.00 3.16
2370 3732 5.509501 CCTTTGTACCACAATGATGCAACTT 60.510 40.000 0.00 0.00 38.00 2.66
2371 3733 4.502171 TGTACCACAATGATGCAACTTG 57.498 40.909 0.00 0.00 0.00 3.16
2372 3734 4.140536 TGTACCACAATGATGCAACTTGA 58.859 39.130 11.75 0.00 0.00 3.02
2373 3735 4.582240 TGTACCACAATGATGCAACTTGAA 59.418 37.500 11.75 0.00 0.00 2.69
2374 3736 4.877378 ACCACAATGATGCAACTTGAAT 57.123 36.364 11.75 0.00 0.00 2.57
2375 3737 4.562082 ACCACAATGATGCAACTTGAATG 58.438 39.130 11.75 2.94 0.00 2.67
2376 3738 4.039488 ACCACAATGATGCAACTTGAATGT 59.961 37.500 11.75 0.00 0.00 2.71
2377 3739 4.992319 CCACAATGATGCAACTTGAATGTT 59.008 37.500 11.75 0.00 0.00 2.71
2378 3740 5.119588 CCACAATGATGCAACTTGAATGTTC 59.880 40.000 11.75 0.00 0.00 3.18
2379 3741 5.692654 CACAATGATGCAACTTGAATGTTCA 59.307 36.000 11.75 0.00 34.92 3.18
2380 3742 6.201234 CACAATGATGCAACTTGAATGTTCAA 59.799 34.615 11.75 7.84 44.31 2.69
2381 3743 6.932400 ACAATGATGCAACTTGAATGTTCAAT 59.068 30.769 8.48 0.00 45.26 2.57
2382 3744 7.442969 ACAATGATGCAACTTGAATGTTCAATT 59.557 29.630 8.48 1.05 45.26 2.32
2383 3745 6.772770 TGATGCAACTTGAATGTTCAATTG 57.227 33.333 8.48 13.92 45.26 2.32
2384 3746 5.697178 TGATGCAACTTGAATGTTCAATTGG 59.303 36.000 19.82 11.42 45.26 3.16
2385 3747 4.378774 TGCAACTTGAATGTTCAATTGGG 58.621 39.130 19.82 9.83 45.26 4.12
2386 3748 4.141756 TGCAACTTGAATGTTCAATTGGGT 60.142 37.500 19.82 10.26 45.26 4.51
2387 3749 4.211794 GCAACTTGAATGTTCAATTGGGTG 59.788 41.667 19.82 14.35 45.26 4.61
2388 3750 5.358922 CAACTTGAATGTTCAATTGGGTGT 58.641 37.500 5.42 0.40 45.26 4.16
2389 3751 5.200368 ACTTGAATGTTCAATTGGGTGTC 57.800 39.130 5.42 0.00 45.26 3.67
2390 3752 4.895297 ACTTGAATGTTCAATTGGGTGTCT 59.105 37.500 5.42 0.00 45.26 3.41
2391 3753 4.852134 TGAATGTTCAATTGGGTGTCTG 57.148 40.909 5.42 0.00 33.55 3.51
2392 3754 3.573538 TGAATGTTCAATTGGGTGTCTGG 59.426 43.478 5.42 0.00 33.55 3.86
2393 3755 1.327303 TGTTCAATTGGGTGTCTGGC 58.673 50.000 5.42 0.00 0.00 4.85
2394 3756 1.133513 TGTTCAATTGGGTGTCTGGCT 60.134 47.619 5.42 0.00 0.00 4.75
2395 3757 1.963515 GTTCAATTGGGTGTCTGGCTT 59.036 47.619 5.42 0.00 0.00 4.35
2396 3758 1.909700 TCAATTGGGTGTCTGGCTTC 58.090 50.000 5.42 0.00 0.00 3.86
2397 3759 1.425066 TCAATTGGGTGTCTGGCTTCT 59.575 47.619 5.42 0.00 0.00 2.85
2398 3760 2.642311 TCAATTGGGTGTCTGGCTTCTA 59.358 45.455 5.42 0.00 0.00 2.10
2399 3761 2.749621 CAATTGGGTGTCTGGCTTCTAC 59.250 50.000 0.00 0.00 0.00 2.59
2400 3762 1.729586 TTGGGTGTCTGGCTTCTACT 58.270 50.000 0.00 0.00 0.00 2.57
2401 3763 1.729586 TGGGTGTCTGGCTTCTACTT 58.270 50.000 0.00 0.00 0.00 2.24
2402 3764 2.054799 TGGGTGTCTGGCTTCTACTTT 58.945 47.619 0.00 0.00 0.00 2.66
2403 3765 2.441750 TGGGTGTCTGGCTTCTACTTTT 59.558 45.455 0.00 0.00 0.00 2.27
2404 3766 3.117663 TGGGTGTCTGGCTTCTACTTTTT 60.118 43.478 0.00 0.00 0.00 1.94
2405 3767 3.502595 GGGTGTCTGGCTTCTACTTTTTC 59.497 47.826 0.00 0.00 0.00 2.29
2870 4495 8.009622 ACTACCAAGTAGCCTCTAAGAAATAC 57.990 38.462 1.69 0.00 39.51 1.89
2927 4552 2.952310 ACAAGCAAAGAACAGGAAGACC 59.048 45.455 0.00 0.00 0.00 3.85
2956 4581 6.344500 ACATCAATCTGACTATGAACCTGTC 58.656 40.000 0.00 0.00 0.00 3.51
3199 4824 7.776933 TTGATATATCTGCAACTCTTGTGTC 57.223 36.000 13.79 0.00 0.00 3.67
3204 4829 1.003545 CTGCAACTCTTGTGTCGTTGG 60.004 52.381 0.00 0.00 38.67 3.77
3389 5014 2.034432 TGCATTGTGATTGAAGCAACGT 59.966 40.909 0.00 0.00 0.00 3.99
3436 5061 5.365895 ACTGGGCCTGGTAGTTAATAACTAG 59.634 44.000 12.70 4.11 44.16 2.57
3813 5458 5.364446 ACATCCGTATGTGGTAGTCCATTTA 59.636 40.000 0.00 0.00 44.79 1.40
3935 6072 8.923270 TCCCAAAATTCTTGTCTTAGATTTGTT 58.077 29.630 0.00 0.00 28.79 2.83
4056 6324 5.590663 TGGTTAACTTTGCTGTGTGAACATA 59.409 36.000 5.42 0.00 0.00 2.29
5003 7301 3.502164 GGATGATGTCCCAACCAGG 57.498 57.895 0.00 0.00 41.50 4.45
5004 7302 0.918983 GGATGATGTCCCAACCAGGA 59.081 55.000 0.00 0.00 41.50 3.86
5005 7303 1.496429 GGATGATGTCCCAACCAGGAT 59.504 52.381 0.00 0.00 41.50 3.24
5006 7304 2.579873 GATGATGTCCCAACCAGGATG 58.420 52.381 0.00 0.00 41.22 3.51
5007 7305 1.667595 TGATGTCCCAACCAGGATGA 58.332 50.000 0.00 0.00 39.69 2.92
5008 7306 2.207988 TGATGTCCCAACCAGGATGAT 58.792 47.619 0.00 0.00 39.69 2.45
5009 7307 2.092267 TGATGTCCCAACCAGGATGATG 60.092 50.000 0.00 0.00 39.69 3.07
5026 7324 1.679153 GATGTCCCAACCGTTTGTGTT 59.321 47.619 0.00 0.00 0.00 3.32
5027 7325 2.414994 TGTCCCAACCGTTTGTGTTA 57.585 45.000 0.00 0.00 0.00 2.41
5070 7385 7.334858 ACTTAGTGTAGGGAGTACTACTGTAC 58.665 42.308 4.77 7.97 46.89 2.90
5079 7394 3.274095 GTACTACTGTACTCCCTCCGT 57.726 52.381 0.00 0.00 44.08 4.69
5080 7395 2.895242 ACTACTGTACTCCCTCCGTT 57.105 50.000 0.00 0.00 0.00 4.44
5081 7396 3.166560 ACTACTGTACTCCCTCCGTTT 57.833 47.619 0.00 0.00 0.00 3.60
5082 7397 3.504375 ACTACTGTACTCCCTCCGTTTT 58.496 45.455 0.00 0.00 0.00 2.43
5083 7398 3.899980 ACTACTGTACTCCCTCCGTTTTT 59.100 43.478 0.00 0.00 0.00 1.94
5084 7399 5.079643 ACTACTGTACTCCCTCCGTTTTTA 58.920 41.667 0.00 0.00 0.00 1.52
5085 7400 5.718607 ACTACTGTACTCCCTCCGTTTTTAT 59.281 40.000 0.00 0.00 0.00 1.40
5086 7401 5.494390 ACTGTACTCCCTCCGTTTTTATT 57.506 39.130 0.00 0.00 0.00 1.40
5087 7402 5.872963 ACTGTACTCCCTCCGTTTTTATTT 58.127 37.500 0.00 0.00 0.00 1.40
5088 7403 7.008021 ACTGTACTCCCTCCGTTTTTATTTA 57.992 36.000 0.00 0.00 0.00 1.40
5089 7404 7.101700 ACTGTACTCCCTCCGTTTTTATTTAG 58.898 38.462 0.00 0.00 0.00 1.85
5090 7405 7.008021 TGTACTCCCTCCGTTTTTATTTAGT 57.992 36.000 0.00 0.00 0.00 2.24
5091 7406 7.452562 TGTACTCCCTCCGTTTTTATTTAGTT 58.547 34.615 0.00 0.00 0.00 2.24
5092 7407 7.603784 TGTACTCCCTCCGTTTTTATTTAGTTC 59.396 37.037 0.00 0.00 0.00 3.01
5093 7408 5.640783 ACTCCCTCCGTTTTTATTTAGTTCG 59.359 40.000 0.00 0.00 0.00 3.95
5094 7409 4.392754 TCCCTCCGTTTTTATTTAGTTCGC 59.607 41.667 0.00 0.00 0.00 4.70
5095 7410 4.154556 CCCTCCGTTTTTATTTAGTTCGCA 59.845 41.667 0.00 0.00 0.00 5.10
5096 7411 5.163693 CCCTCCGTTTTTATTTAGTTCGCAT 60.164 40.000 0.00 0.00 0.00 4.73
5097 7412 6.037391 CCCTCCGTTTTTATTTAGTTCGCATA 59.963 38.462 0.00 0.00 0.00 3.14
5098 7413 7.255001 CCCTCCGTTTTTATTTAGTTCGCATAT 60.255 37.037 0.00 0.00 0.00 1.78
5099 7414 8.126700 CCTCCGTTTTTATTTAGTTCGCATATT 58.873 33.333 0.00 0.00 0.00 1.28
5102 7417 8.889000 CCGTTTTTATTTAGTTCGCATATTAGC 58.111 33.333 0.00 0.00 0.00 3.09
5103 7418 9.646336 CGTTTTTATTTAGTTCGCATATTAGCT 57.354 29.630 0.00 0.00 0.00 3.32
5107 7422 9.944663 TTTATTTAGTTCGCATATTAGCTTTGG 57.055 29.630 0.00 0.00 0.00 3.28
5108 7423 6.995511 TTTAGTTCGCATATTAGCTTTGGT 57.004 33.333 0.00 0.00 0.00 3.67
5109 7424 6.598753 TTAGTTCGCATATTAGCTTTGGTC 57.401 37.500 0.00 0.00 0.00 4.02
5110 7425 4.513442 AGTTCGCATATTAGCTTTGGTCA 58.487 39.130 0.00 0.00 0.00 4.02
5111 7426 4.941263 AGTTCGCATATTAGCTTTGGTCAA 59.059 37.500 0.00 0.00 0.00 3.18
5112 7427 5.414454 AGTTCGCATATTAGCTTTGGTCAAA 59.586 36.000 0.00 0.00 0.00 2.69
5138 7453 9.736023 AGTCAAGCTTTGTAAGTTTTGATTAAG 57.264 29.630 0.00 0.00 36.95 1.85
5139 7454 9.516314 GTCAAGCTTTGTAAGTTTTGATTAAGT 57.484 29.630 0.00 0.00 36.95 2.24
5274 7589 8.865590 TTTCTATAAACTTGGTCAAACTTTGC 57.134 30.769 0.00 0.00 0.00 3.68
5275 7590 7.575414 TCTATAAACTTGGTCAAACTTTGCA 57.425 32.000 0.00 0.00 0.00 4.08
5276 7591 8.001881 TCTATAAACTTGGTCAAACTTTGCAA 57.998 30.769 0.00 0.00 0.00 4.08
5277 7592 8.470805 TCTATAAACTTGGTCAAACTTTGCAAA 58.529 29.630 12.14 12.14 0.00 3.68
5278 7593 5.861222 AAACTTGGTCAAACTTTGCAAAG 57.139 34.783 32.53 32.53 41.73 2.77
5289 7604 3.769536 ACTTTGCAAAGTTTGACTTCGG 58.230 40.909 33.85 11.40 46.52 4.30
5290 7605 3.192633 ACTTTGCAAAGTTTGACTTCGGT 59.807 39.130 33.85 12.02 46.52 4.69
5291 7606 3.414549 TTGCAAAGTTTGACTTCGGTC 57.585 42.857 19.82 0.00 37.47 4.79
5304 7619 5.405331 GACTTCGGTCAAACCTAATATGC 57.595 43.478 0.00 0.00 43.91 3.14
5305 7620 4.839121 ACTTCGGTCAAACCTAATATGCA 58.161 39.130 0.00 0.00 35.66 3.96
5306 7621 4.876107 ACTTCGGTCAAACCTAATATGCAG 59.124 41.667 0.00 0.00 35.66 4.41
5307 7622 4.746535 TCGGTCAAACCTAATATGCAGA 57.253 40.909 0.00 0.00 35.66 4.26
5308 7623 4.439057 TCGGTCAAACCTAATATGCAGAC 58.561 43.478 0.00 0.00 35.66 3.51
5309 7624 4.161565 TCGGTCAAACCTAATATGCAGACT 59.838 41.667 0.00 0.00 35.66 3.24
5310 7625 5.361571 TCGGTCAAACCTAATATGCAGACTA 59.638 40.000 0.00 0.00 35.66 2.59
5311 7626 6.046593 CGGTCAAACCTAATATGCAGACTAA 58.953 40.000 0.00 0.00 35.66 2.24
5312 7627 6.537301 CGGTCAAACCTAATATGCAGACTAAA 59.463 38.462 0.00 0.00 35.66 1.85
5313 7628 7.226720 CGGTCAAACCTAATATGCAGACTAAAT 59.773 37.037 0.00 0.00 35.66 1.40
5314 7629 9.555727 GGTCAAACCTAATATGCAGACTAAATA 57.444 33.333 0.00 0.00 34.73 1.40
5326 7641 8.635765 ATGCAGACTAAATAAAAACAGAAGGA 57.364 30.769 0.00 0.00 0.00 3.36
5327 7642 8.099364 TGCAGACTAAATAAAAACAGAAGGAG 57.901 34.615 0.00 0.00 0.00 3.69
5357 7737 3.715287 ACTTTGGGTTGGTTTGTACCTT 58.285 40.909 0.00 0.00 45.27 3.50
5421 7801 4.374843 TGTGAACATTGCATAATGCTCC 57.625 40.909 1.87 0.00 46.05 4.70
5492 7872 2.357517 CCGTGTTCCTCGCTGCTT 60.358 61.111 0.00 0.00 0.00 3.91
5529 7917 0.802222 CCATGACTGTGGCTACGACG 60.802 60.000 0.00 0.00 31.43 5.12
5630 8018 3.882888 TGATACGGATGAAAATCTTGCCC 59.117 43.478 0.00 0.00 0.00 5.36
5714 8102 1.970917 GAGGCGTGCAACCATCTTCG 61.971 60.000 9.56 0.00 0.00 3.79
5792 8182 3.838271 GATGGCGGCGTCCTCAGA 61.838 66.667 19.92 0.00 0.00 3.27
5793 8183 3.157217 GATGGCGGCGTCCTCAGAT 62.157 63.158 19.92 0.00 0.00 2.90
5794 8184 3.451556 ATGGCGGCGTCCTCAGATG 62.452 63.158 9.84 0.00 0.00 2.90
5795 8185 3.838271 GGCGGCGTCCTCAGATGA 61.838 66.667 9.37 0.00 0.00 2.92
5796 8186 2.419198 GCGGCGTCCTCAGATGAT 59.581 61.111 9.37 0.00 0.00 2.45
5841 8231 0.391597 TGGAGACACGGTTTGGAGAC 59.608 55.000 0.00 0.00 33.40 3.36
5842 8232 0.680061 GGAGACACGGTTTGGAGACT 59.320 55.000 0.00 0.00 0.00 3.24
5849 8239 1.000496 ACGGTTTGGAGACTCTTCGTC 60.000 52.381 1.74 0.00 43.17 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.372459 TCGGCTTGTGTTATAGACCAATATAAT 58.628 33.333 0.00 0.00 31.93 1.28
1 2 7.728148 TCGGCTTGTGTTATAGACCAATATAA 58.272 34.615 0.00 0.00 0.00 0.98
2 3 7.292713 TCGGCTTGTGTTATAGACCAATATA 57.707 36.000 0.00 0.00 0.00 0.86
3 4 6.169557 TCGGCTTGTGTTATAGACCAATAT 57.830 37.500 0.00 0.00 0.00 1.28
143 146 1.943340 CAGCCCTCCTCGAAAATAAGC 59.057 52.381 0.00 0.00 0.00 3.09
144 147 3.198872 GTCAGCCCTCCTCGAAAATAAG 58.801 50.000 0.00 0.00 0.00 1.73
152 155 2.125350 GCTTGTCAGCCCTCCTCG 60.125 66.667 0.00 0.00 40.61 4.63
220 223 5.625311 CACGAAAGAAGTGAAAATAGCAACC 59.375 40.000 0.00 0.00 41.83 3.77
225 228 6.228273 TCAGCACGAAAGAAGTGAAAATAG 57.772 37.500 0.07 0.00 41.83 1.73
228 231 4.574421 TCATCAGCACGAAAGAAGTGAAAA 59.426 37.500 0.07 0.00 41.83 2.29
245 248 5.237996 AGTCACAAACACATGAAGTCATCAG 59.762 40.000 0.00 0.00 42.53 2.90
246 249 5.007921 CAGTCACAAACACATGAAGTCATCA 59.992 40.000 0.00 0.00 43.67 3.07
251 254 3.282021 AGCAGTCACAAACACATGAAGT 58.718 40.909 0.00 0.00 0.00 3.01
260 263 3.632189 CCAAAAGCTAGCAGTCACAAAC 58.368 45.455 18.83 0.00 0.00 2.93
281 284 1.834263 AGTACCTCATGTGGGAGAAGC 59.166 52.381 17.76 0.00 37.05 3.86
317 320 3.739519 GCACCTCTGCGATTGTTATCTCT 60.740 47.826 0.00 0.00 32.44 3.10
318 321 2.541762 GCACCTCTGCGATTGTTATCTC 59.458 50.000 0.00 0.00 32.44 2.75
319 322 2.555199 GCACCTCTGCGATTGTTATCT 58.445 47.619 0.00 0.00 32.44 1.98
336 340 3.172824 GCTAAGAGTGTAACGAGAGCAC 58.827 50.000 0.00 0.00 45.86 4.40
362 366 7.780008 TGTATATCCCTTATGTTTTCACACG 57.220 36.000 0.00 0.00 35.03 4.49
373 377 7.958583 CCAGGCTCCTATATGTATATCCCTTAT 59.041 40.741 0.00 0.00 0.00 1.73
442 446 6.402226 CCTTCAAAGTCGTCTTAAGCCATAAC 60.402 42.308 0.00 0.00 33.09 1.89
466 470 1.668151 GTTCAGCTGACACCGACCC 60.668 63.158 18.03 0.00 0.00 4.46
470 474 1.069765 ACCTGTTCAGCTGACACCG 59.930 57.895 18.03 13.42 0.00 4.94
473 477 1.227943 GCCACCTGTTCAGCTGACA 60.228 57.895 18.03 16.27 0.00 3.58
476 480 2.281070 ACGCCACCTGTTCAGCTG 60.281 61.111 7.63 7.63 0.00 4.24
523 527 3.056328 GGCCACAACTTCTCGGGC 61.056 66.667 0.00 0.00 43.86 6.13
748 754 8.421701 GCACAATGTAAATTTTTAGTTACACCG 58.578 33.333 0.00 0.00 41.63 4.94
750 756 8.960075 ACGCACAATGTAAATTTTTAGTTACAC 58.040 29.630 0.00 0.00 41.63 2.90
753 759 8.959058 CACACGCACAATGTAAATTTTTAGTTA 58.041 29.630 0.00 0.00 0.00 2.24
816 822 8.397575 AGAACCCACTTCTCTTTTTCTTATTC 57.602 34.615 0.00 0.00 33.53 1.75
819 825 8.589701 AAAAGAACCCACTTCTCTTTTTCTTA 57.410 30.769 3.76 0.00 43.48 2.10
855 861 1.035923 GAGATGATGGAGCCGAGACA 58.964 55.000 0.00 0.00 0.00 3.41
856 862 0.039617 CGAGATGATGGAGCCGAGAC 60.040 60.000 0.00 0.00 0.00 3.36
857 863 1.175347 CCGAGATGATGGAGCCGAGA 61.175 60.000 0.00 0.00 0.00 4.04
858 864 1.288439 CCGAGATGATGGAGCCGAG 59.712 63.158 0.00 0.00 0.00 4.63
859 865 2.861101 GCCGAGATGATGGAGCCGA 61.861 63.158 0.00 0.00 0.00 5.54
861 867 1.005156 GAGCCGAGATGATGGAGCC 60.005 63.158 0.00 0.00 0.00 4.70
862 868 0.392336 AAGAGCCGAGATGATGGAGC 59.608 55.000 0.00 0.00 0.00 4.70
864 870 2.079170 AGAAGAGCCGAGATGATGGA 57.921 50.000 0.00 0.00 0.00 3.41
865 871 2.364970 AGAAGAAGAGCCGAGATGATGG 59.635 50.000 0.00 0.00 0.00 3.51
866 872 3.731652 AGAAGAAGAGCCGAGATGATG 57.268 47.619 0.00 0.00 0.00 3.07
867 873 3.181467 CCAAGAAGAAGAGCCGAGATGAT 60.181 47.826 0.00 0.00 0.00 2.45
868 874 2.167281 CCAAGAAGAAGAGCCGAGATGA 59.833 50.000 0.00 0.00 0.00 2.92
869 875 2.548875 CCAAGAAGAAGAGCCGAGATG 58.451 52.381 0.00 0.00 0.00 2.90
870 876 1.484240 CCCAAGAAGAAGAGCCGAGAT 59.516 52.381 0.00 0.00 0.00 2.75
902 908 1.760875 GCCGGGTGGGATACTCAGA 60.761 63.158 2.18 0.00 38.47 3.27
1027 1140 1.213296 TCCTTATTCTCCCTGCCCAC 58.787 55.000 0.00 0.00 0.00 4.61
1156 1269 3.111838 CGTCGGAATGACTCTTCAGATG 58.888 50.000 0.00 0.00 45.87 2.90
1275 1388 4.079827 AGGGCCTCCTCCTGATTG 57.920 61.111 0.00 0.00 39.80 2.67
1461 1576 5.432680 TTTCAGCATCCTCAGAAGATTCT 57.567 39.130 0.00 0.00 38.25 2.40
1654 2019 4.699735 CAGCATCAATGTGGGTAGTGTTAA 59.300 41.667 0.00 0.00 0.00 2.01
1718 2085 1.560923 GAGTGGATTCGATGACACGG 58.439 55.000 7.83 0.00 38.78 4.94
2197 3559 7.643569 TTGTTTTGCATCCATATAGATGTGT 57.356 32.000 11.97 0.00 44.58 3.72
2296 3658 4.874396 ACATAGATGTGTGCTCATTGACTG 59.126 41.667 0.00 0.00 40.03 3.51
2297 3659 5.095145 ACATAGATGTGTGCTCATTGACT 57.905 39.130 0.00 0.00 40.03 3.41
2310 3672 6.534475 AATTGTTTGCATCCACATAGATGT 57.466 33.333 3.69 0.00 44.58 3.06
2332 3694 9.634021 TGTGGTACAAAGGCATCAAATATATAA 57.366 29.630 0.00 0.00 44.16 0.98
2333 3695 9.634021 TTGTGGTACAAAGGCATCAAATATATA 57.366 29.630 0.00 0.00 44.16 0.86
2334 3696 8.532186 TTGTGGTACAAAGGCATCAAATATAT 57.468 30.769 0.00 0.00 44.16 0.86
2335 3697 7.946381 TTGTGGTACAAAGGCATCAAATATA 57.054 32.000 0.00 0.00 44.16 0.86
2336 3698 6.849085 TTGTGGTACAAAGGCATCAAATAT 57.151 33.333 0.00 0.00 44.16 1.28
2337 3699 6.435591 TCATTGTGGTACAAAGGCATCAAATA 59.564 34.615 0.00 0.00 44.16 1.40
2338 3700 5.245751 TCATTGTGGTACAAAGGCATCAAAT 59.754 36.000 0.00 0.00 44.16 2.32
2339 3701 4.586421 TCATTGTGGTACAAAGGCATCAAA 59.414 37.500 0.00 0.00 44.16 2.69
2340 3702 4.148079 TCATTGTGGTACAAAGGCATCAA 58.852 39.130 0.00 0.00 44.16 2.57
2341 3703 3.760738 TCATTGTGGTACAAAGGCATCA 58.239 40.909 0.00 0.00 44.16 3.07
2342 3704 4.675510 CATCATTGTGGTACAAAGGCATC 58.324 43.478 0.00 0.00 44.16 3.91
2343 3705 3.119029 GCATCATTGTGGTACAAAGGCAT 60.119 43.478 0.00 0.00 44.16 4.40
2344 3706 2.230992 GCATCATTGTGGTACAAAGGCA 59.769 45.455 0.00 0.00 44.16 4.75
2345 3707 2.230992 TGCATCATTGTGGTACAAAGGC 59.769 45.455 0.00 0.00 44.16 4.35
2346 3708 4.022068 AGTTGCATCATTGTGGTACAAAGG 60.022 41.667 0.00 0.00 44.16 3.11
2347 3709 5.125100 AGTTGCATCATTGTGGTACAAAG 57.875 39.130 0.00 0.00 44.16 2.77
2348 3710 5.068329 TCAAGTTGCATCATTGTGGTACAAA 59.932 36.000 0.00 0.00 44.16 2.83
2349 3711 4.582240 TCAAGTTGCATCATTGTGGTACAA 59.418 37.500 0.00 0.00 44.16 2.41
2350 3712 4.140536 TCAAGTTGCATCATTGTGGTACA 58.859 39.130 0.00 0.00 0.00 2.90
2351 3713 4.764679 TCAAGTTGCATCATTGTGGTAC 57.235 40.909 0.00 0.00 0.00 3.34
2352 3714 5.243507 ACATTCAAGTTGCATCATTGTGGTA 59.756 36.000 0.00 0.00 0.00 3.25
2353 3715 4.039488 ACATTCAAGTTGCATCATTGTGGT 59.961 37.500 0.00 0.00 0.00 4.16
2354 3716 4.562082 ACATTCAAGTTGCATCATTGTGG 58.438 39.130 0.00 0.00 0.00 4.17
2355 3717 5.692654 TGAACATTCAAGTTGCATCATTGTG 59.307 36.000 0.00 0.00 33.55 3.33
2356 3718 5.845103 TGAACATTCAAGTTGCATCATTGT 58.155 33.333 0.00 0.00 33.55 2.71
2357 3719 6.772770 TTGAACATTCAAGTTGCATCATTG 57.227 33.333 2.89 0.00 41.88 2.82
2370 3732 3.573538 CCAGACACCCAATTGAACATTCA 59.426 43.478 7.12 0.00 34.92 2.57
2371 3733 3.614870 GCCAGACACCCAATTGAACATTC 60.615 47.826 7.12 0.00 0.00 2.67
2372 3734 2.299867 GCCAGACACCCAATTGAACATT 59.700 45.455 7.12 0.00 0.00 2.71
2373 3735 1.895131 GCCAGACACCCAATTGAACAT 59.105 47.619 7.12 0.00 0.00 2.71
2374 3736 1.133513 AGCCAGACACCCAATTGAACA 60.134 47.619 7.12 0.00 0.00 3.18
2375 3737 1.620822 AGCCAGACACCCAATTGAAC 58.379 50.000 7.12 0.00 0.00 3.18
2376 3738 2.158475 AGAAGCCAGACACCCAATTGAA 60.158 45.455 7.12 0.00 0.00 2.69
2377 3739 1.425066 AGAAGCCAGACACCCAATTGA 59.575 47.619 7.12 0.00 0.00 2.57
2378 3740 1.915141 AGAAGCCAGACACCCAATTG 58.085 50.000 0.00 0.00 0.00 2.32
2379 3741 2.644798 AGTAGAAGCCAGACACCCAATT 59.355 45.455 0.00 0.00 0.00 2.32
2380 3742 2.269940 AGTAGAAGCCAGACACCCAAT 58.730 47.619 0.00 0.00 0.00 3.16
2381 3743 1.729586 AGTAGAAGCCAGACACCCAA 58.270 50.000 0.00 0.00 0.00 4.12
2382 3744 1.729586 AAGTAGAAGCCAGACACCCA 58.270 50.000 0.00 0.00 0.00 4.51
2383 3745 2.861147 AAAGTAGAAGCCAGACACCC 57.139 50.000 0.00 0.00 0.00 4.61
2384 3746 4.134563 TGAAAAAGTAGAAGCCAGACACC 58.865 43.478 0.00 0.00 0.00 4.16
2385 3747 4.816925 ACTGAAAAAGTAGAAGCCAGACAC 59.183 41.667 0.00 0.00 37.36 3.67
2386 3748 5.036117 ACTGAAAAAGTAGAAGCCAGACA 57.964 39.130 0.00 0.00 37.36 3.41
2387 3749 5.057149 TGACTGAAAAAGTAGAAGCCAGAC 58.943 41.667 0.00 0.00 40.07 3.51
2388 3750 5.290493 TGACTGAAAAAGTAGAAGCCAGA 57.710 39.130 0.00 0.00 40.07 3.86
2389 3751 6.205464 TCATTGACTGAAAAAGTAGAAGCCAG 59.795 38.462 0.00 0.00 40.07 4.85
2390 3752 6.061441 TCATTGACTGAAAAAGTAGAAGCCA 58.939 36.000 0.00 0.00 40.07 4.75
2391 3753 6.560253 TCATTGACTGAAAAAGTAGAAGCC 57.440 37.500 0.00 0.00 40.07 4.35
2392 3754 6.082984 GCTCATTGACTGAAAAAGTAGAAGC 58.917 40.000 0.00 0.00 40.07 3.86
2393 3755 7.074502 GTGCTCATTGACTGAAAAAGTAGAAG 58.925 38.462 0.00 0.00 40.07 2.85
2394 3756 6.542005 TGTGCTCATTGACTGAAAAAGTAGAA 59.458 34.615 0.00 0.00 40.07 2.10
2395 3757 6.017934 GTGTGCTCATTGACTGAAAAAGTAGA 60.018 38.462 0.00 0.00 40.07 2.59
2396 3758 6.138761 GTGTGCTCATTGACTGAAAAAGTAG 58.861 40.000 0.00 0.00 40.07 2.57
2397 3759 5.588246 TGTGTGCTCATTGACTGAAAAAGTA 59.412 36.000 0.00 0.00 40.07 2.24
2398 3760 4.398988 TGTGTGCTCATTGACTGAAAAAGT 59.601 37.500 0.00 0.00 43.85 2.66
2399 3761 4.923893 TGTGTGCTCATTGACTGAAAAAG 58.076 39.130 0.00 0.00 32.14 2.27
2400 3762 4.979943 TGTGTGCTCATTGACTGAAAAA 57.020 36.364 0.00 0.00 32.14 1.94
2401 3763 4.823442 AGATGTGTGCTCATTGACTGAAAA 59.177 37.500 0.00 0.00 32.14 2.29
2402 3764 4.392047 AGATGTGTGCTCATTGACTGAAA 58.608 39.130 0.00 0.00 32.14 2.69
2403 3765 4.011966 AGATGTGTGCTCATTGACTGAA 57.988 40.909 0.00 0.00 32.14 3.02
2404 3766 3.690475 AGATGTGTGCTCATTGACTGA 57.310 42.857 0.00 0.00 0.00 3.41
2405 3767 6.147328 CCATATAGATGTGTGCTCATTGACTG 59.853 42.308 0.00 0.00 0.00 3.51
2927 4552 6.199908 GGTTCATAGTCAGATTGATGTCTTCG 59.800 42.308 0.00 0.00 0.00 3.79
2956 4581 1.301677 GGAAAACAGGAGCGCTGGAG 61.302 60.000 18.48 6.30 0.00 3.86
3081 4706 5.808366 ATTTCCACTCTGAACACTCTACA 57.192 39.130 0.00 0.00 0.00 2.74
3186 4811 1.014352 ACCAACGACACAAGAGTTGC 58.986 50.000 0.00 0.00 42.60 4.17
3199 4824 2.751436 CCCATCCCAGCACCAACG 60.751 66.667 0.00 0.00 0.00 4.10
3204 4829 0.912486 AGTAGTTCCCATCCCAGCAC 59.088 55.000 0.00 0.00 0.00 4.40
3271 4896 1.422531 TGCCTTTTGCCTTTGACCAT 58.577 45.000 0.00 0.00 40.16 3.55
3389 5014 6.714278 GTTTGGAGTTACCTAACCATCCTAA 58.286 40.000 0.00 2.56 44.44 2.69
3436 5061 1.613437 ACAACACAGCCCATTAGCAAC 59.387 47.619 0.00 0.00 34.23 4.17
3582 5207 2.806244 GTCTCTTTTTAAGCGCCAGTGA 59.194 45.455 2.29 0.00 0.00 3.41
3735 5380 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
3843 5488 1.032794 TCTGCATGCTACTACCTCCG 58.967 55.000 20.33 0.00 0.00 4.63
3906 6043 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3935 6072 8.640063 TTAGTATTAGGTACATCCGCATCTAA 57.360 34.615 0.00 0.00 41.99 2.10
4056 6324 3.515602 AAAGGTTCTGTCCTGCAAGAT 57.484 42.857 0.00 0.00 37.93 2.40
5003 7301 2.095263 CACAAACGGTTGGGACATCATC 60.095 50.000 19.08 0.00 40.98 2.92
5004 7302 1.885887 CACAAACGGTTGGGACATCAT 59.114 47.619 19.08 0.00 40.98 2.45
5005 7303 1.313772 CACAAACGGTTGGGACATCA 58.686 50.000 19.08 0.00 40.98 3.07
5006 7304 1.314730 ACACAAACGGTTGGGACATC 58.685 50.000 25.00 0.00 40.98 3.06
5007 7305 1.770294 AACACAAACGGTTGGGACAT 58.230 45.000 25.00 4.76 40.98 3.06
5008 7306 2.414994 TAACACAAACGGTTGGGACA 57.585 45.000 25.00 5.99 40.98 4.02
5009 7307 3.566742 AGATTAACACAAACGGTTGGGAC 59.433 43.478 25.00 7.74 40.98 4.46
5017 7315 6.712241 AGTCAGATCAGATTAACACAAACG 57.288 37.500 0.00 0.00 0.00 3.60
5070 7385 5.446875 GCGAACTAAATAAAAACGGAGGGAG 60.447 44.000 0.00 0.00 0.00 4.30
5071 7386 4.392754 GCGAACTAAATAAAAACGGAGGGA 59.607 41.667 0.00 0.00 0.00 4.20
5072 7387 4.154556 TGCGAACTAAATAAAAACGGAGGG 59.845 41.667 0.00 0.00 0.00 4.30
5073 7388 5.285798 TGCGAACTAAATAAAAACGGAGG 57.714 39.130 0.00 0.00 0.00 4.30
5076 7391 8.889000 GCTAATATGCGAACTAAATAAAAACGG 58.111 33.333 0.00 0.00 0.00 4.44
5081 7396 9.944663 CCAAAGCTAATATGCGAACTAAATAAA 57.055 29.630 0.00 0.00 38.13 1.40
5082 7397 9.116067 ACCAAAGCTAATATGCGAACTAAATAA 57.884 29.630 0.00 0.00 38.13 1.40
5083 7398 8.671384 ACCAAAGCTAATATGCGAACTAAATA 57.329 30.769 0.00 0.00 38.13 1.40
5084 7399 7.282224 TGACCAAAGCTAATATGCGAACTAAAT 59.718 33.333 0.00 0.00 38.13 1.40
5085 7400 6.596106 TGACCAAAGCTAATATGCGAACTAAA 59.404 34.615 0.00 0.00 38.13 1.85
5086 7401 6.110033 TGACCAAAGCTAATATGCGAACTAA 58.890 36.000 0.00 0.00 38.13 2.24
5087 7402 5.666462 TGACCAAAGCTAATATGCGAACTA 58.334 37.500 0.00 0.00 38.13 2.24
5088 7403 4.513442 TGACCAAAGCTAATATGCGAACT 58.487 39.130 0.00 0.00 38.13 3.01
5089 7404 4.875544 TGACCAAAGCTAATATGCGAAC 57.124 40.909 0.00 0.00 38.13 3.95
5090 7405 5.879237 CTTTGACCAAAGCTAATATGCGAA 58.121 37.500 9.25 0.00 40.94 4.70
5091 7406 5.484173 CTTTGACCAAAGCTAATATGCGA 57.516 39.130 9.25 0.00 40.94 5.10
5112 7427 9.736023 CTTAATCAAAACTTACAAAGCTTGACT 57.264 29.630 0.00 0.00 36.83 3.41
5113 7428 9.516314 ACTTAATCAAAACTTACAAAGCTTGAC 57.484 29.630 0.00 0.00 36.83 3.18
5248 7563 9.308318 GCAAAGTTTGACCAAGTTTATAGAAAA 57.692 29.630 19.82 0.00 36.07 2.29
5249 7564 8.470805 TGCAAAGTTTGACCAAGTTTATAGAAA 58.529 29.630 19.82 0.00 36.07 2.52
5250 7565 8.001881 TGCAAAGTTTGACCAAGTTTATAGAA 57.998 30.769 19.82 0.00 36.07 2.10
5251 7566 7.575414 TGCAAAGTTTGACCAAGTTTATAGA 57.425 32.000 19.82 0.00 36.07 1.98
5252 7567 8.641499 TTTGCAAAGTTTGACCAAGTTTATAG 57.359 30.769 19.82 0.00 36.07 1.31
5253 7568 8.254508 ACTTTGCAAAGTTTGACCAAGTTTATA 58.745 29.630 33.85 0.00 46.52 0.98
5254 7569 7.102993 ACTTTGCAAAGTTTGACCAAGTTTAT 58.897 30.769 33.85 10.04 46.52 1.40
5255 7570 6.459923 ACTTTGCAAAGTTTGACCAAGTTTA 58.540 32.000 33.85 0.00 46.52 2.01
5256 7571 5.304778 ACTTTGCAAAGTTTGACCAAGTTT 58.695 33.333 33.85 11.08 46.52 2.66
5257 7572 4.893608 ACTTTGCAAAGTTTGACCAAGTT 58.106 34.783 33.85 11.27 46.52 2.66
5258 7573 4.535526 ACTTTGCAAAGTTTGACCAAGT 57.464 36.364 33.85 17.53 46.52 3.16
5267 7582 6.128842 GACCGAAGTCAAACTTTGCAAAGTT 61.129 40.000 39.24 39.24 45.31 2.66
5268 7583 4.674362 GACCGAAGTCAAACTTTGCAAAGT 60.674 41.667 33.85 33.85 45.47 2.66
5269 7584 3.769536 ACCGAAGTCAAACTTTGCAAAG 58.230 40.909 32.53 32.53 38.80 2.77
5270 7585 3.765026 GACCGAAGTCAAACTTTGCAAA 58.235 40.909 12.14 12.14 38.80 3.68
5271 7586 3.414549 GACCGAAGTCAAACTTTGCAA 57.585 42.857 0.00 0.00 38.80 4.08
5282 7597 4.873827 TGCATATTAGGTTTGACCGAAGTC 59.126 41.667 0.00 0.00 44.90 3.01
5283 7598 4.839121 TGCATATTAGGTTTGACCGAAGT 58.161 39.130 0.00 0.00 44.90 3.01
5284 7599 5.006746 GTCTGCATATTAGGTTTGACCGAAG 59.993 44.000 0.00 0.00 44.90 3.79
5285 7600 4.873827 GTCTGCATATTAGGTTTGACCGAA 59.126 41.667 0.00 0.00 44.90 4.30
5286 7601 4.161565 AGTCTGCATATTAGGTTTGACCGA 59.838 41.667 0.00 0.00 44.90 4.69
5287 7602 4.442706 AGTCTGCATATTAGGTTTGACCG 58.557 43.478 0.00 0.00 44.90 4.79
5288 7603 7.859325 TTTAGTCTGCATATTAGGTTTGACC 57.141 36.000 0.00 0.00 38.99 4.02
5300 7615 9.733556 TCCTTCTGTTTTTATTTAGTCTGCATA 57.266 29.630 0.00 0.00 0.00 3.14
5301 7616 8.635765 TCCTTCTGTTTTTATTTAGTCTGCAT 57.364 30.769 0.00 0.00 0.00 3.96
5302 7617 7.719633 ACTCCTTCTGTTTTTATTTAGTCTGCA 59.280 33.333 0.00 0.00 0.00 4.41
5303 7618 8.100508 ACTCCTTCTGTTTTTATTTAGTCTGC 57.899 34.615 0.00 0.00 0.00 4.26
5316 7631 9.449719 CCAAAGTATAACATACTCCTTCTGTTT 57.550 33.333 0.00 0.00 35.00 2.83
5317 7632 8.047310 CCCAAAGTATAACATACTCCTTCTGTT 58.953 37.037 0.00 0.00 37.00 3.16
5318 7633 7.182206 ACCCAAAGTATAACATACTCCTTCTGT 59.818 37.037 0.00 0.00 0.00 3.41
5319 7634 7.565680 ACCCAAAGTATAACATACTCCTTCTG 58.434 38.462 0.00 0.00 0.00 3.02
5320 7635 7.750947 ACCCAAAGTATAACATACTCCTTCT 57.249 36.000 0.00 0.00 0.00 2.85
5321 7636 7.282450 CCAACCCAAAGTATAACATACTCCTTC 59.718 40.741 0.00 0.00 0.00 3.46
5322 7637 7.116736 CCAACCCAAAGTATAACATACTCCTT 58.883 38.462 0.00 0.00 0.00 3.36
5323 7638 6.216868 ACCAACCCAAAGTATAACATACTCCT 59.783 38.462 0.00 0.00 0.00 3.69
5324 7639 6.420638 ACCAACCCAAAGTATAACATACTCC 58.579 40.000 0.00 0.00 0.00 3.85
5325 7640 7.933215 AACCAACCCAAAGTATAACATACTC 57.067 36.000 0.00 0.00 0.00 2.59
5326 7641 7.726738 ACAAACCAACCCAAAGTATAACATACT 59.273 33.333 0.00 0.00 0.00 2.12
5327 7642 7.888424 ACAAACCAACCCAAAGTATAACATAC 58.112 34.615 0.00 0.00 0.00 2.39
5357 7737 5.337169 GCAGGTGGGAAATTAAATGCACTAA 60.337 40.000 0.00 0.00 32.79 2.24
5421 7801 8.383619 CAGAAAGACTTATATTTGTGAACGGAG 58.616 37.037 0.00 0.00 33.33 4.63
5492 7872 4.164087 ACCACCGACACCGCACAA 62.164 61.111 0.00 0.00 0.00 3.33
5841 8231 1.137825 GGAGGAGCACGACGAAGAG 59.862 63.158 0.00 0.00 0.00 2.85
5842 8232 2.687805 CGGAGGAGCACGACGAAGA 61.688 63.158 0.00 0.00 0.00 2.87
5862 8252 0.246360 ATCATGGACAGCGACGAACA 59.754 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.