Multiple sequence alignment - TraesCS1A01G061700

Loading Multiple Alignment...

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 TraesCS1A01G061700 chr1A 100.000 6433 0 0 1 6433 42250783 42257215 0.000000e+00 11880.0
1 TraesCS1A01G061700 chr1A 94.004 1134 60 6 4864 5996 42218025 42216899 0.000000e+00 1711.0
2 TraesCS1A01G061700 chr1A 95.078 833 40 1 3762 4594 42220808 42219977 0.000000e+00 1310.0
3 TraesCS1A01G061700 chr1A 95.756 542 12 8 70 606 459051774 459052309 0.000000e+00 863.0
4 TraesCS1A01G061700 chr1A 95.064 547 17 7 65 606 424590067 424590608 0.000000e+00 852.0
5 TraesCS1A01G061700 chr1A 94.863 292 14 1 4587 4878 42218496 42218206 7.600000e-124 455.0
6 TraesCS1A01G061700 chr1A 81.764 499 81 9 3838 4332 42251815 42252307 6.000000e-110 409.0
7 TraesCS1A01G061700 chr1A 81.764 499 81 9 1033 1525 42254620 42255114 6.000000e-110 409.0
8 TraesCS1A01G061700 chr1A 91.034 290 21 3 3392 3676 42221142 42220853 2.810000e-103 387.0
9 TraesCS1A01G061700 chr1A 80.319 376 42 11 1631 1999 42222899 42222549 8.280000e-64 255.0
10 TraesCS1A01G061700 chr1A 91.250 80 6 1 611 690 124238685 124238607 2.450000e-19 108.0
11 TraesCS1A01G061700 chr1A 87.640 89 6 4 2890 2975 42221392 42221306 1.480000e-16 99.0
12 TraesCS1A01G061700 chr1A 85.938 64 8 1 5671 5734 490514083 490514145 4.160000e-07 67.6
13 TraesCS1A01G061700 chr1B 92.055 1825 121 8 3747 5554 62722588 62724405 0.000000e+00 2545.0
14 TraesCS1A01G061700 chr1B 86.293 1357 89 45 790 2092 62719832 62721145 0.000000e+00 1386.0
15 TraesCS1A01G061700 chr1B 91.405 477 25 8 987 1449 429313892 429314366 1.960000e-179 640.0
16 TraesCS1A01G061700 chr1B 82.353 527 79 13 1018 1537 62722666 62723185 4.580000e-121 446.0
17 TraesCS1A01G061700 chr1B 82.456 513 78 11 3826 4332 62720051 62720557 7.660000e-119 438.0
18 TraesCS1A01G061700 chr1B 90.769 325 25 2 6113 6433 62726385 62726708 4.610000e-116 429.0
19 TraesCS1A01G061700 chr1D 91.148 1864 126 14 3713 5549 42762131 42763982 0.000000e+00 2492.0
20 TraesCS1A01G061700 chr1D 87.331 1776 161 24 3291 5059 42712721 42711003 0.000000e+00 1975.0
21 TraesCS1A01G061700 chr1D 89.311 1422 73 46 746 2128 42759409 42760790 0.000000e+00 1711.0
22 TraesCS1A01G061700 chr1D 91.396 709 49 6 3711 4419 42625411 42624715 0.000000e+00 961.0
23 TraesCS1A01G061700 chr1D 90.079 504 44 6 5055 5554 42673784 42673283 0.000000e+00 649.0
24 TraesCS1A01G061700 chr1D 89.881 504 45 6 5055 5554 42700884 42700383 1.510000e-180 643.0
25 TraesCS1A01G061700 chr1D 89.683 504 46 6 5055 5554 42614193 42613692 7.030000e-179 638.0
26 TraesCS1A01G061700 chr1D 92.308 325 18 4 6113 6433 42671454 42671133 7.600000e-124 455.0
27 TraesCS1A01G061700 chr1D 82.685 514 77 11 3825 4332 42759679 42760186 4.580000e-121 446.0
28 TraesCS1A01G061700 chr1D 91.385 325 22 3 6113 6433 42686655 42686333 2.130000e-119 440.0
29 TraesCS1A01G061700 chr1D 81.800 511 83 9 1033 1537 42762263 42762769 2.770000e-113 420.0
30 TraesCS1A01G061700 chr1D 85.864 382 46 5 3291 3665 42625781 42625401 3.610000e-107 399.0
31 TraesCS1A01G061700 chr1D 87.582 306 37 1 5136 5440 42765102 42765407 2.850000e-93 353.0
32 TraesCS1A01G061700 chr1D 78.897 526 97 13 1018 1537 42625307 42624790 1.720000e-90 344.0
33 TraesCS1A01G061700 chr1D 91.020 245 16 3 6113 6353 42611867 42611625 6.220000e-85 326.0
34 TraesCS1A01G061700 chr1D 79.704 473 74 14 2547 3012 31229784 31230241 8.050000e-84 322.0
35 TraesCS1A01G061700 chr1D 81.742 356 60 3 5136 5487 42612711 42612357 6.310000e-75 292.0
36 TraesCS1A01G061700 chr1D 80.178 338 33 16 790 1113 42756469 42756786 8.390000e-54 222.0
37 TraesCS1A01G061700 chr1D 84.375 224 26 6 3436 3658 42761376 42761591 1.820000e-50 211.0
38 TraesCS1A01G061700 chr1D 80.142 282 31 6 2238 2513 42761039 42761301 3.060000e-43 187.0
39 TraesCS1A01G061700 chr1D 81.659 229 23 7 1629 1850 42744648 42744432 8.580000e-39 172.0
40 TraesCS1A01G061700 chr1D 90.805 87 4 1 6113 6195 42765945 42766031 5.270000e-21 113.0
41 TraesCS1A01G061700 chr1D 90.278 72 6 1 2 73 81458682 81458752 6.870000e-15 93.5
42 TraesCS1A01G061700 chr1D 85.075 67 8 2 5671 5737 11958498 11958434 4.160000e-07 67.6
43 TraesCS1A01G061700 chr1D 82.667 75 13 0 5095 5169 436113887 436113961 4.160000e-07 67.6
44 TraesCS1A01G061700 chr1D 85.294 68 7 2 5671 5737 463073050 463072985 4.160000e-07 67.6
45 TraesCS1A01G061700 chr1D 87.719 57 6 1 5679 5734 471123437 471123493 1.500000e-06 65.8
46 TraesCS1A01G061700 chr1D 83.824 68 8 2 5671 5737 422066959 422066894 1.940000e-05 62.1
47 TraesCS1A01G061700 chr1D 83.824 68 8 2 5671 5737 472916700 472916635 1.940000e-05 62.1
48 TraesCS1A01G061700 chr7B 89.062 1024 101 5 4468 5482 572959045 572958024 0.000000e+00 1260.0
49 TraesCS1A01G061700 chr7B 90.429 606 53 2 3743 4346 572959678 572959076 0.000000e+00 793.0
50 TraesCS1A01G061700 chr7B 89.247 279 20 3 4073 4350 147721552 147721283 2.220000e-89 340.0
51 TraesCS1A01G061700 chr7B 92.576 229 17 0 3067 3295 19326312 19326540 4.810000e-86 329.0
52 TraesCS1A01G061700 chr7B 93.846 65 4 0 5 69 79336253 79336189 1.480000e-16 99.0
53 TraesCS1A01G061700 chr7D 89.980 978 90 3 4484 5453 532612382 532611405 0.000000e+00 1256.0
54 TraesCS1A01G061700 chr7D 85.841 904 118 7 4530 5425 5352008 5351107 0.000000e+00 952.0
55 TraesCS1A01G061700 chr7D 91.060 604 52 1 3743 4346 532613022 532612421 0.000000e+00 815.0
56 TraesCS1A01G061700 chr7D 85.795 528 57 5 1018 1527 5352551 5352024 1.580000e-150 544.0
57 TraesCS1A01G061700 chr7D 84.980 253 35 3 2550 2800 567713909 567713658 2.980000e-63 254.0
58 TraesCS1A01G061700 chr7D 85.000 80 11 1 5659 5737 390468598 390468519 5.350000e-11 80.5
59 TraesCS1A01G061700 chr7D 77.953 127 21 6 5598 5723 506871418 506871538 8.950000e-09 73.1
60 TraesCS1A01G061700 chr7A 90.426 940 90 0 4523 5462 612756944 612756005 0.000000e+00 1238.0
61 TraesCS1A01G061700 chr7A 96.133 543 10 7 70 606 426838391 426837854 0.000000e+00 876.0
62 TraesCS1A01G061700 chr7A 90.305 557 51 1 3790 4346 612757587 612757034 0.000000e+00 726.0
63 TraesCS1A01G061700 chr7A 85.938 512 51 5 1037 1527 6802555 6803066 1.590000e-145 527.0
64 TraesCS1A01G061700 chr7A 93.392 227 15 0 3067 3293 184610871 184611097 2.870000e-88 337.0
65 TraesCS1A01G061700 chr7A 85.657 251 36 0 2550 2800 593468404 593468154 1.380000e-66 265.0
66 TraesCS1A01G061700 chr7A 81.553 309 49 7 2550 2852 604510596 604510290 1.390000e-61 248.0
67 TraesCS1A01G061700 chr7A 78.305 295 47 7 2708 2996 654776721 654776438 2.380000e-39 174.0
68 TraesCS1A01G061700 chr7A 92.308 65 5 0 2 66 41039628 41039692 6.870000e-15 93.5
69 TraesCS1A01G061700 chr4A 86.188 905 113 9 4530 5425 737139924 737140825 0.000000e+00 968.0
70 TraesCS1A01G061700 chr4A 95.064 547 15 9 70 611 562503024 562502485 0.000000e+00 850.0
71 TraesCS1A01G061700 chr4A 85.981 535 51 6 1017 1527 737139374 737139908 9.430000e-153 551.0
72 TraesCS1A01G061700 chr4A 92.576 229 17 0 3069 3297 11682475 11682703 4.810000e-86 329.0
73 TraesCS1A01G061700 chr4A 81.029 311 49 9 2546 2852 625324418 625324722 8.340000e-59 239.0
74 TraesCS1A01G061700 chr4A 91.304 69 4 2 5 73 179552111 179552045 6.870000e-15 93.5
75 TraesCS1A01G061700 chr4A 86.567 67 8 1 5671 5737 112854575 112854640 8.950000e-09 73.1
76 TraesCS1A01G061700 chr5A 96.125 542 12 6 69 606 121566272 121566808 0.000000e+00 876.0
77 TraesCS1A01G061700 chr5A 95.580 543 13 8 70 607 367836859 367837395 0.000000e+00 859.0
78 TraesCS1A01G061700 chr5A 95.396 543 16 6 72 610 683796913 683796376 0.000000e+00 856.0
79 TraesCS1A01G061700 chr5A 92.609 230 16 1 3068 3296 422021027 422020798 4.810000e-86 329.0
80 TraesCS1A01G061700 chr3A 95.564 541 16 6 69 606 730263465 730262930 0.000000e+00 859.0
81 TraesCS1A01G061700 chr3A 95.221 544 18 6 71 611 730247081 730246543 0.000000e+00 854.0
82 TraesCS1A01G061700 chr3A 92.952 227 16 0 3067 3293 726353201 726352975 1.340000e-86 331.0
83 TraesCS1A01G061700 chr4B 81.099 455 72 12 2552 2996 128018978 128018528 1.030000e-92 351.0
84 TraesCS1A01G061700 chr4B 87.500 56 7 0 5682 5737 285574941 285574886 1.500000e-06 65.8
85 TraesCS1A01G061700 chr6B 92.609 230 17 0 3067 3296 57289932 57289703 1.340000e-86 331.0
86 TraesCS1A01G061700 chr5B 92.609 230 17 0 3067 3296 570000770 570000541 1.340000e-86 331.0
87 TraesCS1A01G061700 chr6A 92.241 232 18 0 3067 3298 544677827 544677596 4.810000e-86 329.0
88 TraesCS1A01G061700 chr6A 94.937 79 3 1 611 689 14750572 14750495 8.760000e-24 122.0
89 TraesCS1A01G061700 chr6A 88.889 72 7 1 2 73 12399070 12399140 3.200000e-13 87.9
90 TraesCS1A01G061700 chr6A 87.692 65 5 2 5671 5734 1972007 1972069 8.950000e-09 73.1
91 TraesCS1A01G061700 chr6A 89.130 46 3 2 5088 5132 506522807 506522851 1.000000e-03 56.5
92 TraesCS1A01G061700 chr3B 92.241 232 18 0 3066 3297 426807083 426807314 4.810000e-86 329.0
93 TraesCS1A01G061700 chr3B 93.750 80 3 2 611 690 679519808 679519885 1.130000e-22 119.0
94 TraesCS1A01G061700 chr3B 83.696 92 11 4 2268 2356 770188608 770188518 4.130000e-12 84.2
95 TraesCS1A01G061700 chr3B 86.364 66 8 1 5672 5737 397373948 397373884 3.220000e-08 71.3
96 TraesCS1A01G061700 chr4D 80.583 412 72 8 2552 2957 486228078 486227669 1.740000e-80 311.0
97 TraesCS1A01G061700 chr4D 93.333 45 3 0 5690 5734 7924950 7924994 4.160000e-07 67.6
98 TraesCS1A01G061700 chr4D 86.441 59 6 2 5679 5737 456123574 456123518 5.380000e-06 63.9
99 TraesCS1A01G061700 chr3D 80.256 390 68 9 2572 2957 303355616 303355232 1.060000e-72 285.0
100 TraesCS1A01G061700 chr3D 92.405 79 5 1 611 689 486688872 486688949 1.900000e-20 111.0
101 TraesCS1A01G061700 chr3D 87.879 66 7 1 5672 5737 148251149 148251213 6.920000e-10 76.8
102 TraesCS1A01G061700 chr3D 85.938 64 7 2 5671 5734 17523172 17523233 4.160000e-07 67.6
103 TraesCS1A01G061700 chr2D 77.869 488 78 24 2550 3012 373983537 373983055 6.350000e-70 276.0
104 TraesCS1A01G061700 chr2D 76.802 444 63 26 2552 2972 331601770 331602196 5.050000e-51 213.0
105 TraesCS1A01G061700 chr2D 95.000 80 3 1 611 690 638336409 638336331 2.440000e-24 124.0
106 TraesCS1A01G061700 chr2D 90.476 84 6 2 613 696 407215670 407215751 6.820000e-20 110.0
107 TraesCS1A01G061700 chr2D 94.203 69 3 1 5 73 638336473 638336406 3.170000e-18 104.0
108 TraesCS1A01G061700 chr2D 88.889 72 7 1 2 73 582023779 582023849 3.200000e-13 87.9
109 TraesCS1A01G061700 chr2D 85.294 68 9 1 5671 5738 16986804 16986738 1.160000e-07 69.4
110 TraesCS1A01G061700 chr2D 85.075 67 10 0 5671 5737 357894928 357894862 1.160000e-07 69.4
111 TraesCS1A01G061700 chr2D 87.097 62 6 2 6144 6203 460320987 460320926 1.160000e-07 69.4
112 TraesCS1A01G061700 chr2B 93.750 80 4 1 611 690 5788509 5788431 1.130000e-22 119.0
113 TraesCS1A01G061700 chr2B 92.754 69 4 1 5 73 5788573 5788506 1.480000e-16 99.0
114 TraesCS1A01G061700 chr2B 85.294 68 9 1 5671 5738 28878591 28878525 1.160000e-07 69.4
115 TraesCS1A01G061700 chr6D 92.500 80 4 2 611 690 162273620 162273697 5.270000e-21 113.0
116 TraesCS1A01G061700 chr6D 90.278 72 6 1 2 73 162273553 162273623 6.870000e-15 93.5
117 TraesCS1A01G061700 chr6D 86.667 60 7 1 5679 5737 50954159 50954100 1.500000e-06 65.8
118 TraesCS1A01G061700 chrUn 91.667 72 5 1 622 693 412440092 412440162 1.480000e-16 99.0
119 TraesCS1A01G061700 chrUn 88.525 61 5 2 5671 5731 61011368 61011310 8.950000e-09 73.1
120 TraesCS1A01G061700 chrUn 88.525 61 5 2 5671 5731 61012573 61012515 8.950000e-09 73.1
121 TraesCS1A01G061700 chrUn 95.349 43 2 0 5692 5734 57949474 57949516 1.160000e-07 69.4
122 TraesCS1A01G061700 chrUn 87.719 57 4 2 5690 5743 32269520 32269576 5.380000e-06 63.9
123 TraesCS1A01G061700 chrUn 91.111 45 4 0 5690 5734 230312447 230312491 1.940000e-05 62.1
124 TraesCS1A01G061700 chrUn 89.583 48 5 0 5690 5737 452039171 452039124 1.940000e-05 62.1
125 TraesCS1A01G061700 chrUn 85.965 57 7 1 5679 5734 294213807 294213863 6.970000e-05 60.2
126 TraesCS1A01G061700 chrUn 85.965 57 7 1 5679 5734 294240296 294240352 6.970000e-05 60.2
127 TraesCS1A01G061700 chrUn 85.000 60 8 1 5679 5737 320029910 320029851 6.970000e-05 60.2
128 TraesCS1A01G061700 chr5D 89.189 74 5 3 2259 2331 163362941 163362870 8.880000e-14 89.8
129 TraesCS1A01G061700 chr5D 86.301 73 9 1 2259 2331 282442048 282441977 1.920000e-10 78.7
130 TraesCS1A01G061700 chr5D 85.075 67 9 1 5671 5737 42063457 42063392 4.160000e-07 67.6
131 TraesCS1A01G061700 chr5D 97.436 39 1 0 2063 2101 454097124 454097162 4.160000e-07 67.6


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 TraesCS1A01G061700 chr1A 42250783 42257215 6432 False 11880.000000 11880 100.000000 1 6433 1 chr1A.!!$F1 6432
1 TraesCS1A01G061700 chr1A 459051774 459052309 535 False 863.000000 863 95.756000 70 606 1 chr1A.!!$F3 536
2 TraesCS1A01G061700 chr1A 424590067 424590608 541 False 852.000000 852 95.064000 65 606 1 chr1A.!!$F2 541
3 TraesCS1A01G061700 chr1A 42216899 42222899 6000 True 702.833333 1711 90.489667 1631 5996 6 chr1A.!!$R2 4365
4 TraesCS1A01G061700 chr1A 42251815 42255114 3299 False 409.000000 409 81.764000 1033 4332 2 chr1A.!!$F5 3299
5 TraesCS1A01G061700 chr1B 62719832 62726708 6876 False 1048.800000 2545 86.785200 790 6433 5 chr1B.!!$F2 5643
6 TraesCS1A01G061700 chr1D 42711003 42712721 1718 True 1975.000000 1975 87.331000 3291 5059 1 chr1D.!!$R4 1768
7 TraesCS1A01G061700 chr1D 42756469 42766031 9562 False 683.888889 2492 85.336222 746 6195 9 chr1D.!!$F5 5449
8 TraesCS1A01G061700 chr1D 42700383 42700884 501 True 643.000000 643 89.881000 5055 5554 1 chr1D.!!$R3 499
9 TraesCS1A01G061700 chr1D 42624715 42625781 1066 True 568.000000 961 85.385667 1018 4419 3 chr1D.!!$R10 3401
10 TraesCS1A01G061700 chr1D 42671133 42673784 2651 True 552.000000 649 91.193500 5055 6433 2 chr1D.!!$R11 1378
11 TraesCS1A01G061700 chr1D 42611625 42614193 2568 True 418.666667 638 87.481667 5055 6353 3 chr1D.!!$R9 1298
12 TraesCS1A01G061700 chr7B 572958024 572959678 1654 True 1026.500000 1260 89.745500 3743 5482 2 chr7B.!!$R3 1739
13 TraesCS1A01G061700 chr7D 532611405 532613022 1617 True 1035.500000 1256 90.520000 3743 5453 2 chr7D.!!$R4 1710
14 TraesCS1A01G061700 chr7D 5351107 5352551 1444 True 748.000000 952 85.818000 1018 5425 2 chr7D.!!$R3 4407
15 TraesCS1A01G061700 chr7A 612756005 612757587 1582 True 982.000000 1238 90.365500 3790 5462 2 chr7A.!!$R5 1672
16 TraesCS1A01G061700 chr7A 426837854 426838391 537 True 876.000000 876 96.133000 70 606 1 chr7A.!!$R1 536
17 TraesCS1A01G061700 chr7A 6802555 6803066 511 False 527.000000 527 85.938000 1037 1527 1 chr7A.!!$F1 490
18 TraesCS1A01G061700 chr4A 562502485 562503024 539 True 850.000000 850 95.064000 70 611 1 chr4A.!!$R2 541
19 TraesCS1A01G061700 chr4A 737139374 737140825 1451 False 759.500000 968 86.084500 1017 5425 2 chr4A.!!$F4 4408
20 TraesCS1A01G061700 chr5A 121566272 121566808 536 False 876.000000 876 96.125000 69 606 1 chr5A.!!$F1 537
21 TraesCS1A01G061700 chr5A 367836859 367837395 536 False 859.000000 859 95.580000 70 607 1 chr5A.!!$F2 537
22 TraesCS1A01G061700 chr5A 683796376 683796913 537 True 856.000000 856 95.396000 72 610 1 chr5A.!!$R2 538
23 TraesCS1A01G061700 chr3A 730262930 730263465 535 True 859.000000 859 95.564000 69 606 1 chr3A.!!$R3 537
24 TraesCS1A01G061700 chr3A 730246543 730247081 538 True 854.000000 854 95.221000 71 611 1 chr3A.!!$R2 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
784 796 0.034896 CCCGCCACTTTGTACACTCT 59.965 55.000 0.00 0.0 0.00 3.24 F
950 3960 0.820482 TACGTCTATAGCCCAGCGCA 60.820 55.000 11.47 0.0 41.38 6.09 F
953 3963 0.876342 GTCTATAGCCCAGCGCACAC 60.876 60.000 11.47 0.0 41.38 3.82 F
954 3964 1.951130 CTATAGCCCAGCGCACACG 60.951 63.158 11.47 0.0 41.38 4.49 F
990 4000 2.887568 CTGAAGCAGCCGTAGCCG 60.888 66.667 0.00 0.0 41.25 5.52 F
4419 9290 4.096382 AGAGTGCCACTAATATTTTTGCCG 59.904 41.667 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4391 9262 5.567138 AAATATTAGTGGCACTCTGTTGC 57.433 39.130 25.80 0.00 42.18 4.17 R
4666 11053 0.179134 GCAGAGAATGTAGTCGGCGT 60.179 55.000 6.85 0.00 0.00 5.68 R
4677 11064 0.396435 TCCACGGTGTTGCAGAGAAT 59.604 50.000 7.45 0.00 0.00 2.40 R
4732 11119 0.529378 GGCGTAGAAGGGTTTCTCGA 59.471 55.000 10.85 0.00 42.60 4.04 R
4788 11178 4.082523 CATGGAGGTGGCGACGGT 62.083 66.667 0.00 0.00 0.00 4.83 R
5838 13037 0.615850 AGAAGCCTTAAGGAAGCGCT 59.384 50.000 26.21 2.64 39.46 5.92 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
17 18 4.293610 TCAGTGTGGAGGCTCACA 57.706 55.556 17.69 15.16 44.36 3.58
24 25 2.436417 TGTGGAGGCTCACAATTTAGC 58.564 47.619 17.69 0.00 43.70 3.09
25 26 2.224744 TGTGGAGGCTCACAATTTAGCA 60.225 45.455 17.69 0.00 43.70 3.49
26 27 2.819608 GTGGAGGCTCACAATTTAGCAA 59.180 45.455 17.69 0.00 40.61 3.91
27 28 3.255642 GTGGAGGCTCACAATTTAGCAAA 59.744 43.478 17.69 0.00 40.61 3.68
28 29 3.507233 TGGAGGCTCACAATTTAGCAAAG 59.493 43.478 17.69 0.00 40.61 2.77
29 30 3.505836 GAGGCTCACAATTTAGCAAAGC 58.494 45.455 10.25 0.00 40.61 3.51
30 31 2.892852 AGGCTCACAATTTAGCAAAGCA 59.107 40.909 6.55 0.00 40.61 3.91
31 32 3.512724 AGGCTCACAATTTAGCAAAGCAT 59.487 39.130 6.55 0.00 40.61 3.79
32 33 3.615496 GGCTCACAATTTAGCAAAGCATG 59.385 43.478 6.55 0.00 40.61 4.06
45 46 4.398549 CAAAGCATGCATTGAAACTTGG 57.601 40.909 27.17 0.97 0.00 3.61
46 47 2.754946 AGCATGCATTGAAACTTGGG 57.245 45.000 21.98 0.00 0.00 4.12
47 48 1.276989 AGCATGCATTGAAACTTGGGG 59.723 47.619 21.98 0.00 0.00 4.96
48 49 1.002315 GCATGCATTGAAACTTGGGGT 59.998 47.619 14.21 0.00 0.00 4.95
49 50 2.932187 GCATGCATTGAAACTTGGGGTC 60.932 50.000 14.21 0.00 0.00 4.46
50 51 0.958091 TGCATTGAAACTTGGGGTCG 59.042 50.000 0.00 0.00 0.00 4.79
51 52 1.243902 GCATTGAAACTTGGGGTCGA 58.756 50.000 0.00 0.00 0.00 4.20
52 53 1.068541 GCATTGAAACTTGGGGTCGAC 60.069 52.381 7.13 7.13 0.00 4.20
53 54 1.539827 CATTGAAACTTGGGGTCGACC 59.460 52.381 27.04 27.04 39.11 4.79
54 55 0.533308 TTGAAACTTGGGGTCGACCG 60.533 55.000 27.68 16.42 41.60 4.79
176 177 1.219393 CGAGTTCAGGCCCTTCTCC 59.781 63.158 0.00 0.00 0.00 3.71
295 305 3.116317 AGGGGGTGGCTTATATAGAGTGT 60.116 47.826 0.00 0.00 0.00 3.55
324 334 1.265454 CCAGCTCCCCTCCGTTACTT 61.265 60.000 0.00 0.00 0.00 2.24
387 398 9.431887 ACGTCTACAGTAAAATGTCATAAATGT 57.568 29.630 0.00 0.00 34.56 2.71
464 475 1.202486 TGGTGGTCGAGTGTCTTCAAC 60.202 52.381 0.00 0.00 0.00 3.18
529 540 4.527509 TCTCTTCGACTGCTTCTGATTT 57.472 40.909 0.00 0.00 0.00 2.17
607 619 4.835615 CCCTAGGTACATAGCTTCATCAGT 59.164 45.833 9.07 0.00 35.39 3.41
611 623 2.898729 ACATAGCTTCATCAGTCGGG 57.101 50.000 0.00 0.00 0.00 5.14
612 624 2.111384 ACATAGCTTCATCAGTCGGGT 58.889 47.619 0.00 0.00 0.00 5.28
613 625 2.101582 ACATAGCTTCATCAGTCGGGTC 59.898 50.000 0.00 0.00 0.00 4.46
614 626 1.847328 TAGCTTCATCAGTCGGGTCA 58.153 50.000 0.00 0.00 0.00 4.02
615 627 0.247736 AGCTTCATCAGTCGGGTCAC 59.752 55.000 0.00 0.00 0.00 3.67
616 628 0.741221 GCTTCATCAGTCGGGTCACC 60.741 60.000 0.00 0.00 0.00 4.02
617 629 0.108138 CTTCATCAGTCGGGTCACCC 60.108 60.000 1.06 1.06 41.09 4.61
626 638 2.841317 GGGTCACCCCGAAAACCT 59.159 61.111 0.00 0.00 42.41 3.50
627 639 1.303074 GGGTCACCCCGAAAACCTC 60.303 63.158 0.00 0.00 42.41 3.85
628 640 1.759236 GGTCACCCCGAAAACCTCT 59.241 57.895 0.00 0.00 0.00 3.69
629 641 0.321387 GGTCACCCCGAAAACCTCTC 60.321 60.000 0.00 0.00 0.00 3.20
630 642 0.685660 GTCACCCCGAAAACCTCTCT 59.314 55.000 0.00 0.00 0.00 3.10
631 643 1.071857 GTCACCCCGAAAACCTCTCTT 59.928 52.381 0.00 0.00 0.00 2.85
632 644 1.772453 TCACCCCGAAAACCTCTCTTT 59.228 47.619 0.00 0.00 0.00 2.52
633 645 2.152016 CACCCCGAAAACCTCTCTTTC 58.848 52.381 0.00 0.00 0.00 2.62
638 650 2.067013 CGAAAACCTCTCTTTCGTCCC 58.933 52.381 9.02 0.00 46.28 4.46
639 651 2.067013 GAAAACCTCTCTTTCGTCCCG 58.933 52.381 0.00 0.00 0.00 5.14
640 652 0.320697 AAACCTCTCTTTCGTCCCGG 59.679 55.000 0.00 0.00 0.00 5.73
641 653 0.830866 AACCTCTCTTTCGTCCCGGT 60.831 55.000 0.00 0.00 0.00 5.28
642 654 1.249469 ACCTCTCTTTCGTCCCGGTC 61.249 60.000 0.00 0.00 0.00 4.79
643 655 1.511768 CTCTCTTTCGTCCCGGTCC 59.488 63.158 0.00 0.00 0.00 4.46
644 656 1.228644 TCTCTTTCGTCCCGGTCCA 60.229 57.895 0.00 0.00 0.00 4.02
645 657 0.828762 TCTCTTTCGTCCCGGTCCAA 60.829 55.000 0.00 0.00 0.00 3.53
646 658 0.249398 CTCTTTCGTCCCGGTCCAAT 59.751 55.000 0.00 0.00 0.00 3.16
647 659 0.688487 TCTTTCGTCCCGGTCCAATT 59.312 50.000 0.00 0.00 0.00 2.32
648 660 0.802494 CTTTCGTCCCGGTCCAATTG 59.198 55.000 0.00 0.00 0.00 2.32
649 661 0.606944 TTTCGTCCCGGTCCAATTGG 60.607 55.000 19.08 19.08 0.00 3.16
650 662 1.770749 TTCGTCCCGGTCCAATTGGT 61.771 55.000 23.76 0.00 36.34 3.67
651 663 2.038269 CGTCCCGGTCCAATTGGTG 61.038 63.158 23.76 14.39 36.34 4.17
652 664 1.377229 GTCCCGGTCCAATTGGTGA 59.623 57.895 23.76 10.95 36.34 4.02
653 665 0.958876 GTCCCGGTCCAATTGGTGAC 60.959 60.000 23.76 15.28 36.34 3.67
654 666 2.038269 CCCGGTCCAATTGGTGACG 61.038 63.158 23.76 22.85 36.34 4.35
655 667 1.004320 CCGGTCCAATTGGTGACGA 60.004 57.895 27.25 8.80 36.34 4.20
656 668 1.296056 CCGGTCCAATTGGTGACGAC 61.296 60.000 27.25 17.92 36.34 4.34
657 669 1.623081 CGGTCCAATTGGTGACGACG 61.623 60.000 23.76 15.23 36.34 5.12
658 670 0.601841 GGTCCAATTGGTGACGACGT 60.602 55.000 23.76 0.00 36.34 4.34
659 671 1.337074 GGTCCAATTGGTGACGACGTA 60.337 52.381 23.76 0.00 36.34 3.57
660 672 2.406130 GTCCAATTGGTGACGACGTAA 58.594 47.619 23.76 0.00 36.34 3.18
661 673 2.997986 GTCCAATTGGTGACGACGTAAT 59.002 45.455 23.76 0.00 36.34 1.89
662 674 4.175516 GTCCAATTGGTGACGACGTAATA 58.824 43.478 23.76 0.00 36.34 0.98
663 675 4.626604 GTCCAATTGGTGACGACGTAATAA 59.373 41.667 23.76 0.00 36.34 1.40
664 676 5.120519 GTCCAATTGGTGACGACGTAATAAA 59.879 40.000 23.76 0.00 36.34 1.40
665 677 5.349270 TCCAATTGGTGACGACGTAATAAAG 59.651 40.000 23.76 0.00 36.34 1.85
666 678 4.852609 ATTGGTGACGACGTAATAAAGC 57.147 40.909 0.00 0.00 0.00 3.51
667 679 3.581024 TGGTGACGACGTAATAAAGCT 57.419 42.857 0.00 0.00 0.00 3.74
668 680 3.916761 TGGTGACGACGTAATAAAGCTT 58.083 40.909 0.00 0.00 0.00 3.74
669 681 4.309099 TGGTGACGACGTAATAAAGCTTT 58.691 39.130 17.30 17.30 0.00 3.51
670 682 4.150980 TGGTGACGACGTAATAAAGCTTTG 59.849 41.667 22.02 6.93 0.00 2.77
671 683 4.079710 GTGACGACGTAATAAAGCTTTGC 58.920 43.478 22.02 8.14 0.00 3.68
672 684 3.181538 TGACGACGTAATAAAGCTTTGCG 60.182 43.478 22.02 19.89 38.03 4.85
673 685 2.988493 ACGACGTAATAAAGCTTTGCGA 59.012 40.909 22.02 1.88 36.01 5.10
674 686 3.429543 ACGACGTAATAAAGCTTTGCGAA 59.570 39.130 22.02 1.47 36.01 4.70
675 687 4.092383 ACGACGTAATAAAGCTTTGCGAAT 59.908 37.500 22.02 4.09 36.01 3.34
676 688 5.019498 CGACGTAATAAAGCTTTGCGAATT 58.981 37.500 22.02 14.79 36.01 2.17
677 689 5.053932 CGACGTAATAAAGCTTTGCGAATTG 60.054 40.000 22.02 7.85 36.01 2.32
678 690 5.695818 ACGTAATAAAGCTTTGCGAATTGT 58.304 33.333 22.02 8.44 36.01 2.71
679 691 5.793457 ACGTAATAAAGCTTTGCGAATTGTC 59.207 36.000 22.02 9.64 36.01 3.18
680 692 6.021596 CGTAATAAAGCTTTGCGAATTGTCT 58.978 36.000 22.02 0.00 34.67 3.41
681 693 6.192863 CGTAATAAAGCTTTGCGAATTGTCTC 59.807 38.462 22.02 5.65 34.67 3.36
682 694 3.988379 AAAGCTTTGCGAATTGTCTCA 57.012 38.095 11.80 0.00 0.00 3.27
683 695 3.549299 AAGCTTTGCGAATTGTCTCAG 57.451 42.857 0.00 0.00 0.00 3.35
684 696 2.771089 AGCTTTGCGAATTGTCTCAGA 58.229 42.857 0.00 0.00 0.00 3.27
685 697 3.141398 AGCTTTGCGAATTGTCTCAGAA 58.859 40.909 0.00 0.00 0.00 3.02
686 698 3.565482 AGCTTTGCGAATTGTCTCAGAAA 59.435 39.130 0.00 0.00 0.00 2.52
687 699 4.036734 AGCTTTGCGAATTGTCTCAGAAAA 59.963 37.500 0.00 0.00 0.00 2.29
688 700 4.739716 GCTTTGCGAATTGTCTCAGAAAAA 59.260 37.500 0.00 0.00 0.00 1.94
709 721 5.358298 AAAAAGCAACGTCTACTTCATCC 57.642 39.130 0.00 0.00 0.00 3.51
710 722 2.674796 AGCAACGTCTACTTCATCCC 57.325 50.000 0.00 0.00 0.00 3.85
711 723 1.207329 AGCAACGTCTACTTCATCCCC 59.793 52.381 0.00 0.00 0.00 4.81
712 724 1.207329 GCAACGTCTACTTCATCCCCT 59.793 52.381 0.00 0.00 0.00 4.79
713 725 2.738964 GCAACGTCTACTTCATCCCCTC 60.739 54.545 0.00 0.00 0.00 4.30
714 726 2.496070 CAACGTCTACTTCATCCCCTCA 59.504 50.000 0.00 0.00 0.00 3.86
715 727 2.816411 ACGTCTACTTCATCCCCTCAA 58.184 47.619 0.00 0.00 0.00 3.02
716 728 3.170717 ACGTCTACTTCATCCCCTCAAA 58.829 45.455 0.00 0.00 0.00 2.69
717 729 3.581332 ACGTCTACTTCATCCCCTCAAAA 59.419 43.478 0.00 0.00 0.00 2.44
718 730 4.041198 ACGTCTACTTCATCCCCTCAAAAA 59.959 41.667 0.00 0.00 0.00 1.94
719 731 4.631813 CGTCTACTTCATCCCCTCAAAAAG 59.368 45.833 0.00 0.00 0.00 2.27
720 732 5.568825 CGTCTACTTCATCCCCTCAAAAAGA 60.569 44.000 0.00 0.00 0.00 2.52
721 733 6.238648 GTCTACTTCATCCCCTCAAAAAGAA 58.761 40.000 0.00 0.00 0.00 2.52
722 734 6.715264 GTCTACTTCATCCCCTCAAAAAGAAA 59.285 38.462 0.00 0.00 0.00 2.52
723 735 7.230712 GTCTACTTCATCCCCTCAAAAAGAAAA 59.769 37.037 0.00 0.00 0.00 2.29
724 736 6.806668 ACTTCATCCCCTCAAAAAGAAAAA 57.193 33.333 0.00 0.00 0.00 1.94
725 737 6.820335 ACTTCATCCCCTCAAAAAGAAAAAG 58.180 36.000 0.00 0.00 0.00 2.27
726 738 6.611236 ACTTCATCCCCTCAAAAAGAAAAAGA 59.389 34.615 0.00 0.00 0.00 2.52
727 739 7.125659 ACTTCATCCCCTCAAAAAGAAAAAGAA 59.874 33.333 0.00 0.00 0.00 2.52
728 740 7.054491 TCATCCCCTCAAAAAGAAAAAGAAG 57.946 36.000 0.00 0.00 0.00 2.85
729 741 6.838612 TCATCCCCTCAAAAAGAAAAAGAAGA 59.161 34.615 0.00 0.00 0.00 2.87
730 742 7.344352 TCATCCCCTCAAAAAGAAAAAGAAGAA 59.656 33.333 0.00 0.00 0.00 2.52
731 743 7.112452 TCCCCTCAAAAAGAAAAAGAAGAAG 57.888 36.000 0.00 0.00 0.00 2.85
732 744 6.895204 TCCCCTCAAAAAGAAAAAGAAGAAGA 59.105 34.615 0.00 0.00 0.00 2.87
733 745 7.068716 TCCCCTCAAAAAGAAAAAGAAGAAGAG 59.931 37.037 0.00 0.00 0.00 2.85
734 746 7.068716 CCCCTCAAAAAGAAAAAGAAGAAGAGA 59.931 37.037 0.00 0.00 0.00 3.10
735 747 8.470002 CCCTCAAAAAGAAAAAGAAGAAGAGAA 58.530 33.333 0.00 0.00 0.00 2.87
736 748 9.860898 CCTCAAAAAGAAAAAGAAGAAGAGAAA 57.139 29.630 0.00 0.00 0.00 2.52
758 770 3.648179 AAGCTACGTACGTCTACTTCG 57.352 47.619 26.53 6.85 0.00 3.79
759 771 2.611518 AGCTACGTACGTCTACTTCGT 58.388 47.619 26.53 0.00 43.86 3.85
760 772 2.346847 AGCTACGTACGTCTACTTCGTG 59.653 50.000 26.53 6.13 41.62 4.35
761 773 2.535732 GCTACGTACGTCTACTTCGTGG 60.536 54.545 26.53 0.00 41.62 4.94
762 774 1.795768 ACGTACGTCTACTTCGTGGA 58.204 50.000 16.72 0.00 41.62 4.02
763 775 1.728971 ACGTACGTCTACTTCGTGGAG 59.271 52.381 16.72 0.00 41.62 3.86
764 776 1.528603 CGTACGTCTACTTCGTGGAGC 60.529 57.143 7.22 0.00 41.62 4.70
765 777 1.089920 TACGTCTACTTCGTGGAGCC 58.910 55.000 0.00 0.00 41.62 4.70
766 778 1.139095 CGTCTACTTCGTGGAGCCC 59.861 63.158 0.00 0.00 0.00 5.19
767 779 1.516423 GTCTACTTCGTGGAGCCCC 59.484 63.158 0.00 0.00 0.00 5.80
768 780 2.050350 TCTACTTCGTGGAGCCCCG 61.050 63.158 0.00 0.00 34.29 5.73
769 781 3.718210 CTACTTCGTGGAGCCCCGC 62.718 68.421 0.00 0.00 39.56 6.13
776 788 4.659172 TGGAGCCCCGCCACTTTG 62.659 66.667 0.00 0.00 34.29 2.77
777 789 4.660938 GGAGCCCCGCCACTTTGT 62.661 66.667 0.00 0.00 0.00 2.83
778 790 2.349755 GAGCCCCGCCACTTTGTA 59.650 61.111 0.00 0.00 0.00 2.41
779 791 2.033602 AGCCCCGCCACTTTGTAC 59.966 61.111 0.00 0.00 0.00 2.90
780 792 2.281900 GCCCCGCCACTTTGTACA 60.282 61.111 0.00 0.00 0.00 2.90
781 793 2.622962 GCCCCGCCACTTTGTACAC 61.623 63.158 0.00 0.00 0.00 2.90
782 794 1.072505 CCCCGCCACTTTGTACACT 59.927 57.895 0.00 0.00 0.00 3.55
783 795 0.953960 CCCCGCCACTTTGTACACTC 60.954 60.000 0.00 0.00 0.00 3.51
784 796 0.034896 CCCGCCACTTTGTACACTCT 59.965 55.000 0.00 0.00 0.00 3.24
785 797 1.542547 CCCGCCACTTTGTACACTCTT 60.543 52.381 0.00 0.00 0.00 2.85
786 798 1.798813 CCGCCACTTTGTACACTCTTC 59.201 52.381 0.00 0.00 0.00 2.87
787 799 1.798813 CGCCACTTTGTACACTCTTCC 59.201 52.381 0.00 0.00 0.00 3.46
788 800 2.152016 GCCACTTTGTACACTCTTCCC 58.848 52.381 0.00 0.00 0.00 3.97
812 824 1.064134 GGCCAAATGAATCGACCGC 59.936 57.895 0.00 0.00 0.00 5.68
814 826 1.351707 CCAAATGAATCGACCGCGG 59.648 57.895 26.86 26.86 38.28 6.46
841 3835 2.651232 CCTGCGTAGTACGAGCGC 60.651 66.667 26.29 19.40 46.05 5.92
906 3905 2.829023 ACCATTCGTTCTTCCTCCCTA 58.171 47.619 0.00 0.00 0.00 3.53
923 3927 3.117851 TCCCTATCGATCTCACTCACAGT 60.118 47.826 0.00 0.00 0.00 3.55
931 3935 2.379005 TCTCACTCACAGTGTGACACT 58.621 47.619 22.06 13.33 46.03 3.55
939 3949 4.070009 TCACAGTGTGACACTACGTCTAT 58.930 43.478 22.06 0.00 43.43 1.98
940 3950 5.240121 TCACAGTGTGACACTACGTCTATA 58.760 41.667 22.06 0.00 43.43 1.31
950 3960 0.820482 TACGTCTATAGCCCAGCGCA 60.820 55.000 11.47 0.00 41.38 6.09
951 3961 1.661821 CGTCTATAGCCCAGCGCAC 60.662 63.158 11.47 0.00 41.38 5.34
952 3962 1.441729 GTCTATAGCCCAGCGCACA 59.558 57.895 11.47 0.00 41.38 4.57
953 3963 0.876342 GTCTATAGCCCAGCGCACAC 60.876 60.000 11.47 0.00 41.38 3.82
954 3964 1.951130 CTATAGCCCAGCGCACACG 60.951 63.158 11.47 0.00 41.38 4.49
980 3990 4.441695 CTCGCCCTCGCTGAAGCA 62.442 66.667 2.79 0.00 42.21 3.91
990 4000 2.887568 CTGAAGCAGCCGTAGCCG 60.888 66.667 0.00 0.00 41.25 5.52
4391 9262 7.650504 CCACTCCAATATGCTTATGTTTCAATG 59.349 37.037 0.00 0.00 0.00 2.82
4419 9290 4.096382 AGAGTGCCACTAATATTTTTGCCG 59.904 41.667 0.00 0.00 0.00 5.69
4474 9359 7.793948 AGTGAGGGAGTAGTAGTAAATTTGT 57.206 36.000 0.00 0.00 0.00 2.83
4844 11237 1.227823 CCACTGGCTGGACGAACAA 60.228 57.895 0.00 0.00 43.95 2.83
4874 11462 2.166664 GTCCGTGCTCTACATCTCCTTT 59.833 50.000 0.00 0.00 0.00 3.11
5307 11907 1.132849 TGTCTGGGAAAGAGGGTGAGA 60.133 52.381 0.00 0.00 34.84 3.27
5342 11942 0.684535 TGAAGAATGTGAGGGCGACA 59.315 50.000 0.00 0.00 0.00 4.35
5458 12058 2.669133 CGACCAATGGGCCAGGAGA 61.669 63.158 18.07 0.00 37.90 3.71
5554 12630 1.069906 GTCATTGACTCGGTGTTGTGC 60.070 52.381 9.59 0.00 0.00 4.57
5566 12642 3.138304 GGTGTTGTGCAGTGTGATCTTA 58.862 45.455 0.00 0.00 0.00 2.10
5580 12656 8.333908 CAGTGTGATCTTATTTTCTCTGCATAC 58.666 37.037 0.00 0.00 0.00 2.39
5668 12867 3.641437 TGCCTACTGATTTTGTGTTGC 57.359 42.857 0.00 0.00 0.00 4.17
5783 12982 8.394971 AGATGAGATTTGACAATGTTTACACA 57.605 30.769 0.00 0.00 37.31 3.72
5805 13004 2.421388 CCAGTAGATTCGATTTGGGGCA 60.421 50.000 0.00 0.00 0.00 5.36
5808 13007 1.597742 AGATTCGATTTGGGGCATCG 58.402 50.000 0.00 0.00 44.09 3.84
5838 13037 2.111999 CTTGGGCACGAAGGTCTCCA 62.112 60.000 0.00 0.00 40.54 3.86
5903 13102 2.578786 CCCCGGTAGACACAACTTTTT 58.421 47.619 0.00 0.00 0.00 1.94
5908 13948 5.350640 CCCGGTAGACACAACTTTTTCTATC 59.649 44.000 0.00 0.00 0.00 2.08
6067 14261 7.493743 TTTTTGCATACATCAAGTGCATTTT 57.506 28.000 0.00 0.00 46.90 1.82
6275 14511 0.321653 GGGCGCCGAATAGGATTCAT 60.322 55.000 22.54 0.00 45.00 2.57
6322 14558 3.973135 CGTCACGAGCGCTAAATATAACT 59.027 43.478 11.50 0.00 0.00 2.24
6324 14560 3.734231 TCACGAGCGCTAAATATAACTGC 59.266 43.478 11.50 0.00 0.00 4.40
6347 14583 6.052360 GCCCAAACAAACAAATAGAAGGAAA 58.948 36.000 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.162408 GCTAAATTGTGAGCCTCCACAC 59.838 50.000 3.99 0.00 45.62 3.82
6 7 2.877097 TGCTAAATTGTGAGCCTCCA 57.123 45.000 5.15 0.00 37.94 3.86
7 8 3.674410 GCTTTGCTAAATTGTGAGCCTCC 60.674 47.826 5.15 0.00 37.94 4.30
8 9 3.057315 TGCTTTGCTAAATTGTGAGCCTC 60.057 43.478 5.15 0.00 37.94 4.70
9 10 2.892852 TGCTTTGCTAAATTGTGAGCCT 59.107 40.909 5.15 0.00 37.94 4.58
10 11 3.302365 TGCTTTGCTAAATTGTGAGCC 57.698 42.857 5.15 0.00 37.94 4.70
11 12 4.835199 CATGCTTTGCTAAATTGTGAGC 57.165 40.909 1.28 1.28 39.25 4.26
24 25 3.187637 CCCAAGTTTCAATGCATGCTTTG 59.812 43.478 30.58 30.58 33.91 2.77
25 26 3.404899 CCCAAGTTTCAATGCATGCTTT 58.595 40.909 20.33 16.30 0.00 3.51
26 27 2.289819 CCCCAAGTTTCAATGCATGCTT 60.290 45.455 20.33 10.16 0.00 3.91
27 28 1.276989 CCCCAAGTTTCAATGCATGCT 59.723 47.619 20.33 1.07 0.00 3.79
28 29 1.002315 ACCCCAAGTTTCAATGCATGC 59.998 47.619 11.82 11.82 0.00 4.06
29 30 2.671914 CGACCCCAAGTTTCAATGCATG 60.672 50.000 0.00 0.00 0.00 4.06
30 31 1.545582 CGACCCCAAGTTTCAATGCAT 59.454 47.619 0.00 0.00 0.00 3.96
31 32 0.958091 CGACCCCAAGTTTCAATGCA 59.042 50.000 0.00 0.00 0.00 3.96
32 33 1.068541 GTCGACCCCAAGTTTCAATGC 60.069 52.381 3.51 0.00 0.00 3.56
33 34 1.539827 GGTCGACCCCAAGTTTCAATG 59.460 52.381 24.75 0.00 0.00 2.82
34 35 1.880646 CGGTCGACCCCAAGTTTCAAT 60.881 52.381 28.52 0.00 0.00 2.57
35 36 0.533308 CGGTCGACCCCAAGTTTCAA 60.533 55.000 28.52 0.00 0.00 2.69
36 37 1.070105 CGGTCGACCCCAAGTTTCA 59.930 57.895 28.52 0.00 0.00 2.69
37 38 2.322830 GCGGTCGACCCCAAGTTTC 61.323 63.158 28.52 0.58 0.00 2.78
38 39 2.281276 GCGGTCGACCCCAAGTTT 60.281 61.111 28.52 0.00 0.00 2.66
39 40 4.324991 GGCGGTCGACCCCAAGTT 62.325 66.667 28.52 0.00 0.00 2.66
51 52 3.991051 CTGACCAGACACGGCGGT 61.991 66.667 13.24 6.25 35.12 5.68
52 53 3.991051 ACTGACCAGACACGGCGG 61.991 66.667 13.24 2.35 0.00 6.13
53 54 2.734723 CACTGACCAGACACGGCG 60.735 66.667 4.80 4.80 0.00 6.46
54 55 1.664965 GACACTGACCAGACACGGC 60.665 63.158 3.76 0.00 0.00 5.68
55 56 1.371758 CGACACTGACCAGACACGG 60.372 63.158 3.76 0.00 0.00 4.94
56 57 0.934901 CACGACACTGACCAGACACG 60.935 60.000 3.76 8.10 0.00 4.49
57 58 0.597637 CCACGACACTGACCAGACAC 60.598 60.000 3.76 0.00 0.00 3.67
58 59 0.753848 TCCACGACACTGACCAGACA 60.754 55.000 3.76 0.00 0.00 3.41
59 60 0.603569 ATCCACGACACTGACCAGAC 59.396 55.000 3.76 0.00 0.00 3.51
60 61 0.888619 GATCCACGACACTGACCAGA 59.111 55.000 3.76 0.00 0.00 3.86
61 62 0.891373 AGATCCACGACACTGACCAG 59.109 55.000 0.00 0.00 0.00 4.00
62 63 2.209690 TAGATCCACGACACTGACCA 57.790 50.000 0.00 0.00 0.00 4.02
63 64 2.753452 TCTTAGATCCACGACACTGACC 59.247 50.000 0.00 0.00 0.00 4.02
64 65 3.440872 AGTCTTAGATCCACGACACTGAC 59.559 47.826 0.96 0.00 0.00 3.51
65 66 3.440522 CAGTCTTAGATCCACGACACTGA 59.559 47.826 0.96 0.00 33.30 3.41
66 67 3.440522 TCAGTCTTAGATCCACGACACTG 59.559 47.826 0.96 1.70 32.87 3.66
67 68 3.440872 GTCAGTCTTAGATCCACGACACT 59.559 47.826 0.96 0.00 0.00 3.55
176 177 1.202268 CGTAGGGCTGTTACTTCCTCG 60.202 57.143 0.00 0.00 0.00 4.63
324 334 5.708736 TCCTTTATGAGCATTGAACCCTA 57.291 39.130 0.00 0.00 0.00 3.53
464 475 3.971453 ATGCGCTCACTCGACCACG 62.971 63.158 9.73 0.00 41.26 4.94
529 540 3.773560 CCCCCAGGACATCTTTACAAAA 58.226 45.455 0.00 0.00 33.47 2.44
551 562 1.622811 CTGTCCAGCATATCCTCTCCC 59.377 57.143 0.00 0.00 0.00 4.30
552 563 1.622811 CCTGTCCAGCATATCCTCTCC 59.377 57.143 0.00 0.00 0.00 3.71
553 564 1.001860 GCCTGTCCAGCATATCCTCTC 59.998 57.143 0.00 0.00 0.00 3.20
554 565 1.055040 GCCTGTCCAGCATATCCTCT 58.945 55.000 0.00 0.00 0.00 3.69
555 566 0.036022 GGCCTGTCCAGCATATCCTC 59.964 60.000 0.00 0.00 34.01 3.71
611 623 0.685660 AGAGAGGTTTTCGGGGTGAC 59.314 55.000 0.00 0.00 0.00 3.67
612 624 1.430992 AAGAGAGGTTTTCGGGGTGA 58.569 50.000 0.00 0.00 0.00 4.02
613 625 2.152016 GAAAGAGAGGTTTTCGGGGTG 58.848 52.381 0.00 0.00 0.00 4.61
614 626 2.563261 GAAAGAGAGGTTTTCGGGGT 57.437 50.000 0.00 0.00 0.00 4.95
633 645 2.038269 CACCAATTGGACCGGGACG 61.038 63.158 31.22 1.05 46.22 4.79
634 646 0.958876 GTCACCAATTGGACCGGGAC 60.959 60.000 31.22 21.82 38.94 4.46
635 647 1.377229 GTCACCAATTGGACCGGGA 59.623 57.895 31.22 15.63 38.94 5.14
636 648 2.038269 CGTCACCAATTGGACCGGG 61.038 63.158 31.22 13.70 38.94 5.73
637 649 1.004320 TCGTCACCAATTGGACCGG 60.004 57.895 31.22 16.12 38.94 5.28
638 650 1.623081 CGTCGTCACCAATTGGACCG 61.623 60.000 31.22 25.08 38.94 4.79
639 651 0.601841 ACGTCGTCACCAATTGGACC 60.602 55.000 31.22 15.64 38.94 4.46
640 652 2.068837 TACGTCGTCACCAATTGGAC 57.931 50.000 31.22 17.93 38.94 4.02
641 653 2.816204 TTACGTCGTCACCAATTGGA 57.184 45.000 31.22 6.63 38.94 3.53
642 654 5.533533 TTTATTACGTCGTCACCAATTGG 57.466 39.130 23.31 23.31 42.17 3.16
643 655 5.019498 GCTTTATTACGTCGTCACCAATTG 58.981 41.667 0.00 0.00 0.00 2.32
644 656 4.933400 AGCTTTATTACGTCGTCACCAATT 59.067 37.500 0.00 0.00 0.00 2.32
645 657 4.501071 AGCTTTATTACGTCGTCACCAAT 58.499 39.130 0.00 0.00 0.00 3.16
646 658 3.916761 AGCTTTATTACGTCGTCACCAA 58.083 40.909 0.00 0.00 0.00 3.67
647 659 3.581024 AGCTTTATTACGTCGTCACCA 57.419 42.857 0.00 0.00 0.00 4.17
648 660 4.634991 CAAAGCTTTATTACGTCGTCACC 58.365 43.478 12.25 0.00 0.00 4.02
649 661 4.079710 GCAAAGCTTTATTACGTCGTCAC 58.920 43.478 12.25 0.00 0.00 3.67
650 662 3.181538 CGCAAAGCTTTATTACGTCGTCA 60.182 43.478 12.25 0.00 0.00 4.35
651 663 3.059834 TCGCAAAGCTTTATTACGTCGTC 59.940 43.478 12.25 0.00 0.00 4.20
652 664 2.988493 TCGCAAAGCTTTATTACGTCGT 59.012 40.909 12.25 2.21 0.00 4.34
653 665 3.628053 TCGCAAAGCTTTATTACGTCG 57.372 42.857 12.25 7.50 0.00 5.12
654 666 5.793457 ACAATTCGCAAAGCTTTATTACGTC 59.207 36.000 12.25 0.00 0.00 4.34
655 667 5.695818 ACAATTCGCAAAGCTTTATTACGT 58.304 33.333 12.25 0.00 0.00 3.57
656 668 6.021596 AGACAATTCGCAAAGCTTTATTACG 58.978 36.000 12.25 13.15 0.00 3.18
657 669 7.021196 TGAGACAATTCGCAAAGCTTTATTAC 58.979 34.615 12.25 6.14 0.00 1.89
658 670 7.119116 TCTGAGACAATTCGCAAAGCTTTATTA 59.881 33.333 12.25 0.00 30.32 0.98
659 671 6.012658 TGAGACAATTCGCAAAGCTTTATT 57.987 33.333 12.25 5.23 0.00 1.40
660 672 5.412594 TCTGAGACAATTCGCAAAGCTTTAT 59.587 36.000 12.25 0.00 30.32 1.40
661 673 4.754618 TCTGAGACAATTCGCAAAGCTTTA 59.245 37.500 12.25 0.00 30.32 1.85
662 674 3.565482 TCTGAGACAATTCGCAAAGCTTT 59.435 39.130 5.69 5.69 30.32 3.51
663 675 3.141398 TCTGAGACAATTCGCAAAGCTT 58.859 40.909 0.00 0.00 30.32 3.74
664 676 2.771089 TCTGAGACAATTCGCAAAGCT 58.229 42.857 0.00 0.00 30.32 3.74
665 677 3.542712 TTCTGAGACAATTCGCAAAGC 57.457 42.857 0.00 0.00 30.32 3.51
687 699 4.215613 GGGATGAAGTAGACGTTGCTTTTT 59.784 41.667 0.00 0.00 31.34 1.94
688 700 3.751698 GGGATGAAGTAGACGTTGCTTTT 59.248 43.478 0.00 0.00 31.34 2.27
689 701 3.335579 GGGATGAAGTAGACGTTGCTTT 58.664 45.455 0.00 0.00 31.34 3.51
690 702 2.354805 GGGGATGAAGTAGACGTTGCTT 60.355 50.000 0.00 0.00 34.13 3.91
691 703 1.207329 GGGGATGAAGTAGACGTTGCT 59.793 52.381 0.00 0.00 0.00 3.91
692 704 1.207329 AGGGGATGAAGTAGACGTTGC 59.793 52.381 0.00 0.00 0.00 4.17
693 705 2.496070 TGAGGGGATGAAGTAGACGTTG 59.504 50.000 0.00 0.00 0.00 4.10
694 706 2.816411 TGAGGGGATGAAGTAGACGTT 58.184 47.619 0.00 0.00 0.00 3.99
695 707 2.526888 TGAGGGGATGAAGTAGACGT 57.473 50.000 0.00 0.00 0.00 4.34
696 708 3.887621 TTTGAGGGGATGAAGTAGACG 57.112 47.619 0.00 0.00 0.00 4.18
697 709 5.805728 TCTTTTTGAGGGGATGAAGTAGAC 58.194 41.667 0.00 0.00 0.00 2.59
698 710 6.448369 TTCTTTTTGAGGGGATGAAGTAGA 57.552 37.500 0.00 0.00 0.00 2.59
699 711 7.524717 TTTTCTTTTTGAGGGGATGAAGTAG 57.475 36.000 0.00 0.00 0.00 2.57
700 712 7.782644 TCTTTTTCTTTTTGAGGGGATGAAGTA 59.217 33.333 0.00 0.00 0.00 2.24
701 713 6.611236 TCTTTTTCTTTTTGAGGGGATGAAGT 59.389 34.615 0.00 0.00 0.00 3.01
702 714 7.054491 TCTTTTTCTTTTTGAGGGGATGAAG 57.946 36.000 0.00 0.00 0.00 3.02
703 715 7.344352 TCTTCTTTTTCTTTTTGAGGGGATGAA 59.656 33.333 0.00 0.00 0.00 2.57
704 716 6.838612 TCTTCTTTTTCTTTTTGAGGGGATGA 59.161 34.615 0.00 0.00 0.00 2.92
705 717 7.054491 TCTTCTTTTTCTTTTTGAGGGGATG 57.946 36.000 0.00 0.00 0.00 3.51
706 718 7.565029 TCTTCTTCTTTTTCTTTTTGAGGGGAT 59.435 33.333 0.00 0.00 0.00 3.85
707 719 6.895204 TCTTCTTCTTTTTCTTTTTGAGGGGA 59.105 34.615 0.00 0.00 0.00 4.81
708 720 7.068716 TCTCTTCTTCTTTTTCTTTTTGAGGGG 59.931 37.037 0.00 0.00 0.00 4.79
709 721 8.000780 TCTCTTCTTCTTTTTCTTTTTGAGGG 57.999 34.615 0.00 0.00 0.00 4.30
710 722 9.860898 TTTCTCTTCTTCTTTTTCTTTTTGAGG 57.139 29.630 0.00 0.00 0.00 3.86
735 747 4.848299 CGAAGTAGACGTACGTAGCTTTTT 59.152 41.667 22.87 12.12 33.97 1.94
736 748 4.083802 ACGAAGTAGACGTACGTAGCTTTT 60.084 41.667 22.87 12.11 41.94 2.27
737 749 3.433615 ACGAAGTAGACGTACGTAGCTTT 59.566 43.478 22.87 13.54 41.94 3.51
738 750 2.996621 ACGAAGTAGACGTACGTAGCTT 59.003 45.455 22.87 22.79 41.94 3.74
739 751 2.346847 CACGAAGTAGACGTACGTAGCT 59.653 50.000 22.87 17.35 41.61 3.32
740 752 2.535732 CCACGAAGTAGACGTACGTAGC 60.536 54.545 22.87 13.97 41.61 3.58
741 753 2.923655 TCCACGAAGTAGACGTACGTAG 59.076 50.000 22.87 9.15 41.61 3.51
742 754 2.923655 CTCCACGAAGTAGACGTACGTA 59.076 50.000 22.87 3.32 41.61 3.57
743 755 1.728971 CTCCACGAAGTAGACGTACGT 59.271 52.381 23.04 23.04 41.61 3.57
744 756 1.528603 GCTCCACGAAGTAGACGTACG 60.529 57.143 15.01 15.01 41.61 3.67
745 757 1.202121 GGCTCCACGAAGTAGACGTAC 60.202 57.143 0.00 0.00 41.61 3.67
746 758 1.089920 GGCTCCACGAAGTAGACGTA 58.910 55.000 0.00 0.00 41.61 3.57
747 759 1.593296 GGGCTCCACGAAGTAGACGT 61.593 60.000 0.00 0.00 41.61 4.34
748 760 1.139095 GGGCTCCACGAAGTAGACG 59.861 63.158 0.00 0.00 41.61 4.18
749 761 1.516423 GGGGCTCCACGAAGTAGAC 59.484 63.158 0.00 0.00 41.61 2.59
750 762 2.050350 CGGGGCTCCACGAAGTAGA 61.050 63.158 1.96 0.00 41.61 2.59
751 763 2.494918 CGGGGCTCCACGAAGTAG 59.505 66.667 1.96 0.00 41.61 2.57
752 764 3.766691 GCGGGGCTCCACGAAGTA 61.767 66.667 15.62 0.00 41.61 2.24
759 771 4.659172 CAAAGTGGCGGGGCTCCA 62.659 66.667 1.96 0.00 0.00 3.86
760 772 3.262448 TACAAAGTGGCGGGGCTCC 62.262 63.158 0.00 0.00 0.00 4.70
761 773 2.038837 GTACAAAGTGGCGGGGCTC 61.039 63.158 0.00 0.00 0.00 4.70
762 774 2.033602 GTACAAAGTGGCGGGGCT 59.966 61.111 0.00 0.00 0.00 5.19
763 775 2.281900 TGTACAAAGTGGCGGGGC 60.282 61.111 0.00 0.00 0.00 5.80
764 776 0.953960 GAGTGTACAAAGTGGCGGGG 60.954 60.000 0.00 0.00 0.00 5.73
765 777 0.034896 AGAGTGTACAAAGTGGCGGG 59.965 55.000 0.00 0.00 0.00 6.13
766 778 1.798813 GAAGAGTGTACAAAGTGGCGG 59.201 52.381 0.00 0.00 0.00 6.13
767 779 1.798813 GGAAGAGTGTACAAAGTGGCG 59.201 52.381 0.00 0.00 0.00 5.69
768 780 2.152016 GGGAAGAGTGTACAAAGTGGC 58.848 52.381 0.00 0.00 0.00 5.01
769 781 2.105821 TGGGGAAGAGTGTACAAAGTGG 59.894 50.000 0.00 0.00 0.00 4.00
770 782 3.485463 TGGGGAAGAGTGTACAAAGTG 57.515 47.619 0.00 0.00 0.00 3.16
771 783 4.513406 TTTGGGGAAGAGTGTACAAAGT 57.487 40.909 0.00 0.00 0.00 2.66
772 784 4.218417 CCATTTGGGGAAGAGTGTACAAAG 59.782 45.833 0.00 0.00 32.24 2.77
773 785 4.148838 CCATTTGGGGAAGAGTGTACAAA 58.851 43.478 0.00 0.00 33.11 2.83
774 786 3.761897 CCATTTGGGGAAGAGTGTACAA 58.238 45.455 0.00 0.00 0.00 2.41
775 787 2.554344 GCCATTTGGGGAAGAGTGTACA 60.554 50.000 0.00 0.00 37.04 2.90
776 788 2.092323 GCCATTTGGGGAAGAGTGTAC 58.908 52.381 0.00 0.00 37.04 2.90
777 789 1.005450 GGCCATTTGGGGAAGAGTGTA 59.995 52.381 0.00 0.00 37.04 2.90
778 790 0.251787 GGCCATTTGGGGAAGAGTGT 60.252 55.000 0.00 0.00 37.04 3.55
779 791 0.251742 TGGCCATTTGGGGAAGAGTG 60.252 55.000 0.00 0.00 37.04 3.51
780 792 0.486879 TTGGCCATTTGGGGAAGAGT 59.513 50.000 6.09 0.00 37.04 3.24
781 793 1.643310 TTTGGCCATTTGGGGAAGAG 58.357 50.000 6.09 0.00 37.04 2.85
782 794 1.907936 CATTTGGCCATTTGGGGAAGA 59.092 47.619 6.09 0.00 37.04 2.87
783 795 1.907936 TCATTTGGCCATTTGGGGAAG 59.092 47.619 6.09 0.00 37.04 3.46
784 796 2.035910 TCATTTGGCCATTTGGGGAA 57.964 45.000 6.09 0.00 37.04 3.97
785 797 2.035910 TTCATTTGGCCATTTGGGGA 57.964 45.000 6.09 0.00 37.04 4.81
786 798 2.742530 CGATTCATTTGGCCATTTGGGG 60.743 50.000 6.09 0.00 37.04 4.96
787 799 2.168106 TCGATTCATTTGGCCATTTGGG 59.832 45.455 6.09 0.00 40.85 4.12
788 800 3.189285 GTCGATTCATTTGGCCATTTGG 58.811 45.455 6.09 0.00 38.53 3.28
841 3835 3.041940 GGTTGAGCGGTGGACGTG 61.042 66.667 0.00 0.00 46.52 4.49
928 3932 4.820090 GCGCTGGGCTATAGACGTAGTG 62.820 59.091 14.49 14.49 39.36 2.74
931 3935 0.820482 TGCGCTGGGCTATAGACGTA 60.820 55.000 17.81 0.00 44.05 3.57
960 3970 4.742201 TTCAGCGAGGGCGAGTGC 62.742 66.667 0.00 0.00 46.35 4.40
961 3971 2.507992 CTTCAGCGAGGGCGAGTG 60.508 66.667 0.00 0.00 46.35 3.51
962 3972 4.443266 GCTTCAGCGAGGGCGAGT 62.443 66.667 0.00 0.00 46.35 4.18
4391 9262 5.567138 AAATATTAGTGGCACTCTGTTGC 57.433 39.130 25.80 0.00 42.18 4.17
4666 11053 0.179134 GCAGAGAATGTAGTCGGCGT 60.179 55.000 6.85 0.00 0.00 5.68
4677 11064 0.396435 TCCACGGTGTTGCAGAGAAT 59.604 50.000 7.45 0.00 0.00 2.40
4732 11119 0.529378 GGCGTAGAAGGGTTTCTCGA 59.471 55.000 10.85 0.00 42.60 4.04
4788 11178 4.082523 CATGGAGGTGGCGACGGT 62.083 66.667 0.00 0.00 0.00 4.83
5425 12025 0.669625 GGTCGGCTCAGCTTAACGTT 60.670 55.000 5.88 5.88 0.00 3.99
5554 12630 6.732531 TGCAGAGAAAATAAGATCACACTG 57.267 37.500 0.00 0.00 0.00 3.66
5783 12982 2.421529 GCCCCAAATCGAATCTACTGGT 60.422 50.000 0.00 0.00 0.00 4.00
5805 13004 2.436646 CAAGACAAGGGCGGCGAT 60.437 61.111 12.98 0.00 0.00 4.58
5838 13037 0.615850 AGAAGCCTTAAGGAAGCGCT 59.384 50.000 26.21 2.64 39.46 5.92
5908 13948 9.916397 GGTGTATAAAGAAAATGTAGAATGTCG 57.084 33.333 0.00 0.00 0.00 4.35
6094 14288 9.680315 CCGGTTTTAAAAACTGTTAATCATGTA 57.320 29.630 13.85 0.00 0.00 2.29
6096 14290 7.383843 AGCCGGTTTTAAAAACTGTTAATCATG 59.616 33.333 13.85 0.00 0.00 3.07
6098 14292 6.807789 AGCCGGTTTTAAAAACTGTTAATCA 58.192 32.000 13.85 0.00 0.00 2.57
6099 14293 7.539710 CCTAGCCGGTTTTAAAAACTGTTAATC 59.460 37.037 13.85 0.00 0.00 1.75
6100 14294 7.231115 TCCTAGCCGGTTTTAAAAACTGTTAAT 59.769 33.333 13.85 0.00 0.00 1.40
6102 14296 6.060788 TCCTAGCCGGTTTTAAAAACTGTTA 58.939 36.000 13.85 8.72 0.00 2.41
6105 14299 5.441709 TTCCTAGCCGGTTTTAAAAACTG 57.558 39.130 13.85 8.59 0.00 3.16
6106 14300 4.022589 GCTTCCTAGCCGGTTTTAAAAACT 60.023 41.667 13.85 6.80 41.74 2.66
6107 14301 4.232221 GCTTCCTAGCCGGTTTTAAAAAC 58.768 43.478 5.87 5.87 41.74 2.43
6108 14302 4.508461 GCTTCCTAGCCGGTTTTAAAAA 57.492 40.909 1.90 0.00 41.74 1.94
6140 14372 4.082125 AGGGATTTCAATCACTGGTTGAC 58.918 43.478 4.09 0.00 46.97 3.18
6216 14452 1.284982 CGCTACAGACAGGCACACAC 61.285 60.000 0.00 0.00 0.00 3.82
6221 14457 1.153568 GCATCGCTACAGACAGGCA 60.154 57.895 0.00 0.00 0.00 4.75
6225 14461 0.894835 TGAAGGCATCGCTACAGACA 59.105 50.000 0.00 0.00 0.00 3.41
6228 14464 1.009829 GGTTGAAGGCATCGCTACAG 58.990 55.000 0.00 0.00 0.00 2.74
6322 14558 4.651503 TCCTTCTATTTGTTTGTTTGGGCA 59.348 37.500 0.00 0.00 0.00 5.36
6324 14560 8.675705 ATTTTCCTTCTATTTGTTTGTTTGGG 57.324 30.769 0.00 0.00 0.00 4.12
6363 14599 1.410004 AGGTTGTCGTGGAAGACTGA 58.590 50.000 0.00 0.00 41.47 3.41


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

AutoCloner maintained by Alex Coulton.