Multiple sequence alignment - TraesCS5B01G229400

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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 TraesCS5B01G229400 chr5B 100.000 2397 0 0 1 2397 406406917 406404521 0.000000e+00 4427
1 TraesCS5B01G229400 chr5B 96.597 382 13 0 2013 2394 493160512 493160893 3.360000e-178 634
2 TraesCS5B01G229400 chr5B 95.455 88 4 0 1926 2013 699382744 699382831 8.930000e-30 141
3 TraesCS5B01G229400 chr2D 85.199 1081 102 28 537 1587 61299748 61300800 0.000000e+00 1057
4 TraesCS5B01G229400 chr2D 83.946 517 75 6 1 517 439412775 439412267 2.770000e-134 488
5 TraesCS5B01G229400 chr2D 91.525 354 27 3 2005 2357 88351824 88351473 3.580000e-133 484
6 TraesCS5B01G229400 chr2D 88.087 277 26 4 537 808 61271942 61272216 2.970000e-84 322
7 TraesCS5B01G229400 chr5D 89.701 835 57 13 762 1588 345438037 345438850 0.000000e+00 1038
8 TraesCS5B01G229400 chr5D 90.053 754 65 6 64 808 345437291 345438043 0.000000e+00 968
9 TraesCS5B01G229400 chr5D 88.452 407 44 3 17 422 345356955 345357359 2.770000e-134 488
10 TraesCS5B01G229400 chr5D 88.337 403 37 7 414 808 345358123 345358523 2.160000e-130 475
11 TraesCS5B01G229400 chr5D 90.274 329 32 0 211 539 296662659 296662331 4.730000e-117 431
12 TraesCS5B01G229400 chr5D 87.708 301 29 6 762 1059 345358517 345358812 6.340000e-91 344
13 TraesCS5B01G229400 chr5A 87.904 835 79 12 762 1588 445768042 445767222 0.000000e+00 963
14 TraesCS5B01G229400 chr5A 87.530 842 77 15 755 1588 445672315 445671494 0.000000e+00 948
15 TraesCS5B01G229400 chr5A 85.874 807 85 13 788 1588 446039428 446038645 0.000000e+00 832
16 TraesCS5B01G229400 chr5A 89.008 655 65 5 159 807 445768690 445768037 0.000000e+00 804
17 TraesCS5B01G229400 chr5A 88.606 667 64 10 149 808 445810545 445811206 0.000000e+00 800
18 TraesCS5B01G229400 chr5A 84.856 832 79 15 762 1588 445811200 445811989 0.000000e+00 795
19 TraesCS5B01G229400 chr5A 87.801 664 74 5 149 806 446040113 446039451 0.000000e+00 771
20 TraesCS5B01G229400 chr5A 87.500 664 78 3 149 808 446025067 446024405 0.000000e+00 761
21 TraesCS5B01G229400 chr5A 85.047 214 26 3 1 214 703629494 703629287 1.870000e-51 213
22 TraesCS5B01G229400 chr5A 91.558 154 7 1 2 149 445834578 445834731 8.680000e-50 207
23 TraesCS5B01G229400 chr5A 89.610 154 12 2 1 152 445698706 445698555 2.430000e-45 193
24 TraesCS5B01G229400 chr2B 87.696 829 68 11 762 1587 95945805 95946602 0.000000e+00 935
25 TraesCS5B01G229400 chr2B 87.455 829 73 15 762 1587 95995234 95996034 0.000000e+00 926
26 TraesCS5B01G229400 chr2B 86.786 840 73 19 762 1587 95954062 95954877 0.000000e+00 902
27 TraesCS5B01G229400 chr2B 86.988 830 72 12 762 1587 95986931 95987728 0.000000e+00 902
28 TraesCS5B01G229400 chr2B 86.836 828 77 17 762 1586 96020525 96021323 0.000000e+00 896
29 TraesCS5B01G229400 chr2B 86.473 828 69 17 764 1587 95903735 95904523 0.000000e+00 869
30 TraesCS5B01G229400 chr2B 88.889 153 13 3 907 1059 96045712 96045860 4.070000e-43 185
31 TraesCS5B01G229400 chr2B 96.552 87 3 0 1929 2015 693068811 693068725 6.910000e-31 145
32 TraesCS5B01G229400 chr2A 87.334 829 76 8 762 1587 61773420 61774222 0.000000e+00 922
33 TraesCS5B01G229400 chr3B 97.143 385 11 0 2013 2397 778897782 778897398 0.000000e+00 651
34 TraesCS5B01G229400 chr3B 96.623 385 13 0 2013 2397 778969793 778969409 7.230000e-180 640
35 TraesCS5B01G229400 chr3B 96.591 88 2 1 1929 2015 790394401 790394488 6.910000e-31 145
36 TraesCS5B01G229400 chr3B 94.382 89 3 2 1929 2015 611425659 611425571 4.160000e-28 135
37 TraesCS5B01G229400 chr7B 95.584 385 15 2 2012 2394 637211463 637211847 1.220000e-172 616
38 TraesCS5B01G229400 chr7B 94.318 88 4 1 1929 2015 7284028 7283941 1.490000e-27 134
39 TraesCS5B01G229400 chr3A 93.372 347 20 3 2012 2357 507763653 507763309 5.910000e-141 510
40 TraesCS5B01G229400 chr3A 92.219 347 24 3 2012 2357 232867625 232867969 2.770000e-134 488
41 TraesCS5B01G229400 chr3A 90.654 107 3 2 2298 2397 507763195 507763089 4.160000e-28 135
42 TraesCS5B01G229400 chr3A 90.654 107 3 2 2295 2394 743448922 743449028 4.160000e-28 135
43 TraesCS5B01G229400 chr3A 88.785 107 5 2 2295 2394 232868086 232868192 9.000000e-25 124
44 TraesCS5B01G229400 chrUn 92.486 346 24 2 2007 2352 356303 356646 5.950000e-136 494
45 TraesCS5B01G229400 chrUn 90.654 107 3 2 2295 2394 356769 356875 4.160000e-28 135
46 TraesCS5B01G229400 chr1A 92.507 347 23 3 2012 2357 22045846 22046190 5.950000e-136 494
47 TraesCS5B01G229400 chr1D 83.404 470 70 7 71 539 268704132 268704594 1.700000e-116 429
48 TraesCS5B01G229400 chr4D 84.579 214 27 2 1 214 241802578 241802785 8.680000e-50 207
49 TraesCS5B01G229400 chr4D 80.952 168 27 4 628 793 75266745 75266909 6.960000e-26 128
50 TraesCS5B01G229400 chr1B 84.112 214 24 4 1 212 550930208 550930413 5.230000e-47 198
51 TraesCS5B01G229400 chr1B 94.382 89 3 2 1929 2015 564812187 564812275 4.160000e-28 135
52 TraesCS5B01G229400 chr4A 83.226 155 21 4 631 782 596678226 596678378 1.160000e-28 137
53 TraesCS5B01G229400 chr6A 89.720 107 4 2 2295 2394 112605185 112605291 1.930000e-26 130
54 TraesCS5B01G229400 chr7A 93.182 88 5 1 1929 2015 709393179 709393266 6.960000e-26 128
55 TraesCS5B01G229400 chr4B 93.182 88 5 1 1929 2015 33173866 33173953 6.960000e-26 128
56 TraesCS5B01G229400 chr6B 91.398 93 6 2 1925 2015 698981607 698981515 2.500000e-25 126
57 TraesCS5B01G229400 chr6D 86.364 110 15 0 1634 1743 235092346 235092237 1.160000e-23 121


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 TraesCS5B01G229400 chr5B 406404521 406406917 2396 True 4427.000000 4427 100.000000 1 2397 1 chr5B.!!$R1 2396
1 TraesCS5B01G229400 chr2D 61299748 61300800 1052 False 1057.000000 1057 85.199000 537 1587 1 chr2D.!!$F2 1050
2 TraesCS5B01G229400 chr2D 439412267 439412775 508 True 488.000000 488 83.946000 1 517 1 chr2D.!!$R2 516
3 TraesCS5B01G229400 chr5D 345437291 345438850 1559 False 1003.000000 1038 89.877000 64 1588 2 chr5D.!!$F2 1524
4 TraesCS5B01G229400 chr5D 345356955 345358812 1857 False 435.666667 488 88.165667 17 1059 3 chr5D.!!$F1 1042
5 TraesCS5B01G229400 chr5A 445671494 445672315 821 True 948.000000 948 87.530000 755 1588 1 chr5A.!!$R1 833
6 TraesCS5B01G229400 chr5A 445767222 445768690 1468 True 883.500000 963 88.456000 159 1588 2 chr5A.!!$R5 1429
7 TraesCS5B01G229400 chr5A 446038645 446040113 1468 True 801.500000 832 86.837500 149 1588 2 chr5A.!!$R6 1439
8 TraesCS5B01G229400 chr5A 445810545 445811989 1444 False 797.500000 800 86.731000 149 1588 2 chr5A.!!$F2 1439
9 TraesCS5B01G229400 chr5A 446024405 446025067 662 True 761.000000 761 87.500000 149 808 1 chr5A.!!$R3 659
10 TraesCS5B01G229400 chr2B 95945805 95946602 797 False 935.000000 935 87.696000 762 1587 1 chr2B.!!$F2 825
11 TraesCS5B01G229400 chr2B 95995234 95996034 800 False 926.000000 926 87.455000 762 1587 1 chr2B.!!$F5 825
12 TraesCS5B01G229400 chr2B 95954062 95954877 815 False 902.000000 902 86.786000 762 1587 1 chr2B.!!$F3 825
13 TraesCS5B01G229400 chr2B 95986931 95987728 797 False 902.000000 902 86.988000 762 1587 1 chr2B.!!$F4 825
14 TraesCS5B01G229400 chr2B 96020525 96021323 798 False 896.000000 896 86.836000 762 1586 1 chr2B.!!$F6 824
15 TraesCS5B01G229400 chr2B 95903735 95904523 788 False 869.000000 869 86.473000 764 1587 1 chr2B.!!$F1 823
16 TraesCS5B01G229400 chr2A 61773420 61774222 802 False 922.000000 922 87.334000 762 1587 1 chr2A.!!$F1 825
17 TraesCS5B01G229400 chr3A 507763089 507763653 564 True 322.500000 510 92.013000 2012 2397 2 chr3A.!!$R1 385
18 TraesCS5B01G229400 chr3A 232867625 232868192 567 False 306.000000 488 90.502000 2012 2394 2 chr3A.!!$F2 382
19 TraesCS5B01G229400 chrUn 356303 356875 572 False 314.500000 494 91.570000 2007 2394 2 chrUn.!!$F1 387

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
249 250 0.742505 CGATGGCTCCGTACTTGGTA 59.257 55.0 0.0 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 2625 0.036765 TCCAATTAGGAACGCACGCT 60.037 50.0 0.0 0.0 45.65 5.07 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
23 24 4.461198 CCCTCTTGGTCTTGTACAACTTT 58.539 43.478 3.59 0.00 0.00 2.66
38 39 3.074412 CAACTTTGTCACGCCCTTCTAT 58.926 45.455 0.00 0.00 0.00 1.98
41 42 1.568504 TTGTCACGCCCTTCTATCCT 58.431 50.000 0.00 0.00 0.00 3.24
224 225 5.088739 CGACTTCAAAGGTTATTGATGCAC 58.911 41.667 0.00 0.00 38.98 4.57
225 226 5.334802 CGACTTCAAAGGTTATTGATGCACA 60.335 40.000 0.00 0.00 38.98 4.57
249 250 0.742505 CGATGGCTCCGTACTTGGTA 59.257 55.000 0.00 0.00 0.00 3.25
278 280 5.498393 TGTATAAGTCGAAGGACAGAGACT 58.502 41.667 0.00 0.00 45.92 3.24
312 314 1.542915 GTCTACACCACTGGAGCGTAA 59.457 52.381 0.71 0.00 0.00 3.18
314 316 0.892755 TACACCACTGGAGCGTAAGG 59.107 55.000 0.71 0.00 38.28 2.69
367 369 6.544650 ACGGTGTAATCTCTGTATAGGATCT 58.455 40.000 0.00 0.00 0.00 2.75
368 370 7.687388 ACGGTGTAATCTCTGTATAGGATCTA 58.313 38.462 0.00 0.00 0.00 1.98
579 1360 9.878667 TCTTTGATGAATTATTACTTCGGTACA 57.121 29.630 0.00 0.00 0.00 2.90
656 1437 8.493787 ACTCCCTCCGTTTCTAAATATAAGAT 57.506 34.615 0.00 0.00 0.00 2.40
730 1513 9.594478 TTTCAGAGCGTAGATTCACATAATTTA 57.406 29.630 0.00 0.00 0.00 1.40
845 1675 9.754382 AATACTTACCATATGTGTAACTTACCG 57.246 33.333 10.81 5.56 38.04 4.02
848 1678 5.664294 ACCATATGTGTAACTTACCGTCA 57.336 39.130 1.24 0.00 38.04 4.35
850 1680 6.646267 ACCATATGTGTAACTTACCGTCATT 58.354 36.000 1.24 0.00 38.04 2.57
864 1694 2.329379 CGTCATTAGCCGCTCCTATTC 58.671 52.381 0.00 0.00 0.00 1.75
877 1707 3.770666 CTCCTATTCATATACCACGGCG 58.229 50.000 4.80 4.80 0.00 6.46
1141 1997 8.065473 TCATACTACCGGTTAACTGATTTGTA 57.935 34.615 15.04 12.65 0.00 2.41
1149 2005 6.635239 CCGGTTAACTGATTTGTACTTGTTTG 59.365 38.462 16.27 0.00 0.00 2.93
1294 2150 4.849310 GACCATTGCGGCGGGCTA 62.849 66.667 9.78 0.00 44.05 3.93
1321 2177 3.264193 TGGAGCAGTTCATGTGGAAGTAT 59.736 43.478 0.00 0.00 37.04 2.12
1405 2261 7.282224 TGCTCTTTTCTTTGCTAGTTGAACTTA 59.718 33.333 1.97 0.00 0.00 2.24
1423 2279 8.654485 TGAACTTAATGTACAAGGGTAGTAGA 57.346 34.615 0.00 0.00 0.00 2.59
1429 2285 5.080969 TGTACAAGGGTAGTAGACAATGC 57.919 43.478 0.00 0.00 0.00 3.56
1434 2290 3.173965 AGGGTAGTAGACAATGCTGTGT 58.826 45.455 0.00 0.00 35.30 3.72
1465 2321 4.825085 TGGCTCGGAAGAAATAAAACTTGT 59.175 37.500 0.00 0.00 41.32 3.16
1479 2335 5.544136 AAAACTTGTTGCGCATTCTTTTT 57.456 30.435 12.75 10.86 0.00 1.94
1521 2382 4.009675 TCAGCCGCTATTTTGTTCTTGAT 58.990 39.130 0.00 0.00 0.00 2.57
1567 2430 2.017049 CGGGCTCAAAATAGGGACTTG 58.983 52.381 0.00 0.00 41.75 3.16
1570 2433 3.832490 GGGCTCAAAATAGGGACTTGTTT 59.168 43.478 0.00 0.00 41.75 2.83
1588 2451 3.054166 GTTTTTGCCACGGGTAACAATC 58.946 45.455 0.00 0.00 39.74 2.67
1589 2452 2.279935 TTTGCCACGGGTAACAATCT 57.720 45.000 0.00 0.00 39.74 2.40
1590 2453 2.279935 TTGCCACGGGTAACAATCTT 57.720 45.000 0.00 0.00 39.74 2.40
1591 2454 2.279935 TGCCACGGGTAACAATCTTT 57.720 45.000 0.00 0.00 39.74 2.52
1592 2455 3.420300 TGCCACGGGTAACAATCTTTA 57.580 42.857 0.00 0.00 39.74 1.85
1593 2456 3.958018 TGCCACGGGTAACAATCTTTAT 58.042 40.909 0.00 0.00 39.74 1.40
1594 2457 3.942748 TGCCACGGGTAACAATCTTTATC 59.057 43.478 0.00 0.00 39.74 1.75
1595 2458 4.196971 GCCACGGGTAACAATCTTTATCT 58.803 43.478 0.00 0.00 39.74 1.98
1596 2459 4.638865 GCCACGGGTAACAATCTTTATCTT 59.361 41.667 0.00 0.00 39.74 2.40
1597 2460 5.124936 GCCACGGGTAACAATCTTTATCTTT 59.875 40.000 0.00 0.00 39.74 2.52
1598 2461 6.349860 GCCACGGGTAACAATCTTTATCTTTT 60.350 38.462 0.00 0.00 39.74 2.27
1599 2462 7.599171 CCACGGGTAACAATCTTTATCTTTTT 58.401 34.615 0.00 0.00 39.74 1.94
1649 2512 9.286170 CCTTAATTACTATTAAAAGGAGGAGGC 57.714 37.037 0.00 0.00 36.16 4.70
1653 2516 8.982091 ATTACTATTAAAAGGAGGAGGCTTTC 57.018 34.615 0.00 0.00 0.00 2.62
1654 2517 6.388619 ACTATTAAAAGGAGGAGGCTTTCA 57.611 37.500 0.00 0.00 0.00 2.69
1655 2518 6.974795 ACTATTAAAAGGAGGAGGCTTTCAT 58.025 36.000 0.00 0.00 0.00 2.57
1656 2519 8.102484 ACTATTAAAAGGAGGAGGCTTTCATA 57.898 34.615 0.00 0.00 0.00 2.15
1657 2520 8.214364 ACTATTAAAAGGAGGAGGCTTTCATAG 58.786 37.037 0.00 0.00 0.00 2.23
1658 2521 4.936685 AAAAGGAGGAGGCTTTCATAGT 57.063 40.909 0.00 0.00 0.00 2.12
1659 2522 4.936685 AAAGGAGGAGGCTTTCATAGTT 57.063 40.909 0.00 0.00 0.00 2.24
1660 2523 4.495690 AAGGAGGAGGCTTTCATAGTTC 57.504 45.455 0.00 0.00 0.00 3.01
1661 2524 3.730269 AGGAGGAGGCTTTCATAGTTCT 58.270 45.455 0.00 0.00 0.00 3.01
1662 2525 4.107820 AGGAGGAGGCTTTCATAGTTCTT 58.892 43.478 0.00 0.00 0.00 2.52
1663 2526 4.163268 AGGAGGAGGCTTTCATAGTTCTTC 59.837 45.833 0.00 0.00 0.00 2.87
1664 2527 4.080863 GGAGGAGGCTTTCATAGTTCTTCA 60.081 45.833 0.00 0.00 0.00 3.02
1665 2528 5.397334 GGAGGAGGCTTTCATAGTTCTTCAT 60.397 44.000 0.00 0.00 0.00 2.57
1666 2529 6.183361 GGAGGAGGCTTTCATAGTTCTTCATA 60.183 42.308 0.00 0.00 0.00 2.15
1667 2530 6.587273 AGGAGGCTTTCATAGTTCTTCATAC 58.413 40.000 0.00 0.00 0.00 2.39
1668 2531 6.156949 AGGAGGCTTTCATAGTTCTTCATACA 59.843 38.462 0.00 0.00 0.00 2.29
1669 2532 6.995091 GGAGGCTTTCATAGTTCTTCATACAT 59.005 38.462 0.00 0.00 0.00 2.29
1670 2533 7.172361 GGAGGCTTTCATAGTTCTTCATACATC 59.828 40.741 0.00 0.00 0.00 3.06
1671 2534 7.568349 AGGCTTTCATAGTTCTTCATACATCA 58.432 34.615 0.00 0.00 0.00 3.07
1672 2535 8.216423 AGGCTTTCATAGTTCTTCATACATCAT 58.784 33.333 0.00 0.00 0.00 2.45
1673 2536 8.502387 GGCTTTCATAGTTCTTCATACATCATC 58.498 37.037 0.00 0.00 0.00 2.92
1674 2537 8.502387 GCTTTCATAGTTCTTCATACATCATCC 58.498 37.037 0.00 0.00 0.00 3.51
1675 2538 9.775854 CTTTCATAGTTCTTCATACATCATCCT 57.224 33.333 0.00 0.00 0.00 3.24
1710 2573 9.881529 TGTTGATTTTACGTTAACCATAAAGAC 57.118 29.630 0.00 4.91 0.00 3.01
1713 2576 9.491675 TGATTTTACGTTAACCATAAAGACTGA 57.508 29.630 0.00 0.00 0.00 3.41
1714 2577 9.750882 GATTTTACGTTAACCATAAAGACTGAC 57.249 33.333 0.00 0.00 0.00 3.51
1715 2578 6.932901 TTACGTTAACCATAAAGACTGACG 57.067 37.500 0.00 0.00 0.00 4.35
1716 2579 4.240096 ACGTTAACCATAAAGACTGACGG 58.760 43.478 0.00 0.00 32.81 4.79
1717 2580 4.022068 ACGTTAACCATAAAGACTGACGGA 60.022 41.667 0.00 0.00 32.81 4.69
1718 2581 5.107133 CGTTAACCATAAAGACTGACGGAT 58.893 41.667 0.00 0.00 0.00 4.18
1719 2582 5.005394 CGTTAACCATAAAGACTGACGGATG 59.995 44.000 0.00 0.00 0.00 3.51
1720 2583 4.819105 AACCATAAAGACTGACGGATGA 57.181 40.909 0.00 0.00 0.00 2.92
1721 2584 4.392921 ACCATAAAGACTGACGGATGAG 57.607 45.455 0.00 0.00 0.00 2.90
1722 2585 4.023980 ACCATAAAGACTGACGGATGAGA 58.976 43.478 0.00 0.00 0.00 3.27
1723 2586 4.651503 ACCATAAAGACTGACGGATGAGAT 59.348 41.667 0.00 0.00 0.00 2.75
1724 2587 5.129485 ACCATAAAGACTGACGGATGAGATT 59.871 40.000 0.00 0.00 0.00 2.40
1725 2588 6.051717 CCATAAAGACTGACGGATGAGATTT 58.948 40.000 0.00 0.00 0.00 2.17
1726 2589 7.147724 ACCATAAAGACTGACGGATGAGATTTA 60.148 37.037 0.00 0.00 0.00 1.40
1727 2590 7.710907 CCATAAAGACTGACGGATGAGATTTAA 59.289 37.037 0.00 0.00 0.00 1.52
1728 2591 9.098355 CATAAAGACTGACGGATGAGATTTAAA 57.902 33.333 0.00 0.00 0.00 1.52
1729 2592 7.602517 AAAGACTGACGGATGAGATTTAAAG 57.397 36.000 0.00 0.00 0.00 1.85
1730 2593 6.531503 AGACTGACGGATGAGATTTAAAGA 57.468 37.500 0.00 0.00 0.00 2.52
1731 2594 7.118496 AGACTGACGGATGAGATTTAAAGAT 57.882 36.000 0.00 0.00 0.00 2.40
1732 2595 8.239038 AGACTGACGGATGAGATTTAAAGATA 57.761 34.615 0.00 0.00 0.00 1.98
1733 2596 8.356657 AGACTGACGGATGAGATTTAAAGATAG 58.643 37.037 0.00 0.00 0.00 2.08
1734 2597 8.239038 ACTGACGGATGAGATTTAAAGATAGA 57.761 34.615 0.00 0.00 0.00 1.98
1735 2598 8.865090 ACTGACGGATGAGATTTAAAGATAGAT 58.135 33.333 0.00 0.00 0.00 1.98
1774 2637 1.589803 AAAAAGTAGCGTGCGTTCCT 58.410 45.000 0.00 0.00 0.00 3.36
1775 2638 2.443887 AAAAGTAGCGTGCGTTCCTA 57.556 45.000 0.00 0.00 0.00 2.94
1776 2639 2.443887 AAAGTAGCGTGCGTTCCTAA 57.556 45.000 0.00 0.00 0.00 2.69
1777 2640 2.667473 AAGTAGCGTGCGTTCCTAAT 57.333 45.000 0.00 0.00 0.00 1.73
1778 2641 2.667473 AGTAGCGTGCGTTCCTAATT 57.333 45.000 0.00 0.00 0.00 1.40
1779 2642 2.268298 AGTAGCGTGCGTTCCTAATTG 58.732 47.619 0.00 0.00 0.00 2.32
1780 2643 1.326548 GTAGCGTGCGTTCCTAATTGG 59.673 52.381 0.00 0.00 37.10 3.16
1781 2644 0.036765 AGCGTGCGTTCCTAATTGGA 60.037 50.000 0.00 0.00 44.51 3.53
1800 2663 4.926140 GGAATCATTCCCCTCAATTGTC 57.074 45.455 4.89 0.00 44.30 3.18
1801 2664 4.540715 GGAATCATTCCCCTCAATTGTCT 58.459 43.478 4.89 0.00 44.30 3.41
1802 2665 5.694995 GGAATCATTCCCCTCAATTGTCTA 58.305 41.667 4.89 0.00 44.30 2.59
1803 2666 6.129179 GGAATCATTCCCCTCAATTGTCTAA 58.871 40.000 4.89 0.00 44.30 2.10
1804 2667 6.607198 GGAATCATTCCCCTCAATTGTCTAAA 59.393 38.462 4.89 0.00 44.30 1.85
1805 2668 7.124147 GGAATCATTCCCCTCAATTGTCTAAAA 59.876 37.037 4.89 0.00 44.30 1.52
1806 2669 8.434589 AATCATTCCCCTCAATTGTCTAAAAA 57.565 30.769 5.13 0.00 0.00 1.94
1823 2686 0.624254 AAAAAGATCGTCCCCCTCCC 59.376 55.000 0.00 0.00 0.00 4.30
1824 2687 0.549169 AAAAGATCGTCCCCCTCCCA 60.549 55.000 0.00 0.00 0.00 4.37
1825 2688 0.549169 AAAGATCGTCCCCCTCCCAA 60.549 55.000 0.00 0.00 0.00 4.12
1826 2689 0.549169 AAGATCGTCCCCCTCCCAAA 60.549 55.000 0.00 0.00 0.00 3.28
1827 2690 0.549169 AGATCGTCCCCCTCCCAAAA 60.549 55.000 0.00 0.00 0.00 2.44
1828 2691 0.330267 GATCGTCCCCCTCCCAAAAA 59.670 55.000 0.00 0.00 0.00 1.94
1854 2717 9.535878 AAAACTAGAATAGATCGTGATCTTTCC 57.464 33.333 16.88 7.17 45.31 3.13
1855 2718 8.472007 AACTAGAATAGATCGTGATCTTTCCT 57.528 34.615 16.88 12.90 45.31 3.36
1856 2719 8.472007 ACTAGAATAGATCGTGATCTTTCCTT 57.528 34.615 16.88 6.94 45.31 3.36
1857 2720 8.356657 ACTAGAATAGATCGTGATCTTTCCTTG 58.643 37.037 16.88 13.24 45.31 3.61
1858 2721 7.118496 AGAATAGATCGTGATCTTTCCTTGT 57.882 36.000 16.88 3.70 45.31 3.16
1859 2722 7.206687 AGAATAGATCGTGATCTTTCCTTGTC 58.793 38.462 16.88 4.73 45.31 3.18
1860 2723 4.130286 AGATCGTGATCTTTCCTTGTCC 57.870 45.455 6.55 0.00 45.31 4.02
1861 2724 2.762535 TCGTGATCTTTCCTTGTCCC 57.237 50.000 0.00 0.00 0.00 4.46
1862 2725 1.278127 TCGTGATCTTTCCTTGTCCCC 59.722 52.381 0.00 0.00 0.00 4.81
1863 2726 1.003118 CGTGATCTTTCCTTGTCCCCA 59.997 52.381 0.00 0.00 0.00 4.96
1864 2727 2.552155 CGTGATCTTTCCTTGTCCCCAA 60.552 50.000 0.00 0.00 0.00 4.12
1865 2728 3.496331 GTGATCTTTCCTTGTCCCCAAA 58.504 45.455 0.00 0.00 0.00 3.28
1866 2729 3.255888 GTGATCTTTCCTTGTCCCCAAAC 59.744 47.826 0.00 0.00 0.00 2.93
1867 2730 2.375014 TCTTTCCTTGTCCCCAAACC 57.625 50.000 0.00 0.00 0.00 3.27
1868 2731 1.856920 TCTTTCCTTGTCCCCAAACCT 59.143 47.619 0.00 0.00 0.00 3.50
1869 2732 3.057586 TCTTTCCTTGTCCCCAAACCTA 58.942 45.455 0.00 0.00 0.00 3.08
1870 2733 3.073946 TCTTTCCTTGTCCCCAAACCTAG 59.926 47.826 0.00 0.00 0.00 3.02
1871 2734 0.696501 TCCTTGTCCCCAAACCTAGC 59.303 55.000 0.00 0.00 0.00 3.42
1872 2735 0.698818 CCTTGTCCCCAAACCTAGCT 59.301 55.000 0.00 0.00 0.00 3.32
1873 2736 1.913419 CCTTGTCCCCAAACCTAGCTA 59.087 52.381 0.00 0.00 0.00 3.32
1874 2737 2.509964 CCTTGTCCCCAAACCTAGCTAT 59.490 50.000 0.00 0.00 0.00 2.97
1875 2738 3.433740 CCTTGTCCCCAAACCTAGCTATC 60.434 52.174 0.00 0.00 0.00 2.08
1876 2739 1.760613 TGTCCCCAAACCTAGCTATCG 59.239 52.381 0.00 0.00 0.00 2.92
1877 2740 1.761198 GTCCCCAAACCTAGCTATCGT 59.239 52.381 0.00 0.00 0.00 3.73
1878 2741 2.169978 GTCCCCAAACCTAGCTATCGTT 59.830 50.000 0.00 0.00 0.00 3.85
1879 2742 2.433239 TCCCCAAACCTAGCTATCGTTC 59.567 50.000 6.77 0.00 0.00 3.95
1880 2743 2.484947 CCCCAAACCTAGCTATCGTTCC 60.485 54.545 6.77 0.00 0.00 3.62
1881 2744 2.434702 CCCAAACCTAGCTATCGTTCCT 59.565 50.000 6.77 0.00 0.00 3.36
1882 2745 3.640029 CCCAAACCTAGCTATCGTTCCTA 59.360 47.826 6.77 0.00 0.00 2.94
1883 2746 4.100498 CCCAAACCTAGCTATCGTTCCTAA 59.900 45.833 6.77 0.00 0.00 2.69
1884 2747 5.048507 CCAAACCTAGCTATCGTTCCTAAC 58.951 45.833 6.77 0.00 0.00 2.34
1885 2748 5.163437 CCAAACCTAGCTATCGTTCCTAACT 60.163 44.000 6.77 0.00 0.00 2.24
1886 2749 5.517322 AACCTAGCTATCGTTCCTAACTG 57.483 43.478 0.00 0.00 0.00 3.16
1887 2750 3.890147 ACCTAGCTATCGTTCCTAACTGG 59.110 47.826 0.00 0.00 37.10 4.00
1888 2751 4.142790 CCTAGCTATCGTTCCTAACTGGA 58.857 47.826 0.00 0.00 44.51 3.86
1899 2762 2.897969 TCCTAACTGGAATAGATCGCCC 59.102 50.000 0.00 0.00 42.94 6.13
1900 2763 2.028020 CCTAACTGGAATAGATCGCCCC 60.028 54.545 0.00 0.00 38.35 5.80
1901 2764 0.765510 AACTGGAATAGATCGCCCCC 59.234 55.000 0.00 0.00 0.00 5.40
1960 2823 9.773328 TTTAGAATTCTTTGCATTCTAATCACG 57.227 29.630 14.36 0.00 45.88 4.35
1961 2824 7.615582 AGAATTCTTTGCATTCTAATCACGA 57.384 32.000 0.88 0.00 38.89 4.35
1962 2825 8.044060 AGAATTCTTTGCATTCTAATCACGAA 57.956 30.769 0.88 0.00 38.89 3.85
1963 2826 8.514594 AGAATTCTTTGCATTCTAATCACGAAA 58.485 29.630 0.88 0.00 38.89 3.46
1964 2827 8.452989 AATTCTTTGCATTCTAATCACGAAAC 57.547 30.769 0.00 0.00 0.00 2.78
1965 2828 6.552859 TCTTTGCATTCTAATCACGAAACA 57.447 33.333 0.00 0.00 0.00 2.83
1966 2829 6.964908 TCTTTGCATTCTAATCACGAAACAA 58.035 32.000 0.00 0.00 0.00 2.83
1967 2830 7.592938 TCTTTGCATTCTAATCACGAAACAAT 58.407 30.769 0.00 0.00 0.00 2.71
1968 2831 8.726068 TCTTTGCATTCTAATCACGAAACAATA 58.274 29.630 0.00 0.00 0.00 1.90
1969 2832 9.507280 CTTTGCATTCTAATCACGAAACAATAT 57.493 29.630 0.00 0.00 0.00 1.28
1983 2846 9.498307 CACGAAACAATATAAAATAGTTGACCC 57.502 33.333 0.00 0.00 0.00 4.46
1984 2847 9.457436 ACGAAACAATATAAAATAGTTGACCCT 57.543 29.630 0.00 0.00 0.00 4.34
1992 2855 9.914834 ATATAAAATAGTTGACCCTTACAAGCA 57.085 29.630 0.00 0.00 0.00 3.91
1993 2856 5.959618 AAATAGTTGACCCTTACAAGCAC 57.040 39.130 0.00 0.00 0.00 4.40
1994 2857 4.634012 ATAGTTGACCCTTACAAGCACA 57.366 40.909 0.00 0.00 0.00 4.57
1995 2858 2.572290 AGTTGACCCTTACAAGCACAC 58.428 47.619 0.00 0.00 0.00 3.82
1996 2859 2.172717 AGTTGACCCTTACAAGCACACT 59.827 45.455 0.00 0.00 0.00 3.55
1997 2860 2.254546 TGACCCTTACAAGCACACTG 57.745 50.000 0.00 0.00 0.00 3.66
1998 2861 1.765904 TGACCCTTACAAGCACACTGA 59.234 47.619 0.00 0.00 0.00 3.41
1999 2862 2.171659 TGACCCTTACAAGCACACTGAA 59.828 45.455 0.00 0.00 0.00 3.02
2000 2863 3.211045 GACCCTTACAAGCACACTGAAA 58.789 45.455 0.00 0.00 0.00 2.69
2001 2864 2.949644 ACCCTTACAAGCACACTGAAAC 59.050 45.455 0.00 0.00 0.00 2.78
2002 2865 3.214328 CCCTTACAAGCACACTGAAACT 58.786 45.455 0.00 0.00 0.00 2.66
2003 2866 3.251004 CCCTTACAAGCACACTGAAACTC 59.749 47.826 0.00 0.00 0.00 3.01
2004 2867 3.876914 CCTTACAAGCACACTGAAACTCA 59.123 43.478 0.00 0.00 0.00 3.41
2005 2868 4.335315 CCTTACAAGCACACTGAAACTCAA 59.665 41.667 0.00 0.00 0.00 3.02
2006 2869 5.163663 CCTTACAAGCACACTGAAACTCAAA 60.164 40.000 0.00 0.00 0.00 2.69
2007 2870 4.096732 ACAAGCACACTGAAACTCAAAC 57.903 40.909 0.00 0.00 0.00 2.93
2008 2871 3.505680 ACAAGCACACTGAAACTCAAACA 59.494 39.130 0.00 0.00 0.00 2.83
2009 2872 3.764885 AGCACACTGAAACTCAAACAC 57.235 42.857 0.00 0.00 0.00 3.32
2010 2873 3.081061 AGCACACTGAAACTCAAACACA 58.919 40.909 0.00 0.00 0.00 3.72
2051 2914 6.503524 AGCAAATATTAGGCGTTGGTTTATG 58.496 36.000 6.43 0.00 0.00 1.90
2057 2920 3.653539 AGGCGTTGGTTTATGGAAAAC 57.346 42.857 0.00 0.00 32.43 2.43
2136 2999 9.485206 AATGAGTTTGTATAAGACTACGTTTGT 57.515 29.630 0.00 0.00 0.00 2.83
2143 3006 7.208777 TGTATAAGACTACGTTTGTGTTGGAA 58.791 34.615 11.92 0.00 0.00 3.53
2170 3033 5.235616 TGTGTTTGTCAGTTCCTTATTCGAC 59.764 40.000 0.00 0.00 0.00 4.20
2190 3053 9.823647 ATTCGACAATGATTCAGAGTACTATTT 57.176 29.630 0.00 0.00 0.00 1.40
2280 3143 1.824329 ATCGATCTCGCCGGACAGT 60.824 57.895 5.05 0.00 39.60 3.55
2337 3384 2.478539 GGAACAAGCTGGATCGATTTGC 60.479 50.000 0.00 4.75 0.00 3.68
2340 3387 1.332997 CAAGCTGGATCGATTTGCTCC 59.667 52.381 16.93 7.89 33.27 4.70
2348 3395 2.796651 GATTTGCTCCGCTGGCTG 59.203 61.111 0.00 0.00 0.00 4.85
2394 3448 4.555709 ACCTTGGCGGCGACAACA 62.556 61.111 26.68 5.26 35.61 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.589803 AGGGCGTGACAAAGTTGTAC 58.410 50.000 0.00 0.00 42.43 2.90
23 24 2.029623 GTAGGATAGAAGGGCGTGACA 58.970 52.381 0.00 0.00 0.00 3.58
60 61 1.507141 CTGCAACAACGGTCACCCTC 61.507 60.000 0.00 0.00 0.00 4.30
61 62 1.525995 CTGCAACAACGGTCACCCT 60.526 57.895 0.00 0.00 0.00 4.34
62 63 3.030652 CTGCAACAACGGTCACCC 58.969 61.111 0.00 0.00 0.00 4.61
218 219 1.205064 GCCATCGCGTATGTGCATC 59.795 57.895 5.77 0.00 34.05 3.91
224 225 1.002250 GTACGGAGCCATCGCGTATG 61.002 60.000 5.77 8.75 41.18 2.39
225 226 1.170919 AGTACGGAGCCATCGCGTAT 61.171 55.000 5.77 0.00 41.18 3.06
249 250 7.232188 TCTGTCCTTCGACTTATACAGGATAT 58.768 38.462 3.21 0.00 39.94 1.63
290 292 1.583495 CGCTCCAGTGGTGTAGACGA 61.583 60.000 9.54 0.00 0.00 4.20
300 302 1.448540 CTGGCCTTACGCTCCAGTG 60.449 63.158 3.32 0.00 41.76 3.66
312 314 2.079326 GAGAAAACCTCCCTGGCCT 58.921 57.895 3.32 0.00 40.22 5.19
332 334 3.648067 AGATTACACCGTCATCCATGGAT 59.352 43.478 22.15 22.15 34.76 3.41
343 345 6.544650 AGATCCTATACAGAGATTACACCGT 58.455 40.000 0.00 0.00 0.00 4.83
345 347 7.339976 GGGTAGATCCTATACAGAGATTACACC 59.660 44.444 0.00 0.00 36.25 4.16
481 1255 3.066291 TCAAGGTGATACAACCGCATT 57.934 42.857 0.00 0.00 45.53 3.56
538 1319 9.794719 ATTCATCAAAGATATGTGATCTCATGT 57.205 29.630 18.31 12.76 32.06 3.21
569 1350 6.363065 TCTCTACTCCATATTGTACCGAAGT 58.637 40.000 0.00 0.00 0.00 3.01
579 1360 7.770662 TCTTGGTAGGATCTCTACTCCATATT 58.229 38.462 16.24 0.00 45.78 1.28
584 1365 5.390387 ACATCTTGGTAGGATCTCTACTCC 58.610 45.833 16.24 6.28 45.78 3.85
605 1386 7.423341 ACCTTTAATTATTCCCAATGGGTACA 58.577 34.615 19.28 4.07 44.74 2.90
608 1389 7.658260 AGTACCTTTAATTATTCCCAATGGGT 58.342 34.615 19.28 1.88 44.74 4.51
686 1467 7.954248 GCTCTGAAATGCGTCTATATACATTTG 59.046 37.037 11.65 2.60 41.48 2.32
798 1628 9.391006 AGTATTCTATTGCCGTATCTTTTCAAA 57.609 29.630 0.00 0.00 0.00 2.69
803 1633 8.426489 TGGTAAGTATTCTATTGCCGTATCTTT 58.574 33.333 0.00 0.00 34.25 2.52
845 1675 3.386768 TGAATAGGAGCGGCTAATGAC 57.613 47.619 0.60 0.00 0.00 3.06
848 1678 5.661312 TGGTATATGAATAGGAGCGGCTAAT 59.339 40.000 0.60 0.00 0.00 1.73
850 1680 4.401519 GTGGTATATGAATAGGAGCGGCTA 59.598 45.833 0.60 0.00 0.00 3.93
864 1694 1.607148 TCTGTCTCGCCGTGGTATATG 59.393 52.381 0.00 0.00 0.00 1.78
877 1707 1.080434 GGTCAGCCACGTCTGTCTC 60.080 63.158 4.38 0.00 35.63 3.36
888 1718 0.389391 TTCGCTAGCTATGGTCAGCC 59.611 55.000 13.93 0.00 42.84 4.85
889 1719 2.225068 TTTCGCTAGCTATGGTCAGC 57.775 50.000 13.93 0.00 42.12 4.26
891 1721 3.566742 TCGTATTTCGCTAGCTATGGTCA 59.433 43.478 13.93 0.00 39.67 4.02
984 1815 2.819595 ATGATGTGTCGGCACCGC 60.820 61.111 19.06 10.08 44.65 5.68
985 1816 2.463620 CCATGATGTGTCGGCACCG 61.464 63.158 19.06 1.73 44.65 4.94
1073 1922 1.107945 GAAACGGAGAGAGAGAGGGG 58.892 60.000 0.00 0.00 0.00 4.79
1119 1975 7.466746 AGTACAAATCAGTTAACCGGTAGTA 57.533 36.000 8.00 0.00 0.00 1.82
1405 2261 6.070194 AGCATTGTCTACTACCCTTGTACATT 60.070 38.462 0.00 0.00 0.00 2.71
1423 2279 3.260740 CCAAACAACAACACAGCATTGT 58.739 40.909 0.00 0.00 42.07 2.71
1429 2285 1.533756 CCGAGCCAAACAACAACACAG 60.534 52.381 0.00 0.00 0.00 3.66
1434 2290 2.045561 TCTTCCGAGCCAAACAACAA 57.954 45.000 0.00 0.00 0.00 2.83
1479 2335 5.983475 CTGACAAAGCAACAACAACAAAAA 58.017 33.333 0.00 0.00 0.00 1.94
1567 2430 2.580966 TTGTTACCCGTGGCAAAAAC 57.419 45.000 0.00 0.00 0.00 2.43
1570 2433 2.279935 AGATTGTTACCCGTGGCAAA 57.720 45.000 0.00 0.00 0.00 3.68
1623 2486 9.286170 GCCTCCTCCTTTTAATAGTAATTAAGG 57.714 37.037 6.96 6.96 38.48 2.69
1627 2490 9.409918 GAAAGCCTCCTCCTTTTAATAGTAATT 57.590 33.333 0.00 0.00 32.98 1.40
1628 2491 8.557450 TGAAAGCCTCCTCCTTTTAATAGTAAT 58.443 33.333 0.00 0.00 32.98 1.89
1629 2492 7.924541 TGAAAGCCTCCTCCTTTTAATAGTAA 58.075 34.615 0.00 0.00 32.98 2.24
1630 2493 7.504926 TGAAAGCCTCCTCCTTTTAATAGTA 57.495 36.000 0.00 0.00 32.98 1.82
1631 2494 6.388619 TGAAAGCCTCCTCCTTTTAATAGT 57.611 37.500 0.00 0.00 32.98 2.12
1632 2495 8.214364 ACTATGAAAGCCTCCTCCTTTTAATAG 58.786 37.037 0.00 0.00 36.52 1.73
1633 2496 8.102484 ACTATGAAAGCCTCCTCCTTTTAATA 57.898 34.615 0.00 0.00 32.98 0.98
1634 2497 6.974795 ACTATGAAAGCCTCCTCCTTTTAAT 58.025 36.000 0.00 0.00 32.98 1.40
1635 2498 6.388619 ACTATGAAAGCCTCCTCCTTTTAA 57.611 37.500 0.00 0.00 32.98 1.52
1636 2499 6.215636 AGAACTATGAAAGCCTCCTCCTTTTA 59.784 38.462 0.00 0.00 32.98 1.52
1637 2500 4.936685 ACTATGAAAGCCTCCTCCTTTT 57.063 40.909 0.00 0.00 32.98 2.27
1638 2501 4.538089 AGAACTATGAAAGCCTCCTCCTTT 59.462 41.667 0.00 0.00 35.36 3.11
1639 2502 4.107820 AGAACTATGAAAGCCTCCTCCTT 58.892 43.478 0.00 0.00 0.00 3.36
1640 2503 3.730269 AGAACTATGAAAGCCTCCTCCT 58.270 45.455 0.00 0.00 0.00 3.69
1641 2504 4.080863 TGAAGAACTATGAAAGCCTCCTCC 60.081 45.833 0.00 0.00 0.00 4.30
1642 2505 5.091261 TGAAGAACTATGAAAGCCTCCTC 57.909 43.478 0.00 0.00 0.00 3.71
1643 2506 5.707066 ATGAAGAACTATGAAAGCCTCCT 57.293 39.130 0.00 0.00 0.00 3.69
1644 2507 6.349300 TGTATGAAGAACTATGAAAGCCTCC 58.651 40.000 0.00 0.00 0.00 4.30
1645 2508 7.712639 TGATGTATGAAGAACTATGAAAGCCTC 59.287 37.037 0.00 0.00 0.00 4.70
1646 2509 7.568349 TGATGTATGAAGAACTATGAAAGCCT 58.432 34.615 0.00 0.00 0.00 4.58
1647 2510 7.792374 TGATGTATGAAGAACTATGAAAGCC 57.208 36.000 0.00 0.00 0.00 4.35
1648 2511 8.502387 GGATGATGTATGAAGAACTATGAAAGC 58.498 37.037 0.00 0.00 0.00 3.51
1649 2512 9.775854 AGGATGATGTATGAAGAACTATGAAAG 57.224 33.333 0.00 0.00 0.00 2.62
1684 2547 9.881529 GTCTTTATGGTTAACGTAAAATCAACA 57.118 29.630 12.82 0.00 39.40 3.33
1687 2550 9.491675 TCAGTCTTTATGGTTAACGTAAAATCA 57.508 29.630 12.82 0.00 39.40 2.57
1688 2551 9.750882 GTCAGTCTTTATGGTTAACGTAAAATC 57.249 33.333 12.82 9.84 39.40 2.17
1689 2552 8.437742 CGTCAGTCTTTATGGTTAACGTAAAAT 58.562 33.333 12.82 1.11 39.40 1.82
1690 2553 7.095691 CCGTCAGTCTTTATGGTTAACGTAAAA 60.096 37.037 12.82 6.87 39.40 1.52
1691 2554 6.365789 CCGTCAGTCTTTATGGTTAACGTAAA 59.634 38.462 11.80 11.80 38.02 2.01
1692 2555 5.863397 CCGTCAGTCTTTATGGTTAACGTAA 59.137 40.000 0.00 0.00 0.00 3.18
1693 2556 5.182950 TCCGTCAGTCTTTATGGTTAACGTA 59.817 40.000 0.00 0.00 0.00 3.57
1694 2557 4.022068 TCCGTCAGTCTTTATGGTTAACGT 60.022 41.667 0.00 0.00 0.00 3.99
1695 2558 4.487948 TCCGTCAGTCTTTATGGTTAACG 58.512 43.478 0.00 0.00 0.00 3.18
1696 2559 6.103997 TCATCCGTCAGTCTTTATGGTTAAC 58.896 40.000 0.00 0.00 0.00 2.01
1697 2560 6.153851 TCTCATCCGTCAGTCTTTATGGTTAA 59.846 38.462 0.00 0.00 0.00 2.01
1698 2561 5.655090 TCTCATCCGTCAGTCTTTATGGTTA 59.345 40.000 0.00 0.00 0.00 2.85
1699 2562 4.466370 TCTCATCCGTCAGTCTTTATGGTT 59.534 41.667 0.00 0.00 0.00 3.67
1700 2563 4.023980 TCTCATCCGTCAGTCTTTATGGT 58.976 43.478 0.00 0.00 0.00 3.55
1701 2564 4.655762 TCTCATCCGTCAGTCTTTATGG 57.344 45.455 0.00 0.00 0.00 2.74
1702 2565 8.648557 TTAAATCTCATCCGTCAGTCTTTATG 57.351 34.615 0.00 0.00 0.00 1.90
1703 2566 9.319143 CTTTAAATCTCATCCGTCAGTCTTTAT 57.681 33.333 0.00 0.00 0.00 1.40
1704 2567 8.528643 TCTTTAAATCTCATCCGTCAGTCTTTA 58.471 33.333 0.00 0.00 0.00 1.85
1705 2568 7.386851 TCTTTAAATCTCATCCGTCAGTCTTT 58.613 34.615 0.00 0.00 0.00 2.52
1706 2569 6.936279 TCTTTAAATCTCATCCGTCAGTCTT 58.064 36.000 0.00 0.00 0.00 3.01
1707 2570 6.531503 TCTTTAAATCTCATCCGTCAGTCT 57.468 37.500 0.00 0.00 0.00 3.24
1708 2571 8.353684 TCTATCTTTAAATCTCATCCGTCAGTC 58.646 37.037 0.00 0.00 0.00 3.51
1709 2572 8.239038 TCTATCTTTAAATCTCATCCGTCAGT 57.761 34.615 0.00 0.00 0.00 3.41
1755 2618 1.589803 AGGAACGCACGCTACTTTTT 58.410 45.000 0.00 0.00 0.00 1.94
1756 2619 2.443887 TAGGAACGCACGCTACTTTT 57.556 45.000 0.00 0.00 0.00 2.27
1757 2620 2.443887 TTAGGAACGCACGCTACTTT 57.556 45.000 0.00 0.00 0.00 2.66
1758 2621 2.667473 ATTAGGAACGCACGCTACTT 57.333 45.000 0.00 0.00 0.00 2.24
1759 2622 2.268298 CAATTAGGAACGCACGCTACT 58.732 47.619 0.00 0.00 0.00 2.57
1760 2623 1.326548 CCAATTAGGAACGCACGCTAC 59.673 52.381 0.00 0.00 41.22 3.58
1761 2624 1.205179 TCCAATTAGGAACGCACGCTA 59.795 47.619 0.00 0.00 45.65 4.26
1762 2625 0.036765 TCCAATTAGGAACGCACGCT 60.037 50.000 0.00 0.00 45.65 5.07
1763 2626 2.462503 TCCAATTAGGAACGCACGC 58.537 52.632 0.00 0.00 45.65 5.34
1780 2643 7.645058 TTTAGACAATTGAGGGGAATGATTC 57.355 36.000 13.59 0.00 0.00 2.52
1781 2644 8.434589 TTTTTAGACAATTGAGGGGAATGATT 57.565 30.769 13.59 0.00 0.00 2.57
1804 2667 0.624254 GGGAGGGGGACGATCTTTTT 59.376 55.000 0.00 0.00 0.00 1.94
1805 2668 0.549169 TGGGAGGGGGACGATCTTTT 60.549 55.000 0.00 0.00 0.00 2.27
1806 2669 0.549169 TTGGGAGGGGGACGATCTTT 60.549 55.000 0.00 0.00 0.00 2.52
1807 2670 0.549169 TTTGGGAGGGGGACGATCTT 60.549 55.000 0.00 0.00 0.00 2.40
1808 2671 0.549169 TTTTGGGAGGGGGACGATCT 60.549 55.000 0.00 0.00 0.00 2.75
1809 2672 0.330267 TTTTTGGGAGGGGGACGATC 59.670 55.000 0.00 0.00 0.00 3.69
1810 2673 2.481890 TTTTTGGGAGGGGGACGAT 58.518 52.632 0.00 0.00 0.00 3.73
1811 2674 4.005225 TTTTTGGGAGGGGGACGA 57.995 55.556 0.00 0.00 0.00 4.20
1828 2691 9.535878 GGAAAGATCACGATCTATTCTAGTTTT 57.464 33.333 9.90 0.00 46.75 2.43
1829 2692 8.919145 AGGAAAGATCACGATCTATTCTAGTTT 58.081 33.333 9.90 0.00 46.75 2.66
1830 2693 8.472007 AGGAAAGATCACGATCTATTCTAGTT 57.528 34.615 9.90 0.00 46.75 2.24
1831 2694 8.356657 CAAGGAAAGATCACGATCTATTCTAGT 58.643 37.037 9.90 4.25 46.75 2.57
1832 2695 8.356657 ACAAGGAAAGATCACGATCTATTCTAG 58.643 37.037 9.90 10.92 46.75 2.43
1833 2696 8.239038 ACAAGGAAAGATCACGATCTATTCTA 57.761 34.615 9.90 0.00 46.75 2.10
1834 2697 7.118496 ACAAGGAAAGATCACGATCTATTCT 57.882 36.000 9.90 5.36 46.75 2.40
1835 2698 6.422400 GGACAAGGAAAGATCACGATCTATTC 59.578 42.308 9.90 13.73 46.75 1.75
1836 2699 6.284459 GGACAAGGAAAGATCACGATCTATT 58.716 40.000 9.90 6.98 46.75 1.73
1837 2700 5.221541 GGGACAAGGAAAGATCACGATCTAT 60.222 44.000 9.90 0.00 46.75 1.98
1838 2701 4.099573 GGGACAAGGAAAGATCACGATCTA 59.900 45.833 9.90 0.00 46.75 1.98
1840 2703 3.198872 GGGACAAGGAAAGATCACGATC 58.801 50.000 0.00 0.00 38.09 3.69
1841 2704 2.092914 GGGGACAAGGAAAGATCACGAT 60.093 50.000 0.00 0.00 0.00 3.73
1842 2705 1.278127 GGGGACAAGGAAAGATCACGA 59.722 52.381 0.00 0.00 0.00 4.35
1843 2706 1.003118 TGGGGACAAGGAAAGATCACG 59.997 52.381 0.00 0.00 37.44 4.35
1844 2707 2.879103 TGGGGACAAGGAAAGATCAC 57.121 50.000 0.00 0.00 37.44 3.06
1855 2718 4.391467 ACGATAGCTAGGTTTGGGGACAA 61.391 47.826 0.00 0.00 46.38 3.18
1856 2719 1.760613 CGATAGCTAGGTTTGGGGACA 59.239 52.381 0.00 0.00 39.83 4.02
1857 2720 1.761198 ACGATAGCTAGGTTTGGGGAC 59.239 52.381 0.00 0.00 42.67 4.46
1858 2721 2.170012 ACGATAGCTAGGTTTGGGGA 57.830 50.000 0.00 0.00 42.67 4.81
1859 2722 2.484947 GGAACGATAGCTAGGTTTGGGG 60.485 54.545 12.62 0.00 42.67 4.96
1860 2723 2.434702 AGGAACGATAGCTAGGTTTGGG 59.565 50.000 12.62 0.00 42.67 4.12
1861 2724 3.821421 AGGAACGATAGCTAGGTTTGG 57.179 47.619 12.62 0.00 42.67 3.28
1862 2725 5.749109 CAGTTAGGAACGATAGCTAGGTTTG 59.251 44.000 12.62 4.57 42.67 2.93
1863 2726 5.163437 CCAGTTAGGAACGATAGCTAGGTTT 60.163 44.000 12.62 0.00 41.22 3.27
1864 2727 4.341520 CCAGTTAGGAACGATAGCTAGGTT 59.658 45.833 11.54 11.54 41.22 3.50
1865 2728 3.890147 CCAGTTAGGAACGATAGCTAGGT 59.110 47.826 0.00 0.00 41.22 3.08
1866 2729 4.142790 TCCAGTTAGGAACGATAGCTAGG 58.857 47.826 0.00 0.00 45.65 3.02
1879 2742 2.028020 GGGGCGATCTATTCCAGTTAGG 60.028 54.545 0.00 0.00 39.47 2.69
1880 2743 2.028020 GGGGGCGATCTATTCCAGTTAG 60.028 54.545 0.00 0.00 0.00 2.34
1881 2744 1.975680 GGGGGCGATCTATTCCAGTTA 59.024 52.381 0.00 0.00 0.00 2.24
1882 2745 0.765510 GGGGGCGATCTATTCCAGTT 59.234 55.000 0.00 0.00 0.00 3.16
1883 2746 2.453242 GGGGGCGATCTATTCCAGT 58.547 57.895 0.00 0.00 0.00 4.00
1936 2799 8.716646 TCGTGATTAGAATGCAAAGAATTCTA 57.283 30.769 8.75 3.80 41.49 2.10
1937 2800 7.615582 TCGTGATTAGAATGCAAAGAATTCT 57.384 32.000 0.88 0.88 44.56 2.40
1938 2801 8.578769 GTTTCGTGATTAGAATGCAAAGAATTC 58.421 33.333 0.00 0.00 34.80 2.17
1939 2802 8.081633 TGTTTCGTGATTAGAATGCAAAGAATT 58.918 29.630 0.00 0.00 0.00 2.17
1940 2803 7.592938 TGTTTCGTGATTAGAATGCAAAGAAT 58.407 30.769 0.00 0.00 0.00 2.40
1941 2804 6.964908 TGTTTCGTGATTAGAATGCAAAGAA 58.035 32.000 0.00 0.00 0.00 2.52
1942 2805 6.552859 TGTTTCGTGATTAGAATGCAAAGA 57.447 33.333 0.00 0.00 0.00 2.52
1943 2806 7.801547 ATTGTTTCGTGATTAGAATGCAAAG 57.198 32.000 0.00 0.00 31.75 2.77
1957 2820 9.498307 GGGTCAACTATTTTATATTGTTTCGTG 57.502 33.333 0.00 0.00 0.00 4.35
1958 2821 9.457436 AGGGTCAACTATTTTATATTGTTTCGT 57.543 29.630 0.00 0.00 0.00 3.85
1966 2829 9.914834 TGCTTGTAAGGGTCAACTATTTTATAT 57.085 29.630 0.00 0.00 0.00 0.86
1967 2830 9.169592 GTGCTTGTAAGGGTCAACTATTTTATA 57.830 33.333 0.00 0.00 0.00 0.98
1968 2831 7.668052 TGTGCTTGTAAGGGTCAACTATTTTAT 59.332 33.333 0.00 0.00 0.00 1.40
1969 2832 6.999272 TGTGCTTGTAAGGGTCAACTATTTTA 59.001 34.615 0.00 0.00 0.00 1.52
1970 2833 5.830991 TGTGCTTGTAAGGGTCAACTATTTT 59.169 36.000 0.00 0.00 0.00 1.82
1971 2834 5.240844 GTGTGCTTGTAAGGGTCAACTATTT 59.759 40.000 0.00 0.00 0.00 1.40
1972 2835 4.760204 GTGTGCTTGTAAGGGTCAACTATT 59.240 41.667 0.00 0.00 0.00 1.73
1973 2836 4.041691 AGTGTGCTTGTAAGGGTCAACTAT 59.958 41.667 0.00 0.00 0.00 2.12
1974 2837 3.389983 AGTGTGCTTGTAAGGGTCAACTA 59.610 43.478 0.00 0.00 0.00 2.24
1975 2838 2.172717 AGTGTGCTTGTAAGGGTCAACT 59.827 45.455 0.00 0.00 0.00 3.16
1976 2839 2.290641 CAGTGTGCTTGTAAGGGTCAAC 59.709 50.000 0.00 0.00 0.00 3.18
1977 2840 2.171659 TCAGTGTGCTTGTAAGGGTCAA 59.828 45.455 0.00 0.00 0.00 3.18
1978 2841 1.765904 TCAGTGTGCTTGTAAGGGTCA 59.234 47.619 0.00 0.00 0.00 4.02
1979 2842 2.543777 TCAGTGTGCTTGTAAGGGTC 57.456 50.000 0.00 0.00 0.00 4.46
1980 2843 2.949644 GTTTCAGTGTGCTTGTAAGGGT 59.050 45.455 0.00 0.00 0.00 4.34
1981 2844 3.214328 AGTTTCAGTGTGCTTGTAAGGG 58.786 45.455 0.00 0.00 0.00 3.95
1982 2845 3.876914 TGAGTTTCAGTGTGCTTGTAAGG 59.123 43.478 0.00 0.00 0.00 2.69
1983 2846 5.484173 TTGAGTTTCAGTGTGCTTGTAAG 57.516 39.130 0.00 0.00 0.00 2.34
1984 2847 5.182190 TGTTTGAGTTTCAGTGTGCTTGTAA 59.818 36.000 0.00 0.00 0.00 2.41
1985 2848 4.697828 TGTTTGAGTTTCAGTGTGCTTGTA 59.302 37.500 0.00 0.00 0.00 2.41
1986 2849 3.505680 TGTTTGAGTTTCAGTGTGCTTGT 59.494 39.130 0.00 0.00 0.00 3.16
1987 2850 3.853671 GTGTTTGAGTTTCAGTGTGCTTG 59.146 43.478 0.00 0.00 0.00 4.01
1988 2851 3.505680 TGTGTTTGAGTTTCAGTGTGCTT 59.494 39.130 0.00 0.00 0.00 3.91
1989 2852 3.081061 TGTGTTTGAGTTTCAGTGTGCT 58.919 40.909 0.00 0.00 0.00 4.40
1990 2853 3.485947 TGTGTTTGAGTTTCAGTGTGC 57.514 42.857 0.00 0.00 0.00 4.57
1991 2854 4.858692 CCTTTGTGTTTGAGTTTCAGTGTG 59.141 41.667 0.00 0.00 0.00 3.82
1992 2855 4.082245 CCCTTTGTGTTTGAGTTTCAGTGT 60.082 41.667 0.00 0.00 0.00 3.55
1993 2856 4.423732 CCCTTTGTGTTTGAGTTTCAGTG 58.576 43.478 0.00 0.00 0.00 3.66
1994 2857 3.447229 CCCCTTTGTGTTTGAGTTTCAGT 59.553 43.478 0.00 0.00 0.00 3.41
1995 2858 3.447229 ACCCCTTTGTGTTTGAGTTTCAG 59.553 43.478 0.00 0.00 0.00 3.02
1996 2859 3.436243 ACCCCTTTGTGTTTGAGTTTCA 58.564 40.909 0.00 0.00 0.00 2.69
1997 2860 4.180817 CAACCCCTTTGTGTTTGAGTTTC 58.819 43.478 0.00 0.00 0.00 2.78
1998 2861 4.200838 CAACCCCTTTGTGTTTGAGTTT 57.799 40.909 0.00 0.00 0.00 2.66
1999 2862 3.885724 CAACCCCTTTGTGTTTGAGTT 57.114 42.857 0.00 0.00 0.00 3.01
2009 2872 2.896685 TGCTATCCAAACAACCCCTTTG 59.103 45.455 0.00 0.00 41.49 2.77
2010 2873 3.252554 TGCTATCCAAACAACCCCTTT 57.747 42.857 0.00 0.00 0.00 3.11
2051 2914 7.694388 AAAATCAGCTAAAAACTCGTTTTCC 57.306 32.000 8.09 1.68 41.45 3.13
2057 2920 7.851822 TTGCTAAAAATCAGCTAAAAACTCG 57.148 32.000 0.00 0.00 39.83 4.18
2136 2999 3.823873 ACTGACAAACACACTTTCCAACA 59.176 39.130 0.00 0.00 0.00 3.33
2143 3006 6.238374 CGAATAAGGAACTGACAAACACACTT 60.238 38.462 0.00 0.00 40.86 3.16
2190 3053 2.034878 AGAAGCTCACCGCATGATAGA 58.965 47.619 0.00 0.00 42.61 1.98
2195 3058 4.346129 GAAAATAAGAAGCTCACCGCATG 58.654 43.478 0.00 0.00 42.61 4.06
2196 3059 3.378427 GGAAAATAAGAAGCTCACCGCAT 59.622 43.478 0.00 0.00 42.61 4.73
2348 3395 4.204891 GCGTGTACATGCGTCGGC 62.205 66.667 23.44 3.75 40.52 5.54


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

AutoCloner maintained by Alex Coulton.