Multiple sequence alignment - TraesCS5A01G224100

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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 TraesCS5A01G224100 chr5A 100.000 2222 0 0 1 2222 439557245 439555024 0.000000e+00 4104
1 TraesCS5A01G224100 chr5A 96.129 310 10 2 1456 1765 367121006 367120699 2.550000e-139 505
2 TraesCS5A01G224100 chr5B 89.818 1483 97 28 1 1446 397839147 397837682 0.000000e+00 1853
3 TraesCS5A01G224100 chr5B 80.792 505 16 15 1760 2207 397837674 397837194 9.900000e-84 320
4 TraesCS5A01G224100 chr5D 86.471 1057 82 24 410 1446 338666210 338665195 0.000000e+00 1103
5 TraesCS5A01G224100 chr5D 79.859 427 40 19 4 416 338666683 338666289 1.010000e-68 270
6 TraesCS5A01G224100 chr5D 84.581 227 6 9 1760 1962 338665187 338664966 4.840000e-47 198
7 TraesCS5A01G224100 chr6A 97.039 304 8 1 1459 1762 615490703 615491005 5.470000e-141 510
8 TraesCS5A01G224100 chr6A 96.721 305 10 0 1459 1763 535537904 535538208 1.970000e-140 508
9 TraesCS5A01G224100 chr6A 96.104 308 9 3 1456 1761 106002342 106002648 1.180000e-137 499
10 TraesCS5A01G224100 chr6A 79.878 164 33 0 1060 1223 587563970 587564133 1.080000e-23 121
11 TraesCS5A01G224100 chr4A 96.711 304 10 0 1458 1761 210983142 210983445 7.080000e-140 507
12 TraesCS5A01G224100 chr2A 96.721 305 9 1 1459 1763 61341698 61341395 7.080000e-140 507
13 TraesCS5A01G224100 chr2A 96.117 309 11 1 1456 1763 706682813 706682505 9.160000e-139 503
14 TraesCS5A01G224100 chr3A 96.405 306 11 0 1458 1763 6725619 6725924 2.550000e-139 505
15 TraesCS5A01G224100 chr7A 96.382 304 11 0 1458 1761 539609948 539609645 3.290000e-138 501
16 TraesCS5A01G224100 chr6B 79.394 165 34 0 1060 1224 663800525 663800689 1.390000e-22 117
17 TraesCS5A01G224100 chr6D 83.333 120 20 0 1060 1179 438460921 438461040 6.490000e-21 111


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 TraesCS5A01G224100 chr5A 439555024 439557245 2221 True 4104.000000 4104 100.000 1 2222 1 chr5A.!!$R2 2221
1 TraesCS5A01G224100 chr5B 397837194 397839147 1953 True 1086.500000 1853 85.305 1 2207 2 chr5B.!!$R1 2206
2 TraesCS5A01G224100 chr5D 338664966 338666683 1717 True 523.666667 1103 83.637 4 1962 3 chr5D.!!$R1 1958

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
554 702 1.077716 GGTGGTCCCACTATGCACC 60.078 63.158 15.67 0.0 45.52 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1463 1632 0.03582 AACAACGTGCGGGGTATCAT 60.036 50.0 0.0 0.0 0.0 2.45 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
24 25 1.299541 GAGGGTGATGCACAATACCG 58.700 55.000 0.00 0.00 35.86 4.02
90 99 5.988561 CCTAGACATTTGCTGTAGATCCTTC 59.011 44.000 0.00 0.00 38.54 3.46
99 109 6.748333 TGCTGTAGATCCTTCAAATTTGAG 57.252 37.500 19.64 13.84 38.61 3.02
104 114 6.830324 TGTAGATCCTTCAAATTTGAGGATGG 59.170 38.462 33.49 26.09 41.24 3.51
166 176 6.716934 TTTACAAAAGGGTTGTCTATGCAA 57.283 33.333 0.00 0.00 34.11 4.08
167 177 6.716934 TTACAAAAGGGTTGTCTATGCAAA 57.283 33.333 0.00 0.00 34.11 3.68
168 178 5.606348 ACAAAAGGGTTGTCTATGCAAAA 57.394 34.783 0.00 0.00 0.00 2.44
169 179 6.173427 ACAAAAGGGTTGTCTATGCAAAAT 57.827 33.333 0.00 0.00 0.00 1.82
170 180 6.591001 ACAAAAGGGTTGTCTATGCAAAATT 58.409 32.000 0.00 0.00 0.00 1.82
171 181 6.482973 ACAAAAGGGTTGTCTATGCAAAATTG 59.517 34.615 0.00 0.00 0.00 2.32
213 223 5.928264 GGATCTGTTGTTTCCCTTGATTTTG 59.072 40.000 0.00 0.00 0.00 2.44
214 224 6.239289 GGATCTGTTGTTTCCCTTGATTTTGA 60.239 38.462 0.00 0.00 0.00 2.69
219 229 5.287674 TGTTTCCCTTGATTTTGATTGCA 57.712 34.783 0.00 0.00 0.00 4.08
221 231 6.118170 TGTTTCCCTTGATTTTGATTGCAAA 58.882 32.000 1.71 0.00 41.97 3.68
223 233 7.041235 TGTTTCCCTTGATTTTGATTGCAAATC 60.041 33.333 1.71 1.77 43.07 2.17
225 235 6.713276 TCCCTTGATTTTGATTGCAAATCAT 58.287 32.000 1.71 0.00 43.07 2.45
226 236 6.596106 TCCCTTGATTTTGATTGCAAATCATG 59.404 34.615 1.71 9.71 43.07 3.07
228 238 6.596106 CCTTGATTTTGATTGCAAATCATGGA 59.404 34.615 24.97 8.21 43.07 3.41
250 260 5.046663 GGAATTACAAAAGGCTCCATTTGGA 60.047 40.000 17.53 9.00 43.08 3.53
272 292 5.336451 GGATTGGTTTGTTACCTCAACATCC 60.336 44.000 0.00 0.00 46.38 3.51
303 330 4.081031 TGTTGACAACACTGTTAGGGTACA 60.081 41.667 17.02 0.00 36.25 2.90
379 443 4.142816 CCTGCAACTATTGTAGCTGTGTTC 60.143 45.833 0.00 0.00 41.35 3.18
429 577 7.210174 CACAAGGAGCTAGTATGTTGCTATTA 58.790 38.462 0.00 0.00 37.16 0.98
498 646 2.698803 TGTGCTGGCATACACTACTTG 58.301 47.619 18.15 0.00 37.68 3.16
527 675 4.855388 CGAATTGGCTGAATTCTGAACTTG 59.145 41.667 15.79 0.00 45.50 3.16
554 702 1.077716 GGTGGTCCCACTATGCACC 60.078 63.158 15.67 0.00 45.52 5.01
571 719 4.707105 TGCACCACATAATCTGATACTGG 58.293 43.478 0.00 0.00 0.00 4.00
808 959 3.826524 TGAAACAAGTAATCCCAGCACA 58.173 40.909 0.00 0.00 0.00 4.57
862 1013 5.011329 TCCAGGTAACGAAAACTGTGTATCT 59.989 40.000 6.17 0.00 46.39 1.98
882 1033 9.817809 TGTATCTTCTAAAAATACTAGCAGGTG 57.182 33.333 0.00 0.00 0.00 4.00
936 1087 3.996150 ACAATCAAGCTGTTGGTCTTG 57.004 42.857 10.39 0.00 40.62 3.02
958 1109 1.482593 TGCCCCGTTTTGTTTTGACAT 59.517 42.857 0.00 0.00 0.00 3.06
987 1138 6.277605 CACTGATGTGGTACCATTACGATTA 58.722 40.000 19.72 2.07 40.33 1.75
1046 1197 3.058160 CGCCCCAACTGCAGAAGG 61.058 66.667 23.35 20.28 0.00 3.46
1158 1309 2.507944 GTGGAGCATGGCGAGGAT 59.492 61.111 0.00 0.00 0.00 3.24
1236 1387 3.423571 CGTCTGATACGTTTAAGAGCGT 58.576 45.455 0.00 6.93 46.72 5.07
1238 1389 3.477802 GTCTGATACGTTTAAGAGCGTCG 59.522 47.826 0.00 0.00 41.91 5.12
1240 1391 2.179589 GATACGTTTAAGAGCGTCGCA 58.820 47.619 21.09 0.00 41.91 5.10
1241 1392 1.330306 TACGTTTAAGAGCGTCGCAC 58.670 50.000 21.09 13.88 41.91 5.34
1306 1475 4.740822 CCAGTTTGCGGGGAGGGG 62.741 72.222 0.00 0.00 0.00 4.79
1426 1595 6.603201 TGTTTGGAGACATTCTTGTTTCTTCT 59.397 34.615 0.00 0.00 42.32 2.85
1431 1600 6.484977 GGAGACATTCTTGTTTCTTCTTGTCT 59.515 38.462 2.17 2.17 43.70 3.41
1432 1601 7.256756 AGACATTCTTGTTTCTTCTTGTCTG 57.743 36.000 0.00 0.00 40.59 3.51
1440 1609 2.260844 TCTTCTTGTCTGCTGGTTGG 57.739 50.000 0.00 0.00 0.00 3.77
1441 1610 1.202806 TCTTCTTGTCTGCTGGTTGGG 60.203 52.381 0.00 0.00 0.00 4.12
1446 1615 2.853542 TCTGCTGGTTGGGCTGGA 60.854 61.111 0.00 0.00 0.00 3.86
1447 1616 2.233566 TCTGCTGGTTGGGCTGGAT 61.234 57.895 0.00 0.00 0.00 3.41
1448 1617 1.304713 CTGCTGGTTGGGCTGGATT 60.305 57.895 0.00 0.00 0.00 3.01
1449 1618 0.901580 CTGCTGGTTGGGCTGGATTT 60.902 55.000 0.00 0.00 0.00 2.17
1451 1620 0.686789 GCTGGTTGGGCTGGATTTTT 59.313 50.000 0.00 0.00 0.00 1.94
1452 1621 1.338105 GCTGGTTGGGCTGGATTTTTC 60.338 52.381 0.00 0.00 0.00 2.29
1453 1622 1.969923 CTGGTTGGGCTGGATTTTTCA 59.030 47.619 0.00 0.00 0.00 2.69
1454 1623 1.691434 TGGTTGGGCTGGATTTTTCAC 59.309 47.619 0.00 0.00 0.00 3.18
1455 1624 1.970640 GGTTGGGCTGGATTTTTCACT 59.029 47.619 0.00 0.00 0.00 3.41
1456 1625 2.289010 GGTTGGGCTGGATTTTTCACTG 60.289 50.000 0.00 0.00 0.00 3.66
1457 1626 2.627699 GTTGGGCTGGATTTTTCACTGA 59.372 45.455 0.00 0.00 0.00 3.41
1458 1627 2.956132 TGGGCTGGATTTTTCACTGAA 58.044 42.857 0.00 0.00 0.00 3.02
1459 1628 2.627699 TGGGCTGGATTTTTCACTGAAC 59.372 45.455 0.00 0.00 0.00 3.18
1460 1629 2.893489 GGGCTGGATTTTTCACTGAACT 59.107 45.455 0.00 0.00 0.00 3.01
1461 1630 4.079253 GGGCTGGATTTTTCACTGAACTA 58.921 43.478 0.00 0.00 0.00 2.24
1462 1631 4.156739 GGGCTGGATTTTTCACTGAACTAG 59.843 45.833 0.00 0.00 0.00 2.57
1463 1632 5.003804 GGCTGGATTTTTCACTGAACTAGA 58.996 41.667 0.00 0.00 0.00 2.43
1464 1633 5.649831 GGCTGGATTTTTCACTGAACTAGAT 59.350 40.000 0.00 0.00 0.00 1.98
1465 1634 6.404074 GGCTGGATTTTTCACTGAACTAGATG 60.404 42.308 0.00 0.00 0.00 2.90
1466 1635 6.372659 GCTGGATTTTTCACTGAACTAGATGA 59.627 38.462 0.00 0.00 0.00 2.92
1467 1636 7.066766 GCTGGATTTTTCACTGAACTAGATGAT 59.933 37.037 0.00 0.00 0.00 2.45
1468 1637 9.605275 CTGGATTTTTCACTGAACTAGATGATA 57.395 33.333 0.00 0.00 0.00 2.15
1469 1638 9.383519 TGGATTTTTCACTGAACTAGATGATAC 57.616 33.333 0.00 0.00 0.00 2.24
1470 1639 8.831550 GGATTTTTCACTGAACTAGATGATACC 58.168 37.037 0.00 0.00 0.00 2.73
1471 1640 8.738645 ATTTTTCACTGAACTAGATGATACCC 57.261 34.615 0.00 0.00 0.00 3.69
1472 1641 5.871396 TTCACTGAACTAGATGATACCCC 57.129 43.478 0.00 0.00 0.00 4.95
1473 1642 3.889538 TCACTGAACTAGATGATACCCCG 59.110 47.826 0.00 0.00 0.00 5.73
1474 1643 2.628657 ACTGAACTAGATGATACCCCGC 59.371 50.000 0.00 0.00 0.00 6.13
1475 1644 2.628178 CTGAACTAGATGATACCCCGCA 59.372 50.000 0.00 0.00 0.00 5.69
1476 1645 2.364324 TGAACTAGATGATACCCCGCAC 59.636 50.000 0.00 0.00 0.00 5.34
1477 1646 0.959553 ACTAGATGATACCCCGCACG 59.040 55.000 0.00 0.00 0.00 5.34
1478 1647 0.959553 CTAGATGATACCCCGCACGT 59.040 55.000 0.00 0.00 0.00 4.49
1479 1648 1.340248 CTAGATGATACCCCGCACGTT 59.660 52.381 0.00 0.00 0.00 3.99
1480 1649 0.179084 AGATGATACCCCGCACGTTG 60.179 55.000 0.00 0.00 0.00 4.10
1481 1650 0.461339 GATGATACCCCGCACGTTGT 60.461 55.000 0.00 0.00 0.00 3.32
1482 1651 0.035820 ATGATACCCCGCACGTTGTT 60.036 50.000 0.00 0.00 0.00 2.83
1483 1652 0.951525 TGATACCCCGCACGTTGTTG 60.952 55.000 0.00 0.00 0.00 3.33
1484 1653 2.248274 GATACCCCGCACGTTGTTGC 62.248 60.000 0.00 0.00 39.28 4.17
1490 1659 3.595961 GCACGTTGTTGCGGAAAC 58.404 55.556 0.00 0.00 39.41 2.78
1498 1667 2.299993 TGTTGCGGAAACATTTGCAA 57.700 40.000 0.00 0.00 43.96 4.08
1502 1671 3.650070 TGCGGAAACATTTGCAATACA 57.350 38.095 0.00 0.00 33.80 2.29
1503 1672 4.185467 TGCGGAAACATTTGCAATACAT 57.815 36.364 0.00 0.00 33.80 2.29
1504 1673 4.564041 TGCGGAAACATTTGCAATACATT 58.436 34.783 0.00 0.00 33.80 2.71
1505 1674 4.993584 TGCGGAAACATTTGCAATACATTT 59.006 33.333 0.00 0.00 33.80 2.32
1506 1675 5.119898 TGCGGAAACATTTGCAATACATTTC 59.880 36.000 0.00 8.47 33.80 2.17
1507 1676 5.720971 GCGGAAACATTTGCAATACATTTCG 60.721 40.000 0.00 5.96 28.45 3.46
1508 1677 5.570973 CGGAAACATTTGCAATACATTTCGA 59.429 36.000 0.00 0.00 28.45 3.71
1509 1678 6.253298 CGGAAACATTTGCAATACATTTCGAT 59.747 34.615 0.00 0.00 28.45 3.59
1510 1679 7.393327 GGAAACATTTGCAATACATTTCGATG 58.607 34.615 0.00 0.00 28.45 3.84
1511 1680 7.275341 GGAAACATTTGCAATACATTTCGATGA 59.725 33.333 0.00 0.00 28.45 2.92
1512 1681 8.706492 AAACATTTGCAATACATTTCGATGAT 57.294 26.923 0.00 0.00 0.00 2.45
1513 1682 9.800433 AAACATTTGCAATACATTTCGATGATA 57.200 25.926 0.00 0.00 0.00 2.15
1514 1683 9.970395 AACATTTGCAATACATTTCGATGATAT 57.030 25.926 0.00 0.00 0.00 1.63
1515 1684 9.401873 ACATTTGCAATACATTTCGATGATATG 57.598 29.630 0.00 0.00 0.00 1.78
1516 1685 9.401873 CATTTGCAATACATTTCGATGATATGT 57.598 29.630 0.00 7.77 37.77 2.29
1517 1686 8.785468 TTTGCAATACATTTCGATGATATGTG 57.215 30.769 0.00 0.00 35.63 3.21
1518 1687 7.727331 TGCAATACATTTCGATGATATGTGA 57.273 32.000 11.51 0.21 35.63 3.58
1519 1688 8.326680 TGCAATACATTTCGATGATATGTGAT 57.673 30.769 11.51 0.68 35.63 3.06
1520 1689 8.785946 TGCAATACATTTCGATGATATGTGATT 58.214 29.630 11.51 6.35 35.63 2.57
1521 1690 9.616634 GCAATACATTTCGATGATATGTGATTT 57.383 29.630 11.51 2.90 35.63 2.17
1527 1696 9.983804 CATTTCGATGATATGTGATTTCTATGG 57.016 33.333 0.00 0.00 0.00 2.74
1528 1697 9.948964 ATTTCGATGATATGTGATTTCTATGGA 57.051 29.630 0.00 0.00 0.00 3.41
1529 1698 9.777297 TTTCGATGATATGTGATTTCTATGGAA 57.223 29.630 0.00 0.00 0.00 3.53
1530 1699 8.763049 TCGATGATATGTGATTTCTATGGAAC 57.237 34.615 0.00 0.00 0.00 3.62
1531 1700 7.542130 TCGATGATATGTGATTTCTATGGAACG 59.458 37.037 0.00 0.00 0.00 3.95
1532 1701 7.329471 CGATGATATGTGATTTCTATGGAACGT 59.671 37.037 0.00 0.00 0.00 3.99
1533 1702 7.713764 TGATATGTGATTTCTATGGAACGTG 57.286 36.000 0.00 0.00 0.00 4.49
1534 1703 7.496747 TGATATGTGATTTCTATGGAACGTGA 58.503 34.615 0.00 0.00 0.00 4.35
1535 1704 7.984617 TGATATGTGATTTCTATGGAACGTGAA 59.015 33.333 0.00 0.00 0.00 3.18
1536 1705 8.908786 ATATGTGATTTCTATGGAACGTGAAT 57.091 30.769 0.00 0.00 0.00 2.57
1537 1706 9.996554 ATATGTGATTTCTATGGAACGTGAATA 57.003 29.630 0.00 0.00 0.00 1.75
1538 1707 7.770801 TGTGATTTCTATGGAACGTGAATAG 57.229 36.000 0.00 0.00 0.00 1.73
1539 1708 7.327975 TGTGATTTCTATGGAACGTGAATAGT 58.672 34.615 10.50 0.00 0.00 2.12
1540 1709 7.277760 TGTGATTTCTATGGAACGTGAATAGTG 59.722 37.037 10.50 0.00 0.00 2.74
1541 1710 7.491372 GTGATTTCTATGGAACGTGAATAGTGA 59.509 37.037 10.50 4.03 0.00 3.41
1542 1711 8.204160 TGATTTCTATGGAACGTGAATAGTGAT 58.796 33.333 10.50 7.25 0.00 3.06
1543 1712 9.692749 GATTTCTATGGAACGTGAATAGTGATA 57.307 33.333 10.50 0.00 0.00 2.15
1544 1713 8.867112 TTTCTATGGAACGTGAATAGTGATAC 57.133 34.615 10.50 0.00 0.00 2.24
1545 1714 7.818997 TCTATGGAACGTGAATAGTGATACT 57.181 36.000 10.50 0.00 0.00 2.12
1546 1715 8.913487 TCTATGGAACGTGAATAGTGATACTA 57.087 34.615 10.50 0.00 34.82 1.82
1547 1716 9.516546 TCTATGGAACGTGAATAGTGATACTAT 57.483 33.333 10.50 0.00 42.86 2.12
1548 1717 9.561270 CTATGGAACGTGAATAGTGATACTATG 57.439 37.037 2.51 0.00 40.32 2.23
1549 1718 7.576861 TGGAACGTGAATAGTGATACTATGA 57.423 36.000 2.51 0.00 40.32 2.15
1550 1719 8.002984 TGGAACGTGAATAGTGATACTATGAA 57.997 34.615 2.51 0.00 40.32 2.57
1551 1720 8.471609 TGGAACGTGAATAGTGATACTATGAAA 58.528 33.333 2.51 0.00 40.32 2.69
1552 1721 9.309516 GGAACGTGAATAGTGATACTATGAAAA 57.690 33.333 2.51 0.00 40.32 2.29
1554 1723 9.871238 AACGTGAATAGTGATACTATGAAAACT 57.129 29.630 2.51 0.00 40.32 2.66
1569 1738 9.995003 ACTATGAAAACTAAAATTGCAAATCCA 57.005 25.926 1.71 0.00 0.00 3.41
1574 1743 9.706846 GAAAACTAAAATTGCAAATCCATATGC 57.293 29.630 1.71 0.00 42.86 3.14
1575 1744 9.452287 AAAACTAAAATTGCAAATCCATATGCT 57.548 25.926 1.71 0.00 42.97 3.79
1576 1745 9.452287 AAACTAAAATTGCAAATCCATATGCTT 57.548 25.926 1.71 0.00 42.97 3.91
1577 1746 9.452287 AACTAAAATTGCAAATCCATATGCTTT 57.548 25.926 1.71 0.00 42.97 3.51
1582 1751 8.967664 AATTGCAAATCCATATGCTTTATTGT 57.032 26.923 1.71 0.00 42.97 2.71
1583 1752 7.773864 TTGCAAATCCATATGCTTTATTGTG 57.226 32.000 0.00 0.00 42.97 3.33
1584 1753 6.876155 TGCAAATCCATATGCTTTATTGTGT 58.124 32.000 0.00 0.00 42.97 3.72
1585 1754 7.329499 TGCAAATCCATATGCTTTATTGTGTT 58.671 30.769 0.00 0.00 42.97 3.32
1586 1755 7.823310 TGCAAATCCATATGCTTTATTGTGTTT 59.177 29.630 0.00 0.00 42.97 2.83
1587 1756 8.117988 GCAAATCCATATGCTTTATTGTGTTTG 58.882 33.333 0.00 0.00 39.46 2.93
1588 1757 9.368674 CAAATCCATATGCTTTATTGTGTTTGA 57.631 29.630 0.00 0.00 0.00 2.69
1632 1801 8.978874 TCTAATATATGTTTGCATGTTGAGGT 57.021 30.769 0.00 0.00 36.58 3.85
1633 1802 8.839343 TCTAATATATGTTTGCATGTTGAGGTG 58.161 33.333 0.00 0.00 36.58 4.00
1634 1803 4.724074 ATATGTTTGCATGTTGAGGTGG 57.276 40.909 0.00 0.00 36.58 4.61
1635 1804 2.064434 TGTTTGCATGTTGAGGTGGA 57.936 45.000 0.00 0.00 0.00 4.02
1636 1805 2.596346 TGTTTGCATGTTGAGGTGGAT 58.404 42.857 0.00 0.00 0.00 3.41
1637 1806 3.760738 TGTTTGCATGTTGAGGTGGATA 58.239 40.909 0.00 0.00 0.00 2.59
1638 1807 4.343231 TGTTTGCATGTTGAGGTGGATAT 58.657 39.130 0.00 0.00 0.00 1.63
1639 1808 4.771577 TGTTTGCATGTTGAGGTGGATATT 59.228 37.500 0.00 0.00 0.00 1.28
1640 1809 5.245751 TGTTTGCATGTTGAGGTGGATATTT 59.754 36.000 0.00 0.00 0.00 1.40
1641 1810 5.581126 TTGCATGTTGAGGTGGATATTTC 57.419 39.130 0.00 0.00 0.00 2.17
1642 1811 3.953612 TGCATGTTGAGGTGGATATTTCC 59.046 43.478 0.00 0.00 42.94 3.13
1656 1825 4.927425 GGATATTTCCATGTGCATGAATGC 59.073 41.667 13.21 8.36 46.59 3.56
1669 1838 4.036567 CATGAATGCATGTTGTGGTAGG 57.963 45.455 5.39 0.00 45.41 3.18
1670 1839 1.818060 TGAATGCATGTTGTGGTAGGC 59.182 47.619 0.00 0.00 0.00 3.93
1671 1840 1.134946 GAATGCATGTTGTGGTAGGCC 59.865 52.381 0.00 0.00 0.00 5.19
1672 1841 0.332632 ATGCATGTTGTGGTAGGCCT 59.667 50.000 11.78 11.78 35.27 5.19
1673 1842 0.112218 TGCATGTTGTGGTAGGCCTT 59.888 50.000 12.58 0.00 35.27 4.35
1674 1843 1.256812 GCATGTTGTGGTAGGCCTTT 58.743 50.000 12.58 0.00 35.27 3.11
1675 1844 1.618343 GCATGTTGTGGTAGGCCTTTT 59.382 47.619 12.58 0.00 35.27 2.27
1676 1845 2.610232 GCATGTTGTGGTAGGCCTTTTG 60.610 50.000 12.58 0.00 35.27 2.44
1677 1846 1.036707 TGTTGTGGTAGGCCTTTTGC 58.963 50.000 12.58 0.00 40.16 3.68
1687 1856 3.236604 GCCTTTTGCCATGCATGTT 57.763 47.368 24.58 0.00 38.76 2.71
1688 1857 0.800012 GCCTTTTGCCATGCATGTTG 59.200 50.000 24.58 11.90 38.76 3.33
1689 1858 0.800012 CCTTTTGCCATGCATGTTGC 59.200 50.000 24.58 20.96 45.29 4.17
1690 1859 1.609580 CCTTTTGCCATGCATGTTGCT 60.610 47.619 24.58 0.00 45.31 3.91
1691 1860 2.147958 CTTTTGCCATGCATGTTGCTT 58.852 42.857 24.58 0.00 45.31 3.91
1692 1861 1.514003 TTTGCCATGCATGTTGCTTG 58.486 45.000 24.58 9.73 45.31 4.01
1700 1869 3.224884 TGCATGTTGCTTGATGATGTG 57.775 42.857 0.75 0.00 45.31 3.21
1701 1870 2.820787 TGCATGTTGCTTGATGATGTGA 59.179 40.909 0.75 0.00 45.31 3.58
1702 1871 3.176708 GCATGTTGCTTGATGATGTGAC 58.823 45.455 0.00 0.00 40.96 3.67
1703 1872 3.366577 GCATGTTGCTTGATGATGTGACA 60.367 43.478 0.00 0.00 40.96 3.58
1704 1873 4.676986 GCATGTTGCTTGATGATGTGACAT 60.677 41.667 0.00 0.00 40.96 3.06
1705 1874 4.428615 TGTTGCTTGATGATGTGACATG 57.571 40.909 1.23 0.00 0.00 3.21
1706 1875 3.176708 GTTGCTTGATGATGTGACATGC 58.823 45.455 1.23 0.00 35.99 4.06
1707 1876 2.718563 TGCTTGATGATGTGACATGCT 58.281 42.857 1.23 0.00 36.27 3.79
1708 1877 3.086282 TGCTTGATGATGTGACATGCTT 58.914 40.909 1.23 0.00 36.27 3.91
1709 1878 4.263435 TGCTTGATGATGTGACATGCTTA 58.737 39.130 1.23 0.00 36.27 3.09
1710 1879 4.095334 TGCTTGATGATGTGACATGCTTAC 59.905 41.667 1.23 0.00 36.27 2.34
1711 1880 4.095334 GCTTGATGATGTGACATGCTTACA 59.905 41.667 1.23 0.00 33.83 2.41
1712 1881 5.220989 GCTTGATGATGTGACATGCTTACAT 60.221 40.000 1.23 0.00 37.72 2.29
1728 1897 8.743085 ATGCTTACATGTTGAGAGAAATATGT 57.257 30.769 2.30 4.98 42.39 2.29
1729 1898 8.565896 TGCTTACATGTTGAGAGAAATATGTT 57.434 30.769 2.30 0.00 40.81 2.71
1730 1899 9.665719 TGCTTACATGTTGAGAGAAATATGTTA 57.334 29.630 2.30 0.00 40.81 2.41
1734 1903 8.498054 ACATGTTGAGAGAAATATGTTAGTGG 57.502 34.615 0.00 0.00 38.32 4.00
1735 1904 7.554118 ACATGTTGAGAGAAATATGTTAGTGGG 59.446 37.037 0.00 0.00 38.32 4.61
1736 1905 6.414732 TGTTGAGAGAAATATGTTAGTGGGG 58.585 40.000 0.00 0.00 0.00 4.96
1737 1906 5.630415 TGAGAGAAATATGTTAGTGGGGG 57.370 43.478 0.00 0.00 0.00 5.40
1738 1907 4.141482 TGAGAGAAATATGTTAGTGGGGGC 60.141 45.833 0.00 0.00 0.00 5.80
1739 1908 4.047883 AGAGAAATATGTTAGTGGGGGCT 58.952 43.478 0.00 0.00 0.00 5.19
1740 1909 5.224441 AGAGAAATATGTTAGTGGGGGCTA 58.776 41.667 0.00 0.00 0.00 3.93
1741 1910 5.308237 AGAGAAATATGTTAGTGGGGGCTAG 59.692 44.000 0.00 0.00 0.00 3.42
1742 1911 3.790089 AATATGTTAGTGGGGGCTAGC 57.210 47.619 6.04 6.04 0.00 3.42
1743 1912 2.489528 TATGTTAGTGGGGGCTAGCT 57.510 50.000 15.72 0.00 0.00 3.32
1744 1913 2.489528 ATGTTAGTGGGGGCTAGCTA 57.510 50.000 15.72 0.00 0.00 3.32
1745 1914 2.489528 TGTTAGTGGGGGCTAGCTAT 57.510 50.000 15.72 0.00 0.00 2.97
1746 1915 2.771688 TGTTAGTGGGGGCTAGCTATT 58.228 47.619 15.72 0.00 0.00 1.73
1747 1916 3.120108 TGTTAGTGGGGGCTAGCTATTT 58.880 45.455 15.72 0.00 0.00 1.40
1748 1917 4.300345 TGTTAGTGGGGGCTAGCTATTTA 58.700 43.478 15.72 0.00 0.00 1.40
1749 1918 4.347000 TGTTAGTGGGGGCTAGCTATTTAG 59.653 45.833 15.72 0.00 0.00 1.85
1750 1919 3.346146 AGTGGGGGCTAGCTATTTAGA 57.654 47.619 15.72 0.00 0.00 2.10
1751 1920 3.875571 AGTGGGGGCTAGCTATTTAGAT 58.124 45.455 15.72 0.00 0.00 1.98
1752 1921 5.024803 AGTGGGGGCTAGCTATTTAGATA 57.975 43.478 15.72 0.00 0.00 1.98
1753 1922 5.604752 AGTGGGGGCTAGCTATTTAGATAT 58.395 41.667 15.72 0.00 0.00 1.63
1754 1923 6.753134 AGTGGGGGCTAGCTATTTAGATATA 58.247 40.000 15.72 0.00 0.00 0.86
1755 1924 6.841755 AGTGGGGGCTAGCTATTTAGATATAG 59.158 42.308 15.72 0.00 0.00 1.31
1756 1925 6.839657 GTGGGGGCTAGCTATTTAGATATAGA 59.160 42.308 15.72 0.00 31.10 1.98
1757 1926 7.344871 GTGGGGGCTAGCTATTTAGATATAGAA 59.655 40.741 15.72 0.00 31.10 2.10
1758 1927 7.565398 TGGGGGCTAGCTATTTAGATATAGAAG 59.435 40.741 15.72 0.00 31.10 2.85
1779 1948 8.112016 AGAAGATTATCGTGCTAGCATAGTAA 57.888 34.615 22.51 18.42 41.93 2.24
1780 1949 8.744652 AGAAGATTATCGTGCTAGCATAGTAAT 58.255 33.333 22.51 21.77 41.93 1.89
1781 1950 8.694975 AAGATTATCGTGCTAGCATAGTAATG 57.305 34.615 22.51 1.69 41.93 1.90
1822 1991 2.813226 TAATTCTGTTGCCGGCGCCT 62.813 55.000 26.68 2.83 0.00 5.52
1889 2077 4.390603 GTGTTGTGGAATATGTGCTCGTAA 59.609 41.667 0.00 0.00 0.00 3.18
1905 2103 1.161843 GTAACGTGTGGATGGGTTGG 58.838 55.000 0.00 0.00 0.00 3.77
1988 2186 6.211515 TGAACTTTGAGTAGACGAGTTTACC 58.788 40.000 0.00 0.00 31.24 2.85
1997 2195 1.443872 CGAGTTTACCTGCGACGCT 60.444 57.895 22.08 3.01 0.00 5.07
1999 2197 1.956620 GAGTTTACCTGCGACGCTGC 61.957 60.000 22.08 7.24 0.00 5.25
2000 2198 2.740826 TTTACCTGCGACGCTGCC 60.741 61.111 22.08 0.00 0.00 4.85
2102 2321 2.178912 TGCCAGTAACTTCTTTCCCG 57.821 50.000 0.00 0.00 0.00 5.14
2103 2322 1.271163 TGCCAGTAACTTCTTTCCCGG 60.271 52.381 0.00 0.00 0.00 5.73
2112 2331 2.224548 ACTTCTTTCCCGGAAGAGTTGG 60.225 50.000 0.73 0.00 41.71 3.77
2113 2332 0.036306 TCTTTCCCGGAAGAGTTGGC 59.964 55.000 0.73 0.00 32.19 4.52
2114 2333 0.250727 CTTTCCCGGAAGAGTTGGCA 60.251 55.000 0.73 0.00 0.00 4.92
2116 2335 2.045926 CCCGGAAGAGTTGGCAGG 60.046 66.667 0.73 0.00 0.00 4.85
2120 2341 1.160137 CGGAAGAGTTGGCAGGAAAG 58.840 55.000 0.00 0.00 0.00 2.62
2159 2381 2.905415 TGGGCCTCTTTGATTCACAT 57.095 45.000 4.53 0.00 0.00 3.21
2160 2382 3.173953 TGGGCCTCTTTGATTCACATT 57.826 42.857 4.53 0.00 0.00 2.71
2161 2383 3.509442 TGGGCCTCTTTGATTCACATTT 58.491 40.909 4.53 0.00 0.00 2.32
2190 2420 4.388773 TCGGTGAAATTCTTGATCTGTTCG 59.611 41.667 0.00 0.00 0.00 3.95
2202 2432 7.963981 TCTTGATCTGTTCGTAATCAAATCAC 58.036 34.615 0.00 0.00 38.54 3.06
2207 2437 5.867174 TCTGTTCGTAATCAAATCACGACAT 59.133 36.000 0.00 0.00 43.71 3.06
2208 2438 6.367695 TCTGTTCGTAATCAAATCACGACATT 59.632 34.615 0.00 0.00 43.71 2.71
2209 2439 6.893759 TGTTCGTAATCAAATCACGACATTT 58.106 32.000 0.00 0.00 43.71 2.32
2210 2440 7.356540 TGTTCGTAATCAAATCACGACATTTT 58.643 30.769 0.00 0.00 43.71 1.82
2211 2441 8.496751 TGTTCGTAATCAAATCACGACATTTTA 58.503 29.630 0.00 0.00 43.71 1.52
2212 2442 8.985694 GTTCGTAATCAAATCACGACATTTTAG 58.014 33.333 0.00 0.00 43.71 1.85
2213 2443 8.468720 TCGTAATCAAATCACGACATTTTAGA 57.531 30.769 0.00 0.00 39.58 2.10
2214 2444 9.093970 TCGTAATCAAATCACGACATTTTAGAT 57.906 29.630 0.00 0.00 39.58 1.98
2220 2450 9.377312 TCAAATCACGACATTTTAGATATCACA 57.623 29.630 5.32 0.00 0.00 3.58
2221 2451 9.986833 CAAATCACGACATTTTAGATATCACAA 57.013 29.630 5.32 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.068837 TATTGCACAGCTTTGCTTGC 57.931 45.000 24.29 9.77 43.41 4.01
99 109 8.947055 TTAAGACCGTATAACTTTAACCATCC 57.053 34.615 0.00 0.00 0.00 3.51
166 176 4.620589 TGTGTTCCATGATTGGCAATTT 57.379 36.364 14.93 2.43 43.29 1.82
167 177 4.563993 CCTTGTGTTCCATGATTGGCAATT 60.564 41.667 14.93 0.00 43.29 2.32
168 178 3.055675 CCTTGTGTTCCATGATTGGCAAT 60.056 43.478 13.54 13.54 43.29 3.56
169 179 2.299582 CCTTGTGTTCCATGATTGGCAA 59.700 45.455 0.68 0.68 43.29 4.52
170 180 1.894466 CCTTGTGTTCCATGATTGGCA 59.106 47.619 0.00 0.00 43.29 4.92
171 181 2.170166 TCCTTGTGTTCCATGATTGGC 58.830 47.619 0.00 0.00 43.29 4.52
172 182 4.097437 CAGATCCTTGTGTTCCATGATTGG 59.903 45.833 0.00 0.00 45.15 3.16
173 183 4.703575 ACAGATCCTTGTGTTCCATGATTG 59.296 41.667 0.00 0.00 0.00 2.67
213 223 8.392612 CCTTTTGTAATTCCATGATTTGCAATC 58.607 33.333 0.00 0.79 31.63 2.67
214 224 7.148205 GCCTTTTGTAATTCCATGATTTGCAAT 60.148 33.333 0.00 0.00 31.63 3.56
219 229 6.213195 TGGAGCCTTTTGTAATTCCATGATTT 59.787 34.615 0.00 0.00 30.21 2.17
221 231 5.271598 TGGAGCCTTTTGTAATTCCATGAT 58.728 37.500 0.00 0.00 30.21 2.45
223 233 5.603170 ATGGAGCCTTTTGTAATTCCATG 57.397 39.130 3.21 0.00 42.26 3.66
225 235 5.279910 CCAAATGGAGCCTTTTGTAATTCCA 60.280 40.000 20.00 0.00 38.56 3.53
226 236 5.046663 TCCAAATGGAGCCTTTTGTAATTCC 60.047 40.000 20.00 0.00 39.78 3.01
324 351 4.622701 GCCAATGGCGAAATAGATATCC 57.377 45.455 9.14 0.00 39.62 2.59
352 416 4.118410 CAGCTACAATAGTTGCAGGAGAG 58.882 47.826 5.01 0.00 46.76 3.20
379 443 5.580297 GCAATAACAGGAGTCTCAGAAGAAG 59.420 44.000 1.47 0.00 31.93 2.85
498 646 2.947448 ATTCAGCCAATTCGAAAGCC 57.053 45.000 0.00 0.00 0.00 4.35
554 702 8.948631 ACAAAGTACCAGTATCAGATTATGTG 57.051 34.615 0.00 0.00 0.00 3.21
571 719 4.154375 GGCTCTTAGAAGGCAACAAAGTAC 59.846 45.833 0.00 0.00 41.28 2.73
862 1013 6.371548 CACTGCACCTGCTAGTATTTTTAGAA 59.628 38.462 0.00 0.00 42.66 2.10
870 1021 2.834549 AGAACACTGCACCTGCTAGTAT 59.165 45.455 0.00 0.00 42.66 2.12
882 1033 2.481952 CACAGAGGCTTTAGAACACTGC 59.518 50.000 0.00 0.00 0.00 4.40
936 1087 0.179097 TCAAAACAAAACGGGGCAGC 60.179 50.000 0.00 0.00 0.00 5.25
958 1109 3.847671 TGGTACCACATCAGTGTCAAA 57.152 42.857 11.60 0.00 44.39 2.69
987 1138 3.593328 TGTTCCCCATCTCCTCTGAAATT 59.407 43.478 0.00 0.00 0.00 1.82
1020 1171 3.351416 GTTGGGGCGACGGTTGTC 61.351 66.667 0.00 0.00 41.91 3.18
1030 1181 0.827507 TTTCCTTCTGCAGTTGGGGC 60.828 55.000 21.27 0.00 0.00 5.80
1046 1197 1.289066 GGAGCTTGCCCGGTTTTTC 59.711 57.895 0.00 0.00 0.00 2.29
1158 1309 3.950794 GATCCACTTCCCGCACGCA 62.951 63.158 0.00 0.00 0.00 5.24
1228 1379 0.879090 TCAGAAGTGCGACGCTCTTA 59.121 50.000 30.44 16.79 41.46 2.10
1230 1381 0.664767 GTTCAGAAGTGCGACGCTCT 60.665 55.000 22.08 19.97 33.65 4.09
1231 1382 1.775962 GTTCAGAAGTGCGACGCTC 59.224 57.895 22.08 17.80 0.00 5.03
1232 1383 2.016704 CGTTCAGAAGTGCGACGCT 61.017 57.895 22.08 0.00 0.00 5.07
1233 1384 2.014554 TCGTTCAGAAGTGCGACGC 61.015 57.895 14.19 14.19 34.72 5.19
1234 1385 1.767388 GTCGTTCAGAAGTGCGACG 59.233 57.895 8.53 0.00 42.91 5.12
1236 1387 0.029700 TTCGTCGTTCAGAAGTGCGA 59.970 50.000 0.00 0.00 0.00 5.10
1238 1389 1.205657 TGTTCGTCGTTCAGAAGTGC 58.794 50.000 0.00 0.00 0.00 4.40
1240 1391 3.454375 ACATTGTTCGTCGTTCAGAAGT 58.546 40.909 0.00 0.00 0.00 3.01
1241 1392 4.041240 GACATTGTTCGTCGTTCAGAAG 57.959 45.455 0.00 0.00 0.00 2.85
1372 1541 1.028905 TTTGGAGAAAGCCCAACACG 58.971 50.000 0.00 0.00 42.80 4.49
1426 1595 1.529010 CAGCCCAACCAGCAGACAA 60.529 57.895 0.00 0.00 0.00 3.18
1431 1600 0.471591 AAAATCCAGCCCAACCAGCA 60.472 50.000 0.00 0.00 0.00 4.41
1432 1601 0.686789 AAAAATCCAGCCCAACCAGC 59.313 50.000 0.00 0.00 0.00 4.85
1440 1609 5.003804 TCTAGTTCAGTGAAAAATCCAGCC 58.996 41.667 7.25 0.00 0.00 4.85
1441 1610 6.372659 TCATCTAGTTCAGTGAAAAATCCAGC 59.627 38.462 7.25 0.00 0.00 4.85
1446 1615 7.775561 GGGGTATCATCTAGTTCAGTGAAAAAT 59.224 37.037 7.25 0.00 0.00 1.82
1447 1616 7.110155 GGGGTATCATCTAGTTCAGTGAAAAA 58.890 38.462 7.25 0.00 0.00 1.94
1448 1617 6.629515 CGGGGTATCATCTAGTTCAGTGAAAA 60.630 42.308 7.25 0.00 0.00 2.29
1449 1618 5.163447 CGGGGTATCATCTAGTTCAGTGAAA 60.163 44.000 7.25 0.00 0.00 2.69
1451 1620 3.889538 CGGGGTATCATCTAGTTCAGTGA 59.110 47.826 0.00 0.00 0.00 3.41
1452 1621 3.553096 GCGGGGTATCATCTAGTTCAGTG 60.553 52.174 0.00 0.00 0.00 3.66
1453 1622 2.628657 GCGGGGTATCATCTAGTTCAGT 59.371 50.000 0.00 0.00 0.00 3.41
1454 1623 2.628178 TGCGGGGTATCATCTAGTTCAG 59.372 50.000 0.00 0.00 0.00 3.02
1455 1624 2.364324 GTGCGGGGTATCATCTAGTTCA 59.636 50.000 0.00 0.00 0.00 3.18
1456 1625 2.607282 CGTGCGGGGTATCATCTAGTTC 60.607 54.545 0.00 0.00 0.00 3.01
1457 1626 1.340248 CGTGCGGGGTATCATCTAGTT 59.660 52.381 0.00 0.00 0.00 2.24
1458 1627 0.959553 CGTGCGGGGTATCATCTAGT 59.040 55.000 0.00 0.00 0.00 2.57
1459 1628 0.959553 ACGTGCGGGGTATCATCTAG 59.040 55.000 0.00 0.00 0.00 2.43
1460 1629 1.067974 CAACGTGCGGGGTATCATCTA 59.932 52.381 0.00 0.00 0.00 1.98
1461 1630 0.179084 CAACGTGCGGGGTATCATCT 60.179 55.000 0.00 0.00 0.00 2.90
1462 1631 0.461339 ACAACGTGCGGGGTATCATC 60.461 55.000 0.00 0.00 0.00 2.92
1463 1632 0.035820 AACAACGTGCGGGGTATCAT 60.036 50.000 0.00 0.00 0.00 2.45
1464 1633 0.951525 CAACAACGTGCGGGGTATCA 60.952 55.000 0.00 0.00 0.00 2.15
1465 1634 1.791662 CAACAACGTGCGGGGTATC 59.208 57.895 0.00 0.00 0.00 2.24
1466 1635 2.329614 GCAACAACGTGCGGGGTAT 61.330 57.895 0.00 0.00 34.21 2.73
1467 1636 2.973600 GCAACAACGTGCGGGGTA 60.974 61.111 0.00 0.00 34.21 3.69
1473 1642 1.226435 TGTTTCCGCAACAACGTGC 60.226 52.632 0.00 0.00 42.76 5.34
1480 1649 3.738282 TGTATTGCAAATGTTTCCGCAAC 59.262 39.130 1.71 0.00 46.21 4.17
1482 1651 3.650070 TGTATTGCAAATGTTTCCGCA 57.350 38.095 1.71 0.00 0.00 5.69
1483 1652 5.529014 AAATGTATTGCAAATGTTTCCGC 57.471 34.783 1.71 0.00 0.00 5.54
1484 1653 5.570973 TCGAAATGTATTGCAAATGTTTCCG 59.429 36.000 1.71 3.52 0.00 4.30
1485 1654 6.942886 TCGAAATGTATTGCAAATGTTTCC 57.057 33.333 1.71 0.00 0.00 3.13
1486 1655 8.172159 TCATCGAAATGTATTGCAAATGTTTC 57.828 30.769 1.71 10.85 34.32 2.78
1487 1656 8.706492 ATCATCGAAATGTATTGCAAATGTTT 57.294 26.923 1.71 2.69 34.32 2.83
1488 1657 9.970395 ATATCATCGAAATGTATTGCAAATGTT 57.030 25.926 1.71 0.00 34.32 2.71
1489 1658 9.401873 CATATCATCGAAATGTATTGCAAATGT 57.598 29.630 1.71 0.00 34.32 2.71
1490 1659 9.401873 ACATATCATCGAAATGTATTGCAAATG 57.598 29.630 1.71 0.00 32.21 2.32
1491 1660 9.401873 CACATATCATCGAAATGTATTGCAAAT 57.598 29.630 1.71 0.00 32.70 2.32
1492 1661 8.619546 TCACATATCATCGAAATGTATTGCAAA 58.380 29.630 1.71 0.00 32.70 3.68
1493 1662 8.152309 TCACATATCATCGAAATGTATTGCAA 57.848 30.769 0.00 0.00 32.70 4.08
1494 1663 7.727331 TCACATATCATCGAAATGTATTGCA 57.273 32.000 0.00 0.00 32.70 4.08
1495 1664 9.616634 AAATCACATATCATCGAAATGTATTGC 57.383 29.630 0.00 0.00 32.70 3.56
1501 1670 9.983804 CCATAGAAATCACATATCATCGAAATG 57.016 33.333 0.00 0.00 0.00 2.32
1502 1671 9.948964 TCCATAGAAATCACATATCATCGAAAT 57.051 29.630 0.00 0.00 0.00 2.17
1503 1672 9.777297 TTCCATAGAAATCACATATCATCGAAA 57.223 29.630 0.00 0.00 0.00 3.46
1504 1673 9.208022 GTTCCATAGAAATCACATATCATCGAA 57.792 33.333 0.00 0.00 32.58 3.71
1505 1674 7.542130 CGTTCCATAGAAATCACATATCATCGA 59.458 37.037 0.00 0.00 32.58 3.59
1506 1675 7.329471 ACGTTCCATAGAAATCACATATCATCG 59.671 37.037 0.00 0.00 32.58 3.84
1507 1676 8.438513 CACGTTCCATAGAAATCACATATCATC 58.561 37.037 0.00 0.00 32.58 2.92
1508 1677 8.150296 TCACGTTCCATAGAAATCACATATCAT 58.850 33.333 0.00 0.00 32.58 2.45
1509 1678 7.496747 TCACGTTCCATAGAAATCACATATCA 58.503 34.615 0.00 0.00 32.58 2.15
1510 1679 7.946655 TCACGTTCCATAGAAATCACATATC 57.053 36.000 0.00 0.00 32.58 1.63
1511 1680 8.908786 ATTCACGTTCCATAGAAATCACATAT 57.091 30.769 0.00 0.00 32.58 1.78
1512 1681 9.476202 CTATTCACGTTCCATAGAAATCACATA 57.524 33.333 0.00 0.00 32.58 2.29
1513 1682 7.987458 ACTATTCACGTTCCATAGAAATCACAT 59.013 33.333 10.87 0.00 32.58 3.21
1514 1683 7.277760 CACTATTCACGTTCCATAGAAATCACA 59.722 37.037 10.87 0.00 32.58 3.58
1515 1684 7.491372 TCACTATTCACGTTCCATAGAAATCAC 59.509 37.037 10.87 0.00 32.58 3.06
1516 1685 7.552459 TCACTATTCACGTTCCATAGAAATCA 58.448 34.615 10.87 0.00 32.58 2.57
1517 1686 8.594881 ATCACTATTCACGTTCCATAGAAATC 57.405 34.615 10.87 0.00 32.58 2.17
1518 1687 9.477484 GTATCACTATTCACGTTCCATAGAAAT 57.523 33.333 10.87 7.15 32.58 2.17
1519 1688 8.692710 AGTATCACTATTCACGTTCCATAGAAA 58.307 33.333 10.87 1.83 32.58 2.52
1520 1689 8.234136 AGTATCACTATTCACGTTCCATAGAA 57.766 34.615 10.87 0.23 0.00 2.10
1521 1690 7.818997 AGTATCACTATTCACGTTCCATAGA 57.181 36.000 10.87 0.00 0.00 1.98
1522 1691 9.561270 CATAGTATCACTATTCACGTTCCATAG 57.439 37.037 0.00 0.00 39.26 2.23
1523 1692 9.292195 TCATAGTATCACTATTCACGTTCCATA 57.708 33.333 0.00 0.00 39.26 2.74
1524 1693 8.178313 TCATAGTATCACTATTCACGTTCCAT 57.822 34.615 0.00 0.00 39.26 3.41
1525 1694 7.576861 TCATAGTATCACTATTCACGTTCCA 57.423 36.000 0.00 0.00 39.26 3.53
1526 1695 8.867112 TTTCATAGTATCACTATTCACGTTCC 57.133 34.615 0.00 0.00 39.26 3.62
1528 1697 9.871238 AGTTTTCATAGTATCACTATTCACGTT 57.129 29.630 0.00 0.00 39.26 3.99
1543 1712 9.995003 TGGATTTGCAATTTTAGTTTTCATAGT 57.005 25.926 0.00 0.00 0.00 2.12
1548 1717 9.706846 GCATATGGATTTGCAATTTTAGTTTTC 57.293 29.630 0.00 0.00 38.72 2.29
1549 1718 9.452287 AGCATATGGATTTGCAATTTTAGTTTT 57.548 25.926 0.00 0.00 41.35 2.43
1550 1719 9.452287 AAGCATATGGATTTGCAATTTTAGTTT 57.548 25.926 0.00 0.00 41.35 2.66
1551 1720 9.452287 AAAGCATATGGATTTGCAATTTTAGTT 57.548 25.926 0.00 0.00 41.35 2.24
1556 1725 9.398538 ACAATAAAGCATATGGATTTGCAATTT 57.601 25.926 0.00 0.00 41.35 1.82
1557 1726 8.832521 CACAATAAAGCATATGGATTTGCAATT 58.167 29.630 0.00 0.00 41.35 2.32
1558 1727 7.988599 ACACAATAAAGCATATGGATTTGCAAT 59.011 29.630 0.00 0.00 41.35 3.56
1559 1728 7.329499 ACACAATAAAGCATATGGATTTGCAA 58.671 30.769 4.56 0.00 41.35 4.08
1560 1729 6.876155 ACACAATAAAGCATATGGATTTGCA 58.124 32.000 4.56 0.00 41.35 4.08
1561 1730 7.775397 AACACAATAAAGCATATGGATTTGC 57.225 32.000 4.56 0.00 35.54 3.68
1562 1731 9.368674 TCAAACACAATAAAGCATATGGATTTG 57.631 29.630 4.56 3.80 35.54 2.32
1606 1775 9.578576 ACCTCAACATGCAAACATATATTAGAT 57.421 29.630 0.00 0.00 33.67 1.98
1607 1776 8.839343 CACCTCAACATGCAAACATATATTAGA 58.161 33.333 0.00 0.00 33.67 2.10
1608 1777 8.077991 CCACCTCAACATGCAAACATATATTAG 58.922 37.037 0.00 0.00 33.67 1.73
1609 1778 7.777440 TCCACCTCAACATGCAAACATATATTA 59.223 33.333 0.00 0.00 33.67 0.98
1610 1779 6.606796 TCCACCTCAACATGCAAACATATATT 59.393 34.615 0.00 0.00 33.67 1.28
1611 1780 6.128486 TCCACCTCAACATGCAAACATATAT 58.872 36.000 0.00 0.00 33.67 0.86
1612 1781 5.504853 TCCACCTCAACATGCAAACATATA 58.495 37.500 0.00 0.00 33.67 0.86
1613 1782 4.343231 TCCACCTCAACATGCAAACATAT 58.657 39.130 0.00 0.00 33.67 1.78
1614 1783 3.760738 TCCACCTCAACATGCAAACATA 58.239 40.909 0.00 0.00 33.67 2.29
1615 1784 2.596346 TCCACCTCAACATGCAAACAT 58.404 42.857 0.00 0.00 36.79 2.71
1616 1785 2.064434 TCCACCTCAACATGCAAACA 57.936 45.000 0.00 0.00 0.00 2.83
1617 1786 4.989279 ATATCCACCTCAACATGCAAAC 57.011 40.909 0.00 0.00 0.00 2.93
1618 1787 5.105392 GGAAATATCCACCTCAACATGCAAA 60.105 40.000 0.00 0.00 45.79 3.68
1619 1788 4.402155 GGAAATATCCACCTCAACATGCAA 59.598 41.667 0.00 0.00 45.79 4.08
1620 1789 3.953612 GGAAATATCCACCTCAACATGCA 59.046 43.478 0.00 0.00 45.79 3.96
1621 1790 4.574599 GGAAATATCCACCTCAACATGC 57.425 45.455 0.00 0.00 45.79 4.06
1648 1817 6.753409 GGCCTACCACAACATGCATTCATG 62.753 50.000 3.61 3.61 44.80 3.07
1649 1818 2.428171 GCCTACCACAACATGCATTCAT 59.572 45.455 0.00 0.00 0.00 2.57
1650 1819 1.818060 GCCTACCACAACATGCATTCA 59.182 47.619 0.00 0.00 0.00 2.57
1651 1820 1.134946 GGCCTACCACAACATGCATTC 59.865 52.381 0.00 0.00 35.26 2.67
1652 1821 1.185315 GGCCTACCACAACATGCATT 58.815 50.000 0.00 0.00 35.26 3.56
1653 1822 0.332632 AGGCCTACCACAACATGCAT 59.667 50.000 1.29 0.00 39.06 3.96
1654 1823 0.112218 AAGGCCTACCACAACATGCA 59.888 50.000 5.16 0.00 39.06 3.96
1655 1824 1.256812 AAAGGCCTACCACAACATGC 58.743 50.000 5.16 0.00 39.06 4.06
1656 1825 2.610232 GCAAAAGGCCTACCACAACATG 60.610 50.000 5.16 0.00 39.06 3.21
1657 1826 1.618343 GCAAAAGGCCTACCACAACAT 59.382 47.619 5.16 0.00 39.06 2.71
1658 1827 1.036707 GCAAAAGGCCTACCACAACA 58.963 50.000 5.16 0.00 39.06 3.33
1659 1828 3.886044 GCAAAAGGCCTACCACAAC 57.114 52.632 5.16 0.00 39.06 3.32
1669 1838 0.800012 CAACATGCATGGCAAAAGGC 59.200 50.000 29.41 0.00 43.62 4.35
1670 1839 0.800012 GCAACATGCATGGCAAAAGG 59.200 50.000 29.41 11.75 43.62 3.11
1681 1850 3.176708 GTCACATCATCAAGCAACATGC 58.823 45.455 0.00 0.00 45.46 4.06
1682 1851 4.428615 TGTCACATCATCAAGCAACATG 57.571 40.909 0.00 0.00 0.00 3.21
1683 1852 4.676986 GCATGTCACATCATCAAGCAACAT 60.677 41.667 0.00 0.00 0.00 2.71
1684 1853 3.366577 GCATGTCACATCATCAAGCAACA 60.367 43.478 0.00 0.00 0.00 3.33
1685 1854 3.119602 AGCATGTCACATCATCAAGCAAC 60.120 43.478 0.00 0.00 0.00 4.17
1686 1855 3.086282 AGCATGTCACATCATCAAGCAA 58.914 40.909 0.00 0.00 0.00 3.91
1687 1856 2.718563 AGCATGTCACATCATCAAGCA 58.281 42.857 0.00 0.00 0.00 3.91
1688 1857 3.777465 AAGCATGTCACATCATCAAGC 57.223 42.857 0.00 0.00 0.00 4.01
1689 1858 5.806366 TGTAAGCATGTCACATCATCAAG 57.194 39.130 0.00 0.00 0.00 3.02
1690 1859 6.126568 CATGTAAGCATGTCACATCATCAA 57.873 37.500 0.00 0.00 45.48 2.57
1691 1860 5.744666 CATGTAAGCATGTCACATCATCA 57.255 39.130 0.00 0.00 45.48 3.07
1703 1872 8.743085 ACATATTTCTCTCAACATGTAAGCAT 57.257 30.769 0.00 0.00 35.32 3.79
1704 1873 8.565896 AACATATTTCTCTCAACATGTAAGCA 57.434 30.769 0.00 0.00 0.00 3.91
1708 1877 9.599866 CCACTAACATATTTCTCTCAACATGTA 57.400 33.333 0.00 0.00 0.00 2.29
1709 1878 7.554118 CCCACTAACATATTTCTCTCAACATGT 59.446 37.037 0.00 0.00 0.00 3.21
1710 1879 7.012704 CCCCACTAACATATTTCTCTCAACATG 59.987 40.741 0.00 0.00 0.00 3.21
1711 1880 7.056635 CCCCACTAACATATTTCTCTCAACAT 58.943 38.462 0.00 0.00 0.00 2.71
1712 1881 6.414732 CCCCACTAACATATTTCTCTCAACA 58.585 40.000 0.00 0.00 0.00 3.33
1713 1882 5.823045 CCCCCACTAACATATTTCTCTCAAC 59.177 44.000 0.00 0.00 0.00 3.18
1714 1883 5.631481 GCCCCCACTAACATATTTCTCTCAA 60.631 44.000 0.00 0.00 0.00 3.02
1715 1884 4.141482 GCCCCCACTAACATATTTCTCTCA 60.141 45.833 0.00 0.00 0.00 3.27
1716 1885 4.103311 AGCCCCCACTAACATATTTCTCTC 59.897 45.833 0.00 0.00 0.00 3.20
1717 1886 4.047883 AGCCCCCACTAACATATTTCTCT 58.952 43.478 0.00 0.00 0.00 3.10
1718 1887 4.439253 AGCCCCCACTAACATATTTCTC 57.561 45.455 0.00 0.00 0.00 2.87
1719 1888 4.202472 GCTAGCCCCCACTAACATATTTCT 60.202 45.833 2.29 0.00 0.00 2.52
1720 1889 4.072839 GCTAGCCCCCACTAACATATTTC 58.927 47.826 2.29 0.00 0.00 2.17
1721 1890 3.722101 AGCTAGCCCCCACTAACATATTT 59.278 43.478 12.13 0.00 0.00 1.40
1722 1891 3.327439 AGCTAGCCCCCACTAACATATT 58.673 45.455 12.13 0.00 0.00 1.28
1723 1892 2.991580 AGCTAGCCCCCACTAACATAT 58.008 47.619 12.13 0.00 0.00 1.78
1724 1893 2.489528 AGCTAGCCCCCACTAACATA 57.510 50.000 12.13 0.00 0.00 2.29
1725 1894 2.489528 TAGCTAGCCCCCACTAACAT 57.510 50.000 12.13 0.00 0.00 2.71
1726 1895 2.489528 ATAGCTAGCCCCCACTAACA 57.510 50.000 12.13 0.00 0.00 2.41
1727 1896 3.859061 AAATAGCTAGCCCCCACTAAC 57.141 47.619 12.13 0.00 0.00 2.34
1728 1897 4.823107 TCTAAATAGCTAGCCCCCACTAA 58.177 43.478 12.13 0.00 0.00 2.24
1729 1898 4.480777 TCTAAATAGCTAGCCCCCACTA 57.519 45.455 12.13 0.00 0.00 2.74
1730 1899 3.346146 TCTAAATAGCTAGCCCCCACT 57.654 47.619 12.13 0.00 0.00 4.00
1731 1900 5.959583 ATATCTAAATAGCTAGCCCCCAC 57.040 43.478 12.13 0.00 0.00 4.61
1732 1901 6.993408 TCTATATCTAAATAGCTAGCCCCCA 58.007 40.000 12.13 0.00 30.79 4.96
1733 1902 7.785506 TCTTCTATATCTAAATAGCTAGCCCCC 59.214 40.741 12.13 0.00 30.79 5.40
1734 1903 8.770010 TCTTCTATATCTAAATAGCTAGCCCC 57.230 38.462 12.13 0.00 30.79 5.80
1747 1916 9.614792 TGCTAGCACGATAATCTTCTATATCTA 57.385 33.333 14.93 0.00 0.00 1.98
1748 1917 8.512966 TGCTAGCACGATAATCTTCTATATCT 57.487 34.615 14.93 0.00 0.00 1.98
1751 1920 9.397280 ACTATGCTAGCACGATAATCTTCTATA 57.603 33.333 22.07 2.05 0.00 1.31
1752 1921 8.287439 ACTATGCTAGCACGATAATCTTCTAT 57.713 34.615 22.07 0.74 0.00 1.98
1753 1922 7.689446 ACTATGCTAGCACGATAATCTTCTA 57.311 36.000 22.07 2.73 0.00 2.10
1754 1923 6.582677 ACTATGCTAGCACGATAATCTTCT 57.417 37.500 22.07 1.47 0.00 2.85
1755 1924 8.802856 CATTACTATGCTAGCACGATAATCTTC 58.197 37.037 22.07 0.00 0.00 2.87
1756 1925 8.694975 CATTACTATGCTAGCACGATAATCTT 57.305 34.615 22.07 2.89 0.00 2.40
1779 1948 2.590092 GGGGACCGTAAGCAGCAT 59.410 61.111 0.00 0.00 40.86 3.79
1801 1970 1.917782 GCGCCGGCAACAGAATTACA 61.918 55.000 28.98 0.00 39.62 2.41
1826 1995 3.369921 CCAAAGGAGGCAACAGGC 58.630 61.111 0.00 0.00 43.74 4.85
1889 2077 2.434331 CCCAACCCATCCACACGT 59.566 61.111 0.00 0.00 0.00 4.49
2001 2199 3.723348 GAACCAACGGGCTGCGTC 61.723 66.667 0.00 0.00 37.90 5.19
2006 2204 4.612412 TTCGCGAACCAACGGGCT 62.612 61.111 19.38 0.00 43.84 5.19
2007 2205 4.379143 GTTCGCGAACCAACGGGC 62.379 66.667 35.88 12.99 43.84 6.13
2008 2206 4.067016 CGTTCGCGAACCAACGGG 62.067 66.667 38.04 23.25 44.71 5.28
2102 2321 2.568623 TCTTTCCTGCCAACTCTTCC 57.431 50.000 0.00 0.00 0.00 3.46
2103 2322 4.918810 TTTTCTTTCCTGCCAACTCTTC 57.081 40.909 0.00 0.00 0.00 2.87
2127 2348 2.275380 GGCCCAAGTTGGTTCGCAT 61.275 57.895 20.54 0.00 35.17 4.73
2168 2390 4.152402 ACGAACAGATCAAGAATTTCACCG 59.848 41.667 0.00 0.00 0.00 4.94
2178 2408 6.896613 CGTGATTTGATTACGAACAGATCAAG 59.103 38.462 0.00 0.00 43.90 3.02
2181 2411 6.569228 TCGTGATTTGATTACGAACAGATC 57.431 37.500 5.61 0.00 46.16 2.75


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

AutoCloner maintained by Alex Coulton.