Multiple sequence alignment - TraesCS4A01G496200

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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 TraesCS4A01G496200 chr4A 100.000 2267 0 0 1 2267 742790175 742787909 0.000000e+00 4187.0
1 TraesCS4A01G496200 chr4A 80.903 576 98 10 703 1268 469245735 469246308 5.750000e-121 444.0
2 TraesCS4A01G496200 chr7D 93.717 1496 79 9 1 1488 1187292 1185804 0.000000e+00 2228.0
3 TraesCS4A01G496200 chr7D 92.718 412 24 6 1650 2057 1185805 1185396 6.970000e-165 590.0
4 TraesCS4A01G496200 chr7D 92.262 168 13 0 1484 1651 39001282 39001449 2.910000e-59 239.0
5 TraesCS4A01G496200 chr7D 89.189 185 18 2 1470 1653 546102339 546102522 1.750000e-56 230.0
6 TraesCS4A01G496200 chrUn 91.778 1496 106 13 1 1488 316654364 316652878 0.000000e+00 2065.0
7 TraesCS4A01G496200 chrUn 91.711 1496 107 13 1 1488 51486024 51487510 0.000000e+00 2060.0
8 TraesCS4A01G496200 chrUn 90.757 1493 102 15 1 1488 245963564 245965025 0.000000e+00 1960.0
9 TraesCS4A01G496200 chrUn 90.154 1493 114 18 1 1488 269322477 269323941 0.000000e+00 1912.0
10 TraesCS4A01G496200 chrUn 92.718 412 23 6 1650 2057 269323940 269324348 2.510000e-164 588.0
11 TraesCS4A01G496200 chrUn 92.476 412 24 6 1650 2057 245965024 245965432 1.170000e-162 582.0
12 TraesCS4A01G496200 chrUn 91.980 399 25 6 1650 2044 51487509 51487904 9.150000e-154 553.0
13 TraesCS4A01G496200 chrUn 91.980 399 25 6 1650 2044 316652879 316652484 9.150000e-154 553.0
14 TraesCS4A01G496200 chrUn 92.612 379 22 5 1683 2057 351031724 351031348 7.120000e-150 540.0
15 TraesCS4A01G496200 chr4D 80.208 576 102 10 703 1268 106679342 106678769 2.690000e-114 422.0
16 TraesCS4A01G496200 chr3D 91.908 173 14 0 1482 1654 217587729 217587557 2.250000e-60 243.0
17 TraesCS4A01G496200 chr3D 89.418 189 16 3 1487 1672 304588101 304588288 3.760000e-58 235.0
18 TraesCS4A01G496200 chr3D 86.473 207 21 6 1471 1672 78373275 78373479 1.050000e-53 220.0
19 TraesCS4A01G496200 chr6D 89.305 187 14 4 1474 1656 307341051 307340867 1.750000e-56 230.0
20 TraesCS4A01G496200 chr6A 89.189 185 19 1 1479 1662 297678618 297678802 1.750000e-56 230.0
21 TraesCS4A01G496200 chr2D 89.247 186 16 3 1474 1656 213176502 213176318 1.750000e-56 230.0
22 TraesCS4A01G496200 chr1D 88.482 191 18 3 1474 1661 259974621 259974432 6.300000e-56 228.0
23 TraesCS4A01G496200 chr1A 94.231 52 3 0 459 510 6438655 6438604 1.870000e-11 80.5


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 TraesCS4A01G496200 chr4A 742787909 742790175 2266 True 4187.0 4187 100.0000 1 2267 1 chr4A.!!$R1 2266
1 TraesCS4A01G496200 chr4A 469245735 469246308 573 False 444.0 444 80.9030 703 1268 1 chr4A.!!$F1 565
2 TraesCS4A01G496200 chr7D 1185396 1187292 1896 True 1409.0 2228 93.2175 1 2057 2 chr7D.!!$R1 2056
3 TraesCS4A01G496200 chrUn 316652484 316654364 1880 True 1309.0 2065 91.8790 1 2044 2 chrUn.!!$R2 2043
4 TraesCS4A01G496200 chrUn 51486024 51487904 1880 False 1306.5 2060 91.8455 1 2044 2 chrUn.!!$F1 2043
5 TraesCS4A01G496200 chrUn 245963564 245965432 1868 False 1271.0 1960 91.6165 1 2057 2 chrUn.!!$F2 2056
6 TraesCS4A01G496200 chrUn 269322477 269324348 1871 False 1250.0 1912 91.4360 1 2057 2 chrUn.!!$F3 2056
7 TraesCS4A01G496200 chr4D 106678769 106679342 573 True 422.0 422 80.2080 703 1268 1 chr4D.!!$R1 565

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
522 528 0.321653 AGGGTGTCATCGCCTTCAAC 60.322 55.0 0.0 0.0 43.2 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2185 0.036732 GTCCCAGGACACATTGCTGA 59.963 55.0 12.05 0.0 46.53 4.26 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
31 32 2.093658 CCACTTGTACGCCTACCAGAAT 60.094 50.000 1.77 0.00 0.00 2.40
119 120 0.531532 CCTCGCTGCTAATGACTGGG 60.532 60.000 0.00 0.00 0.00 4.45
142 143 1.144057 GTACGATGGTCCTGGCCAG 59.856 63.158 26.87 26.87 42.47 4.85
163 164 1.865788 ATGCAAACCTTGTCGCGCAT 61.866 50.000 8.75 0.00 35.36 4.73
203 204 3.181526 GCTAGCATGGCCAAAGAGT 57.818 52.632 10.96 0.00 36.10 3.24
204 205 0.737219 GCTAGCATGGCCAAAGAGTG 59.263 55.000 10.96 3.67 36.10 3.51
217 218 3.054878 CAAAGAGTGCTGGTTCATTTGC 58.945 45.455 0.00 0.00 0.00 3.68
254 255 7.648112 TCTTCGTCGATCAGAGGTTAATTATTG 59.352 37.037 0.00 0.00 36.24 1.90
284 285 8.001881 TGTCTAGCTTAACTATCTCTCTTTGG 57.998 38.462 0.00 0.00 0.00 3.28
295 296 9.981460 AACTATCTCTCTTTGGAATTTTACCAT 57.019 29.630 0.00 0.00 37.26 3.55
319 324 8.632679 CATATTAATGTTTGTACTGGAGCCATT 58.367 33.333 0.00 0.00 0.00 3.16
360 365 7.571080 TCAAACACCGTAAAGGAAATACTTT 57.429 32.000 0.00 0.00 45.00 2.66
361 366 7.419204 TCAAACACCGTAAAGGAAATACTTTG 58.581 34.615 0.77 0.00 45.00 2.77
362 367 5.366829 ACACCGTAAAGGAAATACTTTGC 57.633 39.130 0.77 0.00 45.00 3.68
371 376 9.489084 GTAAAGGAAATACTTTGCCTTGAAATT 57.511 29.630 0.77 0.00 40.44 1.82
426 431 5.633655 TTACAGGTTCCAGTTTCAAGGTA 57.366 39.130 0.00 0.00 0.00 3.08
483 488 1.303317 GGCAATCGTTGGTGGGACT 60.303 57.895 0.00 0.00 0.00 3.85
504 510 7.151587 GACTGGAGAGTTTGCATATGCACAG 62.152 48.000 29.58 28.29 41.23 3.66
522 528 0.321653 AGGGTGTCATCGCCTTCAAC 60.322 55.000 0.00 0.00 43.20 3.18
531 537 0.400213 TCGCCTTCAACAAGACCCAT 59.600 50.000 0.00 0.00 0.00 4.00
537 543 4.338879 CCTTCAACAAGACCCATCAATCT 58.661 43.478 0.00 0.00 0.00 2.40
579 585 2.416547 GCTTCATGTTCGTGCTATGTGT 59.583 45.455 0.00 0.00 0.00 3.72
613 619 1.141053 GACCTCTGGTGTGTTCCTTGT 59.859 52.381 0.00 0.00 35.25 3.16
615 621 1.417890 CCTCTGGTGTGTTCCTTGTCT 59.582 52.381 0.00 0.00 0.00 3.41
664 670 6.430000 TGTCCAATTCTCTAGCTTGGTTTTAC 59.570 38.462 0.00 0.00 40.28 2.01
665 671 6.655425 GTCCAATTCTCTAGCTTGGTTTTACT 59.345 38.462 0.00 0.00 40.28 2.24
833 840 7.172019 GTCATTGATTCACTTGCATTTTCCTTT 59.828 33.333 0.00 0.00 0.00 3.11
946 961 7.734924 TGACATCTTTTCATATATGAGCACC 57.265 36.000 14.86 2.89 38.19 5.01
1008 1023 6.037940 GTGATCTCTTTTCTTGCATGCAGATA 59.962 38.462 21.50 12.35 0.00 1.98
1041 1056 4.380655 CCTTCAGAGATCGTTACGGAAGTT 60.381 45.833 4.53 0.00 46.40 2.66
1119 1134 3.009695 CCCTCACCATTACCACAAACCTA 59.990 47.826 0.00 0.00 0.00 3.08
1141 1156 2.342650 CCGTACGGTCCCTTCGGAA 61.343 63.158 26.39 0.00 40.92 4.30
1178 1193 0.819259 TTCAGTGTTCCAGTGCAGGC 60.819 55.000 0.00 0.00 35.04 4.85
1218 1233 3.071459 CTTCGCGTGCGCTGGTAAG 62.071 63.158 9.73 3.86 39.59 2.34
1245 1260 2.181525 GCGCTCGGGGTTTACGTA 59.818 61.111 0.00 0.00 0.00 3.57
1257 1272 2.667969 GGTTTACGTACGTTCACCCATC 59.332 50.000 27.92 7.00 0.00 3.51
1270 1285 4.055710 TCACCCATCTCAACCTAGTACA 57.944 45.455 0.00 0.00 0.00 2.90
1276 1291 5.394738 CCATCTCAACCTAGTACATCCCTA 58.605 45.833 0.00 0.00 0.00 3.53
1320 1335 5.627499 TGTCTTCCATGTTTCTATGTTGC 57.373 39.130 0.00 0.00 0.00 4.17
1321 1336 5.069318 TGTCTTCCATGTTTCTATGTTGCA 58.931 37.500 0.00 0.00 0.00 4.08
1401 1420 5.181690 TGTTGGTTTTCTTATCAGCACAC 57.818 39.130 0.00 0.00 0.00 3.82
1402 1421 4.642437 TGTTGGTTTTCTTATCAGCACACA 59.358 37.500 0.00 0.00 0.00 3.72
1403 1422 5.215160 GTTGGTTTTCTTATCAGCACACAG 58.785 41.667 0.00 0.00 0.00 3.66
1404 1423 4.460263 TGGTTTTCTTATCAGCACACAGT 58.540 39.130 0.00 0.00 0.00 3.55
1418 1437 7.386059 TCAGCACACAGTTTCTCTTATCAATA 58.614 34.615 0.00 0.00 0.00 1.90
1421 1440 8.507249 AGCACACAGTTTCTCTTATCAATAAAC 58.493 33.333 0.00 0.00 0.00 2.01
1423 1442 7.957484 CACACAGTTTCTCTTATCAATAAACGG 59.043 37.037 0.00 0.00 35.67 4.44
1457 1477 6.524101 TTGTACCTTTGCAGAGAAACTTTT 57.476 33.333 5.68 0.00 0.00 2.27
1458 1478 6.524101 TGTACCTTTGCAGAGAAACTTTTT 57.476 33.333 5.68 0.00 0.00 1.94
1486 1506 8.850007 TCACGCTCACTATATTCTACTCTATT 57.150 34.615 0.00 0.00 0.00 1.73
1487 1507 9.939802 TCACGCTCACTATATTCTACTCTATTA 57.060 33.333 0.00 0.00 0.00 0.98
1488 1508 9.976255 CACGCTCACTATATTCTACTCTATTAC 57.024 37.037 0.00 0.00 0.00 1.89
1489 1509 9.947433 ACGCTCACTATATTCTACTCTATTACT 57.053 33.333 0.00 0.00 0.00 2.24
1499 1519 8.700439 ATTCTACTCTATTACTCCCTCTGTTC 57.300 38.462 0.00 0.00 0.00 3.18
1500 1520 6.603224 TCTACTCTATTACTCCCTCTGTTCC 58.397 44.000 0.00 0.00 0.00 3.62
1501 1521 5.475398 ACTCTATTACTCCCTCTGTTCCT 57.525 43.478 0.00 0.00 0.00 3.36
1502 1522 6.593759 ACTCTATTACTCCCTCTGTTCCTA 57.406 41.667 0.00 0.00 0.00 2.94
1503 1523 6.982899 ACTCTATTACTCCCTCTGTTCCTAA 58.017 40.000 0.00 0.00 0.00 2.69
1504 1524 7.420029 ACTCTATTACTCCCTCTGTTCCTAAA 58.580 38.462 0.00 0.00 0.00 1.85
1505 1525 8.068733 ACTCTATTACTCCCTCTGTTCCTAAAT 58.931 37.037 0.00 0.00 0.00 1.40
1506 1526 9.589461 CTCTATTACTCCCTCTGTTCCTAAATA 57.411 37.037 0.00 0.00 0.00 1.40
1513 1533 9.453830 ACTCCCTCTGTTCCTAAATATTTATCT 57.546 33.333 8.34 0.00 0.00 1.98
1541 1561 9.619316 TTTACAGATTTCAAATGAATTACCACG 57.381 29.630 0.00 0.00 33.54 4.94
1542 1562 7.214467 ACAGATTTCAAATGAATTACCACGT 57.786 32.000 0.00 0.00 33.54 4.49
1543 1563 8.330466 ACAGATTTCAAATGAATTACCACGTA 57.670 30.769 0.00 0.00 33.54 3.57
1544 1564 8.234546 ACAGATTTCAAATGAATTACCACGTAC 58.765 33.333 0.00 0.00 33.54 3.67
1545 1565 7.425309 CAGATTTCAAATGAATTACCACGTACG 59.575 37.037 15.01 15.01 33.54 3.67
1546 1566 5.533533 TTCAAATGAATTACCACGTACGG 57.466 39.130 21.06 8.46 0.00 4.02
1547 1567 4.818642 TCAAATGAATTACCACGTACGGA 58.181 39.130 21.06 0.00 0.00 4.69
1548 1568 5.421277 TCAAATGAATTACCACGTACGGAT 58.579 37.500 21.06 6.82 0.00 4.18
1549 1569 5.292345 TCAAATGAATTACCACGTACGGATG 59.708 40.000 21.06 9.60 0.00 3.51
1550 1570 3.872511 TGAATTACCACGTACGGATGT 57.127 42.857 21.06 15.02 0.00 3.06
1551 1571 4.979943 TGAATTACCACGTACGGATGTA 57.020 40.909 21.06 14.02 0.00 2.29
1552 1572 5.518848 TGAATTACCACGTACGGATGTAT 57.481 39.130 21.06 4.50 32.11 2.29
1553 1573 6.631971 TGAATTACCACGTACGGATGTATA 57.368 37.500 21.06 8.69 32.11 1.47
1554 1574 7.218228 TGAATTACCACGTACGGATGTATAT 57.782 36.000 21.06 8.96 32.11 0.86
1555 1575 8.334263 TGAATTACCACGTACGGATGTATATA 57.666 34.615 21.06 3.74 32.11 0.86
1556 1576 8.453320 TGAATTACCACGTACGGATGTATATAG 58.547 37.037 21.06 0.00 32.11 1.31
1557 1577 8.565896 AATTACCACGTACGGATGTATATAGA 57.434 34.615 21.06 3.08 32.11 1.98
1558 1578 5.869753 ACCACGTACGGATGTATATAGAC 57.130 43.478 21.06 0.00 32.11 2.59
1559 1579 5.308014 ACCACGTACGGATGTATATAGACA 58.692 41.667 21.06 2.07 32.11 3.41
1560 1580 5.942236 ACCACGTACGGATGTATATAGACAT 59.058 40.000 21.06 12.70 42.82 3.06
1561 1581 7.105588 ACCACGTACGGATGTATATAGACATA 58.894 38.462 21.06 0.00 40.18 2.29
1562 1582 7.772292 ACCACGTACGGATGTATATAGACATAT 59.228 37.037 21.06 5.08 40.18 1.78
1563 1583 8.618677 CCACGTACGGATGTATATAGACATATT 58.381 37.037 21.06 3.62 40.18 1.28
1564 1584 9.999009 CACGTACGGATGTATATAGACATATTT 57.001 33.333 21.06 3.30 40.18 1.40
1589 1609 6.690194 AGAGTGTAGATTCAATCATTTGGC 57.310 37.500 0.00 0.00 35.30 4.52
1590 1610 6.421485 AGAGTGTAGATTCAATCATTTGGCT 58.579 36.000 0.00 0.00 35.30 4.75
1591 1611 6.541641 AGAGTGTAGATTCAATCATTTGGCTC 59.458 38.462 0.00 0.28 35.30 4.70
1592 1612 6.421485 AGTGTAGATTCAATCATTTGGCTCT 58.579 36.000 0.00 0.00 33.44 4.09
1593 1613 6.318144 AGTGTAGATTCAATCATTTGGCTCTG 59.682 38.462 0.00 0.00 33.44 3.35
1594 1614 4.650754 AGATTCAATCATTTGGCTCTGC 57.349 40.909 0.00 0.00 33.44 4.26
1595 1615 4.021229 AGATTCAATCATTTGGCTCTGCA 58.979 39.130 0.00 0.00 33.44 4.41
1596 1616 4.649674 AGATTCAATCATTTGGCTCTGCAT 59.350 37.500 0.00 0.00 33.44 3.96
1597 1617 3.793797 TCAATCATTTGGCTCTGCATG 57.206 42.857 0.00 0.00 33.44 4.06
1598 1618 3.093814 TCAATCATTTGGCTCTGCATGT 58.906 40.909 0.00 0.00 33.44 3.21
1599 1619 4.271661 TCAATCATTTGGCTCTGCATGTA 58.728 39.130 0.00 0.00 33.44 2.29
1600 1620 4.337274 TCAATCATTTGGCTCTGCATGTAG 59.663 41.667 4.14 4.14 33.44 2.74
1601 1621 3.354948 TCATTTGGCTCTGCATGTAGT 57.645 42.857 10.80 0.00 0.00 2.73
1602 1622 3.273434 TCATTTGGCTCTGCATGTAGTC 58.727 45.455 10.80 4.26 0.00 2.59
1603 1623 2.857186 TTTGGCTCTGCATGTAGTCA 57.143 45.000 10.80 3.05 0.00 3.41
1604 1624 2.099141 TTGGCTCTGCATGTAGTCAC 57.901 50.000 10.80 3.04 0.00 3.67
1605 1625 1.269958 TGGCTCTGCATGTAGTCACT 58.730 50.000 10.80 0.00 0.00 3.41
1606 1626 1.625315 TGGCTCTGCATGTAGTCACTT 59.375 47.619 10.80 0.00 0.00 3.16
1607 1627 2.005451 GGCTCTGCATGTAGTCACTTG 58.995 52.381 10.80 0.00 33.92 3.16
1608 1628 2.613977 GGCTCTGCATGTAGTCACTTGT 60.614 50.000 10.80 0.00 33.46 3.16
1609 1629 3.368427 GGCTCTGCATGTAGTCACTTGTA 60.368 47.826 10.80 0.00 33.46 2.41
1610 1630 3.862267 GCTCTGCATGTAGTCACTTGTAG 59.138 47.826 10.80 0.00 41.16 2.74
1611 1631 4.380973 GCTCTGCATGTAGTCACTTGTAGA 60.381 45.833 10.80 9.78 44.02 2.59
1612 1632 5.714047 CTCTGCATGTAGTCACTTGTAGAA 58.286 41.667 10.80 0.00 44.84 2.10
1613 1633 6.096673 TCTGCATGTAGTCACTTGTAGAAA 57.903 37.500 10.80 0.00 43.61 2.52
1614 1634 6.701340 TCTGCATGTAGTCACTTGTAGAAAT 58.299 36.000 10.80 0.00 43.61 2.17
1615 1635 7.161404 TCTGCATGTAGTCACTTGTAGAAATT 58.839 34.615 10.80 0.00 43.61 1.82
1616 1636 7.661437 TCTGCATGTAGTCACTTGTAGAAATTT 59.339 33.333 10.80 0.00 43.61 1.82
1617 1637 7.806690 TGCATGTAGTCACTTGTAGAAATTTC 58.193 34.615 10.33 10.33 33.46 2.17
1618 1638 7.661437 TGCATGTAGTCACTTGTAGAAATTTCT 59.339 33.333 23.53 23.53 34.93 2.52
1619 1639 9.151471 GCATGTAGTCACTTGTAGAAATTTCTA 57.849 33.333 21.46 21.46 33.84 2.10
1646 1666 9.556030 GAAAGACAAATATTTAGAAACGAAGGG 57.444 33.333 0.00 0.00 0.00 3.95
1647 1667 8.857694 AAGACAAATATTTAGAAACGAAGGGA 57.142 30.769 0.00 0.00 0.00 4.20
1648 1668 8.494016 AGACAAATATTTAGAAACGAAGGGAG 57.506 34.615 0.00 0.00 0.00 4.30
1923 1946 2.002586 CCTTACCTCACTTGTCATGCG 58.997 52.381 0.00 0.00 0.00 4.73
1957 1981 8.263640 CCATATGGACCTATGAGATTTTCCTAG 58.736 40.741 17.49 0.00 37.39 3.02
1959 1983 5.788430 TGGACCTATGAGATTTTCCTAGGA 58.212 41.667 7.62 7.62 43.28 2.94
2039 2063 5.542635 TGTTTTGATCACTAGTACAGGACCT 59.457 40.000 0.00 0.00 0.00 3.85
2053 2077 2.038975 ACCTCCTCCTTAGCGGCA 59.961 61.111 1.45 0.00 0.00 5.69
2057 2081 0.250081 CTCCTCCTTAGCGGCATTCC 60.250 60.000 1.45 0.00 0.00 3.01
2067 2091 4.223800 GGCATTCCGATGTGCTCA 57.776 55.556 6.32 0.00 41.04 4.26
2068 2092 1.723870 GGCATTCCGATGTGCTCAC 59.276 57.895 0.00 0.00 41.04 3.51
2069 2093 0.745845 GGCATTCCGATGTGCTCACT 60.746 55.000 1.47 0.00 41.04 3.41
2070 2094 1.473257 GGCATTCCGATGTGCTCACTA 60.473 52.381 1.47 0.00 41.04 2.74
2071 2095 1.863454 GCATTCCGATGTGCTCACTAG 59.137 52.381 1.47 0.00 38.30 2.57
2072 2096 3.935622 GCATTCCGATGTGCTCACTAGC 61.936 54.545 1.47 0.00 40.26 3.42
2081 2105 4.802424 CTCACTAGCAGCGTCTGG 57.198 61.111 8.57 0.00 31.21 3.86
2082 2106 1.140589 CTCACTAGCAGCGTCTGGG 59.859 63.158 8.57 0.00 31.21 4.45
2083 2107 1.599606 CTCACTAGCAGCGTCTGGGT 61.600 60.000 8.57 0.00 31.21 4.51
2084 2108 1.446792 CACTAGCAGCGTCTGGGTG 60.447 63.158 8.57 0.00 46.88 4.61
2085 2109 2.185350 CTAGCAGCGTCTGGGTGG 59.815 66.667 8.57 0.00 44.32 4.61
2086 2110 3.376935 CTAGCAGCGTCTGGGTGGG 62.377 68.421 8.57 0.00 44.32 4.61
2098 2122 3.467226 GGTGGGGCGCTGCTAGTA 61.467 66.667 7.64 0.00 0.00 1.82
2099 2123 2.202892 GTGGGGCGCTGCTAGTAC 60.203 66.667 7.64 0.00 0.00 2.73
2100 2124 3.833645 TGGGGCGCTGCTAGTACG 61.834 66.667 7.64 0.00 0.00 3.67
2101 2125 3.524606 GGGGCGCTGCTAGTACGA 61.525 66.667 7.64 0.00 0.00 3.43
2102 2126 2.278661 GGGCGCTGCTAGTACGAC 60.279 66.667 7.64 4.13 0.00 4.34
2103 2127 2.488355 GGCGCTGCTAGTACGACA 59.512 61.111 7.64 0.00 34.15 4.35
2104 2128 1.872679 GGCGCTGCTAGTACGACAC 60.873 63.158 7.64 0.00 34.15 3.67
2105 2129 2.215604 GCGCTGCTAGTACGACACG 61.216 63.158 0.00 0.00 0.00 4.49
2106 2130 1.422662 CGCTGCTAGTACGACACGA 59.577 57.895 0.00 0.00 0.00 4.35
2107 2131 0.856490 CGCTGCTAGTACGACACGAC 60.856 60.000 0.00 0.00 0.00 4.34
2108 2132 0.447011 GCTGCTAGTACGACACGACT 59.553 55.000 0.00 0.00 0.00 4.18
2109 2133 1.790838 GCTGCTAGTACGACACGACTG 60.791 57.143 0.00 0.00 0.00 3.51
2110 2134 1.730612 CTGCTAGTACGACACGACTGA 59.269 52.381 0.00 0.00 0.00 3.41
2111 2135 2.352034 CTGCTAGTACGACACGACTGAT 59.648 50.000 0.00 0.00 0.00 2.90
2112 2136 3.524541 TGCTAGTACGACACGACTGATA 58.475 45.455 0.00 0.00 0.00 2.15
2113 2137 3.934579 TGCTAGTACGACACGACTGATAA 59.065 43.478 0.00 0.00 0.00 1.75
2114 2138 4.201753 TGCTAGTACGACACGACTGATAAC 60.202 45.833 0.00 0.00 0.00 1.89
2115 2139 4.201753 GCTAGTACGACACGACTGATAACA 60.202 45.833 0.00 0.00 0.00 2.41
2116 2140 4.075763 AGTACGACACGACTGATAACAC 57.924 45.455 0.00 0.00 0.00 3.32
2117 2141 3.499537 AGTACGACACGACTGATAACACA 59.500 43.478 0.00 0.00 0.00 3.72
2118 2142 3.570926 ACGACACGACTGATAACACAT 57.429 42.857 0.00 0.00 0.00 3.21
2119 2143 3.909430 ACGACACGACTGATAACACATT 58.091 40.909 0.00 0.00 0.00 2.71
2120 2144 5.050644 ACGACACGACTGATAACACATTA 57.949 39.130 0.00 0.00 0.00 1.90
2121 2145 4.855388 ACGACACGACTGATAACACATTAC 59.145 41.667 0.00 0.00 0.00 1.89
2122 2146 5.093457 CGACACGACTGATAACACATTACT 58.907 41.667 0.00 0.00 0.00 2.24
2123 2147 5.571741 CGACACGACTGATAACACATTACTT 59.428 40.000 0.00 0.00 0.00 2.24
2124 2148 6.452480 CGACACGACTGATAACACATTACTTG 60.452 42.308 0.00 0.00 0.00 3.16
2125 2149 6.220930 ACACGACTGATAACACATTACTTGT 58.779 36.000 0.00 0.00 39.91 3.16
2126 2150 7.372714 ACACGACTGATAACACATTACTTGTA 58.627 34.615 0.00 0.00 36.57 2.41
2127 2151 7.541091 ACACGACTGATAACACATTACTTGTAG 59.459 37.037 0.00 0.00 36.57 2.74
2128 2152 7.541091 CACGACTGATAACACATTACTTGTAGT 59.459 37.037 0.00 0.00 36.57 2.73
2129 2153 7.541091 ACGACTGATAACACATTACTTGTAGTG 59.459 37.037 0.00 2.43 36.57 2.74
2130 2154 7.541091 CGACTGATAACACATTACTTGTAGTGT 59.459 37.037 3.59 3.59 46.24 3.55
2137 2161 7.347508 ACACATTACTTGTAGTGTTCGATTC 57.652 36.000 6.26 0.00 42.06 2.52
2138 2162 6.926826 ACACATTACTTGTAGTGTTCGATTCA 59.073 34.615 6.26 0.00 42.06 2.57
2139 2163 7.439955 ACACATTACTTGTAGTGTTCGATTCAA 59.560 33.333 6.26 0.00 42.06 2.69
2140 2164 8.279800 CACATTACTTGTAGTGTTCGATTCAAA 58.720 33.333 6.26 0.00 36.57 2.69
2141 2165 8.999431 ACATTACTTGTAGTGTTCGATTCAAAT 58.001 29.630 3.59 0.00 36.57 2.32
2142 2166 9.265938 CATTACTTGTAGTGTTCGATTCAAATG 57.734 33.333 0.00 0.00 0.00 2.32
2143 2167 6.241207 ACTTGTAGTGTTCGATTCAAATGG 57.759 37.500 0.00 0.00 0.00 3.16
2144 2168 5.763204 ACTTGTAGTGTTCGATTCAAATGGT 59.237 36.000 0.00 0.00 0.00 3.55
2145 2169 5.605564 TGTAGTGTTCGATTCAAATGGTG 57.394 39.130 0.00 0.00 0.00 4.17
2146 2170 3.559238 AGTGTTCGATTCAAATGGTGC 57.441 42.857 0.00 0.00 0.00 5.01
2147 2171 3.149196 AGTGTTCGATTCAAATGGTGCT 58.851 40.909 0.00 0.00 0.00 4.40
2148 2172 4.323417 AGTGTTCGATTCAAATGGTGCTA 58.677 39.130 0.00 0.00 0.00 3.49
2149 2173 4.759693 AGTGTTCGATTCAAATGGTGCTAA 59.240 37.500 0.00 0.00 0.00 3.09
2150 2174 5.415701 AGTGTTCGATTCAAATGGTGCTAAT 59.584 36.000 0.00 0.00 0.00 1.73
2151 2175 6.597672 AGTGTTCGATTCAAATGGTGCTAATA 59.402 34.615 0.00 0.00 0.00 0.98
2152 2176 7.283127 AGTGTTCGATTCAAATGGTGCTAATAT 59.717 33.333 0.00 0.00 0.00 1.28
2153 2177 7.376866 GTGTTCGATTCAAATGGTGCTAATATG 59.623 37.037 0.00 0.00 0.00 1.78
2154 2178 7.066887 TGTTCGATTCAAATGGTGCTAATATGT 59.933 33.333 0.00 0.00 0.00 2.29
2155 2179 6.958255 TCGATTCAAATGGTGCTAATATGTG 58.042 36.000 0.00 0.00 0.00 3.21
2156 2180 5.626543 CGATTCAAATGGTGCTAATATGTGC 59.373 40.000 0.00 0.00 0.00 4.57
2157 2181 5.911378 TTCAAATGGTGCTAATATGTGCA 57.089 34.783 0.00 0.00 36.79 4.57
2165 2189 2.880268 TGCTAATATGTGCACCATCAGC 59.120 45.455 15.69 14.70 35.29 4.26
2166 2190 2.880268 GCTAATATGTGCACCATCAGCA 59.120 45.455 15.69 0.00 40.19 4.41
2167 2191 3.316029 GCTAATATGTGCACCATCAGCAA 59.684 43.478 15.69 0.00 44.64 3.91
2168 2192 4.022589 GCTAATATGTGCACCATCAGCAAT 60.023 41.667 15.69 0.45 44.64 3.56
2169 2193 4.316205 AATATGTGCACCATCAGCAATG 57.684 40.909 15.69 0.00 44.64 2.82
2170 2194 1.552578 ATGTGCACCATCAGCAATGT 58.447 45.000 15.69 0.00 44.64 2.71
2171 2195 0.599060 TGTGCACCATCAGCAATGTG 59.401 50.000 15.69 0.00 44.64 3.21
2172 2196 0.599558 GTGCACCATCAGCAATGTGT 59.400 50.000 5.22 0.00 44.64 3.72
2173 2197 0.883153 TGCACCATCAGCAATGTGTC 59.117 50.000 0.00 0.00 39.39 3.67
2174 2198 0.171903 GCACCATCAGCAATGTGTCC 59.828 55.000 0.00 0.00 33.13 4.02
2175 2199 1.830279 CACCATCAGCAATGTGTCCT 58.170 50.000 0.00 0.00 33.13 3.85
2176 2200 1.471287 CACCATCAGCAATGTGTCCTG 59.529 52.381 0.00 0.00 33.13 3.86
2177 2201 1.100510 CCATCAGCAATGTGTCCTGG 58.899 55.000 0.00 0.00 33.13 4.45
2178 2202 1.100510 CATCAGCAATGTGTCCTGGG 58.899 55.000 0.00 0.00 0.00 4.45
2179 2203 0.994247 ATCAGCAATGTGTCCTGGGA 59.006 50.000 0.00 0.00 0.00 4.37
2180 2204 0.036732 TCAGCAATGTGTCCTGGGAC 59.963 55.000 12.43 12.43 44.77 4.46
2181 2205 0.962356 CAGCAATGTGTCCTGGGACC 60.962 60.000 16.07 8.78 43.97 4.46
2182 2206 2.040544 GCAATGTGTCCTGGGACCG 61.041 63.158 16.07 2.56 43.97 4.79
2183 2207 2.040544 CAATGTGTCCTGGGACCGC 61.041 63.158 16.07 10.04 43.97 5.68
2184 2208 2.525124 AATGTGTCCTGGGACCGCA 61.525 57.895 16.07 14.59 43.97 5.69
2185 2209 2.469465 AATGTGTCCTGGGACCGCAG 62.469 60.000 16.07 7.06 43.97 5.18
2188 2212 3.075005 GTCCTGGGACCGCAGCTA 61.075 66.667 8.48 0.00 39.08 3.32
2189 2213 2.759973 TCCTGGGACCGCAGCTAG 60.760 66.667 8.38 0.00 0.00 3.42
2190 2214 3.077556 CCTGGGACCGCAGCTAGT 61.078 66.667 8.38 0.00 0.00 2.57
2191 2215 1.756950 CCTGGGACCGCAGCTAGTA 60.757 63.158 8.38 0.00 0.00 1.82
2192 2216 1.437986 CTGGGACCGCAGCTAGTAC 59.562 63.158 1.13 0.00 0.00 2.73
2193 2217 2.337749 CTGGGACCGCAGCTAGTACG 62.338 65.000 1.13 0.00 0.00 3.67
2197 2221 3.528370 CCGCAGCTAGTACGGGCT 61.528 66.667 11.08 9.27 43.23 5.19
2198 2222 2.191513 CCGCAGCTAGTACGGGCTA 61.192 63.158 13.58 0.00 43.23 3.93
2199 2223 1.524863 CCGCAGCTAGTACGGGCTAT 61.525 60.000 13.58 0.00 43.23 2.97
2200 2224 0.314302 CGCAGCTAGTACGGGCTATT 59.686 55.000 13.58 0.00 37.00 1.73
2201 2225 1.666311 CGCAGCTAGTACGGGCTATTC 60.666 57.143 13.58 7.03 37.00 1.75
2202 2226 1.340248 GCAGCTAGTACGGGCTATTCA 59.660 52.381 13.58 0.00 37.00 2.57
2203 2227 2.608261 GCAGCTAGTACGGGCTATTCAG 60.608 54.545 13.58 4.77 37.00 3.02
2215 2239 2.425989 CTATTCAGCAGCGTTTCACG 57.574 50.000 0.00 0.00 45.88 4.35
2216 2240 1.726791 CTATTCAGCAGCGTTTCACGT 59.273 47.619 0.00 0.00 44.73 4.49
2217 2241 0.944386 ATTCAGCAGCGTTTCACGTT 59.056 45.000 0.00 0.00 44.73 3.99
2224 2248 2.369477 AGCGTTTCACGTTGAACGCC 62.369 55.000 35.27 24.55 46.99 5.68
2232 2256 3.596865 CGTTGAACGCCGCAAATAT 57.403 47.368 4.26 0.00 33.65 1.28
2233 2257 1.179332 CGTTGAACGCCGCAAATATG 58.821 50.000 4.26 0.00 33.65 1.78
2234 2258 1.465020 CGTTGAACGCCGCAAATATGT 60.465 47.619 4.26 0.00 33.65 2.29
2235 2259 2.591133 GTTGAACGCCGCAAATATGTT 58.409 42.857 0.00 0.00 0.00 2.71
2236 2260 3.725305 CGTTGAACGCCGCAAATATGTTA 60.725 43.478 4.26 0.00 33.65 2.41
2237 2261 3.392769 TGAACGCCGCAAATATGTTAC 57.607 42.857 0.00 0.00 0.00 2.50
2238 2262 2.742589 TGAACGCCGCAAATATGTTACA 59.257 40.909 0.00 0.00 0.00 2.41
2239 2263 3.375610 TGAACGCCGCAAATATGTTACAT 59.624 39.130 2.58 2.58 0.00 2.29
2240 2264 4.571176 TGAACGCCGCAAATATGTTACATA 59.429 37.500 7.56 7.56 0.00 2.29
2241 2265 4.461992 ACGCCGCAAATATGTTACATAC 57.538 40.909 7.26 0.00 0.00 2.39
2242 2266 4.124238 ACGCCGCAAATATGTTACATACT 58.876 39.130 7.26 0.00 0.00 2.12
2243 2267 5.291178 ACGCCGCAAATATGTTACATACTA 58.709 37.500 7.26 0.00 0.00 1.82
2244 2268 5.404366 ACGCCGCAAATATGTTACATACTAG 59.596 40.000 7.26 1.88 0.00 2.57
2245 2269 5.404366 CGCCGCAAATATGTTACATACTAGT 59.596 40.000 7.26 0.00 0.00 2.57
2246 2270 6.583427 CGCCGCAAATATGTTACATACTAGTA 59.417 38.462 7.26 4.77 0.00 1.82
2247 2271 7.115236 CGCCGCAAATATGTTACATACTAGTAA 59.885 37.037 7.26 0.00 0.00 2.24
2256 2280 6.744550 GTTACATACTAGTAACGTGCATCC 57.255 41.667 6.70 0.00 42.86 3.51
2257 2281 6.501781 GTTACATACTAGTAACGTGCATCCT 58.498 40.000 6.70 0.00 42.86 3.24
2258 2282 7.642669 GTTACATACTAGTAACGTGCATCCTA 58.357 38.462 6.70 0.00 42.86 2.94
2259 2283 6.069684 ACATACTAGTAACGTGCATCCTAC 57.930 41.667 6.70 0.00 0.00 3.18
2260 2284 5.591472 ACATACTAGTAACGTGCATCCTACA 59.409 40.000 6.70 0.00 0.00 2.74
2261 2285 6.264744 ACATACTAGTAACGTGCATCCTACAT 59.735 38.462 6.70 0.00 0.00 2.29
2262 2286 5.184340 ACTAGTAACGTGCATCCTACATC 57.816 43.478 0.00 0.00 0.00 3.06
2263 2287 4.888239 ACTAGTAACGTGCATCCTACATCT 59.112 41.667 0.00 0.00 0.00 2.90
2264 2288 4.308899 AGTAACGTGCATCCTACATCTC 57.691 45.455 0.00 0.00 0.00 2.75
2265 2289 3.954904 AGTAACGTGCATCCTACATCTCT 59.045 43.478 0.00 0.00 0.00 3.10
2266 2290 2.879002 ACGTGCATCCTACATCTCTG 57.121 50.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.547675 GCATCTGGGGTTTTCTGGACA 60.548 52.381 0.00 0.00 0.00 4.02
119 120 1.518572 CAGGACCATCGTACACGGC 60.519 63.158 1.39 0.00 40.29 5.68
142 143 1.337110 GCGCGACAAGGTTTGCATTC 61.337 55.000 12.10 0.00 0.00 2.67
163 164 1.165907 CGAGGTGCAAACCTTGAGCA 61.166 55.000 6.31 0.00 42.63 4.26
203 204 2.429971 TGTTGAAGCAAATGAACCAGCA 59.570 40.909 0.00 0.00 0.00 4.41
204 205 3.096489 TGTTGAAGCAAATGAACCAGC 57.904 42.857 0.00 0.00 0.00 4.85
217 218 2.672714 TCGACGAAGACCATGTTGAAG 58.327 47.619 0.00 0.00 0.00 3.02
254 255 9.863845 AGAGAGATAGTTAAGCTAGACAAAAAC 57.136 33.333 0.00 0.00 32.45 2.43
294 295 8.632679 CAATGGCTCCAGTACAAACATTAATAT 58.367 33.333 0.00 0.00 0.00 1.28
295 296 7.613801 ACAATGGCTCCAGTACAAACATTAATA 59.386 33.333 0.00 0.00 0.00 0.98
307 312 1.563924 ACCGTACAATGGCTCCAGTA 58.436 50.000 0.00 0.00 0.00 2.74
319 324 5.915758 GTGTTTGAATTGCATAAACCGTACA 59.084 36.000 11.40 0.00 34.32 2.90
351 356 7.437862 TGACACAATTTCAAGGCAAAGTATTTC 59.562 33.333 0.00 0.00 35.03 2.17
360 365 5.301551 ACATAGTTGACACAATTTCAAGGCA 59.698 36.000 0.00 0.00 33.63 4.75
361 366 5.772521 ACATAGTTGACACAATTTCAAGGC 58.227 37.500 0.00 0.00 33.63 4.35
362 367 7.206981 AGACATAGTTGACACAATTTCAAGG 57.793 36.000 0.00 0.00 33.63 3.61
371 376 9.416284 TCCAAGTATATAGACATAGTTGACACA 57.584 33.333 10.75 0.00 41.40 3.72
426 431 0.486879 TGCCTTGAAAGTCCCCCATT 59.513 50.000 0.00 0.00 0.00 3.16
456 461 0.887247 CAACGATTGCCCATTCACCA 59.113 50.000 0.00 0.00 0.00 4.17
504 510 0.605319 TGTTGAAGGCGATGACACCC 60.605 55.000 0.00 0.00 0.00 4.61
522 528 4.750021 TCTCTCAGATTGATGGGTCTTG 57.250 45.455 0.00 0.00 0.00 3.02
531 537 2.354103 CCTGGCGTTTCTCTCAGATTGA 60.354 50.000 0.00 0.00 0.00 2.57
537 543 0.250234 CCATCCTGGCGTTTCTCTCA 59.750 55.000 0.00 0.00 0.00 3.27
579 585 4.044825 ACCAGAGGTCTTAAGAAGGAGAGA 59.955 45.833 6.78 0.00 0.00 3.10
613 619 0.183014 AGTAGCTAGGTAGGCGCAGA 59.817 55.000 10.83 0.00 34.52 4.26
615 621 0.183014 AGAGTAGCTAGGTAGGCGCA 59.817 55.000 10.83 0.00 34.52 6.09
664 670 2.567049 GTCGGACTCGGGTGTCAG 59.433 66.667 0.00 0.00 38.61 3.51
665 671 2.987547 GGTCGGACTCGGGTGTCA 60.988 66.667 8.23 0.00 38.61 3.58
804 811 7.118680 GGAAAATGCAAGTGAATCAATGACAAT 59.881 33.333 0.00 0.00 0.00 2.71
833 840 3.826524 TGGTTCACCAGCTTTGTCAATA 58.173 40.909 0.00 0.00 42.01 1.90
938 953 4.134563 GGAATTACATTACGGGTGCTCAT 58.865 43.478 0.00 0.00 0.00 2.90
1008 1023 0.546267 TCTCTGAAGGGGCAAGCTCT 60.546 55.000 0.00 0.00 0.00 4.09
1141 1156 3.620488 TGAAAGGAGTGCTCTGTGTTTT 58.380 40.909 0.00 0.00 0.00 2.43
1178 1193 6.693315 AGAAACCCACGATGTTATTATTGG 57.307 37.500 0.00 0.00 0.00 3.16
1218 1233 4.849329 CCGAGCGCCTCCACGTAC 62.849 72.222 2.29 0.00 34.88 3.67
1245 1260 1.056660 AGGTTGAGATGGGTGAACGT 58.943 50.000 0.00 0.00 0.00 3.99
1270 1285 2.038557 GTGTGACACAACACCTAGGGAT 59.961 50.000 14.81 0.00 43.84 3.85
1293 1308 8.729756 CAACATAGAAACATGGAAGACATACAA 58.270 33.333 0.00 0.00 37.84 2.41
1320 1335 5.695851 AACACACTTCTTCCTTATTGCTG 57.304 39.130 0.00 0.00 0.00 4.41
1321 1336 7.398024 AGATAACACACTTCTTCCTTATTGCT 58.602 34.615 0.00 0.00 0.00 3.91
1388 1407 5.474578 AGAGAAACTGTGTGCTGATAAGA 57.525 39.130 0.00 0.00 0.00 2.10
1418 1437 9.036671 CAAAGGTACAAACATTATTTTCCGTTT 57.963 29.630 0.00 0.00 31.96 3.60
1421 1440 6.642950 TGCAAAGGTACAAACATTATTTTCCG 59.357 34.615 0.00 0.00 0.00 4.30
1423 1442 8.810652 TCTGCAAAGGTACAAACATTATTTTC 57.189 30.769 0.00 0.00 0.00 2.29
1457 1477 9.286170 AGAGTAGAATATAGTGAGCGTGATAAA 57.714 33.333 0.00 0.00 0.00 1.40
1458 1478 8.850007 AGAGTAGAATATAGTGAGCGTGATAA 57.150 34.615 0.00 0.00 0.00 1.75
1477 1497 6.607019 AGGAACAGAGGGAGTAATAGAGTAG 58.393 44.000 0.00 0.00 0.00 2.57
1487 1507 9.453830 AGATAAATATTTAGGAACAGAGGGAGT 57.546 33.333 13.15 0.00 0.00 3.85
1515 1535 9.619316 CGTGGTAATTCATTTGAAATCTGTAAA 57.381 29.630 0.00 0.00 37.61 2.01
1516 1536 8.788806 ACGTGGTAATTCATTTGAAATCTGTAA 58.211 29.630 0.00 0.00 37.61 2.41
1517 1537 8.330466 ACGTGGTAATTCATTTGAAATCTGTA 57.670 30.769 0.00 0.00 37.61 2.74
1518 1538 7.214467 ACGTGGTAATTCATTTGAAATCTGT 57.786 32.000 0.00 0.00 37.61 3.41
1519 1539 7.425309 CGTACGTGGTAATTCATTTGAAATCTG 59.575 37.037 7.22 0.00 37.61 2.90
1520 1540 7.413657 CCGTACGTGGTAATTCATTTGAAATCT 60.414 37.037 15.21 0.00 37.61 2.40
1521 1541 6.685403 CCGTACGTGGTAATTCATTTGAAATC 59.315 38.462 15.21 0.00 37.61 2.17
1522 1542 6.372103 TCCGTACGTGGTAATTCATTTGAAAT 59.628 34.615 15.21 0.00 37.61 2.17
1523 1543 5.699915 TCCGTACGTGGTAATTCATTTGAAA 59.300 36.000 15.21 0.00 37.61 2.69
1524 1544 5.236282 TCCGTACGTGGTAATTCATTTGAA 58.764 37.500 15.21 0.00 38.56 2.69
1525 1545 4.818642 TCCGTACGTGGTAATTCATTTGA 58.181 39.130 15.21 0.00 0.00 2.69
1526 1546 5.064198 ACATCCGTACGTGGTAATTCATTTG 59.936 40.000 15.21 0.00 0.00 2.32
1527 1547 5.180271 ACATCCGTACGTGGTAATTCATTT 58.820 37.500 15.21 0.00 0.00 2.32
1528 1548 4.761975 ACATCCGTACGTGGTAATTCATT 58.238 39.130 15.21 0.00 0.00 2.57
1529 1549 4.395959 ACATCCGTACGTGGTAATTCAT 57.604 40.909 15.21 0.00 0.00 2.57
1530 1550 3.872511 ACATCCGTACGTGGTAATTCA 57.127 42.857 15.21 0.00 0.00 2.57
1531 1551 8.668353 TCTATATACATCCGTACGTGGTAATTC 58.332 37.037 15.21 0.00 0.00 2.17
1532 1552 8.454106 GTCTATATACATCCGTACGTGGTAATT 58.546 37.037 15.21 7.68 0.00 1.40
1533 1553 7.607607 TGTCTATATACATCCGTACGTGGTAAT 59.392 37.037 15.21 10.95 0.00 1.89
1534 1554 6.934083 TGTCTATATACATCCGTACGTGGTAA 59.066 38.462 15.21 5.39 0.00 2.85
1535 1555 6.463360 TGTCTATATACATCCGTACGTGGTA 58.537 40.000 15.21 13.05 0.00 3.25
1536 1556 5.308014 TGTCTATATACATCCGTACGTGGT 58.692 41.667 15.21 11.27 0.00 4.16
1537 1557 5.868043 TGTCTATATACATCCGTACGTGG 57.132 43.478 15.21 5.54 0.00 4.94
1538 1558 9.999009 AAATATGTCTATATACATCCGTACGTG 57.001 33.333 15.21 9.44 40.52 4.49
1563 1583 8.677300 GCCAAATGATTGAATCTACACTCTAAA 58.323 33.333 6.73 0.00 38.94 1.85
1564 1584 8.049117 AGCCAAATGATTGAATCTACACTCTAA 58.951 33.333 6.73 0.00 38.94 2.10
1565 1585 7.568349 AGCCAAATGATTGAATCTACACTCTA 58.432 34.615 6.73 0.00 38.94 2.43
1566 1586 6.421485 AGCCAAATGATTGAATCTACACTCT 58.579 36.000 6.73 0.00 38.94 3.24
1567 1587 6.541641 AGAGCCAAATGATTGAATCTACACTC 59.458 38.462 6.73 6.17 38.94 3.51
1568 1588 6.318144 CAGAGCCAAATGATTGAATCTACACT 59.682 38.462 6.73 0.00 38.94 3.55
1569 1589 6.493116 CAGAGCCAAATGATTGAATCTACAC 58.507 40.000 6.73 0.00 38.94 2.90
1570 1590 5.066893 GCAGAGCCAAATGATTGAATCTACA 59.933 40.000 6.73 0.00 38.94 2.74
1571 1591 5.066893 TGCAGAGCCAAATGATTGAATCTAC 59.933 40.000 6.73 0.00 38.94 2.59
1572 1592 5.195185 TGCAGAGCCAAATGATTGAATCTA 58.805 37.500 6.73 0.00 38.94 1.98
1573 1593 4.021229 TGCAGAGCCAAATGATTGAATCT 58.979 39.130 6.73 0.00 38.94 2.40
1574 1594 4.380841 TGCAGAGCCAAATGATTGAATC 57.619 40.909 0.00 0.00 38.94 2.52
1575 1595 4.161565 ACATGCAGAGCCAAATGATTGAAT 59.838 37.500 0.00 0.00 38.94 2.57
1576 1596 3.512329 ACATGCAGAGCCAAATGATTGAA 59.488 39.130 0.00 0.00 38.94 2.69
1577 1597 3.093814 ACATGCAGAGCCAAATGATTGA 58.906 40.909 0.00 0.00 38.94 2.57
1578 1598 3.520290 ACATGCAGAGCCAAATGATTG 57.480 42.857 0.00 0.00 36.25 2.67
1579 1599 4.275810 ACTACATGCAGAGCCAAATGATT 58.724 39.130 0.00 0.00 0.00 2.57
1580 1600 3.881688 GACTACATGCAGAGCCAAATGAT 59.118 43.478 0.00 0.00 0.00 2.45
1581 1601 3.273434 GACTACATGCAGAGCCAAATGA 58.727 45.455 0.00 0.00 0.00 2.57
1582 1602 3.011818 TGACTACATGCAGAGCCAAATG 58.988 45.455 0.00 0.00 0.00 2.32
1583 1603 3.012518 GTGACTACATGCAGAGCCAAAT 58.987 45.455 0.00 0.00 0.00 2.32
1584 1604 2.038952 AGTGACTACATGCAGAGCCAAA 59.961 45.455 0.00 0.00 0.00 3.28
1585 1605 1.625315 AGTGACTACATGCAGAGCCAA 59.375 47.619 0.00 0.00 0.00 4.52
1586 1606 1.269958 AGTGACTACATGCAGAGCCA 58.730 50.000 0.00 0.00 0.00 4.75
1587 1607 2.005451 CAAGTGACTACATGCAGAGCC 58.995 52.381 0.00 0.00 0.00 4.70
1588 1608 2.693069 ACAAGTGACTACATGCAGAGC 58.307 47.619 0.00 0.00 0.00 4.09
1589 1609 5.316327 TCTACAAGTGACTACATGCAGAG 57.684 43.478 0.00 0.00 27.93 3.35
1590 1610 5.722021 TTCTACAAGTGACTACATGCAGA 57.278 39.130 0.00 0.00 28.82 4.26
1591 1611 6.974932 ATTTCTACAAGTGACTACATGCAG 57.025 37.500 0.00 0.00 0.00 4.41
1592 1612 7.661437 AGAAATTTCTACAAGTGACTACATGCA 59.339 33.333 19.17 0.00 35.34 3.96
1593 1613 8.034058 AGAAATTTCTACAAGTGACTACATGC 57.966 34.615 19.17 0.00 35.34 4.06
1620 1640 9.556030 CCCTTCGTTTCTAAATATTTGTCTTTC 57.444 33.333 11.05 0.00 0.00 2.62
1621 1641 9.292195 TCCCTTCGTTTCTAAATATTTGTCTTT 57.708 29.630 11.05 0.00 0.00 2.52
1622 1642 8.857694 TCCCTTCGTTTCTAAATATTTGTCTT 57.142 30.769 11.05 0.00 0.00 3.01
1623 1643 8.101419 ACTCCCTTCGTTTCTAAATATTTGTCT 58.899 33.333 11.05 0.00 0.00 3.41
1624 1644 8.265165 ACTCCCTTCGTTTCTAAATATTTGTC 57.735 34.615 11.05 0.00 0.00 3.18
1625 1645 9.379791 CTACTCCCTTCGTTTCTAAATATTTGT 57.620 33.333 11.05 0.00 0.00 2.83
1626 1646 9.595823 TCTACTCCCTTCGTTTCTAAATATTTG 57.404 33.333 11.05 1.65 0.00 2.32
1637 1657 9.955102 ACTATTTATTTTCTACTCCCTTCGTTT 57.045 29.630 0.00 0.00 0.00 3.60
1638 1658 9.379791 CACTATTTATTTTCTACTCCCTTCGTT 57.620 33.333 0.00 0.00 0.00 3.85
1639 1659 8.755977 TCACTATTTATTTTCTACTCCCTTCGT 58.244 33.333 0.00 0.00 0.00 3.85
1640 1660 9.765795 ATCACTATTTATTTTCTACTCCCTTCG 57.234 33.333 0.00 0.00 0.00 3.79
1642 1662 9.343539 GCATCACTATTTATTTTCTACTCCCTT 57.656 33.333 0.00 0.00 0.00 3.95
1643 1663 8.494433 TGCATCACTATTTATTTTCTACTCCCT 58.506 33.333 0.00 0.00 0.00 4.20
1644 1664 8.677148 TGCATCACTATTTATTTTCTACTCCC 57.323 34.615 0.00 0.00 0.00 4.30
1718 1739 4.993705 TTGTGGTCCTTGGACTCTATTT 57.006 40.909 17.99 0.00 0.00 1.40
1763 1784 6.211664 ACTTGTTAGATTCGTGAAAACGAG 57.788 37.500 9.70 9.70 43.33 4.18
1870 1891 8.947115 AGTCTTAACTCCATTAGGAAAATTTCG 58.053 33.333 0.00 0.00 45.19 3.46
1887 1910 8.366401 GTGAGGTAAGGAAGTTTAGTCTTAACT 58.634 37.037 0.00 0.00 40.98 2.24
1923 1946 2.664402 AGGTCCATATGGCCATTCAC 57.336 50.000 26.37 14.68 34.96 3.18
1957 1981 9.845740 AGCCCATTTAATTTTTACCATAATTCC 57.154 29.630 0.00 0.00 0.00 3.01
2039 2063 1.830145 GGAATGCCGCTAAGGAGGA 59.170 57.895 0.00 0.00 45.00 3.71
2064 2088 1.140589 CCCAGACGCTGCTAGTGAG 59.859 63.158 0.00 0.00 0.00 3.51
2065 2089 1.606601 ACCCAGACGCTGCTAGTGA 60.607 57.895 0.00 0.00 0.00 3.41
2066 2090 1.446792 CACCCAGACGCTGCTAGTG 60.447 63.158 0.00 5.38 0.00 2.74
2067 2091 2.650116 CCACCCAGACGCTGCTAGT 61.650 63.158 0.00 0.00 0.00 2.57
2068 2092 2.185350 CCACCCAGACGCTGCTAG 59.815 66.667 0.00 0.00 0.00 3.42
2069 2093 3.390521 CCCACCCAGACGCTGCTA 61.391 66.667 0.00 0.00 0.00 3.49
2081 2105 3.467226 TACTAGCAGCGCCCCACC 61.467 66.667 2.29 0.00 0.00 4.61
2082 2106 2.202892 GTACTAGCAGCGCCCCAC 60.203 66.667 2.29 0.00 0.00 4.61
2083 2107 3.833645 CGTACTAGCAGCGCCCCA 61.834 66.667 2.29 0.00 0.00 4.96
2084 2108 3.524606 TCGTACTAGCAGCGCCCC 61.525 66.667 2.29 0.00 0.00 5.80
2085 2109 2.278661 GTCGTACTAGCAGCGCCC 60.279 66.667 2.29 0.00 0.00 6.13
2086 2110 1.872679 GTGTCGTACTAGCAGCGCC 60.873 63.158 2.29 0.00 0.00 6.53
2087 2111 2.215604 CGTGTCGTACTAGCAGCGC 61.216 63.158 0.00 0.00 0.00 5.92
2088 2112 0.856490 GTCGTGTCGTACTAGCAGCG 60.856 60.000 0.00 0.00 0.00 5.18
2089 2113 0.447011 AGTCGTGTCGTACTAGCAGC 59.553 55.000 0.00 0.00 0.00 5.25
2090 2114 1.730612 TCAGTCGTGTCGTACTAGCAG 59.269 52.381 0.00 0.00 0.00 4.24
2091 2115 1.799544 TCAGTCGTGTCGTACTAGCA 58.200 50.000 0.00 0.00 0.00 3.49
2092 2116 4.201753 TGTTATCAGTCGTGTCGTACTAGC 60.202 45.833 0.00 0.00 0.00 3.42
2093 2117 5.163923 TGTGTTATCAGTCGTGTCGTACTAG 60.164 44.000 0.00 0.00 0.00 2.57
2094 2118 4.690280 TGTGTTATCAGTCGTGTCGTACTA 59.310 41.667 0.00 0.00 0.00 1.82
2095 2119 3.499537 TGTGTTATCAGTCGTGTCGTACT 59.500 43.478 0.00 0.00 0.00 2.73
2096 2120 3.813800 TGTGTTATCAGTCGTGTCGTAC 58.186 45.455 0.00 0.00 0.00 3.67
2097 2121 4.690184 ATGTGTTATCAGTCGTGTCGTA 57.310 40.909 0.00 0.00 0.00 3.43
2098 2122 3.570926 ATGTGTTATCAGTCGTGTCGT 57.429 42.857 0.00 0.00 0.00 4.34
2099 2123 5.093457 AGTAATGTGTTATCAGTCGTGTCG 58.907 41.667 0.00 0.00 0.00 4.35
2100 2124 6.365247 ACAAGTAATGTGTTATCAGTCGTGTC 59.635 38.462 0.00 0.00 41.93 3.67
2101 2125 6.220930 ACAAGTAATGTGTTATCAGTCGTGT 58.779 36.000 0.00 0.00 41.93 4.49
2102 2126 6.706055 ACAAGTAATGTGTTATCAGTCGTG 57.294 37.500 0.00 0.00 41.93 4.35
2103 2127 7.541091 CACTACAAGTAATGTGTTATCAGTCGT 59.459 37.037 0.00 0.00 43.77 4.34
2104 2128 7.541091 ACACTACAAGTAATGTGTTATCAGTCG 59.459 37.037 0.00 0.00 43.77 4.18
2105 2129 8.758633 ACACTACAAGTAATGTGTTATCAGTC 57.241 34.615 0.00 0.00 43.77 3.51
2113 2137 6.926826 TGAATCGAACACTACAAGTAATGTGT 59.073 34.615 0.00 0.00 43.77 3.72
2114 2138 7.346208 TGAATCGAACACTACAAGTAATGTG 57.654 36.000 0.00 0.00 43.77 3.21
2115 2139 7.956420 TTGAATCGAACACTACAAGTAATGT 57.044 32.000 0.00 0.00 46.36 2.71
2116 2140 9.265938 CATTTGAATCGAACACTACAAGTAATG 57.734 33.333 0.00 0.00 0.00 1.90
2117 2141 8.450964 CCATTTGAATCGAACACTACAAGTAAT 58.549 33.333 0.00 0.00 0.00 1.89
2118 2142 7.442969 ACCATTTGAATCGAACACTACAAGTAA 59.557 33.333 0.00 0.00 0.00 2.24
2119 2143 6.932400 ACCATTTGAATCGAACACTACAAGTA 59.068 34.615 0.00 0.00 0.00 2.24
2120 2144 5.763204 ACCATTTGAATCGAACACTACAAGT 59.237 36.000 0.00 0.00 0.00 3.16
2121 2145 6.079763 CACCATTTGAATCGAACACTACAAG 58.920 40.000 0.00 0.00 0.00 3.16
2122 2146 5.561919 GCACCATTTGAATCGAACACTACAA 60.562 40.000 0.00 0.00 0.00 2.41
2123 2147 4.083537 GCACCATTTGAATCGAACACTACA 60.084 41.667 0.00 0.00 0.00 2.74
2124 2148 4.154195 AGCACCATTTGAATCGAACACTAC 59.846 41.667 0.00 0.00 0.00 2.73
2125 2149 4.323417 AGCACCATTTGAATCGAACACTA 58.677 39.130 0.00 0.00 0.00 2.74
2126 2150 3.149196 AGCACCATTTGAATCGAACACT 58.851 40.909 0.00 0.00 0.00 3.55
2127 2151 3.559238 AGCACCATTTGAATCGAACAC 57.441 42.857 0.00 0.00 0.00 3.32
2128 2152 5.895636 ATTAGCACCATTTGAATCGAACA 57.104 34.783 0.00 0.00 0.00 3.18
2129 2153 7.376866 CACATATTAGCACCATTTGAATCGAAC 59.623 37.037 0.00 0.00 0.00 3.95
2130 2154 7.416817 CACATATTAGCACCATTTGAATCGAA 58.583 34.615 0.00 0.00 0.00 3.71
2131 2155 6.513230 GCACATATTAGCACCATTTGAATCGA 60.513 38.462 0.00 0.00 0.00 3.59
2132 2156 5.626543 GCACATATTAGCACCATTTGAATCG 59.373 40.000 0.00 0.00 0.00 3.34
2133 2157 6.506147 TGCACATATTAGCACCATTTGAATC 58.494 36.000 0.00 0.00 35.51 2.52
2134 2158 6.468333 TGCACATATTAGCACCATTTGAAT 57.532 33.333 0.00 0.00 35.51 2.57
2135 2159 5.911378 TGCACATATTAGCACCATTTGAA 57.089 34.783 0.00 0.00 35.51 2.69
2144 2168 2.880268 GCTGATGGTGCACATATTAGCA 59.120 45.455 28.96 15.51 40.72 3.49
2145 2169 2.880268 TGCTGATGGTGCACATATTAGC 59.120 45.455 28.04 28.04 40.72 3.09
2146 2170 5.009310 ACATTGCTGATGGTGCACATATTAG 59.991 40.000 20.43 17.72 40.72 1.73
2147 2171 4.888823 ACATTGCTGATGGTGCACATATTA 59.111 37.500 20.43 8.27 40.72 0.98
2148 2172 3.702548 ACATTGCTGATGGTGCACATATT 59.297 39.130 20.43 0.00 40.72 1.28
2149 2173 3.067601 CACATTGCTGATGGTGCACATAT 59.932 43.478 20.43 12.38 40.72 1.78
2150 2174 2.424246 CACATTGCTGATGGTGCACATA 59.576 45.455 20.43 7.39 40.72 2.29
2151 2175 1.203758 CACATTGCTGATGGTGCACAT 59.796 47.619 20.43 10.28 44.18 3.21
2152 2176 0.599060 CACATTGCTGATGGTGCACA 59.401 50.000 20.43 5.24 40.40 4.57
2153 2177 0.599558 ACACATTGCTGATGGTGCAC 59.400 50.000 8.80 8.80 40.40 4.57
2154 2178 0.883153 GACACATTGCTGATGGTGCA 59.117 50.000 5.78 0.00 40.21 4.57
2155 2179 0.171903 GGACACATTGCTGATGGTGC 59.828 55.000 5.78 3.18 40.21 5.01
2156 2180 1.471287 CAGGACACATTGCTGATGGTG 59.529 52.381 5.78 0.00 46.53 4.17
2157 2181 1.615116 CCAGGACACATTGCTGATGGT 60.615 52.381 5.78 1.64 46.53 3.55
2158 2182 1.100510 CCAGGACACATTGCTGATGG 58.899 55.000 5.78 0.00 46.53 3.51
2159 2183 1.100510 CCCAGGACACATTGCTGATG 58.899 55.000 0.00 0.00 46.53 3.07
2160 2184 0.994247 TCCCAGGACACATTGCTGAT 59.006 50.000 0.00 0.00 46.53 2.90
2161 2185 0.036732 GTCCCAGGACACATTGCTGA 59.963 55.000 12.05 0.00 46.53 4.26
2162 2186 0.962356 GGTCCCAGGACACATTGCTG 60.962 60.000 18.28 0.00 46.20 4.41
2163 2187 1.380302 GGTCCCAGGACACATTGCT 59.620 57.895 18.28 0.00 46.20 3.91
2164 2188 2.040544 CGGTCCCAGGACACATTGC 61.041 63.158 18.28 0.00 46.20 3.56
2165 2189 2.040544 GCGGTCCCAGGACACATTG 61.041 63.158 18.28 3.99 46.20 2.82
2166 2190 2.351276 GCGGTCCCAGGACACATT 59.649 61.111 18.28 0.00 46.20 2.71
2167 2191 2.927856 TGCGGTCCCAGGACACAT 60.928 61.111 18.28 0.00 46.20 3.21
2168 2192 3.625897 CTGCGGTCCCAGGACACA 61.626 66.667 18.28 13.89 46.20 3.72
2170 2194 3.897681 TAGCTGCGGTCCCAGGACA 62.898 63.158 18.28 0.00 46.20 4.02
2171 2195 3.075005 TAGCTGCGGTCCCAGGAC 61.075 66.667 8.40 8.40 43.87 3.85
2172 2196 2.219449 TACTAGCTGCGGTCCCAGGA 62.219 60.000 0.00 0.00 33.44 3.86
2173 2197 1.756950 TACTAGCTGCGGTCCCAGG 60.757 63.158 0.00 0.00 33.44 4.45
2174 2198 1.437986 GTACTAGCTGCGGTCCCAG 59.562 63.158 0.00 3.62 35.93 4.45
2175 2199 2.412323 CGTACTAGCTGCGGTCCCA 61.412 63.158 0.00 0.00 0.00 4.37
2176 2200 2.412112 CGTACTAGCTGCGGTCCC 59.588 66.667 0.00 0.00 0.00 4.46
2177 2201 2.412112 CCGTACTAGCTGCGGTCC 59.588 66.667 11.65 0.00 42.87 4.46
2178 2202 2.412112 CCCGTACTAGCTGCGGTC 59.588 66.667 16.20 0.00 46.22 4.79
2179 2203 2.898920 TAGCCCGTACTAGCTGCGGT 62.899 60.000 14.74 6.55 46.22 5.68
2181 2205 0.314302 AATAGCCCGTACTAGCTGCG 59.686 55.000 14.74 0.00 40.28 5.18
2182 2206 1.340248 TGAATAGCCCGTACTAGCTGC 59.660 52.381 14.74 0.00 40.28 5.25
2183 2207 2.608261 GCTGAATAGCCCGTACTAGCTG 60.608 54.545 14.74 1.61 44.33 4.24
2184 2208 1.614413 GCTGAATAGCCCGTACTAGCT 59.386 52.381 10.82 10.82 44.33 3.32
2185 2209 2.067414 GCTGAATAGCCCGTACTAGC 57.933 55.000 0.00 0.00 44.33 3.42
2208 2232 2.001880 GCGGCGTTCAACGTGAAAC 61.002 57.895 12.40 0.00 44.73 2.78
2209 2233 1.978712 TTGCGGCGTTCAACGTGAAA 61.979 50.000 12.40 2.64 44.73 2.69
2210 2234 1.978712 TTTGCGGCGTTCAACGTGAA 61.979 50.000 12.40 0.00 44.73 3.18
2211 2235 1.777030 ATTTGCGGCGTTCAACGTGA 61.777 50.000 12.40 0.00 44.73 4.35
2212 2236 0.110599 TATTTGCGGCGTTCAACGTG 60.111 50.000 12.40 5.87 44.73 4.49
2213 2237 0.800012 ATATTTGCGGCGTTCAACGT 59.200 45.000 12.40 0.00 44.73 3.99
2214 2238 1.179332 CATATTTGCGGCGTTCAACG 58.821 50.000 5.28 5.28 45.88 4.10
2215 2239 2.256445 ACATATTTGCGGCGTTCAAC 57.744 45.000 9.37 0.00 0.00 3.18
2216 2240 2.999507 AACATATTTGCGGCGTTCAA 57.000 40.000 9.37 1.68 0.00 2.69
2217 2241 2.742589 TGTAACATATTTGCGGCGTTCA 59.257 40.909 9.37 0.00 0.00 3.18
2218 2242 3.392769 TGTAACATATTTGCGGCGTTC 57.607 42.857 9.37 0.00 0.00 3.95
2219 2243 4.573201 AGTATGTAACATATTTGCGGCGTT 59.427 37.500 9.37 0.00 0.00 4.84
2220 2244 4.124238 AGTATGTAACATATTTGCGGCGT 58.876 39.130 9.37 0.00 0.00 5.68
2221 2245 4.725556 AGTATGTAACATATTTGCGGCG 57.274 40.909 0.51 0.51 0.00 6.46
2222 2246 6.780706 ACTAGTATGTAACATATTTGCGGC 57.219 37.500 0.00 0.00 0.00 6.53
2233 2257 6.501781 AGGATGCACGTTACTAGTATGTAAC 58.498 40.000 2.79 0.00 45.06 2.50
2234 2258 6.704289 AGGATGCACGTTACTAGTATGTAA 57.296 37.500 2.79 0.00 0.00 2.41
2235 2259 6.767423 TGTAGGATGCACGTTACTAGTATGTA 59.233 38.462 2.79 0.00 0.00 2.29
2236 2260 5.591472 TGTAGGATGCACGTTACTAGTATGT 59.409 40.000 2.79 3.02 0.00 2.29
2237 2261 6.068473 TGTAGGATGCACGTTACTAGTATG 57.932 41.667 2.79 0.39 0.00 2.39
2238 2262 6.715718 AGATGTAGGATGCACGTTACTAGTAT 59.284 38.462 2.79 0.00 29.56 2.12
2239 2263 6.060136 AGATGTAGGATGCACGTTACTAGTA 58.940 40.000 0.00 0.00 29.56 1.82
2240 2264 4.888239 AGATGTAGGATGCACGTTACTAGT 59.112 41.667 0.00 0.00 29.56 2.57
2241 2265 5.239744 AGAGATGTAGGATGCACGTTACTAG 59.760 44.000 0.00 0.00 29.56 2.57
2242 2266 5.008712 CAGAGATGTAGGATGCACGTTACTA 59.991 44.000 0.00 0.00 29.56 1.82
2243 2267 3.954904 AGAGATGTAGGATGCACGTTACT 59.045 43.478 0.00 0.00 29.56 2.24
2244 2268 4.045104 CAGAGATGTAGGATGCACGTTAC 58.955 47.826 0.00 0.00 29.56 2.50
2245 2269 4.307443 CAGAGATGTAGGATGCACGTTA 57.693 45.455 0.00 0.00 29.56 3.18
2246 2270 3.170791 CAGAGATGTAGGATGCACGTT 57.829 47.619 0.00 0.00 29.56 3.99
2247 2271 2.879002 CAGAGATGTAGGATGCACGT 57.121 50.000 0.00 0.00 29.56 4.49


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

AutoCloner maintained by Alex Coulton.