Multiple sequence alignment - TraesCS7D01G200400

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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 TraesCS7D01G200400 chr7D 100.000 2339 0 0 1 2339 158962629 158964967 0.000000e+00 4320
1 TraesCS7D01G200400 chr7D 95.430 372 16 1 1663 2034 158969909 158970279 2.000000e-165 592
2 TraesCS7D01G200400 chr7D 88.433 268 22 7 1397 1662 157099449 157099709 4.850000e-82 315
3 TraesCS7D01G200400 chr7D 84.270 267 29 9 1384 1647 156916284 156916540 4.990000e-62 248
4 TraesCS7D01G200400 chr7D 95.652 46 2 0 1368 1413 157099380 157099425 8.960000e-10 75
5 TraesCS7D01G200400 chr6D 91.886 1294 93 6 73 1363 356158042 356156758 0.000000e+00 1797
6 TraesCS7D01G200400 chr4D 91.288 1297 103 7 73 1363 349920334 349921626 0.000000e+00 1760
7 TraesCS7D01G200400 chr4D 86.823 683 73 12 1659 2336 435179865 435180535 0.000000e+00 747
8 TraesCS7D01G200400 chr4D 84.085 377 49 11 1663 2034 435185474 435185844 1.030000e-93 353
9 TraesCS7D01G200400 chr4A 91.389 1289 103 6 85 1367 621856355 621857641 0.000000e+00 1759
10 TraesCS7D01G200400 chr7A 90.678 1298 105 14 73 1364 241745450 241744163 0.000000e+00 1712
11 TraesCS7D01G200400 chr6A 90.584 1285 113 7 73 1351 101365468 101364186 0.000000e+00 1696
12 TraesCS7D01G200400 chr5B 90.425 1295 107 12 73 1361 508067987 508066704 0.000000e+00 1688
13 TraesCS7D01G200400 chr5B 88.059 1298 148 6 73 1364 521395061 521396357 0.000000e+00 1531
14 TraesCS7D01G200400 chr4B 90.739 1231 104 8 73 1297 86653064 86651838 0.000000e+00 1633
15 TraesCS7D01G200400 chr3D 88.000 1300 148 5 73 1366 264599552 264600849 0.000000e+00 1530
16 TraesCS7D01G200400 chr5D 80.961 562 97 10 1661 2217 398870521 398871077 9.920000e-119 436
17 TraesCS7D01G200400 chr7B 89.286 280 20 6 1384 1662 119582439 119582709 2.230000e-90 342
18 TraesCS7D01G200400 chr2A 83.491 212 34 1 2120 2330 156659672 156659461 1.830000e-46 196


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 TraesCS7D01G200400 chr7D 158962629 158964967 2338 False 4320 4320 100.000 1 2339 1 chr7D.!!$F2 2338
1 TraesCS7D01G200400 chr6D 356156758 356158042 1284 True 1797 1797 91.886 73 1363 1 chr6D.!!$R1 1290
2 TraesCS7D01G200400 chr4D 349920334 349921626 1292 False 1760 1760 91.288 73 1363 1 chr4D.!!$F1 1290
3 TraesCS7D01G200400 chr4D 435179865 435180535 670 False 747 747 86.823 1659 2336 1 chr4D.!!$F2 677
4 TraesCS7D01G200400 chr4A 621856355 621857641 1286 False 1759 1759 91.389 85 1367 1 chr4A.!!$F1 1282
5 TraesCS7D01G200400 chr7A 241744163 241745450 1287 True 1712 1712 90.678 73 1364 1 chr7A.!!$R1 1291
6 TraesCS7D01G200400 chr6A 101364186 101365468 1282 True 1696 1696 90.584 73 1351 1 chr6A.!!$R1 1278
7 TraesCS7D01G200400 chr5B 508066704 508067987 1283 True 1688 1688 90.425 73 1361 1 chr5B.!!$R1 1288
8 TraesCS7D01G200400 chr5B 521395061 521396357 1296 False 1531 1531 88.059 73 1364 1 chr5B.!!$F1 1291
9 TraesCS7D01G200400 chr4B 86651838 86653064 1226 True 1633 1633 90.739 73 1297 1 chr4B.!!$R1 1224
10 TraesCS7D01G200400 chr3D 264599552 264600849 1297 False 1530 1530 88.000 73 1366 1 chr3D.!!$F1 1293
11 TraesCS7D01G200400 chr5D 398870521 398871077 556 False 436 436 80.961 1661 2217 1 chr5D.!!$F1 556

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
927 938 0.249073 CTGAAGGGTACGATGGAGCG 60.249 60.0 0.0 0.0 37.29 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 1993 0.25589 AGCAATTCCGGCACATACCT 59.744 50.0 0.0 0.0 0.0 3.08 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
56 57 7.582667 AGGCACTTTTGTTGTAATTAGAACT 57.417 32.000 21.92 3.37 27.25 3.01
57 58 8.685838 AGGCACTTTTGTTGTAATTAGAACTA 57.314 30.769 21.92 14.29 27.25 2.24
58 59 8.565416 AGGCACTTTTGTTGTAATTAGAACTAC 58.435 33.333 21.92 5.91 27.25 2.73
59 60 8.565416 GGCACTTTTGTTGTAATTAGAACTACT 58.435 33.333 21.92 2.46 31.45 2.57
60 61 9.946165 GCACTTTTGTTGTAATTAGAACTACTT 57.054 29.630 21.92 4.82 31.45 2.24
167 169 8.783660 ATGAGGACCTGATTAGACAAACTATA 57.216 34.615 0.00 0.00 0.00 1.31
182 184 1.078709 CTATATGGCCCATTGACGCG 58.921 55.000 0.00 3.53 0.00 6.01
198 200 1.131126 ACGCGCAATGGATTCTTTCAG 59.869 47.619 5.73 0.00 0.00 3.02
201 203 2.421424 GCGCAATGGATTCTTTCAGTCT 59.579 45.455 0.30 0.00 0.00 3.24
253 255 5.584649 TCATTGCCTGGAGTTATACGAAAAG 59.415 40.000 0.00 0.00 0.00 2.27
272 274 4.877378 AAGTGGTATGTTCTTGGTACGA 57.123 40.909 0.00 0.00 0.00 3.43
317 319 6.708054 GGAATCATCAGTATGGGAGTAAACTG 59.292 42.308 0.00 0.00 40.54 3.16
371 373 9.866655 ACACATAATCCTATATGGTGTCAAATT 57.133 29.630 0.00 0.00 37.55 1.82
388 390 8.352942 GTGTCAAATTTGGAAGTTATCTTGTCT 58.647 33.333 17.90 0.00 33.64 3.41
439 443 3.025599 ATGGCACCCTCCCATGCT 61.026 61.111 0.00 0.00 41.40 3.79
442 446 3.731728 GCACCCTCCCATGCTGGA 61.732 66.667 4.00 0.00 40.96 3.86
465 469 4.514781 AACACTCGCTAACAGACACATA 57.485 40.909 0.00 0.00 0.00 2.29
492 496 4.028131 TCTCGCCCTCTTGTCCTAATTTA 58.972 43.478 0.00 0.00 0.00 1.40
523 528 7.383687 AGGTTTAGAAGATACGAAACACATGA 58.616 34.615 0.00 0.00 37.20 3.07
652 659 4.658901 ACCTTCTACTTCTTCCTGACCAAA 59.341 41.667 0.00 0.00 0.00 3.28
696 703 6.038271 ACCAAAATGTACGAGAAATGATAGCC 59.962 38.462 0.00 0.00 0.00 3.93
797 805 1.707427 GGGGATCATAGCCCTCACATT 59.293 52.381 0.00 0.00 45.30 2.71
801 809 4.508047 GGGATCATAGCCCTCACATTCAAT 60.508 45.833 0.00 0.00 42.56 2.57
840 851 2.286365 AAGGCGTCCATGAAAAAGGA 57.714 45.000 0.00 0.00 0.00 3.36
889 900 5.493133 TTGTGAAACTTAATGTTGACGCT 57.507 34.783 0.00 0.00 39.13 5.07
927 938 0.249073 CTGAAGGGTACGATGGAGCG 60.249 60.000 0.00 0.00 37.29 5.03
928 939 1.067582 GAAGGGTACGATGGAGCGG 59.932 63.158 0.00 0.00 35.12 5.52
929 940 1.673808 GAAGGGTACGATGGAGCGGT 61.674 60.000 0.00 0.00 35.12 5.68
930 941 0.396139 AAGGGTACGATGGAGCGGTA 60.396 55.000 0.00 0.00 35.12 4.02
932 943 1.361632 GGTACGATGGAGCGGTACC 59.638 63.158 0.16 0.16 33.90 3.34
936 948 2.728817 GATGGAGCGGTACCGAGG 59.271 66.667 37.62 9.90 42.83 4.63
1010 1022 2.679837 CGGATGTTCTGATGGTTGAAGG 59.320 50.000 0.00 0.00 0.00 3.46
1060 1072 1.944234 GCAAAGGGCGGGGTGTAATG 61.944 60.000 0.00 0.00 0.00 1.90
1112 1125 3.566322 GTGATAGAGACTATGCAGGACGT 59.434 47.826 0.00 0.00 0.00 4.34
1264 1278 9.980780 GATTAGCTAGATTTTCTTTGACTTCAC 57.019 33.333 0.00 0.00 0.00 3.18
1299 1313 8.829373 AGGAGCCTCTAAATGAAATTGTAATT 57.171 30.769 0.00 0.00 36.10 1.40
1388 1402 7.396540 AACTATTTTAGTTGGAGATGCCTTG 57.603 36.000 0.00 0.00 46.58 3.61
1389 1403 6.721318 ACTATTTTAGTTGGAGATGCCTTGA 58.279 36.000 0.00 0.00 34.86 3.02
1390 1404 5.904362 ATTTTAGTTGGAGATGCCTTGAC 57.096 39.130 0.00 0.00 37.63 3.18
1391 1405 4.365514 TTTAGTTGGAGATGCCTTGACA 57.634 40.909 0.00 0.00 37.63 3.58
1392 1406 2.957402 AGTTGGAGATGCCTTGACAA 57.043 45.000 0.00 0.00 37.63 3.18
1393 1407 2.787994 AGTTGGAGATGCCTTGACAAG 58.212 47.619 8.31 8.31 37.63 3.16
1394 1408 1.200948 GTTGGAGATGCCTTGACAAGC 59.799 52.381 9.85 6.22 37.63 4.01
1395 1409 0.322816 TGGAGATGCCTTGACAAGCC 60.323 55.000 9.85 5.13 37.63 4.35
1396 1410 0.322816 GGAGATGCCTTGACAAGCCA 60.323 55.000 9.85 5.40 0.00 4.75
1397 1411 1.538047 GAGATGCCTTGACAAGCCAA 58.462 50.000 9.85 0.00 0.00 4.52
1398 1412 1.888512 GAGATGCCTTGACAAGCCAAA 59.111 47.619 9.85 0.00 0.00 3.28
1399 1413 1.615392 AGATGCCTTGACAAGCCAAAC 59.385 47.619 9.85 4.45 0.00 2.93
1400 1414 1.340889 GATGCCTTGACAAGCCAAACA 59.659 47.619 9.85 3.13 0.00 2.83
1401 1415 0.746063 TGCCTTGACAAGCCAAACAG 59.254 50.000 9.85 0.00 0.00 3.16
1402 1416 0.598419 GCCTTGACAAGCCAAACAGC 60.598 55.000 9.85 2.35 0.00 4.40
1404 1418 1.000938 CCTTGACAAGCCAAACAGCTC 60.001 52.381 9.85 0.00 44.11 4.09
1405 1419 0.662619 TTGACAAGCCAAACAGCTCG 59.337 50.000 0.00 0.00 44.11 5.03
1406 1420 0.463654 TGACAAGCCAAACAGCTCGT 60.464 50.000 0.00 0.00 44.11 4.18
1407 1421 0.663153 GACAAGCCAAACAGCTCGTT 59.337 50.000 0.00 0.00 44.11 3.85
1408 1422 0.663153 ACAAGCCAAACAGCTCGTTC 59.337 50.000 2.65 0.00 44.11 3.95
1409 1423 0.040067 CAAGCCAAACAGCTCGTTCC 60.040 55.000 2.65 0.00 44.11 3.62
1410 1424 0.179018 AAGCCAAACAGCTCGTTCCT 60.179 50.000 2.65 0.00 44.11 3.36
1411 1425 0.603975 AGCCAAACAGCTCGTTCCTC 60.604 55.000 2.65 0.00 39.48 3.71
1412 1426 0.884704 GCCAAACAGCTCGTTCCTCA 60.885 55.000 2.65 0.00 36.59 3.86
1413 1427 0.868406 CCAAACAGCTCGTTCCTCAC 59.132 55.000 2.65 0.00 36.59 3.51
1414 1428 0.868406 CAAACAGCTCGTTCCTCACC 59.132 55.000 2.65 0.00 36.59 4.02
1415 1429 0.250338 AAACAGCTCGTTCCTCACCC 60.250 55.000 2.65 0.00 36.59 4.61
1416 1430 2.113243 AACAGCTCGTTCCTCACCCC 62.113 60.000 0.00 0.00 29.27 4.95
1417 1431 3.382832 AGCTCGTTCCTCACCCCG 61.383 66.667 0.00 0.00 0.00 5.73
1418 1432 3.692406 GCTCGTTCCTCACCCCGT 61.692 66.667 0.00 0.00 0.00 5.28
1419 1433 2.261671 CTCGTTCCTCACCCCGTG 59.738 66.667 0.00 0.00 34.45 4.94
1420 1434 3.296709 CTCGTTCCTCACCCCGTGG 62.297 68.421 0.00 0.00 33.87 4.94
1422 1436 2.346365 GTTCCTCACCCCGTGGTC 59.654 66.667 0.00 0.00 45.57 4.02
1423 1437 3.307906 TTCCTCACCCCGTGGTCG 61.308 66.667 0.00 0.00 45.57 4.79
1441 1455 3.735181 GGTAGTGACCGTGGATCAC 57.265 57.895 11.35 11.35 45.70 3.06
1465 1479 2.264480 CCGTGTGGGAGCGAATCA 59.736 61.111 0.00 0.00 38.47 2.57
1466 1480 1.811266 CCGTGTGGGAGCGAATCAG 60.811 63.158 0.00 0.00 38.47 2.90
1467 1481 2.456119 CGTGTGGGAGCGAATCAGC 61.456 63.158 0.00 0.00 37.41 4.26
1475 1489 4.445699 GCGAATCAGCTAGTGGGG 57.554 61.111 0.00 0.00 0.00 4.96
1476 1490 1.227674 GCGAATCAGCTAGTGGGGG 60.228 63.158 0.00 0.00 0.00 5.40
1477 1491 1.686325 GCGAATCAGCTAGTGGGGGA 61.686 60.000 0.00 0.00 0.00 4.81
1478 1492 0.830648 CGAATCAGCTAGTGGGGGAA 59.169 55.000 0.00 0.00 0.00 3.97
1479 1493 1.473434 CGAATCAGCTAGTGGGGGAAC 60.473 57.143 0.00 0.00 0.00 3.62
1480 1494 1.840635 GAATCAGCTAGTGGGGGAACT 59.159 52.381 0.00 0.00 0.00 3.01
1481 1495 1.501582 ATCAGCTAGTGGGGGAACTC 58.498 55.000 0.00 0.00 0.00 3.01
1482 1496 0.413832 TCAGCTAGTGGGGGAACTCT 59.586 55.000 0.00 0.00 0.00 3.24
1483 1497 0.827368 CAGCTAGTGGGGGAACTCTC 59.173 60.000 0.00 0.00 0.00 3.20
1484 1498 0.713579 AGCTAGTGGGGGAACTCTCT 59.286 55.000 0.00 0.00 38.45 3.10
1485 1499 0.827368 GCTAGTGGGGGAACTCTCTG 59.173 60.000 0.00 0.00 34.97 3.35
1486 1500 1.897647 GCTAGTGGGGGAACTCTCTGT 60.898 57.143 0.00 0.00 34.97 3.41
1487 1501 1.827969 CTAGTGGGGGAACTCTCTGTG 59.172 57.143 0.00 0.00 34.97 3.66
1488 1502 1.003233 GTGGGGGAACTCTCTGTGC 60.003 63.158 0.00 0.00 0.00 4.57
1489 1503 2.224159 TGGGGGAACTCTCTGTGCC 61.224 63.158 0.00 0.00 44.01 5.01
1493 1507 1.599576 GGAACTCTCTGTGCCCTCC 59.400 63.158 0.00 0.00 38.50 4.30
1494 1508 1.216710 GAACTCTCTGTGCCCTCCG 59.783 63.158 0.00 0.00 0.00 4.63
1495 1509 2.844072 GAACTCTCTGTGCCCTCCGC 62.844 65.000 0.00 0.00 38.31 5.54
1496 1510 3.073735 CTCTCTGTGCCCTCCGCT 61.074 66.667 0.00 0.00 38.78 5.52
1497 1511 2.604686 TCTCTGTGCCCTCCGCTT 60.605 61.111 0.00 0.00 38.78 4.68
1498 1512 2.125350 CTCTGTGCCCTCCGCTTC 60.125 66.667 0.00 0.00 38.78 3.86
1499 1513 3.997064 CTCTGTGCCCTCCGCTTCG 62.997 68.421 0.00 0.00 38.78 3.79
1527 1541 4.785453 CCGCAGCACTTCCTCCCC 62.785 72.222 0.00 0.00 0.00 4.81
1528 1542 4.785453 CGCAGCACTTCCTCCCCC 62.785 72.222 0.00 0.00 0.00 5.40
1529 1543 3.334054 GCAGCACTTCCTCCCCCT 61.334 66.667 0.00 0.00 0.00 4.79
1530 1544 2.911926 GCAGCACTTCCTCCCCCTT 61.912 63.158 0.00 0.00 0.00 3.95
1531 1545 1.001641 CAGCACTTCCTCCCCCTTG 60.002 63.158 0.00 0.00 0.00 3.61
1532 1546 1.464198 AGCACTTCCTCCCCCTTGT 60.464 57.895 0.00 0.00 0.00 3.16
1533 1547 1.002011 GCACTTCCTCCCCCTTGTC 60.002 63.158 0.00 0.00 0.00 3.18
1534 1548 1.492993 GCACTTCCTCCCCCTTGTCT 61.493 60.000 0.00 0.00 0.00 3.41
1535 1549 1.068121 CACTTCCTCCCCCTTGTCTT 58.932 55.000 0.00 0.00 0.00 3.01
1536 1550 1.003696 CACTTCCTCCCCCTTGTCTTC 59.996 57.143 0.00 0.00 0.00 2.87
1537 1551 1.132365 ACTTCCTCCCCCTTGTCTTCT 60.132 52.381 0.00 0.00 0.00 2.85
1538 1552 1.557371 CTTCCTCCCCCTTGTCTTCTC 59.443 57.143 0.00 0.00 0.00 2.87
1539 1553 0.793617 TCCTCCCCCTTGTCTTCTCT 59.206 55.000 0.00 0.00 0.00 3.10
1540 1554 0.908198 CCTCCCCCTTGTCTTCTCTG 59.092 60.000 0.00 0.00 0.00 3.35
1541 1555 0.251634 CTCCCCCTTGTCTTCTCTGC 59.748 60.000 0.00 0.00 0.00 4.26
1542 1556 1.201429 TCCCCCTTGTCTTCTCTGCC 61.201 60.000 0.00 0.00 0.00 4.85
1543 1557 1.078848 CCCCTTGTCTTCTCTGCCG 60.079 63.158 0.00 0.00 0.00 5.69
1544 1558 1.078848 CCCTTGTCTTCTCTGCCGG 60.079 63.158 0.00 0.00 0.00 6.13
1545 1559 1.743252 CCTTGTCTTCTCTGCCGGC 60.743 63.158 22.73 22.73 0.00 6.13
1546 1560 1.743252 CTTGTCTTCTCTGCCGGCC 60.743 63.158 26.77 5.97 0.00 6.13
1547 1561 2.177594 CTTGTCTTCTCTGCCGGCCT 62.178 60.000 26.77 0.00 0.00 5.19
1548 1562 0.902984 TTGTCTTCTCTGCCGGCCTA 60.903 55.000 26.77 11.23 0.00 3.93
1549 1563 1.142097 GTCTTCTCTGCCGGCCTAC 59.858 63.158 26.77 7.52 0.00 3.18
1550 1564 2.058595 TCTTCTCTGCCGGCCTACC 61.059 63.158 26.77 0.00 0.00 3.18
1551 1565 3.081409 TTCTCTGCCGGCCTACCC 61.081 66.667 26.77 0.00 0.00 3.69
1561 1575 3.613689 GCCTACCCCGATCCGGTC 61.614 72.222 0.00 0.00 46.80 4.79
1562 1576 3.292936 CCTACCCCGATCCGGTCG 61.293 72.222 16.41 16.41 46.80 4.79
1586 1600 3.322466 CCACCGCCTCTCCCAGTT 61.322 66.667 0.00 0.00 0.00 3.16
1587 1601 2.750350 CACCGCCTCTCCCAGTTT 59.250 61.111 0.00 0.00 0.00 2.66
1588 1602 1.376037 CACCGCCTCTCCCAGTTTC 60.376 63.158 0.00 0.00 0.00 2.78
1589 1603 2.269241 CCGCCTCTCCCAGTTTCC 59.731 66.667 0.00 0.00 0.00 3.13
1590 1604 2.592993 CCGCCTCTCCCAGTTTCCA 61.593 63.158 0.00 0.00 0.00 3.53
1591 1605 1.376037 CGCCTCTCCCAGTTTCCAC 60.376 63.158 0.00 0.00 0.00 4.02
1592 1606 1.002011 GCCTCTCCCAGTTTCCACC 60.002 63.158 0.00 0.00 0.00 4.61
1593 1607 1.492993 GCCTCTCCCAGTTTCCACCT 61.493 60.000 0.00 0.00 0.00 4.00
1594 1608 0.326264 CCTCTCCCAGTTTCCACCTG 59.674 60.000 0.00 0.00 0.00 4.00
1595 1609 0.322008 CTCTCCCAGTTTCCACCTGC 60.322 60.000 0.00 0.00 0.00 4.85
1596 1610 1.059584 TCTCCCAGTTTCCACCTGCA 61.060 55.000 0.00 0.00 0.00 4.41
1597 1611 0.890996 CTCCCAGTTTCCACCTGCAC 60.891 60.000 0.00 0.00 0.00 4.57
1598 1612 2.260869 CCCAGTTTCCACCTGCACG 61.261 63.158 0.00 0.00 0.00 5.34
1599 1613 2.639286 CAGTTTCCACCTGCACGC 59.361 61.111 0.00 0.00 0.00 5.34
1600 1614 2.594592 AGTTTCCACCTGCACGCC 60.595 61.111 0.00 0.00 0.00 5.68
1601 1615 2.904866 GTTTCCACCTGCACGCCA 60.905 61.111 0.00 0.00 0.00 5.69
1602 1616 2.115052 TTTCCACCTGCACGCCAT 59.885 55.556 0.00 0.00 0.00 4.40
1603 1617 1.530419 TTTCCACCTGCACGCCATT 60.530 52.632 0.00 0.00 0.00 3.16
1604 1618 1.523154 TTTCCACCTGCACGCCATTC 61.523 55.000 0.00 0.00 0.00 2.67
1605 1619 3.443045 CCACCTGCACGCCATTCC 61.443 66.667 0.00 0.00 0.00 3.01
1606 1620 3.443045 CACCTGCACGCCATTCCC 61.443 66.667 0.00 0.00 0.00 3.97
1607 1621 3.650950 ACCTGCACGCCATTCCCT 61.651 61.111 0.00 0.00 0.00 4.20
1608 1622 3.136123 CCTGCACGCCATTCCCTG 61.136 66.667 0.00 0.00 0.00 4.45
1610 1624 4.738998 TGCACGCCATTCCCTGGG 62.739 66.667 6.33 6.33 46.06 4.45
1616 1630 4.506255 CCATTCCCTGGGGGCGAC 62.506 72.222 14.00 0.00 43.94 5.19
1617 1631 4.856801 CATTCCCTGGGGGCGACG 62.857 72.222 14.00 0.00 43.94 5.12
1634 1648 4.166011 GCCGTCCGCTGCATGTTC 62.166 66.667 0.00 0.00 0.00 3.18
1635 1649 3.499737 CCGTCCGCTGCATGTTCC 61.500 66.667 0.00 0.00 0.00 3.62
1636 1650 3.853330 CGTCCGCTGCATGTTCCG 61.853 66.667 0.00 0.00 0.00 4.30
1637 1651 4.166011 GTCCGCTGCATGTTCCGC 62.166 66.667 0.00 0.00 0.00 5.54
1640 1654 4.465512 CGCTGCATGTTCCGCCAC 62.466 66.667 0.00 0.00 0.00 5.01
1641 1655 4.120331 GCTGCATGTTCCGCCACC 62.120 66.667 0.00 0.00 0.00 4.61
1642 1656 2.360350 CTGCATGTTCCGCCACCT 60.360 61.111 0.00 0.00 0.00 4.00
1643 1657 2.359850 TGCATGTTCCGCCACCTC 60.360 61.111 0.00 0.00 0.00 3.85
1644 1658 2.045926 GCATGTTCCGCCACCTCT 60.046 61.111 0.00 0.00 0.00 3.69
1645 1659 1.220749 GCATGTTCCGCCACCTCTA 59.779 57.895 0.00 0.00 0.00 2.43
1646 1660 1.090052 GCATGTTCCGCCACCTCTAC 61.090 60.000 0.00 0.00 0.00 2.59
1647 1661 0.462047 CATGTTCCGCCACCTCTACC 60.462 60.000 0.00 0.00 0.00 3.18
1648 1662 1.623542 ATGTTCCGCCACCTCTACCC 61.624 60.000 0.00 0.00 0.00 3.69
1649 1663 2.686106 TTCCGCCACCTCTACCCC 60.686 66.667 0.00 0.00 0.00 4.95
1653 1667 3.468140 GCCACCTCTACCCCGGTC 61.468 72.222 0.00 0.00 0.00 4.79
1654 1668 2.038329 CCACCTCTACCCCGGTCA 59.962 66.667 0.00 0.00 0.00 4.02
1655 1669 1.611261 CCACCTCTACCCCGGTCAA 60.611 63.158 0.00 0.00 0.00 3.18
1656 1670 1.595357 CACCTCTACCCCGGTCAAC 59.405 63.158 0.00 0.00 0.00 3.18
1657 1671 1.980772 ACCTCTACCCCGGTCAACG 60.981 63.158 0.00 0.00 43.80 4.10
1666 1680 3.459027 CGGTCAACGGTGATGTCG 58.541 61.111 6.36 7.95 39.42 4.35
1671 1685 3.319198 AACGGTGATGTCGGGCCT 61.319 61.111 0.84 0.00 0.00 5.19
1676 1690 1.296715 GTGATGTCGGGCCTGAGTT 59.703 57.895 16.70 5.00 0.00 3.01
1677 1691 0.535335 GTGATGTCGGGCCTGAGTTA 59.465 55.000 16.70 4.91 0.00 2.24
1680 1694 2.158957 TGATGTCGGGCCTGAGTTAATC 60.159 50.000 16.70 15.65 0.00 1.75
1681 1695 1.568504 TGTCGGGCCTGAGTTAATCT 58.431 50.000 16.70 0.00 0.00 2.40
1682 1696 2.742348 TGTCGGGCCTGAGTTAATCTA 58.258 47.619 16.70 0.00 0.00 1.98
1683 1697 3.305720 TGTCGGGCCTGAGTTAATCTAT 58.694 45.455 16.70 0.00 0.00 1.98
1695 1710 8.944029 CCTGAGTTAATCTATGGCTATGATTTG 58.056 37.037 11.06 0.00 33.24 2.32
1708 1723 5.351458 GCTATGATTTGGGAATTTGTGGAC 58.649 41.667 0.00 0.00 0.00 4.02
1718 1733 4.758165 GGGAATTTGTGGACGAAACTAAGA 59.242 41.667 0.00 0.00 0.00 2.10
1725 1741 7.562454 TTGTGGACGAAACTAAGAGAATTTT 57.438 32.000 0.00 0.00 0.00 1.82
1726 1742 7.186021 TGTGGACGAAACTAAGAGAATTTTC 57.814 36.000 0.00 0.00 0.00 2.29
1727 1743 6.990349 TGTGGACGAAACTAAGAGAATTTTCT 59.010 34.615 0.00 0.00 41.00 2.52
1741 1757 6.690194 AGAATTTTCTCGGGATTTGAGATG 57.310 37.500 0.00 0.00 41.80 2.90
1748 1764 6.425210 TCTCGGGATTTGAGATGTATTGAT 57.575 37.500 0.00 0.00 37.55 2.57
1764 1782 6.931838 TGTATTGATAGTATAAAGGGAGCGG 58.068 40.000 0.00 0.00 0.00 5.52
1769 1787 2.674420 AGTATAAAGGGAGCGGCAGTA 58.326 47.619 1.45 0.00 0.00 2.74
1802 1820 3.398967 AGCCCATAGCATAGAATTTGGGA 59.601 43.478 11.07 0.00 45.47 4.37
1806 1824 6.573094 GCCCATAGCATAGAATTTGGGAAATC 60.573 42.308 11.07 0.00 45.47 2.17
1812 1831 8.537728 AGCATAGAATTTGGGAAATCAACATA 57.462 30.769 0.00 0.00 0.00 2.29
1813 1832 8.416329 AGCATAGAATTTGGGAAATCAACATAC 58.584 33.333 0.00 0.00 0.00 2.39
1842 1861 1.377987 GCCACATCCCGGCTGTTAA 60.378 57.895 0.00 0.00 46.56 2.01
1843 1862 0.963355 GCCACATCCCGGCTGTTAAA 60.963 55.000 0.00 0.00 46.56 1.52
1844 1863 1.094785 CCACATCCCGGCTGTTAAAG 58.905 55.000 0.00 0.00 0.00 1.85
1892 1918 5.237779 CGGAAAAGGTAGAAAAGCAACAGTA 59.762 40.000 0.00 0.00 0.00 2.74
1910 1936 1.546589 TAAACGGTCACGGCCATCCT 61.547 55.000 2.24 0.00 46.48 3.24
1923 1949 1.006102 CATCCTACGGTGGCGATCC 60.006 63.158 0.00 0.00 0.00 3.36
1939 1965 2.496070 CGATCCACTCAACAAGGAGGTA 59.504 50.000 0.00 0.00 39.27 3.08
1950 1976 1.041437 AAGGAGGTAGCCATCGTAGC 58.959 55.000 0.00 0.00 0.00 3.58
1966 1992 2.474816 GTAGCCGTCCATCATCTGAAC 58.525 52.381 0.00 0.00 0.00 3.18
1967 1993 0.904649 AGCCGTCCATCATCTGAACA 59.095 50.000 0.00 0.00 0.00 3.18
1973 1999 4.053983 CGTCCATCATCTGAACAGGTATG 58.946 47.826 1.93 0.45 0.00 2.39
1983 2009 2.290641 TGAACAGGTATGTGCCGGAATT 60.291 45.455 5.05 0.00 40.39 2.17
2007 2034 2.699954 ACAGCGGTAACTGAATCTTGG 58.300 47.619 0.00 0.00 40.25 3.61
2008 2035 2.301870 ACAGCGGTAACTGAATCTTGGA 59.698 45.455 0.00 0.00 40.25 3.53
2010 2037 2.301870 AGCGGTAACTGAATCTTGGACA 59.698 45.455 0.00 0.00 0.00 4.02
2013 2040 3.125316 CGGTAACTGAATCTTGGACAAGC 59.875 47.826 7.18 0.00 38.28 4.01
2014 2041 4.327680 GGTAACTGAATCTTGGACAAGCT 58.672 43.478 7.18 0.00 38.28 3.74
2016 2043 4.843220 AACTGAATCTTGGACAAGCTTG 57.157 40.909 24.84 24.84 38.28 4.01
2056 2083 2.224769 TGCTCCTCCCTTGAAAAACGAT 60.225 45.455 0.00 0.00 0.00 3.73
2068 2095 2.519377 AAAACGATGTGTCCTCACGA 57.481 45.000 0.00 0.00 46.49 4.35
2077 2104 0.669619 TGTCCTCACGACGTTTGCTA 59.330 50.000 0.00 0.00 45.23 3.49
2116 2143 3.391296 TGAGTAGTGGCCTTGAAGAAAGT 59.609 43.478 3.32 0.00 33.66 2.66
2125 2152 3.321968 GCCTTGAAGAAAGTTGGGAATGT 59.678 43.478 0.00 0.00 33.66 2.71
2156 2183 3.244976 GAAATTTGCGTCTTCCCATGTG 58.755 45.455 0.00 0.00 0.00 3.21
2162 2189 0.036010 CGTCTTCCCATGTGGCTTCT 60.036 55.000 0.00 0.00 0.00 2.85
2166 2193 0.112995 TTCCCATGTGGCTTCTGCTT 59.887 50.000 0.00 0.00 39.59 3.91
2170 2197 1.612462 CCATGTGGCTTCTGCTTGAGA 60.612 52.381 0.00 0.00 39.59 3.27
2219 2246 2.078849 CGACAGGCATGTTGTGTCTA 57.921 50.000 5.07 0.00 41.98 2.59
2234 2261 2.094130 GTGTCTAGGTACTTGCCTCACC 60.094 54.545 0.00 0.00 41.75 4.02
2237 2264 2.042569 TCTAGGTACTTGCCTCACCTGA 59.957 50.000 2.77 0.00 42.65 3.86
2243 2270 1.771255 ACTTGCCTCACCTGAAGAACT 59.229 47.619 0.00 0.00 0.00 3.01
2246 2273 1.490490 TGCCTCACCTGAAGAACTTGT 59.510 47.619 0.00 0.00 0.00 3.16
2258 2285 1.518903 GAACTTGTGCAGGCCCTGTC 61.519 60.000 13.35 5.41 33.43 3.51
2276 2303 0.103026 TCTTGATCGTCCCATCAGCG 59.897 55.000 0.00 0.00 34.22 5.18
2285 2312 0.686789 TCCCATCAGCGGATACCATG 59.313 55.000 0.00 0.00 30.87 3.66
2291 2318 1.691976 TCAGCGGATACCATGGGTAAG 59.308 52.381 18.09 4.42 41.85 2.34
2296 2323 3.322828 GCGGATACCATGGGTAAGTTAGA 59.677 47.826 18.09 0.00 41.85 2.10
2303 2330 3.325135 CCATGGGTAAGTTAGAGCTAGGG 59.675 52.174 2.85 0.00 0.00 3.53
2330 2357 3.058224 ACTTACTGCCGATGTGCTTTTTC 60.058 43.478 0.00 0.00 0.00 2.29
2336 2363 2.664916 CCGATGTGCTTTTTCAACTGG 58.335 47.619 0.00 0.00 0.00 4.00
2337 2364 2.053627 CGATGTGCTTTTTCAACTGGC 58.946 47.619 0.00 0.00 0.00 4.85
2338 2365 2.287788 CGATGTGCTTTTTCAACTGGCT 60.288 45.455 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.597255 TCTGCTCTTGAGCTCATTTGAG 58.403 45.455 25.09 25.09 44.75 3.02
10 11 3.690475 TCTGCTCTTGAGCTCATTTGA 57.310 42.857 19.04 14.70 35.49 2.69
11 12 4.379603 CCTTTCTGCTCTTGAGCTCATTTG 60.380 45.833 19.04 11.12 35.49 2.32
12 13 3.757493 CCTTTCTGCTCTTGAGCTCATTT 59.243 43.478 19.04 0.00 35.49 2.32
13 14 3.345414 CCTTTCTGCTCTTGAGCTCATT 58.655 45.455 19.04 0.00 35.49 2.57
14 15 2.940527 GCCTTTCTGCTCTTGAGCTCAT 60.941 50.000 19.04 0.00 35.49 2.90
15 16 1.610102 GCCTTTCTGCTCTTGAGCTCA 60.610 52.381 13.74 13.74 35.49 4.26
16 17 1.085893 GCCTTTCTGCTCTTGAGCTC 58.914 55.000 21.17 6.82 35.49 4.09
17 18 0.399454 TGCCTTTCTGCTCTTGAGCT 59.601 50.000 21.17 0.00 35.49 4.09
18 19 0.520847 GTGCCTTTCTGCTCTTGAGC 59.479 55.000 15.01 15.01 0.00 4.26
19 20 2.181954 AGTGCCTTTCTGCTCTTGAG 57.818 50.000 0.00 0.00 31.42 3.02
20 21 2.645838 AAGTGCCTTTCTGCTCTTGA 57.354 45.000 0.00 0.00 41.88 3.02
21 22 3.181483 ACAAAAGTGCCTTTCTGCTCTTG 60.181 43.478 1.65 0.00 42.43 3.02
22 23 3.026694 ACAAAAGTGCCTTTCTGCTCTT 58.973 40.909 1.37 0.00 44.42 2.85
23 24 2.659428 ACAAAAGTGCCTTTCTGCTCT 58.341 42.857 1.37 0.00 36.70 4.09
24 25 3.118542 CAACAAAAGTGCCTTTCTGCTC 58.881 45.455 1.37 0.00 31.99 4.26
25 26 2.497273 ACAACAAAAGTGCCTTTCTGCT 59.503 40.909 1.37 0.00 31.99 4.24
26 27 2.892374 ACAACAAAAGTGCCTTTCTGC 58.108 42.857 1.37 0.00 31.99 4.26
27 28 8.134895 TCTAATTACAACAAAAGTGCCTTTCTG 58.865 33.333 1.37 5.15 31.99 3.02
28 29 8.232913 TCTAATTACAACAAAAGTGCCTTTCT 57.767 30.769 1.37 0.00 31.99 2.52
29 30 8.752254 GTTCTAATTACAACAAAAGTGCCTTTC 58.248 33.333 0.00 0.00 31.99 2.62
30 31 8.474831 AGTTCTAATTACAACAAAAGTGCCTTT 58.525 29.630 6.41 0.00 34.94 3.11
31 32 8.007405 AGTTCTAATTACAACAAAAGTGCCTT 57.993 30.769 6.41 0.00 0.00 4.35
32 33 7.582667 AGTTCTAATTACAACAAAAGTGCCT 57.417 32.000 6.41 0.00 0.00 4.75
33 34 8.565416 AGTAGTTCTAATTACAACAAAAGTGCC 58.435 33.333 6.41 0.00 0.00 5.01
34 35 9.946165 AAGTAGTTCTAATTACAACAAAAGTGC 57.054 29.630 6.41 0.00 0.00 4.40
54 55 8.799367 GGGGTCACACAAATAAATAAAAGTAGT 58.201 33.333 0.00 0.00 0.00 2.73
55 56 9.020731 AGGGGTCACACAAATAAATAAAAGTAG 57.979 33.333 0.00 0.00 0.00 2.57
56 57 8.943594 AGGGGTCACACAAATAAATAAAAGTA 57.056 30.769 0.00 0.00 0.00 2.24
57 58 7.849322 AGGGGTCACACAAATAAATAAAAGT 57.151 32.000 0.00 0.00 0.00 2.66
58 59 8.466798 CCTAGGGGTCACACAAATAAATAAAAG 58.533 37.037 0.00 0.00 0.00 2.27
59 60 7.397761 CCCTAGGGGTCACACAAATAAATAAAA 59.602 37.037 21.44 0.00 38.25 1.52
60 61 6.893005 CCCTAGGGGTCACACAAATAAATAAA 59.107 38.462 21.44 0.00 38.25 1.40
61 62 6.428295 CCCTAGGGGTCACACAAATAAATAA 58.572 40.000 21.44 0.00 38.25 1.40
62 63 6.008696 CCCTAGGGGTCACACAAATAAATA 57.991 41.667 21.44 0.00 38.25 1.40
63 64 4.867086 CCCTAGGGGTCACACAAATAAAT 58.133 43.478 21.44 0.00 38.25 1.40
64 65 4.310022 CCCTAGGGGTCACACAAATAAA 57.690 45.455 21.44 0.00 38.25 1.40
182 184 4.699257 AGTGAGACTGAAAGAATCCATTGC 59.301 41.667 0.00 0.00 37.43 3.56
186 188 4.991056 CGAAAGTGAGACTGAAAGAATCCA 59.009 41.667 0.00 0.00 37.43 3.41
198 200 5.291858 TCATATCATGTTGCGAAAGTGAGAC 59.708 40.000 0.00 0.00 0.00 3.36
201 203 4.934602 TGTCATATCATGTTGCGAAAGTGA 59.065 37.500 0.00 0.00 0.00 3.41
253 255 4.804139 CAGATCGTACCAAGAACATACCAC 59.196 45.833 0.00 0.00 0.00 4.16
317 319 3.448660 GCCCCATCCCATTAGCATATTTC 59.551 47.826 0.00 0.00 0.00 2.17
324 326 0.251341 ATTCGCCCCATCCCATTAGC 60.251 55.000 0.00 0.00 0.00 3.09
371 373 4.365514 TGCCAGACAAGATAACTTCCAA 57.634 40.909 0.00 0.00 33.70 3.53
439 443 3.508402 TGTCTGTTAGCGAGTGTTATCCA 59.492 43.478 0.00 0.00 0.00 3.41
442 446 4.514781 TGTGTCTGTTAGCGAGTGTTAT 57.485 40.909 0.00 0.00 0.00 1.89
465 469 0.321996 GACAAGAGGGCGAGACCTTT 59.678 55.000 0.00 0.00 42.10 3.11
492 496 8.311836 TGTTTCGTATCTTCTAAACCTTGAGAT 58.688 33.333 0.00 0.00 32.18 2.75
523 528 7.231467 TCCTTTGCTTTACTACAGAGGAAAAT 58.769 34.615 0.19 0.00 42.43 1.82
652 659 8.903059 TTTTGGTACCCCATAATACTCAAATT 57.097 30.769 10.07 0.00 41.49 1.82
696 703 4.336433 CACCATAGGTACCAAGCTGAAATG 59.664 45.833 15.94 4.46 32.11 2.32
797 805 8.843885 TTTGGATGATGCATTTACAAAATTGA 57.156 26.923 15.06 0.00 0.00 2.57
801 809 5.642919 GCCTTTGGATGATGCATTTACAAAA 59.357 36.000 17.03 9.81 29.44 2.44
840 851 0.492276 AGGAGGACAGTACCAACCCT 59.508 55.000 0.00 0.00 32.34 4.34
889 900 6.349860 CCTTCAGCATGTCATGATCAAAAGAA 60.350 38.462 17.24 8.51 37.40 2.52
927 938 1.339291 CCTTTATCGTCCCTCGGTACC 59.661 57.143 0.16 0.16 34.70 3.34
928 939 2.027385 ACCTTTATCGTCCCTCGGTAC 58.973 52.381 0.00 0.00 34.70 3.34
929 940 2.442236 ACCTTTATCGTCCCTCGGTA 57.558 50.000 0.00 0.00 40.32 4.02
930 941 2.305009 CTACCTTTATCGTCCCTCGGT 58.695 52.381 0.00 0.00 40.32 4.69
932 943 2.305009 ACCTACCTTTATCGTCCCTCG 58.695 52.381 0.00 0.00 41.41 4.63
936 948 5.818857 TGCAATAAACCTACCTTTATCGTCC 59.181 40.000 0.00 0.00 0.00 4.79
1010 1022 4.257267 AGGCCAAATTTGAGTGCTAAAC 57.743 40.909 19.86 2.44 0.00 2.01
1060 1072 6.040166 AGGTTGTCTGAATTGATGATTATGCC 59.960 38.462 0.00 0.00 0.00 4.40
1101 1114 3.028130 TGATTGTCCTACGTCCTGCATA 58.972 45.455 0.00 0.00 0.00 3.14
1112 1125 1.220749 GCACCCGCTGATTGTCCTA 59.779 57.895 0.00 0.00 34.30 2.94
1264 1278 7.050377 TCATTTAGAGGCTCCTCAAAATAGTG 58.950 38.462 17.40 10.41 44.99 2.74
1302 1316 8.902540 AGATAACTGTTACATTGTTTGTGAGA 57.097 30.769 1.73 0.00 39.48 3.27
1365 1379 6.599638 GTCAAGGCATCTCCAACTAAAATAGT 59.400 38.462 0.00 0.00 41.73 2.12
1366 1380 6.599244 TGTCAAGGCATCTCCAACTAAAATAG 59.401 38.462 0.00 0.00 37.29 1.73
1367 1381 6.480763 TGTCAAGGCATCTCCAACTAAAATA 58.519 36.000 0.00 0.00 37.29 1.40
1368 1382 5.324409 TGTCAAGGCATCTCCAACTAAAAT 58.676 37.500 0.00 0.00 37.29 1.82
1369 1383 4.724399 TGTCAAGGCATCTCCAACTAAAA 58.276 39.130 0.00 0.00 37.29 1.52
1370 1384 4.365514 TGTCAAGGCATCTCCAACTAAA 57.634 40.909 0.00 0.00 37.29 1.85
1371 1385 4.326826 CTTGTCAAGGCATCTCCAACTAA 58.673 43.478 4.52 0.00 37.29 2.24
1372 1386 3.869912 GCTTGTCAAGGCATCTCCAACTA 60.870 47.826 14.40 0.00 37.29 2.24
1373 1387 2.787994 CTTGTCAAGGCATCTCCAACT 58.212 47.619 4.52 0.00 37.29 3.16
1374 1388 1.200948 GCTTGTCAAGGCATCTCCAAC 59.799 52.381 14.40 0.00 37.29 3.77
1375 1389 1.538047 GCTTGTCAAGGCATCTCCAA 58.462 50.000 14.40 0.00 37.29 3.53
1376 1390 3.254629 GCTTGTCAAGGCATCTCCA 57.745 52.632 14.40 0.00 37.29 3.86
1384 1398 1.000938 GAGCTGTTTGGCTTGTCAAGG 60.001 52.381 14.40 0.00 43.20 3.61
1385 1399 1.334419 CGAGCTGTTTGGCTTGTCAAG 60.334 52.381 8.31 8.31 43.20 3.02
1386 1400 0.662619 CGAGCTGTTTGGCTTGTCAA 59.337 50.000 0.00 0.00 43.20 3.18
1387 1401 2.320215 CGAGCTGTTTGGCTTGTCA 58.680 52.632 0.00 0.00 43.20 3.58
1390 1404 0.040067 GGAACGAGCTGTTTGGCTTG 60.040 55.000 0.00 0.00 46.18 4.01
1391 1405 0.179018 AGGAACGAGCTGTTTGGCTT 60.179 50.000 0.00 0.00 42.09 4.35
1392 1406 0.603975 GAGGAACGAGCTGTTTGGCT 60.604 55.000 0.00 0.00 42.09 4.75
1393 1407 0.884704 TGAGGAACGAGCTGTTTGGC 60.885 55.000 0.00 0.00 42.09 4.52
1394 1408 0.868406 GTGAGGAACGAGCTGTTTGG 59.132 55.000 0.00 0.00 42.09 3.28
1395 1409 0.868406 GGTGAGGAACGAGCTGTTTG 59.132 55.000 0.00 0.00 42.09 2.93
1396 1410 0.250338 GGGTGAGGAACGAGCTGTTT 60.250 55.000 0.00 0.00 42.09 2.83
1397 1411 1.371558 GGGTGAGGAACGAGCTGTT 59.628 57.895 0.00 0.00 45.61 3.16
1398 1412 2.584391 GGGGTGAGGAACGAGCTGT 61.584 63.158 0.00 0.00 0.00 4.40
1399 1413 2.266055 GGGGTGAGGAACGAGCTG 59.734 66.667 0.00 0.00 0.00 4.24
1400 1414 3.382832 CGGGGTGAGGAACGAGCT 61.383 66.667 0.00 0.00 0.00 4.09
1401 1415 3.692406 ACGGGGTGAGGAACGAGC 61.692 66.667 0.00 0.00 0.00 5.03
1402 1416 2.261671 CACGGGGTGAGGAACGAG 59.738 66.667 0.00 0.00 35.23 4.18
1403 1417 3.307906 CCACGGGGTGAGGAACGA 61.308 66.667 0.00 0.00 35.23 3.85
1423 1437 3.735181 GTGATCCACGGTCACTACC 57.265 57.895 9.96 0.00 42.04 3.18
1448 1462 1.811266 CTGATTCGCTCCCACACGG 60.811 63.158 0.00 0.00 0.00 4.94
1449 1463 2.456119 GCTGATTCGCTCCCACACG 61.456 63.158 0.00 0.00 0.00 4.49
1450 1464 0.175760 TAGCTGATTCGCTCCCACAC 59.824 55.000 0.00 0.00 41.30 3.82
1451 1465 0.461548 CTAGCTGATTCGCTCCCACA 59.538 55.000 0.00 0.00 41.30 4.17
1452 1466 0.461961 ACTAGCTGATTCGCTCCCAC 59.538 55.000 0.00 0.00 41.30 4.61
1453 1467 0.461548 CACTAGCTGATTCGCTCCCA 59.538 55.000 0.00 0.00 41.30 4.37
1454 1468 0.249657 CCACTAGCTGATTCGCTCCC 60.250 60.000 0.00 0.00 41.30 4.30
1455 1469 0.249657 CCCACTAGCTGATTCGCTCC 60.250 60.000 0.00 0.00 41.30 4.70
1456 1470 0.249657 CCCCACTAGCTGATTCGCTC 60.250 60.000 0.00 0.00 41.30 5.03
1457 1471 1.690219 CCCCCACTAGCTGATTCGCT 61.690 60.000 0.00 7.85 43.83 4.93
1458 1472 1.227674 CCCCCACTAGCTGATTCGC 60.228 63.158 0.00 0.00 0.00 4.70
1459 1473 0.830648 TTCCCCCACTAGCTGATTCG 59.169 55.000 0.00 0.00 0.00 3.34
1460 1474 1.840635 AGTTCCCCCACTAGCTGATTC 59.159 52.381 0.00 0.00 0.00 2.52
1461 1475 1.840635 GAGTTCCCCCACTAGCTGATT 59.159 52.381 0.00 0.00 0.00 2.57
1462 1476 1.008938 AGAGTTCCCCCACTAGCTGAT 59.991 52.381 0.00 0.00 0.00 2.90
1463 1477 0.413832 AGAGTTCCCCCACTAGCTGA 59.586 55.000 0.00 0.00 0.00 4.26
1464 1478 0.827368 GAGAGTTCCCCCACTAGCTG 59.173 60.000 0.00 0.00 0.00 4.24
1465 1479 0.713579 AGAGAGTTCCCCCACTAGCT 59.286 55.000 0.00 0.00 0.00 3.32
1466 1480 0.827368 CAGAGAGTTCCCCCACTAGC 59.173 60.000 0.00 0.00 0.00 3.42
1467 1481 1.827969 CACAGAGAGTTCCCCCACTAG 59.172 57.143 0.00 0.00 0.00 2.57
1468 1482 1.938585 CACAGAGAGTTCCCCCACTA 58.061 55.000 0.00 0.00 0.00 2.74
1469 1483 1.484444 GCACAGAGAGTTCCCCCACT 61.484 60.000 0.00 0.00 0.00 4.00
1470 1484 1.003233 GCACAGAGAGTTCCCCCAC 60.003 63.158 0.00 0.00 0.00 4.61
1471 1485 2.224159 GGCACAGAGAGTTCCCCCA 61.224 63.158 0.00 0.00 0.00 4.96
1472 1486 2.671682 GGCACAGAGAGTTCCCCC 59.328 66.667 0.00 0.00 0.00 5.40
1473 1487 2.671682 GGGCACAGAGAGTTCCCC 59.328 66.667 0.00 0.00 46.84 4.81
1475 1489 1.599576 GGAGGGCACAGAGAGTTCC 59.400 63.158 0.00 0.00 32.13 3.62
1476 1490 1.216710 CGGAGGGCACAGAGAGTTC 59.783 63.158 0.00 0.00 0.00 3.01
1477 1491 2.948720 GCGGAGGGCACAGAGAGTT 61.949 63.158 0.00 0.00 42.87 3.01
1478 1492 3.386237 GCGGAGGGCACAGAGAGT 61.386 66.667 0.00 0.00 42.87 3.24
1510 1524 4.785453 GGGGAGGAAGTGCTGCGG 62.785 72.222 0.00 0.00 0.00 5.69
1511 1525 4.785453 GGGGGAGGAAGTGCTGCG 62.785 72.222 0.00 0.00 0.00 5.18
1512 1526 2.911926 AAGGGGGAGGAAGTGCTGC 61.912 63.158 0.00 0.00 0.00 5.25
1513 1527 1.001641 CAAGGGGGAGGAAGTGCTG 60.002 63.158 0.00 0.00 0.00 4.41
1514 1528 1.464198 ACAAGGGGGAGGAAGTGCT 60.464 57.895 0.00 0.00 0.00 4.40
1515 1529 1.002011 GACAAGGGGGAGGAAGTGC 60.002 63.158 0.00 0.00 0.00 4.40
1516 1530 1.003696 GAAGACAAGGGGGAGGAAGTG 59.996 57.143 0.00 0.00 0.00 3.16
1517 1531 1.132365 AGAAGACAAGGGGGAGGAAGT 60.132 52.381 0.00 0.00 0.00 3.01
1518 1532 1.557371 GAGAAGACAAGGGGGAGGAAG 59.443 57.143 0.00 0.00 0.00 3.46
1519 1533 1.152271 AGAGAAGACAAGGGGGAGGAA 59.848 52.381 0.00 0.00 0.00 3.36
1520 1534 0.793617 AGAGAAGACAAGGGGGAGGA 59.206 55.000 0.00 0.00 0.00 3.71
1521 1535 0.908198 CAGAGAAGACAAGGGGGAGG 59.092 60.000 0.00 0.00 0.00 4.30
1522 1536 0.251634 GCAGAGAAGACAAGGGGGAG 59.748 60.000 0.00 0.00 0.00 4.30
1523 1537 1.201429 GGCAGAGAAGACAAGGGGGA 61.201 60.000 0.00 0.00 0.00 4.81
1524 1538 1.301293 GGCAGAGAAGACAAGGGGG 59.699 63.158 0.00 0.00 0.00 5.40
1525 1539 1.078848 CGGCAGAGAAGACAAGGGG 60.079 63.158 0.00 0.00 0.00 4.79
1526 1540 1.078848 CCGGCAGAGAAGACAAGGG 60.079 63.158 0.00 0.00 0.00 3.95
1527 1541 1.743252 GCCGGCAGAGAAGACAAGG 60.743 63.158 24.80 0.00 0.00 3.61
1528 1542 1.743252 GGCCGGCAGAGAAGACAAG 60.743 63.158 30.85 0.00 0.00 3.16
1529 1543 0.902984 TAGGCCGGCAGAGAAGACAA 60.903 55.000 30.85 0.00 0.00 3.18
1530 1544 1.304962 TAGGCCGGCAGAGAAGACA 60.305 57.895 30.85 0.00 0.00 3.41
1531 1545 1.142097 GTAGGCCGGCAGAGAAGAC 59.858 63.158 30.85 8.01 0.00 3.01
1532 1546 2.058595 GGTAGGCCGGCAGAGAAGA 61.059 63.158 30.85 0.94 0.00 2.87
1533 1547 2.501610 GGTAGGCCGGCAGAGAAG 59.498 66.667 30.85 0.00 0.00 2.85
1534 1548 3.081409 GGGTAGGCCGGCAGAGAA 61.081 66.667 30.85 4.90 34.97 2.87
1569 1583 2.804828 GAAACTGGGAGAGGCGGTGG 62.805 65.000 0.00 0.00 0.00 4.61
1570 1584 1.376037 GAAACTGGGAGAGGCGGTG 60.376 63.158 0.00 0.00 0.00 4.94
1571 1585 2.593956 GGAAACTGGGAGAGGCGGT 61.594 63.158 0.00 0.00 0.00 5.68
1572 1586 2.269241 GGAAACTGGGAGAGGCGG 59.731 66.667 0.00 0.00 0.00 6.13
1573 1587 1.376037 GTGGAAACTGGGAGAGGCG 60.376 63.158 0.00 0.00 0.00 5.52
1574 1588 1.002011 GGTGGAAACTGGGAGAGGC 60.002 63.158 0.00 0.00 0.00 4.70
1575 1589 0.326264 CAGGTGGAAACTGGGAGAGG 59.674 60.000 0.00 0.00 32.38 3.69
1576 1590 0.322008 GCAGGTGGAAACTGGGAGAG 60.322 60.000 0.00 0.00 36.48 3.20
1577 1591 1.059584 TGCAGGTGGAAACTGGGAGA 61.060 55.000 0.00 0.00 36.48 3.71
1578 1592 0.890996 GTGCAGGTGGAAACTGGGAG 60.891 60.000 0.00 0.00 36.48 4.30
1579 1593 1.150536 GTGCAGGTGGAAACTGGGA 59.849 57.895 0.00 0.00 36.48 4.37
1580 1594 2.260869 CGTGCAGGTGGAAACTGGG 61.261 63.158 0.00 0.00 36.48 4.45
1581 1595 2.908073 GCGTGCAGGTGGAAACTGG 61.908 63.158 8.40 0.00 36.48 4.00
1582 1596 2.639286 GCGTGCAGGTGGAAACTG 59.361 61.111 8.40 0.00 38.95 3.16
1583 1597 2.594592 GGCGTGCAGGTGGAAACT 60.595 61.111 8.40 0.00 0.00 2.66
1584 1598 1.805428 AATGGCGTGCAGGTGGAAAC 61.805 55.000 8.40 0.00 0.00 2.78
1585 1599 1.523154 GAATGGCGTGCAGGTGGAAA 61.523 55.000 8.40 0.00 0.00 3.13
1586 1600 1.971167 GAATGGCGTGCAGGTGGAA 60.971 57.895 8.40 0.00 0.00 3.53
1587 1601 2.359850 GAATGGCGTGCAGGTGGA 60.360 61.111 8.40 0.00 0.00 4.02
1588 1602 3.443045 GGAATGGCGTGCAGGTGG 61.443 66.667 8.40 0.00 0.00 4.61
1589 1603 3.443045 GGGAATGGCGTGCAGGTG 61.443 66.667 8.40 0.00 0.00 4.00
1590 1604 3.650950 AGGGAATGGCGTGCAGGT 61.651 61.111 8.40 0.00 0.00 4.00
1591 1605 3.136123 CAGGGAATGGCGTGCAGG 61.136 66.667 1.01 1.01 0.00 4.85
1592 1606 3.136123 CCAGGGAATGGCGTGCAG 61.136 66.667 0.00 0.00 43.83 4.41
1617 1631 4.166011 GAACATGCAGCGGACGGC 62.166 66.667 0.00 0.00 44.05 5.68
1618 1632 3.499737 GGAACATGCAGCGGACGG 61.500 66.667 0.00 0.00 0.00 4.79
1619 1633 3.853330 CGGAACATGCAGCGGACG 61.853 66.667 0.00 0.00 0.00 4.79
1620 1634 4.166011 GCGGAACATGCAGCGGAC 62.166 66.667 0.00 0.00 0.00 4.79
1623 1637 4.465512 GTGGCGGAACATGCAGCG 62.466 66.667 0.00 0.00 0.00 5.18
1624 1638 4.120331 GGTGGCGGAACATGCAGC 62.120 66.667 0.00 0.00 0.00 5.25
1625 1639 2.360350 AGGTGGCGGAACATGCAG 60.360 61.111 0.00 0.00 0.00 4.41
1626 1640 1.549243 TAGAGGTGGCGGAACATGCA 61.549 55.000 0.00 0.00 0.00 3.96
1627 1641 1.090052 GTAGAGGTGGCGGAACATGC 61.090 60.000 0.00 0.00 0.00 4.06
1628 1642 0.462047 GGTAGAGGTGGCGGAACATG 60.462 60.000 0.00 0.00 0.00 3.21
1629 1643 1.623542 GGGTAGAGGTGGCGGAACAT 61.624 60.000 0.00 0.00 0.00 2.71
1630 1644 2.288025 GGGTAGAGGTGGCGGAACA 61.288 63.158 0.00 0.00 0.00 3.18
1631 1645 2.582978 GGGTAGAGGTGGCGGAAC 59.417 66.667 0.00 0.00 0.00 3.62
1632 1646 2.686106 GGGGTAGAGGTGGCGGAA 60.686 66.667 0.00 0.00 0.00 4.30
1636 1650 3.468140 GACCGGGGTAGAGGTGGC 61.468 72.222 6.32 0.00 41.51 5.01
1637 1651 1.611261 TTGACCGGGGTAGAGGTGG 60.611 63.158 6.32 0.00 41.51 4.61
1638 1652 1.595357 GTTGACCGGGGTAGAGGTG 59.405 63.158 6.32 0.00 41.51 4.00
1639 1653 1.980772 CGTTGACCGGGGTAGAGGT 60.981 63.158 6.32 0.00 44.64 3.85
1640 1654 2.890371 CGTTGACCGGGGTAGAGG 59.110 66.667 6.32 0.00 0.00 3.69
1649 1663 2.092291 CCGACATCACCGTTGACCG 61.092 63.158 0.00 0.00 33.38 4.79
1650 1664 1.740296 CCCGACATCACCGTTGACC 60.740 63.158 0.00 0.00 33.38 4.02
1651 1665 2.388232 GCCCGACATCACCGTTGAC 61.388 63.158 0.00 0.00 33.38 3.18
1652 1666 2.047655 GCCCGACATCACCGTTGA 60.048 61.111 0.00 0.00 35.73 3.18
1653 1667 3.124921 GGCCCGACATCACCGTTG 61.125 66.667 0.00 0.00 0.00 4.10
1654 1668 3.319198 AGGCCCGACATCACCGTT 61.319 61.111 0.00 0.00 0.00 4.44
1655 1669 4.082523 CAGGCCCGACATCACCGT 62.083 66.667 0.00 0.00 0.00 4.83
1656 1670 3.723235 CTCAGGCCCGACATCACCG 62.723 68.421 0.00 0.00 0.00 4.94
1657 1671 2.185310 AACTCAGGCCCGACATCACC 62.185 60.000 0.00 0.00 0.00 4.02
1666 1680 2.373502 AGCCATAGATTAACTCAGGCCC 59.626 50.000 0.00 0.00 44.46 5.80
1671 1685 7.884877 CCCAAATCATAGCCATAGATTAACTCA 59.115 37.037 0.00 0.00 32.11 3.41
1676 1690 9.827198 AAATTCCCAAATCATAGCCATAGATTA 57.173 29.630 0.00 0.00 32.11 1.75
1677 1691 8.591072 CAAATTCCCAAATCATAGCCATAGATT 58.409 33.333 0.00 0.00 33.68 2.40
1680 1694 7.149973 CACAAATTCCCAAATCATAGCCATAG 58.850 38.462 0.00 0.00 0.00 2.23
1681 1695 6.041865 CCACAAATTCCCAAATCATAGCCATA 59.958 38.462 0.00 0.00 0.00 2.74
1682 1696 5.163280 CCACAAATTCCCAAATCATAGCCAT 60.163 40.000 0.00 0.00 0.00 4.40
1683 1697 4.161942 CCACAAATTCCCAAATCATAGCCA 59.838 41.667 0.00 0.00 0.00 4.75
1695 1710 4.758165 TCTTAGTTTCGTCCACAAATTCCC 59.242 41.667 0.00 0.00 0.00 3.97
1718 1733 6.183347 ACATCTCAAATCCCGAGAAAATTCT 58.817 36.000 0.00 0.00 42.57 2.40
1725 1741 5.869649 TCAATACATCTCAAATCCCGAGA 57.130 39.130 0.00 0.00 43.41 4.04
1726 1742 7.382110 ACTATCAATACATCTCAAATCCCGAG 58.618 38.462 0.00 0.00 0.00 4.63
1727 1743 7.303182 ACTATCAATACATCTCAAATCCCGA 57.697 36.000 0.00 0.00 0.00 5.14
1741 1757 5.811100 GCCGCTCCCTTTATACTATCAATAC 59.189 44.000 0.00 0.00 0.00 1.89
1748 1764 2.674420 ACTGCCGCTCCCTTTATACTA 58.326 47.619 0.00 0.00 0.00 1.82
1786 1804 7.953005 TGTTGATTTCCCAAATTCTATGCTA 57.047 32.000 0.00 0.00 0.00 3.49
1788 1806 7.653311 GGTATGTTGATTTCCCAAATTCTATGC 59.347 37.037 0.00 0.00 0.00 3.14
1794 1812 6.263754 AGAGGGTATGTTGATTTCCCAAATT 58.736 36.000 0.00 0.00 40.48 1.82
1798 1816 3.118408 CGAGAGGGTATGTTGATTTCCCA 60.118 47.826 0.00 0.00 40.48 4.37
1799 1817 3.467803 CGAGAGGGTATGTTGATTTCCC 58.532 50.000 0.00 0.00 38.50 3.97
1802 1820 2.238646 TGGCGAGAGGGTATGTTGATTT 59.761 45.455 0.00 0.00 0.00 2.17
1806 1824 0.811616 GCTGGCGAGAGGGTATGTTG 60.812 60.000 0.00 0.00 0.00 3.33
1813 1832 3.746949 GATGTGGCTGGCGAGAGGG 62.747 68.421 0.00 0.00 0.00 4.30
1857 1882 5.195940 TCTACCTTTTCCGTTAGCTAGCTA 58.804 41.667 20.67 20.67 0.00 3.32
1892 1918 1.546589 TAGGATGGCCGTGACCGTTT 61.547 55.000 0.00 0.00 39.96 3.60
1923 1949 1.347707 TGGCTACCTCCTTGTTGAGTG 59.652 52.381 0.00 0.00 0.00 3.51
1927 1953 1.066143 ACGATGGCTACCTCCTTGTTG 60.066 52.381 0.00 0.00 0.00 3.33
1931 1957 1.041437 GCTACGATGGCTACCTCCTT 58.959 55.000 0.00 0.00 0.00 3.36
1939 1965 2.088674 GATGGACGGCTACGATGGCT 62.089 60.000 0.00 0.00 44.60 4.75
1950 1976 1.208052 ACCTGTTCAGATGATGGACGG 59.792 52.381 1.00 0.00 40.75 4.79
1966 1992 0.381801 GCAATTCCGGCACATACCTG 59.618 55.000 0.00 0.00 0.00 4.00
1967 1993 0.255890 AGCAATTCCGGCACATACCT 59.744 50.000 0.00 0.00 0.00 3.08
1973 1999 1.429423 GCTGTAGCAATTCCGGCAC 59.571 57.895 0.00 0.00 41.59 5.01
1983 2009 2.496070 AGATTCAGTTACCGCTGTAGCA 59.504 45.455 4.59 0.00 42.21 3.49
2007 2034 2.739379 GGCTAGTTCAGTCAAGCTTGTC 59.261 50.000 25.19 19.94 35.30 3.18
2008 2035 2.370189 AGGCTAGTTCAGTCAAGCTTGT 59.630 45.455 25.19 4.95 35.30 3.16
2010 2037 2.634940 TCAGGCTAGTTCAGTCAAGCTT 59.365 45.455 0.00 0.00 35.30 3.74
2013 2040 3.667497 TGTCAGGCTAGTTCAGTCAAG 57.333 47.619 0.00 0.00 0.00 3.02
2014 2041 4.318332 CAATGTCAGGCTAGTTCAGTCAA 58.682 43.478 0.00 0.00 0.00 3.18
2016 2043 2.675348 GCAATGTCAGGCTAGTTCAGTC 59.325 50.000 0.00 0.00 0.00 3.51
2056 2083 1.149361 GCAAACGTCGTGAGGACACA 61.149 55.000 0.00 0.00 46.42 3.72
2068 2095 1.084289 GAGGGCGAATTAGCAAACGT 58.916 50.000 12.78 0.00 39.27 3.99
2077 2104 2.025887 ACTCAAGAATGGAGGGCGAATT 60.026 45.455 0.00 0.00 0.00 2.17
2125 2152 8.134895 GGGAAGACGCAAATTTCATCAAATATA 58.865 33.333 0.00 0.00 31.51 0.86
2140 2167 1.971167 GCCACATGGGAAGACGCAA 60.971 57.895 0.00 0.00 41.96 4.85
2156 2183 3.930634 AATTTGTCTCAAGCAGAAGCC 57.069 42.857 0.00 0.00 43.56 4.35
2162 2189 5.070180 TCAATGGGAAAATTTGTCTCAAGCA 59.930 36.000 0.00 0.00 0.00 3.91
2166 2193 7.065120 ACATTCAATGGGAAAATTTGTCTCA 57.935 32.000 1.58 0.00 39.39 3.27
2170 2197 6.934083 GTGGTACATTCAATGGGAAAATTTGT 59.066 34.615 1.58 0.00 44.52 2.83
2210 2237 3.006537 TGAGGCAAGTACCTAGACACAAC 59.993 47.826 0.00 0.00 41.32 3.32
2219 2246 1.625818 CTTCAGGTGAGGCAAGTACCT 59.374 52.381 0.00 0.00 45.36 3.08
2234 2261 0.595095 GGCCTGCACAAGTTCTTCAG 59.405 55.000 0.00 0.00 0.00 3.02
2237 2264 0.825010 CAGGGCCTGCACAAGTTCTT 60.825 55.000 22.68 0.00 0.00 2.52
2243 2270 1.529010 CAAGACAGGGCCTGCACAA 60.529 57.895 33.04 0.00 34.37 3.33
2246 2273 1.300963 GATCAAGACAGGGCCTGCA 59.699 57.895 33.04 12.47 34.37 4.41
2258 2285 0.877649 CCGCTGATGGGACGATCAAG 60.878 60.000 0.00 0.00 31.90 3.02
2276 2303 4.593634 AGCTCTAACTTACCCATGGTATCC 59.406 45.833 11.73 0.00 38.05 2.59
2285 2312 4.900054 TCAATCCCTAGCTCTAACTTACCC 59.100 45.833 0.00 0.00 0.00 3.69
2291 2318 6.508777 CAGTAAGTCAATCCCTAGCTCTAAC 58.491 44.000 0.00 0.00 0.00 2.34
2296 2323 2.436173 GGCAGTAAGTCAATCCCTAGCT 59.564 50.000 0.00 0.00 0.00 3.32
2303 2330 2.030946 GCACATCGGCAGTAAGTCAATC 59.969 50.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.