Multiple sequence alignment - TraesCS4A01G170400

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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 TraesCS4A01G170400 chr4A 100.000 2399 0 0 1 2399 429502174 429504572 0.000000e+00 4431
1 TraesCS4A01G170400 chr4A 92.914 1496 103 3 1 1494 521299093 521300587 0.000000e+00 2172
2 TraesCS4A01G170400 chr4A 88.623 668 56 9 1583 2235 405573928 405574590 0.000000e+00 795
3 TraesCS4A01G170400 chr4A 88.907 613 49 8 1583 2180 607315963 607316571 0.000000e+00 737
4 TraesCS4A01G170400 chr6D 91.845 1496 116 4 1 1494 153176517 153175026 0.000000e+00 2082
5 TraesCS4A01G170400 chr6D 90.703 1409 130 1 1 1408 69504179 69502771 0.000000e+00 1875
6 TraesCS4A01G170400 chr7D 91.255 1498 124 5 1 1494 274862408 274860914 0.000000e+00 2034
7 TraesCS4A01G170400 chr1D 90.897 1505 127 3 1 1495 480940195 480938691 0.000000e+00 2012
8 TraesCS4A01G170400 chr1D 85.089 1462 205 11 1 1455 452586842 452585387 0.000000e+00 1480
9 TraesCS4A01G170400 chr4D 90.709 1496 134 3 1 1494 270688062 270689554 0.000000e+00 1988
10 TraesCS4A01G170400 chr4D 92.143 140 11 0 2229 2368 152886879 152887018 5.230000e-47 198
11 TraesCS4A01G170400 chr4D 88.235 153 18 0 2224 2376 25404688 25404840 1.460000e-42 183
12 TraesCS4A01G170400 chr2D 86.076 1501 200 9 1 1495 10068164 10069661 0.000000e+00 1605
13 TraesCS4A01G170400 chr2D 93.939 132 8 0 2230 2361 139115974 139116105 1.450000e-47 200
14 TraesCS4A01G170400 chr2D 90.345 145 14 0 2232 2376 548746176 548746032 8.750000e-45 191
15 TraesCS4A01G170400 chr2D 89.189 148 13 1 2229 2376 560209835 560209979 5.270000e-42 182
16 TraesCS4A01G170400 chr1A 85.138 1487 211 10 13 1494 544569061 544570542 0.000000e+00 1513
17 TraesCS4A01G170400 chr3B 80.621 1481 272 13 23 1494 125892124 125893598 0.000000e+00 1131
18 TraesCS4A01G170400 chr3B 89.655 145 15 0 2224 2368 225235551 225235695 4.070000e-43 185
19 TraesCS4A01G170400 chr3D 88.167 431 29 8 1583 2002 137715707 137715288 5.960000e-136 494
20 TraesCS4A01G170400 chr3D 77.419 279 44 11 1790 2054 277606584 277606311 5.340000e-32 148
21 TraesCS4A01G170400 chr5A 81.351 681 52 30 1610 2225 567865690 567865020 3.590000e-133 484
22 TraesCS4A01G170400 chr5A 75.452 387 65 18 1690 2052 445582204 445581824 6.860000e-36 161
23 TraesCS4A01G170400 chr5D 89.865 148 15 0 2229 2376 519413918 519414065 8.750000e-45 191
24 TraesCS4A01G170400 chr5D 89.262 149 14 2 2229 2376 73813741 73813888 4.070000e-43 185
25 TraesCS4A01G170400 chr3A 89.262 149 16 0 2229 2377 222039895 222039747 1.130000e-43 187
26 TraesCS4A01G170400 chr3A 75.578 389 66 18 1687 2052 506810119 506810501 5.310000e-37 165
27 TraesCS4A01G170400 chr7A 75.452 387 67 13 1687 2052 45627839 45628218 1.910000e-36 163
28 TraesCS4A01G170400 chr7A 88.496 113 11 1 2117 2227 567728590 567728478 4.160000e-28 135
29 TraesCS4A01G170400 chr2B 75.321 389 67 17 1687 2052 579999574 579999956 2.470000e-35 159
30 TraesCS4A01G170400 chrUn 74.874 398 63 16 1687 2052 108731058 108730666 1.920000e-31 147


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 TraesCS4A01G170400 chr4A 429502174 429504572 2398 False 4431 4431 100.000 1 2399 1 chr4A.!!$F2 2398
1 TraesCS4A01G170400 chr4A 521299093 521300587 1494 False 2172 2172 92.914 1 1494 1 chr4A.!!$F3 1493
2 TraesCS4A01G170400 chr4A 405573928 405574590 662 False 795 795 88.623 1583 2235 1 chr4A.!!$F1 652
3 TraesCS4A01G170400 chr4A 607315963 607316571 608 False 737 737 88.907 1583 2180 1 chr4A.!!$F4 597
4 TraesCS4A01G170400 chr6D 153175026 153176517 1491 True 2082 2082 91.845 1 1494 1 chr6D.!!$R2 1493
5 TraesCS4A01G170400 chr6D 69502771 69504179 1408 True 1875 1875 90.703 1 1408 1 chr6D.!!$R1 1407
6 TraesCS4A01G170400 chr7D 274860914 274862408 1494 True 2034 2034 91.255 1 1494 1 chr7D.!!$R1 1493
7 TraesCS4A01G170400 chr1D 480938691 480940195 1504 True 2012 2012 90.897 1 1495 1 chr1D.!!$R2 1494
8 TraesCS4A01G170400 chr1D 452585387 452586842 1455 True 1480 1480 85.089 1 1455 1 chr1D.!!$R1 1454
9 TraesCS4A01G170400 chr4D 270688062 270689554 1492 False 1988 1988 90.709 1 1494 1 chr4D.!!$F3 1493
10 TraesCS4A01G170400 chr2D 10068164 10069661 1497 False 1605 1605 86.076 1 1495 1 chr2D.!!$F1 1494
11 TraesCS4A01G170400 chr1A 544569061 544570542 1481 False 1513 1513 85.138 13 1494 1 chr1A.!!$F1 1481
12 TraesCS4A01G170400 chr3B 125892124 125893598 1474 False 1131 1131 80.621 23 1494 1 chr3B.!!$F1 1471
13 TraesCS4A01G170400 chr5A 567865020 567865690 670 True 484 484 81.351 1610 2225 1 chr5A.!!$R2 615

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
293 295 0.735471 CTCGACGCCATTCAGAGAGA 59.265 55.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 2350 0.031043 TTTCTTTGCGACTCCGACGA 59.969 50.0 0.0 0.0 38.22 4.2 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
46 48 2.009051 TCGCTGCAACTATTGGATGTG 58.991 47.619 0.00 0.00 0.00 3.21
57 59 5.714863 ACTATTGGATGTGATCTCTCCTCT 58.285 41.667 11.82 5.10 0.00 3.69
144 146 7.662897 ACCCTATCTTAGATAGCTTTCGAAAG 58.337 38.462 29.45 29.45 39.03 2.62
206 208 3.733337 CAAGACTAACCTTGCTCACTGT 58.267 45.455 0.00 0.00 37.35 3.55
287 289 1.067142 AGTTAAGCTCGACGCCATTCA 60.067 47.619 0.00 0.00 40.39 2.57
293 295 0.735471 CTCGACGCCATTCAGAGAGA 59.265 55.000 0.00 0.00 0.00 3.10
311 313 4.962155 AGAGATTTCTTCTGGTCAAACGT 58.038 39.130 0.00 0.00 33.74 3.99
323 325 2.223711 GGTCAAACGTGGAAACTTGCAT 60.224 45.455 0.00 0.00 0.00 3.96
393 395 4.222124 ACTTGGTGGTCTAGGCATTAAG 57.778 45.455 0.00 0.00 0.00 1.85
401 403 5.008118 GTGGTCTAGGCATTAAGAATCTTGC 59.992 44.000 5.64 1.03 0.00 4.01
438 440 6.148315 GCTGCCTGCTTATGAAATTTTCTTTT 59.852 34.615 10.33 0.00 38.95 2.27
439 441 7.424227 TGCCTGCTTATGAAATTTTCTTTTG 57.576 32.000 10.33 2.82 0.00 2.44
459 461 6.521151 TTTGAAATTTTGCAACACCCAAAT 57.479 29.167 0.00 0.00 32.76 2.32
523 525 4.522789 GGATTGCAACAAAAACTCCTAGGA 59.477 41.667 11.98 11.98 0.00 2.94
529 531 4.893829 ACAAAAACTCCTAGGACCTCTC 57.106 45.455 7.62 0.00 0.00 3.20
648 650 3.795688 TGGCTTCTTGAATCACCTCTT 57.204 42.857 0.00 0.00 0.00 2.85
660 662 7.873719 TGAATCACCTCTTCACAAAGTTTTA 57.126 32.000 0.00 0.00 33.95 1.52
672 674 9.449719 CTTCACAAAGTTTTACCTCACCTATAT 57.550 33.333 0.00 0.00 0.00 0.86
696 698 3.181461 CCCACTCCATAGATGACAAGGTC 60.181 52.174 0.00 0.00 0.00 3.85
703 705 4.651503 CCATAGATGACAAGGTCCTAGTGT 59.348 45.833 0.00 0.00 0.00 3.55
705 707 3.100671 AGATGACAAGGTCCTAGTGTCC 58.899 50.000 17.50 6.57 40.79 4.02
899 904 3.519107 TCCATTGTTGCTGATGACTCCTA 59.481 43.478 0.00 0.00 0.00 2.94
979 987 1.899437 TTGGCTTCTCCTCCGCGATT 61.899 55.000 8.23 0.00 35.26 3.34
1005 1013 4.434713 AAATACGAAGGCCAACATGTTC 57.565 40.909 8.48 0.00 0.00 3.18
1051 1059 0.684535 TTGCCCTCGATGTCAAGACA 59.315 50.000 5.24 5.24 46.44 3.41
1090 1098 1.039785 TCTCATCTCCACCTGCTCCG 61.040 60.000 0.00 0.00 0.00 4.63
1168 1177 0.183971 TCACCAACACCCACCGATTT 59.816 50.000 0.00 0.00 0.00 2.17
1188 1198 1.694856 GGGCCTCAACCCCAACATA 59.305 57.895 0.84 0.00 45.00 2.29
1248 1258 2.926838 GGACTCAAGAAATGCTCTCGTC 59.073 50.000 0.00 0.00 31.02 4.20
1377 1390 5.869579 AGACAGTGGCTAAATTTTCTCTCA 58.130 37.500 0.00 0.00 0.00 3.27
1384 1397 4.260948 GGCTAAATTTTCTCTCATCCGCAG 60.261 45.833 0.00 0.00 0.00 5.18
1395 1409 0.390860 CATCCGCAGTCCCTTCTAGG 59.609 60.000 0.00 0.00 34.30 3.02
1461 1478 5.865085 TGAGTGGTAATATATTCAGGTGGC 58.135 41.667 0.00 0.00 0.00 5.01
1511 1535 5.432885 AAAAACGTTGCTACTACATTGCT 57.567 34.783 0.00 0.00 0.00 3.91
1512 1536 6.548441 AAAAACGTTGCTACTACATTGCTA 57.452 33.333 0.00 0.00 0.00 3.49
1513 1537 5.526010 AAACGTTGCTACTACATTGCTAC 57.474 39.130 0.00 0.00 33.04 3.58
1514 1538 4.451629 ACGTTGCTACTACATTGCTACT 57.548 40.909 0.00 0.00 33.90 2.57
1515 1539 4.174009 ACGTTGCTACTACATTGCTACTG 58.826 43.478 0.00 0.00 33.90 2.74
1516 1540 3.551890 CGTTGCTACTACATTGCTACTGG 59.448 47.826 0.00 0.00 33.90 4.00
1517 1541 3.819564 TGCTACTACATTGCTACTGGG 57.180 47.619 0.00 0.00 0.00 4.45
1518 1542 2.158957 TGCTACTACATTGCTACTGGGC 60.159 50.000 0.00 0.00 0.00 5.36
1519 1543 2.807108 GCTACTACATTGCTACTGGGCC 60.807 54.545 0.00 0.00 0.00 5.80
1520 1544 1.584724 ACTACATTGCTACTGGGCCT 58.415 50.000 4.53 0.00 0.00 5.19
1521 1545 1.916181 ACTACATTGCTACTGGGCCTT 59.084 47.619 4.53 0.00 0.00 4.35
1522 1546 3.112263 ACTACATTGCTACTGGGCCTTA 58.888 45.455 4.53 0.00 0.00 2.69
1523 1547 3.716872 ACTACATTGCTACTGGGCCTTAT 59.283 43.478 4.53 0.00 0.00 1.73
1524 1548 3.669939 ACATTGCTACTGGGCCTTATT 57.330 42.857 4.53 0.00 0.00 1.40
1525 1549 3.981212 ACATTGCTACTGGGCCTTATTT 58.019 40.909 4.53 0.00 0.00 1.40
1526 1550 4.352893 ACATTGCTACTGGGCCTTATTTT 58.647 39.130 4.53 0.00 0.00 1.82
1527 1551 4.160252 ACATTGCTACTGGGCCTTATTTTG 59.840 41.667 4.53 0.00 0.00 2.44
1528 1552 3.730215 TGCTACTGGGCCTTATTTTGA 57.270 42.857 4.53 0.00 0.00 2.69
1529 1553 3.620488 TGCTACTGGGCCTTATTTTGAG 58.380 45.455 4.53 0.00 0.00 3.02
1530 1554 3.265737 TGCTACTGGGCCTTATTTTGAGA 59.734 43.478 4.53 0.00 0.00 3.27
1531 1555 3.628032 GCTACTGGGCCTTATTTTGAGAC 59.372 47.826 4.53 0.00 0.00 3.36
1532 1556 4.626529 GCTACTGGGCCTTATTTTGAGACT 60.627 45.833 4.53 0.00 0.00 3.24
1533 1557 4.388577 ACTGGGCCTTATTTTGAGACTT 57.611 40.909 4.53 0.00 0.00 3.01
1534 1558 5.514500 ACTGGGCCTTATTTTGAGACTTA 57.486 39.130 4.53 0.00 0.00 2.24
1535 1559 6.079712 ACTGGGCCTTATTTTGAGACTTAT 57.920 37.500 4.53 0.00 0.00 1.73
1536 1560 6.122964 ACTGGGCCTTATTTTGAGACTTATC 58.877 40.000 4.53 0.00 0.00 1.75
1537 1561 6.073447 TGGGCCTTATTTTGAGACTTATCA 57.927 37.500 4.53 0.00 0.00 2.15
1538 1562 5.885912 TGGGCCTTATTTTGAGACTTATCAC 59.114 40.000 4.53 0.00 0.00 3.06
1539 1563 6.122964 GGGCCTTATTTTGAGACTTATCACT 58.877 40.000 0.84 0.00 0.00 3.41
1540 1564 7.092623 TGGGCCTTATTTTGAGACTTATCACTA 60.093 37.037 4.53 0.00 0.00 2.74
1541 1565 7.442666 GGGCCTTATTTTGAGACTTATCACTAG 59.557 40.741 0.84 0.00 0.00 2.57
1542 1566 7.041712 GGCCTTATTTTGAGACTTATCACTAGC 60.042 40.741 0.00 0.00 0.00 3.42
1543 1567 7.041712 GCCTTATTTTGAGACTTATCACTAGCC 60.042 40.741 0.00 0.00 0.00 3.93
1544 1568 7.987458 CCTTATTTTGAGACTTATCACTAGCCA 59.013 37.037 0.00 0.00 0.00 4.75
1545 1569 8.948631 TTATTTTGAGACTTATCACTAGCCAG 57.051 34.615 0.00 0.00 0.00 4.85
1546 1570 6.605471 TTTTGAGACTTATCACTAGCCAGA 57.395 37.500 0.00 0.00 0.00 3.86
1547 1571 6.798427 TTTGAGACTTATCACTAGCCAGAT 57.202 37.500 0.00 0.00 0.00 2.90
1548 1572 6.798427 TTGAGACTTATCACTAGCCAGATT 57.202 37.500 0.00 0.00 0.00 2.40
1549 1573 6.154203 TGAGACTTATCACTAGCCAGATTG 57.846 41.667 0.00 0.00 0.00 2.67
1550 1574 5.893824 TGAGACTTATCACTAGCCAGATTGA 59.106 40.000 0.00 0.00 0.00 2.57
1551 1575 6.552725 TGAGACTTATCACTAGCCAGATTGAT 59.447 38.462 0.00 0.00 33.31 2.57
1552 1576 6.991938 AGACTTATCACTAGCCAGATTGATC 58.008 40.000 0.00 0.00 31.20 2.92
1553 1577 5.777802 ACTTATCACTAGCCAGATTGATCG 58.222 41.667 0.00 0.00 31.20 3.69
1554 1578 5.536538 ACTTATCACTAGCCAGATTGATCGA 59.463 40.000 0.00 0.00 31.20 3.59
1555 1579 4.944619 ATCACTAGCCAGATTGATCGAA 57.055 40.909 0.00 0.00 0.00 3.71
1556 1580 4.313277 TCACTAGCCAGATTGATCGAAG 57.687 45.455 0.00 0.00 0.00 3.79
1557 1581 3.701542 TCACTAGCCAGATTGATCGAAGT 59.298 43.478 0.00 0.00 0.00 3.01
1558 1582 4.047822 CACTAGCCAGATTGATCGAAGTC 58.952 47.826 0.00 0.00 0.00 3.01
1559 1583 2.215907 AGCCAGATTGATCGAAGTCG 57.784 50.000 0.00 0.00 41.45 4.18
1579 1603 2.933573 GAGGAGATAACTCGACCAGGA 58.066 52.381 0.00 0.00 43.44 3.86
1580 1604 2.882137 GAGGAGATAACTCGACCAGGAG 59.118 54.545 0.00 0.00 43.44 3.69
1581 1605 1.338655 GGAGATAACTCGACCAGGAGC 59.661 57.143 0.00 0.00 43.44 4.70
1588 1612 3.314331 CGACCAGGAGCCACCAGT 61.314 66.667 0.00 0.00 42.04 4.00
1659 1683 1.872237 GCGCAATTAGCCCATCGTCTA 60.872 52.381 0.30 0.00 41.38 2.59
1701 1725 9.985730 TTTGTGAGCATTTAATCTTGATTTCTT 57.014 25.926 0.95 0.00 0.00 2.52
1702 1726 9.985730 TTGTGAGCATTTAATCTTGATTTCTTT 57.014 25.926 0.95 0.00 0.00 2.52
1740 1764 9.844257 CAAGAATAGAGGATTATCTTTGTTCCT 57.156 33.333 0.00 0.00 41.29 3.36
1781 1806 5.664294 ATTGCAGCATCCAGTCAATTTTA 57.336 34.783 0.00 0.00 0.00 1.52
1782 1807 5.664294 TTGCAGCATCCAGTCAATTTTAT 57.336 34.783 0.00 0.00 0.00 1.40
1785 1810 4.098349 GCAGCATCCAGTCAATTTTATGGA 59.902 41.667 5.07 5.07 45.48 3.41
1793 1818 6.496565 TCCAGTCAATTTTATGGATGGTTTGT 59.503 34.615 0.00 0.00 36.92 2.83
1837 1862 6.633856 ACTTGTGAAGAACTGCAAGAAAAAT 58.366 32.000 9.68 0.00 40.30 1.82
1866 1891 7.414762 GGCGAAGTTTATGCACCTAAATTTCTA 60.415 37.037 18.25 0.00 36.20 2.10
1921 1956 7.703621 CCATCATCACTATCCAACATGTTTTTC 59.296 37.037 8.77 0.00 0.00 2.29
1957 2026 7.329226 GGTGTGAACAATGAAGAACAAATATGG 59.671 37.037 0.00 0.00 0.00 2.74
1969 2038 7.230849 AGAACAAATATGGTGATTTGAAGCA 57.769 32.000 14.12 0.00 45.70 3.91
2040 2109 2.621998 CCAACACCGGTATCTATCGACT 59.378 50.000 6.87 0.00 29.66 4.18
2054 2123 6.539649 TCTATCGACTTTGAAAACCAAGTG 57.460 37.500 0.00 0.00 35.94 3.16
2055 2124 6.285224 TCTATCGACTTTGAAAACCAAGTGA 58.715 36.000 0.00 0.00 35.94 3.41
2077 2149 5.538053 TGAATCAAAATAAGAGCAACCACCA 59.462 36.000 0.00 0.00 0.00 4.17
2081 2153 2.332063 ATAAGAGCAACCACCATCCG 57.668 50.000 0.00 0.00 0.00 4.18
2216 2303 0.991920 ACCCATGTCGGAAATCCTGT 59.008 50.000 0.00 0.00 36.56 4.00
2227 2314 1.480954 GAAATCCTGTCTCCGCCACTA 59.519 52.381 0.00 0.00 0.00 2.74
2230 2317 0.965866 TCCTGTCTCCGCCACTACAG 60.966 60.000 0.00 0.00 39.22 2.74
2235 2322 1.448540 CTCCGCCACTACAGCCAAG 60.449 63.158 0.00 0.00 0.00 3.61
2236 2323 2.436646 CCGCCACTACAGCCAAGG 60.437 66.667 0.00 0.00 0.00 3.61
2237 2324 2.347490 CGCCACTACAGCCAAGGT 59.653 61.111 0.00 0.00 0.00 3.50
2238 2325 1.741770 CGCCACTACAGCCAAGGTC 60.742 63.158 0.00 0.00 0.00 3.85
2239 2326 1.679898 GCCACTACAGCCAAGGTCT 59.320 57.895 0.00 0.00 0.00 3.85
2240 2327 0.391793 GCCACTACAGCCAAGGTCTC 60.392 60.000 0.00 0.00 0.00 3.36
2241 2328 0.250513 CCACTACAGCCAAGGTCTCC 59.749 60.000 0.00 0.00 0.00 3.71
2242 2329 1.270907 CACTACAGCCAAGGTCTCCT 58.729 55.000 0.00 0.00 33.87 3.69
2243 2330 1.205893 CACTACAGCCAAGGTCTCCTC 59.794 57.143 0.00 0.00 30.89 3.71
2244 2331 0.827368 CTACAGCCAAGGTCTCCTCC 59.173 60.000 0.00 0.00 30.89 4.30
2245 2332 0.413832 TACAGCCAAGGTCTCCTCCT 59.586 55.000 0.00 0.00 39.84 3.69
2246 2333 0.907230 ACAGCCAAGGTCTCCTCCTC 60.907 60.000 0.00 0.00 36.74 3.71
2247 2334 0.906756 CAGCCAAGGTCTCCTCCTCA 60.907 60.000 0.00 0.00 36.74 3.86
2248 2335 0.043940 AGCCAAGGTCTCCTCCTCAT 59.956 55.000 0.00 0.00 36.74 2.90
2249 2336 0.467804 GCCAAGGTCTCCTCCTCATC 59.532 60.000 0.00 0.00 36.74 2.92
2250 2337 1.871418 CCAAGGTCTCCTCCTCATCA 58.129 55.000 0.00 0.00 36.74 3.07
2251 2338 1.484240 CCAAGGTCTCCTCCTCATCAC 59.516 57.143 0.00 0.00 36.74 3.06
2252 2339 2.465813 CAAGGTCTCCTCCTCATCACT 58.534 52.381 0.00 0.00 36.74 3.41
2253 2340 2.157640 AGGTCTCCTCCTCATCACTG 57.842 55.000 0.00 0.00 31.32 3.66
2254 2341 1.118838 GGTCTCCTCCTCATCACTGG 58.881 60.000 0.00 0.00 0.00 4.00
2255 2342 1.342474 GGTCTCCTCCTCATCACTGGA 60.342 57.143 0.00 0.00 0.00 3.86
2256 2343 1.754226 GTCTCCTCCTCATCACTGGAC 59.246 57.143 0.00 0.00 0.00 4.02
2257 2344 0.743688 CTCCTCCTCATCACTGGACG 59.256 60.000 0.00 0.00 0.00 4.79
2258 2345 0.331616 TCCTCCTCATCACTGGACGA 59.668 55.000 0.00 0.00 0.00 4.20
2259 2346 0.743688 CCTCCTCATCACTGGACGAG 59.256 60.000 0.00 0.00 33.23 4.18
2264 2351 3.090952 CTCATCACTGGACGAGGAATC 57.909 52.381 0.00 0.00 29.87 2.52
2265 2352 1.405463 TCATCACTGGACGAGGAATCG 59.595 52.381 0.00 0.00 39.31 3.34
2272 2359 4.315588 ACGAGGAATCGTCGGAGT 57.684 55.556 25.64 5.80 44.42 3.85
2273 2360 2.096596 ACGAGGAATCGTCGGAGTC 58.903 57.895 25.64 0.00 44.42 3.36
2274 2361 1.011019 CGAGGAATCGTCGGAGTCG 60.011 63.158 16.47 0.00 38.13 4.18
2275 2362 1.298488 GAGGAATCGTCGGAGTCGC 60.298 63.158 0.00 0.00 38.13 5.19
2276 2363 1.989966 GAGGAATCGTCGGAGTCGCA 61.990 60.000 0.00 0.00 38.13 5.10
2277 2364 1.153901 GGAATCGTCGGAGTCGCAA 60.154 57.895 0.00 0.00 38.13 4.85
2278 2365 0.734942 GGAATCGTCGGAGTCGCAAA 60.735 55.000 0.00 0.00 38.13 3.68
2279 2366 0.640768 GAATCGTCGGAGTCGCAAAG 59.359 55.000 0.00 0.00 39.21 2.77
2280 2367 0.242825 AATCGTCGGAGTCGCAAAGA 59.757 50.000 0.00 0.00 39.21 2.52
2281 2368 0.242825 ATCGTCGGAGTCGCAAAGAA 59.757 50.000 0.00 0.00 39.21 2.52
2282 2369 0.031043 TCGTCGGAGTCGCAAAGAAA 59.969 50.000 0.00 0.00 39.21 2.52
2283 2370 0.856641 CGTCGGAGTCGCAAAGAAAA 59.143 50.000 0.00 0.00 36.13 2.29
2284 2371 1.459592 CGTCGGAGTCGCAAAGAAAAT 59.540 47.619 0.00 0.00 36.13 1.82
2285 2372 2.096417 CGTCGGAGTCGCAAAGAAAATT 60.096 45.455 0.00 0.00 36.13 1.82
2286 2373 3.226347 GTCGGAGTCGCAAAGAAAATTG 58.774 45.455 0.00 0.00 36.13 2.32
2287 2374 2.875933 TCGGAGTCGCAAAGAAAATTGT 59.124 40.909 0.00 0.00 36.13 2.71
2288 2375 2.973224 CGGAGTCGCAAAGAAAATTGTG 59.027 45.455 0.00 0.00 41.13 3.33
2289 2376 3.303725 CGGAGTCGCAAAGAAAATTGTGA 60.304 43.478 0.00 0.00 44.94 3.58
2309 2396 2.497107 AAAAAGAACTCGTCGACGGA 57.503 45.000 35.05 21.22 40.29 4.69
2310 2397 2.497107 AAAAGAACTCGTCGACGGAA 57.503 45.000 35.05 18.04 40.29 4.30
2311 2398 2.719426 AAAGAACTCGTCGACGGAAT 57.281 45.000 35.05 21.71 40.29 3.01
2312 2399 2.259505 AAGAACTCGTCGACGGAATC 57.740 50.000 35.05 27.33 40.29 2.52
2313 2400 0.450983 AGAACTCGTCGACGGAATCC 59.549 55.000 35.05 20.57 40.29 3.01
2314 2401 0.169672 GAACTCGTCGACGGAATCCA 59.830 55.000 35.05 15.79 40.29 3.41
2315 2402 0.815734 AACTCGTCGACGGAATCCAT 59.184 50.000 35.05 13.60 40.29 3.41
2316 2403 0.815734 ACTCGTCGACGGAATCCATT 59.184 50.000 35.05 8.55 40.29 3.16
2317 2404 1.203994 ACTCGTCGACGGAATCCATTT 59.796 47.619 35.05 8.42 40.29 2.32
2318 2405 2.268298 CTCGTCGACGGAATCCATTTT 58.732 47.619 35.05 0.00 40.29 1.82
2319 2406 1.996898 TCGTCGACGGAATCCATTTTG 59.003 47.619 35.05 5.02 40.29 2.44
2320 2407 1.730064 CGTCGACGGAATCCATTTTGT 59.270 47.619 29.70 0.00 35.37 2.83
2321 2408 2.924926 CGTCGACGGAATCCATTTTGTA 59.075 45.455 29.70 0.00 35.37 2.41
2322 2409 3.241868 CGTCGACGGAATCCATTTTGTAC 60.242 47.826 29.70 0.00 35.37 2.90
2323 2410 3.063045 GTCGACGGAATCCATTTTGTACC 59.937 47.826 0.00 0.00 0.00 3.34
2324 2411 3.055675 TCGACGGAATCCATTTTGTACCT 60.056 43.478 0.00 0.00 0.00 3.08
2325 2412 3.687698 CGACGGAATCCATTTTGTACCTT 59.312 43.478 0.00 0.00 0.00 3.50
2326 2413 4.436852 CGACGGAATCCATTTTGTACCTTG 60.437 45.833 0.00 0.00 0.00 3.61
2327 2414 3.761752 ACGGAATCCATTTTGTACCTTGG 59.238 43.478 0.00 0.00 0.00 3.61
2328 2415 3.428862 CGGAATCCATTTTGTACCTTGGC 60.429 47.826 0.00 0.00 0.00 4.52
2329 2416 3.513515 GGAATCCATTTTGTACCTTGGCA 59.486 43.478 0.00 0.00 0.00 4.92
2330 2417 4.020662 GGAATCCATTTTGTACCTTGGCAA 60.021 41.667 0.00 0.00 0.00 4.52
2331 2418 5.512232 GGAATCCATTTTGTACCTTGGCAAA 60.512 40.000 0.00 0.00 33.40 3.68
2332 2419 4.329462 TCCATTTTGTACCTTGGCAAAC 57.671 40.909 0.00 0.00 34.77 2.93
2333 2420 3.964031 TCCATTTTGTACCTTGGCAAACT 59.036 39.130 0.00 0.00 34.77 2.66
2334 2421 5.141182 TCCATTTTGTACCTTGGCAAACTA 58.859 37.500 0.00 0.00 34.77 2.24
2335 2422 5.777732 TCCATTTTGTACCTTGGCAAACTAT 59.222 36.000 0.00 0.00 34.77 2.12
2336 2423 6.071616 TCCATTTTGTACCTTGGCAAACTATC 60.072 38.462 0.00 0.00 34.77 2.08
2337 2424 5.365403 TTTTGTACCTTGGCAAACTATCG 57.635 39.130 0.00 0.00 34.77 2.92
2338 2425 3.965379 TGTACCTTGGCAAACTATCGA 57.035 42.857 0.00 0.00 0.00 3.59
2339 2426 4.274602 TGTACCTTGGCAAACTATCGAA 57.725 40.909 0.00 0.00 0.00 3.71
2340 2427 3.998341 TGTACCTTGGCAAACTATCGAAC 59.002 43.478 0.00 0.00 0.00 3.95
2341 2428 3.134574 ACCTTGGCAAACTATCGAACA 57.865 42.857 0.00 0.00 0.00 3.18
2342 2429 3.482436 ACCTTGGCAAACTATCGAACAA 58.518 40.909 0.00 0.00 0.00 2.83
2343 2430 3.252458 ACCTTGGCAAACTATCGAACAAC 59.748 43.478 0.00 0.00 0.00 3.32
2344 2431 3.502211 CCTTGGCAAACTATCGAACAACT 59.498 43.478 0.00 0.00 0.00 3.16
2345 2432 4.023193 CCTTGGCAAACTATCGAACAACTT 60.023 41.667 0.00 0.00 0.00 2.66
2346 2433 4.481930 TGGCAAACTATCGAACAACTTG 57.518 40.909 0.00 0.00 0.00 3.16
2347 2434 3.234386 GGCAAACTATCGAACAACTTGC 58.766 45.455 11.81 11.81 37.54 4.01
2348 2435 2.902484 GCAAACTATCGAACAACTTGCG 59.098 45.455 0.00 0.00 0.00 4.85
2349 2436 3.479006 CAAACTATCGAACAACTTGCGG 58.521 45.455 0.00 0.00 0.00 5.69
2350 2437 1.722011 ACTATCGAACAACTTGCGGG 58.278 50.000 0.00 0.00 0.00 6.13
2351 2438 0.373716 CTATCGAACAACTTGCGGGC 59.626 55.000 0.00 0.00 0.00 6.13
2352 2439 1.355796 TATCGAACAACTTGCGGGCG 61.356 55.000 0.00 0.00 0.00 6.13
2353 2440 3.645975 CGAACAACTTGCGGGCGT 61.646 61.111 0.00 0.00 0.00 5.68
2354 2441 2.251371 GAACAACTTGCGGGCGTC 59.749 61.111 0.00 0.00 0.00 5.19
2355 2442 3.573489 GAACAACTTGCGGGCGTCG 62.573 63.158 0.00 0.00 42.76 5.12
2356 2443 4.595538 ACAACTTGCGGGCGTCGA 62.596 61.111 0.00 0.00 42.43 4.20
2357 2444 4.072088 CAACTTGCGGGCGTCGAC 62.072 66.667 5.18 5.18 42.43 4.20
2358 2445 4.595538 AACTTGCGGGCGTCGACA 62.596 61.111 17.16 0.00 42.43 4.35
2359 2446 4.595538 ACTTGCGGGCGTCGACAA 62.596 61.111 17.16 0.00 42.43 3.18
2360 2447 3.342627 CTTGCGGGCGTCGACAAA 61.343 61.111 17.16 0.00 42.43 2.83
2361 2448 2.666862 TTGCGGGCGTCGACAAAT 60.667 55.556 17.16 0.00 42.43 2.32
2362 2449 2.832818 CTTGCGGGCGTCGACAAATG 62.833 60.000 17.16 3.42 42.43 2.32
2363 2450 3.115892 GCGGGCGTCGACAAATGA 61.116 61.111 17.16 0.00 42.43 2.57
2364 2451 3.081133 CGGGCGTCGACAAATGAG 58.919 61.111 17.16 0.00 42.43 2.90
2365 2452 1.445410 CGGGCGTCGACAAATGAGA 60.445 57.895 17.16 0.00 42.43 3.27
2366 2453 1.683790 CGGGCGTCGACAAATGAGAC 61.684 60.000 17.16 0.00 42.43 3.36
2371 2458 0.982673 GTCGACAAATGAGACGACGG 59.017 55.000 11.55 0.00 43.60 4.79
2372 2459 0.109458 TCGACAAATGAGACGACGGG 60.109 55.000 0.00 0.00 0.00 5.28
2373 2460 1.683790 CGACAAATGAGACGACGGGC 61.684 60.000 0.00 0.00 0.00 6.13
2375 2462 1.445410 CAAATGAGACGACGGGCGA 60.445 57.895 11.73 0.00 44.57 5.54
2376 2463 1.153823 AAATGAGACGACGGGCGAG 60.154 57.895 11.73 0.00 44.57 5.03
2377 2464 3.701604 AATGAGACGACGGGCGAGC 62.702 63.158 11.73 0.66 44.57 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 7.315066 AGATTAATGGGAAAGAGGAGAGATC 57.685 40.000 0.00 0.00 0.00 2.75
57 59 5.232347 AGGCCTAGGTAGATTAATGGGAAA 58.768 41.667 1.29 0.00 0.00 3.13
144 146 1.335597 GCAACCCAACCGAAAAGTAGC 60.336 52.381 0.00 0.00 0.00 3.58
147 149 1.731093 CGCAACCCAACCGAAAAGT 59.269 52.632 0.00 0.00 0.00 2.66
206 208 8.755977 AGTAAATAGTTAAGGAATCGAGGACAA 58.244 33.333 0.00 0.00 0.00 3.18
247 249 4.362677 ACTAGGATAGACTTTGGAAGGCA 58.637 43.478 0.00 0.00 42.77 4.75
252 254 6.039493 CGAGCTTAACTAGGATAGACTTTGGA 59.961 42.308 0.00 0.00 42.77 3.53
255 257 6.238429 CGTCGAGCTTAACTAGGATAGACTTT 60.238 42.308 0.00 0.00 42.77 2.66
287 289 5.221541 ACGTTTGACCAGAAGAAATCTCTCT 60.222 40.000 0.00 0.00 35.73 3.10
293 295 3.815809 TCCACGTTTGACCAGAAGAAAT 58.184 40.909 0.00 0.00 0.00 2.17
323 325 2.377628 GACCAGACACTTCGCACCCA 62.378 60.000 0.00 0.00 0.00 4.51
393 395 3.119708 AGCGGTTCTGAATTGCAAGATTC 60.120 43.478 4.94 5.53 36.73 2.52
401 403 0.169672 CAGGCAGCGGTTCTGAATTG 59.830 55.000 8.54 0.00 45.72 2.32
438 440 6.429385 GGATATTTGGGTGTTGCAAAATTTCA 59.571 34.615 0.00 0.00 0.00 2.69
439 441 6.128035 GGGATATTTGGGTGTTGCAAAATTTC 60.128 38.462 0.00 1.17 0.00 2.17
523 525 7.996758 TTATAATCTTCCAAAGGAGAGAGGT 57.003 36.000 0.00 0.00 31.21 3.85
648 650 9.444600 GAATATAGGTGAGGTAAAACTTTGTGA 57.555 33.333 0.00 0.00 0.00 3.58
660 662 3.051341 TGGAGTGGGAATATAGGTGAGGT 60.051 47.826 0.00 0.00 0.00 3.85
672 674 3.455910 CCTTGTCATCTATGGAGTGGGAA 59.544 47.826 0.00 0.00 0.00 3.97
705 707 0.393820 AGCTGGTTTGCCAAATGGTG 59.606 50.000 0.71 0.00 45.51 4.17
818 823 2.232298 GAGGGACCGCTCTTCTGGTG 62.232 65.000 6.81 0.00 38.99 4.17
825 830 1.610673 ATGTGTGAGGGACCGCTCT 60.611 57.895 13.91 0.00 0.00 4.09
899 904 3.420893 ACAAAATCATGGTGTGGATCGT 58.579 40.909 0.00 0.00 0.00 3.73
1051 1059 4.250116 GATGAAGAGCATCCTCATACGT 57.750 45.455 0.00 0.00 46.23 3.57
1090 1098 2.685897 TGGACCAAACTTGTGTAGCAAC 59.314 45.455 0.00 0.00 32.90 4.17
1195 1205 1.029947 GTTATGGTCAAGGCCACCGG 61.030 60.000 5.01 0.00 41.94 5.28
1222 1232 5.431765 GAGAGCATTTCTTGAGTCCCATAA 58.568 41.667 0.00 0.00 35.87 1.90
1248 1258 4.082517 TGAGAGTGATCTTCGTTCCTGAAG 60.083 45.833 0.00 0.00 45.37 3.02
1298 1308 0.820871 GACCCAGAGCGAGAAGTCAT 59.179 55.000 0.00 0.00 0.00 3.06
1308 1320 1.079057 GAACCGGAAGACCCAGAGC 60.079 63.158 9.46 0.00 34.14 4.09
1336 1349 2.099263 GTCTAGCCGAGTTGCTGTCATA 59.901 50.000 0.00 0.00 42.77 2.15
1377 1390 0.032017 ACCTAGAAGGGACTGCGGAT 60.032 55.000 0.00 0.00 40.58 4.18
1384 1397 5.221581 TGTTACAAGTTCACCTAGAAGGGAC 60.222 44.000 0.00 0.00 40.58 4.46
1395 1409 6.636850 CAGGCAAGTTATTGTTACAAGTTCAC 59.363 38.462 3.63 0.00 38.76 3.18
1495 1519 3.871594 CCCAGTAGCAATGTAGTAGCAAC 59.128 47.826 0.00 0.00 0.00 4.17
1496 1520 3.681594 GCCCAGTAGCAATGTAGTAGCAA 60.682 47.826 0.00 0.00 0.00 3.91
1497 1521 2.158957 GCCCAGTAGCAATGTAGTAGCA 60.159 50.000 0.00 0.00 0.00 3.49
1498 1522 2.484889 GCCCAGTAGCAATGTAGTAGC 58.515 52.381 0.00 0.00 0.00 3.58
1499 1523 2.700897 AGGCCCAGTAGCAATGTAGTAG 59.299 50.000 0.00 0.00 0.00 2.57
1500 1524 2.759355 AGGCCCAGTAGCAATGTAGTA 58.241 47.619 0.00 0.00 0.00 1.82
1501 1525 1.584724 AGGCCCAGTAGCAATGTAGT 58.415 50.000 0.00 0.00 0.00 2.73
1502 1526 2.717639 AAGGCCCAGTAGCAATGTAG 57.282 50.000 0.00 0.00 0.00 2.74
1503 1527 4.788925 AATAAGGCCCAGTAGCAATGTA 57.211 40.909 0.00 0.00 0.00 2.29
1504 1528 3.669939 AATAAGGCCCAGTAGCAATGT 57.330 42.857 0.00 0.00 0.00 2.71
1505 1529 4.402155 TCAAAATAAGGCCCAGTAGCAATG 59.598 41.667 0.00 0.00 0.00 2.82
1506 1530 4.609301 TCAAAATAAGGCCCAGTAGCAAT 58.391 39.130 0.00 0.00 0.00 3.56
1507 1531 4.016444 CTCAAAATAAGGCCCAGTAGCAA 58.984 43.478 0.00 0.00 0.00 3.91
1508 1532 3.265737 TCTCAAAATAAGGCCCAGTAGCA 59.734 43.478 0.00 0.00 0.00 3.49
1509 1533 3.628032 GTCTCAAAATAAGGCCCAGTAGC 59.372 47.826 0.00 0.00 0.00 3.58
1510 1534 5.104259 AGTCTCAAAATAAGGCCCAGTAG 57.896 43.478 0.00 0.00 0.00 2.57
1511 1535 5.514500 AAGTCTCAAAATAAGGCCCAGTA 57.486 39.130 0.00 0.00 0.00 2.74
1512 1536 4.388577 AAGTCTCAAAATAAGGCCCAGT 57.611 40.909 0.00 0.00 0.00 4.00
1513 1537 6.038714 GTGATAAGTCTCAAAATAAGGCCCAG 59.961 42.308 0.00 0.00 0.00 4.45
1514 1538 5.885912 GTGATAAGTCTCAAAATAAGGCCCA 59.114 40.000 0.00 0.00 0.00 5.36
1515 1539 6.122964 AGTGATAAGTCTCAAAATAAGGCCC 58.877 40.000 0.00 0.00 0.00 5.80
1516 1540 7.041712 GCTAGTGATAAGTCTCAAAATAAGGCC 60.042 40.741 0.00 0.00 0.00 5.19
1517 1541 7.041712 GGCTAGTGATAAGTCTCAAAATAAGGC 60.042 40.741 0.00 0.00 0.00 4.35
1518 1542 7.987458 TGGCTAGTGATAAGTCTCAAAATAAGG 59.013 37.037 0.00 0.00 0.00 2.69
1519 1543 8.948631 TGGCTAGTGATAAGTCTCAAAATAAG 57.051 34.615 0.00 0.00 0.00 1.73
1520 1544 8.758829 TCTGGCTAGTGATAAGTCTCAAAATAA 58.241 33.333 0.00 0.00 0.00 1.40
1521 1545 8.306313 TCTGGCTAGTGATAAGTCTCAAAATA 57.694 34.615 0.00 0.00 0.00 1.40
1522 1546 7.187824 TCTGGCTAGTGATAAGTCTCAAAAT 57.812 36.000 0.00 0.00 0.00 1.82
1523 1547 6.605471 TCTGGCTAGTGATAAGTCTCAAAA 57.395 37.500 0.00 0.00 0.00 2.44
1524 1548 6.798427 ATCTGGCTAGTGATAAGTCTCAAA 57.202 37.500 0.00 0.00 0.00 2.69
1525 1549 6.381133 TCAATCTGGCTAGTGATAAGTCTCAA 59.619 38.462 0.00 0.00 0.00 3.02
1526 1550 5.893824 TCAATCTGGCTAGTGATAAGTCTCA 59.106 40.000 0.00 0.00 0.00 3.27
1527 1551 6.398234 TCAATCTGGCTAGTGATAAGTCTC 57.602 41.667 0.00 0.00 0.00 3.36
1528 1552 6.294453 CGATCAATCTGGCTAGTGATAAGTCT 60.294 42.308 3.57 0.00 30.94 3.24
1529 1553 5.861251 CGATCAATCTGGCTAGTGATAAGTC 59.139 44.000 3.57 0.00 30.94 3.01
1530 1554 5.536538 TCGATCAATCTGGCTAGTGATAAGT 59.463 40.000 3.57 0.00 30.94 2.24
1531 1555 6.018589 TCGATCAATCTGGCTAGTGATAAG 57.981 41.667 3.57 2.55 30.94 1.73
1532 1556 6.040955 ACTTCGATCAATCTGGCTAGTGATAA 59.959 38.462 3.57 0.00 30.94 1.75
1533 1557 5.536538 ACTTCGATCAATCTGGCTAGTGATA 59.463 40.000 3.57 0.00 30.94 2.15
1534 1558 4.343526 ACTTCGATCAATCTGGCTAGTGAT 59.656 41.667 3.25 3.25 33.45 3.06
1535 1559 3.701542 ACTTCGATCAATCTGGCTAGTGA 59.298 43.478 0.00 0.00 0.00 3.41
1536 1560 4.047822 GACTTCGATCAATCTGGCTAGTG 58.952 47.826 0.00 0.00 0.00 2.74
1537 1561 3.243234 CGACTTCGATCAATCTGGCTAGT 60.243 47.826 0.00 0.00 43.02 2.57
1538 1562 3.003793 TCGACTTCGATCAATCTGGCTAG 59.996 47.826 0.00 0.00 44.22 3.42
1539 1563 2.949644 TCGACTTCGATCAATCTGGCTA 59.050 45.455 0.00 0.00 44.22 3.93
1540 1564 1.751351 TCGACTTCGATCAATCTGGCT 59.249 47.619 0.00 0.00 44.22 4.75
1541 1565 2.209838 TCGACTTCGATCAATCTGGC 57.790 50.000 0.00 0.00 44.22 4.85
1559 1583 2.882137 CTCCTGGTCGAGTTATCTCCTC 59.118 54.545 0.00 0.00 37.40 3.71
1560 1584 2.938838 CTCCTGGTCGAGTTATCTCCT 58.061 52.381 0.00 0.00 37.40 3.69
1561 1585 1.338655 GCTCCTGGTCGAGTTATCTCC 59.661 57.143 0.00 0.00 37.40 3.71
1562 1586 1.338655 GGCTCCTGGTCGAGTTATCTC 59.661 57.143 0.00 0.00 37.35 2.75
1563 1587 1.342076 TGGCTCCTGGTCGAGTTATCT 60.342 52.381 0.00 0.00 32.11 1.98
1564 1588 1.112113 TGGCTCCTGGTCGAGTTATC 58.888 55.000 0.00 0.00 32.11 1.75
1565 1589 0.824759 GTGGCTCCTGGTCGAGTTAT 59.175 55.000 0.00 0.00 32.11 1.89
1566 1590 1.255667 GGTGGCTCCTGGTCGAGTTA 61.256 60.000 0.00 0.00 32.11 2.24
1567 1591 2.584391 GGTGGCTCCTGGTCGAGTT 61.584 63.158 0.00 0.00 32.11 3.01
1568 1592 2.997897 GGTGGCTCCTGGTCGAGT 60.998 66.667 0.00 0.00 32.11 4.18
1569 1593 2.997315 TGGTGGCTCCTGGTCGAG 60.997 66.667 7.19 0.00 37.07 4.04
1570 1594 2.997315 CTGGTGGCTCCTGGTCGA 60.997 66.667 7.19 0.00 37.07 4.20
1571 1595 3.314331 ACTGGTGGCTCCTGGTCG 61.314 66.667 15.54 0.00 39.12 4.79
1572 1596 2.348998 CACTGGTGGCTCCTGGTC 59.651 66.667 15.54 0.00 39.12 4.02
1573 1597 3.958860 GCACTGGTGGCTCCTGGT 61.959 66.667 15.54 7.91 39.12 4.00
1574 1598 3.278072 ATGCACTGGTGGCTCCTGG 62.278 63.158 15.54 7.35 39.12 4.45
1575 1599 2.044555 CATGCACTGGTGGCTCCTG 61.045 63.158 10.48 10.48 40.38 3.86
1576 1600 2.226315 TCATGCACTGGTGGCTCCT 61.226 57.895 7.19 0.00 37.07 3.69
1577 1601 2.042831 GTCATGCACTGGTGGCTCC 61.043 63.158 0.00 0.00 0.00 4.70
1578 1602 2.393768 CGTCATGCACTGGTGGCTC 61.394 63.158 0.00 0.00 0.00 4.70
1579 1603 2.359107 CGTCATGCACTGGTGGCT 60.359 61.111 0.00 0.00 0.00 4.75
1580 1604 4.107051 GCGTCATGCACTGGTGGC 62.107 66.667 0.00 0.00 45.45 5.01
1600 1624 4.194640 TCTGTCTTCTAGATGGCAAATGC 58.805 43.478 13.31 0.00 41.14 3.56
1601 1625 5.177142 CGATCTGTCTTCTAGATGGCAAATG 59.823 44.000 13.31 3.58 35.14 2.32
1602 1626 5.295950 CGATCTGTCTTCTAGATGGCAAAT 58.704 41.667 13.31 6.57 35.14 2.32
1603 1627 4.686972 CGATCTGTCTTCTAGATGGCAAA 58.313 43.478 13.31 1.69 35.14 3.68
1604 1628 4.313277 CGATCTGTCTTCTAGATGGCAA 57.687 45.455 13.31 6.11 35.14 4.52
1659 1683 6.183360 TGCTCACAAAGAACAATCAGTCAATT 60.183 34.615 0.00 0.00 0.00 2.32
1781 1806 3.956199 CAGAGCCAATACAAACCATCCAT 59.044 43.478 0.00 0.00 0.00 3.41
1782 1807 3.245229 ACAGAGCCAATACAAACCATCCA 60.245 43.478 0.00 0.00 0.00 3.41
1785 1810 5.179452 AGTACAGAGCCAATACAAACCAT 57.821 39.130 0.00 0.00 0.00 3.55
1786 1811 4.634012 AGTACAGAGCCAATACAAACCA 57.366 40.909 0.00 0.00 0.00 3.67
1793 1818 9.378551 CACAAGTTTTATAGTACAGAGCCAATA 57.621 33.333 0.00 0.00 0.00 1.90
1837 1862 3.343941 AGGTGCATAAACTTCGCCTTA 57.656 42.857 0.00 0.00 37.43 2.69
1876 1901 6.709281 TGATGGCATGGTGTAAATTTGAATT 58.291 32.000 3.81 0.00 0.00 2.17
1887 1912 3.497405 GGATAGTGATGATGGCATGGTGT 60.497 47.826 3.81 0.00 34.11 4.16
1921 1956 6.983474 TCATTGTTCACACCTATACACATG 57.017 37.500 0.00 0.00 0.00 3.21
1957 2026 3.328505 CCCCACAAATGCTTCAAATCAC 58.671 45.455 0.00 0.00 0.00 3.06
1969 2038 1.075601 TGAAGCTCTCCCCCACAAAT 58.924 50.000 0.00 0.00 0.00 2.32
2008 2077 0.234625 CGGTGTTGGTGTTGATGTCG 59.765 55.000 0.00 0.00 0.00 4.35
2054 2123 6.024552 TGGTGGTTGCTCTTATTTTGATTC 57.975 37.500 0.00 0.00 0.00 2.52
2055 2124 6.351286 GGATGGTGGTTGCTCTTATTTTGATT 60.351 38.462 0.00 0.00 0.00 2.57
2077 2149 0.456221 CCAACTGTAGCTCGTCGGAT 59.544 55.000 0.00 0.00 0.00 4.18
2081 2153 0.038159 AGTGCCAACTGTAGCTCGTC 60.038 55.000 0.00 0.00 34.48 4.20
2183 2267 3.942748 GACATGGGTATGCGGAGTAAAAA 59.057 43.478 0.00 0.00 37.85 1.94
2193 2280 1.880027 GGATTTCCGACATGGGTATGC 59.120 52.381 0.00 0.00 37.85 3.14
2216 2303 1.888436 CTTGGCTGTAGTGGCGGAGA 61.888 60.000 0.00 0.00 35.06 3.71
2227 2314 0.907230 GAGGAGGAGACCTTGGCTGT 60.907 60.000 0.00 0.00 40.73 4.40
2230 2317 0.467804 GATGAGGAGGAGACCTTGGC 59.532 60.000 0.00 0.00 40.73 4.52
2235 2322 1.118838 CCAGTGATGAGGAGGAGACC 58.881 60.000 0.00 0.00 0.00 3.85
2236 2323 1.754226 GTCCAGTGATGAGGAGGAGAC 59.246 57.143 0.00 0.00 33.85 3.36
2237 2324 1.683319 CGTCCAGTGATGAGGAGGAGA 60.683 57.143 0.00 0.00 41.16 3.71
2238 2325 0.743688 CGTCCAGTGATGAGGAGGAG 59.256 60.000 0.00 0.00 41.16 3.69
2239 2326 0.331616 TCGTCCAGTGATGAGGAGGA 59.668 55.000 0.00 0.00 44.07 3.71
2240 2327 0.743688 CTCGTCCAGTGATGAGGAGG 59.256 60.000 9.83 0.00 46.57 4.30
2245 2332 1.405463 CGATTCCTCGTCCAGTGATGA 59.595 52.381 0.00 0.00 40.07 2.92
2246 2333 1.845266 CGATTCCTCGTCCAGTGATG 58.155 55.000 0.00 0.00 40.07 3.07
2256 2343 2.968330 GCGACTCCGACGATTCCTCG 62.968 65.000 0.00 0.00 42.56 4.63
2257 2344 1.298488 GCGACTCCGACGATTCCTC 60.298 63.158 0.00 0.00 38.22 3.71
2258 2345 1.592400 TTGCGACTCCGACGATTCCT 61.592 55.000 0.00 0.00 38.22 3.36
2259 2346 0.734942 TTTGCGACTCCGACGATTCC 60.735 55.000 0.00 0.00 38.22 3.01
2260 2347 0.640768 CTTTGCGACTCCGACGATTC 59.359 55.000 0.00 0.00 38.22 2.52
2261 2348 0.242825 TCTTTGCGACTCCGACGATT 59.757 50.000 0.00 0.00 38.22 3.34
2262 2349 0.242825 TTCTTTGCGACTCCGACGAT 59.757 50.000 0.00 0.00 38.22 3.73
2263 2350 0.031043 TTTCTTTGCGACTCCGACGA 59.969 50.000 0.00 0.00 38.22 4.20
2264 2351 0.856641 TTTTCTTTGCGACTCCGACG 59.143 50.000 0.00 0.00 38.22 5.12
2265 2352 3.226347 CAATTTTCTTTGCGACTCCGAC 58.774 45.455 0.00 0.00 38.22 4.79
2266 2353 2.875933 ACAATTTTCTTTGCGACTCCGA 59.124 40.909 0.00 0.00 38.22 4.55
2267 2354 2.973224 CACAATTTTCTTTGCGACTCCG 59.027 45.455 0.00 0.00 39.16 4.63
2268 2355 4.223320 TCACAATTTTCTTTGCGACTCC 57.777 40.909 0.00 0.00 0.00 3.85
2269 2356 6.567769 TTTTCACAATTTTCTTTGCGACTC 57.432 33.333 0.00 0.00 0.00 3.36
2270 2357 6.959671 TTTTTCACAATTTTCTTTGCGACT 57.040 29.167 0.00 0.00 0.00 4.18
2290 2377 2.497107 TCCGTCGACGAGTTCTTTTT 57.503 45.000 37.65 0.00 43.02 1.94
2291 2378 2.497107 TTCCGTCGACGAGTTCTTTT 57.503 45.000 37.65 0.00 43.02 2.27
2292 2379 2.593257 GATTCCGTCGACGAGTTCTTT 58.407 47.619 37.65 15.17 43.02 2.52
2293 2380 1.135460 GGATTCCGTCGACGAGTTCTT 60.135 52.381 37.65 16.21 43.02 2.52
2294 2381 0.450983 GGATTCCGTCGACGAGTTCT 59.549 55.000 37.65 17.45 43.02 3.01
2295 2382 0.169672 TGGATTCCGTCGACGAGTTC 59.830 55.000 37.65 26.78 43.02 3.01
2296 2383 0.815734 ATGGATTCCGTCGACGAGTT 59.184 50.000 37.65 21.16 43.02 3.01
2297 2384 0.815734 AATGGATTCCGTCGACGAGT 59.184 50.000 37.65 22.44 43.02 4.18
2298 2385 1.922570 AAATGGATTCCGTCGACGAG 58.077 50.000 37.65 26.30 43.02 4.18
2299 2386 1.996898 CAAAATGGATTCCGTCGACGA 59.003 47.619 37.65 20.57 43.02 4.20
2300 2387 1.730064 ACAAAATGGATTCCGTCGACG 59.270 47.619 30.33 30.33 39.44 5.12
2301 2388 3.063045 GGTACAAAATGGATTCCGTCGAC 59.937 47.826 5.18 5.18 0.00 4.20
2302 2389 3.055675 AGGTACAAAATGGATTCCGTCGA 60.056 43.478 0.00 0.00 0.00 4.20
2303 2390 3.267483 AGGTACAAAATGGATTCCGTCG 58.733 45.455 0.00 0.00 0.00 5.12
2304 2391 4.142469 CCAAGGTACAAAATGGATTCCGTC 60.142 45.833 0.00 0.00 34.82 4.79
2305 2392 3.761752 CCAAGGTACAAAATGGATTCCGT 59.238 43.478 0.00 0.00 34.82 4.69
2306 2393 3.428862 GCCAAGGTACAAAATGGATTCCG 60.429 47.826 8.99 0.00 34.82 4.30
2307 2394 3.513515 TGCCAAGGTACAAAATGGATTCC 59.486 43.478 8.99 0.00 34.82 3.01
2308 2395 4.799564 TGCCAAGGTACAAAATGGATTC 57.200 40.909 8.99 0.00 34.82 2.52
2309 2396 5.071653 AGTTTGCCAAGGTACAAAATGGATT 59.928 36.000 8.99 0.00 37.50 3.01
2310 2397 4.592778 AGTTTGCCAAGGTACAAAATGGAT 59.407 37.500 8.99 0.00 37.50 3.41
2311 2398 3.964031 AGTTTGCCAAGGTACAAAATGGA 59.036 39.130 8.99 0.00 37.50 3.41
2312 2399 4.335400 AGTTTGCCAAGGTACAAAATGG 57.665 40.909 0.00 0.00 37.50 3.16
2313 2400 5.799936 CGATAGTTTGCCAAGGTACAAAATG 59.200 40.000 0.00 0.00 37.50 2.32
2314 2401 5.708230 TCGATAGTTTGCCAAGGTACAAAAT 59.292 36.000 0.00 0.00 37.50 1.82
2315 2402 5.064558 TCGATAGTTTGCCAAGGTACAAAA 58.935 37.500 0.00 0.00 37.50 2.44
2316 2403 4.643463 TCGATAGTTTGCCAAGGTACAAA 58.357 39.130 0.00 0.00 33.55 2.83
2317 2404 4.274602 TCGATAGTTTGCCAAGGTACAA 57.725 40.909 0.00 0.00 37.40 2.41
2318 2405 3.965379 TCGATAGTTTGCCAAGGTACA 57.035 42.857 0.00 0.00 37.40 2.90
2319 2406 3.998341 TGTTCGATAGTTTGCCAAGGTAC 59.002 43.478 0.00 0.00 37.40 3.34
2320 2407 4.274602 TGTTCGATAGTTTGCCAAGGTA 57.725 40.909 0.00 0.00 37.40 3.08
2321 2408 3.134574 TGTTCGATAGTTTGCCAAGGT 57.865 42.857 0.00 0.00 37.40 3.50
2322 2409 3.502211 AGTTGTTCGATAGTTTGCCAAGG 59.498 43.478 0.00 0.00 37.40 3.61
2323 2410 4.749245 AGTTGTTCGATAGTTTGCCAAG 57.251 40.909 0.00 0.00 37.40 3.61
2324 2411 4.791411 GCAAGTTGTTCGATAGTTTGCCAA 60.791 41.667 4.48 0.00 34.85 4.52
2325 2412 3.304391 GCAAGTTGTTCGATAGTTTGCCA 60.304 43.478 4.48 0.00 34.85 4.92
2326 2413 3.234386 GCAAGTTGTTCGATAGTTTGCC 58.766 45.455 4.48 0.00 34.85 4.52
2327 2414 2.902484 CGCAAGTTGTTCGATAGTTTGC 59.098 45.455 4.48 10.34 36.88 3.68
2328 2415 3.479006 CCGCAAGTTGTTCGATAGTTTG 58.521 45.455 4.48 0.00 37.40 2.93
2329 2416 2.482721 CCCGCAAGTTGTTCGATAGTTT 59.517 45.455 4.48 0.00 37.40 2.66
2330 2417 2.073816 CCCGCAAGTTGTTCGATAGTT 58.926 47.619 4.48 0.00 37.40 2.24
2331 2418 1.722011 CCCGCAAGTTGTTCGATAGT 58.278 50.000 4.48 0.00 37.40 2.12
2332 2419 0.373716 GCCCGCAAGTTGTTCGATAG 59.626 55.000 4.48 0.00 0.00 2.08
2333 2420 1.355796 CGCCCGCAAGTTGTTCGATA 61.356 55.000 4.48 0.00 0.00 2.92
2334 2421 2.677003 CGCCCGCAAGTTGTTCGAT 61.677 57.895 4.48 0.00 0.00 3.59
2335 2422 3.342627 CGCCCGCAAGTTGTTCGA 61.343 61.111 4.48 0.00 0.00 3.71
2336 2423 3.573489 GACGCCCGCAAGTTGTTCG 62.573 63.158 4.48 5.81 0.00 3.95
2337 2424 2.251371 GACGCCCGCAAGTTGTTC 59.749 61.111 4.48 0.00 0.00 3.18
2338 2425 3.645975 CGACGCCCGCAAGTTGTT 61.646 61.111 4.48 0.00 0.00 2.83
2339 2426 4.595538 TCGACGCCCGCAAGTTGT 62.596 61.111 4.48 0.00 38.37 3.32
2340 2427 4.072088 GTCGACGCCCGCAAGTTG 62.072 66.667 0.00 0.00 38.37 3.16
2341 2428 4.595538 TGTCGACGCCCGCAAGTT 62.596 61.111 11.62 0.00 38.37 2.66
2342 2429 4.595538 TTGTCGACGCCCGCAAGT 62.596 61.111 11.62 0.00 38.37 3.16
2343 2430 2.677003 ATTTGTCGACGCCCGCAAG 61.677 57.895 11.62 0.00 36.34 4.01
2344 2431 2.666862 ATTTGTCGACGCCCGCAA 60.667 55.556 11.62 0.00 38.37 4.85
2345 2432 3.418913 CATTTGTCGACGCCCGCA 61.419 61.111 11.62 0.00 38.37 5.69
2346 2433 3.083600 CTCATTTGTCGACGCCCGC 62.084 63.158 11.62 0.00 38.37 6.13
2347 2434 1.445410 TCTCATTTGTCGACGCCCG 60.445 57.895 11.62 0.00 40.25 6.13
2348 2435 1.683790 CGTCTCATTTGTCGACGCCC 61.684 60.000 11.62 0.00 43.02 6.13
2349 2436 1.702299 CGTCTCATTTGTCGACGCC 59.298 57.895 11.62 0.00 43.02 5.68
2352 2439 0.982673 CCGTCGTCTCATTTGTCGAC 59.017 55.000 9.11 9.11 45.70 4.20
2353 2440 0.109458 CCCGTCGTCTCATTTGTCGA 60.109 55.000 0.00 0.00 0.00 4.20
2354 2441 1.683790 GCCCGTCGTCTCATTTGTCG 61.684 60.000 0.00 0.00 0.00 4.35
2355 2442 1.683790 CGCCCGTCGTCTCATTTGTC 61.684 60.000 0.00 0.00 0.00 3.18
2356 2443 1.736645 CGCCCGTCGTCTCATTTGT 60.737 57.895 0.00 0.00 0.00 2.83
2357 2444 1.413767 CTCGCCCGTCGTCTCATTTG 61.414 60.000 0.00 0.00 39.67 2.32
2358 2445 1.153823 CTCGCCCGTCGTCTCATTT 60.154 57.895 0.00 0.00 39.67 2.32
2359 2446 2.490217 CTCGCCCGTCGTCTCATT 59.510 61.111 0.00 0.00 39.67 2.57
2360 2447 4.194720 GCTCGCCCGTCGTCTCAT 62.195 66.667 0.00 0.00 39.67 2.90


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

AutoCloner maintained by Alex Coulton.