Multiple sequence alignment - TraesCS6A01G027200

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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 TraesCS6A01G027200 chr6A 100.000 2411 0 0 1 2411 13686040 13683630 0.000000e+00 4453.0
1 TraesCS6A01G027200 chr2B 98.734 948 11 1 497 1444 717090404 717089458 0.000000e+00 1683.0
2 TraesCS6A01G027200 chr2B 98.185 551 7 1 898 1445 261045387 261045937 0.000000e+00 959.0
3 TraesCS6A01G027200 chr2B 98.253 458 8 0 1 458 717090862 717090405 0.000000e+00 802.0
4 TraesCS6A01G027200 chr6D 89.251 614 52 12 1806 2411 12329243 12328636 0.000000e+00 756.0
5 TraesCS6A01G027200 chr6D 75.630 357 60 16 1972 2313 12314281 12313937 4.150000e-33 152.0
6 TraesCS6A01G027200 chr6B 86.179 615 66 17 1806 2411 22647216 22646612 0.000000e+00 647.0
7 TraesCS6A01G027200 chr6B 78.440 218 44 1 1972 2186 22581445 22581228 3.230000e-29 139.0
8 TraesCS6A01G027200 chr3D 74.777 1459 331 29 2 1444 56567564 56569001 2.630000e-174 621.0
9 TraesCS6A01G027200 chr3D 75.059 850 161 28 1 844 480415285 480414481 4.930000e-92 348.0
10 TraesCS6A01G027200 chrUn 77.412 850 176 13 1 844 68204072 68204911 2.150000e-135 492.0
11 TraesCS6A01G027200 chr7D 75.383 849 199 10 1 844 535773155 535773998 3.730000e-108 401.0
12 TraesCS6A01G027200 chr7D 75.132 378 84 10 236 608 22616868 22617240 4.120000e-38 169.0
13 TraesCS6A01G027200 chr5B 73.988 642 144 20 122 750 10578872 10579503 3.100000e-59 239.0
14 TraesCS6A01G027200 chr2A 76.056 426 86 16 331 748 196510091 196510508 8.740000e-50 207.0
15 TraesCS6A01G027200 chr3A 75.708 424 91 12 331 748 214129817 214129400 4.060000e-48 202.0
16 TraesCS6A01G027200 chr3A 76.176 340 67 13 302 634 690083248 690083580 1.480000e-37 167.0
17 TraesCS6A01G027200 chr1D 97.826 46 1 0 1386 1431 20657880 20657925 1.990000e-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 TraesCS6A01G027200 chr6A 13683630 13686040 2410 True 4453.0 4453 100.0000 1 2411 1 chr6A.!!$R1 2410
1 TraesCS6A01G027200 chr2B 717089458 717090862 1404 True 1242.5 1683 98.4935 1 1444 2 chr2B.!!$R1 1443
2 TraesCS6A01G027200 chr2B 261045387 261045937 550 False 959.0 959 98.1850 898 1445 1 chr2B.!!$F1 547
3 TraesCS6A01G027200 chr6D 12328636 12329243 607 True 756.0 756 89.2510 1806 2411 1 chr6D.!!$R2 605
4 TraesCS6A01G027200 chr6B 22646612 22647216 604 True 647.0 647 86.1790 1806 2411 1 chr6B.!!$R2 605
5 TraesCS6A01G027200 chr3D 56567564 56569001 1437 False 621.0 621 74.7770 2 1444 1 chr3D.!!$F1 1442
6 TraesCS6A01G027200 chr3D 480414481 480415285 804 True 348.0 348 75.0590 1 844 1 chr3D.!!$R1 843
7 TraesCS6A01G027200 chrUn 68204072 68204911 839 False 492.0 492 77.4120 1 844 1 chrUn.!!$F1 843
8 TraesCS6A01G027200 chr7D 535773155 535773998 843 False 401.0 401 75.3830 1 844 1 chr7D.!!$F2 843
9 TraesCS6A01G027200 chr5B 10578872 10579503 631 False 239.0 239 73.9880 122 750 1 chr5B.!!$F1 628

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
687 691 3.162666 TGAACGACTACCAGTCCTCATT 58.837 45.455 0.0 0.0 42.12 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 2417 0.036199 TGCCCGGTGTACACATAACC 60.036 55.0 26.51 8.79 0.0 2.85 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
465 469 5.336770 GCTTGCTACCTTGGAAAATAAAGCT 60.337 40.000 0.00 0.00 34.82 3.74
468 472 7.768807 TGCTACCTTGGAAAATAAAGCTAAA 57.231 32.000 0.00 0.00 0.00 1.85
474 478 8.148351 ACCTTGGAAAATAAAGCTAAAAGGAAC 58.852 33.333 4.72 0.00 36.11 3.62
687 691 3.162666 TGAACGACTACCAGTCCTCATT 58.837 45.455 0.00 0.00 42.12 2.57
1264 1274 1.512926 ATCTGGACGTGAAGTTGTGC 58.487 50.000 0.00 0.00 0.00 4.57
1268 1278 1.014352 GGACGTGAAGTTGTGCTGTT 58.986 50.000 0.00 0.00 0.00 3.16
1490 1500 6.817270 CAAATTATTGCAGGTAATGTGCTC 57.183 37.500 9.74 0.00 41.78 4.26
1491 1501 6.567050 CAAATTATTGCAGGTAATGTGCTCT 58.433 36.000 9.74 0.00 41.78 4.09
1492 1502 6.780457 AATTATTGCAGGTAATGTGCTCTT 57.220 33.333 7.06 0.00 41.78 2.85
1493 1503 6.780457 ATTATTGCAGGTAATGTGCTCTTT 57.220 33.333 5.84 0.00 41.78 2.52
1494 1504 4.708726 ATTGCAGGTAATGTGCTCTTTC 57.291 40.909 0.00 0.00 41.78 2.62
1495 1505 2.076100 TGCAGGTAATGTGCTCTTTCG 58.924 47.619 0.00 0.00 41.78 3.46
1496 1506 2.289382 TGCAGGTAATGTGCTCTTTCGA 60.289 45.455 0.00 0.00 41.78 3.71
1497 1507 2.094417 GCAGGTAATGTGCTCTTTCGAC 59.906 50.000 0.00 0.00 37.96 4.20
1498 1508 3.325870 CAGGTAATGTGCTCTTTCGACA 58.674 45.455 0.00 0.00 0.00 4.35
1499 1509 3.745975 CAGGTAATGTGCTCTTTCGACAA 59.254 43.478 0.00 0.00 0.00 3.18
1500 1510 3.997021 AGGTAATGTGCTCTTTCGACAAG 59.003 43.478 0.00 0.00 0.00 3.16
1501 1511 2.977405 AATGTGCTCTTTCGACAAGC 57.023 45.000 6.03 6.03 36.56 4.01
1502 1512 2.175878 ATGTGCTCTTTCGACAAGCT 57.824 45.000 12.50 0.00 36.96 3.74
1503 1513 2.812358 TGTGCTCTTTCGACAAGCTA 57.188 45.000 12.50 1.95 36.96 3.32
1504 1514 2.677199 TGTGCTCTTTCGACAAGCTAG 58.323 47.619 12.50 0.00 36.96 3.42
1505 1515 1.996191 GTGCTCTTTCGACAAGCTAGG 59.004 52.381 12.50 0.00 36.96 3.02
1506 1516 1.618837 TGCTCTTTCGACAAGCTAGGT 59.381 47.619 12.50 0.00 36.96 3.08
1507 1517 2.823747 TGCTCTTTCGACAAGCTAGGTA 59.176 45.455 12.50 0.00 36.96 3.08
1508 1518 3.119459 TGCTCTTTCGACAAGCTAGGTAG 60.119 47.826 12.50 0.00 36.96 3.18
1509 1519 3.128938 GCTCTTTCGACAAGCTAGGTAGA 59.871 47.826 0.00 0.00 33.23 2.59
1510 1520 4.202070 GCTCTTTCGACAAGCTAGGTAGAT 60.202 45.833 0.00 0.00 33.23 1.98
1511 1521 5.502153 TCTTTCGACAAGCTAGGTAGATC 57.498 43.478 0.00 0.00 0.00 2.75
1512 1522 4.948004 TCTTTCGACAAGCTAGGTAGATCA 59.052 41.667 0.00 0.00 0.00 2.92
1513 1523 4.902443 TTCGACAAGCTAGGTAGATCAG 57.098 45.455 0.00 0.00 0.00 2.90
1514 1524 2.619177 TCGACAAGCTAGGTAGATCAGC 59.381 50.000 0.00 0.00 35.49 4.26
1515 1525 2.359214 CGACAAGCTAGGTAGATCAGCA 59.641 50.000 0.00 0.00 37.78 4.41
1516 1526 3.005261 CGACAAGCTAGGTAGATCAGCAT 59.995 47.826 0.00 0.00 37.78 3.79
1517 1527 4.555262 GACAAGCTAGGTAGATCAGCATC 58.445 47.826 0.00 0.00 37.78 3.91
1518 1528 3.963374 ACAAGCTAGGTAGATCAGCATCA 59.037 43.478 0.00 0.00 37.78 3.07
1519 1529 4.039004 ACAAGCTAGGTAGATCAGCATCAG 59.961 45.833 0.00 0.00 37.78 2.90
1520 1530 2.562298 AGCTAGGTAGATCAGCATCAGC 59.438 50.000 4.95 1.78 37.78 4.26
1532 1542 2.539346 GCATCAGCTGTTTGCACTAG 57.461 50.000 27.83 5.81 45.94 2.57
1533 1543 1.131883 GCATCAGCTGTTTGCACTAGG 59.868 52.381 27.83 7.18 45.94 3.02
1534 1544 1.741706 CATCAGCTGTTTGCACTAGGG 59.258 52.381 14.67 0.00 45.94 3.53
1535 1545 0.606401 TCAGCTGTTTGCACTAGGGC 60.606 55.000 10.98 10.98 45.94 5.19
1536 1546 0.890542 CAGCTGTTTGCACTAGGGCA 60.891 55.000 17.75 17.75 45.94 5.36
1537 1547 0.607489 AGCTGTTTGCACTAGGGCAG 60.607 55.000 20.92 9.78 45.88 4.85
1538 1548 0.890996 GCTGTTTGCACTAGGGCAGT 60.891 55.000 20.92 0.00 45.88 4.40
1539 1549 1.610624 GCTGTTTGCACTAGGGCAGTA 60.611 52.381 20.92 9.81 45.88 2.74
1540 1550 2.350522 CTGTTTGCACTAGGGCAGTAG 58.649 52.381 20.92 15.21 45.88 2.57
1541 1551 1.697432 TGTTTGCACTAGGGCAGTAGT 59.303 47.619 20.92 0.00 45.88 2.73
1542 1552 2.901192 TGTTTGCACTAGGGCAGTAGTA 59.099 45.455 20.92 1.17 45.88 1.82
1543 1553 3.259902 GTTTGCACTAGGGCAGTAGTAC 58.740 50.000 20.92 10.57 45.88 2.73
1544 1554 1.481871 TGCACTAGGGCAGTAGTACC 58.518 55.000 17.75 0.00 39.25 3.34
1545 1555 1.272816 TGCACTAGGGCAGTAGTACCA 60.273 52.381 17.75 0.00 39.25 3.25
1546 1556 1.829222 GCACTAGGGCAGTAGTACCAA 59.171 52.381 13.43 0.00 34.98 3.67
1547 1557 2.434702 GCACTAGGGCAGTAGTACCAAT 59.565 50.000 13.43 0.00 34.98 3.16
1548 1558 3.741388 GCACTAGGGCAGTAGTACCAATG 60.741 52.174 13.43 0.00 34.98 2.82
1549 1559 3.704566 CACTAGGGCAGTAGTACCAATGA 59.295 47.826 0.00 0.00 34.98 2.57
1550 1560 3.961408 ACTAGGGCAGTAGTACCAATGAG 59.039 47.826 0.00 0.00 34.98 2.90
1551 1561 2.119495 AGGGCAGTAGTACCAATGAGG 58.881 52.381 0.00 0.00 45.67 3.86
1552 1562 1.475213 GGGCAGTAGTACCAATGAGGC 60.475 57.143 0.00 0.00 43.14 4.70
1553 1563 1.209504 GGCAGTAGTACCAATGAGGCA 59.790 52.381 0.00 0.00 43.14 4.75
1554 1564 2.158755 GGCAGTAGTACCAATGAGGCAT 60.159 50.000 0.00 0.00 43.14 4.40
1555 1565 3.071023 GGCAGTAGTACCAATGAGGCATA 59.929 47.826 0.00 0.00 43.14 3.14
1556 1566 4.444306 GGCAGTAGTACCAATGAGGCATAA 60.444 45.833 0.00 0.00 43.14 1.90
1557 1567 4.511826 GCAGTAGTACCAATGAGGCATAAC 59.488 45.833 0.00 0.00 43.14 1.89
1558 1568 5.670485 CAGTAGTACCAATGAGGCATAACA 58.330 41.667 0.00 0.00 43.14 2.41
1559 1569 6.291377 CAGTAGTACCAATGAGGCATAACAT 58.709 40.000 0.00 0.00 43.14 2.71
1560 1570 7.441836 CAGTAGTACCAATGAGGCATAACATA 58.558 38.462 0.00 0.00 43.14 2.29
1561 1571 7.931407 CAGTAGTACCAATGAGGCATAACATAA 59.069 37.037 0.00 0.00 43.14 1.90
1562 1572 8.491134 AGTAGTACCAATGAGGCATAACATAAA 58.509 33.333 0.00 0.00 43.14 1.40
1563 1573 7.807977 AGTACCAATGAGGCATAACATAAAG 57.192 36.000 0.00 0.00 43.14 1.85
1564 1574 5.520376 ACCAATGAGGCATAACATAAAGC 57.480 39.130 0.00 0.00 43.14 3.51
1565 1575 4.955450 ACCAATGAGGCATAACATAAAGCA 59.045 37.500 0.00 0.00 43.14 3.91
1566 1576 5.421693 ACCAATGAGGCATAACATAAAGCAA 59.578 36.000 0.00 0.00 43.14 3.91
1567 1577 5.750067 CCAATGAGGCATAACATAAAGCAAC 59.250 40.000 0.00 0.00 0.00 4.17
1568 1578 4.981806 TGAGGCATAACATAAAGCAACC 57.018 40.909 0.00 0.00 0.00 3.77
1569 1579 4.599041 TGAGGCATAACATAAAGCAACCT 58.401 39.130 0.00 0.00 0.00 3.50
1570 1580 4.398988 TGAGGCATAACATAAAGCAACCTG 59.601 41.667 0.00 0.00 0.00 4.00
1571 1581 3.701040 AGGCATAACATAAAGCAACCTGG 59.299 43.478 0.00 0.00 0.00 4.45
1572 1582 3.447742 GCATAACATAAAGCAACCTGGC 58.552 45.455 0.00 0.00 0.00 4.85
1573 1583 3.694734 CATAACATAAAGCAACCTGGCG 58.305 45.455 0.00 0.00 39.27 5.69
1574 1584 0.243636 AACATAAAGCAACCTGGCGC 59.756 50.000 0.00 0.00 39.27 6.53
1575 1585 0.893270 ACATAAAGCAACCTGGCGCA 60.893 50.000 10.83 0.00 39.27 6.09
1576 1586 0.457035 CATAAAGCAACCTGGCGCAT 59.543 50.000 10.83 0.00 39.27 4.73
1577 1587 0.740737 ATAAAGCAACCTGGCGCATC 59.259 50.000 10.83 0.00 39.27 3.91
1578 1588 0.322456 TAAAGCAACCTGGCGCATCT 60.322 50.000 10.83 0.00 39.27 2.90
1579 1589 0.322456 AAAGCAACCTGGCGCATCTA 60.322 50.000 10.83 0.00 39.27 1.98
1580 1590 0.107017 AAGCAACCTGGCGCATCTAT 60.107 50.000 10.83 0.00 39.27 1.98
1581 1591 0.533755 AGCAACCTGGCGCATCTATC 60.534 55.000 10.83 0.00 39.27 2.08
1582 1592 0.533755 GCAACCTGGCGCATCTATCT 60.534 55.000 10.83 0.00 0.00 1.98
1583 1593 1.506493 CAACCTGGCGCATCTATCTC 58.494 55.000 10.83 0.00 0.00 2.75
1584 1594 1.123077 AACCTGGCGCATCTATCTCA 58.877 50.000 10.83 0.00 0.00 3.27
1585 1595 1.346062 ACCTGGCGCATCTATCTCAT 58.654 50.000 10.83 0.00 0.00 2.90
1586 1596 1.001746 ACCTGGCGCATCTATCTCATG 59.998 52.381 10.83 0.00 0.00 3.07
1587 1597 1.001746 CCTGGCGCATCTATCTCATGT 59.998 52.381 10.83 0.00 0.00 3.21
1588 1598 2.335752 CTGGCGCATCTATCTCATGTC 58.664 52.381 10.83 0.00 0.00 3.06
1589 1599 1.966354 TGGCGCATCTATCTCATGTCT 59.034 47.619 10.83 0.00 0.00 3.41
1590 1600 2.366590 TGGCGCATCTATCTCATGTCTT 59.633 45.455 10.83 0.00 0.00 3.01
1591 1601 3.181462 TGGCGCATCTATCTCATGTCTTT 60.181 43.478 10.83 0.00 0.00 2.52
1592 1602 3.812053 GGCGCATCTATCTCATGTCTTTT 59.188 43.478 10.83 0.00 0.00 2.27
1593 1603 4.274459 GGCGCATCTATCTCATGTCTTTTT 59.726 41.667 10.83 0.00 0.00 1.94
1667 1677 9.255029 TCATACCAGCATATTAGCATAAGTAGA 57.745 33.333 0.00 0.00 36.85 2.59
1668 1678 9.875691 CATACCAGCATATTAGCATAAGTAGAA 57.124 33.333 0.00 0.00 36.85 2.10
1669 1679 9.877178 ATACCAGCATATTAGCATAAGTAGAAC 57.123 33.333 0.00 0.00 36.85 3.01
1670 1680 7.967908 ACCAGCATATTAGCATAAGTAGAACT 58.032 34.615 0.00 0.00 36.85 3.01
1671 1681 7.875041 ACCAGCATATTAGCATAAGTAGAACTG 59.125 37.037 0.00 0.00 36.85 3.16
1672 1682 8.090831 CCAGCATATTAGCATAAGTAGAACTGA 58.909 37.037 0.00 0.00 36.85 3.41
1673 1683 9.650539 CAGCATATTAGCATAAGTAGAACTGAT 57.349 33.333 0.00 0.00 36.85 2.90
1674 1684 9.650539 AGCATATTAGCATAAGTAGAACTGATG 57.349 33.333 0.66 0.66 39.59 3.07
1675 1685 9.645059 GCATATTAGCATAAGTAGAACTGATGA 57.355 33.333 8.35 0.00 39.04 2.92
1694 1704 9.790344 ACTGATGATTATATTGGAAGAAAGAGG 57.210 33.333 0.00 0.00 0.00 3.69
1695 1705 8.627208 TGATGATTATATTGGAAGAAAGAGGC 57.373 34.615 0.00 0.00 0.00 4.70
1696 1706 8.219868 TGATGATTATATTGGAAGAAAGAGGCA 58.780 33.333 0.00 0.00 0.00 4.75
1697 1707 9.071276 GATGATTATATTGGAAGAAAGAGGCAA 57.929 33.333 0.00 0.00 0.00 4.52
1698 1708 8.821686 TGATTATATTGGAAGAAAGAGGCAAA 57.178 30.769 0.00 0.00 0.00 3.68
1699 1709 8.906867 TGATTATATTGGAAGAAAGAGGCAAAG 58.093 33.333 0.00 0.00 0.00 2.77
1700 1710 3.949842 ATTGGAAGAAAGAGGCAAAGC 57.050 42.857 0.00 0.00 0.00 3.51
1701 1711 2.363306 TGGAAGAAAGAGGCAAAGCA 57.637 45.000 0.00 0.00 0.00 3.91
1702 1712 2.665165 TGGAAGAAAGAGGCAAAGCAA 58.335 42.857 0.00 0.00 0.00 3.91
1703 1713 3.233507 TGGAAGAAAGAGGCAAAGCAAT 58.766 40.909 0.00 0.00 0.00 3.56
1704 1714 3.642848 TGGAAGAAAGAGGCAAAGCAATT 59.357 39.130 0.00 0.00 0.00 2.32
1705 1715 4.240888 GGAAGAAAGAGGCAAAGCAATTC 58.759 43.478 0.00 0.00 0.00 2.17
1706 1716 3.949842 AGAAAGAGGCAAAGCAATTCC 57.050 42.857 0.00 0.00 0.00 3.01
1707 1717 2.229784 AGAAAGAGGCAAAGCAATTCCG 59.770 45.455 0.00 0.00 0.00 4.30
1708 1718 0.890683 AAGAGGCAAAGCAATTCCGG 59.109 50.000 0.00 0.00 0.00 5.14
1709 1719 0.038166 AGAGGCAAAGCAATTCCGGA 59.962 50.000 0.00 0.00 0.00 5.14
1710 1720 0.887933 GAGGCAAAGCAATTCCGGAA 59.112 50.000 21.37 21.37 0.00 4.30
1711 1721 0.603065 AGGCAAAGCAATTCCGGAAC 59.397 50.000 21.56 7.16 0.00 3.62
1712 1722 0.316841 GGCAAAGCAATTCCGGAACA 59.683 50.000 21.56 0.00 0.00 3.18
1713 1723 1.066929 GGCAAAGCAATTCCGGAACAT 60.067 47.619 21.56 8.97 0.00 2.71
1714 1724 2.165437 GGCAAAGCAATTCCGGAACATA 59.835 45.455 21.56 0.00 0.00 2.29
1715 1725 3.438360 GCAAAGCAATTCCGGAACATAG 58.562 45.455 21.56 10.69 0.00 2.23
1716 1726 3.119495 GCAAAGCAATTCCGGAACATAGT 60.119 43.478 21.56 0.00 0.00 2.12
1717 1727 4.414852 CAAAGCAATTCCGGAACATAGTG 58.585 43.478 21.56 13.38 0.00 2.74
1718 1728 3.627395 AGCAATTCCGGAACATAGTGA 57.373 42.857 21.56 0.00 0.00 3.41
1719 1729 3.950397 AGCAATTCCGGAACATAGTGAA 58.050 40.909 21.56 0.00 0.00 3.18
1720 1730 3.689649 AGCAATTCCGGAACATAGTGAAC 59.310 43.478 21.56 1.76 0.00 3.18
1721 1731 3.438781 GCAATTCCGGAACATAGTGAACA 59.561 43.478 21.56 0.00 0.00 3.18
1722 1732 4.083003 GCAATTCCGGAACATAGTGAACAA 60.083 41.667 21.56 0.00 0.00 2.83
1723 1733 5.631026 CAATTCCGGAACATAGTGAACAAG 58.369 41.667 21.56 0.00 0.00 3.16
1724 1734 4.345859 TTCCGGAACATAGTGAACAAGT 57.654 40.909 14.35 0.00 0.00 3.16
1725 1735 4.345859 TCCGGAACATAGTGAACAAGTT 57.654 40.909 0.00 0.00 0.00 2.66
1726 1736 4.062293 TCCGGAACATAGTGAACAAGTTG 58.938 43.478 0.00 0.00 0.00 3.16
1727 1737 4.062293 CCGGAACATAGTGAACAAGTTGA 58.938 43.478 10.54 0.00 0.00 3.18
1728 1738 4.152402 CCGGAACATAGTGAACAAGTTGAG 59.848 45.833 10.54 0.00 0.00 3.02
1729 1739 4.152402 CGGAACATAGTGAACAAGTTGAGG 59.848 45.833 10.54 0.00 0.00 3.86
1730 1740 5.305585 GGAACATAGTGAACAAGTTGAGGA 58.694 41.667 10.54 0.00 0.00 3.71
1731 1741 5.940470 GGAACATAGTGAACAAGTTGAGGAT 59.060 40.000 10.54 0.00 0.00 3.24
1732 1742 6.092807 GGAACATAGTGAACAAGTTGAGGATC 59.907 42.308 10.54 3.15 0.00 3.36
1733 1743 6.365970 ACATAGTGAACAAGTTGAGGATCT 57.634 37.500 10.54 4.10 34.92 2.75
1734 1744 6.773638 ACATAGTGAACAAGTTGAGGATCTT 58.226 36.000 10.54 0.00 34.92 2.40
1735 1745 7.227156 ACATAGTGAACAAGTTGAGGATCTTT 58.773 34.615 10.54 0.00 34.92 2.52
1736 1746 7.721399 ACATAGTGAACAAGTTGAGGATCTTTT 59.279 33.333 10.54 0.00 34.92 2.27
1737 1747 8.571336 CATAGTGAACAAGTTGAGGATCTTTTT 58.429 33.333 10.54 0.00 34.92 1.94
1762 1772 8.966155 TTTTCTCCATTTTTAGGGGAATAAGT 57.034 30.769 0.00 0.00 44.71 2.24
1763 1773 8.966155 TTTCTCCATTTTTAGGGGAATAAGTT 57.034 30.769 0.00 0.00 44.71 2.66
1764 1774 8.966155 TTCTCCATTTTTAGGGGAATAAGTTT 57.034 30.769 0.00 0.00 40.64 2.66
1765 1775 8.966155 TCTCCATTTTTAGGGGAATAAGTTTT 57.034 30.769 0.00 0.00 31.16 2.43
1766 1776 9.387397 TCTCCATTTTTAGGGGAATAAGTTTTT 57.613 29.630 0.00 0.00 31.16 1.94
1788 1798 7.846101 TTTTTACGGGTTTTTAGGGGAATAA 57.154 32.000 0.00 0.00 0.00 1.40
1789 1799 7.465353 TTTTACGGGTTTTTAGGGGAATAAG 57.535 36.000 0.00 0.00 0.00 1.73
1790 1800 4.662966 ACGGGTTTTTAGGGGAATAAGT 57.337 40.909 0.00 0.00 0.00 2.24
1791 1801 5.001833 ACGGGTTTTTAGGGGAATAAGTT 57.998 39.130 0.00 0.00 0.00 2.66
1792 1802 5.396485 ACGGGTTTTTAGGGGAATAAGTTT 58.604 37.500 0.00 0.00 0.00 2.66
1793 1803 5.840149 ACGGGTTTTTAGGGGAATAAGTTTT 59.160 36.000 0.00 0.00 0.00 2.43
1794 1804 6.327104 ACGGGTTTTTAGGGGAATAAGTTTTT 59.673 34.615 0.00 0.00 0.00 1.94
1838 1850 7.228308 GGAATAAGTTGAGGATCTCAGAATTGG 59.772 40.741 0.00 0.00 41.75 3.16
1860 1872 0.684535 TCTGTGTCATCGAAGCCCAA 59.315 50.000 0.00 0.00 0.00 4.12
1891 1903 1.222387 CCGGCCCAATTTAGTCCGA 59.778 57.895 0.00 0.00 42.43 4.55
1900 1927 3.068307 CCAATTTAGTCCGATCCGACTCT 59.932 47.826 18.29 4.51 42.19 3.24
1901 1928 4.291783 CAATTTAGTCCGATCCGACTCTC 58.708 47.826 18.29 0.00 42.19 3.20
1902 1929 1.964552 TTAGTCCGATCCGACTCTCC 58.035 55.000 18.29 0.00 42.19 3.71
1915 1942 2.037144 GACTCTCCCACGCCCTAATAA 58.963 52.381 0.00 0.00 0.00 1.40
1916 1943 2.036089 GACTCTCCCACGCCCTAATAAG 59.964 54.545 0.00 0.00 0.00 1.73
1917 1944 2.040178 CTCTCCCACGCCCTAATAAGT 58.960 52.381 0.00 0.00 0.00 2.24
1918 1945 3.228453 CTCTCCCACGCCCTAATAAGTA 58.772 50.000 0.00 0.00 0.00 2.24
1919 1946 3.833070 CTCTCCCACGCCCTAATAAGTAT 59.167 47.826 0.00 0.00 0.00 2.12
1920 1947 3.830755 TCTCCCACGCCCTAATAAGTATC 59.169 47.826 0.00 0.00 0.00 2.24
1922 1949 2.559668 CCCACGCCCTAATAAGTATCGA 59.440 50.000 0.00 0.00 0.00 3.59
1923 1950 3.572584 CCACGCCCTAATAAGTATCGAC 58.427 50.000 0.00 0.00 0.00 4.20
1924 1951 3.255149 CCACGCCCTAATAAGTATCGACT 59.745 47.826 0.00 0.00 37.59 4.18
1925 1952 4.456911 CCACGCCCTAATAAGTATCGACTA 59.543 45.833 0.00 0.00 33.58 2.59
1979 2006 1.867233 GTTGCGCAGATAACGATGGAT 59.133 47.619 11.31 0.00 0.00 3.41
2017 2044 1.134965 GGATCTGACGCAGCAACTACT 60.135 52.381 0.00 0.00 0.00 2.57
2046 2073 1.448540 CTCGCCAATGTCTTCCGCT 60.449 57.895 0.00 0.00 0.00 5.52
2147 2174 4.194720 CTCGCGGACCTCCCTTCG 62.195 72.222 6.13 0.00 0.00 3.79
2169 2196 1.266175 ACTCGCTGACCGGTATATTCG 59.734 52.381 7.34 7.50 37.59 3.34
2208 2235 0.676736 GCTCCCCAGATACTTCTCGG 59.323 60.000 0.00 0.00 30.52 4.63
2219 2246 3.074369 TTCTCGGCCGCCTCATCA 61.074 61.111 23.51 0.00 0.00 3.07
2227 2254 1.300465 CCGCCTCATCATCCGTGAG 60.300 63.158 0.00 0.00 42.11 3.51
2233 2260 0.598419 TCATCATCCGTGAGCATCGC 60.598 55.000 0.00 0.00 43.58 4.58
2247 2274 0.541863 CATCGCCCCTTTGGACTACT 59.458 55.000 0.00 0.00 35.39 2.57
2253 2280 2.945890 GCCCCTTTGGACTACTTGGATG 60.946 54.545 0.00 0.00 35.39 3.51
2256 2283 2.369394 CTTTGGACTACTTGGATGCCC 58.631 52.381 0.00 0.00 0.00 5.36
2257 2284 1.367346 TTGGACTACTTGGATGCCCA 58.633 50.000 0.00 0.00 41.64 5.36
2261 2291 0.249398 ACTACTTGGATGCCCACGAC 59.751 55.000 0.00 0.00 43.41 4.34
2271 2301 1.135939 GCCCACGACGCCATTAAAC 59.864 57.895 0.00 0.00 0.00 2.01
2272 2302 1.579084 GCCCACGACGCCATTAAACA 61.579 55.000 0.00 0.00 0.00 2.83
2273 2303 1.091537 CCCACGACGCCATTAAACAT 58.908 50.000 0.00 0.00 0.00 2.71
2276 2306 3.127203 CCCACGACGCCATTAAACATTTA 59.873 43.478 0.00 0.00 0.00 1.40
2279 2309 3.026349 CGACGCCATTAAACATTTAGCG 58.974 45.455 12.32 12.32 39.32 4.26
2315 2345 2.588989 GGCCTCCTCCTGCTCAAG 59.411 66.667 0.00 0.00 0.00 3.02
2324 2354 2.049156 CTGCTCAAGGACGACGCA 60.049 61.111 0.00 0.00 0.00 5.24
2325 2355 2.049156 TGCTCAAGGACGACGCAG 60.049 61.111 0.00 0.00 0.00 5.18
2326 2356 3.482783 GCTCAAGGACGACGCAGC 61.483 66.667 0.00 0.00 0.00 5.25
2334 2364 0.170561 GGACGACGCAGCTAAAGAGA 59.829 55.000 0.00 0.00 0.00 3.10
2335 2365 1.202313 GGACGACGCAGCTAAAGAGAT 60.202 52.381 0.00 0.00 0.00 2.75
2336 2366 2.113289 GACGACGCAGCTAAAGAGATC 58.887 52.381 0.00 0.00 0.00 2.75
2381 2411 1.521681 GTGGACGCATCTGCCTACC 60.522 63.158 0.00 0.00 37.91 3.18
2387 2417 3.142393 CATCTGCCTACCCCTCCG 58.858 66.667 0.00 0.00 0.00 4.63
2388 2418 2.122813 ATCTGCCTACCCCTCCGG 60.123 66.667 0.00 0.00 37.81 5.14
2390 2420 2.547123 ATCTGCCTACCCCTCCGGTT 62.547 60.000 0.00 0.00 45.36 4.44
2396 2426 1.492764 CTACCCCTCCGGTTATGTGT 58.507 55.000 0.00 0.00 45.36 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
361 365 3.239464 TGCTTCCCAGACAGCACA 58.761 55.556 0.00 0.00 41.20 4.57
474 478 6.522165 GCGCACATATATCAGATTTCACAATG 59.478 38.462 0.30 0.00 0.00 2.82
620 624 0.469917 CAGTAGCCATTCCGGTCCAT 59.530 55.000 0.00 0.00 36.97 3.41
687 691 0.601558 GCCACGTTCTCCAGAGTGTA 59.398 55.000 0.00 0.00 33.14 2.90
1264 1274 2.263077 GCCTCGTCTCACATGTAACAG 58.737 52.381 0.00 0.00 0.00 3.16
1268 1278 1.262417 TTGGCCTCGTCTCACATGTA 58.738 50.000 3.32 0.00 0.00 2.29
1467 1477 6.567050 AGAGCACATTACCTGCAATAATTTG 58.433 36.000 10.26 10.26 37.08 2.32
1468 1478 6.780457 AGAGCACATTACCTGCAATAATTT 57.220 33.333 1.03 0.00 37.08 1.82
1469 1479 6.780457 AAGAGCACATTACCTGCAATAATT 57.220 33.333 1.03 0.00 37.08 1.40
1470 1480 6.458751 CGAAAGAGCACATTACCTGCAATAAT 60.459 38.462 0.00 0.00 37.08 1.28
1471 1481 5.163764 CGAAAGAGCACATTACCTGCAATAA 60.164 40.000 0.00 0.00 37.08 1.40
1472 1482 4.332543 CGAAAGAGCACATTACCTGCAATA 59.667 41.667 0.00 0.00 37.08 1.90
1473 1483 3.127548 CGAAAGAGCACATTACCTGCAAT 59.872 43.478 0.00 0.00 37.08 3.56
1474 1484 2.483877 CGAAAGAGCACATTACCTGCAA 59.516 45.455 0.00 0.00 37.08 4.08
1475 1485 2.076100 CGAAAGAGCACATTACCTGCA 58.924 47.619 0.00 0.00 37.08 4.41
1476 1486 2.094417 GTCGAAAGAGCACATTACCTGC 59.906 50.000 0.00 0.00 43.49 4.85
1477 1487 3.325870 TGTCGAAAGAGCACATTACCTG 58.674 45.455 0.00 0.00 43.49 4.00
1478 1488 3.678056 TGTCGAAAGAGCACATTACCT 57.322 42.857 0.00 0.00 43.49 3.08
1479 1489 3.424962 GCTTGTCGAAAGAGCACATTACC 60.425 47.826 10.11 0.00 43.49 2.85
1480 1490 3.433615 AGCTTGTCGAAAGAGCACATTAC 59.566 43.478 15.55 0.00 43.49 1.89
1481 1491 3.664107 AGCTTGTCGAAAGAGCACATTA 58.336 40.909 15.55 0.00 43.49 1.90
1482 1492 2.498167 AGCTTGTCGAAAGAGCACATT 58.502 42.857 15.55 0.00 43.49 2.71
1483 1493 2.175878 AGCTTGTCGAAAGAGCACAT 57.824 45.000 15.55 0.00 43.49 3.21
1484 1494 2.610479 CCTAGCTTGTCGAAAGAGCACA 60.610 50.000 15.55 5.01 43.49 4.57
1485 1495 1.996191 CCTAGCTTGTCGAAAGAGCAC 59.004 52.381 15.55 0.00 43.49 4.40
1486 1496 1.618837 ACCTAGCTTGTCGAAAGAGCA 59.381 47.619 15.55 0.00 43.49 4.26
1487 1497 2.371910 ACCTAGCTTGTCGAAAGAGC 57.628 50.000 0.00 9.03 43.49 4.09
1488 1498 4.966965 TCTACCTAGCTTGTCGAAAGAG 57.033 45.455 0.00 0.20 43.49 2.85
1489 1499 4.948004 TGATCTACCTAGCTTGTCGAAAGA 59.052 41.667 0.00 0.00 38.16 2.52
1490 1500 5.250235 TGATCTACCTAGCTTGTCGAAAG 57.750 43.478 0.00 0.00 0.00 2.62
1491 1501 4.440250 GCTGATCTACCTAGCTTGTCGAAA 60.440 45.833 0.00 0.00 34.70 3.46
1492 1502 3.066900 GCTGATCTACCTAGCTTGTCGAA 59.933 47.826 0.00 0.00 34.70 3.71
1493 1503 2.619177 GCTGATCTACCTAGCTTGTCGA 59.381 50.000 0.00 0.00 34.70 4.20
1494 1504 2.359214 TGCTGATCTACCTAGCTTGTCG 59.641 50.000 0.00 0.00 38.25 4.35
1495 1505 4.038522 TGATGCTGATCTACCTAGCTTGTC 59.961 45.833 0.00 1.39 38.25 3.18
1496 1506 3.963374 TGATGCTGATCTACCTAGCTTGT 59.037 43.478 0.00 0.00 38.25 3.16
1497 1507 4.558178 CTGATGCTGATCTACCTAGCTTG 58.442 47.826 0.00 0.00 38.25 4.01
1498 1508 3.006752 GCTGATGCTGATCTACCTAGCTT 59.993 47.826 0.00 0.00 38.25 3.74
1499 1509 2.562298 GCTGATGCTGATCTACCTAGCT 59.438 50.000 3.91 0.00 38.25 3.32
1500 1510 2.958213 GCTGATGCTGATCTACCTAGC 58.042 52.381 0.00 0.00 37.93 3.42
1513 1523 1.131883 CCTAGTGCAAACAGCTGATGC 59.868 52.381 29.63 29.63 45.94 3.91
1514 1524 1.741706 CCCTAGTGCAAACAGCTGATG 59.258 52.381 23.35 19.16 45.94 3.07
1515 1525 1.952367 GCCCTAGTGCAAACAGCTGAT 60.952 52.381 23.35 5.41 45.94 2.90
1516 1526 0.606401 GCCCTAGTGCAAACAGCTGA 60.606 55.000 23.35 0.00 45.94 4.26
1517 1527 0.890542 TGCCCTAGTGCAAACAGCTG 60.891 55.000 13.48 13.48 45.94 4.24
1518 1528 0.607489 CTGCCCTAGTGCAAACAGCT 60.607 55.000 0.45 0.00 45.94 4.24
1519 1529 0.890996 ACTGCCCTAGTGCAAACAGC 60.891 55.000 0.45 0.00 41.51 4.40
1520 1530 2.289694 ACTACTGCCCTAGTGCAAACAG 60.290 50.000 0.45 1.54 41.51 3.16
1521 1531 1.697432 ACTACTGCCCTAGTGCAAACA 59.303 47.619 0.45 0.00 41.51 2.83
1522 1532 2.474410 ACTACTGCCCTAGTGCAAAC 57.526 50.000 0.45 0.00 41.51 2.93
1523 1533 2.235402 GGTACTACTGCCCTAGTGCAAA 59.765 50.000 0.45 0.00 41.51 3.68
1524 1534 1.829222 GGTACTACTGCCCTAGTGCAA 59.171 52.381 0.45 0.00 41.51 4.08
1525 1535 1.272816 TGGTACTACTGCCCTAGTGCA 60.273 52.381 0.00 0.00 40.65 4.57
1526 1536 1.481871 TGGTACTACTGCCCTAGTGC 58.518 55.000 0.00 0.00 40.65 4.40
1527 1537 3.704566 TCATTGGTACTACTGCCCTAGTG 59.295 47.826 0.00 0.00 40.65 2.74
1528 1538 3.961408 CTCATTGGTACTACTGCCCTAGT 59.039 47.826 0.00 0.00 43.56 2.57
1529 1539 3.322254 CCTCATTGGTACTACTGCCCTAG 59.678 52.174 0.00 0.00 0.00 3.02
1530 1540 3.305720 CCTCATTGGTACTACTGCCCTA 58.694 50.000 0.00 0.00 0.00 3.53
1531 1541 2.119495 CCTCATTGGTACTACTGCCCT 58.881 52.381 0.00 0.00 0.00 5.19
1532 1542 1.475213 GCCTCATTGGTACTACTGCCC 60.475 57.143 0.00 0.00 38.35 5.36
1533 1543 1.209504 TGCCTCATTGGTACTACTGCC 59.790 52.381 0.00 0.00 38.35 4.85
1534 1544 2.691409 TGCCTCATTGGTACTACTGC 57.309 50.000 0.00 0.00 38.35 4.40
1535 1545 5.670485 TGTTATGCCTCATTGGTACTACTG 58.330 41.667 0.00 0.00 38.35 2.74
1536 1546 5.950544 TGTTATGCCTCATTGGTACTACT 57.049 39.130 0.00 0.00 38.35 2.57
1537 1547 8.671384 TTTATGTTATGCCTCATTGGTACTAC 57.329 34.615 0.00 0.00 38.35 2.73
1538 1548 7.444183 GCTTTATGTTATGCCTCATTGGTACTA 59.556 37.037 0.00 0.00 38.35 1.82
1539 1549 6.263168 GCTTTATGTTATGCCTCATTGGTACT 59.737 38.462 0.00 0.00 38.35 2.73
1540 1550 6.039270 TGCTTTATGTTATGCCTCATTGGTAC 59.961 38.462 0.00 0.00 38.35 3.34
1541 1551 6.125719 TGCTTTATGTTATGCCTCATTGGTA 58.874 36.000 0.00 0.00 38.35 3.25
1542 1552 4.955450 TGCTTTATGTTATGCCTCATTGGT 59.045 37.500 0.00 0.00 38.35 3.67
1543 1553 5.518848 TGCTTTATGTTATGCCTCATTGG 57.481 39.130 0.00 0.00 39.35 3.16
1544 1554 5.750067 GGTTGCTTTATGTTATGCCTCATTG 59.250 40.000 0.00 0.00 0.00 2.82
1545 1555 5.658190 AGGTTGCTTTATGTTATGCCTCATT 59.342 36.000 0.00 0.00 0.00 2.57
1546 1556 5.068198 CAGGTTGCTTTATGTTATGCCTCAT 59.932 40.000 0.00 0.00 0.00 2.90
1547 1557 4.398988 CAGGTTGCTTTATGTTATGCCTCA 59.601 41.667 0.00 0.00 0.00 3.86
1548 1558 4.202050 CCAGGTTGCTTTATGTTATGCCTC 60.202 45.833 0.00 0.00 0.00 4.70
1549 1559 3.701040 CCAGGTTGCTTTATGTTATGCCT 59.299 43.478 0.00 0.00 0.00 4.75
1550 1560 3.737972 GCCAGGTTGCTTTATGTTATGCC 60.738 47.826 0.00 0.00 0.00 4.40
1551 1561 3.447742 GCCAGGTTGCTTTATGTTATGC 58.552 45.455 0.00 0.00 0.00 3.14
1552 1562 3.694734 CGCCAGGTTGCTTTATGTTATG 58.305 45.455 0.00 0.00 0.00 1.90
1553 1563 2.099098 GCGCCAGGTTGCTTTATGTTAT 59.901 45.455 0.00 0.00 0.00 1.89
1554 1564 1.470890 GCGCCAGGTTGCTTTATGTTA 59.529 47.619 0.00 0.00 0.00 2.41
1555 1565 0.243636 GCGCCAGGTTGCTTTATGTT 59.756 50.000 0.00 0.00 0.00 2.71
1556 1566 0.893270 TGCGCCAGGTTGCTTTATGT 60.893 50.000 4.18 0.00 0.00 2.29
1557 1567 0.457035 ATGCGCCAGGTTGCTTTATG 59.543 50.000 4.18 0.00 0.00 1.90
1558 1568 0.740737 GATGCGCCAGGTTGCTTTAT 59.259 50.000 4.18 0.00 0.00 1.40
1559 1569 0.322456 AGATGCGCCAGGTTGCTTTA 60.322 50.000 4.18 0.00 0.00 1.85
1560 1570 0.322456 TAGATGCGCCAGGTTGCTTT 60.322 50.000 4.18 0.00 0.00 3.51
1561 1571 0.107017 ATAGATGCGCCAGGTTGCTT 60.107 50.000 4.18 1.34 0.00 3.91
1562 1572 0.533755 GATAGATGCGCCAGGTTGCT 60.534 55.000 4.18 0.00 0.00 3.91
1563 1573 0.533755 AGATAGATGCGCCAGGTTGC 60.534 55.000 4.18 0.00 0.00 4.17
1564 1574 1.202568 TGAGATAGATGCGCCAGGTTG 60.203 52.381 4.18 0.00 0.00 3.77
1565 1575 1.123077 TGAGATAGATGCGCCAGGTT 58.877 50.000 4.18 0.00 0.00 3.50
1566 1576 1.001746 CATGAGATAGATGCGCCAGGT 59.998 52.381 4.18 0.00 0.00 4.00
1567 1577 1.001746 ACATGAGATAGATGCGCCAGG 59.998 52.381 4.18 0.00 0.00 4.45
1568 1578 2.029200 AGACATGAGATAGATGCGCCAG 60.029 50.000 4.18 0.00 0.00 4.85
1569 1579 1.966354 AGACATGAGATAGATGCGCCA 59.034 47.619 4.18 0.00 0.00 5.69
1570 1580 2.739885 AGACATGAGATAGATGCGCC 57.260 50.000 4.18 0.00 0.00 6.53
1571 1581 5.415415 AAAAAGACATGAGATAGATGCGC 57.585 39.130 0.00 0.00 0.00 6.09
1641 1651 9.255029 TCTACTTATGCTAATATGCTGGTATGA 57.745 33.333 0.00 0.00 0.00 2.15
1642 1652 9.875691 TTCTACTTATGCTAATATGCTGGTATG 57.124 33.333 0.00 0.00 0.00 2.39
1643 1653 9.877178 GTTCTACTTATGCTAATATGCTGGTAT 57.123 33.333 0.00 0.00 0.00 2.73
1644 1654 9.090103 AGTTCTACTTATGCTAATATGCTGGTA 57.910 33.333 0.00 0.00 0.00 3.25
1645 1655 7.875041 CAGTTCTACTTATGCTAATATGCTGGT 59.125 37.037 0.00 0.00 0.00 4.00
1646 1656 8.090831 TCAGTTCTACTTATGCTAATATGCTGG 58.909 37.037 0.00 0.00 0.00 4.85
1647 1657 9.650539 ATCAGTTCTACTTATGCTAATATGCTG 57.349 33.333 0.00 0.00 0.00 4.41
1648 1658 9.650539 CATCAGTTCTACTTATGCTAATATGCT 57.349 33.333 0.00 0.00 0.00 3.79
1649 1659 9.645059 TCATCAGTTCTACTTATGCTAATATGC 57.355 33.333 0.00 0.00 31.62 3.14
1668 1678 9.790344 CCTCTTTCTTCCAATATAATCATCAGT 57.210 33.333 0.00 0.00 0.00 3.41
1669 1679 8.728833 GCCTCTTTCTTCCAATATAATCATCAG 58.271 37.037 0.00 0.00 0.00 2.90
1670 1680 8.219868 TGCCTCTTTCTTCCAATATAATCATCA 58.780 33.333 0.00 0.00 0.00 3.07
1671 1681 8.627208 TGCCTCTTTCTTCCAATATAATCATC 57.373 34.615 0.00 0.00 0.00 2.92
1672 1682 9.425248 TTTGCCTCTTTCTTCCAATATAATCAT 57.575 29.630 0.00 0.00 0.00 2.45
1673 1683 8.821686 TTTGCCTCTTTCTTCCAATATAATCA 57.178 30.769 0.00 0.00 0.00 2.57
1674 1684 7.864882 GCTTTGCCTCTTTCTTCCAATATAATC 59.135 37.037 0.00 0.00 0.00 1.75
1675 1685 7.342799 TGCTTTGCCTCTTTCTTCCAATATAAT 59.657 33.333 0.00 0.00 0.00 1.28
1676 1686 6.663093 TGCTTTGCCTCTTTCTTCCAATATAA 59.337 34.615 0.00 0.00 0.00 0.98
1677 1687 6.186957 TGCTTTGCCTCTTTCTTCCAATATA 58.813 36.000 0.00 0.00 0.00 0.86
1678 1688 5.018809 TGCTTTGCCTCTTTCTTCCAATAT 58.981 37.500 0.00 0.00 0.00 1.28
1679 1689 4.406456 TGCTTTGCCTCTTTCTTCCAATA 58.594 39.130 0.00 0.00 0.00 1.90
1680 1690 3.233507 TGCTTTGCCTCTTTCTTCCAAT 58.766 40.909 0.00 0.00 0.00 3.16
1681 1691 2.665165 TGCTTTGCCTCTTTCTTCCAA 58.335 42.857 0.00 0.00 0.00 3.53
1682 1692 2.363306 TGCTTTGCCTCTTTCTTCCA 57.637 45.000 0.00 0.00 0.00 3.53
1683 1693 3.949842 ATTGCTTTGCCTCTTTCTTCC 57.050 42.857 0.00 0.00 0.00 3.46
1684 1694 4.240888 GGAATTGCTTTGCCTCTTTCTTC 58.759 43.478 0.00 0.00 0.00 2.87
1685 1695 3.305608 CGGAATTGCTTTGCCTCTTTCTT 60.306 43.478 0.00 0.00 0.00 2.52
1686 1696 2.229784 CGGAATTGCTTTGCCTCTTTCT 59.770 45.455 0.00 0.00 0.00 2.52
1687 1697 2.599659 CGGAATTGCTTTGCCTCTTTC 58.400 47.619 0.00 0.00 0.00 2.62
1688 1698 1.273327 CCGGAATTGCTTTGCCTCTTT 59.727 47.619 0.00 0.00 0.00 2.52
1689 1699 0.890683 CCGGAATTGCTTTGCCTCTT 59.109 50.000 0.00 0.00 0.00 2.85
1690 1700 0.038166 TCCGGAATTGCTTTGCCTCT 59.962 50.000 0.00 0.00 0.00 3.69
1691 1701 0.887933 TTCCGGAATTGCTTTGCCTC 59.112 50.000 14.35 0.00 0.00 4.70
1692 1702 0.603065 GTTCCGGAATTGCTTTGCCT 59.397 50.000 22.04 0.00 0.00 4.75
1693 1703 0.316841 TGTTCCGGAATTGCTTTGCC 59.683 50.000 22.04 4.34 0.00 4.52
1694 1704 2.368655 ATGTTCCGGAATTGCTTTGC 57.631 45.000 22.04 5.12 0.00 3.68
1695 1705 4.155826 TCACTATGTTCCGGAATTGCTTTG 59.844 41.667 22.04 13.33 0.00 2.77
1696 1706 4.331968 TCACTATGTTCCGGAATTGCTTT 58.668 39.130 22.04 4.60 0.00 3.51
1697 1707 3.950397 TCACTATGTTCCGGAATTGCTT 58.050 40.909 22.04 8.44 0.00 3.91
1698 1708 3.627395 TCACTATGTTCCGGAATTGCT 57.373 42.857 22.04 8.00 0.00 3.91
1699 1709 3.438781 TGTTCACTATGTTCCGGAATTGC 59.561 43.478 22.04 8.35 0.00 3.56
1700 1710 5.181245 ACTTGTTCACTATGTTCCGGAATTG 59.819 40.000 22.04 12.89 0.00 2.32
1701 1711 5.313712 ACTTGTTCACTATGTTCCGGAATT 58.686 37.500 22.04 13.71 0.00 2.17
1702 1712 4.906618 ACTTGTTCACTATGTTCCGGAAT 58.093 39.130 22.04 7.98 0.00 3.01
1703 1713 4.345859 ACTTGTTCACTATGTTCCGGAA 57.654 40.909 14.35 14.35 0.00 4.30
1704 1714 4.062293 CAACTTGTTCACTATGTTCCGGA 58.938 43.478 0.00 0.00 0.00 5.14
1705 1715 4.062293 TCAACTTGTTCACTATGTTCCGG 58.938 43.478 0.00 0.00 0.00 5.14
1706 1716 4.152402 CCTCAACTTGTTCACTATGTTCCG 59.848 45.833 0.00 0.00 0.00 4.30
1707 1717 5.305585 TCCTCAACTTGTTCACTATGTTCC 58.694 41.667 0.00 0.00 0.00 3.62
1708 1718 6.876257 AGATCCTCAACTTGTTCACTATGTTC 59.124 38.462 0.00 0.00 0.00 3.18
1709 1719 6.773638 AGATCCTCAACTTGTTCACTATGTT 58.226 36.000 0.00 0.00 0.00 2.71
1710 1720 6.365970 AGATCCTCAACTTGTTCACTATGT 57.634 37.500 0.00 0.00 0.00 2.29
1711 1721 7.678947 AAAGATCCTCAACTTGTTCACTATG 57.321 36.000 0.00 0.00 0.00 2.23
1712 1722 8.697507 AAAAAGATCCTCAACTTGTTCACTAT 57.302 30.769 0.00 0.00 0.00 2.12
1736 1746 9.387397 ACTTATTCCCCTAAAAATGGAGAAAAA 57.613 29.630 0.00 0.00 0.00 1.94
1737 1747 8.966155 ACTTATTCCCCTAAAAATGGAGAAAA 57.034 30.769 0.00 0.00 0.00 2.29
1738 1748 8.966155 AACTTATTCCCCTAAAAATGGAGAAA 57.034 30.769 0.00 0.00 0.00 2.52
1739 1749 8.966155 AAACTTATTCCCCTAAAAATGGAGAA 57.034 30.769 0.00 0.00 0.00 2.87
1740 1750 8.966155 AAAACTTATTCCCCTAAAAATGGAGA 57.034 30.769 0.00 0.00 0.00 3.71
1764 1774 7.508636 ACTTATTCCCCTAAAAACCCGTAAAAA 59.491 33.333 0.00 0.00 0.00 1.94
1765 1775 7.009550 ACTTATTCCCCTAAAAACCCGTAAAA 58.990 34.615 0.00 0.00 0.00 1.52
1766 1776 6.551085 ACTTATTCCCCTAAAAACCCGTAAA 58.449 36.000 0.00 0.00 0.00 2.01
1767 1777 6.138391 ACTTATTCCCCTAAAAACCCGTAA 57.862 37.500 0.00 0.00 0.00 3.18
1768 1778 5.777526 ACTTATTCCCCTAAAAACCCGTA 57.222 39.130 0.00 0.00 0.00 4.02
1769 1779 4.662966 ACTTATTCCCCTAAAAACCCGT 57.337 40.909 0.00 0.00 0.00 5.28
1770 1780 5.988310 AAACTTATTCCCCTAAAAACCCG 57.012 39.130 0.00 0.00 0.00 5.28
1798 1808 9.734984 CTCAACTTATTCCCCTAAAAGTTTCTA 57.265 33.333 0.00 0.00 39.50 2.10
1799 1809 7.670140 CCTCAACTTATTCCCCTAAAAGTTTCT 59.330 37.037 0.00 0.00 39.50 2.52
1800 1810 7.668469 TCCTCAACTTATTCCCCTAAAAGTTTC 59.332 37.037 0.00 0.00 39.50 2.78
1801 1811 7.532199 TCCTCAACTTATTCCCCTAAAAGTTT 58.468 34.615 0.00 0.00 39.50 2.66
1802 1812 7.098845 TCCTCAACTTATTCCCCTAAAAGTT 57.901 36.000 0.00 0.00 41.56 2.66
1803 1813 6.713731 TCCTCAACTTATTCCCCTAAAAGT 57.286 37.500 0.00 0.00 33.72 2.66
1804 1814 7.578203 AGATCCTCAACTTATTCCCCTAAAAG 58.422 38.462 0.00 0.00 0.00 2.27
1805 1815 7.183839 TGAGATCCTCAACTTATTCCCCTAAAA 59.816 37.037 0.00 0.00 37.57 1.52
1806 1816 6.676632 TGAGATCCTCAACTTATTCCCCTAAA 59.323 38.462 0.00 0.00 37.57 1.85
1807 1817 6.209774 TGAGATCCTCAACTTATTCCCCTAA 58.790 40.000 0.00 0.00 37.57 2.69
1808 1818 5.788430 TGAGATCCTCAACTTATTCCCCTA 58.212 41.667 0.00 0.00 37.57 3.53
1809 1819 4.635473 TGAGATCCTCAACTTATTCCCCT 58.365 43.478 0.00 0.00 37.57 4.79
1838 1850 2.159099 TGGGCTTCGATGACACAGATAC 60.159 50.000 6.48 0.00 0.00 2.24
1860 1872 2.426023 GCCGGCCGAACTATCCAT 59.574 61.111 30.73 0.00 0.00 3.41
1891 1903 3.148279 GGCGTGGGAGAGTCGGAT 61.148 66.667 0.00 0.00 0.00 4.18
1900 1927 2.559668 CGATACTTATTAGGGCGTGGGA 59.440 50.000 0.00 0.00 0.00 4.37
1901 1928 2.559668 TCGATACTTATTAGGGCGTGGG 59.440 50.000 0.00 0.00 0.00 4.61
1902 1929 3.255149 AGTCGATACTTATTAGGGCGTGG 59.745 47.826 0.00 0.00 29.00 4.94
1920 1947 6.161911 TCGAGTATAATGGTTCGATAGTCG 57.838 41.667 9.74 9.74 44.64 4.18
1963 1990 3.502920 GTCCTATCCATCGTTATCTGCG 58.497 50.000 0.00 0.00 0.00 5.18
1964 1991 3.190744 TCGTCCTATCCATCGTTATCTGC 59.809 47.826 0.00 0.00 0.00 4.26
1979 2006 4.758251 TCCGCCGACGTCGTCCTA 62.758 66.667 33.49 15.56 37.70 2.94
2134 2161 1.712977 CGAGTACGAAGGGAGGTCCG 61.713 65.000 0.00 0.00 42.66 4.79
2144 2171 0.673333 TACCGGTCAGCGAGTACGAA 60.673 55.000 12.40 0.00 42.66 3.85
2147 2174 3.666374 CGAATATACCGGTCAGCGAGTAC 60.666 52.174 12.40 0.00 0.00 2.73
2208 2235 2.969238 CACGGATGATGAGGCGGC 60.969 66.667 0.00 0.00 0.00 6.53
2219 2246 4.241555 GGGGCGATGCTCACGGAT 62.242 66.667 0.00 0.00 0.00 4.18
2227 2254 1.095807 GTAGTCCAAAGGGGCGATGC 61.096 60.000 0.00 0.00 46.12 3.91
2233 2260 2.945890 GCATCCAAGTAGTCCAAAGGGG 60.946 54.545 0.00 0.00 38.37 4.79
2253 2280 1.135939 GTTTAATGGCGTCGTGGGC 59.864 57.895 0.00 0.00 0.00 5.36
2256 2283 3.783943 GCTAAATGTTTAATGGCGTCGTG 59.216 43.478 0.00 0.00 0.00 4.35
2257 2284 3.484557 CGCTAAATGTTTAATGGCGTCGT 60.485 43.478 8.54 0.00 33.17 4.34
2261 2291 4.670621 GTGATCGCTAAATGTTTAATGGCG 59.329 41.667 0.00 9.82 36.67 5.69
2315 2345 0.170561 TCTCTTTAGCTGCGTCGTCC 59.829 55.000 0.00 0.00 0.00 4.79
2323 2353 2.170187 AGCACCCAGATCTCTTTAGCTG 59.830 50.000 0.00 0.00 0.00 4.24
2324 2354 2.476199 AGCACCCAGATCTCTTTAGCT 58.524 47.619 0.00 0.00 0.00 3.32
2325 2355 2.998316 AGCACCCAGATCTCTTTAGC 57.002 50.000 0.00 0.00 0.00 3.09
2326 2356 5.994668 GGATTAAGCACCCAGATCTCTTTAG 59.005 44.000 0.00 0.00 0.00 1.85
2334 2364 0.179018 GCGGGATTAAGCACCCAGAT 60.179 55.000 13.23 0.00 45.83 2.90
2335 2365 1.223487 GCGGGATTAAGCACCCAGA 59.777 57.895 13.23 0.00 45.83 3.86
2336 2366 1.823899 GGCGGGATTAAGCACCCAG 60.824 63.158 13.23 8.38 45.83 4.45
2360 2390 1.257750 TAGGCAGATGCGTCCACTGT 61.258 55.000 1.23 0.00 43.26 3.55
2387 2417 0.036199 TGCCCGGTGTACACATAACC 60.036 55.000 26.51 8.79 0.00 2.85
2388 2418 1.668751 CATGCCCGGTGTACACATAAC 59.331 52.381 26.51 13.64 0.00 1.89
2389 2419 1.407575 CCATGCCCGGTGTACACATAA 60.408 52.381 26.51 8.25 0.00 1.90
2390 2420 0.179234 CCATGCCCGGTGTACACATA 59.821 55.000 26.51 8.57 0.00 2.29


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

AutoCloner maintained by Alex Coulton.