Multiple sequence alignment - TraesCS2D01G179900

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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 TraesCS2D01G179900 chr2D 100.000 2414 0 0 1 2414 124066738 124064325 0.000000e+00 4458.0
1 TraesCS2D01G179900 chr2D 76.000 175 33 7 1271 1440 361240869 361241039 5.530000e-12 82.4
2 TraesCS2D01G179900 chr5D 94.040 1443 78 5 1 1440 3936730 3935293 0.000000e+00 2182.0
3 TraesCS2D01G179900 chr5D 93.268 1233 80 3 177 1408 545617567 545618797 0.000000e+00 1814.0
4 TraesCS2D01G179900 chr5D 97.959 49 1 0 1393 1441 545618813 545618861 4.280000e-13 86.1
5 TraesCS2D01G179900 chr5D 79.200 125 18 7 1322 1441 416436329 416436208 1.990000e-11 80.5
6 TraesCS2D01G179900 chr5A 93.495 1399 86 4 1 1396 205016869 205015473 0.000000e+00 2074.0
7 TraesCS2D01G179900 chr5B 92.862 1387 96 3 1 1385 688357228 688358613 0.000000e+00 2010.0
8 TraesCS2D01G179900 chr2B 94.136 1313 65 3 129 1440 772395116 772393815 0.000000e+00 1988.0
9 TraesCS2D01G179900 chr2B 96.571 729 23 2 1687 2414 176709178 176708451 0.000000e+00 1206.0
10 TraesCS2D01G179900 chr2B 93.145 248 14 2 1441 1688 504193167 504193411 6.340000e-96 361.0
11 TraesCS2D01G179900 chr2A 97.846 650 13 1 1766 2414 129867906 129868555 0.000000e+00 1122.0
12 TraesCS2D01G179900 chr4D 78.700 1446 282 21 10 1441 213419191 213417758 0.000000e+00 941.0
13 TraesCS2D01G179900 chr4D 76.842 1425 323 6 7 1427 85014075 85012654 0.000000e+00 797.0
14 TraesCS2D01G179900 chr4D 76.301 173 28 10 1280 1443 505310250 505310418 1.990000e-11 80.5
15 TraesCS2D01G179900 chr3B 77.992 1454 297 20 1 1443 252352269 252353710 0.000000e+00 891.0
16 TraesCS2D01G179900 chrUn 78.033 1434 281 23 10 1434 29529422 29528014 0.000000e+00 872.0
17 TraesCS2D01G179900 chr7D 94.231 416 24 0 1032 1447 158942415 158942830 9.410000e-179 636.0
18 TraesCS2D01G179900 chr7D 95.349 172 8 0 1441 1612 197818272 197818101 8.500000e-70 274.0
19 TraesCS2D01G179900 chr6D 95.968 248 10 0 1441 1688 453724846 453725093 1.040000e-108 403.0
20 TraesCS2D01G179900 chr7B 79.699 133 19 8 1280 1408 423764008 423764136 3.310000e-14 89.8


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 TraesCS2D01G179900 chr2D 124064325 124066738 2413 True 4458.00 4458 100.0000 1 2414 1 chr2D.!!$R1 2413
1 TraesCS2D01G179900 chr5D 3935293 3936730 1437 True 2182.00 2182 94.0400 1 1440 1 chr5D.!!$R1 1439
2 TraesCS2D01G179900 chr5D 545617567 545618861 1294 False 950.05 1814 95.6135 177 1441 2 chr5D.!!$F1 1264
3 TraesCS2D01G179900 chr5A 205015473 205016869 1396 True 2074.00 2074 93.4950 1 1396 1 chr5A.!!$R1 1395
4 TraesCS2D01G179900 chr5B 688357228 688358613 1385 False 2010.00 2010 92.8620 1 1385 1 chr5B.!!$F1 1384
5 TraesCS2D01G179900 chr2B 772393815 772395116 1301 True 1988.00 1988 94.1360 129 1440 1 chr2B.!!$R2 1311
6 TraesCS2D01G179900 chr2B 176708451 176709178 727 True 1206.00 1206 96.5710 1687 2414 1 chr2B.!!$R1 727
7 TraesCS2D01G179900 chr2A 129867906 129868555 649 False 1122.00 1122 97.8460 1766 2414 1 chr2A.!!$F1 648
8 TraesCS2D01G179900 chr4D 213417758 213419191 1433 True 941.00 941 78.7000 10 1441 1 chr4D.!!$R2 1431
9 TraesCS2D01G179900 chr4D 85012654 85014075 1421 True 797.00 797 76.8420 7 1427 1 chr4D.!!$R1 1420
10 TraesCS2D01G179900 chr3B 252352269 252353710 1441 False 891.00 891 77.9920 1 1443 1 chr3B.!!$F1 1442
11 TraesCS2D01G179900 chrUn 29528014 29529422 1408 True 872.00 872 78.0330 10 1434 1 chrUn.!!$R1 1424

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
440 443 0.463295 CCTCGAATGTGGCTGCTGAT 60.463 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 1698 0.240145 GCTTGCAGTAAAACGGGGTC 59.76 55.0 0.0 0.0 0.0 4.46 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
166 167 3.006112 TCGACTGTATCCTCTTCTGCT 57.994 47.619 0.00 0.00 0.00 4.24
440 443 0.463295 CCTCGAATGTGGCTGCTGAT 60.463 55.000 0.00 0.00 0.00 2.90
457 460 3.307339 GCTGATGAGAAGAGTTGGAAGGT 60.307 47.826 0.00 0.00 0.00 3.50
568 571 1.028330 CGCCATGTTCCTGATGCTGT 61.028 55.000 0.00 0.00 0.00 4.40
618 621 2.191908 TGGAGCACGCCACACTTT 59.808 55.556 0.00 0.00 31.66 2.66
839 843 3.643763 CTCCACATCCTCGTATTACAGC 58.356 50.000 0.00 0.00 0.00 4.40
931 935 3.244561 TGAGTCTTCTTCACCCAATCCAC 60.245 47.826 0.00 0.00 0.00 4.02
1222 1228 3.244976 GGCAAAATTGATCGTTCCAGTG 58.755 45.455 0.00 0.00 0.00 3.66
1230 1236 1.200716 GATCGTTCCAGTGTCGGTACA 59.799 52.381 0.00 0.00 0.00 2.90
1275 1281 1.108727 CAAGGGGCTTTGTGTCTGCA 61.109 55.000 0.00 0.00 0.00 4.41
1298 1304 0.602638 TTCAAGCATGTTCGTCGGCT 60.603 50.000 0.00 0.00 38.45 5.52
1299 1305 0.602638 TCAAGCATGTTCGTCGGCTT 60.603 50.000 0.00 0.55 46.71 4.35
1324 1330 7.053498 TGTTAATGTGGCTGCTCATCTATTAA 58.947 34.615 0.00 6.78 0.00 1.40
1464 1506 6.288426 GCTATACCTAGCTAAAAAGTGTGC 57.712 41.667 0.00 0.00 45.78 4.57
1465 1507 5.236695 GCTATACCTAGCTAAAAAGTGTGCC 59.763 44.000 0.00 0.00 45.78 5.01
1466 1508 3.502123 ACCTAGCTAAAAAGTGTGCCA 57.498 42.857 0.00 0.00 0.00 4.92
1467 1509 3.412386 ACCTAGCTAAAAAGTGTGCCAG 58.588 45.455 0.00 0.00 0.00 4.85
1468 1510 2.162408 CCTAGCTAAAAAGTGTGCCAGC 59.838 50.000 0.00 0.00 0.00 4.85
1469 1511 1.986882 AGCTAAAAAGTGTGCCAGCT 58.013 45.000 0.00 0.00 34.63 4.24
1470 1512 2.310538 AGCTAAAAAGTGTGCCAGCTT 58.689 42.857 0.00 0.00 35.94 3.74
1471 1513 3.486383 AGCTAAAAAGTGTGCCAGCTTA 58.514 40.909 0.00 0.00 35.94 3.09
1472 1514 4.082125 AGCTAAAAAGTGTGCCAGCTTAT 58.918 39.130 0.00 0.00 35.94 1.73
1473 1515 4.524328 AGCTAAAAAGTGTGCCAGCTTATT 59.476 37.500 0.00 0.00 35.94 1.40
1474 1516 5.710099 AGCTAAAAAGTGTGCCAGCTTATTA 59.290 36.000 0.00 0.00 35.94 0.98
1475 1517 6.030228 GCTAAAAAGTGTGCCAGCTTATTAG 58.970 40.000 0.00 0.00 0.00 1.73
1485 1527 2.235546 GCTTATTAGCTTCCCGCGG 58.764 57.895 21.04 21.04 44.27 6.46
1486 1528 1.228657 GCTTATTAGCTTCCCGCGGG 61.229 60.000 39.13 39.13 44.27 6.13
1487 1529 1.227734 TTATTAGCTTCCCGCGGGC 60.228 57.895 39.89 27.37 45.59 6.13
1488 1530 1.973816 TTATTAGCTTCCCGCGGGCA 61.974 55.000 39.89 29.47 45.59 5.36
1489 1531 1.973816 TATTAGCTTCCCGCGGGCAA 61.974 55.000 39.89 29.52 45.59 4.52
1490 1532 2.624674 ATTAGCTTCCCGCGGGCAAT 62.625 55.000 39.89 25.93 45.59 3.56
1514 1556 4.686839 CGAAAGGAAACAGAAGGGATTC 57.313 45.455 0.00 0.00 0.00 2.52
1515 1557 3.440522 CGAAAGGAAACAGAAGGGATTCC 59.559 47.826 0.00 0.00 41.32 3.01
1516 1558 4.407365 GAAAGGAAACAGAAGGGATTCCA 58.593 43.478 4.80 0.00 43.03 3.53
1517 1559 4.682021 AAGGAAACAGAAGGGATTCCAT 57.318 40.909 4.80 0.00 43.03 3.41
1518 1560 3.973425 AGGAAACAGAAGGGATTCCATG 58.027 45.455 4.80 0.36 43.03 3.66
1519 1561 2.428530 GGAAACAGAAGGGATTCCATGC 59.571 50.000 4.80 0.00 40.81 4.06
1520 1562 1.755179 AACAGAAGGGATTCCATGCG 58.245 50.000 4.80 0.00 34.83 4.73
1521 1563 0.749454 ACAGAAGGGATTCCATGCGC 60.749 55.000 0.00 0.00 34.83 6.09
1522 1564 0.465097 CAGAAGGGATTCCATGCGCT 60.465 55.000 9.73 0.00 34.83 5.92
1523 1565 1.131638 AGAAGGGATTCCATGCGCTA 58.868 50.000 9.73 0.00 34.83 4.26
1524 1566 1.490490 AGAAGGGATTCCATGCGCTAA 59.510 47.619 9.73 0.00 34.83 3.09
1525 1567 2.107204 AGAAGGGATTCCATGCGCTAAT 59.893 45.455 9.73 3.12 34.83 1.73
1526 1568 2.664402 AGGGATTCCATGCGCTAATT 57.336 45.000 9.73 0.00 34.83 1.40
1527 1569 2.508526 AGGGATTCCATGCGCTAATTC 58.491 47.619 9.73 2.08 34.83 2.17
1528 1570 2.158623 AGGGATTCCATGCGCTAATTCA 60.159 45.455 9.73 0.00 34.83 2.57
1529 1571 2.622942 GGGATTCCATGCGCTAATTCAA 59.377 45.455 9.73 0.00 0.00 2.69
1530 1572 3.068024 GGGATTCCATGCGCTAATTCAAA 59.932 43.478 9.73 0.00 0.00 2.69
1531 1573 4.293415 GGATTCCATGCGCTAATTCAAAG 58.707 43.478 9.73 0.00 0.00 2.77
1532 1574 2.849880 TCCATGCGCTAATTCAAAGC 57.150 45.000 9.73 0.00 36.60 3.51
1533 1575 2.090760 TCCATGCGCTAATTCAAAGCA 58.909 42.857 9.73 0.69 40.08 3.91
1534 1576 2.097954 TCCATGCGCTAATTCAAAGCAG 59.902 45.455 9.73 0.00 41.34 4.24
1535 1577 2.159338 CCATGCGCTAATTCAAAGCAGT 60.159 45.455 9.73 0.00 41.34 4.40
1536 1578 2.900122 TGCGCTAATTCAAAGCAGTC 57.100 45.000 9.73 0.00 40.08 3.51
1537 1579 1.468520 TGCGCTAATTCAAAGCAGTCC 59.531 47.619 9.73 0.00 40.08 3.85
1538 1580 1.468520 GCGCTAATTCAAAGCAGTCCA 59.531 47.619 0.00 0.00 40.08 4.02
1539 1581 2.729156 GCGCTAATTCAAAGCAGTCCAC 60.729 50.000 0.00 0.00 40.08 4.02
1540 1582 2.744202 CGCTAATTCAAAGCAGTCCACT 59.256 45.455 0.00 0.00 40.08 4.00
1541 1583 3.932710 CGCTAATTCAAAGCAGTCCACTA 59.067 43.478 0.00 0.00 40.08 2.74
1542 1584 4.033358 CGCTAATTCAAAGCAGTCCACTAG 59.967 45.833 0.00 0.00 40.08 2.57
1543 1585 5.178797 GCTAATTCAAAGCAGTCCACTAGA 58.821 41.667 0.00 0.00 39.83 2.43
1544 1586 5.643777 GCTAATTCAAAGCAGTCCACTAGAA 59.356 40.000 0.00 0.00 39.83 2.10
1545 1587 6.317391 GCTAATTCAAAGCAGTCCACTAGAAT 59.683 38.462 0.00 0.00 39.83 2.40
1546 1588 6.506500 AATTCAAAGCAGTCCACTAGAATG 57.493 37.500 0.00 0.00 43.53 2.67
1547 1589 3.942829 TCAAAGCAGTCCACTAGAATGG 58.057 45.455 0.00 0.00 40.96 3.16
1548 1590 3.012518 CAAAGCAGTCCACTAGAATGGG 58.987 50.000 0.00 0.00 40.96 4.00
1549 1591 0.543749 AGCAGTCCACTAGAATGGGC 59.456 55.000 0.00 0.00 45.38 5.36
1552 1594 3.065575 GTCCACTAGAATGGGCGTG 57.934 57.895 0.00 0.00 40.49 5.34
1553 1595 0.249398 GTCCACTAGAATGGGCGTGT 59.751 55.000 0.00 0.00 40.49 4.49
1554 1596 1.479323 GTCCACTAGAATGGGCGTGTA 59.521 52.381 0.00 0.00 40.49 2.90
1555 1597 2.093869 GTCCACTAGAATGGGCGTGTAA 60.094 50.000 0.00 0.00 40.49 2.41
1556 1598 2.167693 TCCACTAGAATGGGCGTGTAAG 59.832 50.000 0.00 0.00 40.49 2.34
1557 1599 2.550978 CACTAGAATGGGCGTGTAAGG 58.449 52.381 0.00 0.00 0.00 2.69
1558 1600 2.167693 CACTAGAATGGGCGTGTAAGGA 59.832 50.000 0.00 0.00 0.00 3.36
1559 1601 2.167900 ACTAGAATGGGCGTGTAAGGAC 59.832 50.000 0.00 0.00 0.00 3.85
1560 1602 1.276622 AGAATGGGCGTGTAAGGACT 58.723 50.000 0.00 0.00 0.00 3.85
1561 1603 1.207329 AGAATGGGCGTGTAAGGACTC 59.793 52.381 0.00 0.00 0.00 3.36
1562 1604 0.252197 AATGGGCGTGTAAGGACTCC 59.748 55.000 0.00 0.00 0.00 3.85
1563 1605 0.907704 ATGGGCGTGTAAGGACTCCA 60.908 55.000 0.00 0.00 0.00 3.86
1564 1606 1.218316 GGGCGTGTAAGGACTCCAG 59.782 63.158 0.00 0.00 0.00 3.86
1565 1607 1.255667 GGGCGTGTAAGGACTCCAGA 61.256 60.000 0.00 0.00 0.00 3.86
1566 1608 0.824759 GGCGTGTAAGGACTCCAGAT 59.175 55.000 0.00 0.00 0.00 2.90
1567 1609 1.207329 GGCGTGTAAGGACTCCAGATT 59.793 52.381 0.00 0.00 0.00 2.40
1568 1610 2.354805 GGCGTGTAAGGACTCCAGATTT 60.355 50.000 0.00 0.00 0.00 2.17
1569 1611 2.930682 GCGTGTAAGGACTCCAGATTTC 59.069 50.000 0.00 0.00 0.00 2.17
1570 1612 3.616560 GCGTGTAAGGACTCCAGATTTCA 60.617 47.826 0.00 0.00 0.00 2.69
1571 1613 4.759782 CGTGTAAGGACTCCAGATTTCAT 58.240 43.478 0.00 0.00 0.00 2.57
1572 1614 5.178797 CGTGTAAGGACTCCAGATTTCATT 58.821 41.667 0.00 0.00 0.00 2.57
1573 1615 5.063944 CGTGTAAGGACTCCAGATTTCATTG 59.936 44.000 0.00 0.00 0.00 2.82
1574 1616 4.943705 TGTAAGGACTCCAGATTTCATTGC 59.056 41.667 0.00 0.00 0.00 3.56
1575 1617 3.010200 AGGACTCCAGATTTCATTGCC 57.990 47.619 0.00 0.00 0.00 4.52
1576 1618 2.309755 AGGACTCCAGATTTCATTGCCA 59.690 45.455 0.00 0.00 0.00 4.92
1577 1619 2.424956 GGACTCCAGATTTCATTGCCAC 59.575 50.000 0.00 0.00 0.00 5.01
1578 1620 3.350833 GACTCCAGATTTCATTGCCACT 58.649 45.455 0.00 0.00 0.00 4.00
1579 1621 3.760684 GACTCCAGATTTCATTGCCACTT 59.239 43.478 0.00 0.00 0.00 3.16
1580 1622 4.154942 ACTCCAGATTTCATTGCCACTTT 58.845 39.130 0.00 0.00 0.00 2.66
1581 1623 4.590222 ACTCCAGATTTCATTGCCACTTTT 59.410 37.500 0.00 0.00 0.00 2.27
1582 1624 4.885413 TCCAGATTTCATTGCCACTTTTG 58.115 39.130 0.00 0.00 0.00 2.44
1583 1625 4.588106 TCCAGATTTCATTGCCACTTTTGA 59.412 37.500 0.00 0.00 0.00 2.69
1584 1626 5.070180 TCCAGATTTCATTGCCACTTTTGAA 59.930 36.000 0.00 0.00 0.00 2.69
1585 1627 5.759273 CCAGATTTCATTGCCACTTTTGAAA 59.241 36.000 0.00 0.00 40.99 2.69
1586 1628 6.073440 CCAGATTTCATTGCCACTTTTGAAAG 60.073 38.462 2.06 2.06 40.32 2.62
1587 1629 5.467735 AGATTTCATTGCCACTTTTGAAAGC 59.532 36.000 3.48 4.78 42.03 3.51
1588 1630 3.815856 TCATTGCCACTTTTGAAAGCA 57.184 38.095 3.48 0.00 39.63 3.91
1589 1631 4.339872 TCATTGCCACTTTTGAAAGCAT 57.660 36.364 3.48 0.00 39.63 3.79
1590 1632 4.309099 TCATTGCCACTTTTGAAAGCATC 58.691 39.130 3.48 0.00 39.63 3.91
1591 1633 2.818130 TGCCACTTTTGAAAGCATCC 57.182 45.000 3.48 0.00 39.63 3.51
1592 1634 2.037901 TGCCACTTTTGAAAGCATCCA 58.962 42.857 3.48 0.00 39.63 3.41
1593 1635 2.224018 TGCCACTTTTGAAAGCATCCAC 60.224 45.455 3.48 0.00 39.63 4.02
1594 1636 2.036346 GCCACTTTTGAAAGCATCCACT 59.964 45.455 3.48 0.00 39.63 4.00
1595 1637 3.255642 GCCACTTTTGAAAGCATCCACTA 59.744 43.478 3.48 0.00 39.63 2.74
1596 1638 4.616835 GCCACTTTTGAAAGCATCCACTAG 60.617 45.833 3.48 0.00 39.63 2.57
1597 1639 4.520492 CCACTTTTGAAAGCATCCACTAGT 59.480 41.667 3.48 0.00 39.63 2.57
1598 1640 5.010012 CCACTTTTGAAAGCATCCACTAGTT 59.990 40.000 0.00 0.00 39.63 2.24
1599 1641 6.145535 CACTTTTGAAAGCATCCACTAGTTC 58.854 40.000 0.00 0.00 39.63 3.01
1600 1642 5.241728 ACTTTTGAAAGCATCCACTAGTTCC 59.758 40.000 0.00 0.00 39.63 3.62
1601 1643 4.365514 TTGAAAGCATCCACTAGTTCCA 57.634 40.909 0.00 0.00 0.00 3.53
1602 1644 3.942829 TGAAAGCATCCACTAGTTCCAG 58.057 45.455 0.00 0.00 0.00 3.86
1603 1645 3.274288 GAAAGCATCCACTAGTTCCAGG 58.726 50.000 0.00 0.00 0.00 4.45
1604 1646 0.543749 AGCATCCACTAGTTCCAGGC 59.456 55.000 0.00 0.00 0.00 4.85
1605 1647 0.253044 GCATCCACTAGTTCCAGGCA 59.747 55.000 0.00 0.00 0.00 4.75
1606 1648 1.340017 GCATCCACTAGTTCCAGGCAA 60.340 52.381 0.00 0.00 0.00 4.52
1607 1649 2.684927 GCATCCACTAGTTCCAGGCAAT 60.685 50.000 0.00 0.00 0.00 3.56
1608 1650 3.209410 CATCCACTAGTTCCAGGCAATC 58.791 50.000 0.00 0.00 0.00 2.67
1609 1651 2.265367 TCCACTAGTTCCAGGCAATCA 58.735 47.619 0.00 0.00 0.00 2.57
1610 1652 2.237143 TCCACTAGTTCCAGGCAATCAG 59.763 50.000 0.00 0.00 0.00 2.90
1611 1653 2.237143 CCACTAGTTCCAGGCAATCAGA 59.763 50.000 0.00 0.00 0.00 3.27
1612 1654 3.118112 CCACTAGTTCCAGGCAATCAGAT 60.118 47.826 0.00 0.00 0.00 2.90
1613 1655 4.521146 CACTAGTTCCAGGCAATCAGATT 58.479 43.478 0.00 0.00 0.00 2.40
1614 1656 4.574013 CACTAGTTCCAGGCAATCAGATTC 59.426 45.833 0.00 0.00 0.00 2.52
1615 1657 3.010200 AGTTCCAGGCAATCAGATTCC 57.990 47.619 0.00 0.00 0.00 3.01
1616 1658 2.309755 AGTTCCAGGCAATCAGATTCCA 59.690 45.455 11.86 0.00 0.00 3.53
1617 1659 2.424956 GTTCCAGGCAATCAGATTCCAC 59.575 50.000 11.86 0.00 0.00 4.02
1618 1660 1.918262 TCCAGGCAATCAGATTCCACT 59.082 47.619 11.86 1.31 0.00 4.00
1619 1661 2.022195 CCAGGCAATCAGATTCCACTG 58.978 52.381 11.86 10.78 39.02 3.66
1620 1662 2.619849 CCAGGCAATCAGATTCCACTGT 60.620 50.000 13.37 0.00 38.79 3.55
1621 1663 3.087031 CAGGCAATCAGATTCCACTGTT 58.913 45.455 11.86 0.00 38.79 3.16
1622 1664 4.264253 CAGGCAATCAGATTCCACTGTTA 58.736 43.478 11.86 0.00 38.79 2.41
1623 1665 4.095483 CAGGCAATCAGATTCCACTGTTAC 59.905 45.833 11.86 0.00 38.79 2.50
1624 1666 4.018960 AGGCAATCAGATTCCACTGTTACT 60.019 41.667 11.86 0.00 38.79 2.24
1625 1667 4.333926 GGCAATCAGATTCCACTGTTACTC 59.666 45.833 0.00 0.00 38.79 2.59
1626 1668 5.181748 GCAATCAGATTCCACTGTTACTCT 58.818 41.667 0.00 0.00 38.79 3.24
1627 1669 5.064452 GCAATCAGATTCCACTGTTACTCTG 59.936 44.000 0.00 0.00 38.79 3.35
1628 1670 4.808414 TCAGATTCCACTGTTACTCTGG 57.192 45.455 0.00 0.00 38.79 3.86
1629 1671 4.416516 TCAGATTCCACTGTTACTCTGGA 58.583 43.478 0.00 0.00 38.79 3.86
1630 1672 4.838423 TCAGATTCCACTGTTACTCTGGAA 59.162 41.667 13.84 13.84 45.87 3.53
1631 1673 4.932200 CAGATTCCACTGTTACTCTGGAAC 59.068 45.833 13.78 9.56 44.88 3.62
1632 1674 4.593206 AGATTCCACTGTTACTCTGGAACA 59.407 41.667 13.78 0.00 44.88 3.18
1633 1675 4.974645 TTCCACTGTTACTCTGGAACAT 57.025 40.909 9.30 0.00 38.83 2.71
1634 1676 4.537135 TCCACTGTTACTCTGGAACATC 57.463 45.455 0.00 0.00 38.20 3.06
1635 1677 3.260884 TCCACTGTTACTCTGGAACATCC 59.739 47.826 0.00 0.00 38.20 3.51
1636 1678 3.261897 CCACTGTTACTCTGGAACATCCT 59.738 47.826 0.00 0.00 38.20 3.24
1637 1679 4.499183 CACTGTTACTCTGGAACATCCTC 58.501 47.826 0.00 0.00 38.20 3.71
1638 1680 4.221703 CACTGTTACTCTGGAACATCCTCT 59.778 45.833 0.00 0.00 38.20 3.69
1639 1681 4.841246 ACTGTTACTCTGGAACATCCTCTT 59.159 41.667 0.00 0.00 38.20 2.85
1640 1682 5.308237 ACTGTTACTCTGGAACATCCTCTTT 59.692 40.000 0.00 0.00 38.20 2.52
1641 1683 5.794894 TGTTACTCTGGAACATCCTCTTTC 58.205 41.667 0.00 0.00 38.20 2.62
1642 1684 5.306937 TGTTACTCTGGAACATCCTCTTTCA 59.693 40.000 0.00 0.00 38.20 2.69
1643 1685 4.982241 ACTCTGGAACATCCTCTTTCAA 57.018 40.909 0.00 0.00 38.20 2.69
1644 1686 5.310409 ACTCTGGAACATCCTCTTTCAAA 57.690 39.130 0.00 0.00 38.20 2.69
1645 1687 5.312079 ACTCTGGAACATCCTCTTTCAAAG 58.688 41.667 0.00 0.00 38.20 2.77
1646 1688 5.072329 ACTCTGGAACATCCTCTTTCAAAGA 59.928 40.000 0.00 0.00 38.20 2.52
1647 1689 5.555017 TCTGGAACATCCTCTTTCAAAGAG 58.445 41.667 18.99 18.99 46.60 2.85
1648 1690 4.155644 CTGGAACATCCTCTTTCAAAGAGC 59.844 45.833 20.30 6.64 46.06 4.09
1649 1691 6.263710 CTGGAACATCCTCTTTCAAAGAGCA 61.264 44.000 20.30 7.49 46.06 4.26
1650 1692 7.524068 CTGGAACATCCTCTTTCAAAGAGCAT 61.524 42.308 20.30 9.70 46.06 3.79
1651 1693 9.223557 CTGGAACATCCTCTTTCAAAGAGCATC 62.224 44.444 20.30 12.48 46.06 3.91
1662 1704 4.844420 GAGCATCTTCAGACCCCG 57.156 61.111 0.00 0.00 0.00 5.73
1663 1705 1.901085 GAGCATCTTCAGACCCCGT 59.099 57.895 0.00 0.00 0.00 5.28
1664 1706 0.250513 GAGCATCTTCAGACCCCGTT 59.749 55.000 0.00 0.00 0.00 4.44
1665 1707 0.693049 AGCATCTTCAGACCCCGTTT 59.307 50.000 0.00 0.00 0.00 3.60
1666 1708 1.073923 AGCATCTTCAGACCCCGTTTT 59.926 47.619 0.00 0.00 0.00 2.43
1667 1709 2.304761 AGCATCTTCAGACCCCGTTTTA 59.695 45.455 0.00 0.00 0.00 1.52
1668 1710 2.418976 GCATCTTCAGACCCCGTTTTAC 59.581 50.000 0.00 0.00 0.00 2.01
1669 1711 3.868754 GCATCTTCAGACCCCGTTTTACT 60.869 47.826 0.00 0.00 0.00 2.24
1670 1712 3.396260 TCTTCAGACCCCGTTTTACTG 57.604 47.619 0.00 0.00 0.00 2.74
1671 1713 1.804748 CTTCAGACCCCGTTTTACTGC 59.195 52.381 0.00 0.00 0.00 4.40
1672 1714 0.759959 TCAGACCCCGTTTTACTGCA 59.240 50.000 0.00 0.00 0.00 4.41
1673 1715 1.141254 TCAGACCCCGTTTTACTGCAA 59.859 47.619 0.00 0.00 0.00 4.08
1674 1716 1.535462 CAGACCCCGTTTTACTGCAAG 59.465 52.381 0.00 0.00 42.29 4.01
1675 1717 0.240145 GACCCCGTTTTACTGCAAGC 59.760 55.000 0.00 0.00 37.60 4.01
1676 1718 1.209127 CCCCGTTTTACTGCAAGCG 59.791 57.895 0.00 0.00 37.60 4.68
1677 1719 1.442017 CCCGTTTTACTGCAAGCGC 60.442 57.895 0.00 0.00 37.60 5.92
1678 1720 1.442017 CCGTTTTACTGCAAGCGCC 60.442 57.895 2.29 0.00 37.60 6.53
1679 1721 1.574428 CGTTTTACTGCAAGCGCCT 59.426 52.632 2.29 0.00 37.60 5.52
1680 1722 0.452784 CGTTTTACTGCAAGCGCCTC 60.453 55.000 2.29 0.00 37.60 4.70
1681 1723 0.875059 GTTTTACTGCAAGCGCCTCT 59.125 50.000 2.29 0.00 37.60 3.69
1682 1724 0.874390 TTTTACTGCAAGCGCCTCTG 59.126 50.000 2.29 0.00 37.60 3.35
1683 1725 1.577328 TTTACTGCAAGCGCCTCTGC 61.577 55.000 17.23 17.23 37.60 4.26
1685 1727 1.604147 TACTGCAAGCGCCTCTGCTA 61.604 55.000 22.46 9.13 46.60 3.49
1699 1741 4.333926 GCCTCTGCTATTAACCTCAAACAG 59.666 45.833 0.00 0.00 33.53 3.16
1701 1743 5.582665 CCTCTGCTATTAACCTCAAACAGAC 59.417 44.000 0.00 0.00 0.00 3.51
1723 1765 2.365635 CCAGACCATCCCGGACCT 60.366 66.667 0.73 0.00 38.63 3.85
1805 1848 3.422603 CGAAACCAATACGTGAACTTCCG 60.423 47.826 0.00 0.00 0.00 4.30
1898 1942 0.180406 CCATAGACTTCAACCCCGGG 59.820 60.000 15.80 15.80 0.00 5.73
1954 1998 2.505819 CCCACATAGAGCCAAAGGTAGT 59.494 50.000 0.00 0.00 0.00 2.73
2015 2059 5.239963 TCGCCCTTAAGAGAAAACGATTTTT 59.760 36.000 3.36 0.00 37.65 1.94
2343 2387 4.752594 TTCGGGAAGGGGAGGGGG 62.753 72.222 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 4.788925 ACCTTGGCATTAGCAGGTATAA 57.211 40.909 6.02 0.00 43.24 0.98
248 249 3.457610 TCTGCAGCAATATCATCACGA 57.542 42.857 9.47 0.00 0.00 4.35
440 443 5.104776 CCATATCACCTTCCAACTCTTCTCA 60.105 44.000 0.00 0.00 0.00 3.27
457 460 6.508030 TGGGTGCTTTAATAGACCATATCA 57.492 37.500 0.00 0.00 0.00 2.15
517 520 1.305213 GCCCCAGATGGAAGGCAAA 60.305 57.895 12.68 0.00 40.77 3.68
568 571 1.102154 CCCACAGAAGCAACAACACA 58.898 50.000 0.00 0.00 0.00 3.72
618 621 3.122613 CAGTTTTTGCACGCAGACAAAAA 59.877 39.130 13.43 13.43 46.05 1.94
752 755 3.132824 CCAAAAAGAAACAGCCAGAACCT 59.867 43.478 0.00 0.00 0.00 3.50
839 843 6.042777 TCAGTATAAGCACGGATTTTCTCAG 58.957 40.000 0.00 0.00 0.00 3.35
931 935 2.738521 CGGCGGCGGAATCCATAG 60.739 66.667 25.36 0.00 0.00 2.23
1119 1123 1.289109 CGTCCTTTGCCAGGTACACG 61.289 60.000 0.00 0.00 44.37 4.49
1222 1228 8.812147 TTGATATCATTAATCACTGTACCGAC 57.188 34.615 6.17 0.00 33.18 4.79
1275 1281 2.061773 CGACGAACATGCTTGAACTCT 58.938 47.619 6.60 0.00 0.00 3.24
1298 1304 3.689347 AGATGAGCAGCCACATTAACAA 58.311 40.909 4.50 0.00 0.00 2.83
1299 1305 3.354948 AGATGAGCAGCCACATTAACA 57.645 42.857 4.50 0.00 0.00 2.41
1442 1484 6.346096 TGGCACACTTTTTAGCTAGGTATAG 58.654 40.000 1.80 3.98 0.00 1.31
1443 1485 6.302535 TGGCACACTTTTTAGCTAGGTATA 57.697 37.500 1.80 0.00 0.00 1.47
1444 1486 5.174037 TGGCACACTTTTTAGCTAGGTAT 57.826 39.130 1.80 0.00 0.00 2.73
1445 1487 4.575885 CTGGCACACTTTTTAGCTAGGTA 58.424 43.478 0.00 0.00 32.73 3.08
1446 1488 3.412386 CTGGCACACTTTTTAGCTAGGT 58.588 45.455 0.00 0.00 32.73 3.08
1447 1489 2.162408 GCTGGCACACTTTTTAGCTAGG 59.838 50.000 0.00 0.00 36.29 3.02
1448 1490 3.077359 AGCTGGCACACTTTTTAGCTAG 58.923 45.455 0.00 0.00 39.50 3.42
1449 1491 3.140325 AGCTGGCACACTTTTTAGCTA 57.860 42.857 0.00 0.00 39.50 3.32
1450 1492 1.986882 AGCTGGCACACTTTTTAGCT 58.013 45.000 0.00 0.00 36.74 3.32
1451 1493 2.800881 AAGCTGGCACACTTTTTAGC 57.199 45.000 0.00 0.00 0.00 3.09
1452 1494 6.030228 GCTAATAAGCTGGCACACTTTTTAG 58.970 40.000 20.01 20.01 45.85 1.85
1453 1495 5.949735 GCTAATAAGCTGGCACACTTTTTA 58.050 37.500 3.57 6.00 45.85 1.52
1454 1496 4.809673 GCTAATAAGCTGGCACACTTTTT 58.190 39.130 3.57 5.26 45.85 1.94
1455 1497 4.440839 GCTAATAAGCTGGCACACTTTT 57.559 40.909 3.57 2.34 45.85 2.27
1467 1509 1.228657 CCCGCGGGAAGCTAATAAGC 61.229 60.000 41.82 0.00 45.59 3.09
1468 1510 2.914379 CCCGCGGGAAGCTAATAAG 58.086 57.895 41.82 6.81 45.59 1.73
1485 1527 0.316841 TGTTTCCTTTCGGCATTGCC 59.683 50.000 18.10 18.10 46.75 4.52
1486 1528 1.269448 TCTGTTTCCTTTCGGCATTGC 59.731 47.619 0.00 0.00 0.00 3.56
1487 1529 3.568538 CTTCTGTTTCCTTTCGGCATTG 58.431 45.455 0.00 0.00 0.00 2.82
1488 1530 2.558359 CCTTCTGTTTCCTTTCGGCATT 59.442 45.455 0.00 0.00 0.00 3.56
1489 1531 2.162681 CCTTCTGTTTCCTTTCGGCAT 58.837 47.619 0.00 0.00 0.00 4.40
1490 1532 1.604604 CCTTCTGTTTCCTTTCGGCA 58.395 50.000 0.00 0.00 0.00 5.69
1491 1533 0.881796 CCCTTCTGTTTCCTTTCGGC 59.118 55.000 0.00 0.00 0.00 5.54
1492 1534 2.561478 TCCCTTCTGTTTCCTTTCGG 57.439 50.000 0.00 0.00 0.00 4.30
1493 1535 3.440522 GGAATCCCTTCTGTTTCCTTTCG 59.559 47.826 0.00 0.00 35.74 3.46
1494 1536 4.407365 TGGAATCCCTTCTGTTTCCTTTC 58.593 43.478 0.00 0.00 38.73 2.62
1495 1537 4.469469 TGGAATCCCTTCTGTTTCCTTT 57.531 40.909 0.00 0.00 38.73 3.11
1496 1538 4.347607 CATGGAATCCCTTCTGTTTCCTT 58.652 43.478 0.00 0.00 38.73 3.36
1497 1539 3.879321 GCATGGAATCCCTTCTGTTTCCT 60.879 47.826 0.00 0.00 38.73 3.36
1498 1540 2.428530 GCATGGAATCCCTTCTGTTTCC 59.571 50.000 0.00 0.00 38.48 3.13
1499 1541 2.098117 CGCATGGAATCCCTTCTGTTTC 59.902 50.000 0.00 0.00 0.00 2.78
1500 1542 2.094675 CGCATGGAATCCCTTCTGTTT 58.905 47.619 0.00 0.00 0.00 2.83
1501 1543 1.755179 CGCATGGAATCCCTTCTGTT 58.245 50.000 0.00 0.00 0.00 3.16
1502 1544 0.749454 GCGCATGGAATCCCTTCTGT 60.749 55.000 0.30 0.00 0.00 3.41
1503 1545 0.465097 AGCGCATGGAATCCCTTCTG 60.465 55.000 11.47 0.00 0.00 3.02
1504 1546 1.131638 TAGCGCATGGAATCCCTTCT 58.868 50.000 11.47 0.00 0.00 2.85
1505 1547 1.967319 TTAGCGCATGGAATCCCTTC 58.033 50.000 11.47 0.00 0.00 3.46
1506 1548 2.664402 ATTAGCGCATGGAATCCCTT 57.336 45.000 11.47 0.00 0.00 3.95
1507 1549 2.158623 TGAATTAGCGCATGGAATCCCT 60.159 45.455 11.47 0.00 0.00 4.20
1508 1550 2.229792 TGAATTAGCGCATGGAATCCC 58.770 47.619 11.47 0.77 0.00 3.85
1509 1551 3.988379 TTGAATTAGCGCATGGAATCC 57.012 42.857 11.47 0.00 0.00 3.01
1510 1552 3.732721 GCTTTGAATTAGCGCATGGAATC 59.267 43.478 11.47 0.14 0.00 2.52
1511 1553 3.130869 TGCTTTGAATTAGCGCATGGAAT 59.869 39.130 11.47 0.02 41.54 3.01
1512 1554 2.491298 TGCTTTGAATTAGCGCATGGAA 59.509 40.909 11.47 0.00 41.54 3.53
1513 1555 2.090760 TGCTTTGAATTAGCGCATGGA 58.909 42.857 11.47 0.00 41.54 3.41
1514 1556 2.159338 ACTGCTTTGAATTAGCGCATGG 60.159 45.455 11.47 0.00 41.54 3.66
1515 1557 3.103738 GACTGCTTTGAATTAGCGCATG 58.896 45.455 11.47 0.00 41.54 4.06
1516 1558 2.098117 GGACTGCTTTGAATTAGCGCAT 59.902 45.455 11.47 0.00 41.54 4.73
1517 1559 1.468520 GGACTGCTTTGAATTAGCGCA 59.531 47.619 11.47 0.00 41.54 6.09
1518 1560 1.468520 TGGACTGCTTTGAATTAGCGC 59.531 47.619 0.00 0.00 41.54 5.92
1519 1561 2.744202 AGTGGACTGCTTTGAATTAGCG 59.256 45.455 0.00 0.00 41.54 4.26
1520 1562 5.178797 TCTAGTGGACTGCTTTGAATTAGC 58.821 41.667 0.00 0.00 39.10 3.09
1521 1563 7.201679 CCATTCTAGTGGACTGCTTTGAATTAG 60.202 40.741 0.00 0.00 42.02 1.73
1522 1564 6.599244 CCATTCTAGTGGACTGCTTTGAATTA 59.401 38.462 0.00 0.00 42.02 1.40
1523 1565 5.416952 CCATTCTAGTGGACTGCTTTGAATT 59.583 40.000 0.00 0.00 42.02 2.17
1524 1566 4.946157 CCATTCTAGTGGACTGCTTTGAAT 59.054 41.667 0.00 0.00 42.02 2.57
1525 1567 4.326826 CCATTCTAGTGGACTGCTTTGAA 58.673 43.478 0.00 0.00 42.02 2.69
1526 1568 3.307691 CCCATTCTAGTGGACTGCTTTGA 60.308 47.826 0.91 0.00 42.02 2.69
1527 1569 3.012518 CCCATTCTAGTGGACTGCTTTG 58.987 50.000 0.91 0.00 42.02 2.77
1528 1570 2.619074 GCCCATTCTAGTGGACTGCTTT 60.619 50.000 0.91 0.00 42.02 3.51
1529 1571 1.065126 GCCCATTCTAGTGGACTGCTT 60.065 52.381 0.91 0.00 42.02 3.91
1530 1572 0.543749 GCCCATTCTAGTGGACTGCT 59.456 55.000 0.91 0.00 42.02 4.24
1531 1573 0.811616 CGCCCATTCTAGTGGACTGC 60.812 60.000 0.91 0.00 42.02 4.40
1532 1574 0.537188 ACGCCCATTCTAGTGGACTG 59.463 55.000 0.91 0.00 42.02 3.51
1533 1575 0.537188 CACGCCCATTCTAGTGGACT 59.463 55.000 0.91 0.00 42.02 3.85
1534 1576 0.249398 ACACGCCCATTCTAGTGGAC 59.751 55.000 0.91 0.00 42.02 4.02
1535 1577 1.855295 TACACGCCCATTCTAGTGGA 58.145 50.000 0.91 0.00 42.02 4.02
1536 1578 2.550978 CTTACACGCCCATTCTAGTGG 58.449 52.381 0.00 0.00 38.78 4.00
1537 1579 2.167693 TCCTTACACGCCCATTCTAGTG 59.832 50.000 0.00 0.00 40.17 2.74
1538 1580 2.167900 GTCCTTACACGCCCATTCTAGT 59.832 50.000 0.00 0.00 0.00 2.57
1539 1581 2.431057 AGTCCTTACACGCCCATTCTAG 59.569 50.000 0.00 0.00 0.00 2.43
1540 1582 2.429610 GAGTCCTTACACGCCCATTCTA 59.570 50.000 0.00 0.00 0.00 2.10
1541 1583 1.207329 GAGTCCTTACACGCCCATTCT 59.793 52.381 0.00 0.00 0.00 2.40
1542 1584 1.653151 GAGTCCTTACACGCCCATTC 58.347 55.000 0.00 0.00 0.00 2.67
1543 1585 0.252197 GGAGTCCTTACACGCCCATT 59.748 55.000 0.41 0.00 30.27 3.16
1544 1586 0.907704 TGGAGTCCTTACACGCCCAT 60.908 55.000 11.33 0.00 35.45 4.00
1545 1587 1.534476 TGGAGTCCTTACACGCCCA 60.534 57.895 11.33 0.00 35.45 5.36
1546 1588 1.218316 CTGGAGTCCTTACACGCCC 59.782 63.158 11.33 0.00 35.45 6.13
1547 1589 0.824759 ATCTGGAGTCCTTACACGCC 59.175 55.000 11.33 0.00 36.80 5.68
1548 1590 2.674796 AATCTGGAGTCCTTACACGC 57.325 50.000 11.33 0.00 0.00 5.34
1549 1591 4.188247 TGAAATCTGGAGTCCTTACACG 57.812 45.455 11.33 0.00 0.00 4.49
1550 1592 5.163713 GCAATGAAATCTGGAGTCCTTACAC 60.164 44.000 11.33 0.00 0.00 2.90
1551 1593 4.943705 GCAATGAAATCTGGAGTCCTTACA 59.056 41.667 11.33 2.99 0.00 2.41
1552 1594 4.336713 GGCAATGAAATCTGGAGTCCTTAC 59.663 45.833 11.33 0.00 0.00 2.34
1553 1595 4.018506 TGGCAATGAAATCTGGAGTCCTTA 60.019 41.667 11.33 0.00 0.00 2.69
1554 1596 3.245371 TGGCAATGAAATCTGGAGTCCTT 60.245 43.478 11.33 0.00 0.00 3.36
1555 1597 2.309755 TGGCAATGAAATCTGGAGTCCT 59.690 45.455 11.33 0.00 0.00 3.85
1556 1598 2.424956 GTGGCAATGAAATCTGGAGTCC 59.575 50.000 0.73 0.73 0.00 3.85
1557 1599 3.350833 AGTGGCAATGAAATCTGGAGTC 58.649 45.455 0.00 0.00 0.00 3.36
1558 1600 3.446442 AGTGGCAATGAAATCTGGAGT 57.554 42.857 0.00 0.00 0.00 3.85
1559 1601 4.796038 AAAGTGGCAATGAAATCTGGAG 57.204 40.909 0.00 0.00 0.00 3.86
1560 1602 4.588106 TCAAAAGTGGCAATGAAATCTGGA 59.412 37.500 0.00 0.00 0.00 3.86
1561 1603 4.885413 TCAAAAGTGGCAATGAAATCTGG 58.115 39.130 0.00 0.00 0.00 3.86
1562 1604 6.565247 GCTTTCAAAAGTGGCAATGAAATCTG 60.565 38.462 15.02 8.45 40.03 2.90
1563 1605 5.467735 GCTTTCAAAAGTGGCAATGAAATCT 59.532 36.000 15.02 0.00 40.03 2.40
1564 1606 5.236911 TGCTTTCAAAAGTGGCAATGAAATC 59.763 36.000 15.02 12.70 40.03 2.17
1565 1607 5.124645 TGCTTTCAAAAGTGGCAATGAAAT 58.875 33.333 15.02 0.00 40.03 2.17
1566 1608 4.511527 TGCTTTCAAAAGTGGCAATGAAA 58.488 34.783 14.32 14.32 38.92 2.69
1567 1609 4.134379 TGCTTTCAAAAGTGGCAATGAA 57.866 36.364 4.54 0.00 38.28 2.57
1568 1610 3.815856 TGCTTTCAAAAGTGGCAATGA 57.184 38.095 4.54 0.00 38.28 2.57
1569 1611 3.434299 GGATGCTTTCAAAAGTGGCAATG 59.566 43.478 4.54 0.00 38.28 2.82
1570 1612 3.071312 TGGATGCTTTCAAAAGTGGCAAT 59.929 39.130 4.54 0.00 38.28 3.56
1571 1613 2.433604 TGGATGCTTTCAAAAGTGGCAA 59.566 40.909 4.54 0.00 38.28 4.52
1572 1614 2.037901 TGGATGCTTTCAAAAGTGGCA 58.962 42.857 4.54 0.00 38.28 4.92
1573 1615 2.036346 AGTGGATGCTTTCAAAAGTGGC 59.964 45.455 4.54 0.00 38.28 5.01
1574 1616 4.520492 ACTAGTGGATGCTTTCAAAAGTGG 59.480 41.667 0.00 0.00 38.28 4.00
1575 1617 5.695851 ACTAGTGGATGCTTTCAAAAGTG 57.304 39.130 0.00 0.00 38.28 3.16
1576 1618 5.241728 GGAACTAGTGGATGCTTTCAAAAGT 59.758 40.000 0.00 0.00 38.28 2.66
1577 1619 5.241506 TGGAACTAGTGGATGCTTTCAAAAG 59.758 40.000 0.00 0.00 39.03 2.27
1578 1620 5.136828 TGGAACTAGTGGATGCTTTCAAAA 58.863 37.500 0.00 0.00 0.00 2.44
1579 1621 4.724399 TGGAACTAGTGGATGCTTTCAAA 58.276 39.130 0.00 0.00 0.00 2.69
1580 1622 4.326826 CTGGAACTAGTGGATGCTTTCAA 58.673 43.478 0.00 0.00 0.00 2.69
1581 1623 3.307691 CCTGGAACTAGTGGATGCTTTCA 60.308 47.826 0.00 0.00 0.00 2.69
1582 1624 3.274288 CCTGGAACTAGTGGATGCTTTC 58.726 50.000 0.00 0.00 0.00 2.62
1583 1625 2.619074 GCCTGGAACTAGTGGATGCTTT 60.619 50.000 0.00 0.00 0.00 3.51
1584 1626 1.065126 GCCTGGAACTAGTGGATGCTT 60.065 52.381 0.00 0.00 0.00 3.91
1585 1627 0.543749 GCCTGGAACTAGTGGATGCT 59.456 55.000 0.00 0.00 0.00 3.79
1586 1628 0.253044 TGCCTGGAACTAGTGGATGC 59.747 55.000 0.00 0.00 0.00 3.91
1587 1629 2.787473 TTGCCTGGAACTAGTGGATG 57.213 50.000 0.00 0.00 0.00 3.51
1588 1630 2.846206 TGATTGCCTGGAACTAGTGGAT 59.154 45.455 0.00 0.00 0.00 3.41
1589 1631 2.237143 CTGATTGCCTGGAACTAGTGGA 59.763 50.000 0.00 0.00 0.00 4.02
1590 1632 2.237143 TCTGATTGCCTGGAACTAGTGG 59.763 50.000 0.00 0.00 0.00 4.00
1591 1633 3.616956 TCTGATTGCCTGGAACTAGTG 57.383 47.619 0.00 0.00 0.00 2.74
1592 1634 4.384647 GGAATCTGATTGCCTGGAACTAGT 60.385 45.833 7.78 0.00 0.00 2.57
1593 1635 4.133078 GGAATCTGATTGCCTGGAACTAG 58.867 47.826 7.78 0.00 0.00 2.57
1594 1636 3.523157 TGGAATCTGATTGCCTGGAACTA 59.477 43.478 17.58 0.00 0.00 2.24
1595 1637 2.309755 TGGAATCTGATTGCCTGGAACT 59.690 45.455 17.58 0.00 0.00 3.01
1596 1638 2.424956 GTGGAATCTGATTGCCTGGAAC 59.575 50.000 17.58 6.51 0.00 3.62
1597 1639 2.309755 AGTGGAATCTGATTGCCTGGAA 59.690 45.455 17.58 0.00 0.00 3.53
1598 1640 1.918262 AGTGGAATCTGATTGCCTGGA 59.082 47.619 17.58 0.00 0.00 3.86
1599 1641 2.022195 CAGTGGAATCTGATTGCCTGG 58.978 52.381 21.40 9.48 37.61 4.45
1600 1642 2.719739 ACAGTGGAATCTGATTGCCTG 58.280 47.619 24.52 24.52 38.63 4.85
1601 1643 3.446442 AACAGTGGAATCTGATTGCCT 57.554 42.857 17.58 11.79 38.63 4.75
1602 1644 4.265073 AGTAACAGTGGAATCTGATTGCC 58.735 43.478 17.58 13.47 38.63 4.52
1603 1645 5.064452 CAGAGTAACAGTGGAATCTGATTGC 59.936 44.000 15.73 14.15 37.03 3.56
1604 1646 5.583854 CCAGAGTAACAGTGGAATCTGATTG 59.416 44.000 20.15 0.00 37.03 2.67
1605 1647 5.485353 TCCAGAGTAACAGTGGAATCTGATT 59.515 40.000 20.15 1.81 37.43 2.57
1606 1648 5.026121 TCCAGAGTAACAGTGGAATCTGAT 58.974 41.667 20.15 0.00 37.43 2.90
1607 1649 4.416516 TCCAGAGTAACAGTGGAATCTGA 58.583 43.478 20.15 8.57 37.43 3.27
1608 1650 4.808414 TCCAGAGTAACAGTGGAATCTG 57.192 45.455 14.46 14.46 37.43 2.90
1612 1654 4.262894 GGATGTTCCAGAGTAACAGTGGAA 60.263 45.833 5.05 5.05 46.01 3.53
1613 1655 3.260884 GGATGTTCCAGAGTAACAGTGGA 59.739 47.826 0.00 0.00 40.00 4.02
1614 1656 3.261897 AGGATGTTCCAGAGTAACAGTGG 59.738 47.826 0.00 0.00 40.00 4.00
1615 1657 4.221703 AGAGGATGTTCCAGAGTAACAGTG 59.778 45.833 0.00 0.00 40.00 3.66
1616 1658 4.421131 AGAGGATGTTCCAGAGTAACAGT 58.579 43.478 0.00 0.00 40.00 3.55
1617 1659 5.413309 AAGAGGATGTTCCAGAGTAACAG 57.587 43.478 0.00 0.00 40.00 3.16
1618 1660 5.306937 TGAAAGAGGATGTTCCAGAGTAACA 59.693 40.000 0.00 0.00 39.61 2.41
1619 1661 5.794894 TGAAAGAGGATGTTCCAGAGTAAC 58.205 41.667 0.00 0.00 39.61 2.50
1620 1662 6.433847 TTGAAAGAGGATGTTCCAGAGTAA 57.566 37.500 0.00 0.00 39.61 2.24
1621 1663 6.270000 TCTTTGAAAGAGGATGTTCCAGAGTA 59.730 38.462 3.02 0.00 39.61 2.59
1622 1664 4.982241 TTGAAAGAGGATGTTCCAGAGT 57.018 40.909 0.00 0.00 39.61 3.24
1623 1665 5.555017 TCTTTGAAAGAGGATGTTCCAGAG 58.445 41.667 3.02 0.00 39.61 3.35
1624 1666 5.567037 TCTTTGAAAGAGGATGTTCCAGA 57.433 39.130 3.02 0.00 39.61 3.86
1636 1678 4.999950 GGTCTGAAGATGCTCTTTGAAAGA 59.000 41.667 7.49 7.49 36.73 2.52
1637 1679 4.155644 GGGTCTGAAGATGCTCTTTGAAAG 59.844 45.833 0.00 0.00 36.73 2.62
1638 1680 4.074970 GGGTCTGAAGATGCTCTTTGAAA 58.925 43.478 0.86 0.00 36.73 2.69
1639 1681 3.560025 GGGGTCTGAAGATGCTCTTTGAA 60.560 47.826 0.86 0.00 36.73 2.69
1640 1682 2.026822 GGGGTCTGAAGATGCTCTTTGA 60.027 50.000 0.86 1.26 36.73 2.69
1641 1683 2.363683 GGGGTCTGAAGATGCTCTTTG 58.636 52.381 0.86 0.00 36.73 2.77
1642 1684 1.065854 CGGGGTCTGAAGATGCTCTTT 60.066 52.381 0.86 0.00 36.73 2.52
1643 1685 0.539051 CGGGGTCTGAAGATGCTCTT 59.461 55.000 0.00 0.00 39.87 2.85
1644 1686 0.616111 ACGGGGTCTGAAGATGCTCT 60.616 55.000 0.00 0.00 0.00 4.09
1645 1687 0.250513 AACGGGGTCTGAAGATGCTC 59.749 55.000 0.00 0.00 0.00 4.26
1646 1688 0.693049 AAACGGGGTCTGAAGATGCT 59.307 50.000 0.00 0.00 0.00 3.79
1647 1689 1.534729 AAAACGGGGTCTGAAGATGC 58.465 50.000 0.00 0.00 0.00 3.91
1648 1690 3.684788 CAGTAAAACGGGGTCTGAAGATG 59.315 47.826 0.00 0.00 0.00 2.90
1649 1691 3.868754 GCAGTAAAACGGGGTCTGAAGAT 60.869 47.826 0.00 0.00 0.00 2.40
1650 1692 2.549349 GCAGTAAAACGGGGTCTGAAGA 60.549 50.000 0.00 0.00 0.00 2.87
1651 1693 1.804748 GCAGTAAAACGGGGTCTGAAG 59.195 52.381 0.00 0.00 0.00 3.02
1652 1694 1.141254 TGCAGTAAAACGGGGTCTGAA 59.859 47.619 0.00 0.00 0.00 3.02
1653 1695 0.759959 TGCAGTAAAACGGGGTCTGA 59.240 50.000 0.00 0.00 0.00 3.27
1654 1696 1.535462 CTTGCAGTAAAACGGGGTCTG 59.465 52.381 0.00 0.00 0.00 3.51
1655 1697 1.892209 CTTGCAGTAAAACGGGGTCT 58.108 50.000 0.00 0.00 0.00 3.85
1656 1698 0.240145 GCTTGCAGTAAAACGGGGTC 59.760 55.000 0.00 0.00 0.00 4.46
1657 1699 1.512156 CGCTTGCAGTAAAACGGGGT 61.512 55.000 0.00 0.00 0.00 4.95
1658 1700 1.209127 CGCTTGCAGTAAAACGGGG 59.791 57.895 0.00 0.00 0.00 5.73
1659 1701 1.442017 GCGCTTGCAGTAAAACGGG 60.442 57.895 0.00 0.00 38.92 5.28
1660 1702 1.442017 GGCGCTTGCAGTAAAACGG 60.442 57.895 7.64 0.00 41.71 4.44
1661 1703 0.452784 GAGGCGCTTGCAGTAAAACG 60.453 55.000 7.64 0.00 41.71 3.60
1662 1704 0.875059 AGAGGCGCTTGCAGTAAAAC 59.125 50.000 7.64 0.00 41.71 2.43
1663 1705 0.874390 CAGAGGCGCTTGCAGTAAAA 59.126 50.000 7.64 0.00 41.71 1.52
1664 1706 1.577328 GCAGAGGCGCTTGCAGTAAA 61.577 55.000 21.21 0.00 41.71 2.01
1665 1707 2.034879 GCAGAGGCGCTTGCAGTAA 61.035 57.895 21.21 0.00 41.71 2.24
1666 1708 2.434884 GCAGAGGCGCTTGCAGTA 60.435 61.111 21.21 0.00 41.71 2.74
1676 1718 4.261801 TGTTTGAGGTTAATAGCAGAGGC 58.738 43.478 0.00 0.00 41.61 4.70
1677 1719 5.582665 GTCTGTTTGAGGTTAATAGCAGAGG 59.417 44.000 0.00 0.00 33.22 3.69
1678 1720 5.289675 CGTCTGTTTGAGGTTAATAGCAGAG 59.710 44.000 0.00 0.00 33.22 3.35
1679 1721 5.168569 CGTCTGTTTGAGGTTAATAGCAGA 58.831 41.667 0.00 0.00 0.00 4.26
1680 1722 4.201724 GCGTCTGTTTGAGGTTAATAGCAG 60.202 45.833 0.00 0.00 33.47 4.24
1681 1723 3.682858 GCGTCTGTTTGAGGTTAATAGCA 59.317 43.478 0.00 0.00 33.47 3.49
1682 1724 3.241995 CGCGTCTGTTTGAGGTTAATAGC 60.242 47.826 0.00 0.00 33.47 2.97
1683 1725 3.306166 CCGCGTCTGTTTGAGGTTAATAG 59.694 47.826 4.92 0.00 33.47 1.73
1684 1726 3.255725 CCGCGTCTGTTTGAGGTTAATA 58.744 45.455 4.92 0.00 33.47 0.98
1685 1727 2.073816 CCGCGTCTGTTTGAGGTTAAT 58.926 47.619 4.92 0.00 33.47 1.40
1717 1759 1.301401 TTTGCCACGAGAAGGTCCG 60.301 57.895 0.00 0.00 0.00 4.79
1719 1761 1.002792 GTTGTTTGCCACGAGAAGGTC 60.003 52.381 0.00 0.00 0.00 3.85
1898 1942 1.823169 TTGGGAGTAGACGTGTGGGC 61.823 60.000 0.00 0.00 0.00 5.36
2343 2387 4.253685 CTCGTCCATCTCTCTATCTCTCC 58.746 52.174 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.