Multiple sequence alignment - TraesCS7B01G013100

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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 TraesCS7B01G013100 chr7B 100.000 3258 0 0 1 3258 9701478 9704735 0.000000e+00 6017
1 TraesCS7B01G013100 chr7D 94.004 1401 53 15 1784 3170 68416977 68415594 0.000000e+00 2093
2 TraesCS7B01G013100 chr7D 90.236 1567 81 37 1 1508 68418557 68417004 0.000000e+00 1980
3 TraesCS7B01G013100 chr7A 90.798 1554 65 41 1 1507 71668852 71670374 0.000000e+00 2006
4 TraesCS7B01G013100 chr7A 91.990 1161 38 19 1784 2904 71670399 71671544 0.000000e+00 1578
5 TraesCS7B01G013100 chr3B 98.155 271 3 1 1502 1770 782679636 782679906 3.800000e-129 472
6 TraesCS7B01G013100 chr3B 94.361 266 13 1 1505 1768 564249934 564250199 1.090000e-109 407
7 TraesCS7B01G013100 chr3B 85.253 217 32 0 2034 2250 158716006 158715790 1.180000e-54 224
8 TraesCS7B01G013100 chr5A 97.070 273 5 2 1502 1772 686507720 686507991 1.070000e-124 457
9 TraesCS7B01G013100 chr4A 97.727 264 4 1 1505 1766 694884932 694884669 1.380000e-123 453
10 TraesCS7B01G013100 chr4A 96.970 264 6 1 1506 1767 669675757 669676020 2.980000e-120 442
11 TraesCS7B01G013100 chr5B 97.719 263 4 1 1506 1766 100551543 100551281 4.960000e-123 451
12 TraesCS7B01G013100 chr1A 95.896 268 8 2 1505 1769 550727639 550727372 6.460000e-117 431
13 TraesCS7B01G013100 chr1B 95.455 264 8 2 1506 1767 522355992 522355731 5.030000e-113 418
14 TraesCS7B01G013100 chr2B 94.182 275 12 3 1503 1774 104069831 104069558 1.810000e-112 416
15 TraesCS7B01G013100 chr3D 85.253 217 32 0 2034 2250 107678837 107678621 1.180000e-54 224


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 TraesCS7B01G013100 chr7B 9701478 9704735 3257 False 6017.0 6017 100.000 1 3258 1 chr7B.!!$F1 3257
1 TraesCS7B01G013100 chr7D 68415594 68418557 2963 True 2036.5 2093 92.120 1 3170 2 chr7D.!!$R1 3169
2 TraesCS7B01G013100 chr7A 71668852 71671544 2692 False 1792.0 2006 91.394 1 2904 2 chr7A.!!$F1 2903

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
961 1026 0.032267 CGTACCCTAGCTAGCAAGGC 59.968 60.0 18.83 3.29 0.00 4.35 F
1764 1858 0.033796 TATTCGTGGACGGAGGGAGT 60.034 55.0 0.00 0.00 40.29 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2060 0.173708 TGTAGACACACACACGCACA 59.826 50.0 0.0 0.0 0.00 4.57 R
3107 3263 0.105760 TCAAGCCAAGGCCAGGAAAA 60.106 50.0 17.7 0.0 43.17 2.29 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
138 145 2.363795 ATCGTCCTTGAGCCGGGA 60.364 61.111 2.18 0.00 0.00 5.14
174 181 8.964476 ATATATATTCTCGCGGGAAAATGATT 57.036 30.769 27.43 10.71 0.00 2.57
268 291 1.433053 CTTTCCGACCACGCACACAA 61.433 55.000 0.00 0.00 38.29 3.33
286 309 2.694628 ACAACCAGCAGCAAGAATGAAA 59.305 40.909 0.00 0.00 0.00 2.69
450 477 0.453390 CAAATCGAGCCAAGGAAGCC 59.547 55.000 0.00 0.00 0.00 4.35
470 497 4.373116 CACCCCAGTCACCGTCGG 62.373 72.222 10.48 10.48 0.00 4.79
583 610 3.958147 CTACACCCCAGCAGGCACG 62.958 68.421 0.00 0.00 0.00 5.34
703 755 2.281208 GCTGCCGGTTACACCACA 60.281 61.111 1.90 0.00 38.47 4.17
719 771 2.892852 ACCACATCCACAGAACCAATTG 59.107 45.455 0.00 0.00 0.00 2.32
829 891 2.694065 CATGGACATGTACCCTGCG 58.306 57.895 5.38 0.00 34.23 5.18
927 989 2.909504 TACTCCTGCTCCAGAGAACT 57.090 50.000 0.00 0.00 32.44 3.01
946 1011 0.670546 TTCTGCTTGCTGCCTCGTAC 60.671 55.000 0.00 0.00 42.00 3.67
958 1023 1.688772 CCTCGTACCCTAGCTAGCAA 58.311 55.000 18.83 0.00 0.00 3.91
959 1024 1.609555 CCTCGTACCCTAGCTAGCAAG 59.390 57.143 18.83 8.50 0.00 4.01
960 1025 1.609555 CTCGTACCCTAGCTAGCAAGG 59.390 57.143 18.83 16.15 0.00 3.61
961 1026 0.032267 CGTACCCTAGCTAGCAAGGC 59.968 60.000 18.83 3.29 0.00 4.35
962 1027 1.120530 GTACCCTAGCTAGCAAGGCA 58.879 55.000 18.83 1.78 0.00 4.75
963 1028 1.485066 GTACCCTAGCTAGCAAGGCAA 59.515 52.381 18.83 3.60 0.00 4.52
964 1029 0.543749 ACCCTAGCTAGCAAGGCAAG 59.456 55.000 18.83 4.08 0.00 4.01
965 1030 0.817229 CCCTAGCTAGCAAGGCAAGC 60.817 60.000 18.83 0.00 0.00 4.01
966 1031 0.179936 CCTAGCTAGCAAGGCAAGCT 59.820 55.000 18.83 8.71 45.77 3.74
986 1054 3.556775 GCTAGCCGGTCGATCTATACTAG 59.443 52.174 2.29 2.11 0.00 2.57
997 1065 4.399934 CGATCTATACTAGGAAGGAAGGGC 59.600 50.000 0.00 0.00 0.00 5.19
998 1066 5.585894 GATCTATACTAGGAAGGAAGGGCT 58.414 45.833 0.00 0.00 0.00 5.19
1014 1082 2.067197 GCTAATGGCCGGTAGGGAT 58.933 57.895 1.90 0.00 38.47 3.85
1228 1296 5.449999 CGTACACAGTCACTATCTAATGCCA 60.450 44.000 0.00 0.00 0.00 4.92
1231 1299 6.418101 ACACAGTCACTATCTAATGCCAATT 58.582 36.000 0.00 0.00 0.00 2.32
1249 1325 5.124457 GCCAATTTATCTCTGAAAGTGCTCA 59.876 40.000 0.00 0.00 32.07 4.26
1276 1352 1.325647 CACATGATCGATCGAGCTCG 58.674 55.000 30.86 30.03 39.99 5.03
1291 1369 3.919197 CGAGCTCGATCTATAGTACGTGA 59.081 47.826 32.06 0.00 43.02 4.35
1297 1375 5.614308 TCGATCTATAGTACGTGAGGGAAA 58.386 41.667 16.04 0.00 0.00 3.13
1298 1376 6.236409 TCGATCTATAGTACGTGAGGGAAAT 58.764 40.000 16.04 0.00 0.00 2.17
1304 1382 8.701895 TCTATAGTACGTGAGGGAAATTGATTT 58.298 33.333 0.00 0.00 0.00 2.17
1329 1410 3.082698 TGCTTCTGTTCACATGTTTGC 57.917 42.857 0.00 0.00 0.00 3.68
1332 1413 3.854784 GCTTCTGTTCACATGTTTGCCTC 60.855 47.826 0.00 0.00 0.00 4.70
1333 1414 2.929641 TCTGTTCACATGTTTGCCTCA 58.070 42.857 0.00 0.00 0.00 3.86
1377 1458 2.910199 TCTTGCATATGTCTCTGTGCC 58.090 47.619 4.29 0.00 36.79 5.01
1400 1485 5.186409 CCCTCTGGTGTTGATCATGATTTTT 59.814 40.000 10.14 0.00 0.00 1.94
1425 1515 2.168521 TGCTTCTTCTATGTTCGGGGAG 59.831 50.000 0.00 0.00 0.00 4.30
1430 1520 3.199946 TCTTCTATGTTCGGGGAGCATTT 59.800 43.478 0.37 0.00 35.31 2.32
1436 1526 5.675684 ATGTTCGGGGAGCATTTATTTTT 57.324 34.783 0.00 0.00 29.54 1.94
1483 1577 0.038251 TGTCCTAGCAAGCACACGAG 60.038 55.000 0.00 0.00 0.00 4.18
1513 1607 9.953697 TTAAAGCTCGATCTTAAATACTCTCTC 57.046 33.333 1.27 0.00 0.00 3.20
1514 1608 6.569179 AGCTCGATCTTAAATACTCTCTCC 57.431 41.667 0.00 0.00 0.00 3.71
1515 1609 5.180492 AGCTCGATCTTAAATACTCTCTCCG 59.820 44.000 0.00 0.00 0.00 4.63
1516 1610 5.049267 GCTCGATCTTAAATACTCTCTCCGT 60.049 44.000 0.00 0.00 0.00 4.69
1517 1611 6.542574 TCGATCTTAAATACTCTCTCCGTC 57.457 41.667 0.00 0.00 0.00 4.79
1518 1612 5.469421 TCGATCTTAAATACTCTCTCCGTCC 59.531 44.000 0.00 0.00 0.00 4.79
1519 1613 5.615106 CGATCTTAAATACTCTCTCCGTCCG 60.615 48.000 0.00 0.00 0.00 4.79
1520 1614 4.774124 TCTTAAATACTCTCTCCGTCCGA 58.226 43.478 0.00 0.00 0.00 4.55
1521 1615 5.188434 TCTTAAATACTCTCTCCGTCCGAA 58.812 41.667 0.00 0.00 0.00 4.30
1522 1616 5.826737 TCTTAAATACTCTCTCCGTCCGAAT 59.173 40.000 0.00 0.00 0.00 3.34
1523 1617 6.994496 TCTTAAATACTCTCTCCGTCCGAATA 59.006 38.462 0.00 0.00 0.00 1.75
1524 1618 7.500227 TCTTAAATACTCTCTCCGTCCGAATAA 59.500 37.037 0.00 0.00 0.00 1.40
1525 1619 6.461110 AAATACTCTCTCCGTCCGAATAAA 57.539 37.500 0.00 0.00 0.00 1.40
1526 1620 6.651975 AATACTCTCTCCGTCCGAATAAAT 57.348 37.500 0.00 0.00 0.00 1.40
1527 1621 4.308899 ACTCTCTCCGTCCGAATAAATG 57.691 45.455 0.00 0.00 0.00 2.32
1528 1622 3.700038 ACTCTCTCCGTCCGAATAAATGT 59.300 43.478 0.00 0.00 0.00 2.71
1529 1623 4.885907 ACTCTCTCCGTCCGAATAAATGTA 59.114 41.667 0.00 0.00 0.00 2.29
1530 1624 5.179045 TCTCTCCGTCCGAATAAATGTAC 57.821 43.478 0.00 0.00 0.00 2.90
1531 1625 4.885907 TCTCTCCGTCCGAATAAATGTACT 59.114 41.667 0.00 0.00 0.00 2.73
1532 1626 5.359009 TCTCTCCGTCCGAATAAATGTACTT 59.641 40.000 0.00 0.00 0.00 2.24
1533 1627 5.585390 TCTCCGTCCGAATAAATGTACTTC 58.415 41.667 0.00 0.00 0.00 3.01
1534 1628 5.359009 TCTCCGTCCGAATAAATGTACTTCT 59.641 40.000 0.00 0.00 0.00 2.85
1535 1629 6.543465 TCTCCGTCCGAATAAATGTACTTCTA 59.457 38.462 0.00 0.00 0.00 2.10
1536 1630 6.732154 TCCGTCCGAATAAATGTACTTCTAG 58.268 40.000 0.00 0.00 0.00 2.43
1537 1631 5.401674 CCGTCCGAATAAATGTACTTCTAGC 59.598 44.000 0.00 0.00 0.00 3.42
1538 1632 6.207213 CGTCCGAATAAATGTACTTCTAGCT 58.793 40.000 0.00 0.00 0.00 3.32
1539 1633 6.696148 CGTCCGAATAAATGTACTTCTAGCTT 59.304 38.462 0.00 0.00 0.00 3.74
1540 1634 7.222224 CGTCCGAATAAATGTACTTCTAGCTTT 59.778 37.037 0.00 0.00 0.00 3.51
1541 1635 8.880750 GTCCGAATAAATGTACTTCTAGCTTTT 58.119 33.333 0.00 0.00 0.00 2.27
1542 1636 8.879759 TCCGAATAAATGTACTTCTAGCTTTTG 58.120 33.333 0.00 0.00 0.00 2.44
1543 1637 8.665685 CCGAATAAATGTACTTCTAGCTTTTGT 58.334 33.333 0.00 0.00 0.00 2.83
1544 1638 9.690434 CGAATAAATGTACTTCTAGCTTTTGTC 57.310 33.333 0.00 0.00 0.00 3.18
1550 1644 9.780186 AATGTACTTCTAGCTTTTGTCTTAAGT 57.220 29.630 1.63 0.00 0.00 2.24
1551 1645 8.813643 TGTACTTCTAGCTTTTGTCTTAAGTC 57.186 34.615 1.63 0.00 0.00 3.01
1552 1646 8.418662 TGTACTTCTAGCTTTTGTCTTAAGTCA 58.581 33.333 1.63 0.00 0.00 3.41
1553 1647 9.257651 GTACTTCTAGCTTTTGTCTTAAGTCAA 57.742 33.333 10.54 10.54 0.00 3.18
1554 1648 8.732746 ACTTCTAGCTTTTGTCTTAAGTCAAA 57.267 30.769 19.60 19.60 32.81 2.69
1555 1649 8.831550 ACTTCTAGCTTTTGTCTTAAGTCAAAG 58.168 33.333 21.47 17.68 35.29 2.77
1556 1650 8.732746 TTCTAGCTTTTGTCTTAAGTCAAAGT 57.267 30.769 21.47 15.13 35.29 2.66
1557 1651 8.732746 TCTAGCTTTTGTCTTAAGTCAAAGTT 57.267 30.769 21.47 17.02 35.29 2.66
1558 1652 9.174166 TCTAGCTTTTGTCTTAAGTCAAAGTTT 57.826 29.630 21.47 15.16 35.29 2.66
1559 1653 9.788960 CTAGCTTTTGTCTTAAGTCAAAGTTTT 57.211 29.630 21.47 13.93 35.29 2.43
1592 1686 8.331730 TGACCAACTTTATAGGAAAAAGTAGC 57.668 34.615 1.96 0.00 44.35 3.58
1593 1687 7.940137 TGACCAACTTTATAGGAAAAAGTAGCA 59.060 33.333 1.96 0.00 44.35 3.49
1594 1688 8.336801 ACCAACTTTATAGGAAAAAGTAGCAG 57.663 34.615 1.96 0.00 44.35 4.24
1595 1689 7.094334 ACCAACTTTATAGGAAAAAGTAGCAGC 60.094 37.037 1.96 0.00 44.35 5.25
1596 1690 7.094377 CCAACTTTATAGGAAAAAGTAGCAGCA 60.094 37.037 0.00 0.00 44.35 4.41
1597 1691 8.462016 CAACTTTATAGGAAAAAGTAGCAGCAT 58.538 33.333 0.00 0.00 44.35 3.79
1598 1692 8.581253 ACTTTATAGGAAAAAGTAGCAGCATT 57.419 30.769 0.00 0.00 43.54 3.56
1599 1693 9.025041 ACTTTATAGGAAAAAGTAGCAGCATTT 57.975 29.630 0.00 0.00 43.54 2.32
1603 1697 8.752005 ATAGGAAAAAGTAGCAGCATTTATGA 57.248 30.769 0.00 0.00 0.00 2.15
1604 1698 6.856895 AGGAAAAAGTAGCAGCATTTATGAC 58.143 36.000 0.00 0.00 0.00 3.06
1605 1699 6.434028 AGGAAAAAGTAGCAGCATTTATGACA 59.566 34.615 0.00 0.00 0.00 3.58
1606 1700 6.528072 GGAAAAAGTAGCAGCATTTATGACAC 59.472 38.462 0.00 0.00 0.00 3.67
1607 1701 6.824305 AAAAGTAGCAGCATTTATGACACT 57.176 33.333 0.00 0.00 0.00 3.55
1608 1702 7.921786 AAAAGTAGCAGCATTTATGACACTA 57.078 32.000 0.00 0.00 0.00 2.74
1609 1703 7.921786 AAAGTAGCAGCATTTATGACACTAA 57.078 32.000 0.00 0.00 0.00 2.24
1610 1704 7.921786 AAGTAGCAGCATTTATGACACTAAA 57.078 32.000 0.00 0.00 0.00 1.85
1611 1705 8.511604 AAGTAGCAGCATTTATGACACTAAAT 57.488 30.769 0.00 0.00 32.76 1.40
1612 1706 8.511604 AGTAGCAGCATTTATGACACTAAATT 57.488 30.769 0.00 0.00 30.68 1.82
1613 1707 9.613428 AGTAGCAGCATTTATGACACTAAATTA 57.387 29.630 0.00 0.00 30.68 1.40
1614 1708 9.869844 GTAGCAGCATTTATGACACTAAATTAG 57.130 33.333 0.00 0.00 30.68 1.73
1615 1709 8.511604 AGCAGCATTTATGACACTAAATTAGT 57.488 30.769 0.00 0.00 40.28 2.24
1616 1710 9.613428 AGCAGCATTTATGACACTAAATTAGTA 57.387 29.630 5.23 0.00 37.23 1.82
1639 1733 9.436957 AGTATCACTAGATTCGTTTTGAAATGT 57.563 29.630 0.00 0.00 40.71 2.71
1753 1847 8.530269 AAAACTAGAAGTACACTTATTCGTGG 57.470 34.615 0.00 0.00 39.19 4.94
1754 1848 7.458409 AACTAGAAGTACACTTATTCGTGGA 57.542 36.000 0.00 0.00 39.19 4.02
1755 1849 6.850555 ACTAGAAGTACACTTATTCGTGGAC 58.149 40.000 0.00 0.00 46.77 4.02
1758 1852 3.492421 GTACACTTATTCGTGGACGGA 57.508 47.619 0.00 0.00 38.82 4.69
1759 1853 2.649331 ACACTTATTCGTGGACGGAG 57.351 50.000 0.00 0.00 39.19 4.63
1760 1854 1.203994 ACACTTATTCGTGGACGGAGG 59.796 52.381 0.00 0.00 39.19 4.30
1761 1855 0.822164 ACTTATTCGTGGACGGAGGG 59.178 55.000 0.00 0.00 40.29 4.30
1762 1856 1.108776 CTTATTCGTGGACGGAGGGA 58.891 55.000 0.00 0.00 40.29 4.20
1763 1857 1.067212 CTTATTCGTGGACGGAGGGAG 59.933 57.143 0.00 0.00 40.29 4.30
1764 1858 0.033796 TATTCGTGGACGGAGGGAGT 60.034 55.000 0.00 0.00 40.29 3.85
1815 1919 0.374758 GATCATGATGTGCACGCGTT 59.625 50.000 14.30 0.00 0.00 4.84
1955 2059 6.887002 TCCCTAGATATACACACTAGCTCATG 59.113 42.308 0.00 0.00 34.21 3.07
1956 2060 6.661377 CCCTAGATATACACACTAGCTCATGT 59.339 42.308 0.00 0.00 34.21 3.21
2020 2144 2.740826 CCCGGTACAACTGGTGCG 60.741 66.667 0.00 0.00 43.22 5.34
2092 2216 2.126618 CACCGCTTCGTGCTCGTA 60.127 61.111 8.17 0.00 40.11 3.43
2110 2234 1.323271 TACTCTTCCAGCAGCTCGGG 61.323 60.000 10.08 2.16 0.00 5.14
2266 2390 5.930135 AGGATGTACAATTGATCTACCCAC 58.070 41.667 13.59 0.00 0.00 4.61
2285 2409 4.814294 GCCCTCGTACGCCACCAG 62.814 72.222 11.24 1.80 0.00 4.00
2373 2501 3.792124 GCCAGCCACGAATTAAGCATTAC 60.792 47.826 0.00 0.00 0.00 1.89
2509 2649 5.880164 TGGCTTGGTACTGCACTATATAA 57.120 39.130 0.00 0.00 0.00 0.98
2510 2650 6.241882 TGGCTTGGTACTGCACTATATAAA 57.758 37.500 0.00 0.00 0.00 1.40
2553 2693 4.837972 TGCCAATAGTATACAGCACACAA 58.162 39.130 5.50 0.00 0.00 3.33
2623 2770 0.819259 TCTGCAGGTTGGTCTTGTGC 60.819 55.000 15.13 0.00 34.62 4.57
2694 2841 3.505680 TGCATGGGAGACAAACATGTAAC 59.494 43.478 0.00 0.00 42.89 2.50
2730 2877 5.455849 GCTACAAGACACAGTGATATGTACG 59.544 44.000 7.81 7.99 0.00 3.67
2841 2988 1.251527 TGAGACCGGTGGCTTCTCTC 61.252 60.000 14.63 11.38 0.00 3.20
2842 2989 0.968393 GAGACCGGTGGCTTCTCTCT 60.968 60.000 14.63 0.00 0.00 3.10
2848 2995 1.066573 CGGTGGCTTCTCTCTGTGATT 60.067 52.381 0.00 0.00 0.00 2.57
2853 3000 5.049167 GTGGCTTCTCTCTGTGATTATGAG 58.951 45.833 0.00 0.00 0.00 2.90
2894 3045 4.318618 GCGCTCATCAATCTGTGTCTTATG 60.319 45.833 0.00 0.00 0.00 1.90
2898 3049 6.649973 GCTCATCAATCTGTGTCTTATGCTAT 59.350 38.462 0.00 0.00 0.00 2.97
2965 3116 4.750598 GCCGTCCTAGGTTTCAGAAATATC 59.249 45.833 9.08 0.00 0.00 1.63
3047 3199 5.635280 AGTGCAGATAATAATCGGTTCATCG 59.365 40.000 0.00 0.00 37.19 3.84
3053 3205 1.835121 TAATCGGTTCATCGTCAGCG 58.165 50.000 0.00 0.00 39.92 5.18
3083 3235 4.201920 GCCTTTTCGAACTTCAAAGTGAGT 60.202 41.667 0.00 0.00 39.66 3.41
3097 3253 9.737427 CTTCAAAGTGAGTATATATCGACAACT 57.263 33.333 0.00 0.00 0.00 3.16
3099 3255 9.731819 TCAAAGTGAGTATATATCGACAACTTC 57.268 33.333 0.00 0.00 29.54 3.01
3113 3269 7.619964 TCGACAACTTCTTTAACTTTTTCCT 57.380 32.000 0.00 0.00 0.00 3.36
3119 3275 5.661312 ACTTCTTTAACTTTTTCCTGGCCTT 59.339 36.000 3.32 0.00 0.00 4.35
3126 3282 0.105760 TTTTCCTGGCCTTGGCTTGA 60.106 50.000 11.71 3.27 0.00 3.02
3129 3285 0.612732 TCCTGGCCTTGGCTTGATTG 60.613 55.000 11.71 0.00 0.00 2.67
3136 3292 2.353109 GCCTTGGCTTGATTGGACTTTC 60.353 50.000 4.11 0.00 0.00 2.62
3147 3303 2.175878 TGGACTTTCTCAGCTCTTGC 57.824 50.000 0.00 0.00 40.05 4.01
3170 3326 4.214310 CATTCAGCTTCCTCTCTCCTCTA 58.786 47.826 0.00 0.00 0.00 2.43
3171 3327 3.290948 TCAGCTTCCTCTCTCCTCTAC 57.709 52.381 0.00 0.00 0.00 2.59
3172 3328 2.092103 TCAGCTTCCTCTCTCCTCTACC 60.092 54.545 0.00 0.00 0.00 3.18
3173 3329 1.216930 AGCTTCCTCTCTCCTCTACCC 59.783 57.143 0.00 0.00 0.00 3.69
3174 3330 1.975660 CTTCCTCTCTCCTCTACCCG 58.024 60.000 0.00 0.00 0.00 5.28
3175 3331 0.106619 TTCCTCTCTCCTCTACCCGC 60.107 60.000 0.00 0.00 0.00 6.13
3176 3332 1.227664 CCTCTCTCCTCTACCCGCA 59.772 63.158 0.00 0.00 0.00 5.69
3177 3333 0.395862 CCTCTCTCCTCTACCCGCAA 60.396 60.000 0.00 0.00 0.00 4.85
3178 3334 1.475403 CTCTCTCCTCTACCCGCAAA 58.525 55.000 0.00 0.00 0.00 3.68
3179 3335 1.825474 CTCTCTCCTCTACCCGCAAAA 59.175 52.381 0.00 0.00 0.00 2.44
3180 3336 2.233922 CTCTCTCCTCTACCCGCAAAAA 59.766 50.000 0.00 0.00 0.00 1.94
3204 3360 4.551702 AAAAAGCTTCCTCTCTCCTCTC 57.448 45.455 0.00 0.00 0.00 3.20
3205 3361 3.473113 AAAGCTTCCTCTCTCCTCTCT 57.527 47.619 0.00 0.00 0.00 3.10
3206 3362 2.736670 AGCTTCCTCTCTCCTCTCTC 57.263 55.000 0.00 0.00 0.00 3.20
3207 3363 1.922447 AGCTTCCTCTCTCCTCTCTCA 59.078 52.381 0.00 0.00 0.00 3.27
3208 3364 2.311542 AGCTTCCTCTCTCCTCTCTCAA 59.688 50.000 0.00 0.00 0.00 3.02
3209 3365 2.427095 GCTTCCTCTCTCCTCTCTCAAC 59.573 54.545 0.00 0.00 0.00 3.18
3210 3366 3.877735 GCTTCCTCTCTCCTCTCTCAACT 60.878 52.174 0.00 0.00 0.00 3.16
3211 3367 4.344104 CTTCCTCTCTCCTCTCTCAACTT 58.656 47.826 0.00 0.00 0.00 2.66
3212 3368 3.696045 TCCTCTCTCCTCTCTCAACTTG 58.304 50.000 0.00 0.00 0.00 3.16
3213 3369 3.075283 TCCTCTCTCCTCTCTCAACTTGT 59.925 47.826 0.00 0.00 0.00 3.16
3214 3370 3.443681 CCTCTCTCCTCTCTCAACTTGTC 59.556 52.174 0.00 0.00 0.00 3.18
3215 3371 4.335416 CTCTCTCCTCTCTCAACTTGTCT 58.665 47.826 0.00 0.00 0.00 3.41
3216 3372 4.735369 TCTCTCCTCTCTCAACTTGTCTT 58.265 43.478 0.00 0.00 0.00 3.01
3217 3373 5.144100 TCTCTCCTCTCTCAACTTGTCTTT 58.856 41.667 0.00 0.00 0.00 2.52
3218 3374 5.242838 TCTCTCCTCTCTCAACTTGTCTTTC 59.757 44.000 0.00 0.00 0.00 2.62
3219 3375 4.022762 TCTCCTCTCTCAACTTGTCTTTCG 60.023 45.833 0.00 0.00 0.00 3.46
3220 3376 3.005897 TCCTCTCTCAACTTGTCTTTCGG 59.994 47.826 0.00 0.00 0.00 4.30
3221 3377 3.243907 CCTCTCTCAACTTGTCTTTCGGT 60.244 47.826 0.00 0.00 0.00 4.69
3222 3378 4.022242 CCTCTCTCAACTTGTCTTTCGGTA 60.022 45.833 0.00 0.00 0.00 4.02
3223 3379 5.122512 TCTCTCAACTTGTCTTTCGGTAG 57.877 43.478 0.00 0.00 0.00 3.18
3224 3380 4.825634 TCTCTCAACTTGTCTTTCGGTAGA 59.174 41.667 0.00 0.00 0.00 2.59
3225 3381 5.477291 TCTCTCAACTTGTCTTTCGGTAGAT 59.523 40.000 0.00 0.00 0.00 1.98
3226 3382 5.470368 TCTCAACTTGTCTTTCGGTAGATG 58.530 41.667 0.00 0.00 0.00 2.90
3227 3383 4.566004 TCAACTTGTCTTTCGGTAGATGG 58.434 43.478 0.00 0.00 0.00 3.51
3228 3384 2.973945 ACTTGTCTTTCGGTAGATGGC 58.026 47.619 0.00 0.00 0.00 4.40
3229 3385 2.301870 ACTTGTCTTTCGGTAGATGGCA 59.698 45.455 0.00 0.00 0.00 4.92
3230 3386 3.055094 ACTTGTCTTTCGGTAGATGGCAT 60.055 43.478 0.00 0.00 0.00 4.40
3231 3387 3.627395 TGTCTTTCGGTAGATGGCATT 57.373 42.857 0.00 0.00 0.00 3.56
3232 3388 4.746535 TGTCTTTCGGTAGATGGCATTA 57.253 40.909 0.00 0.00 0.00 1.90
3233 3389 4.693283 TGTCTTTCGGTAGATGGCATTAG 58.307 43.478 0.00 0.00 0.00 1.73
3234 3390 4.058817 GTCTTTCGGTAGATGGCATTAGG 58.941 47.826 0.00 0.00 0.00 2.69
3235 3391 3.964688 TCTTTCGGTAGATGGCATTAGGA 59.035 43.478 0.00 0.00 0.00 2.94
3236 3392 4.407621 TCTTTCGGTAGATGGCATTAGGAA 59.592 41.667 0.00 0.00 0.00 3.36
3237 3393 4.336889 TTCGGTAGATGGCATTAGGAAG 57.663 45.455 0.00 0.00 0.00 3.46
3238 3394 3.305720 TCGGTAGATGGCATTAGGAAGT 58.694 45.455 0.00 0.00 0.00 3.01
3239 3395 4.476297 TCGGTAGATGGCATTAGGAAGTA 58.524 43.478 0.00 0.00 0.00 2.24
3240 3396 4.523173 TCGGTAGATGGCATTAGGAAGTAG 59.477 45.833 0.00 0.00 0.00 2.57
3241 3397 4.322049 CGGTAGATGGCATTAGGAAGTAGG 60.322 50.000 0.00 0.00 0.00 3.18
3242 3398 4.020128 GGTAGATGGCATTAGGAAGTAGGG 60.020 50.000 0.00 0.00 0.00 3.53
3243 3399 2.373502 AGATGGCATTAGGAAGTAGGGC 59.626 50.000 0.00 0.00 0.00 5.19
3244 3400 1.893315 TGGCATTAGGAAGTAGGGCT 58.107 50.000 0.00 0.00 0.00 5.19
3245 3401 1.768870 TGGCATTAGGAAGTAGGGCTC 59.231 52.381 0.00 0.00 0.00 4.70
3246 3402 1.072489 GGCATTAGGAAGTAGGGCTCC 59.928 57.143 0.00 0.00 0.00 4.70
3247 3403 1.768870 GCATTAGGAAGTAGGGCTCCA 59.231 52.381 0.00 0.00 0.00 3.86
3248 3404 2.373502 GCATTAGGAAGTAGGGCTCCAT 59.626 50.000 0.00 0.00 0.00 3.41
3249 3405 3.808618 GCATTAGGAAGTAGGGCTCCATG 60.809 52.174 0.00 0.00 0.00 3.66
3250 3406 1.424638 TAGGAAGTAGGGCTCCATGC 58.575 55.000 0.00 0.00 41.94 4.06
3251 3407 0.327000 AGGAAGTAGGGCTCCATGCT 60.327 55.000 0.00 0.00 42.39 3.79
3252 3408 0.548510 GGAAGTAGGGCTCCATGCTT 59.451 55.000 3.68 3.68 42.39 3.91
3253 3409 1.768870 GGAAGTAGGGCTCCATGCTTA 59.231 52.381 4.02 0.00 42.39 3.09
3254 3410 2.224402 GGAAGTAGGGCTCCATGCTTAG 60.224 54.545 4.02 0.00 42.39 2.18
3255 3411 2.478872 AGTAGGGCTCCATGCTTAGA 57.521 50.000 0.00 0.00 42.39 2.10
3256 3412 2.764269 AGTAGGGCTCCATGCTTAGAA 58.236 47.619 0.00 0.00 42.39 2.10
3257 3413 2.703007 AGTAGGGCTCCATGCTTAGAAG 59.297 50.000 0.00 0.00 42.39 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.812571 TCCCTTTGAGCGCATCTTTTC 59.187 47.619 11.47 0.00 0.00 2.29
40 41 7.797038 TCTTTTTAATATACCCTCCGCTTTC 57.203 36.000 0.00 0.00 0.00 2.62
71 72 7.519032 TCGAAATAAACCCTCTGATTGTTTT 57.481 32.000 9.14 0.00 34.33 2.43
75 82 4.035675 GGCTCGAAATAAACCCTCTGATTG 59.964 45.833 0.00 0.00 0.00 2.67
84 91 1.064979 TCCCTGGGCTCGAAATAAACC 60.065 52.381 8.22 0.00 0.00 3.27
138 145 5.450137 GCGAGAATATATATACAGTGCCGGT 60.450 44.000 1.90 0.00 0.00 5.28
150 157 7.822334 ACAATCATTTTCCCGCGAGAATATATA 59.178 33.333 8.23 0.00 0.00 0.86
268 291 1.615392 GGTTTCATTCTTGCTGCTGGT 59.385 47.619 0.00 0.00 0.00 4.00
286 309 2.122768 GGAGATCATTGGAGGACAGGT 58.877 52.381 0.00 0.00 0.00 4.00
376 399 2.032071 AAGGTGTCGAAAGCCCGG 59.968 61.111 0.00 0.00 0.00 5.73
450 477 3.883744 GACGGTGACTGGGGTGCAG 62.884 68.421 0.00 0.00 0.00 4.41
469 496 1.510480 CTGCCAATTAGCTAGCGGCC 61.510 60.000 22.80 9.56 42.27 6.13
470 497 0.532862 TCTGCCAATTAGCTAGCGGC 60.533 55.000 20.06 20.06 43.28 6.53
471 498 1.221414 GTCTGCCAATTAGCTAGCGG 58.779 55.000 9.55 5.07 0.00 5.52
583 610 4.929211 GCAAATTAATGGTGGTTTCTGTCC 59.071 41.667 0.00 0.00 0.00 4.02
585 612 4.038642 ACGCAAATTAATGGTGGTTTCTGT 59.961 37.500 0.00 0.00 0.00 3.41
696 748 0.843309 TGGTTCTGTGGATGTGGTGT 59.157 50.000 0.00 0.00 0.00 4.16
703 755 5.241403 TCTGTACAATTGGTTCTGTGGAT 57.759 39.130 10.83 0.00 0.00 3.41
719 771 1.716826 CTCGTCGCCTCCCTCTGTAC 61.717 65.000 0.00 0.00 0.00 2.90
829 891 2.614829 TATAGGGCCGAAAAGCTCAC 57.385 50.000 0.00 0.00 34.85 3.51
938 1003 0.822532 TGCTAGCTAGGGTACGAGGC 60.823 60.000 22.10 5.91 0.00 4.70
946 1011 3.393472 CTTGCCTTGCTAGCTAGGG 57.607 57.895 35.92 24.98 38.94 3.53
960 1025 1.951631 GATCGACCGGCTAGCTTGC 60.952 63.158 15.72 12.01 0.00 4.01
961 1026 0.952280 TAGATCGACCGGCTAGCTTG 59.048 55.000 15.72 8.56 0.00 4.01
962 1027 1.912417 ATAGATCGACCGGCTAGCTT 58.088 50.000 15.72 0.00 0.00 3.74
963 1028 2.027007 AGTATAGATCGACCGGCTAGCT 60.027 50.000 15.72 0.00 0.00 3.32
964 1029 2.358015 AGTATAGATCGACCGGCTAGC 58.642 52.381 6.04 6.04 0.00 3.42
965 1030 4.121317 CCTAGTATAGATCGACCGGCTAG 58.879 52.174 0.00 0.00 42.77 3.42
966 1031 3.771479 TCCTAGTATAGATCGACCGGCTA 59.229 47.826 0.00 0.00 42.77 3.93
986 1054 3.117657 GCCATTAGCCCTTCCTTCC 57.882 57.895 0.00 0.00 34.35 3.46
997 1065 1.831736 CCTATCCCTACCGGCCATTAG 59.168 57.143 0.00 1.60 0.00 1.73
998 1066 1.553884 CCCTATCCCTACCGGCCATTA 60.554 57.143 0.00 0.00 0.00 1.90
1008 1076 1.155390 CAGCGGGTCCCTATCCCTA 59.845 63.158 6.29 0.00 42.56 3.53
1228 1296 6.150140 GTGGTGAGCACTTTCAGAGATAAATT 59.850 38.462 7.64 0.00 0.00 1.82
1231 1299 4.040339 TGTGGTGAGCACTTTCAGAGATAA 59.960 41.667 16.26 0.00 0.00 1.75
1249 1325 0.108186 ATCGATCATGTGCGTGTGGT 60.108 50.000 0.00 0.00 0.00 4.16
1276 1352 7.883217 TCAATTTCCCTCACGTACTATAGATC 58.117 38.462 6.78 0.00 0.00 2.75
1279 1355 8.888579 AAATCAATTTCCCTCACGTACTATAG 57.111 34.615 0.00 0.00 0.00 1.31
1291 1369 5.420104 AGAAGCATCGAAAATCAATTTCCCT 59.580 36.000 0.00 0.00 43.77 4.20
1297 1375 6.088824 GTGAACAGAAGCATCGAAAATCAAT 58.911 36.000 0.00 0.00 0.00 2.57
1298 1376 5.008514 TGTGAACAGAAGCATCGAAAATCAA 59.991 36.000 0.00 0.00 0.00 2.57
1304 1382 3.402110 ACATGTGAACAGAAGCATCGAA 58.598 40.909 0.00 0.00 0.00 3.71
1329 1410 2.391616 TAGTCATGTGCTTGCTGAGG 57.608 50.000 0.00 0.00 0.00 3.86
1332 1413 2.422479 AGCATTAGTCATGTGCTTGCTG 59.578 45.455 14.00 5.69 46.29 4.41
1333 1414 2.719739 AGCATTAGTCATGTGCTTGCT 58.280 42.857 2.10 7.42 46.29 3.91
1368 1449 0.764369 AACACCAGAGGGCACAGAGA 60.764 55.000 0.00 0.00 37.90 3.10
1377 1458 5.909621 AAAATCATGATCAACACCAGAGG 57.090 39.130 9.06 0.00 0.00 3.69
1400 1485 4.039245 CCCCGAACATAGAAGAAGCATAGA 59.961 45.833 0.00 0.00 0.00 1.98
1412 1497 6.391227 AAAATAAATGCTCCCCGAACATAG 57.609 37.500 0.00 0.00 0.00 2.23
1414 1499 5.675684 AAAAATAAATGCTCCCCGAACAT 57.324 34.783 0.00 0.00 0.00 2.71
1436 1526 7.175467 ACATGAAACATGTCAAGAGAAGCATAA 59.825 33.333 10.94 0.00 0.00 1.90
1437 1527 6.656270 ACATGAAACATGTCAAGAGAAGCATA 59.344 34.615 10.94 0.00 0.00 3.14
1446 1536 5.835257 AGGACAAACATGAAACATGTCAAG 58.165 37.500 15.96 11.66 41.60 3.02
1508 1602 4.885907 AGTACATTTATTCGGACGGAGAGA 59.114 41.667 0.00 0.00 0.00 3.10
1509 1603 5.184340 AGTACATTTATTCGGACGGAGAG 57.816 43.478 0.00 0.00 0.00 3.20
1510 1604 5.359009 AGAAGTACATTTATTCGGACGGAGA 59.641 40.000 0.00 0.00 0.00 3.71
1511 1605 5.589192 AGAAGTACATTTATTCGGACGGAG 58.411 41.667 0.00 0.00 0.00 4.63
1512 1606 5.587388 AGAAGTACATTTATTCGGACGGA 57.413 39.130 0.00 0.00 0.00 4.69
1513 1607 5.401674 GCTAGAAGTACATTTATTCGGACGG 59.598 44.000 0.00 0.00 0.00 4.79
1514 1608 6.207213 AGCTAGAAGTACATTTATTCGGACG 58.793 40.000 0.00 0.00 0.00 4.79
1515 1609 8.421673 AAAGCTAGAAGTACATTTATTCGGAC 57.578 34.615 0.00 0.00 0.00 4.79
1516 1610 8.879759 CAAAAGCTAGAAGTACATTTATTCGGA 58.120 33.333 0.00 0.00 0.00 4.55
1517 1611 8.665685 ACAAAAGCTAGAAGTACATTTATTCGG 58.334 33.333 0.00 0.00 0.00 4.30
1518 1612 9.690434 GACAAAAGCTAGAAGTACATTTATTCG 57.310 33.333 0.00 0.00 0.00 3.34
1524 1618 9.780186 ACTTAAGACAAAAGCTAGAAGTACATT 57.220 29.630 10.09 0.00 0.00 2.71
1525 1619 9.425577 GACTTAAGACAAAAGCTAGAAGTACAT 57.574 33.333 10.09 0.00 0.00 2.29
1526 1620 8.418662 TGACTTAAGACAAAAGCTAGAAGTACA 58.581 33.333 10.09 0.00 0.00 2.90
1527 1621 8.813643 TGACTTAAGACAAAAGCTAGAAGTAC 57.186 34.615 10.09 0.00 0.00 2.73
1528 1622 9.826574 TTTGACTTAAGACAAAAGCTAGAAGTA 57.173 29.630 24.34 4.07 36.92 2.24
1529 1623 8.732746 TTTGACTTAAGACAAAAGCTAGAAGT 57.267 30.769 24.34 0.00 36.92 3.01
1530 1624 8.831550 ACTTTGACTTAAGACAAAAGCTAGAAG 58.168 33.333 25.68 17.12 38.68 2.85
1531 1625 8.732746 ACTTTGACTTAAGACAAAAGCTAGAA 57.267 30.769 25.68 8.67 38.68 2.10
1532 1626 8.732746 AACTTTGACTTAAGACAAAAGCTAGA 57.267 30.769 25.68 9.24 38.68 2.43
1533 1627 9.788960 AAAACTTTGACTTAAGACAAAAGCTAG 57.211 29.630 25.68 18.71 38.68 3.42
1566 1660 8.789762 GCTACTTTTTCCTATAAAGTTGGTCAA 58.210 33.333 6.33 0.00 41.69 3.18
1567 1661 7.940137 TGCTACTTTTTCCTATAAAGTTGGTCA 59.060 33.333 6.33 0.00 41.69 4.02
1568 1662 8.331730 TGCTACTTTTTCCTATAAAGTTGGTC 57.668 34.615 6.33 0.00 41.69 4.02
1569 1663 7.094334 GCTGCTACTTTTTCCTATAAAGTTGGT 60.094 37.037 6.33 0.00 41.69 3.67
1570 1664 7.094377 TGCTGCTACTTTTTCCTATAAAGTTGG 60.094 37.037 0.00 2.81 41.69 3.77
1571 1665 7.816640 TGCTGCTACTTTTTCCTATAAAGTTG 58.183 34.615 0.00 6.06 41.69 3.16
1572 1666 7.996098 TGCTGCTACTTTTTCCTATAAAGTT 57.004 32.000 0.00 0.00 41.69 2.66
1573 1667 8.581253 AATGCTGCTACTTTTTCCTATAAAGT 57.419 30.769 0.00 0.00 45.19 2.66
1577 1671 9.845740 TCATAAATGCTGCTACTTTTTCCTATA 57.154 29.630 0.00 0.00 0.00 1.31
1578 1672 8.624776 GTCATAAATGCTGCTACTTTTTCCTAT 58.375 33.333 0.00 0.00 0.00 2.57
1579 1673 7.609918 TGTCATAAATGCTGCTACTTTTTCCTA 59.390 33.333 0.00 0.00 0.00 2.94
1580 1674 6.434028 TGTCATAAATGCTGCTACTTTTTCCT 59.566 34.615 0.00 0.00 0.00 3.36
1581 1675 6.528072 GTGTCATAAATGCTGCTACTTTTTCC 59.472 38.462 0.00 0.00 0.00 3.13
1582 1676 7.308435 AGTGTCATAAATGCTGCTACTTTTTC 58.692 34.615 0.00 0.00 0.00 2.29
1583 1677 7.219484 AGTGTCATAAATGCTGCTACTTTTT 57.781 32.000 0.00 0.00 0.00 1.94
1584 1678 6.824305 AGTGTCATAAATGCTGCTACTTTT 57.176 33.333 0.00 0.00 0.00 2.27
1585 1679 7.921786 TTAGTGTCATAAATGCTGCTACTTT 57.078 32.000 0.00 1.23 0.00 2.66
1586 1680 7.921786 TTTAGTGTCATAAATGCTGCTACTT 57.078 32.000 0.00 0.00 0.00 2.24
1587 1681 8.511604 AATTTAGTGTCATAAATGCTGCTACT 57.488 30.769 0.00 0.00 35.91 2.57
1588 1682 9.869844 CTAATTTAGTGTCATAAATGCTGCTAC 57.130 33.333 0.00 0.00 35.91 3.58
1589 1683 9.613428 ACTAATTTAGTGTCATAAATGCTGCTA 57.387 29.630 8.27 0.00 37.69 3.49
1590 1684 8.511604 ACTAATTTAGTGTCATAAATGCTGCT 57.488 30.769 8.27 0.00 37.69 4.24
1613 1707 9.436957 ACATTTCAAAACGAATCTAGTGATACT 57.563 29.630 0.00 0.00 32.32 2.12
1727 1821 8.985805 CCACGAATAAGTGTACTTCTAGTTTTT 58.014 33.333 0.00 0.00 40.33 1.94
1728 1822 8.362639 TCCACGAATAAGTGTACTTCTAGTTTT 58.637 33.333 0.00 0.00 40.33 2.43
1729 1823 7.811713 GTCCACGAATAAGTGTACTTCTAGTTT 59.188 37.037 0.00 0.00 40.33 2.66
1730 1824 7.311408 GTCCACGAATAAGTGTACTTCTAGTT 58.689 38.462 0.00 0.00 40.33 2.24
1731 1825 6.402983 CGTCCACGAATAAGTGTACTTCTAGT 60.403 42.308 0.00 0.00 43.02 2.57
1732 1826 5.964168 CGTCCACGAATAAGTGTACTTCTAG 59.036 44.000 0.00 0.00 43.02 2.43
1733 1827 5.163723 CCGTCCACGAATAAGTGTACTTCTA 60.164 44.000 0.00 0.00 43.02 2.10
1734 1828 4.380233 CCGTCCACGAATAAGTGTACTTCT 60.380 45.833 0.00 0.00 43.02 2.85
1735 1829 3.855950 CCGTCCACGAATAAGTGTACTTC 59.144 47.826 0.00 0.00 43.02 3.01
1736 1830 3.507233 TCCGTCCACGAATAAGTGTACTT 59.493 43.478 0.00 2.51 43.02 2.24
1737 1831 3.084039 TCCGTCCACGAATAAGTGTACT 58.916 45.455 0.00 0.00 43.02 2.73
1738 1832 3.432782 CTCCGTCCACGAATAAGTGTAC 58.567 50.000 0.00 0.00 43.02 2.90
1739 1833 2.424601 CCTCCGTCCACGAATAAGTGTA 59.575 50.000 0.00 0.00 43.02 2.90
1740 1834 1.203994 CCTCCGTCCACGAATAAGTGT 59.796 52.381 0.00 0.00 43.02 3.55
1741 1835 1.470979 CCCTCCGTCCACGAATAAGTG 60.471 57.143 0.00 0.00 43.02 3.16
1742 1836 0.822164 CCCTCCGTCCACGAATAAGT 59.178 55.000 0.00 0.00 43.02 2.24
1743 1837 1.067212 CTCCCTCCGTCCACGAATAAG 59.933 57.143 0.00 0.00 43.02 1.73
1744 1838 1.108776 CTCCCTCCGTCCACGAATAA 58.891 55.000 0.00 0.00 43.02 1.40
1745 1839 0.033796 ACTCCCTCCGTCCACGAATA 60.034 55.000 0.00 0.00 43.02 1.75
1746 1840 0.033796 TACTCCCTCCGTCCACGAAT 60.034 55.000 0.00 0.00 43.02 3.34
1747 1841 0.033796 ATACTCCCTCCGTCCACGAA 60.034 55.000 0.00 0.00 43.02 3.85
1748 1842 0.839277 TATACTCCCTCCGTCCACGA 59.161 55.000 0.00 0.00 43.02 4.35
1749 1843 1.540267 CATATACTCCCTCCGTCCACG 59.460 57.143 0.00 0.00 39.44 4.94
1750 1844 1.272769 GCATATACTCCCTCCGTCCAC 59.727 57.143 0.00 0.00 0.00 4.02
1751 1845 1.147191 AGCATATACTCCCTCCGTCCA 59.853 52.381 0.00 0.00 0.00 4.02
1752 1846 1.926108 AGCATATACTCCCTCCGTCC 58.074 55.000 0.00 0.00 0.00 4.79
1753 1847 4.463186 ACATAAGCATATACTCCCTCCGTC 59.537 45.833 0.00 0.00 0.00 4.79
1754 1848 4.417437 ACATAAGCATATACTCCCTCCGT 58.583 43.478 0.00 0.00 0.00 4.69
1755 1849 5.067936 CCTACATAAGCATATACTCCCTCCG 59.932 48.000 0.00 0.00 0.00 4.63
1756 1850 5.958987 ACCTACATAAGCATATACTCCCTCC 59.041 44.000 0.00 0.00 0.00 4.30
1757 1851 7.835181 ACTACCTACATAAGCATATACTCCCTC 59.165 40.741 0.00 0.00 0.00 4.30
1758 1852 7.710579 ACTACCTACATAAGCATATACTCCCT 58.289 38.462 0.00 0.00 0.00 4.20
1759 1853 7.957992 ACTACCTACATAAGCATATACTCCC 57.042 40.000 0.00 0.00 0.00 4.30
1760 1854 9.683870 AGTACTACCTACATAAGCATATACTCC 57.316 37.037 0.00 0.00 0.00 3.85
1815 1919 1.078497 CATCACCTGCGGGCAGTAA 60.078 57.895 12.89 4.87 42.15 2.24
1955 2059 0.575390 GTAGACACACACACGCACAC 59.425 55.000 0.00 0.00 0.00 3.82
1956 2060 0.173708 TGTAGACACACACACGCACA 59.826 50.000 0.00 0.00 0.00 4.57
1957 2061 1.192312 CATGTAGACACACACACGCAC 59.808 52.381 0.00 0.00 37.54 5.34
1958 2062 1.202475 ACATGTAGACACACACACGCA 60.202 47.619 0.00 0.00 37.54 5.24
1959 2063 1.192312 CACATGTAGACACACACACGC 59.808 52.381 0.00 0.00 37.54 5.34
1960 2064 2.218530 CACACATGTAGACACACACACG 59.781 50.000 0.00 0.00 37.54 4.49
2020 2144 3.692406 ACCTCCTGCCCGAACGAC 61.692 66.667 0.00 0.00 0.00 4.34
2092 2216 2.654079 CCCGAGCTGCTGGAAGAGT 61.654 63.158 13.55 0.00 34.07 3.24
2343 2467 2.024176 TTCGTGGCTGGCTTCTTATC 57.976 50.000 2.00 0.00 0.00 1.75
2373 2501 9.151471 GTAGTGTATGTGTTGCCAATATATAGG 57.849 37.037 0.00 0.00 0.00 2.57
2471 2602 3.567478 AGCCATTGATCTAGGGTTCAC 57.433 47.619 9.54 0.00 0.00 3.18
2509 2649 7.720957 TGGCATCAGTTTATTGCAGACTATATT 59.279 33.333 0.00 0.00 38.12 1.28
2510 2650 7.226441 TGGCATCAGTTTATTGCAGACTATAT 58.774 34.615 0.00 0.00 38.12 0.86
2553 2693 3.113260 GCGTGTAGCTCCTCCAATATT 57.887 47.619 0.00 0.00 44.04 1.28
2623 2770 1.393196 TCATGCACGCATAAGTGAACG 59.607 47.619 3.80 0.00 44.43 3.95
2730 2877 0.796312 TTTGCTACTGCGCTAAGTGC 59.204 50.000 9.73 11.43 43.34 4.40
2813 2960 2.159014 GCCACCGGTCTCATACATAACA 60.159 50.000 2.59 0.00 0.00 2.41
2848 2995 6.147656 CGCACCAGACATTAATATTGCTCATA 59.852 38.462 0.00 0.00 0.00 2.15
2853 3000 3.003689 AGCGCACCAGACATTAATATTGC 59.996 43.478 11.47 0.00 0.00 3.56
2894 3045 3.628487 ACGCTACCTAGCTAGCATATAGC 59.372 47.826 18.83 20.40 46.85 2.97
2898 3049 3.008157 AGAGACGCTACCTAGCTAGCATA 59.992 47.826 18.83 8.75 46.85 3.14
3028 3180 5.864474 GCTGACGATGAACCGATTATTATCT 59.136 40.000 0.00 0.00 0.00 1.98
3029 3181 5.220043 CGCTGACGATGAACCGATTATTATC 60.220 44.000 0.00 0.00 43.93 1.75
3035 3187 1.421410 GCGCTGACGATGAACCGATT 61.421 55.000 0.00 0.00 43.93 3.34
3097 3253 5.163353 CCAAGGCCAGGAAAAAGTTAAAGAA 60.163 40.000 5.01 0.00 0.00 2.52
3099 3255 4.631131 CCAAGGCCAGGAAAAAGTTAAAG 58.369 43.478 5.01 0.00 0.00 1.85
3107 3263 0.105760 TCAAGCCAAGGCCAGGAAAA 60.106 50.000 17.70 0.00 43.17 2.29
3113 3269 0.899717 GTCCAATCAAGCCAAGGCCA 60.900 55.000 5.01 0.00 43.17 5.36
3119 3275 3.415212 CTGAGAAAGTCCAATCAAGCCA 58.585 45.455 0.00 0.00 0.00 4.75
3126 3282 3.080319 GCAAGAGCTGAGAAAGTCCAAT 58.920 45.455 0.00 0.00 37.91 3.16
3129 3285 1.271054 TGGCAAGAGCTGAGAAAGTCC 60.271 52.381 0.00 0.00 41.70 3.85
3136 3292 0.733729 GCTGAATGGCAAGAGCTGAG 59.266 55.000 0.00 0.00 41.70 3.35
3147 3303 2.102925 GAGGAGAGAGGAAGCTGAATGG 59.897 54.545 0.00 0.00 0.00 3.16
3183 3339 4.167319 AGAGAGGAGAGAGGAAGCTTTTT 58.833 43.478 0.00 0.00 0.00 1.94
3184 3340 3.769300 GAGAGAGGAGAGAGGAAGCTTTT 59.231 47.826 0.00 0.00 0.00 2.27
3185 3341 3.245586 TGAGAGAGGAGAGAGGAAGCTTT 60.246 47.826 0.00 0.00 0.00 3.51
3186 3342 2.311542 TGAGAGAGGAGAGAGGAAGCTT 59.688 50.000 0.00 0.00 0.00 3.74
3187 3343 1.922447 TGAGAGAGGAGAGAGGAAGCT 59.078 52.381 0.00 0.00 0.00 3.74
3188 3344 2.427095 GTTGAGAGAGGAGAGAGGAAGC 59.573 54.545 0.00 0.00 0.00 3.86
3189 3345 3.968265 AGTTGAGAGAGGAGAGAGGAAG 58.032 50.000 0.00 0.00 0.00 3.46
3190 3346 4.085733 CAAGTTGAGAGAGGAGAGAGGAA 58.914 47.826 0.00 0.00 0.00 3.36
3191 3347 3.075283 ACAAGTTGAGAGAGGAGAGAGGA 59.925 47.826 10.54 0.00 0.00 3.71
3192 3348 3.430453 ACAAGTTGAGAGAGGAGAGAGG 58.570 50.000 10.54 0.00 0.00 3.69
3193 3349 4.335416 AGACAAGTTGAGAGAGGAGAGAG 58.665 47.826 10.54 0.00 0.00 3.20
3194 3350 4.380843 AGACAAGTTGAGAGAGGAGAGA 57.619 45.455 10.54 0.00 0.00 3.10
3195 3351 5.467035 AAAGACAAGTTGAGAGAGGAGAG 57.533 43.478 10.54 0.00 0.00 3.20
3196 3352 4.022762 CGAAAGACAAGTTGAGAGAGGAGA 60.023 45.833 10.54 0.00 0.00 3.71
3197 3353 4.233789 CGAAAGACAAGTTGAGAGAGGAG 58.766 47.826 10.54 0.00 0.00 3.69
3198 3354 3.005897 CCGAAAGACAAGTTGAGAGAGGA 59.994 47.826 10.54 0.00 0.00 3.71
3199 3355 3.243907 ACCGAAAGACAAGTTGAGAGAGG 60.244 47.826 10.54 7.99 0.00 3.69
3200 3356 3.983741 ACCGAAAGACAAGTTGAGAGAG 58.016 45.455 10.54 0.00 0.00 3.20
3201 3357 4.825634 TCTACCGAAAGACAAGTTGAGAGA 59.174 41.667 10.54 0.00 0.00 3.10
3202 3358 5.122512 TCTACCGAAAGACAAGTTGAGAG 57.877 43.478 10.54 0.00 0.00 3.20
3203 3359 5.470368 CATCTACCGAAAGACAAGTTGAGA 58.530 41.667 10.54 0.00 0.00 3.27
3204 3360 4.627467 CCATCTACCGAAAGACAAGTTGAG 59.373 45.833 10.54 0.00 0.00 3.02
3205 3361 4.566004 CCATCTACCGAAAGACAAGTTGA 58.434 43.478 10.54 0.00 0.00 3.18
3206 3362 3.125316 GCCATCTACCGAAAGACAAGTTG 59.875 47.826 0.00 0.00 0.00 3.16
3207 3363 3.244422 TGCCATCTACCGAAAGACAAGTT 60.244 43.478 0.00 0.00 0.00 2.66
3208 3364 2.301870 TGCCATCTACCGAAAGACAAGT 59.698 45.455 0.00 0.00 0.00 3.16
3209 3365 2.972625 TGCCATCTACCGAAAGACAAG 58.027 47.619 0.00 0.00 0.00 3.16
3210 3366 3.627395 ATGCCATCTACCGAAAGACAA 57.373 42.857 0.00 0.00 0.00 3.18
3211 3367 3.627395 AATGCCATCTACCGAAAGACA 57.373 42.857 0.00 0.00 0.00 3.41
3212 3368 4.058817 CCTAATGCCATCTACCGAAAGAC 58.941 47.826 0.00 0.00 0.00 3.01
3213 3369 3.964688 TCCTAATGCCATCTACCGAAAGA 59.035 43.478 0.00 0.00 0.00 2.52
3214 3370 4.336889 TCCTAATGCCATCTACCGAAAG 57.663 45.455 0.00 0.00 0.00 2.62
3215 3371 4.163458 ACTTCCTAATGCCATCTACCGAAA 59.837 41.667 0.00 0.00 0.00 3.46
3216 3372 3.709653 ACTTCCTAATGCCATCTACCGAA 59.290 43.478 0.00 0.00 0.00 4.30
3217 3373 3.305720 ACTTCCTAATGCCATCTACCGA 58.694 45.455 0.00 0.00 0.00 4.69
3218 3374 3.753294 ACTTCCTAATGCCATCTACCG 57.247 47.619 0.00 0.00 0.00 4.02
3219 3375 4.020128 CCCTACTTCCTAATGCCATCTACC 60.020 50.000 0.00 0.00 0.00 3.18
3220 3376 4.563786 GCCCTACTTCCTAATGCCATCTAC 60.564 50.000 0.00 0.00 0.00 2.59
3221 3377 3.583086 GCCCTACTTCCTAATGCCATCTA 59.417 47.826 0.00 0.00 0.00 1.98
3222 3378 2.373502 GCCCTACTTCCTAATGCCATCT 59.626 50.000 0.00 0.00 0.00 2.90
3223 3379 2.373502 AGCCCTACTTCCTAATGCCATC 59.626 50.000 0.00 0.00 0.00 3.51
3224 3380 2.373502 GAGCCCTACTTCCTAATGCCAT 59.626 50.000 0.00 0.00 0.00 4.40
3225 3381 1.768870 GAGCCCTACTTCCTAATGCCA 59.231 52.381 0.00 0.00 0.00 4.92
3226 3382 1.072489 GGAGCCCTACTTCCTAATGCC 59.928 57.143 0.00 0.00 0.00 4.40
3227 3383 1.768870 TGGAGCCCTACTTCCTAATGC 59.231 52.381 0.00 0.00 0.00 3.56
3228 3384 3.808618 GCATGGAGCCCTACTTCCTAATG 60.809 52.174 0.00 0.00 37.23 1.90
3229 3385 2.373502 GCATGGAGCCCTACTTCCTAAT 59.626 50.000 0.00 0.00 37.23 1.73
3230 3386 1.768870 GCATGGAGCCCTACTTCCTAA 59.231 52.381 0.00 0.00 37.23 2.69
3231 3387 1.424638 GCATGGAGCCCTACTTCCTA 58.575 55.000 0.00 0.00 37.23 2.94
3232 3388 2.225792 GCATGGAGCCCTACTTCCT 58.774 57.895 0.00 0.00 37.23 3.36
3233 3389 4.887615 GCATGGAGCCCTACTTCC 57.112 61.111 0.00 0.00 37.23 3.46


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

AutoCloner maintained by Alex Coulton.