Multiple sequence alignment - TraesCS6A01G386300

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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 TraesCS6A01G386300 chr6A 100.000 3406 0 0 1 3406 603265833 603269238 0.000000e+00 6290
1 TraesCS6A01G386300 chr7A 96.144 752 29 0 1 752 39476032 39476783 0.000000e+00 1229
2 TraesCS6A01G386300 chr6D 90.645 930 63 15 2225 3139 456544656 456545576 0.000000e+00 1214
3 TraesCS6A01G386300 chr6D 96.213 713 21 2 759 1468 456543256 456543965 0.000000e+00 1162
4 TraesCS6A01G386300 chr6D 93.186 499 20 9 1576 2073 456544003 456544488 0.000000e+00 721
5 TraesCS6A01G386300 chr6D 90.196 204 13 5 3125 3323 456545633 456545834 3.370000e-65 259
6 TraesCS6A01G386300 chr6B 89.541 937 65 19 2225 3139 694341800 694342725 0.000000e+00 1157
7 TraesCS6A01G386300 chr6B 88.947 760 40 18 759 1489 694340397 694341141 0.000000e+00 898
8 TraesCS6A01G386300 chr6B 90.977 532 29 12 1572 2095 694341162 694341682 0.000000e+00 699
9 TraesCS6A01G386300 chr6B 88.421 285 27 2 3125 3404 694342788 694343071 4.210000e-89 339
10 TraesCS6A01G386300 chr2D 91.064 761 56 10 1 752 594565932 594566689 0.000000e+00 1018
11 TraesCS6A01G386300 chr1B 86.720 753 97 3 1 752 271735492 271734742 0.000000e+00 833
12 TraesCS6A01G386300 chr3B 85.619 751 108 0 1 751 545084899 545084149 0.000000e+00 789
13 TraesCS6A01G386300 chr4B 84.595 753 114 2 1 752 201656501 201657252 0.000000e+00 747
14 TraesCS6A01G386300 chr7B 81.719 640 115 2 120 758 658121695 658121057 1.800000e-147 532


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 TraesCS6A01G386300 chr6A 603265833 603269238 3405 False 6290.00 6290 100.0000 1 3406 1 chr6A.!!$F1 3405
1 TraesCS6A01G386300 chr7A 39476032 39476783 751 False 1229.00 1229 96.1440 1 752 1 chr7A.!!$F1 751
2 TraesCS6A01G386300 chr6D 456543256 456545834 2578 False 839.00 1214 92.5600 759 3323 4 chr6D.!!$F1 2564
3 TraesCS6A01G386300 chr6B 694340397 694343071 2674 False 773.25 1157 89.4715 759 3404 4 chr6B.!!$F1 2645
4 TraesCS6A01G386300 chr2D 594565932 594566689 757 False 1018.00 1018 91.0640 1 752 1 chr2D.!!$F1 751
5 TraesCS6A01G386300 chr1B 271734742 271735492 750 True 833.00 833 86.7200 1 752 1 chr1B.!!$R1 751
6 TraesCS6A01G386300 chr3B 545084149 545084899 750 True 789.00 789 85.6190 1 751 1 chr3B.!!$R1 750
7 TraesCS6A01G386300 chr4B 201656501 201657252 751 False 747.00 747 84.5950 1 752 1 chr4B.!!$F1 751
8 TraesCS6A01G386300 chr7B 658121057 658121695 638 True 532.00 532 81.7190 120 758 1 chr7B.!!$R1 638

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
93 94 0.825010 ACAAACTCAAGCAGGCTGGG 60.825 55.0 17.64 0.0 0.0 4.45 F
1218 1236 0.614979 AGGCGCAGGAGGAAGAAGTA 60.615 55.0 10.83 0.0 0.0 2.24 F
1553 1595 0.037790 GAGCTCATCCGGCATCCTAC 60.038 60.0 9.40 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1576 0.037790 GTAGGATGCCGGATGAGCTC 60.038 60.0 5.05 6.82 0.00 4.09 R
2337 2436 0.238289 ATTTCCTGCAAGACGCGTTG 59.762 50.0 15.53 10.38 46.97 4.10 R
3175 3367 0.384309 TGTTAGCCTCTATCCGCGTG 59.616 55.0 4.92 0.00 0.00 5.34 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
93 94 0.825010 ACAAACTCAAGCAGGCTGGG 60.825 55.000 17.64 0.00 0.00 4.45
298 301 2.823747 GTTTGGAAAGTATCGGGCCTTT 59.176 45.455 0.84 0.00 33.74 3.11
323 326 0.975556 TTGAGCGCATAGGGACTCCA 60.976 55.000 11.47 0.00 41.75 3.86
330 333 2.169769 CGCATAGGGACTCCAGGTTTTA 59.830 50.000 0.00 0.00 41.75 1.52
343 346 3.119849 CCAGGTTTTAGATCAAACGCCAG 60.120 47.826 0.00 0.00 37.50 4.85
392 395 4.349048 TGAAGCTATGCATATCCCTGAACT 59.651 41.667 6.92 0.00 0.00 3.01
424 431 3.026630 TGAGCTTTAGACCGTGTCAAG 57.973 47.619 6.78 4.13 34.60 3.02
491 498 3.496870 GCTCCACCAATACTTCCCCATAG 60.497 52.174 0.00 0.00 0.00 2.23
536 543 4.569943 TGACTTTGTCAGATAGAAGCACC 58.430 43.478 0.00 0.00 37.67 5.01
575 582 2.127118 CCTGCGCAACTGCTTTCG 60.127 61.111 13.05 0.00 39.32 3.46
752 759 4.565652 GGATGTGTATGGTCTGTTTCACCT 60.566 45.833 0.00 0.00 34.66 4.00
754 761 3.646162 TGTGTATGGTCTGTTTCACCTCT 59.354 43.478 0.00 0.00 34.66 3.69
1182 1200 3.621805 TTGGCGTCGCAGGAGGAA 61.622 61.111 20.50 0.00 0.00 3.36
1215 1233 2.660064 GGAGGCGCAGGAGGAAGAA 61.660 63.158 10.83 0.00 0.00 2.52
1216 1234 1.153469 GAGGCGCAGGAGGAAGAAG 60.153 63.158 10.83 0.00 0.00 2.85
1217 1235 1.893919 GAGGCGCAGGAGGAAGAAGT 61.894 60.000 10.83 0.00 0.00 3.01
1218 1236 0.614979 AGGCGCAGGAGGAAGAAGTA 60.615 55.000 10.83 0.00 0.00 2.24
1231 1252 3.118702 GGAAGAAGTAGTACAGGAAGCCC 60.119 52.174 2.52 0.00 0.00 5.19
1277 1301 4.467107 AGGGGAGGTCGAGGAGCC 62.467 72.222 0.00 0.00 0.00 4.70
1459 1501 1.453762 CCCGGAGATGGTCGAGGTAC 61.454 65.000 0.73 0.00 0.00 3.34
1490 1532 1.411394 CACGCTGTTTGCTGAAATGG 58.589 50.000 0.00 0.00 40.11 3.16
1491 1533 1.032014 ACGCTGTTTGCTGAAATGGT 58.968 45.000 0.00 0.00 40.11 3.55
1493 1535 2.621055 ACGCTGTTTGCTGAAATGGTTA 59.379 40.909 0.00 0.00 40.11 2.85
1494 1536 2.979813 CGCTGTTTGCTGAAATGGTTAC 59.020 45.455 0.00 0.00 40.11 2.50
1495 1537 3.317150 GCTGTTTGCTGAAATGGTTACC 58.683 45.455 0.00 0.00 38.95 2.85
1496 1538 3.005791 GCTGTTTGCTGAAATGGTTACCT 59.994 43.478 2.07 0.00 38.95 3.08
1497 1539 4.501400 GCTGTTTGCTGAAATGGTTACCTT 60.501 41.667 2.07 0.00 38.95 3.50
1498 1540 5.278758 GCTGTTTGCTGAAATGGTTACCTTA 60.279 40.000 2.07 0.00 38.95 2.69
1501 1543 7.731054 TGTTTGCTGAAATGGTTACCTTAATT 58.269 30.769 2.07 0.00 0.00 1.40
1502 1544 7.870445 TGTTTGCTGAAATGGTTACCTTAATTC 59.130 33.333 2.07 2.93 0.00 2.17
1504 1546 6.013379 TGCTGAAATGGTTACCTTAATTCCA 58.987 36.000 2.07 0.00 0.00 3.53
1505 1547 6.071616 TGCTGAAATGGTTACCTTAATTCCAC 60.072 38.462 2.07 0.00 0.00 4.02
1506 1548 6.071616 GCTGAAATGGTTACCTTAATTCCACA 60.072 38.462 2.07 0.00 0.00 4.17
1507 1549 7.363793 GCTGAAATGGTTACCTTAATTCCACAT 60.364 37.037 2.07 0.00 0.00 3.21
1508 1550 9.184523 CTGAAATGGTTACCTTAATTCCACATA 57.815 33.333 2.07 0.00 0.00 2.29
1509 1551 8.962679 TGAAATGGTTACCTTAATTCCACATAC 58.037 33.333 2.07 0.00 0.00 2.39
1510 1552 8.887264 AAATGGTTACCTTAATTCCACATACA 57.113 30.769 2.07 0.00 0.00 2.29
1511 1553 9.487442 AAATGGTTACCTTAATTCCACATACAT 57.513 29.630 2.07 0.00 0.00 2.29
1512 1554 7.873719 TGGTTACCTTAATTCCACATACATG 57.126 36.000 2.07 0.00 0.00 3.21
1513 1555 7.634718 TGGTTACCTTAATTCCACATACATGA 58.365 34.615 2.07 0.00 0.00 3.07
1514 1556 8.278639 TGGTTACCTTAATTCCACATACATGAT 58.721 33.333 2.07 0.00 0.00 2.45
1515 1557 8.784043 GGTTACCTTAATTCCACATACATGATC 58.216 37.037 0.00 0.00 0.00 2.92
1516 1558 9.337396 GTTACCTTAATTCCACATACATGATCA 57.663 33.333 0.00 0.00 0.00 2.92
1517 1559 9.559732 TTACCTTAATTCCACATACATGATCAG 57.440 33.333 0.00 0.00 0.00 2.90
1518 1560 7.805163 ACCTTAATTCCACATACATGATCAGA 58.195 34.615 0.00 0.00 0.00 3.27
1519 1561 8.443176 ACCTTAATTCCACATACATGATCAGAT 58.557 33.333 0.00 0.00 0.00 2.90
1520 1562 8.944029 CCTTAATTCCACATACATGATCAGATC 58.056 37.037 0.00 3.11 0.00 2.75
1521 1563 9.498176 CTTAATTCCACATACATGATCAGATCA 57.502 33.333 15.69 15.69 44.55 2.92
1522 1564 7.741027 AATTCCACATACATGATCAGATCAC 57.259 36.000 15.67 0.00 43.01 3.06
1523 1565 6.490241 TTCCACATACATGATCAGATCACT 57.510 37.500 15.67 6.47 43.01 3.41
1524 1566 7.601705 TTCCACATACATGATCAGATCACTA 57.398 36.000 15.67 8.43 43.01 2.74
1525 1567 7.787623 TCCACATACATGATCAGATCACTAT 57.212 36.000 15.67 10.24 43.01 2.12
1526 1568 8.198807 TCCACATACATGATCAGATCACTATT 57.801 34.615 15.67 3.10 43.01 1.73
1527 1569 8.654094 TCCACATACATGATCAGATCACTATTT 58.346 33.333 15.67 4.42 43.01 1.40
1528 1570 9.281371 CCACATACATGATCAGATCACTATTTT 57.719 33.333 15.67 0.00 43.01 1.82
1534 1576 9.761504 ACATGATCAGATCACTATTTTGACTAG 57.238 33.333 15.67 0.00 43.01 2.57
1535 1577 9.978044 CATGATCAGATCACTATTTTGACTAGA 57.022 33.333 15.67 0.00 43.01 2.43
1537 1579 8.140628 TGATCAGATCACTATTTTGACTAGAGC 58.859 37.037 9.21 0.00 33.59 4.09
1538 1580 7.652524 TCAGATCACTATTTTGACTAGAGCT 57.347 36.000 0.00 0.00 0.00 4.09
1539 1581 7.711846 TCAGATCACTATTTTGACTAGAGCTC 58.288 38.462 5.27 5.27 0.00 4.09
1540 1582 7.340487 TCAGATCACTATTTTGACTAGAGCTCA 59.660 37.037 17.77 0.82 0.00 4.26
1541 1583 8.143193 CAGATCACTATTTTGACTAGAGCTCAT 58.857 37.037 17.77 0.00 0.00 2.90
1542 1584 8.359642 AGATCACTATTTTGACTAGAGCTCATC 58.640 37.037 17.77 10.89 0.00 2.92
1543 1585 6.810911 TCACTATTTTGACTAGAGCTCATCC 58.189 40.000 17.77 2.50 0.00 3.51
1544 1586 5.689514 CACTATTTTGACTAGAGCTCATCCG 59.310 44.000 17.77 3.28 0.00 4.18
1545 1587 3.526931 TTTTGACTAGAGCTCATCCGG 57.473 47.619 17.77 0.00 0.00 5.14
1546 1588 0.747255 TTGACTAGAGCTCATCCGGC 59.253 55.000 17.77 3.44 0.00 6.13
1547 1589 0.395724 TGACTAGAGCTCATCCGGCA 60.396 55.000 17.77 6.25 0.00 5.69
1548 1590 0.965439 GACTAGAGCTCATCCGGCAT 59.035 55.000 17.77 0.00 0.00 4.40
1549 1591 0.965439 ACTAGAGCTCATCCGGCATC 59.035 55.000 17.77 0.00 0.00 3.91
1550 1592 0.246086 CTAGAGCTCATCCGGCATCC 59.754 60.000 17.77 0.00 0.00 3.51
1551 1593 0.178950 TAGAGCTCATCCGGCATCCT 60.179 55.000 17.77 0.00 0.00 3.24
1552 1594 0.178950 AGAGCTCATCCGGCATCCTA 60.179 55.000 17.77 0.00 0.00 2.94
1553 1595 0.037790 GAGCTCATCCGGCATCCTAC 60.038 60.000 9.40 0.00 0.00 3.18
1554 1596 0.470833 AGCTCATCCGGCATCCTACT 60.471 55.000 0.00 0.00 0.00 2.57
1555 1597 0.394565 GCTCATCCGGCATCCTACTT 59.605 55.000 0.00 0.00 0.00 2.24
1556 1598 1.618837 GCTCATCCGGCATCCTACTTA 59.381 52.381 0.00 0.00 0.00 2.24
1557 1599 2.037251 GCTCATCCGGCATCCTACTTAA 59.963 50.000 0.00 0.00 0.00 1.85
1558 1600 3.654414 CTCATCCGGCATCCTACTTAAC 58.346 50.000 0.00 0.00 0.00 2.01
1559 1601 2.367567 TCATCCGGCATCCTACTTAACC 59.632 50.000 0.00 0.00 0.00 2.85
1560 1602 2.170012 TCCGGCATCCTACTTAACCT 57.830 50.000 0.00 0.00 0.00 3.50
1561 1603 1.760613 TCCGGCATCCTACTTAACCTG 59.239 52.381 0.00 0.00 0.00 4.00
1562 1604 1.583054 CGGCATCCTACTTAACCTGC 58.417 55.000 0.00 0.00 0.00 4.85
1563 1605 1.134521 CGGCATCCTACTTAACCTGCA 60.135 52.381 0.00 0.00 0.00 4.41
1564 1606 2.485479 CGGCATCCTACTTAACCTGCAT 60.485 50.000 0.00 0.00 0.00 3.96
1565 1607 2.880890 GGCATCCTACTTAACCTGCATG 59.119 50.000 0.00 0.00 0.00 4.06
1566 1608 3.433598 GGCATCCTACTTAACCTGCATGA 60.434 47.826 0.00 0.00 0.00 3.07
1567 1609 4.392940 GCATCCTACTTAACCTGCATGAT 58.607 43.478 0.00 0.00 0.00 2.45
1568 1610 4.453819 GCATCCTACTTAACCTGCATGATC 59.546 45.833 0.00 0.00 0.00 2.92
1569 1611 4.322080 TCCTACTTAACCTGCATGATCG 57.678 45.455 0.00 0.00 0.00 3.69
1570 1612 3.958147 TCCTACTTAACCTGCATGATCGA 59.042 43.478 0.00 0.00 0.00 3.59
1591 1633 1.159285 CTTGATCTCAAACGCCTGCA 58.841 50.000 0.00 0.00 35.15 4.41
1592 1634 1.741706 CTTGATCTCAAACGCCTGCAT 59.258 47.619 0.00 0.00 35.15 3.96
1593 1635 1.825090 TGATCTCAAACGCCTGCATT 58.175 45.000 0.00 0.00 0.00 3.56
1594 1636 1.469703 TGATCTCAAACGCCTGCATTG 59.530 47.619 0.00 0.00 0.00 2.82
1595 1637 0.171903 ATCTCAAACGCCTGCATTGC 59.828 50.000 0.46 0.46 0.00 3.56
1596 1638 1.171549 TCTCAAACGCCTGCATTGCA 61.172 50.000 11.50 11.50 36.92 4.08
1597 1639 0.108992 CTCAAACGCCTGCATTGCAT 60.109 50.000 12.53 0.00 38.13 3.96
1610 1652 2.158841 GCATTGCATTTTTCAGGTGCTG 59.841 45.455 3.15 0.00 39.52 4.41
1673 1715 1.361993 GATGAGCACGCTCGAGGAT 59.638 57.895 15.58 2.17 45.48 3.24
1739 1781 6.073981 TCTGCTCAATCTATCTACCATCACT 58.926 40.000 0.00 0.00 0.00 3.41
1743 1785 4.218635 TCAATCTATCTACCATCACTCCGC 59.781 45.833 0.00 0.00 0.00 5.54
1747 1789 0.817654 TCTACCATCACTCCGCACAG 59.182 55.000 0.00 0.00 0.00 3.66
1748 1790 0.532573 CTACCATCACTCCGCACAGT 59.467 55.000 0.00 0.00 0.00 3.55
1749 1791 0.246360 TACCATCACTCCGCACAGTG 59.754 55.000 5.79 5.79 44.61 3.66
1750 1792 2.393768 CCATCACTCCGCACAGTGC 61.394 63.158 16.21 16.21 43.18 4.40
1751 1793 1.375140 CATCACTCCGCACAGTGCT 60.375 57.895 23.15 1.17 43.18 4.40
1752 1794 1.375140 ATCACTCCGCACAGTGCTG 60.375 57.895 23.15 16.99 43.18 4.41
1753 1795 3.720193 CACTCCGCACAGTGCTGC 61.720 66.667 23.15 7.40 42.25 5.25
1754 1796 4.240103 ACTCCGCACAGTGCTGCA 62.240 61.111 23.15 0.00 42.25 4.41
1755 1797 2.974148 CTCCGCACAGTGCTGCAA 60.974 61.111 23.15 5.07 42.25 4.08
1756 1798 2.281692 TCCGCACAGTGCTGCAAT 60.282 55.556 23.15 0.00 42.25 3.56
1757 1799 2.126618 CCGCACAGTGCTGCAATG 60.127 61.111 26.33 26.33 42.25 2.82
1758 1800 2.126618 CGCACAGTGCTGCAATGG 60.127 61.111 30.16 20.59 42.25 3.16
1759 1801 2.619165 CGCACAGTGCTGCAATGGA 61.619 57.895 30.16 0.00 42.25 3.41
1760 1802 1.661480 GCACAGTGCTGCAATGGAA 59.339 52.632 30.16 0.00 40.96 3.53
1761 1803 0.245539 GCACAGTGCTGCAATGGAAT 59.754 50.000 30.16 10.19 40.96 3.01
1766 1808 3.186909 CAGTGCTGCAATGGAATTCATG 58.813 45.455 21.28 4.41 31.22 3.07
1767 1809 3.093814 AGTGCTGCAATGGAATTCATGA 58.906 40.909 2.77 0.00 31.22 3.07
1768 1810 3.704566 AGTGCTGCAATGGAATTCATGAT 59.295 39.130 2.77 0.00 31.22 2.45
1770 1812 3.243267 TGCTGCAATGGAATTCATGATCG 60.243 43.478 7.93 0.00 31.22 3.69
1771 1813 3.004002 GCTGCAATGGAATTCATGATCGA 59.996 43.478 7.93 0.00 31.22 3.59
1772 1814 4.321008 GCTGCAATGGAATTCATGATCGAT 60.321 41.667 7.93 0.00 31.22 3.59
1774 1816 6.151663 TGCAATGGAATTCATGATCGATTT 57.848 33.333 7.93 0.00 31.22 2.17
1775 1817 6.575267 TGCAATGGAATTCATGATCGATTTT 58.425 32.000 7.93 0.00 31.22 1.82
1777 1819 7.648908 TGCAATGGAATTCATGATCGATTTTAC 59.351 33.333 7.93 0.00 31.22 2.01
1778 1820 7.149080 GCAATGGAATTCATGATCGATTTTACG 60.149 37.037 7.93 0.00 31.22 3.18
1779 1821 6.918892 TGGAATTCATGATCGATTTTACGT 57.081 33.333 7.93 0.00 34.70 3.57
1780 1822 7.315247 TGGAATTCATGATCGATTTTACGTT 57.685 32.000 7.93 0.00 34.70 3.99
1784 1826 5.383984 TCATGATCGATTTTACGTTTCGG 57.616 39.130 0.00 0.00 33.82 4.30
1787 1829 4.948588 TGATCGATTTTACGTTTCGGTTG 58.051 39.130 0.00 0.00 33.82 3.77
1788 1830 4.448395 TGATCGATTTTACGTTTCGGTTGT 59.552 37.500 0.00 0.00 33.82 3.32
1790 1832 4.760683 TCGATTTTACGTTTCGGTTGTTC 58.239 39.130 0.00 0.00 33.82 3.18
1925 1967 2.187946 GTCACCCCGGAGATGCTG 59.812 66.667 0.73 0.00 0.00 4.41
2087 2132 1.156736 CGGTAAGAAACACTGCCTGG 58.843 55.000 0.00 0.00 0.00 4.45
2097 2160 2.124403 CTGCCTGGCACCATCTCC 60.124 66.667 19.30 0.00 33.79 3.71
2102 2165 1.565390 CCTGGCACCATCTCCCTTCA 61.565 60.000 0.00 0.00 0.00 3.02
2103 2166 0.549950 CTGGCACCATCTCCCTTCAT 59.450 55.000 0.00 0.00 0.00 2.57
2104 2167 0.256752 TGGCACCATCTCCCTTCATG 59.743 55.000 0.00 0.00 0.00 3.07
2107 2170 2.450476 GCACCATCTCCCTTCATGTTT 58.550 47.619 0.00 0.00 0.00 2.83
2108 2171 2.165030 GCACCATCTCCCTTCATGTTTG 59.835 50.000 0.00 0.00 0.00 2.93
2124 2187 2.813754 TGTTTGGTACATGAGAAGCTGC 59.186 45.455 0.00 0.00 39.30 5.25
2125 2188 2.813754 GTTTGGTACATGAGAAGCTGCA 59.186 45.455 0.00 0.00 39.30 4.41
2126 2189 2.391616 TGGTACATGAGAAGCTGCAG 57.608 50.000 10.11 10.11 0.00 4.41
2129 2192 2.871022 GGTACATGAGAAGCTGCAGATG 59.129 50.000 20.43 13.43 0.00 2.90
2130 2193 2.783609 ACATGAGAAGCTGCAGATGT 57.216 45.000 20.43 14.13 0.00 3.06
2131 2194 2.357075 ACATGAGAAGCTGCAGATGTG 58.643 47.619 20.43 8.80 0.00 3.21
2162 2225 6.554334 TGGTACAAGCTACTGAATTGTTTC 57.446 37.500 0.00 0.00 38.14 2.78
2163 2226 5.472137 TGGTACAAGCTACTGAATTGTTTCC 59.528 40.000 0.00 0.00 38.14 3.13
2164 2227 5.705905 GGTACAAGCTACTGAATTGTTTCCT 59.294 40.000 0.00 0.00 38.14 3.36
2165 2228 6.877322 GGTACAAGCTACTGAATTGTTTCCTA 59.123 38.462 0.00 0.00 38.14 2.94
2166 2229 7.389607 GGTACAAGCTACTGAATTGTTTCCTAA 59.610 37.037 0.00 0.00 38.14 2.69
2167 2230 8.947115 GTACAAGCTACTGAATTGTTTCCTAAT 58.053 33.333 0.00 0.00 38.14 1.73
2168 2231 7.820648 ACAAGCTACTGAATTGTTTCCTAATG 58.179 34.615 0.00 0.00 33.49 1.90
2169 2232 7.448469 ACAAGCTACTGAATTGTTTCCTAATGT 59.552 33.333 0.00 0.00 33.49 2.71
2170 2233 7.383102 AGCTACTGAATTGTTTCCTAATGTG 57.617 36.000 0.00 0.00 0.00 3.21
2171 2234 6.375455 AGCTACTGAATTGTTTCCTAATGTGG 59.625 38.462 0.00 0.00 0.00 4.17
2172 2235 6.151144 GCTACTGAATTGTTTCCTAATGTGGT 59.849 38.462 0.00 0.00 0.00 4.16
2173 2236 6.331369 ACTGAATTGTTTCCTAATGTGGTG 57.669 37.500 0.00 0.00 0.00 4.17
2174 2237 6.068010 ACTGAATTGTTTCCTAATGTGGTGA 58.932 36.000 0.00 0.00 0.00 4.02
2175 2238 6.721208 ACTGAATTGTTTCCTAATGTGGTGAT 59.279 34.615 0.00 0.00 0.00 3.06
2176 2239 6.923012 TGAATTGTTTCCTAATGTGGTGATG 58.077 36.000 0.00 0.00 0.00 3.07
2177 2240 6.718912 TGAATTGTTTCCTAATGTGGTGATGA 59.281 34.615 0.00 0.00 0.00 2.92
2178 2241 7.396907 TGAATTGTTTCCTAATGTGGTGATGAT 59.603 33.333 0.00 0.00 0.00 2.45
2188 2251 4.206477 TGTGGTGATGATCACTAACCTG 57.794 45.455 23.28 0.00 46.19 4.00
2196 2259 5.952347 TGATGATCACTAACCTGACACTAGT 59.048 40.000 0.00 0.00 0.00 2.57
2202 2265 3.762823 ACTAACCTGACACTAGTACCTGC 59.237 47.826 0.00 0.00 0.00 4.85
2212 2275 2.976882 ACTAGTACCTGCAAACCCTTCA 59.023 45.455 0.00 0.00 0.00 3.02
2226 2318 2.564062 ACCCTTCAAATGCAGAATGTGG 59.436 45.455 0.00 0.00 39.31 4.17
2238 2330 3.427233 GCAGAATGTGGCAAGATGAACTC 60.427 47.826 0.00 0.00 39.31 3.01
2259 2351 7.933215 ACTCTGTTTTGTTAACTAACTTGGT 57.067 32.000 18.46 13.14 37.12 3.67
2261 2353 8.456471 ACTCTGTTTTGTTAACTAACTTGGTTC 58.544 33.333 18.46 0.21 37.12 3.62
2264 2356 7.030768 TGTTTTGTTAACTAACTTGGTTCTGC 58.969 34.615 18.46 0.00 37.12 4.26
2265 2357 7.094118 TGTTTTGTTAACTAACTTGGTTCTGCT 60.094 33.333 18.46 0.00 37.12 4.24
2267 2360 6.371809 TGTTAACTAACTTGGTTCTGCTTG 57.628 37.500 7.22 0.00 37.12 4.01
2278 2371 5.549742 TGGTTCTGCTTGGAAATTCATTT 57.450 34.783 0.00 0.00 0.00 2.32
2286 2379 5.759273 TGCTTGGAAATTCATTTTTCACAGG 59.241 36.000 0.00 0.00 37.34 4.00
2287 2380 5.759763 GCTTGGAAATTCATTTTTCACAGGT 59.240 36.000 0.00 0.00 37.34 4.00
2298 2391 9.844257 TTCATTTTTCACAGGTCCAATAAAAAT 57.156 25.926 9.44 9.44 37.13 1.82
2305 2404 9.527157 TTCACAGGTCCAATAAAAATAATCAGA 57.473 29.630 0.00 0.00 0.00 3.27
2346 2445 4.986659 AGTTAACTGAATAACAACGCGTCT 59.013 37.500 14.44 2.44 38.07 4.18
2416 2515 6.010219 GGAAGAGATACTAGAGAGCTGGATT 58.990 44.000 0.00 0.00 0.00 3.01
2487 2586 0.656259 CAATGCAGATCACGGAGCAG 59.344 55.000 0.00 0.00 40.71 4.24
2513 2612 2.537560 GCCATCGATTGCTCGTGGG 61.538 63.158 13.89 2.13 45.25 4.61
2533 2632 1.226974 GCGCATTCCGAGAGCAGTA 60.227 57.895 0.30 0.00 40.02 2.74
2572 2671 2.807837 CGCCTGATCTGATATGCCAACA 60.808 50.000 0.38 0.00 0.00 3.33
2777 2889 4.941263 TGGAACCACATTCTTTTAGATCCG 59.059 41.667 0.00 0.00 37.48 4.18
2921 3035 4.437930 GCCAGATTCATGTGAACACTAAGC 60.438 45.833 6.51 4.59 36.80 3.09
2944 3058 5.755813 CTGTTGTTTGGAGAATCAACTCAG 58.244 41.667 0.00 0.00 40.34 3.35
2946 3060 5.528690 TGTTGTTTGGAGAATCAACTCAGAG 59.471 40.000 0.00 0.00 40.34 3.35
3028 3143 9.107177 CACTGCAATACTAATTTTCTGAGAGAT 57.893 33.333 0.00 0.00 0.00 2.75
3029 3144 9.107177 ACTGCAATACTAATTTTCTGAGAGATG 57.893 33.333 0.00 0.00 0.00 2.90
3074 3189 7.045416 AGAGTACAAAGACACATACACAAACA 58.955 34.615 0.00 0.00 0.00 2.83
3081 3196 4.692625 AGACACATACACAAACATCAGAGC 59.307 41.667 0.00 0.00 0.00 4.09
3118 3233 8.301720 TCGTAAGTTGTAAGTATTGTGACAGAT 58.698 33.333 0.00 0.00 39.48 2.90
3123 3238 9.507329 AGTTGTAAGTATTGTGACAGATCATTT 57.493 29.630 0.00 0.00 37.14 2.32
3129 3244 8.357796 AGTATTGTGACAGATCATTTATGACG 57.642 34.615 0.00 0.00 40.03 4.35
3141 3333 8.184192 AGATCATTTATGACGGTGACAATTTTC 58.816 33.333 0.00 0.00 40.03 2.29
3164 3356 4.935352 TCCACCTTTTCTTGGTTTGATG 57.065 40.909 0.00 0.00 35.28 3.07
3175 3367 1.579429 GTTTGATGGCGACCACACC 59.421 57.895 0.50 0.00 35.80 4.16
3176 3368 1.149401 TTTGATGGCGACCACACCA 59.851 52.632 0.50 0.00 41.06 4.17
3177 3369 1.169661 TTTGATGGCGACCACACCAC 61.170 55.000 0.50 0.00 39.19 4.16
3184 3381 2.574929 GACCACACCACGCGGATA 59.425 61.111 12.47 0.00 35.59 2.59
3222 3419 5.184711 AGCAAAGTTTTCTTTTCATTGGCA 58.815 33.333 0.00 0.00 46.55 4.92
3230 3427 9.657419 AGTTTTCTTTTCATTGGCATATTAAGG 57.343 29.630 0.00 0.00 0.00 2.69
3249 3446 1.906574 GGGGAATTTGGGGGAAAAGAC 59.093 52.381 0.00 0.00 0.00 3.01
3250 3447 2.615391 GGGAATTTGGGGGAAAAGACA 58.385 47.619 0.00 0.00 0.00 3.41
3324 3522 8.692110 TCATAGCTGCTTTTATGTTTTGATTG 57.308 30.769 7.79 0.00 0.00 2.67
3362 3560 0.247655 GTACAATGCATGCACGACGG 60.248 55.000 25.37 13.00 0.00 4.79
3373 3571 1.740296 CACGACGGGGGTGAACATC 60.740 63.158 0.00 0.00 37.60 3.06
3374 3572 2.211410 ACGACGGGGGTGAACATCA 61.211 57.895 0.00 0.00 0.00 3.07
3376 3574 1.078426 GACGGGGGTGAACATCAGG 60.078 63.158 0.00 0.00 0.00 3.86
3390 3588 3.744660 ACATCAGGGACAAGTCAAAGAC 58.255 45.455 2.29 0.00 0.00 3.01
3404 3602 4.778143 AGACGATGCCGCCCCAAC 62.778 66.667 0.00 0.00 39.95 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 1.203137 AGGTTTTAACTCCAAGGGGGC 60.203 52.381 0.00 0.00 36.21 5.80
245 246 2.388735 AGATGTCGTGGCTAAGGATGA 58.611 47.619 0.00 0.00 0.00 2.92
298 301 3.388024 AGTCCCTATGCGCTCAAATTCTA 59.612 43.478 9.73 0.00 0.00 2.10
323 326 4.015872 TCTGGCGTTTGATCTAAAACCT 57.984 40.909 9.69 0.00 36.83 3.50
343 346 1.797635 GCTATGCTTTCTCGGCAGATC 59.202 52.381 0.00 0.00 43.15 2.75
392 395 1.633774 AAAGCTCAAGGAGGACTCGA 58.366 50.000 0.00 0.00 0.00 4.04
424 431 3.486383 TCACTGGATCAGTTGGGAAAAC 58.514 45.455 0.00 0.00 42.59 2.43
491 498 2.747446 TCTGCCAAGAATTAAGTTCGCC 59.253 45.455 0.00 0.00 41.84 5.54
536 543 2.872245 CCATACCAACCTTCGCTATGTG 59.128 50.000 0.00 0.00 0.00 3.21
575 582 3.588210 AGTAGGGAAGGAGACTCTAGC 57.412 52.381 1.74 0.00 42.68 3.42
678 685 2.530661 TCCCGGTCCATGTGGGTT 60.531 61.111 0.00 0.00 43.75 4.11
752 759 4.456911 CCACTTGCATTTTTCTCTAGCAGA 59.543 41.667 0.00 0.00 36.47 4.26
754 761 4.144297 ACCACTTGCATTTTTCTCTAGCA 58.856 39.130 0.00 0.00 0.00 3.49
1165 1183 3.589654 CTTCCTCCTGCGACGCCAA 62.590 63.158 18.69 0.00 0.00 4.52
1215 1233 0.686769 CCGGGGCTTCCTGTACTACT 60.687 60.000 0.00 0.00 35.10 2.57
1216 1234 1.683418 CCCGGGGCTTCCTGTACTAC 61.683 65.000 14.71 0.00 35.10 2.73
1217 1235 1.382146 CCCGGGGCTTCCTGTACTA 60.382 63.158 14.71 0.00 35.10 1.82
1218 1236 2.687566 CCCGGGGCTTCCTGTACT 60.688 66.667 14.71 0.00 35.10 2.73
1231 1252 4.479993 CTCTTCCAGCTGCCCCGG 62.480 72.222 8.66 0.00 0.00 5.73
1482 1524 7.461182 TGTGGAATTAAGGTAACCATTTCAG 57.539 36.000 0.00 0.00 33.19 3.02
1490 1532 9.337396 TGATCATGTATGTGGAATTAAGGTAAC 57.663 33.333 0.00 0.00 0.00 2.50
1491 1533 9.559732 CTGATCATGTATGTGGAATTAAGGTAA 57.440 33.333 0.00 0.00 0.00 2.85
1493 1535 7.805163 TCTGATCATGTATGTGGAATTAAGGT 58.195 34.615 0.00 0.00 0.00 3.50
1494 1536 8.859236 ATCTGATCATGTATGTGGAATTAAGG 57.141 34.615 0.00 0.00 0.00 2.69
1495 1537 9.498176 TGATCTGATCATGTATGTGGAATTAAG 57.502 33.333 16.06 0.00 33.59 1.85
1496 1538 9.276590 GTGATCTGATCATGTATGTGGAATTAA 57.723 33.333 22.09 0.00 42.04 1.40
1497 1539 8.654094 AGTGATCTGATCATGTATGTGGAATTA 58.346 33.333 22.09 0.00 42.04 1.40
1498 1540 7.515586 AGTGATCTGATCATGTATGTGGAATT 58.484 34.615 22.09 0.00 42.04 2.17
1501 1543 7.787623 ATAGTGATCTGATCATGTATGTGGA 57.212 36.000 22.09 2.70 42.04 4.02
1502 1544 8.843885 AAATAGTGATCTGATCATGTATGTGG 57.156 34.615 22.09 0.00 42.04 4.17
1508 1550 9.761504 CTAGTCAAAATAGTGATCTGATCATGT 57.238 33.333 22.09 15.10 42.04 3.21
1509 1551 9.978044 TCTAGTCAAAATAGTGATCTGATCATG 57.022 33.333 22.09 15.07 42.04 3.07
1511 1553 8.140628 GCTCTAGTCAAAATAGTGATCTGATCA 58.859 37.037 16.06 16.06 36.84 2.92
1512 1554 8.359642 AGCTCTAGTCAAAATAGTGATCTGATC 58.640 37.037 10.72 10.72 0.00 2.92
1513 1555 8.248904 AGCTCTAGTCAAAATAGTGATCTGAT 57.751 34.615 0.00 0.00 0.00 2.90
1514 1556 7.340487 TGAGCTCTAGTCAAAATAGTGATCTGA 59.660 37.037 16.19 0.00 32.92 3.27
1515 1557 7.487484 TGAGCTCTAGTCAAAATAGTGATCTG 58.513 38.462 16.19 0.00 32.92 2.90
1516 1558 7.652524 TGAGCTCTAGTCAAAATAGTGATCT 57.347 36.000 16.19 0.00 32.92 2.75
1517 1559 7.598493 GGATGAGCTCTAGTCAAAATAGTGATC 59.402 40.741 16.19 3.31 32.55 2.92
1518 1560 7.441017 GGATGAGCTCTAGTCAAAATAGTGAT 58.559 38.462 16.19 0.00 0.00 3.06
1519 1561 6.460261 CGGATGAGCTCTAGTCAAAATAGTGA 60.460 42.308 16.19 0.00 0.00 3.41
1520 1562 5.689514 CGGATGAGCTCTAGTCAAAATAGTG 59.310 44.000 16.19 0.00 0.00 2.74
1521 1563 5.221342 CCGGATGAGCTCTAGTCAAAATAGT 60.221 44.000 16.19 0.00 0.00 2.12
1522 1564 5.226396 CCGGATGAGCTCTAGTCAAAATAG 58.774 45.833 16.19 0.00 0.00 1.73
1523 1565 4.501571 GCCGGATGAGCTCTAGTCAAAATA 60.502 45.833 16.19 0.00 0.00 1.40
1524 1566 3.742640 GCCGGATGAGCTCTAGTCAAAAT 60.743 47.826 16.19 0.00 0.00 1.82
1525 1567 2.418746 GCCGGATGAGCTCTAGTCAAAA 60.419 50.000 16.19 0.00 0.00 2.44
1526 1568 1.137086 GCCGGATGAGCTCTAGTCAAA 59.863 52.381 16.19 0.00 0.00 2.69
1527 1569 0.747255 GCCGGATGAGCTCTAGTCAA 59.253 55.000 16.19 0.00 0.00 3.18
1528 1570 0.395724 TGCCGGATGAGCTCTAGTCA 60.396 55.000 16.19 2.80 0.00 3.41
1529 1571 0.965439 ATGCCGGATGAGCTCTAGTC 59.035 55.000 16.19 10.19 0.00 2.59
1530 1572 0.965439 GATGCCGGATGAGCTCTAGT 59.035 55.000 16.19 0.50 0.00 2.57
1531 1573 0.246086 GGATGCCGGATGAGCTCTAG 59.754 60.000 16.19 3.44 0.00 2.43
1532 1574 0.178950 AGGATGCCGGATGAGCTCTA 60.179 55.000 16.19 1.49 0.00 2.43
1533 1575 0.178950 TAGGATGCCGGATGAGCTCT 60.179 55.000 16.19 0.00 0.00 4.09
1534 1576 0.037790 GTAGGATGCCGGATGAGCTC 60.038 60.000 5.05 6.82 0.00 4.09
1535 1577 0.470833 AGTAGGATGCCGGATGAGCT 60.471 55.000 5.05 0.00 0.00 4.09
1536 1578 0.394565 AAGTAGGATGCCGGATGAGC 59.605 55.000 5.05 0.00 0.00 4.26
1537 1579 3.555168 GGTTAAGTAGGATGCCGGATGAG 60.555 52.174 5.05 0.00 0.00 2.90
1538 1580 2.367567 GGTTAAGTAGGATGCCGGATGA 59.632 50.000 5.05 0.00 0.00 2.92
1539 1581 2.368875 AGGTTAAGTAGGATGCCGGATG 59.631 50.000 5.05 0.00 0.00 3.51
1540 1582 2.368875 CAGGTTAAGTAGGATGCCGGAT 59.631 50.000 5.05 0.00 0.00 4.18
1541 1583 1.760613 CAGGTTAAGTAGGATGCCGGA 59.239 52.381 5.05 0.00 0.00 5.14
1542 1584 1.810412 GCAGGTTAAGTAGGATGCCGG 60.810 57.143 0.00 0.00 0.00 6.13
1543 1585 1.134521 TGCAGGTTAAGTAGGATGCCG 60.135 52.381 0.00 0.00 32.77 5.69
1544 1586 2.710096 TGCAGGTTAAGTAGGATGCC 57.290 50.000 0.00 0.00 32.77 4.40
1545 1587 3.808728 TCATGCAGGTTAAGTAGGATGC 58.191 45.455 0.00 0.00 31.02 3.91
1546 1588 4.687948 CGATCATGCAGGTTAAGTAGGATG 59.312 45.833 0.00 0.00 0.00 3.51
1547 1589 4.588951 TCGATCATGCAGGTTAAGTAGGAT 59.411 41.667 0.00 0.00 0.00 3.24
1548 1590 3.958147 TCGATCATGCAGGTTAAGTAGGA 59.042 43.478 0.00 0.00 0.00 2.94
1549 1591 4.322080 TCGATCATGCAGGTTAAGTAGG 57.678 45.455 0.00 0.00 0.00 3.18
1550 1592 5.777802 AGATCGATCATGCAGGTTAAGTAG 58.222 41.667 26.47 0.00 0.00 2.57
1551 1593 5.791336 AGATCGATCATGCAGGTTAAGTA 57.209 39.130 26.47 0.00 0.00 2.24
1552 1594 4.679373 AGATCGATCATGCAGGTTAAGT 57.321 40.909 26.47 0.00 0.00 2.24
1553 1595 5.052481 TCAAGATCGATCATGCAGGTTAAG 58.948 41.667 26.47 0.70 0.00 1.85
1554 1596 5.022282 TCAAGATCGATCATGCAGGTTAA 57.978 39.130 26.47 5.13 0.00 2.01
1555 1597 4.670896 TCAAGATCGATCATGCAGGTTA 57.329 40.909 26.47 5.83 0.00 2.85
1556 1598 3.548745 TCAAGATCGATCATGCAGGTT 57.451 42.857 26.47 7.99 0.00 3.50
1557 1599 3.324268 AGATCAAGATCGATCATGCAGGT 59.676 43.478 26.47 11.62 43.61 4.00
1558 1600 3.927758 GAGATCAAGATCGATCATGCAGG 59.072 47.826 26.47 9.39 43.61 4.85
1559 1601 4.557205 TGAGATCAAGATCGATCATGCAG 58.443 43.478 26.47 11.32 43.61 4.41
1560 1602 4.595762 TGAGATCAAGATCGATCATGCA 57.404 40.909 26.47 14.73 43.61 3.96
1561 1603 5.612059 CGTTTGAGATCAAGATCGATCATGC 60.612 44.000 26.47 13.06 43.61 4.06
1562 1604 5.612059 GCGTTTGAGATCAAGATCGATCATG 60.612 44.000 26.47 23.95 43.61 3.07
1563 1605 4.447054 GCGTTTGAGATCAAGATCGATCAT 59.553 41.667 26.47 13.02 43.61 2.45
1564 1606 3.798878 GCGTTTGAGATCAAGATCGATCA 59.201 43.478 26.47 7.29 43.61 2.92
1565 1607 3.183373 GGCGTTTGAGATCAAGATCGATC 59.817 47.826 17.91 17.91 42.48 3.69
1566 1608 3.126831 GGCGTTTGAGATCAAGATCGAT 58.873 45.455 0.00 0.00 42.48 3.59
1567 1609 2.166459 AGGCGTTTGAGATCAAGATCGA 59.834 45.455 15.50 0.00 42.48 3.59
1568 1610 2.283617 CAGGCGTTTGAGATCAAGATCG 59.716 50.000 4.54 10.32 42.48 3.69
1569 1611 2.031437 GCAGGCGTTTGAGATCAAGATC 59.969 50.000 1.81 1.81 37.15 2.75
1570 1612 2.012673 GCAGGCGTTTGAGATCAAGAT 58.987 47.619 0.00 0.00 37.15 2.40
1591 1633 3.756933 ACAGCACCTGAAAAATGCAAT 57.243 38.095 0.00 0.00 41.97 3.56
1592 1634 3.549827 CGTACAGCACCTGAAAAATGCAA 60.550 43.478 0.00 0.00 41.97 4.08
1593 1635 2.031245 CGTACAGCACCTGAAAAATGCA 60.031 45.455 0.00 0.00 41.97 3.96
1594 1636 2.225491 TCGTACAGCACCTGAAAAATGC 59.775 45.455 0.00 0.00 39.74 3.56
1595 1637 3.364964 GGTCGTACAGCACCTGAAAAATG 60.365 47.826 0.00 0.00 35.18 2.32
1596 1638 2.812011 GGTCGTACAGCACCTGAAAAAT 59.188 45.455 0.00 0.00 35.18 1.82
1597 1639 2.215196 GGTCGTACAGCACCTGAAAAA 58.785 47.619 0.00 0.00 35.18 1.94
1673 1715 1.741401 CTTGATGACCCGCTCGCAA 60.741 57.895 0.00 0.00 0.00 4.85
1730 1772 0.246360 CACTGTGCGGAGTGATGGTA 59.754 55.000 8.86 0.00 45.39 3.25
1743 1785 2.029739 TGAATTCCATTGCAGCACTGTG 60.030 45.455 11.51 2.76 0.00 3.66
1747 1789 3.513680 TCATGAATTCCATTGCAGCAC 57.486 42.857 2.27 0.00 31.94 4.40
1748 1790 3.243267 CGATCATGAATTCCATTGCAGCA 60.243 43.478 0.00 0.00 31.94 4.41
1749 1791 3.004002 TCGATCATGAATTCCATTGCAGC 59.996 43.478 0.00 0.00 31.94 5.25
1750 1792 4.823790 TCGATCATGAATTCCATTGCAG 57.176 40.909 0.00 0.00 31.94 4.41
1751 1793 5.777850 AATCGATCATGAATTCCATTGCA 57.222 34.783 0.00 0.00 31.94 4.08
1752 1794 7.149080 CGTAAAATCGATCATGAATTCCATTGC 60.149 37.037 0.00 0.00 31.94 3.56
1753 1795 7.857389 ACGTAAAATCGATCATGAATTCCATTG 59.143 33.333 0.00 0.00 32.15 2.82
1754 1796 7.930217 ACGTAAAATCGATCATGAATTCCATT 58.070 30.769 0.00 0.00 32.15 3.16
1755 1797 7.496529 ACGTAAAATCGATCATGAATTCCAT 57.503 32.000 0.00 0.00 33.57 3.41
1756 1798 6.918892 ACGTAAAATCGATCATGAATTCCA 57.081 33.333 0.00 0.00 34.70 3.53
1757 1799 7.110216 CGAAACGTAAAATCGATCATGAATTCC 59.890 37.037 0.00 0.00 38.82 3.01
1758 1800 7.110216 CCGAAACGTAAAATCGATCATGAATTC 59.890 37.037 0.00 0.00 38.82 2.17
1759 1801 6.905076 CCGAAACGTAAAATCGATCATGAATT 59.095 34.615 0.00 0.00 38.82 2.17
1760 1802 6.036735 ACCGAAACGTAAAATCGATCATGAAT 59.963 34.615 0.00 0.00 38.82 2.57
1761 1803 5.349270 ACCGAAACGTAAAATCGATCATGAA 59.651 36.000 0.00 0.00 38.82 2.57
1766 1808 4.949756 ACAACCGAAACGTAAAATCGATC 58.050 39.130 0.00 0.00 38.82 3.69
1767 1809 4.996062 ACAACCGAAACGTAAAATCGAT 57.004 36.364 12.62 0.00 38.82 3.59
1768 1810 4.507388 AGAACAACCGAAACGTAAAATCGA 59.493 37.500 12.62 0.00 38.82 3.59
1770 1812 6.687958 TGAAAGAACAACCGAAACGTAAAATC 59.312 34.615 0.00 0.00 0.00 2.17
1771 1813 6.553524 TGAAAGAACAACCGAAACGTAAAAT 58.446 32.000 0.00 0.00 0.00 1.82
1772 1814 5.936054 TGAAAGAACAACCGAAACGTAAAA 58.064 33.333 0.00 0.00 0.00 1.52
1774 1816 4.494526 GCTGAAAGAACAACCGAAACGTAA 60.495 41.667 0.00 0.00 34.07 3.18
1775 1817 3.001533 GCTGAAAGAACAACCGAAACGTA 59.998 43.478 0.00 0.00 34.07 3.57
1777 1819 2.031683 AGCTGAAAGAACAACCGAAACG 59.968 45.455 0.00 0.00 34.07 3.60
1778 1820 3.181500 ACAGCTGAAAGAACAACCGAAAC 60.181 43.478 23.35 0.00 34.07 2.78
1779 1821 3.013921 ACAGCTGAAAGAACAACCGAAA 58.986 40.909 23.35 0.00 34.07 3.46
1780 1822 2.639065 ACAGCTGAAAGAACAACCGAA 58.361 42.857 23.35 0.00 34.07 4.30
2080 2125 2.124403 GGAGATGGTGCCAGGCAG 60.124 66.667 16.83 0.00 40.08 4.85
2087 2132 2.134789 AACATGAAGGGAGATGGTGC 57.865 50.000 0.00 0.00 0.00 5.01
2103 2166 2.813754 GCAGCTTCTCATGTACCAAACA 59.186 45.455 0.00 0.00 43.86 2.83
2104 2167 2.813754 TGCAGCTTCTCATGTACCAAAC 59.186 45.455 0.00 0.00 0.00 2.93
2107 2170 1.901833 TCTGCAGCTTCTCATGTACCA 59.098 47.619 9.47 0.00 0.00 3.25
2108 2171 2.680312 TCTGCAGCTTCTCATGTACC 57.320 50.000 9.47 0.00 0.00 3.34
2123 2186 1.171308 ACCAAGACATGCACATCTGC 58.829 50.000 2.39 0.00 44.52 4.26
2124 2187 3.337358 TGTACCAAGACATGCACATCTG 58.663 45.455 2.39 0.00 0.00 2.90
2125 2188 3.701205 TGTACCAAGACATGCACATCT 57.299 42.857 0.00 0.00 0.00 2.90
2126 2189 3.426695 GCTTGTACCAAGACATGCACATC 60.427 47.826 8.11 0.00 45.25 3.06
2129 2192 2.619013 GCTTGTACCAAGACATGCAC 57.381 50.000 8.11 0.00 45.25 4.57
2131 2194 3.372206 CAGTAGCTTGTACCAAGACATGC 59.628 47.826 8.11 6.36 45.90 4.06
2134 2197 4.948341 TTCAGTAGCTTGTACCAAGACA 57.052 40.909 8.11 0.00 0.00 3.41
2135 2198 5.701290 ACAATTCAGTAGCTTGTACCAAGAC 59.299 40.000 8.11 0.00 31.62 3.01
2136 2199 5.865085 ACAATTCAGTAGCTTGTACCAAGA 58.135 37.500 8.11 0.00 31.62 3.02
2137 2200 6.560253 AACAATTCAGTAGCTTGTACCAAG 57.440 37.500 0.00 0.00 33.01 3.61
2138 2201 6.016610 GGAAACAATTCAGTAGCTTGTACCAA 60.017 38.462 0.00 0.00 37.29 3.67
2139 2202 5.472137 GGAAACAATTCAGTAGCTTGTACCA 59.528 40.000 0.00 0.00 37.29 3.25
2140 2203 5.705905 AGGAAACAATTCAGTAGCTTGTACC 59.294 40.000 0.00 0.00 37.29 3.34
2141 2204 6.803154 AGGAAACAATTCAGTAGCTTGTAC 57.197 37.500 0.00 0.00 37.29 2.90
2142 2205 8.946085 CATTAGGAAACAATTCAGTAGCTTGTA 58.054 33.333 0.00 0.00 37.29 2.41
2146 2209 6.375455 CCACATTAGGAAACAATTCAGTAGCT 59.625 38.462 0.00 0.00 37.29 3.32
2147 2210 6.151144 ACCACATTAGGAAACAATTCAGTAGC 59.849 38.462 0.00 0.00 37.29 3.58
2148 2211 7.390440 TCACCACATTAGGAAACAATTCAGTAG 59.610 37.037 0.00 0.00 37.29 2.57
2149 2212 7.227873 TCACCACATTAGGAAACAATTCAGTA 58.772 34.615 0.00 0.00 37.29 2.74
2150 2213 6.068010 TCACCACATTAGGAAACAATTCAGT 58.932 36.000 0.00 0.00 37.29 3.41
2151 2214 6.573664 TCACCACATTAGGAAACAATTCAG 57.426 37.500 0.00 0.00 37.29 3.02
2152 2215 6.718912 TCATCACCACATTAGGAAACAATTCA 59.281 34.615 0.00 0.00 37.29 2.57
2153 2216 7.156876 TCATCACCACATTAGGAAACAATTC 57.843 36.000 0.00 0.00 34.66 2.17
2154 2217 7.396907 TGATCATCACCACATTAGGAAACAATT 59.603 33.333 0.00 0.00 0.00 2.32
2155 2218 6.891361 TGATCATCACCACATTAGGAAACAAT 59.109 34.615 0.00 0.00 0.00 2.71
2156 2219 6.150976 GTGATCATCACCACATTAGGAAACAA 59.849 38.462 6.50 0.00 41.37 2.83
2157 2220 5.647658 GTGATCATCACCACATTAGGAAACA 59.352 40.000 6.50 0.00 41.37 2.83
2158 2221 6.124088 GTGATCATCACCACATTAGGAAAC 57.876 41.667 6.50 0.00 41.37 2.78
2172 2235 5.952347 ACTAGTGTCAGGTTAGTGATCATCA 59.048 40.000 0.00 0.00 0.00 3.07
2173 2236 6.458232 ACTAGTGTCAGGTTAGTGATCATC 57.542 41.667 0.00 0.00 0.00 2.92
2174 2237 6.321690 GGTACTAGTGTCAGGTTAGTGATCAT 59.678 42.308 5.39 0.00 0.00 2.45
2175 2238 5.651139 GGTACTAGTGTCAGGTTAGTGATCA 59.349 44.000 5.39 0.00 0.00 2.92
2176 2239 5.887035 AGGTACTAGTGTCAGGTTAGTGATC 59.113 44.000 5.39 0.00 36.02 2.92
2177 2240 5.652891 CAGGTACTAGTGTCAGGTTAGTGAT 59.347 44.000 5.39 0.00 36.02 3.06
2178 2241 5.008331 CAGGTACTAGTGTCAGGTTAGTGA 58.992 45.833 5.39 0.00 36.02 3.41
2188 2251 2.302157 AGGGTTTGCAGGTACTAGTGTC 59.698 50.000 5.39 0.00 36.02 3.67
2196 2259 2.298729 GCATTTGAAGGGTTTGCAGGTA 59.701 45.455 0.00 0.00 33.58 3.08
2202 2265 4.449743 CACATTCTGCATTTGAAGGGTTTG 59.550 41.667 4.23 0.00 30.61 2.93
2212 2275 3.512329 TCATCTTGCCACATTCTGCATTT 59.488 39.130 0.00 0.00 37.33 2.32
2226 2318 7.196331 AGTTAACAAAACAGAGTTCATCTTGC 58.804 34.615 8.61 0.00 35.47 4.01
2238 2330 7.220108 GCAGAACCAAGTTAGTTAACAAAACAG 59.780 37.037 19.79 13.71 38.62 3.16
2259 2351 7.046652 TGTGAAAAATGAATTTCCAAGCAGAA 58.953 30.769 0.00 0.00 38.30 3.02
2261 2353 6.073440 CCTGTGAAAAATGAATTTCCAAGCAG 60.073 38.462 0.00 0.00 38.30 4.24
2264 2356 6.424812 GGACCTGTGAAAAATGAATTTCCAAG 59.575 38.462 0.00 0.00 38.30 3.61
2265 2357 6.126940 TGGACCTGTGAAAAATGAATTTCCAA 60.127 34.615 0.00 0.00 38.30 3.53
2267 2360 5.852827 TGGACCTGTGAAAAATGAATTTCC 58.147 37.500 0.00 0.00 38.30 3.13
2300 2393 9.458727 AACTTCAGTTATGTCATGAAATCTGAT 57.541 29.630 14.83 2.83 36.32 2.90
2324 2423 5.260027 AGACGCGTTGTTATTCAGTTAAC 57.740 39.130 15.53 0.00 33.56 2.01
2337 2436 0.238289 ATTTCCTGCAAGACGCGTTG 59.762 50.000 15.53 10.38 46.97 4.10
2341 2440 0.796312 TTCGATTTCCTGCAAGACGC 59.204 50.000 0.00 0.00 42.89 5.19
2346 2445 1.167851 CTGCCTTCGATTTCCTGCAA 58.832 50.000 0.00 0.00 0.00 4.08
2416 2515 5.007626 CGAGTTTCTCCAATGTGAAGAAACA 59.992 40.000 22.94 0.00 46.10 2.83
2487 2586 3.303406 GAGCAATCGATGGCTTATTTGC 58.697 45.455 27.68 17.19 41.22 3.68
2513 2612 2.202797 TGCTCTCGGAATGCGCTC 60.203 61.111 9.73 0.00 0.00 5.03
2533 2632 1.068333 GCGATGCAAGAACCATGTGTT 60.068 47.619 0.00 0.00 40.81 3.32
2572 2671 3.882888 CGAAGCCACCAAATATACACCAT 59.117 43.478 0.00 0.00 0.00 3.55
2760 2872 4.142622 TGCAAGCGGATCTAAAAGAATGTG 60.143 41.667 0.00 0.00 0.00 3.21
2761 2873 4.009675 TGCAAGCGGATCTAAAAGAATGT 58.990 39.130 0.00 0.00 0.00 2.71
2777 2889 5.733226 AAACATAAAACCAAGTTGCAAGC 57.267 34.783 0.00 0.00 0.00 4.01
2899 3013 4.940046 AGCTTAGTGTTCACATGAATCTGG 59.060 41.667 0.00 0.96 36.33 3.86
2921 3035 5.528690 TCTGAGTTGATTCTCCAAACAACAG 59.471 40.000 0.00 0.00 44.06 3.16
2957 3072 7.638295 GCAATATGCATTGACAATGTTGAATTG 59.362 33.333 25.18 24.77 43.67 2.32
2985 3100 5.820131 TGCAGTGTATATTACATTTGCAGC 58.180 37.500 17.98 0.00 46.92 5.25
2999 3114 9.890629 TCTCAGAAAATTAGTATTGCAGTGTAT 57.109 29.630 0.00 0.00 0.00 2.29
3035 3150 7.982354 GTCTTTGTACTCTTGCCTCTAATGTAT 59.018 37.037 0.00 0.00 0.00 2.29
3037 3152 6.166982 GTCTTTGTACTCTTGCCTCTAATGT 58.833 40.000 0.00 0.00 0.00 2.71
3058 3173 4.692625 GCTCTGATGTTTGTGTATGTGTCT 59.307 41.667 0.00 0.00 0.00 3.41
3081 3196 3.067106 ACAACTTACGAGCTTCATGGTG 58.933 45.455 0.00 0.00 0.00 4.17
3118 3233 7.447374 AGAAAATTGTCACCGTCATAAATGA 57.553 32.000 0.00 0.00 0.00 2.57
3121 3236 6.263392 TGGAAGAAAATTGTCACCGTCATAAA 59.737 34.615 0.00 0.00 0.00 1.40
3123 3238 5.180492 GTGGAAGAAAATTGTCACCGTCATA 59.820 40.000 0.00 0.00 0.00 2.15
3129 3244 4.937201 AAGGTGGAAGAAAATTGTCACC 57.063 40.909 0.00 0.00 43.41 4.02
3141 3333 5.291971 CATCAAACCAAGAAAAGGTGGAAG 58.708 41.667 0.00 0.00 39.86 3.46
3175 3367 0.384309 TGTTAGCCTCTATCCGCGTG 59.616 55.000 4.92 0.00 0.00 5.34
3176 3368 1.108776 TTGTTAGCCTCTATCCGCGT 58.891 50.000 4.92 0.00 0.00 6.01
3177 3369 2.128035 CTTTGTTAGCCTCTATCCGCG 58.872 52.381 0.00 0.00 0.00 6.46
3179 3371 4.202121 TGCTACTTTGTTAGCCTCTATCCG 60.202 45.833 0.00 0.00 38.48 4.18
3184 3381 4.974399 ACTTTGCTACTTTGTTAGCCTCT 58.026 39.130 0.00 0.00 38.48 3.69
3222 3419 5.777187 TTCCCCCAAATTCCCCTTAATAT 57.223 39.130 0.00 0.00 0.00 1.28
3230 3427 2.615391 TGTCTTTTCCCCCAAATTCCC 58.385 47.619 0.00 0.00 0.00 3.97
3331 3529 2.032302 TGCATTGTACAACACCAACGAC 59.968 45.455 11.22 0.00 0.00 4.34
3334 3532 2.730928 GCATGCATTGTACAACACCAAC 59.269 45.455 14.21 2.30 0.00 3.77
3338 3536 1.978097 CGTGCATGCATTGTACAACAC 59.022 47.619 25.64 11.97 40.62 3.32
3362 3560 0.404040 TTGTCCCTGATGTTCACCCC 59.596 55.000 0.00 0.00 0.00 4.95
3365 3563 3.126001 TGACTTGTCCCTGATGTTCAC 57.874 47.619 0.00 0.00 0.00 3.18
3373 3571 2.526304 TCGTCTTTGACTTGTCCCTG 57.474 50.000 0.00 0.00 0.00 4.45
3374 3572 2.872038 GCATCGTCTTTGACTTGTCCCT 60.872 50.000 0.00 0.00 0.00 4.20
3376 3574 1.464997 GGCATCGTCTTTGACTTGTCC 59.535 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.