Multiple sequence alignment - TraesCS1D01G272400

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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 TraesCS1D01G272400 chr1D 100.000 2339 0 0 1 2339 366238378 366240716 0.000000e+00 4320.0
1 TraesCS1D01G272400 chr1B 93.124 829 41 8 1 819 491250768 491249946 0.000000e+00 1201.0
2 TraesCS1D01G272400 chr1B 95.037 403 17 2 1908 2310 491249638 491249239 4.240000e-177 630.0
3 TraesCS1D01G272400 chr1B 87.724 391 31 3 1528 1912 572521612 572521991 7.670000e-120 440.0
4 TraesCS1D01G272400 chr1A 91.586 725 39 11 1 720 465507945 465507238 0.000000e+00 981.0
5 TraesCS1D01G272400 chr1A 85.648 432 58 2 1908 2339 23033734 23033307 3.540000e-123 451.0
6 TraesCS1D01G272400 chr2B 93.956 546 30 2 819 1362 579986674 579986130 0.000000e+00 822.0
7 TraesCS1D01G272400 chr2B 88.083 386 32 10 1529 1912 691463123 691463496 1.650000e-121 446.0
8 TraesCS1D01G272400 chr3A 92.831 544 39 0 819 1362 688909904 688909361 0.000000e+00 789.0
9 TraesCS1D01G272400 chr3A 83.214 280 40 7 1910 2187 706552382 706552656 1.390000e-62 250.0
10 TraesCS1D01G272400 chr4B 91.376 545 46 1 819 1363 461164825 461165368 0.000000e+00 745.0
11 TraesCS1D01G272400 chr4B 89.890 544 55 0 819 1362 245672194 245671651 0.000000e+00 701.0
12 TraesCS1D01G272400 chr4B 82.506 423 70 4 1919 2339 404118742 404118322 3.670000e-98 368.0
13 TraesCS1D01G272400 chr7B 91.176 544 48 0 819 1362 81434279 81433736 0.000000e+00 739.0
14 TraesCS1D01G272400 chr7B 84.570 337 52 0 1996 2332 546939323 546938987 3.720000e-88 335.0
15 TraesCS1D01G272400 chr7B 78.155 412 85 5 1914 2322 750288223 750288632 8.290000e-65 257.0
16 TraesCS1D01G272400 chr3D 90.494 547 52 0 819 1365 434892532 434891986 0.000000e+00 723.0
17 TraesCS1D01G272400 chr6B 89.299 542 57 1 819 1360 583185005 583185545 0.000000e+00 678.0
18 TraesCS1D01G272400 chr6B 87.080 387 30 8 1528 1912 130299362 130298994 1.000000e-113 420.0
19 TraesCS1D01G272400 chr6B 93.585 265 15 2 1649 1912 165905761 165905498 6.060000e-106 394.0
20 TraesCS1D01G272400 chr6A 88.971 544 60 0 819 1362 404692714 404693257 0.000000e+00 673.0
21 TraesCS1D01G272400 chr5D 86.813 546 65 5 819 1362 167049847 167049307 9.250000e-169 603.0
22 TraesCS1D01G272400 chr5D 91.517 389 29 4 1526 1912 189022361 189021975 1.230000e-147 532.0
23 TraesCS1D01G272400 chr5A 91.906 383 30 1 1531 1912 686517850 686517468 3.420000e-148 534.0
24 TraesCS1D01G272400 chr7A 88.144 388 39 5 1529 1912 110399559 110399943 2.740000e-124 455.0
25 TraesCS1D01G272400 chr4D 81.905 420 71 5 1910 2326 17851214 17850797 1.330000e-92 350.0
26 TraesCS1D01G272400 chr2D 91.228 57 4 1 1527 1583 170816746 170816801 2.490000e-10 76.8


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 TraesCS1D01G272400 chr1D 366238378 366240716 2338 False 4320.0 4320 100.0000 1 2339 1 chr1D.!!$F1 2338
1 TraesCS1D01G272400 chr1B 491249239 491250768 1529 True 915.5 1201 94.0805 1 2310 2 chr1B.!!$R1 2309
2 TraesCS1D01G272400 chr1A 465507238 465507945 707 True 981.0 981 91.5860 1 720 1 chr1A.!!$R2 719
3 TraesCS1D01G272400 chr2B 579986130 579986674 544 True 822.0 822 93.9560 819 1362 1 chr2B.!!$R1 543
4 TraesCS1D01G272400 chr3A 688909361 688909904 543 True 789.0 789 92.8310 819 1362 1 chr3A.!!$R1 543
5 TraesCS1D01G272400 chr4B 461164825 461165368 543 False 745.0 745 91.3760 819 1363 1 chr4B.!!$F1 544
6 TraesCS1D01G272400 chr4B 245671651 245672194 543 True 701.0 701 89.8900 819 1362 1 chr4B.!!$R1 543
7 TraesCS1D01G272400 chr7B 81433736 81434279 543 True 739.0 739 91.1760 819 1362 1 chr7B.!!$R1 543
8 TraesCS1D01G272400 chr3D 434891986 434892532 546 True 723.0 723 90.4940 819 1365 1 chr3D.!!$R1 546
9 TraesCS1D01G272400 chr6B 583185005 583185545 540 False 678.0 678 89.2990 819 1360 1 chr6B.!!$F1 541
10 TraesCS1D01G272400 chr6A 404692714 404693257 543 False 673.0 673 88.9710 819 1362 1 chr6A.!!$F1 543
11 TraesCS1D01G272400 chr5D 167049307 167049847 540 True 603.0 603 86.8130 819 1362 1 chr5D.!!$R1 543

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
848 863 0.333652 ATAAGAAACGGGGGTTGGGG 59.666 55.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1910 0.031111 ATCCTCCCGAATGGTCCTGA 60.031 55.0 0.0 0.0 34.77 3.86 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
77 78 1.207329 GACTACATCAACTCGGGCCTT 59.793 52.381 0.84 0.00 0.00 4.35
161 162 4.373116 GTCTCCGCCCTCGCACAA 62.373 66.667 0.00 0.00 34.03 3.33
272 273 0.969894 CCCTCGTCCTGTTTGAGAGT 59.030 55.000 0.00 0.00 31.31 3.24
275 276 2.035961 CCTCGTCCTGTTTGAGAGTGAA 59.964 50.000 0.00 0.00 31.31 3.18
375 376 2.644676 TGCAGAGTCTGTAGATACGCT 58.355 47.619 21.06 0.00 33.43 5.07
414 417 2.743928 CTTGGCTGCCACTCGGTC 60.744 66.667 23.30 0.00 30.78 4.79
462 466 8.661352 TTTTCTTTTTAGGAAGCTTTGAATGG 57.339 30.769 0.00 0.00 0.00 3.16
484 488 5.013495 TGGTCCTTCAGATGTGAATTCTCTT 59.987 40.000 5.65 1.17 41.96 2.85
487 491 4.880696 CCTTCAGATGTGAATTCTCTTCCC 59.119 45.833 5.65 2.12 41.96 3.97
509 513 2.549754 GACTGCTGCTTTGTCTTTGCTA 59.450 45.455 0.00 0.00 0.00 3.49
511 515 3.571401 ACTGCTGCTTTGTCTTTGCTATT 59.429 39.130 0.00 0.00 0.00 1.73
513 517 3.822735 TGCTGCTTTGTCTTTGCTATTCT 59.177 39.130 0.00 0.00 0.00 2.40
514 518 4.083110 TGCTGCTTTGTCTTTGCTATTCTC 60.083 41.667 0.00 0.00 0.00 2.87
554 566 4.577283 CGAGTTCTCCCTTGTTGGTTTAAA 59.423 41.667 0.00 0.00 0.00 1.52
678 691 3.057946 GTGTTTCTGGTTGATCCTTGCTC 60.058 47.826 0.00 0.00 37.07 4.26
679 692 3.149196 GTTTCTGGTTGATCCTTGCTCA 58.851 45.455 0.00 0.00 37.07 4.26
707 720 2.290896 TGTAGCAACTGGGATTGAAGGG 60.291 50.000 0.00 0.00 0.00 3.95
720 733 2.552599 TGAAGGGCACGTTGATGTTA 57.447 45.000 0.00 0.00 36.18 2.41
740 753 6.668323 TGTTAAAAGATGCTTGAGTAACTGC 58.332 36.000 0.00 0.00 0.00 4.40
748 761 2.341257 CTTGAGTAACTGCGCTGTGAT 58.659 47.619 21.17 8.75 0.00 3.06
749 762 2.455674 TGAGTAACTGCGCTGTGATT 57.544 45.000 21.17 10.27 0.00 2.57
780 793 6.869206 TCTAAAGCTATGACAACTAGGGTT 57.131 37.500 0.00 0.00 35.86 4.11
782 795 7.328737 TCTAAAGCTATGACAACTAGGGTTTC 58.671 38.462 0.00 0.00 32.73 2.78
794 807 2.669240 GGTTTCCCCTCTCCGTGG 59.331 66.667 0.00 0.00 0.00 4.94
816 829 9.013490 CGTGGCAAATTAATTTCTTCTAATCAG 57.987 33.333 10.53 0.00 0.00 2.90
837 850 4.092091 CAGACAAGAGCGTCCATAAGAAAC 59.908 45.833 0.00 0.00 36.52 2.78
847 862 1.470051 CATAAGAAACGGGGGTTGGG 58.530 55.000 0.00 0.00 0.00 4.12
848 863 0.333652 ATAAGAAACGGGGGTTGGGG 59.666 55.000 0.00 0.00 0.00 4.96
860 875 2.044450 TTGGGGCTGCCCTCCTAT 59.956 61.111 34.99 0.00 44.66 2.57
906 921 4.180817 ACGCGTCTTTTGATCATGACATA 58.819 39.130 5.58 0.00 0.00 2.29
917 932 4.838423 TGATCATGACATACTAACGGGGAT 59.162 41.667 0.00 0.00 0.00 3.85
965 980 5.367945 AAAGATAGGTTTATTGCGGGAGA 57.632 39.130 0.00 0.00 0.00 3.71
1062 1077 1.844544 AAAGGGCGGGGTGTAATCGT 61.845 55.000 0.00 0.00 0.00 3.73
1110 1125 2.422519 GGTGATTGAGACCATGCAGGAT 60.423 50.000 0.00 0.00 41.22 3.24
1178 1193 6.145858 TGTTTTCACTATGCATGTGATTTTGC 59.854 34.615 23.49 15.71 42.95 3.68
1388 1404 5.745312 TCTTCTAATCAGACTGCCTTCAA 57.255 39.130 0.00 0.00 0.00 2.69
1393 1409 8.498054 TTCTAATCAGACTGCCTTCAATAAAG 57.502 34.615 0.00 0.00 34.52 1.85
1426 1442 1.133513 TGAAAAGTGTGGTCATGGCCT 60.134 47.619 19.09 0.00 0.00 5.19
1484 1501 5.574188 AGTGGGTTGATTCTTAAGCTTGAT 58.426 37.500 9.86 0.00 0.00 2.57
1487 1504 7.836183 AGTGGGTTGATTCTTAAGCTTGATTAT 59.164 33.333 9.86 0.00 0.00 1.28
1528 1545 6.410540 AGAGTTGTTAGCTGGGATTTCTTAG 58.589 40.000 0.00 0.00 0.00 2.18
1529 1546 5.501156 AGTTGTTAGCTGGGATTTCTTAGG 58.499 41.667 0.00 0.00 0.00 2.69
1530 1547 4.503714 TGTTAGCTGGGATTTCTTAGGG 57.496 45.455 0.00 0.00 0.00 3.53
1531 1548 4.108570 TGTTAGCTGGGATTTCTTAGGGA 58.891 43.478 0.00 0.00 0.00 4.20
1533 1550 5.014755 TGTTAGCTGGGATTTCTTAGGGAAA 59.985 40.000 0.00 0.00 46.33 3.13
1535 1552 4.604156 AGCTGGGATTTCTTAGGGAAAAG 58.396 43.478 0.00 0.00 45.56 2.27
1536 1553 4.292306 AGCTGGGATTTCTTAGGGAAAAGA 59.708 41.667 0.00 0.00 45.56 2.52
1537 1554 5.043806 AGCTGGGATTTCTTAGGGAAAAGAT 60.044 40.000 0.00 0.00 45.56 2.40
1539 1556 6.183360 GCTGGGATTTCTTAGGGAAAAGATTC 60.183 42.308 0.00 0.00 45.56 2.52
1552 1569 0.395724 AAGATTCCCATCAACCGGCC 60.396 55.000 0.00 0.00 0.00 6.13
1553 1570 2.124320 ATTCCCATCAACCGGCCG 60.124 61.111 21.04 21.04 0.00 6.13
1554 1571 2.602746 GATTCCCATCAACCGGCCGA 62.603 60.000 30.73 6.75 0.00 5.54
1555 1572 1.994885 ATTCCCATCAACCGGCCGAT 61.995 55.000 30.73 6.36 0.00 4.18
1556 1573 2.124320 CCCATCAACCGGCCGATT 60.124 61.111 30.73 15.33 0.00 3.34
1557 1574 1.147376 CCCATCAACCGGCCGATTA 59.853 57.895 30.73 9.54 0.00 1.75
1558 1575 1.164041 CCCATCAACCGGCCGATTAC 61.164 60.000 30.73 0.00 0.00 1.89
1559 1576 0.462937 CCATCAACCGGCCGATTACA 60.463 55.000 30.73 6.02 0.00 2.41
1560 1577 1.374560 CATCAACCGGCCGATTACAA 58.625 50.000 30.73 4.93 0.00 2.41
1561 1578 1.946768 CATCAACCGGCCGATTACAAT 59.053 47.619 30.73 7.49 0.00 2.71
1562 1579 1.658994 TCAACCGGCCGATTACAATC 58.341 50.000 30.73 0.00 0.00 2.67
1572 1589 2.347023 GATTACAATCGCAACGTCCG 57.653 50.000 0.00 0.00 0.00 4.79
1573 1590 0.372334 ATTACAATCGCAACGTCCGC 59.628 50.000 3.94 2.02 0.00 5.54
1574 1591 1.628447 TTACAATCGCAACGTCCGCC 61.628 55.000 4.50 0.00 0.00 6.13
1581 1598 3.186047 CAACGTCCGCCGCCTTAG 61.186 66.667 0.00 0.00 41.42 2.18
1583 1600 3.637926 AACGTCCGCCGCCTTAGAC 62.638 63.158 0.00 0.00 41.42 2.59
1584 1601 4.124351 CGTCCGCCGCCTTAGACA 62.124 66.667 0.00 0.00 0.00 3.41
1585 1602 2.508663 GTCCGCCGCCTTAGACAC 60.509 66.667 0.00 0.00 0.00 3.67
1586 1603 4.124351 TCCGCCGCCTTAGACACG 62.124 66.667 0.00 0.00 0.00 4.49
1592 1609 3.488090 GCCTTAGACACGCGCCAC 61.488 66.667 5.73 0.00 0.00 5.01
1608 1625 3.224324 ACGCGTCCTGTGTGAGGT 61.224 61.111 5.58 0.00 43.37 3.85
1609 1626 2.734723 CGCGTCCTGTGTGAGGTG 60.735 66.667 0.00 0.00 43.37 4.00
1610 1627 2.734591 GCGTCCTGTGTGAGGTGA 59.265 61.111 0.00 0.00 43.37 4.02
1612 1629 0.946221 GCGTCCTGTGTGAGGTGAAG 60.946 60.000 0.00 0.00 43.37 3.02
1613 1630 0.946221 CGTCCTGTGTGAGGTGAAGC 60.946 60.000 0.00 0.00 43.37 3.86
1616 1633 0.037303 CCTGTGTGAGGTGAAGCCAT 59.963 55.000 0.00 0.00 40.61 4.40
1617 1634 1.446907 CTGTGTGAGGTGAAGCCATC 58.553 55.000 0.00 0.00 40.61 3.51
1618 1635 0.764271 TGTGTGAGGTGAAGCCATCA 59.236 50.000 0.00 0.00 40.61 3.07
1625 1642 3.067985 TGAAGCCATCACCGCTCA 58.932 55.556 0.00 0.00 34.84 4.26
1626 1643 1.603842 TGAAGCCATCACCGCTCAT 59.396 52.632 0.00 0.00 34.84 2.90
1627 1644 0.462581 TGAAGCCATCACCGCTCATC 60.463 55.000 0.00 0.00 34.84 2.92
1628 1645 1.153086 AAGCCATCACCGCTCATCC 60.153 57.895 0.00 0.00 34.84 3.51
1629 1646 2.592861 GCCATCACCGCTCATCCC 60.593 66.667 0.00 0.00 0.00 3.85
1631 1648 2.446848 CCATCACCGCTCATCCCCT 61.447 63.158 0.00 0.00 0.00 4.79
1632 1649 1.528824 CATCACCGCTCATCCCCTT 59.471 57.895 0.00 0.00 0.00 3.95
1636 1653 0.830648 CACCGCTCATCCCCTTCTTA 59.169 55.000 0.00 0.00 0.00 2.10
1637 1654 1.417890 CACCGCTCATCCCCTTCTTAT 59.582 52.381 0.00 0.00 0.00 1.73
1638 1655 1.694696 ACCGCTCATCCCCTTCTTATC 59.305 52.381 0.00 0.00 0.00 1.75
1640 1657 2.370189 CCGCTCATCCCCTTCTTATCTT 59.630 50.000 0.00 0.00 0.00 2.40
1641 1658 3.556004 CCGCTCATCCCCTTCTTATCTTC 60.556 52.174 0.00 0.00 0.00 2.87
1642 1659 3.070159 CGCTCATCCCCTTCTTATCTTCA 59.930 47.826 0.00 0.00 0.00 3.02
1644 1661 5.629125 GCTCATCCCCTTCTTATCTTCATT 58.371 41.667 0.00 0.00 0.00 2.57
1645 1662 5.704978 GCTCATCCCCTTCTTATCTTCATTC 59.295 44.000 0.00 0.00 0.00 2.67
1646 1663 5.858381 TCATCCCCTTCTTATCTTCATTCG 58.142 41.667 0.00 0.00 0.00 3.34
1647 1664 5.366768 TCATCCCCTTCTTATCTTCATTCGT 59.633 40.000 0.00 0.00 0.00 3.85
1648 1665 5.277857 TCCCCTTCTTATCTTCATTCGTC 57.722 43.478 0.00 0.00 0.00 4.20
1651 1668 4.509600 CCCTTCTTATCTTCATTCGTCTGC 59.490 45.833 0.00 0.00 0.00 4.26
1652 1669 5.111989 CCTTCTTATCTTCATTCGTCTGCA 58.888 41.667 0.00 0.00 0.00 4.41
1653 1670 5.757320 CCTTCTTATCTTCATTCGTCTGCAT 59.243 40.000 0.00 0.00 0.00 3.96
1655 1672 6.154203 TCTTATCTTCATTCGTCTGCATCT 57.846 37.500 0.00 0.00 0.00 2.90
1656 1673 7.277174 TCTTATCTTCATTCGTCTGCATCTA 57.723 36.000 0.00 0.00 0.00 1.98
1657 1674 7.366513 TCTTATCTTCATTCGTCTGCATCTAG 58.633 38.462 0.00 0.00 0.00 2.43
1658 1675 3.711086 TCTTCATTCGTCTGCATCTAGC 58.289 45.455 0.00 0.00 45.96 3.42
1659 1676 3.382865 TCTTCATTCGTCTGCATCTAGCT 59.617 43.478 0.00 0.00 45.94 3.32
1660 1677 3.089573 TCATTCGTCTGCATCTAGCTG 57.910 47.619 0.00 0.00 45.94 4.24
1661 1678 1.526041 CATTCGTCTGCATCTAGCTGC 59.474 52.381 11.65 11.65 45.94 5.25
1685 1702 4.576879 TGCTCAGATGCATATCTCAATCC 58.423 43.478 0.00 0.00 41.71 3.01
1688 1705 5.122554 GCTCAGATGCATATCTCAATCCAAG 59.877 44.000 0.00 0.00 41.71 3.61
1689 1706 5.001874 TCAGATGCATATCTCAATCCAAGC 58.998 41.667 0.00 0.00 41.71 4.01
1690 1707 4.001652 AGATGCATATCTCAATCCAAGCG 58.998 43.478 0.00 0.00 39.46 4.68
1691 1708 3.198409 TGCATATCTCAATCCAAGCGT 57.802 42.857 0.00 0.00 0.00 5.07
1692 1709 3.544684 TGCATATCTCAATCCAAGCGTT 58.455 40.909 0.00 0.00 0.00 4.84
1693 1710 3.313249 TGCATATCTCAATCCAAGCGTTG 59.687 43.478 0.00 0.00 0.00 4.10
1694 1711 3.561310 GCATATCTCAATCCAAGCGTTGA 59.439 43.478 0.15 0.00 33.63 3.18
1695 1712 4.553547 GCATATCTCAATCCAAGCGTTGAC 60.554 45.833 0.15 0.00 31.55 3.18
1696 1713 1.808411 TCTCAATCCAAGCGTTGACC 58.192 50.000 0.15 0.00 31.55 4.02
1697 1714 1.347707 TCTCAATCCAAGCGTTGACCT 59.652 47.619 0.15 0.00 31.55 3.85
1698 1715 2.154462 CTCAATCCAAGCGTTGACCTT 58.846 47.619 0.15 0.00 31.55 3.50
1699 1716 1.879380 TCAATCCAAGCGTTGACCTTG 59.121 47.619 0.00 0.00 39.44 3.61
1700 1717 1.608590 CAATCCAAGCGTTGACCTTGT 59.391 47.619 9.76 0.00 38.36 3.16
1701 1718 1.523758 ATCCAAGCGTTGACCTTGTC 58.476 50.000 9.76 0.00 38.36 3.18
1702 1719 0.534203 TCCAAGCGTTGACCTTGTCC 60.534 55.000 9.76 0.00 38.36 4.02
1703 1720 0.817634 CCAAGCGTTGACCTTGTCCA 60.818 55.000 9.76 0.00 38.36 4.02
1704 1721 1.238439 CAAGCGTTGACCTTGTCCAT 58.762 50.000 0.00 0.00 35.97 3.41
1705 1722 1.069022 CAAGCGTTGACCTTGTCCATG 60.069 52.381 0.00 0.00 35.97 3.66
1706 1723 0.396435 AGCGTTGACCTTGTCCATGA 59.604 50.000 0.00 0.00 0.00 3.07
1707 1724 0.517316 GCGTTGACCTTGTCCATGAC 59.483 55.000 0.00 0.00 0.00 3.06
1708 1725 0.790207 CGTTGACCTTGTCCATGACG 59.210 55.000 0.00 0.00 34.95 4.35
1709 1726 1.604438 CGTTGACCTTGTCCATGACGA 60.604 52.381 0.00 0.00 34.95 4.20
1710 1727 2.069273 GTTGACCTTGTCCATGACGAG 58.931 52.381 0.00 4.76 42.12 4.18
1711 1728 1.338107 TGACCTTGTCCATGACGAGT 58.662 50.000 9.91 0.00 41.20 4.18
1712 1729 2.521126 TGACCTTGTCCATGACGAGTA 58.479 47.619 9.91 0.00 41.20 2.59
1713 1730 2.492088 TGACCTTGTCCATGACGAGTAG 59.508 50.000 9.91 0.12 41.20 2.57
1714 1731 1.204941 ACCTTGTCCATGACGAGTAGC 59.795 52.381 9.91 0.00 41.20 3.58
1715 1732 1.204704 CCTTGTCCATGACGAGTAGCA 59.795 52.381 9.91 0.00 41.20 3.49
1716 1733 2.263077 CTTGTCCATGACGAGTAGCAC 58.737 52.381 0.00 0.00 38.77 4.40
1717 1734 0.530744 TGTCCATGACGAGTAGCACC 59.469 55.000 0.00 0.00 34.95 5.01
1718 1735 0.179108 GTCCATGACGAGTAGCACCC 60.179 60.000 0.00 0.00 0.00 4.61
1719 1736 1.144057 CCATGACGAGTAGCACCCC 59.856 63.158 0.00 0.00 0.00 4.95
1720 1737 1.613317 CCATGACGAGTAGCACCCCA 61.613 60.000 0.00 0.00 0.00 4.96
1721 1738 0.465705 CATGACGAGTAGCACCCCAT 59.534 55.000 0.00 0.00 0.00 4.00
1722 1739 0.465705 ATGACGAGTAGCACCCCATG 59.534 55.000 0.00 0.00 0.00 3.66
1723 1740 1.144057 GACGAGTAGCACCCCATGG 59.856 63.158 4.14 4.14 37.80 3.66
1724 1741 2.203070 CGAGTAGCACCCCATGGC 60.203 66.667 6.09 0.00 33.59 4.40
1725 1742 2.193248 GAGTAGCACCCCATGGCC 59.807 66.667 6.09 0.00 33.59 5.36
1726 1743 3.757248 GAGTAGCACCCCATGGCCG 62.757 68.421 6.09 0.10 33.59 6.13
1727 1744 4.875713 GTAGCACCCCATGGCCGG 62.876 72.222 6.09 5.77 33.59 6.13
1757 1774 3.264897 CGGCCTGCGAGTATGCAC 61.265 66.667 0.00 0.00 40.62 4.57
1758 1775 2.187946 GGCCTGCGAGTATGCACT 59.812 61.111 0.00 0.00 40.62 4.40
1759 1776 1.441729 GGCCTGCGAGTATGCACTA 59.558 57.895 0.00 0.00 40.62 2.74
1760 1777 0.598680 GGCCTGCGAGTATGCACTAG 60.599 60.000 0.00 0.00 40.62 2.57
1763 1780 3.923614 GCGAGTATGCACTAGCGG 58.076 61.111 0.00 0.00 42.40 5.52
1764 1781 2.303676 GCGAGTATGCACTAGCGGC 61.304 63.158 0.00 0.00 42.40 6.53
1765 1782 1.360551 CGAGTATGCACTAGCGGCT 59.639 57.895 7.98 7.98 46.23 5.52
1766 1783 0.936764 CGAGTATGCACTAGCGGCTG 60.937 60.000 13.86 5.32 46.23 4.85
1767 1784 0.385751 GAGTATGCACTAGCGGCTGA 59.614 55.000 13.86 0.00 46.23 4.26
1768 1785 1.000283 GAGTATGCACTAGCGGCTGAT 60.000 52.381 13.86 0.00 46.23 2.90
1769 1786 1.414181 AGTATGCACTAGCGGCTGATT 59.586 47.619 13.86 0.00 46.23 2.57
1770 1787 2.158900 AGTATGCACTAGCGGCTGATTT 60.159 45.455 13.86 0.00 46.23 2.17
1771 1788 1.755179 ATGCACTAGCGGCTGATTTT 58.245 45.000 13.86 0.00 46.23 1.82
1772 1789 0.804364 TGCACTAGCGGCTGATTTTG 59.196 50.000 13.86 3.46 46.23 2.44
1773 1790 0.804989 GCACTAGCGGCTGATTTTGT 59.195 50.000 13.86 0.00 0.00 2.83
1774 1791 1.200020 GCACTAGCGGCTGATTTTGTT 59.800 47.619 13.86 0.00 0.00 2.83
1775 1792 2.855180 CACTAGCGGCTGATTTTGTTG 58.145 47.619 13.86 0.00 0.00 3.33
1776 1793 2.483877 CACTAGCGGCTGATTTTGTTGA 59.516 45.455 13.86 0.00 0.00 3.18
1777 1794 3.127548 CACTAGCGGCTGATTTTGTTGAT 59.872 43.478 13.86 0.00 0.00 2.57
1778 1795 2.642139 AGCGGCTGATTTTGTTGATG 57.358 45.000 0.00 0.00 0.00 3.07
1779 1796 0.994263 GCGGCTGATTTTGTTGATGC 59.006 50.000 0.00 0.00 0.00 3.91
1780 1797 1.403249 GCGGCTGATTTTGTTGATGCT 60.403 47.619 0.00 0.00 0.00 3.79
1781 1798 2.256174 CGGCTGATTTTGTTGATGCTG 58.744 47.619 0.00 0.00 0.00 4.41
1782 1799 2.613691 GGCTGATTTTGTTGATGCTGG 58.386 47.619 0.00 0.00 0.00 4.85
1783 1800 2.231964 GGCTGATTTTGTTGATGCTGGA 59.768 45.455 0.00 0.00 0.00 3.86
1784 1801 3.306225 GGCTGATTTTGTTGATGCTGGAA 60.306 43.478 0.00 0.00 0.00 3.53
1785 1802 3.924686 GCTGATTTTGTTGATGCTGGAAG 59.075 43.478 0.00 0.00 0.00 3.46
1808 1825 4.969196 CACTCGGGTGCTGCGTGT 62.969 66.667 0.51 0.00 36.61 4.49
1809 1826 4.664677 ACTCGGGTGCTGCGTGTC 62.665 66.667 0.00 0.00 0.00 3.67
1877 1894 3.423154 CCGTTGAAGCCTGCCGTC 61.423 66.667 0.00 0.00 0.00 4.79
1878 1895 3.777925 CGTTGAAGCCTGCCGTCG 61.778 66.667 0.00 0.00 0.00 5.12
1879 1896 4.090057 GTTGAAGCCTGCCGTCGC 62.090 66.667 0.00 0.00 0.00 5.19
1880 1897 4.314440 TTGAAGCCTGCCGTCGCT 62.314 61.111 0.00 0.00 36.74 4.93
1881 1898 4.742201 TGAAGCCTGCCGTCGCTC 62.742 66.667 0.00 0.00 33.09 5.03
1890 1907 4.394078 CCGTCGCTCGTCGTTCCA 62.394 66.667 7.93 0.00 39.67 3.53
1891 1908 3.164011 CGTCGCTCGTCGTTCCAC 61.164 66.667 1.17 0.00 39.67 4.02
1892 1909 3.164011 GTCGCTCGTCGTTCCACG 61.164 66.667 0.00 0.00 44.19 4.94
1893 1910 3.653009 TCGCTCGTCGTTCCACGT 61.653 61.111 0.00 0.00 43.14 4.49
1894 1911 3.164011 CGCTCGTCGTTCCACGTC 61.164 66.667 0.00 0.00 43.14 4.34
1895 1912 2.050714 GCTCGTCGTTCCACGTCA 60.051 61.111 0.00 0.00 43.14 4.35
1896 1913 2.081212 GCTCGTCGTTCCACGTCAG 61.081 63.158 0.00 0.00 43.14 3.51
1897 1914 1.442184 CTCGTCGTTCCACGTCAGG 60.442 63.158 0.00 0.00 43.14 3.86
1898 1915 1.848932 CTCGTCGTTCCACGTCAGGA 61.849 60.000 0.00 0.00 43.14 3.86
1899 1916 1.728426 CGTCGTTCCACGTCAGGAC 60.728 63.158 0.00 0.00 43.14 3.85
1900 1917 1.372623 GTCGTTCCACGTCAGGACC 60.373 63.158 0.00 0.00 43.14 4.46
1901 1918 1.829096 TCGTTCCACGTCAGGACCA 60.829 57.895 0.00 0.00 43.14 4.02
1902 1919 1.183030 TCGTTCCACGTCAGGACCAT 61.183 55.000 0.00 0.00 43.14 3.55
1903 1920 0.320421 CGTTCCACGTCAGGACCATT 60.320 55.000 0.00 0.00 37.42 3.16
1904 1921 1.439679 GTTCCACGTCAGGACCATTC 58.560 55.000 0.00 0.00 37.42 2.67
1905 1922 0.037697 TTCCACGTCAGGACCATTCG 60.038 55.000 0.00 0.00 37.42 3.34
1906 1923 1.447838 CCACGTCAGGACCATTCGG 60.448 63.158 0.00 0.00 38.77 4.30
1917 1934 3.328050 AGGACCATTCGGGAGGATTAATC 59.672 47.826 6.93 6.93 41.15 1.75
2013 2030 3.608316 AGAGACTCTCTTGATTGTGCC 57.392 47.619 2.39 0.00 37.60 5.01
2019 2036 4.464008 ACTCTCTTGATTGTGCCAAGAAA 58.536 39.130 0.00 0.00 46.29 2.52
2022 2039 6.716628 ACTCTCTTGATTGTGCCAAGAAATTA 59.283 34.615 0.00 0.00 46.29 1.40
2049 2066 7.781056 AGTGGATCTTAACTTGCTTTGAAAAA 58.219 30.769 0.00 0.00 0.00 1.94
2057 2074 9.139174 CTTAACTTGCTTTGAAAAACTTTCTGA 57.861 29.630 1.22 0.00 0.00 3.27
2110 2127 6.198650 TGCATACCATGAATGTTTCTGAAG 57.801 37.500 0.00 0.00 0.00 3.02
2136 2153 6.599244 CCATGTCTAAAGAATTTGCTCAGGTA 59.401 38.462 0.00 0.00 39.63 3.08
2142 2159 9.077885 TCTAAAGAATTTGCTCAGGTATTTTGT 57.922 29.630 0.00 0.00 39.63 2.83
2290 2307 8.854117 GGAAACATCTTTCATATAGAGGCAAAT 58.146 33.333 0.00 0.00 38.04 2.32
2305 2322 7.187824 AGAGGCAAATTGATCTTACTCACTA 57.812 36.000 0.00 0.00 0.00 2.74
2310 2327 7.119846 GGCAAATTGATCTTACTCACTACTTGT 59.880 37.037 0.00 0.00 0.00 3.16
2311 2328 9.151471 GCAAATTGATCTTACTCACTACTTGTA 57.849 33.333 0.00 0.00 0.00 2.41
2315 2332 8.703604 TTGATCTTACTCACTACTTGTATTGC 57.296 34.615 0.00 0.00 0.00 3.56
2316 2333 7.265673 TGATCTTACTCACTACTTGTATTGCC 58.734 38.462 0.00 0.00 0.00 4.52
2317 2334 6.599356 TCTTACTCACTACTTGTATTGCCA 57.401 37.500 0.00 0.00 0.00 4.92
2318 2335 6.631016 TCTTACTCACTACTTGTATTGCCAG 58.369 40.000 0.00 0.00 0.00 4.85
2319 2336 4.891992 ACTCACTACTTGTATTGCCAGT 57.108 40.909 0.00 0.00 0.00 4.00
2320 2337 5.995565 ACTCACTACTTGTATTGCCAGTA 57.004 39.130 0.00 0.00 0.00 2.74
2321 2338 6.546428 ACTCACTACTTGTATTGCCAGTAT 57.454 37.500 0.00 0.00 0.00 2.12
2322 2339 6.574350 ACTCACTACTTGTATTGCCAGTATC 58.426 40.000 0.00 0.00 0.00 2.24
2323 2340 5.914033 TCACTACTTGTATTGCCAGTATCC 58.086 41.667 0.00 0.00 0.00 2.59
2324 2341 5.057149 CACTACTTGTATTGCCAGTATCCC 58.943 45.833 0.00 0.00 0.00 3.85
2325 2342 4.969359 ACTACTTGTATTGCCAGTATCCCT 59.031 41.667 0.00 0.00 0.00 4.20
2326 2343 4.156455 ACTTGTATTGCCAGTATCCCTG 57.844 45.455 0.00 0.00 41.15 4.45
2327 2344 2.638480 TGTATTGCCAGTATCCCTGC 57.362 50.000 0.00 0.00 40.06 4.85
2328 2345 1.142870 TGTATTGCCAGTATCCCTGCC 59.857 52.381 0.00 0.00 40.06 4.85
2329 2346 1.421646 GTATTGCCAGTATCCCTGCCT 59.578 52.381 0.00 0.00 40.06 4.75
2330 2347 1.819753 ATTGCCAGTATCCCTGCCTA 58.180 50.000 0.00 0.00 40.06 3.93
2331 2348 1.819753 TTGCCAGTATCCCTGCCTAT 58.180 50.000 0.00 0.00 40.06 2.57
2332 2349 1.819753 TGCCAGTATCCCTGCCTATT 58.180 50.000 0.00 0.00 40.06 1.73
2333 2350 2.135189 TGCCAGTATCCCTGCCTATTT 58.865 47.619 0.00 0.00 40.06 1.40
2334 2351 3.322862 TGCCAGTATCCCTGCCTATTTA 58.677 45.455 0.00 0.00 40.06 1.40
2335 2352 3.719479 TGCCAGTATCCCTGCCTATTTAA 59.281 43.478 0.00 0.00 40.06 1.52
2336 2353 4.353788 TGCCAGTATCCCTGCCTATTTAAT 59.646 41.667 0.00 0.00 40.06 1.40
2337 2354 4.702131 GCCAGTATCCCTGCCTATTTAATG 59.298 45.833 0.00 0.00 40.06 1.90
2338 2355 5.749032 GCCAGTATCCCTGCCTATTTAATGT 60.749 44.000 0.00 0.00 40.06 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 273 2.035155 TCGGTCGCCTCCTCTTCA 59.965 61.111 0.00 0.00 0.00 3.02
327 328 2.029666 CGAGATCCGGATGGTGCC 59.970 66.667 24.82 6.85 36.30 5.01
375 376 3.073062 GCAAAAGCTATATCCCTGGGAGA 59.927 47.826 21.99 17.87 34.05 3.71
406 409 1.666888 GCAAAAGCATTGGACCGAGTG 60.667 52.381 4.67 0.00 0.00 3.51
414 417 0.883833 AGAGGACGCAAAAGCATTGG 59.116 50.000 4.67 0.00 0.00 3.16
462 466 5.584251 GGAAGAGAATTCACATCTGAAGGAC 59.416 44.000 8.44 0.00 39.83 3.85
484 488 1.301716 GACAAAGCAGCAGTCGGGA 60.302 57.895 0.00 0.00 0.00 5.14
487 491 1.923316 GCAAAGACAAAGCAGCAGTCG 60.923 52.381 0.00 0.00 37.36 4.18
513 517 2.680352 GGACGTGGCTCAGGGAGA 60.680 66.667 0.00 0.00 0.00 3.71
514 518 3.775654 GGGACGTGGCTCAGGGAG 61.776 72.222 0.00 0.00 0.00 4.30
554 566 2.834549 CAGTACAATCCTCTGGTCACCT 59.165 50.000 0.00 0.00 0.00 4.00
707 720 4.475944 AGCATCTTTTAACATCAACGTGC 58.524 39.130 0.00 0.00 0.00 5.34
720 733 3.365364 GCGCAGTTACTCAAGCATCTTTT 60.365 43.478 0.30 0.00 0.00 2.27
785 798 5.567138 AGAAATTAATTTGCCACGGAGAG 57.433 39.130 17.98 0.00 0.00 3.20
790 803 8.909708 TGATTAGAAGAAATTAATTTGCCACG 57.090 30.769 17.98 0.00 0.00 4.94
816 829 3.060895 CGTTTCTTATGGACGCTCTTGTC 59.939 47.826 0.00 0.00 38.17 3.18
817 830 2.993899 CGTTTCTTATGGACGCTCTTGT 59.006 45.455 0.00 0.00 0.00 3.16
860 875 3.482436 ACATTTAGTTTCACGAAGCCCA 58.518 40.909 0.00 0.00 0.00 5.36
906 921 0.837272 CACCCATCATCCCCGTTAGT 59.163 55.000 0.00 0.00 0.00 2.24
917 932 1.277273 CTCTCAAGACTGCACCCATCA 59.723 52.381 0.00 0.00 0.00 3.07
942 957 6.488769 TCTCCCGCAATAAACCTATCTTTA 57.511 37.500 0.00 0.00 0.00 1.85
965 980 8.342634 CCGTACAATATTCGATCTTTCCATTTT 58.657 33.333 0.00 0.00 0.00 1.82
1062 1077 8.927411 TCCATATTGTCTGAGTTGATGATTAGA 58.073 33.333 0.00 0.00 0.00 2.10
1110 1125 1.918293 ACCCGCTGATTGTCCTCCA 60.918 57.895 0.00 0.00 0.00 3.86
1178 1193 4.174009 ACAATGTTCGAATCTAGTCACGG 58.826 43.478 0.00 0.00 0.00 4.94
1207 1223 4.144297 TCATGAGCTACTTTGTTTGCCTT 58.856 39.130 0.00 0.00 0.00 4.35
1365 1381 5.745312 TGAAGGCAGTCTGATTAGAAGAA 57.255 39.130 3.32 0.00 34.01 2.52
1366 1382 5.745312 TTGAAGGCAGTCTGATTAGAAGA 57.255 39.130 3.32 0.00 34.01 2.87
1367 1383 8.498054 TTTATTGAAGGCAGTCTGATTAGAAG 57.502 34.615 3.32 0.00 34.01 2.85
1368 1384 8.498054 CTTTATTGAAGGCAGTCTGATTAGAA 57.502 34.615 3.32 0.00 34.01 2.10
1388 1404 9.413734 CACTTTTCAGGATAAATCTCCCTTTAT 57.586 33.333 0.00 0.00 35.79 1.40
1393 1409 5.358160 CCACACTTTTCAGGATAAATCTCCC 59.642 44.000 0.00 0.00 35.79 4.30
1405 1421 1.270550 GGCCATGACCACACTTTTCAG 59.729 52.381 0.00 0.00 0.00 3.02
1451 1467 1.668826 TCAACCCACTAGCCCAGATT 58.331 50.000 0.00 0.00 0.00 2.40
1487 1504 8.450578 AACAACTCTTGTCATATGTTTTCTCA 57.549 30.769 1.90 0.00 44.59 3.27
1494 1511 5.877012 CCAGCTAACAACTCTTGTCATATGT 59.123 40.000 1.90 0.00 44.59 2.29
1495 1512 5.295292 CCCAGCTAACAACTCTTGTCATATG 59.705 44.000 0.00 0.00 44.59 1.78
1502 1519 5.006386 AGAAATCCCAGCTAACAACTCTTG 58.994 41.667 0.00 0.00 0.00 3.02
1504 1521 4.917906 AGAAATCCCAGCTAACAACTCT 57.082 40.909 0.00 0.00 0.00 3.24
1505 1522 5.586643 CCTAAGAAATCCCAGCTAACAACTC 59.413 44.000 0.00 0.00 0.00 3.01
1506 1523 5.501156 CCTAAGAAATCCCAGCTAACAACT 58.499 41.667 0.00 0.00 0.00 3.16
1507 1524 4.640647 CCCTAAGAAATCCCAGCTAACAAC 59.359 45.833 0.00 0.00 0.00 3.32
1508 1525 4.538490 TCCCTAAGAAATCCCAGCTAACAA 59.462 41.667 0.00 0.00 0.00 2.83
1509 1526 4.108570 TCCCTAAGAAATCCCAGCTAACA 58.891 43.478 0.00 0.00 0.00 2.41
1530 1547 2.159240 GCCGGTTGATGGGAATCTTTTC 60.159 50.000 1.90 0.00 0.00 2.29
1531 1548 1.824852 GCCGGTTGATGGGAATCTTTT 59.175 47.619 1.90 0.00 0.00 2.27
1533 1550 0.395724 GGCCGGTTGATGGGAATCTT 60.396 55.000 1.90 0.00 0.00 2.40
1535 1552 2.186826 CGGCCGGTTGATGGGAATC 61.187 63.158 20.10 0.00 0.00 2.52
1536 1553 1.994885 ATCGGCCGGTTGATGGGAAT 61.995 55.000 27.83 3.72 0.00 3.01
1537 1554 2.204865 AATCGGCCGGTTGATGGGAA 62.205 55.000 25.77 0.00 0.00 3.97
1539 1556 1.147376 TAATCGGCCGGTTGATGGG 59.853 57.895 33.45 0.00 0.00 4.00
1541 1558 1.374560 TTGTAATCGGCCGGTTGATG 58.625 50.000 33.45 0.00 0.00 3.07
1542 1559 2.218603 GATTGTAATCGGCCGGTTGAT 58.781 47.619 33.45 22.52 0.00 2.57
1553 1570 1.591394 GCGGACGTTGCGATTGTAATC 60.591 52.381 0.00 0.00 30.86 1.75
1554 1571 0.372334 GCGGACGTTGCGATTGTAAT 59.628 50.000 0.00 0.00 30.86 1.89
1555 1572 1.628447 GGCGGACGTTGCGATTGTAA 61.628 55.000 7.51 0.00 30.86 2.41
1556 1573 2.095847 GGCGGACGTTGCGATTGTA 61.096 57.895 7.51 0.00 30.86 2.41
1557 1574 3.419759 GGCGGACGTTGCGATTGT 61.420 61.111 7.51 0.00 30.86 2.71
1558 1575 4.499023 CGGCGGACGTTGCGATTG 62.499 66.667 0.00 0.00 37.93 2.67
1564 1581 3.186047 CTAAGGCGGCGGACGTTG 61.186 66.667 9.78 0.00 46.52 4.10
1565 1582 3.376078 TCTAAGGCGGCGGACGTT 61.376 61.111 9.78 3.22 46.52 3.99
1566 1583 4.125695 GTCTAAGGCGGCGGACGT 62.126 66.667 9.78 0.00 46.52 4.34
1568 1585 2.508663 GTGTCTAAGGCGGCGGAC 60.509 66.667 19.56 19.56 0.00 4.79
1569 1586 4.124351 CGTGTCTAAGGCGGCGGA 62.124 66.667 9.78 0.33 0.00 5.54
1576 1593 3.179265 CGTGGCGCGTGTCTAAGG 61.179 66.667 13.13 0.00 35.54 2.69
1577 1594 3.838795 GCGTGGCGCGTGTCTAAG 61.839 66.667 22.49 0.00 44.55 2.18
1588 1605 4.961511 TCACACAGGACGCGTGGC 62.962 66.667 20.70 1.83 38.74 5.01
1598 1615 1.271001 TGATGGCTTCACCTCACACAG 60.271 52.381 0.00 0.00 40.22 3.66
1599 1616 0.764271 TGATGGCTTCACCTCACACA 59.236 50.000 0.00 0.00 40.22 3.72
1608 1625 0.462581 GATGAGCGGTGATGGCTTCA 60.463 55.000 0.00 0.00 41.72 3.02
1609 1626 1.162800 GGATGAGCGGTGATGGCTTC 61.163 60.000 0.00 0.00 41.72 3.86
1610 1627 1.153086 GGATGAGCGGTGATGGCTT 60.153 57.895 0.00 0.00 41.72 4.35
1612 1629 2.592861 GGGATGAGCGGTGATGGC 60.593 66.667 0.00 0.00 0.00 4.40
1613 1630 1.987807 AAGGGGATGAGCGGTGATGG 61.988 60.000 0.00 0.00 0.00 3.51
1616 1633 0.909610 AAGAAGGGGATGAGCGGTGA 60.910 55.000 0.00 0.00 0.00 4.02
1617 1634 0.830648 TAAGAAGGGGATGAGCGGTG 59.169 55.000 0.00 0.00 0.00 4.94
1618 1635 1.694696 GATAAGAAGGGGATGAGCGGT 59.305 52.381 0.00 0.00 0.00 5.68
1619 1636 1.974236 AGATAAGAAGGGGATGAGCGG 59.026 52.381 0.00 0.00 0.00 5.52
1620 1637 3.070159 TGAAGATAAGAAGGGGATGAGCG 59.930 47.826 0.00 0.00 0.00 5.03
1621 1638 4.696479 TGAAGATAAGAAGGGGATGAGC 57.304 45.455 0.00 0.00 0.00 4.26
1622 1639 5.931146 CGAATGAAGATAAGAAGGGGATGAG 59.069 44.000 0.00 0.00 0.00 2.90
1623 1640 5.366768 ACGAATGAAGATAAGAAGGGGATGA 59.633 40.000 0.00 0.00 0.00 2.92
1625 1642 5.604650 AGACGAATGAAGATAAGAAGGGGAT 59.395 40.000 0.00 0.00 0.00 3.85
1626 1643 4.962995 AGACGAATGAAGATAAGAAGGGGA 59.037 41.667 0.00 0.00 0.00 4.81
1627 1644 5.053145 CAGACGAATGAAGATAAGAAGGGG 58.947 45.833 0.00 0.00 0.00 4.79
1628 1645 4.509600 GCAGACGAATGAAGATAAGAAGGG 59.490 45.833 0.00 0.00 0.00 3.95
1629 1646 5.111989 TGCAGACGAATGAAGATAAGAAGG 58.888 41.667 0.00 0.00 0.00 3.46
1631 1648 6.577103 AGATGCAGACGAATGAAGATAAGAA 58.423 36.000 0.00 0.00 0.00 2.52
1632 1649 6.154203 AGATGCAGACGAATGAAGATAAGA 57.846 37.500 0.00 0.00 0.00 2.10
1636 1653 4.039004 AGCTAGATGCAGACGAATGAAGAT 59.961 41.667 0.00 0.00 45.94 2.40
1637 1654 3.382865 AGCTAGATGCAGACGAATGAAGA 59.617 43.478 0.00 0.00 45.94 2.87
1638 1655 3.490155 CAGCTAGATGCAGACGAATGAAG 59.510 47.826 0.00 0.00 45.94 3.02
1640 1657 2.800985 GCAGCTAGATGCAGACGAATGA 60.801 50.000 27.32 0.00 45.77 2.57
1641 1658 1.526041 GCAGCTAGATGCAGACGAATG 59.474 52.381 27.32 0.00 45.77 2.67
1642 1659 1.863267 GCAGCTAGATGCAGACGAAT 58.137 50.000 27.32 0.00 45.77 3.34
1664 1681 4.576879 TGGATTGAGATATGCATCTGAGC 58.423 43.478 0.19 0.00 41.78 4.26
1665 1682 5.122554 GCTTGGATTGAGATATGCATCTGAG 59.877 44.000 0.19 0.00 41.78 3.35
1667 1684 4.142881 CGCTTGGATTGAGATATGCATCTG 60.143 45.833 0.19 0.00 41.78 2.90
1669 1686 3.750130 ACGCTTGGATTGAGATATGCATC 59.250 43.478 0.19 0.00 0.00 3.91
1670 1687 3.748083 ACGCTTGGATTGAGATATGCAT 58.252 40.909 3.79 3.79 0.00 3.96
1672 1689 3.561310 TCAACGCTTGGATTGAGATATGC 59.439 43.478 0.00 0.00 31.29 3.14
1673 1690 4.024556 GGTCAACGCTTGGATTGAGATATG 60.025 45.833 0.00 0.00 35.55 1.78
1674 1691 4.130118 GGTCAACGCTTGGATTGAGATAT 58.870 43.478 0.00 0.00 35.55 1.63
1676 1693 2.026822 AGGTCAACGCTTGGATTGAGAT 60.027 45.455 0.00 0.00 35.55 2.75
1677 1694 1.347707 AGGTCAACGCTTGGATTGAGA 59.652 47.619 0.00 0.00 35.55 3.27
1678 1695 1.813513 AGGTCAACGCTTGGATTGAG 58.186 50.000 0.00 0.00 35.55 3.02
1679 1696 1.879380 CAAGGTCAACGCTTGGATTGA 59.121 47.619 0.00 0.00 32.44 2.57
1680 1697 1.608590 ACAAGGTCAACGCTTGGATTG 59.391 47.619 12.74 6.74 32.27 2.67
1681 1698 1.880027 GACAAGGTCAACGCTTGGATT 59.120 47.619 12.74 0.00 32.27 3.01
1683 1700 0.534203 GGACAAGGTCAACGCTTGGA 60.534 55.000 12.74 0.00 33.68 3.53
1684 1701 0.817634 TGGACAAGGTCAACGCTTGG 60.818 55.000 12.74 0.00 33.68 3.61
1685 1702 1.069022 CATGGACAAGGTCAACGCTTG 60.069 52.381 0.00 0.00 33.68 4.01
1688 1705 0.517316 GTCATGGACAAGGTCAACGC 59.483 55.000 0.00 0.00 33.68 4.84
1689 1706 0.790207 CGTCATGGACAAGGTCAACG 59.210 55.000 0.00 0.00 33.68 4.10
1690 1707 2.069273 CTCGTCATGGACAAGGTCAAC 58.931 52.381 0.00 0.00 33.68 3.18
1691 1708 1.691976 ACTCGTCATGGACAAGGTCAA 59.308 47.619 0.00 0.00 33.68 3.18
1692 1709 1.338107 ACTCGTCATGGACAAGGTCA 58.662 50.000 0.00 0.00 33.68 4.02
1693 1710 2.735762 GCTACTCGTCATGGACAAGGTC 60.736 54.545 0.00 0.00 32.09 3.85
1694 1711 1.204941 GCTACTCGTCATGGACAAGGT 59.795 52.381 0.00 0.00 32.09 3.50
1695 1712 1.204704 TGCTACTCGTCATGGACAAGG 59.795 52.381 0.00 0.00 32.09 3.61
1696 1713 2.263077 GTGCTACTCGTCATGGACAAG 58.737 52.381 0.00 0.00 32.09 3.16
1697 1714 1.067142 GGTGCTACTCGTCATGGACAA 60.067 52.381 0.00 0.00 32.09 3.18
1698 1715 0.530744 GGTGCTACTCGTCATGGACA 59.469 55.000 0.00 0.00 32.09 4.02
1699 1716 0.179108 GGGTGCTACTCGTCATGGAC 60.179 60.000 0.00 0.00 0.00 4.02
1700 1717 1.327690 GGGGTGCTACTCGTCATGGA 61.328 60.000 0.00 0.00 0.00 3.41
1701 1718 1.144057 GGGGTGCTACTCGTCATGG 59.856 63.158 0.00 0.00 0.00 3.66
1702 1719 0.465705 ATGGGGTGCTACTCGTCATG 59.534 55.000 0.00 0.00 0.00 3.07
1703 1720 0.465705 CATGGGGTGCTACTCGTCAT 59.534 55.000 0.00 0.00 0.00 3.06
1704 1721 1.613317 CCATGGGGTGCTACTCGTCA 61.613 60.000 2.85 0.00 0.00 4.35
1705 1722 1.144057 CCATGGGGTGCTACTCGTC 59.856 63.158 2.85 0.00 0.00 4.20
1706 1723 3.031417 GCCATGGGGTGCTACTCGT 62.031 63.158 15.13 0.00 36.17 4.18
1707 1724 2.203070 GCCATGGGGTGCTACTCG 60.203 66.667 15.13 0.00 36.17 4.18
1708 1725 2.193248 GGCCATGGGGTGCTACTC 59.807 66.667 15.13 0.00 36.17 2.59
1709 1726 3.797353 CGGCCATGGGGTGCTACT 61.797 66.667 15.13 0.00 36.17 2.57
1710 1727 4.875713 CCGGCCATGGGGTGCTAC 62.876 72.222 15.13 0.00 36.17 3.58
1732 1749 4.435436 TCGCAGGCCGCTGTACTG 62.435 66.667 15.78 0.00 39.08 2.74
1733 1750 4.135153 CTCGCAGGCCGCTGTACT 62.135 66.667 15.78 0.00 39.08 2.73
1734 1751 2.351336 ATACTCGCAGGCCGCTGTAC 62.351 60.000 15.78 0.00 39.08 2.90
1735 1752 2.125326 ATACTCGCAGGCCGCTGTA 61.125 57.895 15.78 16.52 39.08 2.74
1736 1753 3.461773 ATACTCGCAGGCCGCTGT 61.462 61.111 15.78 15.27 39.08 4.40
1737 1754 2.963854 CATACTCGCAGGCCGCTG 60.964 66.667 15.78 11.24 39.08 5.18
1738 1755 4.899239 GCATACTCGCAGGCCGCT 62.899 66.667 15.78 2.38 39.08 5.52
1740 1757 2.349969 TAGTGCATACTCGCAGGCCG 62.350 60.000 0.00 0.00 44.05 6.13
1741 1758 0.598680 CTAGTGCATACTCGCAGGCC 60.599 60.000 0.00 0.00 44.05 5.19
1742 1759 1.218230 GCTAGTGCATACTCGCAGGC 61.218 60.000 0.00 0.00 44.05 4.85
1743 1760 0.936764 CGCTAGTGCATACTCGCAGG 60.937 60.000 0.00 0.00 43.63 4.85
1744 1761 0.936764 CCGCTAGTGCATACTCGCAG 60.937 60.000 0.00 0.00 43.63 5.18
1745 1762 1.065764 CCGCTAGTGCATACTCGCA 59.934 57.895 0.00 0.00 43.63 5.10
1746 1763 2.303676 GCCGCTAGTGCATACTCGC 61.304 63.158 0.00 0.00 40.97 5.03
1747 1764 0.936764 CAGCCGCTAGTGCATACTCG 60.937 60.000 8.74 0.00 38.36 4.18
1748 1765 0.385751 TCAGCCGCTAGTGCATACTC 59.614 55.000 8.74 0.00 38.36 2.59
1749 1766 1.043816 ATCAGCCGCTAGTGCATACT 58.956 50.000 8.74 0.00 40.99 2.12
1750 1767 1.871080 AATCAGCCGCTAGTGCATAC 58.129 50.000 8.74 0.00 39.64 2.39
1751 1768 2.613595 CAAAATCAGCCGCTAGTGCATA 59.386 45.455 8.74 0.00 39.64 3.14
1752 1769 1.402968 CAAAATCAGCCGCTAGTGCAT 59.597 47.619 8.74 0.00 39.64 3.96
1753 1770 0.804364 CAAAATCAGCCGCTAGTGCA 59.196 50.000 8.74 0.00 39.64 4.57
1754 1771 0.804989 ACAAAATCAGCCGCTAGTGC 59.195 50.000 0.00 0.00 0.00 4.40
1755 1772 2.483877 TCAACAAAATCAGCCGCTAGTG 59.516 45.455 0.00 0.00 0.00 2.74
1756 1773 2.778299 TCAACAAAATCAGCCGCTAGT 58.222 42.857 0.00 0.00 0.00 2.57
1757 1774 3.688272 CATCAACAAAATCAGCCGCTAG 58.312 45.455 0.00 0.00 0.00 3.42
1758 1775 2.159393 GCATCAACAAAATCAGCCGCTA 60.159 45.455 0.00 0.00 0.00 4.26
1759 1776 1.403249 GCATCAACAAAATCAGCCGCT 60.403 47.619 0.00 0.00 0.00 5.52
1760 1777 0.994263 GCATCAACAAAATCAGCCGC 59.006 50.000 0.00 0.00 0.00 6.53
1761 1778 2.256174 CAGCATCAACAAAATCAGCCG 58.744 47.619 0.00 0.00 0.00 5.52
1762 1779 2.231964 TCCAGCATCAACAAAATCAGCC 59.768 45.455 0.00 0.00 0.00 4.85
1763 1780 3.581024 TCCAGCATCAACAAAATCAGC 57.419 42.857 0.00 0.00 0.00 4.26
1764 1781 3.924686 GCTTCCAGCATCAACAAAATCAG 59.075 43.478 0.00 0.00 41.89 2.90
1765 1782 3.306225 GGCTTCCAGCATCAACAAAATCA 60.306 43.478 0.00 0.00 44.75 2.57
1766 1783 3.256558 GGCTTCCAGCATCAACAAAATC 58.743 45.455 0.00 0.00 44.75 2.17
1767 1784 2.353011 CGGCTTCCAGCATCAACAAAAT 60.353 45.455 0.00 0.00 44.75 1.82
1768 1785 1.000385 CGGCTTCCAGCATCAACAAAA 60.000 47.619 0.00 0.00 44.75 2.44
1769 1786 0.597568 CGGCTTCCAGCATCAACAAA 59.402 50.000 0.00 0.00 44.75 2.83
1770 1787 1.243342 CCGGCTTCCAGCATCAACAA 61.243 55.000 0.00 0.00 44.75 2.83
1771 1788 1.675310 CCGGCTTCCAGCATCAACA 60.675 57.895 0.00 0.00 44.75 3.33
1772 1789 3.056313 GCCGGCTTCCAGCATCAAC 62.056 63.158 22.15 0.00 44.75 3.18
1773 1790 2.751436 GCCGGCTTCCAGCATCAA 60.751 61.111 22.15 0.00 44.75 2.57
1774 1791 4.802051 GGCCGGCTTCCAGCATCA 62.802 66.667 28.56 0.00 44.75 3.07
1775 1792 4.802051 TGGCCGGCTTCCAGCATC 62.802 66.667 28.56 6.48 44.75 3.91
1792 1809 4.664677 GACACGCAGCACCCGAGT 62.665 66.667 0.00 0.00 32.44 4.18
1860 1877 3.423154 GACGGCAGGCTTCAACGG 61.423 66.667 0.00 0.00 0.00 4.44
1861 1878 3.777925 CGACGGCAGGCTTCAACG 61.778 66.667 1.16 0.00 0.00 4.10
1862 1879 4.090057 GCGACGGCAGGCTTCAAC 62.090 66.667 0.00 0.00 39.62 3.18
1863 1880 4.314440 AGCGACGGCAGGCTTCAA 62.314 61.111 0.00 0.00 43.41 2.69
1864 1881 4.742201 GAGCGACGGCAGGCTTCA 62.742 66.667 0.00 0.00 43.41 3.02
1874 1891 3.164011 GTGGAACGACGAGCGACG 61.164 66.667 12.54 12.54 44.57 5.12
1885 1902 1.439679 GAATGGTCCTGACGTGGAAC 58.560 55.000 3.02 3.02 43.84 3.62
1886 1903 0.037697 CGAATGGTCCTGACGTGGAA 60.038 55.000 0.00 0.00 37.93 3.53
1887 1904 1.589630 CGAATGGTCCTGACGTGGA 59.410 57.895 0.00 0.00 0.00 4.02
1888 1905 1.447838 CCGAATGGTCCTGACGTGG 60.448 63.158 0.00 0.00 0.00 4.94
1889 1906 1.447838 CCCGAATGGTCCTGACGTG 60.448 63.158 0.00 0.00 0.00 4.49
1890 1907 1.605058 CTCCCGAATGGTCCTGACGT 61.605 60.000 0.00 0.00 34.77 4.34
1891 1908 1.141881 CTCCCGAATGGTCCTGACG 59.858 63.158 0.00 0.00 34.77 4.35
1892 1909 0.976073 TCCTCCCGAATGGTCCTGAC 60.976 60.000 0.00 0.00 34.77 3.51
1893 1910 0.031111 ATCCTCCCGAATGGTCCTGA 60.031 55.000 0.00 0.00 34.77 3.86
1894 1911 0.839946 AATCCTCCCGAATGGTCCTG 59.160 55.000 0.00 0.00 34.77 3.86
1895 1912 2.489528 TAATCCTCCCGAATGGTCCT 57.510 50.000 0.00 0.00 34.77 3.85
1896 1913 3.328050 AGATTAATCCTCCCGAATGGTCC 59.672 47.826 11.92 0.00 34.77 4.46
1897 1914 4.202367 ACAGATTAATCCTCCCGAATGGTC 60.202 45.833 11.92 0.00 34.77 4.02
1898 1915 3.716872 ACAGATTAATCCTCCCGAATGGT 59.283 43.478 11.92 0.00 34.77 3.55
1899 1916 4.067896 CACAGATTAATCCTCCCGAATGG 58.932 47.826 11.92 0.00 0.00 3.16
1900 1917 4.067896 CCACAGATTAATCCTCCCGAATG 58.932 47.826 11.92 3.97 0.00 2.67
1901 1918 3.073062 CCCACAGATTAATCCTCCCGAAT 59.927 47.826 11.92 0.00 0.00 3.34
1902 1919 2.438021 CCCACAGATTAATCCTCCCGAA 59.562 50.000 11.92 0.00 0.00 4.30
1903 1920 2.047061 CCCACAGATTAATCCTCCCGA 58.953 52.381 11.92 0.00 0.00 5.14
1904 1921 1.543429 GCCCACAGATTAATCCTCCCG 60.543 57.143 11.92 0.00 0.00 5.14
1905 1922 1.777272 AGCCCACAGATTAATCCTCCC 59.223 52.381 11.92 0.00 0.00 4.30
1906 1923 3.137360 AGAAGCCCACAGATTAATCCTCC 59.863 47.826 11.92 0.00 0.00 4.30
1987 2004 7.766278 GGCACAATCAAGAGAGTCTCTAATAAA 59.234 37.037 22.93 7.56 40.28 1.40
2019 2036 9.077885 TCAAAGCAAGTTAAGATCCACTTTAAT 57.922 29.630 0.78 0.00 39.72 1.40
2022 2039 6.959639 TCAAAGCAAGTTAAGATCCACTTT 57.040 33.333 0.78 0.00 39.72 2.66
2064 2081 8.637986 TGCAAGTCACTTTTATGGAAGTTAATT 58.362 29.630 0.00 0.00 37.76 1.40
2073 2090 5.895636 TGGTATGCAAGTCACTTTTATGG 57.104 39.130 0.00 0.00 0.00 2.74
2110 2127 5.314923 TGAGCAAATTCTTTAGACATGGC 57.685 39.130 0.00 0.00 0.00 4.40
2142 2159 1.691434 GGGAAGTCACCAAATTGGCAA 59.309 47.619 12.67 0.68 42.67 4.52
2204 2221 6.606241 TTATTGGTTGGATATCCTCCCTTT 57.394 37.500 22.35 14.12 44.23 3.11
2207 2224 6.434340 GTCAATTATTGGTTGGATATCCTCCC 59.566 42.308 22.35 20.07 44.23 4.30
2251 2268 1.045911 TGTTTCCCCAACCAACCAGC 61.046 55.000 0.00 0.00 33.97 4.85
2290 2307 7.764443 GGCAATACAAGTAGTGAGTAAGATCAA 59.236 37.037 11.40 0.00 33.41 2.57
2305 2322 4.156455 CAGGGATACTGGCAATACAAGT 57.844 45.455 0.00 0.00 43.70 3.16


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

AutoCloner maintained by Alex Coulton.