Multiple sequence alignment - TraesCS4A01G445400

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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 TraesCS4A01G445400 chr4A 100.000 2571 0 0 1 2571 713394590 713392020 0.000000e+00 4748
1 TraesCS4A01G445400 chr1A 96.195 1603 59 2 1 1602 309728797 309727196 0.000000e+00 2621
2 TraesCS4A01G445400 chr1A 83.664 655 74 14 1941 2568 22647136 22647784 1.020000e-163 586
3 TraesCS4A01G445400 chr1D 96.007 1603 57 5 1 1602 104018001 104019597 0.000000e+00 2599
4 TraesCS4A01G445400 chr1D 84.170 657 71 10 1939 2568 489983180 489983830 7.870000e-170 606
5 TraesCS4A01G445400 chr1D 83.213 691 62 10 1925 2568 342115811 342116494 3.690000e-163 584
6 TraesCS4A01G445400 chr1D 81.358 692 80 25 1922 2571 10133491 10132807 3.790000e-143 518
7 TraesCS4A01G445400 chr2B 90.872 1490 130 4 114 1602 625970500 625969016 0.000000e+00 1993
8 TraesCS4A01G445400 chr2B 84.451 656 70 8 1941 2568 101157214 101157865 3.630000e-173 617
9 TraesCS4A01G445400 chr2B 83.580 676 58 16 1941 2568 18621732 18622402 3.690000e-163 584
10 TraesCS4A01G445400 chr2B 80.832 673 71 26 1947 2567 179742707 179742041 2.310000e-130 475
11 TraesCS4A01G445400 chr2B 83.490 533 55 10 1920 2422 721300233 721300762 1.390000e-127 466
12 TraesCS4A01G445400 chr2D 84.884 688 56 17 1928 2568 592373885 592373199 0.000000e+00 651
13 TraesCS4A01G445400 chr7D 84.992 653 68 9 1941 2566 215099145 215099794 1.000000e-178 636
14 TraesCS4A01G445400 chr7D 84.294 694 58 12 1925 2571 614082738 614082049 4.670000e-177 630
15 TraesCS4A01G445400 chr3D 84.249 692 53 16 1929 2568 607326554 607327241 7.810000e-175 623
16 TraesCS4A01G445400 chr3D 84.627 644 66 8 1938 2554 373870109 373869472 6.080000e-171 610
17 TraesCS4A01G445400 chr3D 83.612 659 75 9 1941 2568 154178543 154179199 2.850000e-164 588
18 TraesCS4A01G445400 chr4D 83.590 713 61 12 1911 2571 329142578 329141870 3.630000e-173 617
19 TraesCS4A01G445400 chr4D 84.686 653 62 17 1944 2566 403143586 403142942 3.630000e-173 617
20 TraesCS4A01G445400 chr6A 83.759 665 80 6 1932 2571 617987802 617987141 2.830000e-169 604
21 TraesCS4A01G445400 chr6B 83.205 649 90 15 1934 2568 88321603 88322246 6.170000e-161 577
22 TraesCS4A01G445400 chr6B 82.695 705 67 14 1919 2571 523508062 523507361 2.220000e-160 575
23 TraesCS4A01G445400 chr4B 82.180 679 65 28 1944 2571 173513290 173512617 1.350000e-147 532
24 TraesCS4A01G445400 chr5B 81.213 676 65 39 1947 2568 450540825 450540158 2.970000e-134 488
25 TraesCS4A01G445400 chr5B 86.387 382 25 10 2216 2570 528383716 528383335 2.400000e-105 392
26 TraesCS4A01G445400 chr3B 80.811 641 65 33 1981 2568 807943990 807944625 1.400000e-122 449
27 TraesCS4A01G445400 chr3B 85.422 391 29 14 2208 2571 109900645 109900256 5.190000e-102 381
28 TraesCS4A01G445400 chr1B 84.962 266 16 8 2326 2568 57647165 57647429 5.490000e-62 248


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 TraesCS4A01G445400 chr4A 713392020 713394590 2570 True 4748 4748 100.000 1 2571 1 chr4A.!!$R1 2570
1 TraesCS4A01G445400 chr1A 309727196 309728797 1601 True 2621 2621 96.195 1 1602 1 chr1A.!!$R1 1601
2 TraesCS4A01G445400 chr1A 22647136 22647784 648 False 586 586 83.664 1941 2568 1 chr1A.!!$F1 627
3 TraesCS4A01G445400 chr1D 104018001 104019597 1596 False 2599 2599 96.007 1 1602 1 chr1D.!!$F1 1601
4 TraesCS4A01G445400 chr1D 489983180 489983830 650 False 606 606 84.170 1939 2568 1 chr1D.!!$F3 629
5 TraesCS4A01G445400 chr1D 342115811 342116494 683 False 584 584 83.213 1925 2568 1 chr1D.!!$F2 643
6 TraesCS4A01G445400 chr1D 10132807 10133491 684 True 518 518 81.358 1922 2571 1 chr1D.!!$R1 649
7 TraesCS4A01G445400 chr2B 625969016 625970500 1484 True 1993 1993 90.872 114 1602 1 chr2B.!!$R2 1488
8 TraesCS4A01G445400 chr2B 101157214 101157865 651 False 617 617 84.451 1941 2568 1 chr2B.!!$F2 627
9 TraesCS4A01G445400 chr2B 18621732 18622402 670 False 584 584 83.580 1941 2568 1 chr2B.!!$F1 627
10 TraesCS4A01G445400 chr2B 179742041 179742707 666 True 475 475 80.832 1947 2567 1 chr2B.!!$R1 620
11 TraesCS4A01G445400 chr2B 721300233 721300762 529 False 466 466 83.490 1920 2422 1 chr2B.!!$F3 502
12 TraesCS4A01G445400 chr2D 592373199 592373885 686 True 651 651 84.884 1928 2568 1 chr2D.!!$R1 640
13 TraesCS4A01G445400 chr7D 215099145 215099794 649 False 636 636 84.992 1941 2566 1 chr7D.!!$F1 625
14 TraesCS4A01G445400 chr7D 614082049 614082738 689 True 630 630 84.294 1925 2571 1 chr7D.!!$R1 646
15 TraesCS4A01G445400 chr3D 607326554 607327241 687 False 623 623 84.249 1929 2568 1 chr3D.!!$F2 639
16 TraesCS4A01G445400 chr3D 373869472 373870109 637 True 610 610 84.627 1938 2554 1 chr3D.!!$R1 616
17 TraesCS4A01G445400 chr3D 154178543 154179199 656 False 588 588 83.612 1941 2568 1 chr3D.!!$F1 627
18 TraesCS4A01G445400 chr4D 329141870 329142578 708 True 617 617 83.590 1911 2571 1 chr4D.!!$R1 660
19 TraesCS4A01G445400 chr4D 403142942 403143586 644 True 617 617 84.686 1944 2566 1 chr4D.!!$R2 622
20 TraesCS4A01G445400 chr6A 617987141 617987802 661 True 604 604 83.759 1932 2571 1 chr6A.!!$R1 639
21 TraesCS4A01G445400 chr6B 88321603 88322246 643 False 577 577 83.205 1934 2568 1 chr6B.!!$F1 634
22 TraesCS4A01G445400 chr6B 523507361 523508062 701 True 575 575 82.695 1919 2571 1 chr6B.!!$R1 652
23 TraesCS4A01G445400 chr4B 173512617 173513290 673 True 532 532 82.180 1944 2571 1 chr4B.!!$R1 627
24 TraesCS4A01G445400 chr5B 450540158 450540825 667 True 488 488 81.213 1947 2568 1 chr5B.!!$R1 621
25 TraesCS4A01G445400 chr3B 807943990 807944625 635 False 449 449 80.811 1981 2568 1 chr3B.!!$F1 587

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
536 538 0.319986 TCGGCGTACAAGTTGCATCA 60.32 50.0 6.85 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 1697 0.040692 CACGTGTCTTTCTCCGACGA 60.041 55.0 7.58 0.0 34.17 4.2 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
73 74 0.971386 CTTTCAACCTGGCCATGCTT 59.029 50.000 5.51 0.00 0.00 3.91
204 205 5.780793 AGGGTATGTCATATACTTGGAGGAC 59.219 44.000 0.00 0.00 0.00 3.85
267 268 1.462928 GGGTGGGTGATGGTTCCAA 59.537 57.895 0.00 0.00 31.73 3.53
385 386 4.513442 TGTTTGATCCATACACAGGTAGC 58.487 43.478 0.00 0.00 31.88 3.58
445 446 2.372264 GATGCCTCTTTGATCCTTGCA 58.628 47.619 0.00 0.00 0.00 4.08
536 538 0.319986 TCGGCGTACAAGTTGCATCA 60.320 50.000 6.85 0.00 0.00 3.07
544 546 4.378770 CGTACAAGTTGCATCAGCTCATTT 60.379 41.667 1.81 0.00 42.74 2.32
617 619 9.818270 ATTTCATTGGTATGATATCTGGAATGT 57.182 29.630 3.98 0.00 40.37 2.71
619 621 8.625786 TCATTGGTATGATATCTGGAATGTTG 57.374 34.615 3.98 0.00 35.87 3.33
668 670 1.528129 TGGCGCATCACACACAATAA 58.472 45.000 10.83 0.00 0.00 1.40
670 672 1.467374 GGCGCATCACACACAATAACC 60.467 52.381 10.83 0.00 0.00 2.85
677 679 3.495331 TCACACACAATAACCTGCCAAT 58.505 40.909 0.00 0.00 0.00 3.16
716 718 4.021544 GCGAAGAGGGATTGAGACTGATAT 60.022 45.833 0.00 0.00 0.00 1.63
739 741 1.507141 CTGCCCAGTTTGTCACCGTC 61.507 60.000 0.00 0.00 0.00 4.79
794 796 4.990426 GTGTAAGGAGGTACGCAAAGTTTA 59.010 41.667 0.00 0.00 35.10 2.01
855 857 1.901833 GAATGTGTTGGCCCCAAAGAT 59.098 47.619 0.00 0.00 37.70 2.40
1032 1034 7.706607 ACTGATTTTGAGACTTTTTGCCTTAAC 59.293 33.333 0.00 0.00 0.00 2.01
1108 1110 7.666623 TGACACACTGAAGATTAACACAGATA 58.333 34.615 0.00 0.00 34.88 1.98
1113 1115 7.179338 ACACTGAAGATTAACACAGATAGGAGT 59.821 37.037 0.00 0.00 34.88 3.85
1157 1159 0.178924 AGGCTGGGGCTTTGTGATTT 60.179 50.000 0.00 0.00 33.67 2.17
1219 1221 4.645535 AGCTCAATTACTTGCAAGACTCA 58.354 39.130 32.50 12.99 32.11 3.41
1294 1296 2.224257 GGGCATGACAAACATTGTGGTT 60.224 45.455 0.00 0.00 45.52 3.67
1504 1506 2.516225 GACCCCCAAGCCGTATGC 60.516 66.667 0.00 0.00 41.71 3.14
1529 1531 1.844497 GTGGAGCCCCTACCTTTGTAT 59.156 52.381 0.00 0.00 0.00 2.29
1550 1552 0.829990 TGACTTGATGGCCAGCGATA 59.170 50.000 17.68 3.14 0.00 2.92
1554 1556 2.224606 CTTGATGGCCAGCGATATTGT 58.775 47.619 17.68 0.00 0.00 2.71
1587 1589 7.232534 TGCTGGTTAATGGAATAGAGTTTGTTT 59.767 33.333 0.00 0.00 0.00 2.83
1589 1591 8.934023 TGGTTAATGGAATAGAGTTTGTTTCT 57.066 30.769 0.00 0.00 0.00 2.52
1615 1617 3.263941 AAAAAGAGCGCGCGGAAT 58.736 50.000 33.06 8.15 0.00 3.01
1616 1618 1.154225 AAAAAGAGCGCGCGGAATG 60.154 52.632 33.06 2.79 0.00 2.67
1617 1619 2.527547 AAAAAGAGCGCGCGGAATGG 62.528 55.000 33.06 1.90 0.00 3.16
1625 1627 3.746889 CGCGGAATGGCTTGGCAA 61.747 61.111 0.00 0.00 0.00 4.52
1626 1628 2.125952 GCGGAATGGCTTGGCAAC 60.126 61.111 0.00 0.00 0.00 4.17
1651 1653 4.923942 CCGGCGCCATGCTCTGAT 62.924 66.667 28.98 0.00 45.43 2.90
1652 1654 3.646976 CGGCGCCATGCTCTGATG 61.647 66.667 28.98 0.98 45.43 3.07
1653 1655 3.285215 GGCGCCATGCTCTGATGG 61.285 66.667 24.80 0.00 45.20 3.51
1654 1656 2.203112 GCGCCATGCTCTGATGGA 60.203 61.111 5.00 0.00 45.24 3.41
1655 1657 1.820906 GCGCCATGCTCTGATGGAA 60.821 57.895 5.00 0.00 45.24 3.53
1656 1658 1.378882 GCGCCATGCTCTGATGGAAA 61.379 55.000 5.00 0.00 45.24 3.13
1657 1659 1.097232 CGCCATGCTCTGATGGAAAA 58.903 50.000 5.00 0.00 45.24 2.29
1658 1660 1.065102 CGCCATGCTCTGATGGAAAAG 59.935 52.381 5.00 0.00 45.24 2.27
1659 1661 2.372264 GCCATGCTCTGATGGAAAAGA 58.628 47.619 5.00 0.00 45.24 2.52
1660 1662 2.756760 GCCATGCTCTGATGGAAAAGAA 59.243 45.455 5.00 0.00 45.24 2.52
1661 1663 3.428589 GCCATGCTCTGATGGAAAAGAAC 60.429 47.826 5.00 0.00 45.24 3.01
1662 1664 3.181503 CCATGCTCTGATGGAAAAGAACG 60.182 47.826 0.00 0.00 45.24 3.95
1663 1665 2.426522 TGCTCTGATGGAAAAGAACGG 58.573 47.619 0.00 0.00 0.00 4.44
1664 1666 2.038426 TGCTCTGATGGAAAAGAACGGA 59.962 45.455 0.00 0.00 0.00 4.69
1665 1667 2.675348 GCTCTGATGGAAAAGAACGGAG 59.325 50.000 0.00 0.00 37.14 4.63
1666 1668 3.265791 CTCTGATGGAAAAGAACGGAGG 58.734 50.000 0.00 0.00 32.42 4.30
1667 1669 2.903784 TCTGATGGAAAAGAACGGAGGA 59.096 45.455 0.00 0.00 0.00 3.71
1668 1670 3.055819 TCTGATGGAAAAGAACGGAGGAG 60.056 47.826 0.00 0.00 0.00 3.69
1669 1671 2.027192 TGATGGAAAAGAACGGAGGAGG 60.027 50.000 0.00 0.00 0.00 4.30
1670 1672 0.690762 TGGAAAAGAACGGAGGAGGG 59.309 55.000 0.00 0.00 0.00 4.30
1671 1673 0.981943 GGAAAAGAACGGAGGAGGGA 59.018 55.000 0.00 0.00 0.00 4.20
1672 1674 1.338864 GGAAAAGAACGGAGGAGGGAC 60.339 57.143 0.00 0.00 0.00 4.46
1673 1675 0.320697 AAAAGAACGGAGGAGGGACG 59.679 55.000 0.00 0.00 0.00 4.79
1674 1676 2.168666 AAAGAACGGAGGAGGGACGC 62.169 60.000 0.00 0.00 0.00 5.19
1675 1677 3.379445 GAACGGAGGAGGGACGCA 61.379 66.667 0.00 0.00 0.00 5.24
1676 1678 3.358076 GAACGGAGGAGGGACGCAG 62.358 68.421 0.00 0.00 0.00 5.18
1679 1681 4.154347 GGAGGAGGGACGCAGCTG 62.154 72.222 10.11 10.11 0.00 4.24
1680 1682 4.828925 GAGGAGGGACGCAGCTGC 62.829 72.222 29.12 29.12 37.78 5.25
1682 1684 4.479993 GGAGGGACGCAGCTGCAT 62.480 66.667 36.03 25.08 42.21 3.96
1683 1685 3.200593 GAGGGACGCAGCTGCATG 61.201 66.667 36.03 23.84 42.21 4.06
1684 1686 3.670637 GAGGGACGCAGCTGCATGA 62.671 63.158 36.03 0.00 42.21 3.07
1685 1687 2.747460 GGGACGCAGCTGCATGAA 60.747 61.111 36.03 0.00 42.21 2.57
1686 1688 2.482374 GGACGCAGCTGCATGAAC 59.518 61.111 36.03 20.83 42.21 3.18
1687 1689 2.482374 GACGCAGCTGCATGAACC 59.518 61.111 36.03 14.98 42.21 3.62
1688 1690 3.372676 GACGCAGCTGCATGAACCG 62.373 63.158 36.03 20.96 42.21 4.44
1689 1691 4.824166 CGCAGCTGCATGAACCGC 62.824 66.667 36.03 8.20 42.21 5.68
1690 1692 4.487412 GCAGCTGCATGAACCGCC 62.487 66.667 33.36 0.00 41.59 6.13
1691 1693 3.818787 CAGCTGCATGAACCGCCC 61.819 66.667 0.00 0.00 0.00 6.13
1692 1694 4.039092 AGCTGCATGAACCGCCCT 62.039 61.111 1.02 0.00 0.00 5.19
1693 1695 3.064324 GCTGCATGAACCGCCCTT 61.064 61.111 0.00 0.00 0.00 3.95
1694 1696 2.639327 GCTGCATGAACCGCCCTTT 61.639 57.895 0.00 0.00 0.00 3.11
1695 1697 1.966762 CTGCATGAACCGCCCTTTT 59.033 52.632 0.00 0.00 0.00 2.27
1696 1698 0.109132 CTGCATGAACCGCCCTTTTC 60.109 55.000 0.00 0.00 0.00 2.29
1697 1699 1.154035 GCATGAACCGCCCTTTTCG 60.154 57.895 0.00 0.00 0.00 3.46
1698 1700 1.862602 GCATGAACCGCCCTTTTCGT 61.863 55.000 0.00 0.00 0.00 3.85
1699 1701 0.168128 CATGAACCGCCCTTTTCGTC 59.832 55.000 0.00 0.00 0.00 4.20
1700 1702 1.296056 ATGAACCGCCCTTTTCGTCG 61.296 55.000 0.00 0.00 0.00 5.12
1701 1703 2.667199 AACCGCCCTTTTCGTCGG 60.667 61.111 0.00 0.00 46.61 4.79
1702 1704 3.167822 AACCGCCCTTTTCGTCGGA 62.168 57.895 6.52 0.00 44.23 4.55
1703 1705 2.813908 CCGCCCTTTTCGTCGGAG 60.814 66.667 0.00 0.00 44.23 4.63
1704 1706 2.260434 CGCCCTTTTCGTCGGAGA 59.740 61.111 0.00 0.00 0.00 3.71
1705 1707 1.373748 CGCCCTTTTCGTCGGAGAA 60.374 57.895 0.00 0.00 39.69 2.87
1706 1708 0.947180 CGCCCTTTTCGTCGGAGAAA 60.947 55.000 0.00 2.83 39.69 2.52
1707 1709 0.796927 GCCCTTTTCGTCGGAGAAAG 59.203 55.000 6.39 1.50 40.66 2.62
1708 1710 1.607251 GCCCTTTTCGTCGGAGAAAGA 60.607 52.381 14.18 0.18 40.66 2.52
1709 1711 2.067013 CCCTTTTCGTCGGAGAAAGAC 58.933 52.381 14.18 0.00 40.66 3.01
1710 1712 2.547218 CCCTTTTCGTCGGAGAAAGACA 60.547 50.000 14.18 0.00 40.66 3.41
1711 1713 2.475487 CCTTTTCGTCGGAGAAAGACAC 59.525 50.000 14.18 0.00 40.66 3.67
1712 1714 1.762419 TTTCGTCGGAGAAAGACACG 58.238 50.000 0.00 0.00 39.69 4.49
1713 1715 0.664761 TTCGTCGGAGAAAGACACGT 59.335 50.000 0.00 0.00 39.69 4.49
1714 1716 0.040692 TCGTCGGAGAAAGACACGTG 60.041 55.000 15.48 15.48 39.69 4.49
1715 1717 1.606350 CGTCGGAGAAAGACACGTGC 61.606 60.000 17.22 8.74 39.69 5.34
1716 1718 0.318784 GTCGGAGAAAGACACGTGCT 60.319 55.000 17.22 11.14 39.69 4.40
1717 1719 0.387929 TCGGAGAAAGACACGTGCTT 59.612 50.000 17.22 16.62 0.00 3.91
1718 1720 1.202486 TCGGAGAAAGACACGTGCTTT 60.202 47.619 26.83 26.83 38.22 3.51
1719 1721 1.597663 CGGAGAAAGACACGTGCTTTT 59.402 47.619 27.04 21.83 35.83 2.27
1720 1722 2.798283 CGGAGAAAGACACGTGCTTTTA 59.202 45.455 27.04 0.00 35.83 1.52
1721 1723 3.362693 CGGAGAAAGACACGTGCTTTTAC 60.363 47.826 27.04 23.15 35.83 2.01
1722 1724 3.808174 GGAGAAAGACACGTGCTTTTACT 59.192 43.478 27.04 22.29 35.83 2.24
1723 1725 4.272748 GGAGAAAGACACGTGCTTTTACTT 59.727 41.667 27.04 17.84 35.83 2.24
1724 1726 5.405331 AGAAAGACACGTGCTTTTACTTC 57.595 39.130 27.04 18.74 35.83 3.01
1725 1727 3.854286 AAGACACGTGCTTTTACTTCG 57.146 42.857 17.22 0.00 0.00 3.79
1726 1728 2.132762 AGACACGTGCTTTTACTTCGG 58.867 47.619 17.22 0.00 0.00 4.30
1727 1729 0.584876 ACACGTGCTTTTACTTCGGC 59.415 50.000 17.22 0.00 0.00 5.54
1728 1730 0.584396 CACGTGCTTTTACTTCGGCA 59.416 50.000 0.82 0.00 0.00 5.69
1729 1731 1.196808 CACGTGCTTTTACTTCGGCAT 59.803 47.619 0.82 0.00 37.05 4.40
1730 1732 1.463444 ACGTGCTTTTACTTCGGCATC 59.537 47.619 0.00 0.00 37.05 3.91
1731 1733 1.526986 CGTGCTTTTACTTCGGCATCG 60.527 52.381 0.00 0.00 37.05 3.84
1732 1734 1.730064 GTGCTTTTACTTCGGCATCGA 59.270 47.619 0.00 0.00 44.44 3.59
1733 1735 2.351726 GTGCTTTTACTTCGGCATCGAT 59.648 45.455 0.00 0.00 45.51 3.59
1734 1736 2.351418 TGCTTTTACTTCGGCATCGATG 59.649 45.455 21.27 21.27 45.51 3.84
1745 1747 3.924238 CATCGATGCTTTTTCCGGG 57.076 52.632 13.37 0.00 0.00 5.73
1746 1748 1.378531 CATCGATGCTTTTTCCGGGA 58.621 50.000 13.37 0.00 0.00 5.14
1747 1749 1.949525 CATCGATGCTTTTTCCGGGAT 59.050 47.619 13.37 0.00 0.00 3.85
1748 1750 1.378531 TCGATGCTTTTTCCGGGATG 58.621 50.000 0.00 0.00 0.00 3.51
1749 1751 1.094785 CGATGCTTTTTCCGGGATGT 58.905 50.000 0.00 0.00 0.00 3.06
1750 1752 1.472480 CGATGCTTTTTCCGGGATGTT 59.528 47.619 0.00 0.00 0.00 2.71
1751 1753 2.477863 CGATGCTTTTTCCGGGATGTTC 60.478 50.000 0.00 0.00 0.00 3.18
1752 1754 2.286365 TGCTTTTTCCGGGATGTTCT 57.714 45.000 0.00 0.00 0.00 3.01
1753 1755 2.593026 TGCTTTTTCCGGGATGTTCTT 58.407 42.857 0.00 0.00 0.00 2.52
1754 1756 2.556622 TGCTTTTTCCGGGATGTTCTTC 59.443 45.455 0.00 0.00 0.00 2.87
1755 1757 2.820197 GCTTTTTCCGGGATGTTCTTCT 59.180 45.455 0.00 0.00 0.00 2.85
1756 1758 3.255888 GCTTTTTCCGGGATGTTCTTCTT 59.744 43.478 0.00 0.00 0.00 2.52
1757 1759 4.616143 GCTTTTTCCGGGATGTTCTTCTTC 60.616 45.833 0.00 0.00 0.00 2.87
1758 1760 2.781681 TTCCGGGATGTTCTTCTTCC 57.218 50.000 0.00 0.00 38.99 3.46
1763 1765 2.797177 GGATGTTCTTCTTCCCTGCT 57.203 50.000 0.00 0.00 35.21 4.24
1764 1766 2.637947 GGATGTTCTTCTTCCCTGCTC 58.362 52.381 0.00 0.00 35.21 4.26
1765 1767 2.637947 GATGTTCTTCTTCCCTGCTCC 58.362 52.381 0.00 0.00 0.00 4.70
1766 1768 1.734655 TGTTCTTCTTCCCTGCTCCT 58.265 50.000 0.00 0.00 0.00 3.69
1767 1769 2.057922 TGTTCTTCTTCCCTGCTCCTT 58.942 47.619 0.00 0.00 0.00 3.36
1768 1770 2.224621 TGTTCTTCTTCCCTGCTCCTTG 60.225 50.000 0.00 0.00 0.00 3.61
1769 1771 0.987294 TCTTCTTCCCTGCTCCTTGG 59.013 55.000 0.00 0.00 0.00 3.61
1770 1772 0.679321 CTTCTTCCCTGCTCCTTGGC 60.679 60.000 0.00 0.00 0.00 4.52
1771 1773 1.136329 TTCTTCCCTGCTCCTTGGCT 61.136 55.000 0.00 0.00 0.00 4.75
1772 1774 1.136329 TCTTCCCTGCTCCTTGGCTT 61.136 55.000 0.00 0.00 0.00 4.35
1773 1775 0.251519 CTTCCCTGCTCCTTGGCTTT 60.252 55.000 0.00 0.00 0.00 3.51
1774 1776 1.004745 CTTCCCTGCTCCTTGGCTTTA 59.995 52.381 0.00 0.00 0.00 1.85
1775 1777 1.072266 TCCCTGCTCCTTGGCTTTAA 58.928 50.000 0.00 0.00 0.00 1.52
1776 1778 1.427368 TCCCTGCTCCTTGGCTTTAAA 59.573 47.619 0.00 0.00 0.00 1.52
1777 1779 2.158385 TCCCTGCTCCTTGGCTTTAAAA 60.158 45.455 0.00 0.00 0.00 1.52
1778 1780 2.833943 CCCTGCTCCTTGGCTTTAAAAT 59.166 45.455 0.00 0.00 0.00 1.82
1779 1781 4.023291 CCCTGCTCCTTGGCTTTAAAATA 58.977 43.478 0.00 0.00 0.00 1.40
1780 1782 4.651045 CCCTGCTCCTTGGCTTTAAAATAT 59.349 41.667 0.00 0.00 0.00 1.28
1781 1783 5.833131 CCCTGCTCCTTGGCTTTAAAATATA 59.167 40.000 0.00 0.00 0.00 0.86
1782 1784 6.494835 CCCTGCTCCTTGGCTTTAAAATATAT 59.505 38.462 0.00 0.00 0.00 0.86
1783 1785 7.015584 CCCTGCTCCTTGGCTTTAAAATATATT 59.984 37.037 0.00 0.00 0.00 1.28
1784 1786 9.077885 CCTGCTCCTTGGCTTTAAAATATATTA 57.922 33.333 0.00 0.00 0.00 0.98
1787 1789 9.914131 GCTCCTTGGCTTTAAAATATATTAAGG 57.086 33.333 11.00 11.00 33.91 2.69
1880 1882 9.645059 ATCAACGATATCGAATTTGTATCAGAT 57.355 29.630 30.75 10.43 43.02 2.90
1881 1883 9.129209 TCAACGATATCGAATTTGTATCAGATC 57.871 33.333 30.75 0.00 43.02 2.75
1882 1884 8.376203 CAACGATATCGAATTTGTATCAGATCC 58.624 37.037 30.75 0.00 43.02 3.36
1883 1885 7.036220 ACGATATCGAATTTGTATCAGATCCC 58.964 38.462 30.75 0.00 43.02 3.85
1884 1886 7.035612 CGATATCGAATTTGTATCAGATCCCA 58.964 38.462 20.50 0.00 43.02 4.37
1885 1887 7.009631 CGATATCGAATTTGTATCAGATCCCAC 59.990 40.741 20.50 0.00 43.02 4.61
1886 1888 5.351948 TCGAATTTGTATCAGATCCCACA 57.648 39.130 0.00 0.00 0.00 4.17
1887 1889 5.928976 TCGAATTTGTATCAGATCCCACAT 58.071 37.500 0.00 0.00 0.00 3.21
1888 1890 5.759763 TCGAATTTGTATCAGATCCCACATG 59.240 40.000 0.00 0.00 0.00 3.21
1889 1891 5.759763 CGAATTTGTATCAGATCCCACATGA 59.240 40.000 0.00 0.00 0.00 3.07
1890 1892 6.260714 CGAATTTGTATCAGATCCCACATGAA 59.739 38.462 0.00 0.00 0.00 2.57
1891 1893 7.201723 CGAATTTGTATCAGATCCCACATGAAA 60.202 37.037 0.00 0.00 0.00 2.69
1892 1894 7.959658 ATTTGTATCAGATCCCACATGAAAA 57.040 32.000 0.00 0.00 0.00 2.29
1893 1895 6.757897 TTGTATCAGATCCCACATGAAAAC 57.242 37.500 0.00 0.00 0.00 2.43
1894 1896 6.065976 TGTATCAGATCCCACATGAAAACT 57.934 37.500 0.00 0.00 0.00 2.66
1895 1897 7.194112 TGTATCAGATCCCACATGAAAACTA 57.806 36.000 0.00 0.00 0.00 2.24
1896 1898 7.805163 TGTATCAGATCCCACATGAAAACTAT 58.195 34.615 0.00 0.00 0.00 2.12
1897 1899 8.274322 TGTATCAGATCCCACATGAAAACTATT 58.726 33.333 0.00 0.00 0.00 1.73
1898 1900 9.125026 GTATCAGATCCCACATGAAAACTATTT 57.875 33.333 0.00 0.00 0.00 1.40
1899 1901 8.599624 ATCAGATCCCACATGAAAACTATTTT 57.400 30.769 0.00 0.00 35.12 1.82
1901 1903 7.122650 TCAGATCCCACATGAAAACTATTTTCC 59.877 37.037 0.00 0.00 46.49 3.13
1902 1904 7.123247 CAGATCCCACATGAAAACTATTTTCCT 59.877 37.037 0.00 0.00 46.49 3.36
1903 1905 8.336235 AGATCCCACATGAAAACTATTTTCCTA 58.664 33.333 0.00 0.00 46.49 2.94
1904 1906 9.136323 GATCCCACATGAAAACTATTTTCCTAT 57.864 33.333 0.00 0.00 46.49 2.57
1905 1907 8.893563 TCCCACATGAAAACTATTTTCCTATT 57.106 30.769 0.00 0.00 46.49 1.73
1906 1908 9.320295 TCCCACATGAAAACTATTTTCCTATTT 57.680 29.630 0.00 0.00 46.49 1.40
1942 1945 7.976135 TTGTGGATGTTGATTTTTATTTGGG 57.024 32.000 0.00 0.00 0.00 4.12
2013 2022 3.792458 TATAGCACACAGACTGCGCCG 62.792 57.143 4.18 0.00 39.79 6.46
2136 2147 2.351336 AATCCCTCGCGACGTGATCC 62.351 60.000 12.13 0.00 0.00 3.36
2157 2168 7.338196 TGATCCTCGAAACTAGATCTCATATCC 59.662 40.741 0.00 0.00 36.82 2.59
2395 2489 9.696917 ATTTTCATGGTCAAAGTACTGAAATTC 57.303 29.630 0.00 0.00 33.91 2.17
2460 2578 4.819105 AAGCACTATGGCAACTACAGTA 57.181 40.909 0.00 0.00 35.83 2.74
2466 2584 6.018180 GCACTATGGCAACTACAGTATAAACC 60.018 42.308 0.00 0.00 37.61 3.27
2555 2678 4.516092 CGTTGAGACGGATTTAATGGTC 57.484 45.455 0.00 0.00 45.32 4.02
2568 2691 7.201401 CGGATTTAATGGTCAAAACGGATTTTC 60.201 37.037 0.00 0.00 35.79 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.664873 CCGCCATCCTTGTTTTGCA 59.335 52.632 0.00 0.00 0.00 4.08
161 162 0.320421 TCTTTCGGCTGTGCACCTAC 60.320 55.000 15.69 3.13 0.00 3.18
204 205 4.558095 GCAGCTCAATACCTTGCAATATGG 60.558 45.833 0.00 0.00 34.99 2.74
267 268 5.784398 TGGATCTGCCCATATATTGATGT 57.216 39.130 0.00 0.00 34.97 3.06
385 386 3.733337 GTGGACAAGCTGTATATCCCAG 58.267 50.000 0.00 0.00 0.00 4.45
536 538 2.224523 TGTTCCCTTCGTCAAATGAGCT 60.225 45.455 0.00 0.00 0.00 4.09
544 546 1.301401 CCGCTTGTTCCCTTCGTCA 60.301 57.895 0.00 0.00 0.00 4.35
628 630 5.387958 GCCATAAAAATTGTTTTGTCGTCGG 60.388 40.000 0.00 0.00 37.51 4.79
634 636 5.468072 TGATGCGCCATAAAAATTGTTTTGT 59.532 32.000 4.18 0.00 37.51 2.83
668 670 2.749044 CGAGCAGCATTGGCAGGT 60.749 61.111 0.00 0.00 44.61 4.00
716 718 0.108585 GTGACAAACTGGGCAGAGGA 59.891 55.000 0.00 0.00 0.00 3.71
739 741 2.094286 AGTGAGCTCCGTCTTCATCAAG 60.094 50.000 12.15 0.00 0.00 3.02
855 857 6.208599 CCCATTTCAGTAGCCTGTTTAAGAAA 59.791 38.462 0.00 0.00 39.82 2.52
1265 1267 0.033208 TTTGTCATGCCCCATCCCTC 60.033 55.000 0.00 0.00 0.00 4.30
1294 1296 4.058124 CAAGTTCACAAGAATCCGTCTCA 58.942 43.478 0.00 0.00 34.56 3.27
1457 1459 1.167155 TTCGCACCAAAAGCCGCTAA 61.167 50.000 0.00 0.00 0.00 3.09
1529 1531 1.672030 CGCTGGCCATCAAGTCACA 60.672 57.895 5.51 0.00 0.00 3.58
1550 1552 0.893270 TAACCAGCAGGCGCAACAAT 60.893 50.000 10.83 0.00 42.27 2.71
1554 1556 1.594194 CCATTAACCAGCAGGCGCAA 61.594 55.000 10.83 0.00 42.27 4.85
1608 1610 3.746889 TTGCCAAGCCATTCCGCG 61.747 61.111 0.00 0.00 0.00 6.46
1609 1611 2.125952 GTTGCCAAGCCATTCCGC 60.126 61.111 0.00 0.00 0.00 5.54
1610 1612 1.080569 GTGTTGCCAAGCCATTCCG 60.081 57.895 0.00 0.00 0.00 4.30
1611 1613 1.080569 CGTGTTGCCAAGCCATTCC 60.081 57.895 0.00 0.00 0.00 3.01
1612 1614 1.734117 GCGTGTTGCCAAGCCATTC 60.734 57.895 0.00 0.00 39.77 2.67
1613 1615 2.339712 GCGTGTTGCCAAGCCATT 59.660 55.556 0.00 0.00 39.77 3.16
1614 1616 4.041917 CGCGTGTTGCCAAGCCAT 62.042 61.111 0.00 0.00 42.25 4.40
1634 1636 4.923942 ATCAGAGCATGGCGCCGG 62.924 66.667 23.90 18.06 44.04 6.13
1635 1637 3.646976 CATCAGAGCATGGCGCCG 61.647 66.667 23.90 9.82 44.04 6.46
1636 1638 3.285215 CCATCAGAGCATGGCGCC 61.285 66.667 22.73 22.73 44.04 6.53
1637 1639 1.378882 TTTCCATCAGAGCATGGCGC 61.379 55.000 0.00 0.00 42.97 6.53
1638 1640 1.065102 CTTTTCCATCAGAGCATGGCG 59.935 52.381 0.00 0.00 42.97 5.69
1639 1641 2.372264 TCTTTTCCATCAGAGCATGGC 58.628 47.619 0.00 0.00 42.97 4.40
1640 1642 3.181503 CGTTCTTTTCCATCAGAGCATGG 60.182 47.826 0.00 0.00 44.45 3.66
1641 1643 3.181503 CCGTTCTTTTCCATCAGAGCATG 60.182 47.826 0.00 0.00 0.00 4.06
1642 1644 3.012518 CCGTTCTTTTCCATCAGAGCAT 58.987 45.455 0.00 0.00 0.00 3.79
1643 1645 2.038426 TCCGTTCTTTTCCATCAGAGCA 59.962 45.455 0.00 0.00 0.00 4.26
1644 1646 2.675348 CTCCGTTCTTTTCCATCAGAGC 59.325 50.000 0.00 0.00 0.00 4.09
1645 1647 3.055819 TCCTCCGTTCTTTTCCATCAGAG 60.056 47.826 0.00 0.00 0.00 3.35
1646 1648 2.903784 TCCTCCGTTCTTTTCCATCAGA 59.096 45.455 0.00 0.00 0.00 3.27
1647 1649 3.265791 CTCCTCCGTTCTTTTCCATCAG 58.734 50.000 0.00 0.00 0.00 2.90
1648 1650 2.027192 CCTCCTCCGTTCTTTTCCATCA 60.027 50.000 0.00 0.00 0.00 3.07
1649 1651 2.633488 CCTCCTCCGTTCTTTTCCATC 58.367 52.381 0.00 0.00 0.00 3.51
1650 1652 1.282157 CCCTCCTCCGTTCTTTTCCAT 59.718 52.381 0.00 0.00 0.00 3.41
1651 1653 0.690762 CCCTCCTCCGTTCTTTTCCA 59.309 55.000 0.00 0.00 0.00 3.53
1652 1654 0.981943 TCCCTCCTCCGTTCTTTTCC 59.018 55.000 0.00 0.00 0.00 3.13
1653 1655 1.672145 CGTCCCTCCTCCGTTCTTTTC 60.672 57.143 0.00 0.00 0.00 2.29
1654 1656 0.320697 CGTCCCTCCTCCGTTCTTTT 59.679 55.000 0.00 0.00 0.00 2.27
1655 1657 1.972978 CGTCCCTCCTCCGTTCTTT 59.027 57.895 0.00 0.00 0.00 2.52
1656 1658 2.647158 GCGTCCCTCCTCCGTTCTT 61.647 63.158 0.00 0.00 0.00 2.52
1657 1659 3.069318 GCGTCCCTCCTCCGTTCT 61.069 66.667 0.00 0.00 0.00 3.01
1658 1660 3.358076 CTGCGTCCCTCCTCCGTTC 62.358 68.421 0.00 0.00 0.00 3.95
1659 1661 3.382832 CTGCGTCCCTCCTCCGTT 61.383 66.667 0.00 0.00 0.00 4.44
1662 1664 4.154347 CAGCTGCGTCCCTCCTCC 62.154 72.222 0.00 0.00 0.00 4.30
1663 1665 4.828925 GCAGCTGCGTCCCTCCTC 62.829 72.222 25.23 0.00 0.00 3.71
1665 1667 4.479993 ATGCAGCTGCGTCCCTCC 62.480 66.667 32.11 5.47 45.83 4.30
1666 1668 3.200593 CATGCAGCTGCGTCCCTC 61.201 66.667 30.32 4.25 45.83 4.30
1667 1669 3.258228 TTCATGCAGCTGCGTCCCT 62.258 57.895 30.32 10.84 45.83 4.20
1668 1670 2.747460 TTCATGCAGCTGCGTCCC 60.747 61.111 30.32 5.84 45.83 4.46
1669 1671 2.482374 GTTCATGCAGCTGCGTCC 59.518 61.111 30.32 16.91 45.83 4.79
1670 1672 2.482374 GGTTCATGCAGCTGCGTC 59.518 61.111 30.32 18.88 45.83 5.19
1671 1673 3.425713 CGGTTCATGCAGCTGCGT 61.426 61.111 32.11 30.01 45.83 5.24
1672 1674 4.824166 GCGGTTCATGCAGCTGCG 62.824 66.667 32.11 19.83 45.83 5.18
1673 1675 4.487412 GGCGGTTCATGCAGCTGC 62.487 66.667 31.89 31.89 42.50 5.25
1674 1676 3.818787 GGGCGGTTCATGCAGCTG 61.819 66.667 10.11 10.11 0.00 4.24
1675 1677 3.574074 AAGGGCGGTTCATGCAGCT 62.574 57.895 0.00 0.00 0.00 4.24
1676 1678 2.158561 AAAAGGGCGGTTCATGCAGC 62.159 55.000 0.00 0.00 0.00 5.25
1677 1679 0.109132 GAAAAGGGCGGTTCATGCAG 60.109 55.000 0.00 0.00 0.00 4.41
1678 1680 1.861542 CGAAAAGGGCGGTTCATGCA 61.862 55.000 0.00 0.00 0.00 3.96
1679 1681 1.154035 CGAAAAGGGCGGTTCATGC 60.154 57.895 0.00 0.00 0.00 4.06
1680 1682 0.168128 GACGAAAAGGGCGGTTCATG 59.832 55.000 0.00 0.00 0.00 3.07
1681 1683 1.296056 CGACGAAAAGGGCGGTTCAT 61.296 55.000 0.00 0.00 0.00 2.57
1682 1684 1.957186 CGACGAAAAGGGCGGTTCA 60.957 57.895 0.00 0.00 0.00 3.18
1683 1685 2.674084 CCGACGAAAAGGGCGGTTC 61.674 63.158 0.00 0.00 37.22 3.62
1684 1686 2.667199 CCGACGAAAAGGGCGGTT 60.667 61.111 0.00 0.00 37.22 4.44
1685 1687 3.584868 CTCCGACGAAAAGGGCGGT 62.585 63.158 6.75 0.00 40.95 5.68
1686 1688 2.775032 TTCTCCGACGAAAAGGGCGG 62.775 60.000 0.00 0.00 41.32 6.13
1687 1689 0.947180 TTTCTCCGACGAAAAGGGCG 60.947 55.000 0.00 0.00 30.49 6.13
1688 1690 0.796927 CTTTCTCCGACGAAAAGGGC 59.203 55.000 0.00 0.00 32.95 5.19
1689 1691 2.067013 GTCTTTCTCCGACGAAAAGGG 58.933 52.381 13.61 0.00 32.95 3.95
1690 1692 2.475487 GTGTCTTTCTCCGACGAAAAGG 59.525 50.000 13.61 0.00 32.95 3.11
1691 1693 2.153247 CGTGTCTTTCTCCGACGAAAAG 59.847 50.000 0.00 3.85 32.95 2.27
1692 1694 2.121786 CGTGTCTTTCTCCGACGAAAA 58.878 47.619 0.00 0.00 32.95 2.29
1693 1695 1.066002 ACGTGTCTTTCTCCGACGAAA 59.934 47.619 0.00 0.00 34.17 3.46
1694 1696 0.664761 ACGTGTCTTTCTCCGACGAA 59.335 50.000 0.00 0.00 34.17 3.85
1695 1697 0.040692 CACGTGTCTTTCTCCGACGA 60.041 55.000 7.58 0.00 34.17 4.20
1696 1698 1.606350 GCACGTGTCTTTCTCCGACG 61.606 60.000 18.38 0.00 34.17 5.12
1697 1699 0.318784 AGCACGTGTCTTTCTCCGAC 60.319 55.000 18.38 0.00 0.00 4.79
1698 1700 0.387929 AAGCACGTGTCTTTCTCCGA 59.612 50.000 18.38 0.00 0.00 4.55
1699 1701 1.217882 AAAGCACGTGTCTTTCTCCG 58.782 50.000 23.38 0.00 0.00 4.63
1700 1702 3.808174 AGTAAAAGCACGTGTCTTTCTCC 59.192 43.478 26.72 19.79 33.06 3.71
1701 1703 5.405331 AAGTAAAAGCACGTGTCTTTCTC 57.595 39.130 26.72 22.47 33.06 2.87
1702 1704 4.025979 CGAAGTAAAAGCACGTGTCTTTCT 60.026 41.667 26.72 20.50 33.06 2.52
1703 1705 4.201576 CGAAGTAAAAGCACGTGTCTTTC 58.798 43.478 26.72 19.21 33.06 2.62
1704 1706 3.001939 CCGAAGTAAAAGCACGTGTCTTT 59.998 43.478 23.38 23.38 35.47 2.52
1705 1707 2.542595 CCGAAGTAAAAGCACGTGTCTT 59.457 45.455 18.38 17.11 0.00 3.01
1706 1708 2.132762 CCGAAGTAAAAGCACGTGTCT 58.867 47.619 18.38 11.90 0.00 3.41
1707 1709 1.398071 GCCGAAGTAAAAGCACGTGTC 60.398 52.381 18.38 9.62 0.00 3.67
1708 1710 0.584876 GCCGAAGTAAAAGCACGTGT 59.415 50.000 18.38 0.68 0.00 4.49
1709 1711 0.584396 TGCCGAAGTAAAAGCACGTG 59.416 50.000 12.28 12.28 0.00 4.49
1710 1712 1.463444 GATGCCGAAGTAAAAGCACGT 59.537 47.619 0.00 0.00 38.21 4.49
1711 1713 1.526986 CGATGCCGAAGTAAAAGCACG 60.527 52.381 0.00 0.00 38.21 5.34
1712 1714 1.730064 TCGATGCCGAAGTAAAAGCAC 59.270 47.619 0.00 0.00 42.51 4.40
1713 1715 2.087501 TCGATGCCGAAGTAAAAGCA 57.912 45.000 0.00 0.00 42.51 3.91
1727 1729 1.378531 TCCCGGAAAAAGCATCGATG 58.621 50.000 21.27 21.27 0.00 3.84
1728 1730 1.949525 CATCCCGGAAAAAGCATCGAT 59.050 47.619 0.73 0.00 0.00 3.59
1729 1731 1.339631 ACATCCCGGAAAAAGCATCGA 60.340 47.619 0.73 0.00 0.00 3.59
1730 1732 1.094785 ACATCCCGGAAAAAGCATCG 58.905 50.000 0.73 0.00 0.00 3.84
1731 1733 2.755103 AGAACATCCCGGAAAAAGCATC 59.245 45.455 0.73 0.00 0.00 3.91
1732 1734 2.807676 AGAACATCCCGGAAAAAGCAT 58.192 42.857 0.73 0.00 0.00 3.79
1733 1735 2.286365 AGAACATCCCGGAAAAAGCA 57.714 45.000 0.73 0.00 0.00 3.91
1734 1736 2.820197 AGAAGAACATCCCGGAAAAAGC 59.180 45.455 0.73 0.00 0.00 3.51
1735 1737 4.082733 GGAAGAAGAACATCCCGGAAAAAG 60.083 45.833 0.73 0.00 30.97 2.27
1736 1738 3.824443 GGAAGAAGAACATCCCGGAAAAA 59.176 43.478 0.73 0.00 30.97 1.94
1737 1739 3.418047 GGAAGAAGAACATCCCGGAAAA 58.582 45.455 0.73 0.00 30.97 2.29
1738 1740 2.290705 GGGAAGAAGAACATCCCGGAAA 60.291 50.000 0.73 0.00 44.89 3.13
1739 1741 1.280998 GGGAAGAAGAACATCCCGGAA 59.719 52.381 0.73 0.00 44.89 4.30
1740 1742 0.909623 GGGAAGAAGAACATCCCGGA 59.090 55.000 0.73 0.00 44.89 5.14
1741 1743 3.478540 GGGAAGAAGAACATCCCGG 57.521 57.895 0.00 0.00 44.89 5.73
1744 1746 2.637947 GAGCAGGGAAGAAGAACATCC 58.362 52.381 0.00 0.00 35.84 3.51
1745 1747 2.238395 AGGAGCAGGGAAGAAGAACATC 59.762 50.000 0.00 0.00 0.00 3.06
1746 1748 2.273619 AGGAGCAGGGAAGAAGAACAT 58.726 47.619 0.00 0.00 0.00 2.71
1747 1749 1.734655 AGGAGCAGGGAAGAAGAACA 58.265 50.000 0.00 0.00 0.00 3.18
1748 1750 2.431454 CAAGGAGCAGGGAAGAAGAAC 58.569 52.381 0.00 0.00 0.00 3.01
1749 1751 1.352352 CCAAGGAGCAGGGAAGAAGAA 59.648 52.381 0.00 0.00 0.00 2.52
1750 1752 0.987294 CCAAGGAGCAGGGAAGAAGA 59.013 55.000 0.00 0.00 0.00 2.87
1751 1753 0.679321 GCCAAGGAGCAGGGAAGAAG 60.679 60.000 0.00 0.00 0.00 2.85
1752 1754 1.136329 AGCCAAGGAGCAGGGAAGAA 61.136 55.000 0.00 0.00 34.23 2.52
1753 1755 1.136329 AAGCCAAGGAGCAGGGAAGA 61.136 55.000 0.00 0.00 34.23 2.87
1754 1756 0.251519 AAAGCCAAGGAGCAGGGAAG 60.252 55.000 0.00 0.00 34.23 3.46
1755 1757 1.072266 TAAAGCCAAGGAGCAGGGAA 58.928 50.000 0.00 0.00 34.23 3.97
1756 1758 1.072266 TTAAAGCCAAGGAGCAGGGA 58.928 50.000 0.00 0.00 34.23 4.20
1757 1759 1.923356 TTTAAAGCCAAGGAGCAGGG 58.077 50.000 0.00 0.00 34.23 4.45
1758 1760 5.859205 ATATTTTAAAGCCAAGGAGCAGG 57.141 39.130 0.00 0.00 34.23 4.85
1761 1763 9.914131 CCTTAATATATTTTAAAGCCAAGGAGC 57.086 33.333 11.54 0.00 32.36 4.70
1854 1856 9.645059 ATCTGATACAAATTCGATATCGTTGAT 57.355 29.630 25.08 16.65 40.80 2.57
1855 1857 9.129209 GATCTGATACAAATTCGATATCGTTGA 57.871 33.333 25.08 14.54 40.80 3.18
1856 1858 8.376203 GGATCTGATACAAATTCGATATCGTTG 58.624 37.037 23.61 21.31 40.80 4.10
1857 1859 7.545965 GGGATCTGATACAAATTCGATATCGTT 59.454 37.037 23.61 9.88 40.80 3.85
1858 1860 7.036220 GGGATCTGATACAAATTCGATATCGT 58.964 38.462 23.61 6.93 40.80 3.73
1859 1861 7.009631 GTGGGATCTGATACAAATTCGATATCG 59.990 40.741 19.14 19.14 41.45 2.92
1860 1862 7.819415 TGTGGGATCTGATACAAATTCGATATC 59.181 37.037 1.67 0.00 0.00 1.63
1861 1863 7.679783 TGTGGGATCTGATACAAATTCGATAT 58.320 34.615 1.67 0.00 0.00 1.63
1862 1864 7.061566 TGTGGGATCTGATACAAATTCGATA 57.938 36.000 1.67 0.00 0.00 2.92
1863 1865 5.928976 TGTGGGATCTGATACAAATTCGAT 58.071 37.500 1.67 0.00 0.00 3.59
1864 1866 5.351948 TGTGGGATCTGATACAAATTCGA 57.648 39.130 1.67 0.00 0.00 3.71
1865 1867 5.759763 TCATGTGGGATCTGATACAAATTCG 59.240 40.000 1.67 0.00 0.00 3.34
1866 1868 7.572523 TTCATGTGGGATCTGATACAAATTC 57.427 36.000 1.67 0.00 0.00 2.17
1867 1869 7.959658 TTTCATGTGGGATCTGATACAAATT 57.040 32.000 1.67 0.00 0.00 1.82
1868 1870 7.616935 AGTTTTCATGTGGGATCTGATACAAAT 59.383 33.333 1.67 0.00 0.00 2.32
1869 1871 6.947733 AGTTTTCATGTGGGATCTGATACAAA 59.052 34.615 1.67 0.00 0.00 2.83
1870 1872 6.484288 AGTTTTCATGTGGGATCTGATACAA 58.516 36.000 1.67 0.00 0.00 2.41
1871 1873 6.065976 AGTTTTCATGTGGGATCTGATACA 57.934 37.500 1.67 0.00 0.00 2.29
1872 1874 8.682936 AATAGTTTTCATGTGGGATCTGATAC 57.317 34.615 0.00 0.00 0.00 2.24
1873 1875 9.699410 AAAATAGTTTTCATGTGGGATCTGATA 57.301 29.630 0.00 0.00 0.00 2.15
1874 1876 8.599624 AAAATAGTTTTCATGTGGGATCTGAT 57.400 30.769 0.00 0.00 0.00 2.90
1875 1877 8.055279 GAAAATAGTTTTCATGTGGGATCTGA 57.945 34.615 9.59 0.00 46.34 3.27
1916 1918 9.664332 CCCAAATAAAAATCAACATCCACAATA 57.336 29.630 0.00 0.00 0.00 1.90
1917 1919 7.121020 GCCCAAATAAAAATCAACATCCACAAT 59.879 33.333 0.00 0.00 0.00 2.71
1929 1931 6.704819 CATTAGCGTTGCCCAAATAAAAATC 58.295 36.000 0.00 0.00 0.00 2.17
1936 1938 3.739077 GCATTAGCGTTGCCCAAAT 57.261 47.368 0.00 0.00 33.95 2.32
1942 1945 1.670811 ACATGTAGGCATTAGCGTTGC 59.329 47.619 0.00 0.59 43.41 4.17
1956 1959 1.945580 TAGCTCCCACCACACATGTA 58.054 50.000 0.00 0.00 0.00 2.29
2023 2032 7.384660 TCCAAAAAGATTTTCACATGTATGCAC 59.615 33.333 0.00 0.00 0.00 4.57
2178 2192 4.616953 ACATGGCAACTTTTAACCGAAAG 58.383 39.130 0.00 0.00 41.34 2.62
2272 2362 8.030106 AGTCTAGTTTCTTAATTCTCCGTCTTG 58.970 37.037 0.00 0.00 0.00 3.02
2275 2365 7.201453 GCAAGTCTAGTTTCTTAATTCTCCGTC 60.201 40.741 0.00 0.00 0.00 4.79
2433 2551 5.411361 TGTAGTTGCCATAGTGCTTAAACTG 59.589 40.000 0.00 0.00 30.51 3.16
2460 2578 4.020307 CCCAAAAGTTGCCATGAGGTTTAT 60.020 41.667 0.00 0.00 37.19 1.40
2466 2584 0.680618 TGCCCAAAAGTTGCCATGAG 59.319 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.