Multiple sequence alignment - TraesCS1A01G138300

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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 TraesCS1A01G138300 chr1A 100.000 5294 0 0 1 5294 230473558 230468265 0.000000e+00 9777.0
1 TraesCS1A01G138300 chr1B 96.949 3146 84 9 1842 4986 238675576 238672442 0.000000e+00 5267.0
2 TraesCS1A01G138300 chr1B 93.570 762 28 7 820 1566 238676329 238675574 0.000000e+00 1116.0
3 TraesCS1A01G138300 chr1B 91.393 244 18 3 420 663 647160424 647160664 1.100000e-86 331.0
4 TraesCS1A01G138300 chr1B 92.035 113 7 2 703 813 238676510 238676398 1.970000e-34 158.0
5 TraesCS1A01G138300 chr1D 97.397 2804 58 5 1679 4482 165476137 165473349 0.000000e+00 4759.0
6 TraesCS1A01G138300 chr1D 97.362 834 18 2 786 1616 165476965 165476133 0.000000e+00 1415.0
7 TraesCS1A01G138300 chr1D 93.127 742 43 3 4466 5200 165473331 165472591 0.000000e+00 1081.0
8 TraesCS1A01G138300 chr2D 90.385 676 55 5 1 669 380980457 380979785 0.000000e+00 880.0
9 TraesCS1A01G138300 chr2D 89.645 676 59 5 1 669 637743636 637742965 0.000000e+00 850.0
10 TraesCS1A01G138300 chr2D 91.837 98 8 0 5193 5290 606191222 606191319 2.570000e-28 137.0
11 TraesCS1A01G138300 chr2D 89.216 102 11 0 5193 5294 637016018 637015917 1.550000e-25 128.0
12 TraesCS1A01G138300 chr7B 88.872 665 45 15 1 663 61444578 61445215 0.000000e+00 791.0
13 TraesCS1A01G138300 chr7B 87.500 664 54 12 1 663 39975595 39976230 0.000000e+00 739.0
14 TraesCS1A01G138300 chr7B 94.286 35 2 0 1645 1679 462244930 462244964 3.000000e-03 54.7
15 TraesCS1A01G138300 chr7B 94.286 35 2 0 1651 1685 742113360 742113326 3.000000e-03 54.7
16 TraesCS1A01G138300 chrUn 88.722 665 46 15 1 663 187828023 187828660 0.000000e+00 785.0
17 TraesCS1A01G138300 chrUn 88.571 665 47 15 1 663 187852662 187853299 0.000000e+00 780.0
18 TraesCS1A01G138300 chrUn 88.376 671 49 15 1 669 332815711 332815068 0.000000e+00 780.0
19 TraesCS1A01G138300 chrUn 88.438 666 45 16 1 663 196517821 196518457 0.000000e+00 774.0
20 TraesCS1A01G138300 chrUn 88.215 594 42 8 77 669 352156241 352155675 0.000000e+00 684.0
21 TraesCS1A01G138300 chrUn 90.566 212 20 0 4986 5197 163043122 163043333 1.120000e-71 281.0
22 TraesCS1A01G138300 chrUn 90.094 212 21 0 4986 5197 162956372 162956583 5.220000e-70 276.0
23 TraesCS1A01G138300 chrUn 90.094 212 21 0 4986 5197 375463239 375463450 5.220000e-70 276.0
24 TraesCS1A01G138300 chrUn 89.352 216 22 1 4982 5197 162982413 162982627 2.430000e-68 270.0
25 TraesCS1A01G138300 chrUn 100.000 30 0 0 1652 1681 228898086 228898057 7.410000e-04 56.5
26 TraesCS1A01G138300 chrUn 100.000 30 0 0 1652 1681 302118910 302118881 7.410000e-04 56.5
27 TraesCS1A01G138300 chr4A 87.332 671 54 9 1 669 584301230 584300589 0.000000e+00 739.0
28 TraesCS1A01G138300 chr6D 86.542 587 67 5 1 577 211908670 211909254 2.080000e-178 636.0
29 TraesCS1A01G138300 chr7D 91.038 212 19 0 4986 5197 167590235 167590446 2.410000e-73 287.0
30 TraesCS1A01G138300 chr7D 91.176 102 9 0 5193 5294 167590474 167590575 7.150000e-29 139.0
31 TraesCS1A01G138300 chr7D 91.000 100 9 0 5193 5292 458522551 458522650 9.250000e-28 135.0
32 TraesCS1A01G138300 chr3D 90.698 215 20 0 4983 5197 178403964 178404178 2.410000e-73 287.0
33 TraesCS1A01G138300 chr3D 91.176 102 9 0 5193 5294 178404212 178404313 7.150000e-29 139.0
34 TraesCS1A01G138300 chr3D 89.216 102 11 0 5193 5294 74327121 74327222 1.550000e-25 128.0
35 TraesCS1A01G138300 chr3D 89.691 97 10 0 5196 5292 45359572 45359476 2.000000e-24 124.0
36 TraesCS1A01G138300 chr3D 88.235 102 12 0 5193 5294 608662274 608662173 7.200000e-24 122.0
37 TraesCS1A01G138300 chr2A 90.566 212 20 0 4986 5197 16711075 16710864 1.120000e-71 281.0
38 TraesCS1A01G138300 chr2A 92.500 40 2 1 1652 1691 44028725 44028687 7.410000e-04 56.5
39 TraesCS1A01G138300 chr2A 100.000 30 0 0 1652 1681 231350054 231350025 7.410000e-04 56.5
40 TraesCS1A01G138300 chr6B 88.839 224 21 4 4976 5197 43801692 43801913 6.760000e-69 272.0
41 TraesCS1A01G138300 chr5D 90.909 99 7 2 5197 5294 242233997 242233900 1.200000e-26 132.0
42 TraesCS1A01G138300 chr5A 100.000 30 0 0 1652 1681 667072790 667072761 7.410000e-04 56.5
43 TraesCS1A01G138300 chr5A 94.286 35 2 0 1652 1686 601439062 601439028 3.000000e-03 54.7
44 TraesCS1A01G138300 chr3B 100.000 30 0 0 1651 1680 790745035 790745006 7.410000e-04 56.5


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 TraesCS1A01G138300 chr1A 230468265 230473558 5293 True 9777.000000 9777 100.000000 1 5294 1 chr1A.!!$R1 5293
1 TraesCS1A01G138300 chr1B 238672442 238676510 4068 True 2180.333333 5267 94.184667 703 4986 3 chr1B.!!$R1 4283
2 TraesCS1A01G138300 chr1D 165472591 165476965 4374 True 2418.333333 4759 95.962000 786 5200 3 chr1D.!!$R1 4414
3 TraesCS1A01G138300 chr2D 380979785 380980457 672 True 880.000000 880 90.385000 1 669 1 chr2D.!!$R1 668
4 TraesCS1A01G138300 chr2D 637742965 637743636 671 True 850.000000 850 89.645000 1 669 1 chr2D.!!$R3 668
5 TraesCS1A01G138300 chr7B 61444578 61445215 637 False 791.000000 791 88.872000 1 663 1 chr7B.!!$F2 662
6 TraesCS1A01G138300 chr7B 39975595 39976230 635 False 739.000000 739 87.500000 1 663 1 chr7B.!!$F1 662
7 TraesCS1A01G138300 chrUn 187828023 187828660 637 False 785.000000 785 88.722000 1 663 1 chrUn.!!$F4 662
8 TraesCS1A01G138300 chrUn 187852662 187853299 637 False 780.000000 780 88.571000 1 663 1 chrUn.!!$F5 662
9 TraesCS1A01G138300 chrUn 332815068 332815711 643 True 780.000000 780 88.376000 1 669 1 chrUn.!!$R3 668
10 TraesCS1A01G138300 chrUn 196517821 196518457 636 False 774.000000 774 88.438000 1 663 1 chrUn.!!$F6 662
11 TraesCS1A01G138300 chrUn 352155675 352156241 566 True 684.000000 684 88.215000 77 669 1 chrUn.!!$R4 592
12 TraesCS1A01G138300 chr4A 584300589 584301230 641 True 739.000000 739 87.332000 1 669 1 chr4A.!!$R1 668
13 TraesCS1A01G138300 chr6D 211908670 211909254 584 False 636.000000 636 86.542000 1 577 1 chr6D.!!$F1 576

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
814 835 0.963962 TAGTTCAGTTTCGCGAGGGT 59.036 50.0 9.59 0.0 0.00 4.34 F
1631 1735 0.030504 TCGCTGTTGTGCCAAATGTG 59.969 50.0 0.00 0.0 0.00 3.21 F
1634 1738 0.104487 CTGTTGTGCCAAATGTGCCA 59.896 50.0 0.00 0.0 0.00 4.92 F
3129 3233 0.532862 TCGCCTGCTTGCTTATAGCC 60.533 55.0 0.00 0.0 41.51 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 1780 0.585357 GCTGATAGCCAGTGCGATTG 59.415 55.000 0.00 0.00 44.71 2.67 R
3129 3233 2.121116 AACTCGATGGATCTTACGCG 57.879 50.000 3.53 3.53 0.00 6.01 R
3389 3493 3.529319 ACCCAGGATAGAAGCTTCCATTT 59.471 43.478 22.81 7.01 34.27 2.32 R
5098 5244 0.178301 TCTAACGCCCACACAACACA 59.822 50.000 0.00 0.00 0.00 3.72 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
64 65 1.066858 CCGCAGACCTGACTTACACAT 60.067 52.381 0.47 0.00 0.00 3.21
116 117 5.507985 GGGAGGAGAAGTTGTTTGAAACATG 60.508 44.000 11.97 0.00 41.79 3.21
131 132 9.262472 GTTTGAAACATGTCATCGATAACTTAC 57.738 33.333 0.00 0.00 0.00 2.34
134 135 7.969508 TGAAACATGTCATCGATAACTTACGTA 59.030 33.333 0.00 0.00 0.00 3.57
178 179 5.623596 CGGATGACAAGTGTGGTAACTCATA 60.624 44.000 0.00 0.00 42.88 2.15
248 249 9.256477 ACGTATCACGATAAATCATGTGTAAAT 57.744 29.630 5.61 0.00 46.05 1.40
376 386 1.475403 ATAGGTCTCGTCACAGTGGG 58.525 55.000 0.00 0.00 0.00 4.61
495 511 3.395607 ACCTTCTAATGCATGCCTCCATA 59.604 43.478 16.68 0.00 0.00 2.74
526 542 7.622081 TGTGAAGGGAAGATTACAAGACCTATA 59.378 37.037 0.00 0.00 0.00 1.31
673 693 8.997621 ATGAGATCTAGTTTTAAACGTTAGCA 57.002 30.769 0.00 0.00 36.23 3.49
674 694 8.236084 TGAGATCTAGTTTTAAACGTTAGCAC 57.764 34.615 0.00 0.00 36.23 4.40
675 695 7.868922 TGAGATCTAGTTTTAAACGTTAGCACA 59.131 33.333 0.00 0.00 36.23 4.57
676 696 8.240883 AGATCTAGTTTTAAACGTTAGCACAG 57.759 34.615 0.00 0.00 36.23 3.66
677 697 7.871463 AGATCTAGTTTTAAACGTTAGCACAGT 59.129 33.333 0.00 0.00 36.23 3.55
678 698 7.398834 TCTAGTTTTAAACGTTAGCACAGTC 57.601 36.000 0.00 0.00 36.23 3.51
679 699 5.413969 AGTTTTAAACGTTAGCACAGTCC 57.586 39.130 0.00 0.00 36.23 3.85
680 700 5.121105 AGTTTTAAACGTTAGCACAGTCCT 58.879 37.500 0.00 0.00 36.23 3.85
681 701 5.587443 AGTTTTAAACGTTAGCACAGTCCTT 59.413 36.000 0.00 0.00 36.23 3.36
682 702 6.094464 AGTTTTAAACGTTAGCACAGTCCTTT 59.906 34.615 0.00 0.00 36.23 3.11
683 703 7.280652 AGTTTTAAACGTTAGCACAGTCCTTTA 59.719 33.333 0.00 0.00 36.23 1.85
684 704 6.774354 TTAAACGTTAGCACAGTCCTTTAG 57.226 37.500 0.00 0.00 0.00 1.85
685 705 4.595762 AACGTTAGCACAGTCCTTTAGA 57.404 40.909 0.00 0.00 0.00 2.10
686 706 4.175787 ACGTTAGCACAGTCCTTTAGAG 57.824 45.455 0.00 0.00 0.00 2.43
687 707 3.825014 ACGTTAGCACAGTCCTTTAGAGA 59.175 43.478 0.00 0.00 0.00 3.10
688 708 4.280174 ACGTTAGCACAGTCCTTTAGAGAA 59.720 41.667 0.00 0.00 0.00 2.87
689 709 5.047235 ACGTTAGCACAGTCCTTTAGAGAAT 60.047 40.000 0.00 0.00 0.00 2.40
690 710 5.869888 CGTTAGCACAGTCCTTTAGAGAATT 59.130 40.000 0.00 0.00 0.00 2.17
691 711 7.033791 CGTTAGCACAGTCCTTTAGAGAATTA 58.966 38.462 0.00 0.00 0.00 1.40
692 712 7.707035 CGTTAGCACAGTCCTTTAGAGAATTAT 59.293 37.037 0.00 0.00 0.00 1.28
693 713 9.384764 GTTAGCACAGTCCTTTAGAGAATTATT 57.615 33.333 0.00 0.00 0.00 1.40
694 714 9.959721 TTAGCACAGTCCTTTAGAGAATTATTT 57.040 29.630 0.00 0.00 0.00 1.40
695 715 8.870075 AGCACAGTCCTTTAGAGAATTATTTT 57.130 30.769 0.00 0.00 0.00 1.82
696 716 9.301897 AGCACAGTCCTTTAGAGAATTATTTTT 57.698 29.630 0.00 0.00 0.00 1.94
751 772 3.849708 GCTAAAATCGGCCTTAAAACACG 59.150 43.478 0.00 0.00 0.00 4.49
756 777 3.779271 TCGGCCTTAAAACACGTTTTT 57.221 38.095 12.73 11.37 42.22 1.94
759 780 3.727227 CGGCCTTAAAACACGTTTTTCTC 59.273 43.478 12.73 1.94 42.22 2.87
814 835 0.963962 TAGTTCAGTTTCGCGAGGGT 59.036 50.000 9.59 0.00 0.00 4.34
942 1025 1.134037 AGCGTCTCGTCTTATCCTCCT 60.134 52.381 0.00 0.00 0.00 3.69
943 1026 1.264826 GCGTCTCGTCTTATCCTCCTC 59.735 57.143 0.00 0.00 0.00 3.71
944 1027 1.874872 CGTCTCGTCTTATCCTCCTCC 59.125 57.143 0.00 0.00 0.00 4.30
1005 1094 1.368345 CCGCATCCGCTTCAATGTCA 61.368 55.000 0.00 0.00 35.30 3.58
1094 1183 4.134623 AGCGTCGCTGGAAAACAA 57.865 50.000 21.02 0.00 37.57 2.83
1245 1334 0.402504 TTACAAGGGGACGGCATGTT 59.597 50.000 0.00 0.00 0.00 2.71
1275 1364 6.315642 CGTATCCTAGATGTGATACATACCGT 59.684 42.308 13.79 0.00 42.13 4.83
1429 1518 1.341852 TCTCCGTCAATTCCACGACAA 59.658 47.619 7.84 0.00 39.75 3.18
1434 1523 3.314553 CGTCAATTCCACGACAAGTACT 58.685 45.455 0.89 0.00 39.75 2.73
1535 1639 6.757237 TGAACATTTCCTTGCACATATTTGT 58.243 32.000 0.00 0.00 36.15 2.83
1599 1703 0.466372 TCGGTGTGCCAAATGTTCCA 60.466 50.000 0.00 0.00 34.09 3.53
1615 1719 6.604735 ATGTTCCAAAATGTAGTAGATCGC 57.395 37.500 0.00 0.00 0.00 4.58
1616 1720 5.730550 TGTTCCAAAATGTAGTAGATCGCT 58.269 37.500 0.00 0.00 0.00 4.93
1617 1721 5.580691 TGTTCCAAAATGTAGTAGATCGCTG 59.419 40.000 3.57 0.00 0.00 5.18
1618 1722 5.339008 TCCAAAATGTAGTAGATCGCTGT 57.661 39.130 3.57 0.00 0.00 4.40
1619 1723 5.730550 TCCAAAATGTAGTAGATCGCTGTT 58.269 37.500 3.57 0.00 0.00 3.16
1620 1724 5.580691 TCCAAAATGTAGTAGATCGCTGTTG 59.419 40.000 3.57 0.00 0.00 3.33
1621 1725 5.351465 CCAAAATGTAGTAGATCGCTGTTGT 59.649 40.000 3.57 0.00 0.00 3.32
1622 1726 6.243551 CAAAATGTAGTAGATCGCTGTTGTG 58.756 40.000 3.57 0.00 0.00 3.33
1623 1727 2.876091 TGTAGTAGATCGCTGTTGTGC 58.124 47.619 3.57 0.00 0.00 4.57
1624 1728 2.194271 GTAGTAGATCGCTGTTGTGCC 58.806 52.381 3.57 0.00 0.00 5.01
1625 1729 0.608130 AGTAGATCGCTGTTGTGCCA 59.392 50.000 0.00 0.00 0.00 4.92
1626 1730 1.001974 AGTAGATCGCTGTTGTGCCAA 59.998 47.619 0.00 0.00 0.00 4.52
1627 1731 1.804151 GTAGATCGCTGTTGTGCCAAA 59.196 47.619 0.00 0.00 0.00 3.28
1628 1732 1.538047 AGATCGCTGTTGTGCCAAAT 58.462 45.000 0.00 0.00 0.00 2.32
1629 1733 1.200716 AGATCGCTGTTGTGCCAAATG 59.799 47.619 0.00 0.00 0.00 2.32
1630 1734 0.961019 ATCGCTGTTGTGCCAAATGT 59.039 45.000 0.00 0.00 0.00 2.71
1631 1735 0.030504 TCGCTGTTGTGCCAAATGTG 59.969 50.000 0.00 0.00 0.00 3.21
1632 1736 1.550659 CGCTGTTGTGCCAAATGTGC 61.551 55.000 0.00 0.00 0.00 4.57
1633 1737 1.223417 GCTGTTGTGCCAAATGTGCC 61.223 55.000 0.00 0.00 0.00 5.01
1634 1738 0.104487 CTGTTGTGCCAAATGTGCCA 59.896 50.000 0.00 0.00 0.00 4.92
1635 1739 0.538584 TGTTGTGCCAAATGTGCCAA 59.461 45.000 0.00 0.00 0.00 4.52
1636 1740 1.065926 TGTTGTGCCAAATGTGCCAAA 60.066 42.857 0.00 0.00 0.00 3.28
1637 1741 2.220313 GTTGTGCCAAATGTGCCAAAT 58.780 42.857 0.00 0.00 0.00 2.32
1638 1742 1.880271 TGTGCCAAATGTGCCAAATG 58.120 45.000 0.00 0.00 0.00 2.32
1639 1743 1.140452 TGTGCCAAATGTGCCAAATGT 59.860 42.857 0.00 0.00 0.00 2.71
1640 1744 2.220313 GTGCCAAATGTGCCAAATGTT 58.780 42.857 0.00 0.00 0.00 2.71
1641 1745 2.617774 GTGCCAAATGTGCCAAATGTTT 59.382 40.909 0.00 0.00 0.00 2.83
1642 1746 2.877168 TGCCAAATGTGCCAAATGTTTC 59.123 40.909 0.00 0.00 0.00 2.78
1643 1747 2.877168 GCCAAATGTGCCAAATGTTTCA 59.123 40.909 0.00 0.00 0.00 2.69
1644 1748 3.314635 GCCAAATGTGCCAAATGTTTCAA 59.685 39.130 0.00 0.00 0.00 2.69
1645 1749 4.201990 GCCAAATGTGCCAAATGTTTCAAA 60.202 37.500 0.00 0.00 0.00 2.69
1646 1750 5.507650 GCCAAATGTGCCAAATGTTTCAAAT 60.508 36.000 0.00 0.00 0.00 2.32
1647 1751 5.915758 CCAAATGTGCCAAATGTTTCAAATG 59.084 36.000 0.00 0.00 0.00 2.32
1648 1752 6.459848 CCAAATGTGCCAAATGTTTCAAATGT 60.460 34.615 0.00 0.00 0.00 2.71
1649 1753 6.696441 AATGTGCCAAATGTTTCAAATGTT 57.304 29.167 0.00 0.00 0.00 2.71
1650 1754 6.696441 ATGTGCCAAATGTTTCAAATGTTT 57.304 29.167 0.00 0.00 0.00 2.83
1651 1755 6.116680 TGTGCCAAATGTTTCAAATGTTTC 57.883 33.333 0.00 0.00 0.00 2.78
1652 1756 5.065731 TGTGCCAAATGTTTCAAATGTTTCC 59.934 36.000 0.00 0.00 0.00 3.13
1653 1757 5.065731 GTGCCAAATGTTTCAAATGTTTCCA 59.934 36.000 0.00 0.00 0.00 3.53
1654 1758 5.826737 TGCCAAATGTTTCAAATGTTTCCAT 59.173 32.000 0.00 0.00 0.00 3.41
1655 1759 6.320672 TGCCAAATGTTTCAAATGTTTCCATT 59.679 30.769 0.00 0.00 43.14 3.16
1656 1760 7.500227 TGCCAAATGTTTCAAATGTTTCCATTA 59.500 29.630 0.00 0.00 40.42 1.90
1657 1761 8.016801 GCCAAATGTTTCAAATGTTTCCATTAG 58.983 33.333 0.00 0.00 40.42 1.73
1658 1762 8.505625 CCAAATGTTTCAAATGTTTCCATTAGG 58.494 33.333 0.00 0.00 40.42 2.69
1659 1763 7.671495 AATGTTTCAAATGTTTCCATTAGGC 57.329 32.000 0.00 0.00 40.42 3.93
1660 1764 5.546526 TGTTTCAAATGTTTCCATTAGGCC 58.453 37.500 0.00 0.00 40.42 5.19
1661 1765 4.817318 TTCAAATGTTTCCATTAGGCCC 57.183 40.909 0.00 0.00 40.42 5.80
1662 1766 3.784178 TCAAATGTTTCCATTAGGCCCA 58.216 40.909 0.00 0.00 40.42 5.36
1663 1767 4.360889 TCAAATGTTTCCATTAGGCCCAT 58.639 39.130 0.00 0.00 40.42 4.00
1664 1768 4.782156 TCAAATGTTTCCATTAGGCCCATT 59.218 37.500 0.00 0.00 40.42 3.16
1665 1769 5.960811 TCAAATGTTTCCATTAGGCCCATTA 59.039 36.000 0.00 0.00 40.42 1.90
1666 1770 5.869649 AATGTTTCCATTAGGCCCATTAC 57.130 39.130 0.00 0.00 39.52 1.89
1667 1771 3.283751 TGTTTCCATTAGGCCCATTACG 58.716 45.455 0.00 0.00 33.74 3.18
1668 1772 3.284617 GTTTCCATTAGGCCCATTACGT 58.715 45.455 0.00 0.00 33.74 3.57
1669 1773 4.080469 TGTTTCCATTAGGCCCATTACGTA 60.080 41.667 0.00 0.00 33.74 3.57
1670 1774 3.756933 TCCATTAGGCCCATTACGTAC 57.243 47.619 0.00 0.00 33.74 3.67
1671 1775 3.311091 TCCATTAGGCCCATTACGTACT 58.689 45.455 0.00 0.00 33.74 2.73
1672 1776 3.322828 TCCATTAGGCCCATTACGTACTC 59.677 47.826 0.00 0.00 33.74 2.59
1673 1777 3.323979 CCATTAGGCCCATTACGTACTCT 59.676 47.826 0.00 0.00 0.00 3.24
1674 1778 4.525487 CCATTAGGCCCATTACGTACTCTA 59.475 45.833 0.00 0.00 0.00 2.43
1675 1779 5.011329 CCATTAGGCCCATTACGTACTCTAA 59.989 44.000 0.00 0.00 0.00 2.10
1676 1780 5.520376 TTAGGCCCATTACGTACTCTAAC 57.480 43.478 0.00 0.00 0.00 2.34
1677 1781 3.368248 AGGCCCATTACGTACTCTAACA 58.632 45.455 0.00 0.00 0.00 2.41
1678 1782 3.770933 AGGCCCATTACGTACTCTAACAA 59.229 43.478 0.00 0.00 0.00 2.83
1679 1783 4.407945 AGGCCCATTACGTACTCTAACAAT 59.592 41.667 0.00 0.00 0.00 2.71
1680 1784 4.748600 GGCCCATTACGTACTCTAACAATC 59.251 45.833 0.00 0.00 0.00 2.67
1681 1785 4.443394 GCCCATTACGTACTCTAACAATCG 59.557 45.833 0.00 0.00 0.00 3.34
1742 1846 5.126545 TGATTGCTTCTGAATCTTCCATTGG 59.873 40.000 0.00 0.00 32.04 3.16
1782 1886 4.202264 ACCTGTCTCGTGATTGTTCTCTTT 60.202 41.667 0.00 0.00 0.00 2.52
1824 1928 6.091305 TGAGTCTGTTCTTATTGCAGAAATCG 59.909 38.462 0.00 0.00 40.40 3.34
1870 1974 1.349026 TGAAGAAGGGGAGTTCTGCTG 59.651 52.381 0.00 0.00 36.86 4.41
1887 1991 0.609131 CTGGCCTTCCCAACGTGAAT 60.609 55.000 3.32 0.00 44.81 2.57
1920 2024 4.679372 GCTTCTGCCACAAAACCAACTTTA 60.679 41.667 0.00 0.00 0.00 1.85
2096 2200 1.151810 TGGAAAGCCCTGGTCCTCT 60.152 57.895 3.10 0.00 35.38 3.69
2323 2427 2.612212 CCTACCCCAATCGAAAATGACG 59.388 50.000 0.00 0.00 0.00 4.35
2377 2481 6.655003 GGATCCAGAATTGTGTTCAACTCTTA 59.345 38.462 6.95 0.00 37.93 2.10
2724 2828 1.244816 ATGCATTGCTCCATCATCCG 58.755 50.000 10.49 0.00 0.00 4.18
2785 2889 4.904253 GACCGCCTGTCTATATCTATCC 57.096 50.000 0.00 0.00 41.03 2.59
2957 3061 7.754069 TTCAGAAGCTAAACACACAAAAATG 57.246 32.000 0.00 0.00 0.00 2.32
3129 3233 0.532862 TCGCCTGCTTGCTTATAGCC 60.533 55.000 0.00 0.00 41.51 3.93
3330 3434 1.373570 CCTGCCGATTGACTTTCCTC 58.626 55.000 0.00 0.00 0.00 3.71
3389 3493 3.181455 ACACAGATAACACAGGTTCTGCA 60.181 43.478 0.00 0.00 38.45 4.41
3513 3617 8.201554 ACACATAAGCATAATTACTGACACTG 57.798 34.615 0.00 0.00 0.00 3.66
3653 3757 5.599999 TCCAGCTTACTCAACCTATTCTC 57.400 43.478 0.00 0.00 0.00 2.87
3995 4099 2.756840 GGTACTACACCGGCTTTTCT 57.243 50.000 0.00 0.00 37.63 2.52
3998 4102 2.632987 ACTACACCGGCTTTTCTGTT 57.367 45.000 0.00 0.00 0.00 3.16
4057 4161 0.546122 ACAGCCAACACAAGGTGAGA 59.454 50.000 2.98 0.00 36.96 3.27
4073 4177 0.315568 GAGAGAGTGCCGTCAACAGT 59.684 55.000 0.00 0.00 0.00 3.55
4143 4248 1.777272 GCCTTCTCCATATGTTCCCCT 59.223 52.381 1.24 0.00 0.00 4.79
4178 4283 1.810030 GAAGAAGTACTGCCCGCCG 60.810 63.158 0.00 0.00 0.00 6.46
4361 4466 9.303116 TGTTGTTAGTTGATTGGTGGTATATTT 57.697 29.630 0.00 0.00 0.00 1.40
4418 4523 1.477553 TGATTGGAAGGAGGCAATGC 58.522 50.000 0.00 0.00 0.00 3.56
4471 4576 4.517952 TTTAAATGCTTAGCTGCTGCAA 57.482 36.364 17.06 8.95 42.74 4.08
4508 4647 7.013274 GGGTATGTAGTGTACGTTATAGTCCAA 59.987 40.741 0.00 0.00 0.00 3.53
4565 4704 3.194861 TCTTGGAGTGTGACGTCAAAAG 58.805 45.455 21.95 15.76 0.00 2.27
4634 4773 6.465948 TCTAGCGGTGGTTATTCTAAACAAA 58.534 36.000 0.00 0.00 0.00 2.83
4635 4774 6.935771 TCTAGCGGTGGTTATTCTAAACAAAA 59.064 34.615 0.00 0.00 0.00 2.44
4673 4812 3.313249 TGACACAACAGTCTGAATGCAAG 59.687 43.478 6.91 0.00 39.27 4.01
4694 4833 8.849168 TGCAAGAAAAGAAAAGTCTGAATCATA 58.151 29.630 0.00 0.00 33.05 2.15
4920 5065 4.930696 TCCTATAACTGGTCTCACTCACA 58.069 43.478 0.00 0.00 0.00 3.58
4957 5102 1.078324 TCGTCTTAGGGGGAACTTCCT 59.922 52.381 7.77 0.00 36.57 3.36
5006 5152 5.937540 TCTCAAATGATAACATCCACACGTT 59.062 36.000 0.00 0.00 35.50 3.99
5032 5178 1.237533 ATTTGCACATCGCTCACACA 58.762 45.000 0.00 0.00 43.06 3.72
5041 5187 0.037326 TCGCTCACACACCTTGATCC 60.037 55.000 0.00 0.00 0.00 3.36
5051 5197 3.441572 CACACCTTGATCCACCTTGATTC 59.558 47.826 0.00 0.00 0.00 2.52
5061 5207 3.068024 TCCACCTTGATTCTGTTTTGCAC 59.932 43.478 0.00 0.00 0.00 4.57
5066 5212 4.618489 CCTTGATTCTGTTTTGCACGAATC 59.382 41.667 11.73 11.73 39.45 2.52
5069 5215 5.000591 TGATTCTGTTTTGCACGAATCCTA 58.999 37.500 14.21 1.53 38.93 2.94
5073 5219 5.060506 TCTGTTTTGCACGAATCCTAAAGA 58.939 37.500 0.00 0.00 0.00 2.52
5077 5223 6.861055 TGTTTTGCACGAATCCTAAAGAAATC 59.139 34.615 0.00 0.00 0.00 2.17
5116 5262 0.306533 GTGTGTTGTGTGGGCGTTAG 59.693 55.000 0.00 0.00 0.00 2.34
5181 5327 2.665185 GTGCGCGAACCAGTTCCT 60.665 61.111 12.10 0.00 36.27 3.36
5197 5343 2.281761 CTGCCCACACAGTCACCC 60.282 66.667 0.00 0.00 32.78 4.61
5200 5346 2.915079 CCCACACAGTCACCCACA 59.085 61.111 0.00 0.00 0.00 4.17
5201 5347 1.525995 CCCACACAGTCACCCACAC 60.526 63.158 0.00 0.00 0.00 3.82
5202 5348 1.887242 CCACACAGTCACCCACACG 60.887 63.158 0.00 0.00 0.00 4.49
5203 5349 1.142965 CACACAGTCACCCACACGA 59.857 57.895 0.00 0.00 0.00 4.35
5204 5350 1.143183 ACACAGTCACCCACACGAC 59.857 57.895 0.00 0.00 0.00 4.34
5205 5351 1.949133 CACAGTCACCCACACGACG 60.949 63.158 0.00 0.00 37.23 5.12
5206 5352 3.036084 CAGTCACCCACACGACGC 61.036 66.667 0.00 0.00 37.23 5.19
5207 5353 3.224324 AGTCACCCACACGACGCT 61.224 61.111 0.00 0.00 37.23 5.07
5208 5354 2.733593 GTCACCCACACGACGCTC 60.734 66.667 0.00 0.00 0.00 5.03
5209 5355 4.337060 TCACCCACACGACGCTCG 62.337 66.667 0.00 5.97 46.93 5.03
5218 5364 2.402388 CGACGCTCGTACGGTGAT 59.598 61.111 16.52 0.00 37.37 3.06
5219 5365 1.637934 CGACGCTCGTACGGTGATA 59.362 57.895 16.52 0.00 37.37 2.15
5220 5366 0.382758 CGACGCTCGTACGGTGATAG 60.383 60.000 16.52 5.97 37.37 2.08
5221 5367 0.933097 GACGCTCGTACGGTGATAGA 59.067 55.000 16.52 0.00 37.37 1.98
5222 5368 1.530293 GACGCTCGTACGGTGATAGAT 59.470 52.381 16.52 0.00 37.37 1.98
5223 5369 1.263484 ACGCTCGTACGGTGATAGATG 59.737 52.381 16.52 4.03 37.37 2.90
5224 5370 1.399855 CGCTCGTACGGTGATAGATGG 60.400 57.143 16.52 0.00 0.00 3.51
5225 5371 1.666311 GCTCGTACGGTGATAGATGGC 60.666 57.143 16.52 1.49 0.00 4.40
5226 5372 1.607148 CTCGTACGGTGATAGATGGCA 59.393 52.381 16.52 0.00 0.00 4.92
5227 5373 2.025898 TCGTACGGTGATAGATGGCAA 58.974 47.619 16.52 0.00 0.00 4.52
5228 5374 2.124903 CGTACGGTGATAGATGGCAAC 58.875 52.381 7.57 0.00 0.00 4.17
5229 5375 2.223735 CGTACGGTGATAGATGGCAACT 60.224 50.000 7.57 1.95 37.61 3.16
5230 5376 2.315925 ACGGTGATAGATGGCAACTG 57.684 50.000 7.62 0.00 37.61 3.16
5231 5377 0.940126 CGGTGATAGATGGCAACTGC 59.060 55.000 7.62 0.28 41.14 4.40
5232 5378 1.743431 CGGTGATAGATGGCAACTGCA 60.743 52.381 7.62 2.98 44.36 4.41
5233 5379 2.368439 GGTGATAGATGGCAACTGCAA 58.632 47.619 7.62 0.00 44.36 4.08
5234 5380 2.954318 GGTGATAGATGGCAACTGCAAT 59.046 45.455 7.62 0.00 44.36 3.56
5235 5381 3.382546 GGTGATAGATGGCAACTGCAATT 59.617 43.478 7.62 0.00 44.36 2.32
5236 5382 4.357142 GTGATAGATGGCAACTGCAATTG 58.643 43.478 2.92 2.92 44.36 2.32
5241 5387 4.324424 GCAACTGCAATTGCGTGT 57.676 50.000 24.58 21.50 45.08 4.49
5242 5388 3.470520 GCAACTGCAATTGCGTGTA 57.529 47.368 24.58 6.97 45.08 2.90
5243 5389 1.981254 GCAACTGCAATTGCGTGTAT 58.019 45.000 24.58 13.25 45.08 2.29
5244 5390 1.650153 GCAACTGCAATTGCGTGTATG 59.350 47.619 24.58 21.83 45.08 2.39
5245 5391 1.650153 CAACTGCAATTGCGTGTATGC 59.350 47.619 24.58 0.00 45.83 3.14
5246 5392 0.179192 ACTGCAATTGCGTGTATGCG 60.179 50.000 24.58 8.23 45.83 4.73
5247 5393 0.862701 CTGCAATTGCGTGTATGCGG 60.863 55.000 24.58 0.83 45.83 5.69
5248 5394 2.223549 GCAATTGCGTGTATGCGGC 61.224 57.895 15.87 0.00 37.81 6.53
5249 5395 1.136356 CAATTGCGTGTATGCGGCA 59.864 52.632 4.58 4.58 37.81 5.69
5250 5396 0.455802 CAATTGCGTGTATGCGGCAA 60.456 50.000 6.82 12.91 37.81 4.52
5251 5397 0.455410 AATTGCGTGTATGCGGCAAT 59.545 45.000 6.82 15.68 38.85 3.56
5252 5398 0.455410 ATTGCGTGTATGCGGCAATT 59.545 45.000 6.82 0.00 36.22 2.32
5253 5399 1.087501 TTGCGTGTATGCGGCAATTA 58.912 45.000 6.82 0.00 37.81 1.40
5254 5400 1.087501 TGCGTGTATGCGGCAATTAA 58.912 45.000 6.82 0.00 37.81 1.40
5255 5401 1.468914 TGCGTGTATGCGGCAATTAAA 59.531 42.857 6.82 0.00 37.81 1.52
5256 5402 2.098280 TGCGTGTATGCGGCAATTAAAT 59.902 40.909 6.82 0.00 37.81 1.40
5257 5403 3.312697 TGCGTGTATGCGGCAATTAAATA 59.687 39.130 6.82 0.00 37.81 1.40
5258 5404 4.201920 TGCGTGTATGCGGCAATTAAATAA 60.202 37.500 6.82 0.00 37.81 1.40
5259 5405 4.735822 GCGTGTATGCGGCAATTAAATAAA 59.264 37.500 6.82 0.00 0.00 1.40
5260 5406 5.331235 GCGTGTATGCGGCAATTAAATAAAC 60.331 40.000 6.82 0.00 0.00 2.01
5261 5407 5.739630 CGTGTATGCGGCAATTAAATAAACA 59.260 36.000 6.82 0.00 0.00 2.83
5262 5408 6.290851 CGTGTATGCGGCAATTAAATAAACAC 60.291 38.462 6.82 9.20 0.00 3.32
5263 5409 6.528423 GTGTATGCGGCAATTAAATAAACACA 59.472 34.615 6.82 0.00 34.12 3.72
5264 5410 6.528423 TGTATGCGGCAATTAAATAAACACAC 59.472 34.615 6.82 0.00 0.00 3.82
5265 5411 4.871513 TGCGGCAATTAAATAAACACACA 58.128 34.783 0.00 0.00 0.00 3.72
5266 5412 5.473931 TGCGGCAATTAAATAAACACACAT 58.526 33.333 0.00 0.00 0.00 3.21
5267 5413 5.347093 TGCGGCAATTAAATAAACACACATG 59.653 36.000 0.00 0.00 0.00 3.21
5268 5414 5.220378 GCGGCAATTAAATAAACACACATGG 60.220 40.000 0.00 0.00 0.00 3.66
5269 5415 5.220378 CGGCAATTAAATAAACACACATGGC 60.220 40.000 0.00 0.00 0.00 4.40
5270 5416 5.641209 GGCAATTAAATAAACACACATGGCA 59.359 36.000 0.00 0.00 0.00 4.92
5271 5417 6.148480 GGCAATTAAATAAACACACATGGCAA 59.852 34.615 0.00 0.00 0.00 4.52
5272 5418 7.014702 GCAATTAAATAAACACACATGGCAAC 58.985 34.615 0.00 0.00 0.00 4.17
5273 5419 7.095271 GCAATTAAATAAACACACATGGCAACT 60.095 33.333 0.00 0.00 37.61 3.16
5274 5420 9.416794 CAATTAAATAAACACACATGGCAACTA 57.583 29.630 0.00 0.00 37.61 2.24
5280 5426 9.801873 AATAAACACACATGGCAACTATATTTC 57.198 29.630 0.00 0.00 37.61 2.17
5281 5427 5.484173 ACACACATGGCAACTATATTTCG 57.516 39.130 0.00 0.00 37.61 3.46
5282 5428 4.941263 ACACACATGGCAACTATATTTCGT 59.059 37.500 0.00 0.00 37.61 3.85
5283 5429 5.414454 ACACACATGGCAACTATATTTCGTT 59.586 36.000 0.00 0.00 37.61 3.85
5284 5430 5.738693 CACACATGGCAACTATATTTCGTTG 59.261 40.000 0.00 0.00 42.47 4.10
5285 5431 5.163663 ACACATGGCAACTATATTTCGTTGG 60.164 40.000 0.00 2.02 40.52 3.77
5286 5432 4.947388 ACATGGCAACTATATTTCGTTGGT 59.053 37.500 0.00 2.45 40.52 3.67
5287 5433 6.037720 CACATGGCAACTATATTTCGTTGGTA 59.962 38.462 0.00 0.00 40.52 3.25
5288 5434 6.260050 ACATGGCAACTATATTTCGTTGGTAG 59.740 38.462 0.00 0.00 40.52 3.18
5289 5435 5.979993 TGGCAACTATATTTCGTTGGTAGA 58.020 37.500 11.65 0.00 40.52 2.59
5290 5436 6.588204 TGGCAACTATATTTCGTTGGTAGAT 58.412 36.000 11.65 0.00 40.52 1.98
5291 5437 6.481976 TGGCAACTATATTTCGTTGGTAGATG 59.518 38.462 11.65 0.00 40.52 2.90
5292 5438 6.073222 GGCAACTATATTTCGTTGGTAGATGG 60.073 42.308 11.65 0.00 40.52 3.51
5293 5439 6.565999 GCAACTATATTTCGTTGGTAGATGGC 60.566 42.308 11.65 0.00 40.52 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.376299 AGGTCTGCGGTTCGTATATTATCATA 59.624 38.462 0.00 0.00 0.00 2.15
64 65 2.543430 GTCAAAGTTACCGCGGTGTTTA 59.457 45.455 40.02 18.69 0.00 2.01
131 132 5.331013 CGTACATTACCACGCTGTTTATACG 60.331 44.000 0.00 0.00 0.00 3.06
134 135 3.866910 CCGTACATTACCACGCTGTTTAT 59.133 43.478 0.00 0.00 36.85 1.40
139 140 1.858458 CATCCGTACATTACCACGCTG 59.142 52.381 0.00 0.00 36.85 5.18
178 179 0.462403 AGTTACCGCGGTGTTTGTGT 60.462 50.000 40.02 13.86 0.00 3.72
345 355 6.592607 GTGACGAGACCTATAAAACCAAATCA 59.407 38.462 0.00 0.00 0.00 2.57
357 367 1.272536 ACCCACTGTGACGAGACCTAT 60.273 52.381 9.86 0.00 0.00 2.57
473 489 1.565759 TGGAGGCATGCATTAGAAGGT 59.434 47.619 21.36 0.00 0.00 3.50
495 511 4.858850 TGTAATCTTCCCTTCACATGCAT 58.141 39.130 0.00 0.00 0.00 3.96
558 575 9.471084 CATGTCGGTTGTGTATAACTTATCATA 57.529 33.333 0.00 0.00 0.00 2.15
647 667 9.431887 TGCTAACGTTTAAAACTAGATCTCATT 57.568 29.630 5.91 0.00 0.00 2.57
663 683 4.952460 TCTAAAGGACTGTGCTAACGTTT 58.048 39.130 5.91 0.00 0.00 3.60
666 686 4.436242 TCTCTAAAGGACTGTGCTAACG 57.564 45.455 1.14 0.00 0.00 3.18
669 689 9.959721 AAAATAATTCTCTAAAGGACTGTGCTA 57.040 29.630 1.14 0.00 0.00 3.49
670 690 8.870075 AAAATAATTCTCTAAAGGACTGTGCT 57.130 30.769 0.00 0.00 0.00 4.40
689 709 9.896263 GTCCGTTTAATCAACCTGTAAAAATAA 57.104 29.630 0.00 0.00 30.65 1.40
690 710 8.513774 GGTCCGTTTAATCAACCTGTAAAAATA 58.486 33.333 0.00 0.00 30.65 1.40
691 711 7.231925 AGGTCCGTTTAATCAACCTGTAAAAAT 59.768 33.333 6.75 0.00 38.88 1.82
692 712 6.546772 AGGTCCGTTTAATCAACCTGTAAAAA 59.453 34.615 6.75 0.00 38.88 1.94
693 713 6.063404 AGGTCCGTTTAATCAACCTGTAAAA 58.937 36.000 6.75 0.00 38.88 1.52
694 714 5.623169 AGGTCCGTTTAATCAACCTGTAAA 58.377 37.500 6.75 0.00 38.88 2.01
695 715 5.231702 AGGTCCGTTTAATCAACCTGTAA 57.768 39.130 6.75 0.00 38.88 2.41
696 716 4.895668 AGGTCCGTTTAATCAACCTGTA 57.104 40.909 6.75 0.00 38.88 2.74
697 717 3.782656 AGGTCCGTTTAATCAACCTGT 57.217 42.857 6.75 0.00 38.88 4.00
699 719 3.782656 ACAGGTCCGTTTAATCAACCT 57.217 42.857 3.00 3.00 40.97 3.50
700 720 3.057806 CCAACAGGTCCGTTTAATCAACC 60.058 47.826 0.00 0.00 30.65 3.77
701 721 3.057806 CCCAACAGGTCCGTTTAATCAAC 60.058 47.826 0.00 0.00 0.00 3.18
702 722 3.150767 CCCAACAGGTCCGTTTAATCAA 58.849 45.455 0.00 0.00 0.00 2.57
703 723 2.785562 CCCAACAGGTCCGTTTAATCA 58.214 47.619 0.00 0.00 0.00 2.57
704 724 1.471287 GCCCAACAGGTCCGTTTAATC 59.529 52.381 0.00 0.00 38.26 1.75
705 725 1.541379 GCCCAACAGGTCCGTTTAAT 58.459 50.000 0.00 0.00 38.26 1.40
706 726 0.537828 GGCCCAACAGGTCCGTTTAA 60.538 55.000 0.00 0.00 38.26 1.52
707 727 1.073548 GGCCCAACAGGTCCGTTTA 59.926 57.895 0.00 0.00 38.26 2.01
708 728 2.203437 GGCCCAACAGGTCCGTTT 60.203 61.111 0.00 0.00 38.26 3.60
709 729 4.636435 CGGCCCAACAGGTCCGTT 62.636 66.667 0.00 0.00 45.08 4.44
751 772 1.302271 AGTCCGGGCCGAGAAAAAC 60.302 57.895 30.79 14.60 0.00 2.43
809 830 1.599576 GCCAACTCTCCTCACCCTC 59.400 63.158 0.00 0.00 0.00 4.30
814 835 3.003173 CCCCGCCAACTCTCCTCA 61.003 66.667 0.00 0.00 0.00 3.86
942 1025 3.132139 CGCCGAAGACGAGGAGGA 61.132 66.667 0.00 0.00 42.66 3.71
943 1026 3.132139 TCGCCGAAGACGAGGAGG 61.132 66.667 0.00 0.00 42.66 4.30
1245 1334 6.531021 TGTATCACATCTAGGATACGTCTCA 58.469 40.000 3.17 0.00 45.57 3.27
1275 1364 9.679661 TTATCCAATAAATCTGCTCAACAAGTA 57.320 29.630 0.00 0.00 0.00 2.24
1599 1703 5.163854 GCACAACAGCGATCTACTACATTTT 60.164 40.000 0.00 0.00 0.00 1.82
1623 1727 5.496133 TTTGAAACATTTGGCACATTTGG 57.504 34.783 0.00 0.00 39.30 3.28
1624 1728 6.496571 ACATTTGAAACATTTGGCACATTTG 58.503 32.000 0.00 0.00 39.30 2.32
1625 1729 6.696441 ACATTTGAAACATTTGGCACATTT 57.304 29.167 0.00 0.00 39.30 2.32
1626 1730 6.696441 AACATTTGAAACATTTGGCACATT 57.304 29.167 0.00 0.00 39.30 2.71
1627 1731 6.238703 GGAAACATTTGAAACATTTGGCACAT 60.239 34.615 0.00 0.00 39.30 3.21
1628 1732 5.065731 GGAAACATTTGAAACATTTGGCACA 59.934 36.000 0.00 0.00 0.00 4.57
1629 1733 5.065731 TGGAAACATTTGAAACATTTGGCAC 59.934 36.000 0.00 0.00 33.40 5.01
1630 1734 5.188434 TGGAAACATTTGAAACATTTGGCA 58.812 33.333 0.00 0.00 33.40 4.92
1631 1735 5.747951 TGGAAACATTTGAAACATTTGGC 57.252 34.783 0.00 0.00 33.40 4.52
1647 1751 3.284617 ACGTAATGGGCCTAATGGAAAC 58.715 45.455 4.53 0.00 34.57 2.78
1648 1752 3.655615 ACGTAATGGGCCTAATGGAAA 57.344 42.857 4.53 0.00 34.57 3.13
1649 1753 3.712733 AGTACGTAATGGGCCTAATGGAA 59.287 43.478 4.53 0.00 34.57 3.53
1650 1754 3.311091 AGTACGTAATGGGCCTAATGGA 58.689 45.455 4.53 0.00 34.57 3.41
1651 1755 3.323979 AGAGTACGTAATGGGCCTAATGG 59.676 47.826 4.53 0.00 0.00 3.16
1652 1756 4.602340 AGAGTACGTAATGGGCCTAATG 57.398 45.455 4.53 0.00 0.00 1.90
1653 1757 5.599656 TGTTAGAGTACGTAATGGGCCTAAT 59.400 40.000 4.53 0.00 0.00 1.73
1654 1758 4.955450 TGTTAGAGTACGTAATGGGCCTAA 59.045 41.667 4.53 0.00 0.00 2.69
1655 1759 4.535781 TGTTAGAGTACGTAATGGGCCTA 58.464 43.478 4.53 0.00 0.00 3.93
1656 1760 3.368248 TGTTAGAGTACGTAATGGGCCT 58.632 45.455 4.53 0.00 0.00 5.19
1657 1761 3.806625 TGTTAGAGTACGTAATGGGCC 57.193 47.619 0.00 0.00 0.00 5.80
1658 1762 4.443394 CGATTGTTAGAGTACGTAATGGGC 59.557 45.833 0.00 0.00 0.00 5.36
1659 1763 4.443394 GCGATTGTTAGAGTACGTAATGGG 59.557 45.833 0.00 0.00 0.00 4.00
1660 1764 5.038683 TGCGATTGTTAGAGTACGTAATGG 58.961 41.667 0.00 0.00 0.00 3.16
1661 1765 5.742453 AGTGCGATTGTTAGAGTACGTAATG 59.258 40.000 0.00 0.00 0.00 1.90
1662 1766 5.742453 CAGTGCGATTGTTAGAGTACGTAAT 59.258 40.000 0.00 0.00 0.00 1.89
1663 1767 5.090757 CAGTGCGATTGTTAGAGTACGTAA 58.909 41.667 0.00 0.00 0.00 3.18
1664 1768 4.437794 CCAGTGCGATTGTTAGAGTACGTA 60.438 45.833 0.00 0.00 0.00 3.57
1665 1769 3.499048 CAGTGCGATTGTTAGAGTACGT 58.501 45.455 0.00 0.00 0.00 3.57
1666 1770 2.852413 CCAGTGCGATTGTTAGAGTACG 59.148 50.000 0.00 0.00 0.00 3.67
1667 1771 2.603560 GCCAGTGCGATTGTTAGAGTAC 59.396 50.000 0.00 0.00 0.00 2.73
1668 1772 2.496070 AGCCAGTGCGATTGTTAGAGTA 59.504 45.455 0.00 0.00 44.33 2.59
1669 1773 1.276421 AGCCAGTGCGATTGTTAGAGT 59.724 47.619 0.00 0.00 44.33 3.24
1670 1774 2.015736 AGCCAGTGCGATTGTTAGAG 57.984 50.000 0.00 0.00 44.33 2.43
1671 1775 3.132111 TGATAGCCAGTGCGATTGTTAGA 59.868 43.478 0.00 0.00 44.33 2.10
1672 1776 3.457234 TGATAGCCAGTGCGATTGTTAG 58.543 45.455 0.00 0.00 44.33 2.34
1673 1777 3.457234 CTGATAGCCAGTGCGATTGTTA 58.543 45.455 0.00 0.00 44.33 2.41
1674 1778 2.283298 CTGATAGCCAGTGCGATTGTT 58.717 47.619 0.00 0.00 44.33 2.83
1675 1779 1.945387 CTGATAGCCAGTGCGATTGT 58.055 50.000 0.00 0.00 44.33 2.71
1676 1780 0.585357 GCTGATAGCCAGTGCGATTG 59.415 55.000 0.00 0.00 44.71 2.67
1677 1781 2.997899 GCTGATAGCCAGTGCGATT 58.002 52.632 0.00 0.00 44.71 3.34
1678 1782 4.766970 GCTGATAGCCAGTGCGAT 57.233 55.556 0.00 0.00 44.71 4.58
1722 1826 3.760151 CACCAATGGAAGATTCAGAAGCA 59.240 43.478 6.16 0.00 0.00 3.91
1742 1846 7.113124 CGAGACAGGTAATACATAACGAATCAC 59.887 40.741 0.00 0.00 0.00 3.06
1782 1886 2.016318 CTCAGTGAAACAGCACAACCA 58.984 47.619 0.00 0.00 41.43 3.67
1870 1974 1.379527 CTATTCACGTTGGGAAGGCC 58.620 55.000 0.00 0.00 0.00 5.19
1920 2024 2.048127 GCTCGCTCAAACCGGTCT 60.048 61.111 8.04 0.00 0.00 3.85
1974 2078 0.664166 GCACAGATGGGCAACAAACG 60.664 55.000 1.27 0.00 45.57 3.60
2096 2200 4.592942 AGAAGCTGCATTGTCAAGGAATA 58.407 39.130 1.02 0.00 0.00 1.75
2323 2427 6.904011 CAGTGCGTTTCAATCTCAAAGATATC 59.096 38.462 0.00 0.00 32.89 1.63
2673 2777 6.106648 AGAGATGTGAGTGAATGAGAAACA 57.893 37.500 0.00 0.00 0.00 2.83
2724 2828 3.715628 AAGCAAAGACATGGACAACAC 57.284 42.857 0.00 0.00 0.00 3.32
2957 3061 7.325338 GCAAAAAGGTAACCGATTAGAAGAAAC 59.675 37.037 0.00 0.00 37.17 2.78
3129 3233 2.121116 AACTCGATGGATCTTACGCG 57.879 50.000 3.53 3.53 0.00 6.01
3185 3289 7.750229 AAGCATATCAGAACAGAAACAAGAA 57.250 32.000 0.00 0.00 0.00 2.52
3186 3290 7.750229 AAAGCATATCAGAACAGAAACAAGA 57.250 32.000 0.00 0.00 0.00 3.02
3389 3493 3.529319 ACCCAGGATAGAAGCTTCCATTT 59.471 43.478 22.81 7.01 34.27 2.32
3530 3634 4.577693 GCATGCAGAAATCTCCTATTGTCA 59.422 41.667 14.21 0.00 0.00 3.58
3653 3757 4.691359 AAAGCTGGGCCCTGCAGG 62.691 66.667 43.72 26.87 42.23 4.85
3995 4099 1.134551 GTTGCTTCCAAGGCCAAAACA 60.135 47.619 5.01 0.00 0.00 2.83
3998 4102 0.398381 AGGTTGCTTCCAAGGCCAAA 60.398 50.000 5.01 0.00 0.00 3.28
4057 4161 3.402628 AATTACTGTTGACGGCACTCT 57.597 42.857 0.00 0.00 0.00 3.24
4073 4177 9.665719 GAAAGGGAATTAAATGCTTCCAAATTA 57.334 29.630 7.66 0.00 42.29 1.40
4143 4248 9.132521 GTACTTCTTCGCTACAAATTTGTACTA 57.867 33.333 23.91 9.20 42.35 1.82
4361 4466 3.449018 ACAGGTTTTGCCAACAATGTACA 59.551 39.130 0.00 0.00 40.61 2.90
4418 4523 2.929531 ACTACAGACAGCATCACGAG 57.070 50.000 0.00 0.00 0.00 4.18
4471 4576 6.374417 ACACTACATACCCAAGAAACAGAT 57.626 37.500 0.00 0.00 0.00 2.90
4508 4647 3.386078 AGCAAGGTGTGACGAGATATGAT 59.614 43.478 0.00 0.00 0.00 2.45
4565 4704 7.280876 TGCCTATAGTCAACACATTCATCTTTC 59.719 37.037 0.00 0.00 0.00 2.62
4634 4773 5.013547 TGTGTCAACCGGGATGAAAATATT 58.986 37.500 8.72 0.00 0.00 1.28
4635 4774 4.594970 TGTGTCAACCGGGATGAAAATAT 58.405 39.130 8.72 0.00 0.00 1.28
4645 4784 0.179056 AGACTGTTGTGTCAACCGGG 60.179 55.000 6.32 0.00 39.27 5.73
4753 4898 0.755686 GGGGACATGCCAAACAACAA 59.244 50.000 8.20 0.00 38.95 2.83
4885 5030 9.408069 GACCAGTTATAGGAACACGATAATTAG 57.592 37.037 0.00 0.00 30.90 1.73
4893 5038 4.158025 AGTGAGACCAGTTATAGGAACACG 59.842 45.833 0.00 0.00 34.80 4.49
4957 5102 4.837093 AAATCCTCGGTAAGGTCATTCA 57.163 40.909 0.00 0.00 46.32 2.57
4983 5128 5.801350 ACGTGTGGATGTTATCATTTGAG 57.199 39.130 0.00 0.00 34.06 3.02
4989 5135 2.486203 GCCAAACGTGTGGATGTTATCA 59.514 45.455 29.47 0.00 41.65 2.15
4997 5143 3.567576 CAAATATGCCAAACGTGTGGA 57.432 42.857 29.47 13.76 41.65 4.02
5026 5172 1.434188 AGGTGGATCAAGGTGTGTGA 58.566 50.000 0.00 0.00 0.00 3.58
5032 5178 3.331889 ACAGAATCAAGGTGGATCAAGGT 59.668 43.478 0.00 0.00 0.00 3.50
5041 5187 3.044986 CGTGCAAAACAGAATCAAGGTG 58.955 45.455 0.00 0.00 0.00 4.00
5051 5197 5.356882 TCTTTAGGATTCGTGCAAAACAG 57.643 39.130 0.00 0.00 0.00 3.16
5061 5207 5.007136 GGCACTCAGATTTCTTTAGGATTCG 59.993 44.000 0.00 0.00 0.00 3.34
5066 5212 3.372206 CGTGGCACTCAGATTTCTTTAGG 59.628 47.826 16.72 0.00 0.00 2.69
5069 5215 2.851195 ACGTGGCACTCAGATTTCTTT 58.149 42.857 16.72 0.00 0.00 2.52
5073 5219 2.386661 CCTACGTGGCACTCAGATTT 57.613 50.000 16.72 0.00 0.00 2.17
5098 5244 0.178301 TCTAACGCCCACACAACACA 59.822 50.000 0.00 0.00 0.00 3.72
5163 5309 2.970324 GGAACTGGTTCGCGCACA 60.970 61.111 11.73 4.14 40.37 4.57
5181 5327 3.093172 TGGGTGACTGTGTGGGCA 61.093 61.111 0.00 0.00 0.00 5.36
5201 5347 0.382758 CTATCACCGTACGAGCGTCG 60.383 60.000 18.76 0.48 46.93 5.12
5202 5348 0.933097 TCTATCACCGTACGAGCGTC 59.067 55.000 18.76 0.00 0.00 5.19
5203 5349 1.263484 CATCTATCACCGTACGAGCGT 59.737 52.381 18.76 2.91 0.00 5.07
5204 5350 1.399855 CCATCTATCACCGTACGAGCG 60.400 57.143 18.76 2.16 0.00 5.03
5205 5351 1.666311 GCCATCTATCACCGTACGAGC 60.666 57.143 18.76 0.00 0.00 5.03
5206 5352 1.607148 TGCCATCTATCACCGTACGAG 59.393 52.381 18.76 9.56 0.00 4.18
5207 5353 1.682740 TGCCATCTATCACCGTACGA 58.317 50.000 18.76 0.00 0.00 3.43
5208 5354 2.124903 GTTGCCATCTATCACCGTACG 58.875 52.381 8.69 8.69 0.00 3.67
5209 5355 3.123804 CAGTTGCCATCTATCACCGTAC 58.876 50.000 0.00 0.00 0.00 3.67
5210 5356 2.483013 GCAGTTGCCATCTATCACCGTA 60.483 50.000 0.00 0.00 34.31 4.02
5211 5357 1.743772 GCAGTTGCCATCTATCACCGT 60.744 52.381 0.00 0.00 34.31 4.83
5212 5358 0.940126 GCAGTTGCCATCTATCACCG 59.060 55.000 0.00 0.00 34.31 4.94
5213 5359 2.042686 TGCAGTTGCCATCTATCACC 57.957 50.000 1.06 0.00 41.18 4.02
5214 5360 4.357142 CAATTGCAGTTGCCATCTATCAC 58.643 43.478 9.16 0.00 41.18 3.06
5215 5361 3.181484 GCAATTGCAGTTGCCATCTATCA 60.181 43.478 30.49 0.00 46.69 2.15
5216 5362 3.378339 GCAATTGCAGTTGCCATCTATC 58.622 45.455 30.49 6.00 46.69 2.08
5217 5363 3.447918 GCAATTGCAGTTGCCATCTAT 57.552 42.857 30.49 0.00 46.69 1.98
5218 5364 2.945447 GCAATTGCAGTTGCCATCTA 57.055 45.000 30.49 0.00 46.69 1.98
5219 5365 3.826637 GCAATTGCAGTTGCCATCT 57.173 47.368 30.49 0.00 46.69 2.90
5225 5371 1.650153 GCATACACGCAATTGCAGTTG 59.350 47.619 28.77 22.61 42.21 3.16
5226 5372 1.728825 CGCATACACGCAATTGCAGTT 60.729 47.619 28.77 14.45 42.21 3.16
5227 5373 0.179192 CGCATACACGCAATTGCAGT 60.179 50.000 28.77 25.88 42.21 4.40
5228 5374 0.862701 CCGCATACACGCAATTGCAG 60.863 55.000 28.77 21.95 42.21 4.41
5229 5375 1.136356 CCGCATACACGCAATTGCA 59.864 52.632 28.77 10.89 42.21 4.08
5230 5376 2.223549 GCCGCATACACGCAATTGC 61.224 57.895 20.76 20.76 37.78 3.56
5231 5377 0.455802 TTGCCGCATACACGCAATTG 60.456 50.000 0.00 0.00 0.00 2.32
5232 5378 0.455410 ATTGCCGCATACACGCAATT 59.545 45.000 0.00 0.00 36.85 2.32
5233 5379 0.455410 AATTGCCGCATACACGCAAT 59.545 45.000 0.00 0.83 39.61 3.56
5234 5380 1.087501 TAATTGCCGCATACACGCAA 58.912 45.000 0.00 0.00 35.00 4.85
5235 5381 1.087501 TTAATTGCCGCATACACGCA 58.912 45.000 0.00 0.00 0.00 5.24
5236 5382 2.181426 TTTAATTGCCGCATACACGC 57.819 45.000 0.00 0.00 0.00 5.34
5237 5383 5.739630 TGTTTATTTAATTGCCGCATACACG 59.260 36.000 0.00 0.00 0.00 4.49
5238 5384 6.528423 TGTGTTTATTTAATTGCCGCATACAC 59.472 34.615 0.00 0.00 33.52 2.90
5239 5385 6.528423 GTGTGTTTATTTAATTGCCGCATACA 59.472 34.615 0.00 0.00 0.00 2.29
5240 5386 6.528423 TGTGTGTTTATTTAATTGCCGCATAC 59.472 34.615 0.00 0.00 0.00 2.39
5241 5387 6.621613 TGTGTGTTTATTTAATTGCCGCATA 58.378 32.000 0.00 0.00 0.00 3.14
5242 5388 5.473931 TGTGTGTTTATTTAATTGCCGCAT 58.526 33.333 0.00 0.00 0.00 4.73
5243 5389 4.871513 TGTGTGTTTATTTAATTGCCGCA 58.128 34.783 0.00 0.00 0.00 5.69
5244 5390 5.220378 CCATGTGTGTTTATTTAATTGCCGC 60.220 40.000 0.00 0.00 0.00 6.53
5245 5391 5.220378 GCCATGTGTGTTTATTTAATTGCCG 60.220 40.000 0.00 0.00 0.00 5.69
5246 5392 5.641209 TGCCATGTGTGTTTATTTAATTGCC 59.359 36.000 0.00 0.00 0.00 4.52
5247 5393 6.718454 TGCCATGTGTGTTTATTTAATTGC 57.282 33.333 0.00 0.00 0.00 3.56
5248 5394 8.309163 AGTTGCCATGTGTGTTTATTTAATTG 57.691 30.769 0.00 0.00 0.00 2.32
5254 5400 9.801873 GAAATATAGTTGCCATGTGTGTTTATT 57.198 29.630 0.00 0.00 0.00 1.40
5255 5401 8.128582 CGAAATATAGTTGCCATGTGTGTTTAT 58.871 33.333 0.00 0.00 0.00 1.40
5256 5402 7.119992 ACGAAATATAGTTGCCATGTGTGTTTA 59.880 33.333 0.00 0.00 0.00 2.01
5257 5403 6.072175 ACGAAATATAGTTGCCATGTGTGTTT 60.072 34.615 0.00 0.00 0.00 2.83
5258 5404 5.414454 ACGAAATATAGTTGCCATGTGTGTT 59.586 36.000 0.00 0.00 0.00 3.32
5259 5405 4.941263 ACGAAATATAGTTGCCATGTGTGT 59.059 37.500 0.00 0.00 0.00 3.72
5260 5406 5.484173 ACGAAATATAGTTGCCATGTGTG 57.516 39.130 0.00 0.00 0.00 3.82
5261 5407 5.163663 CCAACGAAATATAGTTGCCATGTGT 60.164 40.000 11.10 0.00 44.45 3.72
5262 5408 5.163663 ACCAACGAAATATAGTTGCCATGTG 60.164 40.000 11.10 2.88 44.45 3.21
5263 5409 4.947388 ACCAACGAAATATAGTTGCCATGT 59.053 37.500 11.10 4.07 44.45 3.21
5264 5410 5.499139 ACCAACGAAATATAGTTGCCATG 57.501 39.130 11.10 0.00 44.45 3.66
5265 5411 6.588204 TCTACCAACGAAATATAGTTGCCAT 58.412 36.000 11.10 4.51 44.45 4.40
5266 5412 5.979993 TCTACCAACGAAATATAGTTGCCA 58.020 37.500 11.10 3.41 44.45 4.92
5267 5413 6.073222 CCATCTACCAACGAAATATAGTTGCC 60.073 42.308 11.10 0.00 44.45 4.52
5268 5414 6.565999 GCCATCTACCAACGAAATATAGTTGC 60.566 42.308 11.10 0.00 44.45 4.17
5269 5415 6.888430 GCCATCTACCAACGAAATATAGTTG 58.112 40.000 10.10 10.10 45.14 3.16


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

AutoCloner maintained by Alex Coulton.