Multiple sequence alignment - TraesCS2D01G380000

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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 TraesCS2D01G380000 chr2D 100.000 2558 0 0 1 2558 484380071 484382628 0.000000e+00 4724.0
1 TraesCS2D01G380000 chr2D 90.671 954 59 16 745 1687 484833970 484834904 0.000000e+00 1242.0
2 TraesCS2D01G380000 chr2D 98.054 411 8 0 2148 2558 615121637 615121227 0.000000e+00 715.0
3 TraesCS2D01G380000 chr2D 92.814 334 14 5 1688 2016 521336438 521336110 2.300000e-130 475.0
4 TraesCS2D01G380000 chr2D 98.077 52 1 0 2018 2069 637965454 637965403 9.750000e-15 91.6
5 TraesCS2D01G380000 chr2B 89.989 949 61 16 745 1683 569485688 569486612 0.000000e+00 1195.0
6 TraesCS2D01G380000 chr2B 92.237 657 32 9 1 657 569125750 569125113 0.000000e+00 913.0
7 TraesCS2D01G380000 chr2B 91.176 340 25 3 1682 2019 704735821 704736157 8.340000e-125 457.0
8 TraesCS2D01G380000 chr2B 93.814 97 6 0 652 748 569113429 569113333 2.050000e-31 147.0
9 TraesCS2D01G380000 chr2B 95.714 70 3 0 745 814 569113273 569113204 2.080000e-21 113.0
10 TraesCS2D01G380000 chr2B 95.238 63 3 0 686 748 569485566 569485628 1.620000e-17 100.0
11 TraesCS2D01G380000 chr5D 98.844 519 6 0 2040 2558 278284743 278285261 0.000000e+00 926.0
12 TraesCS2D01G380000 chr5D 91.667 336 19 4 1688 2018 243874373 243874042 8.340000e-125 457.0
13 TraesCS2D01G380000 chr2A 93.548 620 18 10 1 614 628677896 628678499 0.000000e+00 904.0
14 TraesCS2D01G380000 chr7D 97.647 425 10 0 2134 2558 75227769 75228193 0.000000e+00 730.0
15 TraesCS2D01G380000 chr7D 93.600 125 6 2 2018 2142 160872179 160872057 4.350000e-43 185.0
16 TraesCS2D01G380000 chr3D 95.455 330 12 1 1688 2017 574246416 574246742 8.110000e-145 523.0
17 TraesCS2D01G380000 chr3D 76.943 386 74 11 2176 2557 55977501 55977875 3.340000e-49 206.0
18 TraesCS2D01G380000 chr1A 94.910 334 13 2 1684 2016 415634755 415634425 1.050000e-143 520.0
19 TraesCS2D01G380000 chr3A 94.848 330 12 3 1688 2016 358860741 358860416 6.310000e-141 510.0
20 TraesCS2D01G380000 chr3A 90.000 50 3 2 2018 2067 691701524 691701571 2.120000e-06 63.9
21 TraesCS2D01G380000 chr5A 93.586 343 18 2 1677 2019 544444381 544444043 2.270000e-140 508.0
22 TraesCS2D01G380000 chr7A 94.260 331 15 2 1689 2019 700168872 700169198 1.060000e-138 503.0
23 TraesCS2D01G380000 chr7A 90.000 50 3 2 2018 2067 734568350 734568397 2.120000e-06 63.9
24 TraesCS2D01G380000 chr6D 91.964 336 18 4 1688 2018 38838937 38838606 1.790000e-126 462.0
25 TraesCS2D01G380000 chr6A 71.812 298 76 8 2265 2558 431177919 431178212 7.590000e-11 78.7


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 TraesCS2D01G380000 chr2D 484380071 484382628 2557 False 4724.0 4724 100.0000 1 2558 1 chr2D.!!$F1 2557
1 TraesCS2D01G380000 chr2D 484833970 484834904 934 False 1242.0 1242 90.6710 745 1687 1 chr2D.!!$F2 942
2 TraesCS2D01G380000 chr2B 569125113 569125750 637 True 913.0 913 92.2370 1 657 1 chr2B.!!$R1 656
3 TraesCS2D01G380000 chr2B 569485566 569486612 1046 False 647.5 1195 92.6135 686 1683 2 chr2B.!!$F2 997
4 TraesCS2D01G380000 chr5D 278284743 278285261 518 False 926.0 926 98.8440 2040 2558 1 chr5D.!!$F1 518
5 TraesCS2D01G380000 chr2A 628677896 628678499 603 False 904.0 904 93.5480 1 614 1 chr2A.!!$F1 613

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
659 666 0.031314 CGATCTCTAGTGCGCACCAT 59.969 55.0 35.51 21.57 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1812 0.106719 CGACCACTGGGCCCATTTAT 60.107 55.0 28.82 12.16 37.9 1.4 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
69 70 2.203294 GTTGCCCACCCACTTCGT 60.203 61.111 0.00 0.00 0.00 3.85
83 84 3.277211 TTCGTCCGCCTGTTCTCCG 62.277 63.158 0.00 0.00 0.00 4.63
246 247 6.272318 CACCTGTTTGATTTGAAAGCTTGTA 58.728 36.000 0.00 0.00 0.00 2.41
376 382 2.594131 ACCAGCTAAACCAGAAAACCC 58.406 47.619 0.00 0.00 0.00 4.11
386 392 0.038310 CAGAAAACCCCTCCCCAGTC 59.962 60.000 0.00 0.00 0.00 3.51
412 418 2.837591 TGGGTCGATTCTTTCTCCATGA 59.162 45.455 0.00 0.00 0.00 3.07
453 460 1.153289 CTGTCCCCCAAGCAGATCG 60.153 63.158 0.00 0.00 32.39 3.69
492 499 2.923655 CAGCGACCGCCTTGTATATATG 59.076 50.000 11.03 0.00 43.17 1.78
648 655 6.540438 AAAAACTGGTACCATCGATCTCTA 57.460 37.500 16.75 0.00 0.00 2.43
649 656 5.776173 AAACTGGTACCATCGATCTCTAG 57.224 43.478 16.75 1.69 0.00 2.43
650 657 4.440826 ACTGGTACCATCGATCTCTAGT 57.559 45.455 16.75 2.40 0.00 2.57
651 658 4.138290 ACTGGTACCATCGATCTCTAGTG 58.862 47.826 16.75 0.90 0.00 2.74
652 659 2.885266 TGGTACCATCGATCTCTAGTGC 59.115 50.000 11.60 0.00 0.00 4.40
653 660 2.095668 GGTACCATCGATCTCTAGTGCG 60.096 54.545 7.15 0.00 0.00 5.34
654 661 0.312416 ACCATCGATCTCTAGTGCGC 59.688 55.000 0.00 0.00 0.00 6.09
655 662 0.312102 CCATCGATCTCTAGTGCGCA 59.688 55.000 5.66 5.66 0.00 6.09
656 663 1.403493 CATCGATCTCTAGTGCGCAC 58.597 55.000 32.79 32.79 0.00 5.34
657 664 0.312416 ATCGATCTCTAGTGCGCACC 59.688 55.000 35.51 17.89 0.00 5.01
658 665 1.029947 TCGATCTCTAGTGCGCACCA 61.030 55.000 35.51 23.16 0.00 4.17
659 666 0.031314 CGATCTCTAGTGCGCACCAT 59.969 55.000 35.51 21.57 0.00 3.55
660 667 1.536922 CGATCTCTAGTGCGCACCATT 60.537 52.381 35.51 20.80 0.00 3.16
661 668 2.131183 GATCTCTAGTGCGCACCATTC 58.869 52.381 35.51 19.64 0.00 2.67
662 669 0.175760 TCTCTAGTGCGCACCATTCC 59.824 55.000 35.51 11.40 0.00 3.01
663 670 1.148157 CTCTAGTGCGCACCATTCCG 61.148 60.000 35.51 17.53 0.00 4.30
664 671 2.125310 TAGTGCGCACCATTCCGG 60.125 61.111 35.51 0.00 42.50 5.14
674 681 2.914379 CCATTCCGGTAGCGATTCC 58.086 57.895 17.33 0.00 0.00 3.01
675 682 0.602905 CCATTCCGGTAGCGATTCCC 60.603 60.000 17.33 0.00 0.00 3.97
676 683 0.602905 CATTCCGGTAGCGATTCCCC 60.603 60.000 17.33 0.00 0.00 4.81
677 684 1.765597 ATTCCGGTAGCGATTCCCCC 61.766 60.000 17.33 0.00 0.00 5.40
678 685 3.158648 CCGGTAGCGATTCCCCCA 61.159 66.667 17.33 0.00 0.00 4.96
679 686 2.108362 CGGTAGCGATTCCCCCAC 59.892 66.667 9.07 0.00 0.00 4.61
680 687 2.727392 CGGTAGCGATTCCCCCACA 61.727 63.158 9.07 0.00 0.00 4.17
681 688 1.146263 GGTAGCGATTCCCCCACAG 59.854 63.158 0.00 0.00 0.00 3.66
682 689 1.146263 GTAGCGATTCCCCCACAGG 59.854 63.158 0.00 0.00 0.00 4.00
702 709 4.993584 CAGGGGAACTCAATCGATTGATAG 59.006 45.833 34.40 26.79 44.92 2.08
716 723 4.387256 CGATTGATAGCCTTCTCCGAAATC 59.613 45.833 0.00 0.00 0.00 2.17
767 837 5.705441 GTCAAATCCTACATGAACTCCACAA 59.295 40.000 0.00 0.00 0.00 3.33
768 838 5.939883 TCAAATCCTACATGAACTCCACAAG 59.060 40.000 0.00 0.00 0.00 3.16
797 868 2.764128 GATCCGGGCTGTCTGGGA 60.764 66.667 7.39 0.94 42.31 4.37
798 869 3.083997 ATCCGGGCTGTCTGGGAC 61.084 66.667 7.39 0.00 42.31 4.46
799 870 3.625632 ATCCGGGCTGTCTGGGACT 62.626 63.158 7.39 0.00 42.31 3.85
800 871 4.087892 CCGGGCTGTCTGGGACTG 62.088 72.222 0.00 0.38 38.27 3.51
801 872 3.314331 CGGGCTGTCTGGGACTGT 61.314 66.667 6.47 0.00 34.68 3.55
802 873 2.348998 GGGCTGTCTGGGACTGTG 59.651 66.667 6.47 0.00 34.68 3.66
803 874 2.348998 GGCTGTCTGGGACTGTGG 59.651 66.667 6.47 0.00 34.68 4.17
804 875 2.348998 GCTGTCTGGGACTGTGGG 59.651 66.667 6.47 0.00 34.68 4.61
835 909 2.394632 AGCATAATGTACCCGAGGACA 58.605 47.619 0.00 0.00 0.00 4.02
846 920 0.109226 CCGAGGACAGGAAACGAGAC 60.109 60.000 0.00 0.00 0.00 3.36
847 921 0.596577 CGAGGACAGGAAACGAGACA 59.403 55.000 0.00 0.00 0.00 3.41
848 922 1.202582 CGAGGACAGGAAACGAGACAT 59.797 52.381 0.00 0.00 0.00 3.06
849 923 2.732597 CGAGGACAGGAAACGAGACATC 60.733 54.545 0.00 0.00 0.00 3.06
850 924 2.494073 GAGGACAGGAAACGAGACATCT 59.506 50.000 0.00 0.00 0.00 2.90
851 925 2.900546 AGGACAGGAAACGAGACATCTT 59.099 45.455 0.00 0.00 0.00 2.40
852 926 3.325135 AGGACAGGAAACGAGACATCTTT 59.675 43.478 0.00 0.00 0.00 2.52
898 972 1.195985 CGCGCGTGAATACATCGAC 59.804 57.895 24.19 0.00 0.00 4.20
900 974 1.818221 GCGCGTGAATACATCGACCC 61.818 60.000 8.43 0.00 0.00 4.46
901 975 0.526739 CGCGTGAATACATCGACCCA 60.527 55.000 0.00 0.00 0.00 4.51
902 976 0.928229 GCGTGAATACATCGACCCAC 59.072 55.000 0.00 0.00 0.00 4.61
903 977 1.470979 GCGTGAATACATCGACCCACT 60.471 52.381 0.00 0.00 0.00 4.00
904 978 2.193447 CGTGAATACATCGACCCACTG 58.807 52.381 0.00 0.00 0.00 3.66
914 988 1.377725 GACCCACTGCACCATGGAG 60.378 63.158 21.47 12.70 41.93 3.86
923 997 0.681175 GCACCATGGAGGCAAAACTT 59.319 50.000 21.47 0.00 43.14 2.66
926 1000 2.029649 CACCATGGAGGCAAAACTTCTG 60.030 50.000 21.47 0.00 43.14 3.02
929 1003 1.321474 TGGAGGCAAAACTTCTGCAG 58.679 50.000 7.63 7.63 41.78 4.41
930 1004 0.038801 GGAGGCAAAACTTCTGCAGC 60.039 55.000 9.47 0.00 41.78 5.25
934 1008 0.936297 GCAAAACTTCTGCAGCACGG 60.936 55.000 9.47 1.19 39.69 4.94
969 1043 4.207281 CTTCGATGGAGCGCCGGA 62.207 66.667 5.05 0.00 36.79 5.14
971 1045 4.508128 TCGATGGAGCGCCGGAAC 62.508 66.667 5.05 0.00 36.79 3.62
1044 1118 2.794981 CGTTCTGTGTATAGTCGGCCTG 60.795 54.545 0.00 0.00 0.00 4.85
1125 1199 3.153024 CGTGGTCATGGACGGATTT 57.847 52.632 0.00 0.00 32.65 2.17
1168 1242 1.683790 GCGGACGTTCAATCTCACCG 61.684 60.000 0.00 0.00 41.44 4.94
1186 1260 1.194547 CCGTGGTCATCAACAACTTCG 59.805 52.381 0.00 0.00 28.55 3.79
1242 1316 3.066900 CAGTGGTCTTATACGGAGGAGTG 59.933 52.174 0.00 0.00 0.00 3.51
1302 1376 0.868406 CCAAGTGCTCCACGAAGTTC 59.132 55.000 0.00 0.00 41.61 3.01
1339 1413 2.762875 GAGGGGTGGGTCTACCGG 60.763 72.222 0.00 0.00 44.64 5.28
1373 1447 2.125552 CATGGCGGACGAGAAGCA 60.126 61.111 0.00 0.00 0.00 3.91
1433 1507 3.774702 GAAGCACCGGTCGTTCGC 61.775 66.667 2.59 4.54 0.00 4.70
1560 1641 1.674221 CCCGGCTTTCTGTTCTGAGAG 60.674 57.143 0.00 0.00 0.00 3.20
1564 1645 2.289320 GGCTTTCTGTTCTGAGAGAGCA 60.289 50.000 13.26 0.00 46.97 4.26
1584 1665 4.717233 CATGTATGCCTTTGCCAGTTTA 57.283 40.909 0.00 0.00 36.33 2.01
1585 1666 4.423732 CATGTATGCCTTTGCCAGTTTAC 58.576 43.478 0.00 0.00 36.33 2.01
1626 1707 4.205065 TCCCGTTGGTACATAATTCGTT 57.795 40.909 0.00 0.00 39.30 3.85
1630 1711 5.754406 CCCGTTGGTACATAATTCGTTCATA 59.246 40.000 0.00 0.00 39.30 2.15
1683 1766 1.134401 TGCTCTGGCCTATGTACTTGC 60.134 52.381 3.32 0.00 37.74 4.01
1687 1770 2.104792 TCTGGCCTATGTACTTGCATCC 59.895 50.000 3.32 0.00 0.00 3.51
1688 1771 1.843206 TGGCCTATGTACTTGCATCCA 59.157 47.619 3.32 0.00 0.00 3.41
1689 1772 2.158769 TGGCCTATGTACTTGCATCCAG 60.159 50.000 3.32 0.00 0.00 3.86
1690 1773 2.498167 GCCTATGTACTTGCATCCAGG 58.502 52.381 0.00 0.00 31.16 4.45
1691 1774 2.811873 GCCTATGTACTTGCATCCAGGG 60.812 54.545 0.00 0.00 29.55 4.45
1692 1775 2.498167 CTATGTACTTGCATCCAGGGC 58.502 52.381 0.00 0.00 0.00 5.19
1693 1776 0.106519 ATGTACTTGCATCCAGGGCC 60.107 55.000 0.00 0.00 0.00 5.80
1694 1777 1.819632 GTACTTGCATCCAGGGCCG 60.820 63.158 0.00 0.00 0.00 6.13
1695 1778 3.042733 TACTTGCATCCAGGGCCGG 62.043 63.158 0.00 0.00 0.00 6.13
1707 1790 3.062466 GGCCGGGCCTGAAGTTTC 61.062 66.667 30.86 0.00 46.69 2.78
1708 1791 3.431725 GCCGGGCCTGAAGTTTCG 61.432 66.667 15.09 0.00 0.00 3.46
1709 1792 2.746277 CCGGGCCTGAAGTTTCGG 60.746 66.667 15.09 5.66 0.00 4.30
1710 1793 2.345991 CGGGCCTGAAGTTTCGGA 59.654 61.111 5.28 0.00 35.56 4.55
1711 1794 1.741770 CGGGCCTGAAGTTTCGGAG 60.742 63.158 5.28 0.00 35.56 4.63
1712 1795 1.377333 GGGCCTGAAGTTTCGGAGG 60.377 63.158 0.84 0.00 35.56 4.30
1713 1796 2.041115 GGCCTGAAGTTTCGGAGGC 61.041 63.158 12.46 12.46 42.53 4.70
1714 1797 2.041115 GCCTGAAGTTTCGGAGGCC 61.041 63.158 10.58 0.00 39.30 5.19
1715 1798 1.377333 CCTGAAGTTTCGGAGGCCC 60.377 63.158 0.00 0.00 35.56 5.80
1716 1799 1.679898 CTGAAGTTTCGGAGGCCCT 59.320 57.895 0.00 0.00 35.56 5.19
1717 1800 0.902531 CTGAAGTTTCGGAGGCCCTA 59.097 55.000 0.00 0.00 35.56 3.53
1718 1801 0.902531 TGAAGTTTCGGAGGCCCTAG 59.097 55.000 0.00 0.00 0.00 3.02
1719 1802 0.178301 GAAGTTTCGGAGGCCCTAGG 59.822 60.000 0.06 0.06 0.00 3.02
1720 1803 1.272554 AAGTTTCGGAGGCCCTAGGG 61.273 60.000 24.89 24.89 38.57 3.53
1735 1818 5.520376 CCCTAGGGCAAACTCAATAAATG 57.480 43.478 16.90 0.00 0.00 2.32
1736 1819 4.342092 CCCTAGGGCAAACTCAATAAATGG 59.658 45.833 16.90 0.00 0.00 3.16
1737 1820 4.342092 CCTAGGGCAAACTCAATAAATGGG 59.658 45.833 0.00 0.00 34.78 4.00
1738 1821 2.501316 AGGGCAAACTCAATAAATGGGC 59.499 45.455 0.00 0.00 30.00 5.36
1739 1822 2.419990 GGGCAAACTCAATAAATGGGCC 60.420 50.000 0.00 0.00 38.15 5.80
1740 1823 2.419990 GGCAAACTCAATAAATGGGCCC 60.420 50.000 17.59 17.59 30.00 5.80
1741 1824 2.235898 GCAAACTCAATAAATGGGCCCA 59.764 45.455 30.92 30.92 30.00 5.36
1742 1825 3.679639 GCAAACTCAATAAATGGGCCCAG 60.680 47.826 31.97 15.77 30.00 4.45
1743 1826 3.473113 AACTCAATAAATGGGCCCAGT 57.527 42.857 31.97 27.20 30.00 4.00
1744 1827 2.738743 ACTCAATAAATGGGCCCAGTG 58.261 47.619 31.97 20.99 30.00 3.66
1745 1828 2.034124 CTCAATAAATGGGCCCAGTGG 58.966 52.381 31.97 17.84 0.00 4.00
1746 1829 1.360852 TCAATAAATGGGCCCAGTGGT 59.639 47.619 31.97 16.64 0.00 4.16
1747 1830 1.756538 CAATAAATGGGCCCAGTGGTC 59.243 52.381 31.97 0.00 34.57 4.02
1748 1831 0.106719 ATAAATGGGCCCAGTGGTCG 60.107 55.000 31.97 0.00 36.99 4.79
1749 1832 1.202099 TAAATGGGCCCAGTGGTCGA 61.202 55.000 31.97 8.77 36.99 4.20
1750 1833 2.075355 AAATGGGCCCAGTGGTCGAA 62.075 55.000 31.97 2.06 36.99 3.71
1751 1834 2.484287 AATGGGCCCAGTGGTCGAAG 62.484 60.000 31.97 0.00 36.99 3.79
1752 1835 3.637273 GGGCCCAGTGGTCGAAGT 61.637 66.667 19.95 0.00 36.99 3.01
1753 1836 2.358737 GGCCCAGTGGTCGAAGTG 60.359 66.667 8.74 0.00 0.00 3.16
1754 1837 2.426023 GCCCAGTGGTCGAAGTGT 59.574 61.111 8.74 0.00 0.00 3.55
1755 1838 1.227853 GCCCAGTGGTCGAAGTGTT 60.228 57.895 8.74 0.00 0.00 3.32
1756 1839 1.228657 GCCCAGTGGTCGAAGTGTTC 61.229 60.000 8.74 0.00 0.00 3.18
1757 1840 0.393077 CCCAGTGGTCGAAGTGTTCT 59.607 55.000 8.74 0.00 0.00 3.01
1758 1841 1.605712 CCCAGTGGTCGAAGTGTTCTC 60.606 57.143 8.74 0.00 0.00 2.87
1759 1842 1.341531 CCAGTGGTCGAAGTGTTCTCT 59.658 52.381 0.00 0.00 0.00 3.10
1760 1843 2.224066 CCAGTGGTCGAAGTGTTCTCTT 60.224 50.000 0.00 0.00 0.00 2.85
1761 1844 3.458189 CAGTGGTCGAAGTGTTCTCTTT 58.542 45.455 0.00 0.00 0.00 2.52
1762 1845 3.871594 CAGTGGTCGAAGTGTTCTCTTTT 59.128 43.478 0.00 0.00 0.00 2.27
1763 1846 4.332819 CAGTGGTCGAAGTGTTCTCTTTTT 59.667 41.667 0.00 0.00 0.00 1.94
1764 1847 5.522460 CAGTGGTCGAAGTGTTCTCTTTTTA 59.478 40.000 0.00 0.00 0.00 1.52
1765 1848 5.753921 AGTGGTCGAAGTGTTCTCTTTTTAG 59.246 40.000 0.00 0.00 0.00 1.85
1766 1849 5.751990 GTGGTCGAAGTGTTCTCTTTTTAGA 59.248 40.000 0.00 0.00 0.00 2.10
1767 1850 6.424207 GTGGTCGAAGTGTTCTCTTTTTAGAT 59.576 38.462 0.00 0.00 0.00 1.98
1768 1851 6.990349 TGGTCGAAGTGTTCTCTTTTTAGATT 59.010 34.615 0.00 0.00 0.00 2.40
1769 1852 7.170998 TGGTCGAAGTGTTCTCTTTTTAGATTC 59.829 37.037 0.00 0.00 0.00 2.52
1770 1853 7.360185 GGTCGAAGTGTTCTCTTTTTAGATTCC 60.360 40.741 0.00 0.00 0.00 3.01
1771 1854 7.170998 GTCGAAGTGTTCTCTTTTTAGATTCCA 59.829 37.037 0.00 0.00 0.00 3.53
1772 1855 7.878127 TCGAAGTGTTCTCTTTTTAGATTCCAT 59.122 33.333 0.00 0.00 0.00 3.41
1773 1856 9.151471 CGAAGTGTTCTCTTTTTAGATTCCATA 57.849 33.333 0.00 0.00 0.00 2.74
1775 1858 9.793259 AAGTGTTCTCTTTTTAGATTCCATACA 57.207 29.630 0.00 0.00 0.00 2.29
1776 1859 9.965902 AGTGTTCTCTTTTTAGATTCCATACAT 57.034 29.630 0.00 0.00 0.00 2.29
1868 1951 9.748708 TCTAGTAACAATGTTGTACTTTTACGT 57.251 29.630 9.15 0.00 41.31 3.57
1871 1954 9.101655 AGTAACAATGTTGTACTTTTACGTTCT 57.898 29.630 9.15 0.00 41.31 3.01
1874 1957 8.876275 ACAATGTTGTACTTTTACGTTCTAGA 57.124 30.769 0.00 0.00 40.16 2.43
1875 1958 9.485206 ACAATGTTGTACTTTTACGTTCTAGAT 57.515 29.630 0.00 0.00 40.16 1.98
1876 1959 9.953825 CAATGTTGTACTTTTACGTTCTAGATC 57.046 33.333 0.00 0.00 0.00 2.75
1877 1960 9.701098 AATGTTGTACTTTTACGTTCTAGATCA 57.299 29.630 0.00 0.00 0.00 2.92
1878 1961 9.701098 ATGTTGTACTTTTACGTTCTAGATCAA 57.299 29.630 0.00 0.00 0.00 2.57
1879 1962 9.531942 TGTTGTACTTTTACGTTCTAGATCAAA 57.468 29.630 0.00 0.00 0.00 2.69
1901 1984 9.665719 TCAAATATCAATAAGTTACAGAGCACA 57.334 29.630 0.00 0.00 0.00 4.57
1904 1987 9.448438 AATATCAATAAGTTACAGAGCACAACA 57.552 29.630 0.00 0.00 0.00 3.33
1905 1988 7.744087 ATCAATAAGTTACAGAGCACAACAA 57.256 32.000 0.00 0.00 0.00 2.83
1906 1989 7.561021 TCAATAAGTTACAGAGCACAACAAA 57.439 32.000 0.00 0.00 0.00 2.83
1907 1990 7.990917 TCAATAAGTTACAGAGCACAACAAAA 58.009 30.769 0.00 0.00 0.00 2.44
1908 1991 8.462811 TCAATAAGTTACAGAGCACAACAAAAA 58.537 29.630 0.00 0.00 0.00 1.94
1938 2021 9.868277 AATGCCTTTAATAATCATGAAAAACGA 57.132 25.926 0.00 0.00 0.00 3.85
1939 2022 8.682128 TGCCTTTAATAATCATGAAAAACGAC 57.318 30.769 0.00 0.00 0.00 4.34
1940 2023 8.519526 TGCCTTTAATAATCATGAAAAACGACT 58.480 29.630 0.00 0.00 0.00 4.18
1941 2024 9.010366 GCCTTTAATAATCATGAAAAACGACTC 57.990 33.333 0.00 0.00 0.00 3.36
1942 2025 9.503427 CCTTTAATAATCATGAAAAACGACTCC 57.497 33.333 0.00 0.00 0.00 3.85
1943 2026 9.210426 CTTTAATAATCATGAAAAACGACTCCG 57.790 33.333 0.00 0.00 42.50 4.63
1957 2040 4.600012 CGACTCCGTGCATTTTTCTATT 57.400 40.909 0.00 0.00 0.00 1.73
1958 2041 4.578601 CGACTCCGTGCATTTTTCTATTC 58.421 43.478 0.00 0.00 0.00 1.75
1959 2042 4.092821 CGACTCCGTGCATTTTTCTATTCA 59.907 41.667 0.00 0.00 0.00 2.57
1960 2043 5.390461 CGACTCCGTGCATTTTTCTATTCAA 60.390 40.000 0.00 0.00 0.00 2.69
1961 2044 6.325919 ACTCCGTGCATTTTTCTATTCAAA 57.674 33.333 0.00 0.00 0.00 2.69
1962 2045 6.744112 ACTCCGTGCATTTTTCTATTCAAAA 58.256 32.000 0.00 0.00 0.00 2.44
1963 2046 7.206687 ACTCCGTGCATTTTTCTATTCAAAAA 58.793 30.769 0.00 0.00 39.09 1.94
1964 2047 7.872483 ACTCCGTGCATTTTTCTATTCAAAAAT 59.128 29.630 0.00 0.00 43.63 1.82
1965 2048 8.238481 TCCGTGCATTTTTCTATTCAAAAATC 57.762 30.769 0.00 0.04 41.82 2.17
1966 2049 7.869937 TCCGTGCATTTTTCTATTCAAAAATCA 59.130 29.630 0.00 2.06 41.82 2.57
1967 2050 8.658609 CCGTGCATTTTTCTATTCAAAAATCAT 58.341 29.630 0.00 0.00 41.82 2.45
1968 2051 9.679596 CGTGCATTTTTCTATTCAAAAATCATC 57.320 29.630 0.00 0.00 41.82 2.92
1981 2064 7.757941 TCAAAAATCATCAATGGTAGTGTCA 57.242 32.000 0.00 0.00 0.00 3.58
1982 2065 8.175925 TCAAAAATCATCAATGGTAGTGTCAA 57.824 30.769 0.00 0.00 0.00 3.18
1983 2066 8.298854 TCAAAAATCATCAATGGTAGTGTCAAG 58.701 33.333 0.00 0.00 0.00 3.02
1984 2067 8.298854 CAAAAATCATCAATGGTAGTGTCAAGA 58.701 33.333 0.00 0.00 0.00 3.02
1985 2068 8.585471 AAAATCATCAATGGTAGTGTCAAGAT 57.415 30.769 0.00 0.00 0.00 2.40
1986 2069 8.585471 AAATCATCAATGGTAGTGTCAAGATT 57.415 30.769 0.00 0.00 0.00 2.40
1987 2070 9.685276 AAATCATCAATGGTAGTGTCAAGATTA 57.315 29.630 0.00 0.00 0.00 1.75
1988 2071 9.685276 AATCATCAATGGTAGTGTCAAGATTAA 57.315 29.630 0.00 0.00 0.00 1.40
1989 2072 9.857656 ATCATCAATGGTAGTGTCAAGATTAAT 57.142 29.630 0.00 0.00 0.00 1.40
1990 2073 9.112725 TCATCAATGGTAGTGTCAAGATTAATG 57.887 33.333 0.00 0.00 0.00 1.90
1991 2074 9.112725 CATCAATGGTAGTGTCAAGATTAATGA 57.887 33.333 0.00 0.00 0.00 2.57
1992 2075 9.857656 ATCAATGGTAGTGTCAAGATTAATGAT 57.142 29.630 0.00 0.00 0.00 2.45
2019 2102 9.088512 AGTAATTTATCTGCTCTTTTACTGTCG 57.911 33.333 0.00 0.00 29.79 4.35
2020 2103 9.084164 GTAATTTATCTGCTCTTTTACTGTCGA 57.916 33.333 0.00 0.00 0.00 4.20
2021 2104 8.547967 AATTTATCTGCTCTTTTACTGTCGAA 57.452 30.769 0.00 0.00 0.00 3.71
2022 2105 7.582435 TTTATCTGCTCTTTTACTGTCGAAG 57.418 36.000 0.00 0.00 0.00 3.79
2023 2106 3.914312 TCTGCTCTTTTACTGTCGAAGG 58.086 45.455 0.00 0.00 0.00 3.46
2024 2107 2.996621 CTGCTCTTTTACTGTCGAAGGG 59.003 50.000 0.00 0.00 0.00 3.95
2025 2108 1.732809 GCTCTTTTACTGTCGAAGGGC 59.267 52.381 10.81 10.81 39.43 5.19
2026 2109 2.347731 CTCTTTTACTGTCGAAGGGCC 58.652 52.381 0.00 0.00 0.00 5.80
2027 2110 1.695242 TCTTTTACTGTCGAAGGGCCA 59.305 47.619 6.18 0.00 0.00 5.36
2028 2111 2.304761 TCTTTTACTGTCGAAGGGCCAT 59.695 45.455 6.18 0.00 0.00 4.40
2029 2112 2.871096 TTTACTGTCGAAGGGCCATT 57.129 45.000 0.07 0.07 0.00 3.16
2030 2113 2.107950 TTACTGTCGAAGGGCCATTG 57.892 50.000 7.73 0.00 0.00 2.82
2031 2114 0.251916 TACTGTCGAAGGGCCATTGG 59.748 55.000 7.73 6.59 0.00 3.16
2069 2152 7.574607 AGAAAGGGAAAGAAAGAGTACAAAGA 58.425 34.615 0.00 0.00 0.00 2.52
2220 2303 0.523966 CTCCAGACGCCGATATCCTC 59.476 60.000 0.00 0.00 0.00 3.71
2425 2508 1.216427 GGGATCAGGAAATCAGCCCTT 59.784 52.381 0.00 0.00 0.00 3.95
2449 2532 1.002251 CGTGCCTTAAAACGAAGCCAA 60.002 47.619 0.00 0.00 42.32 4.52
2527 2610 1.699656 CGCAAAGAGGACAGATGCCG 61.700 60.000 0.00 0.00 33.55 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 179 0.599204 TCAACGCGTTCAGGAGTTCC 60.599 55.000 23.92 0.00 0.00 3.62
246 247 7.383843 CCAGGTTTGTGTATTTTTCGCTTTATT 59.616 33.333 0.00 0.00 0.00 1.40
264 265 4.081406 TCATCAATCTGGTTCCAGGTTTG 58.919 43.478 13.90 17.36 35.45 2.93
303 308 1.150567 CCTTCTCCTTCGCAGCATCG 61.151 60.000 0.00 0.00 0.00 3.84
386 392 3.375299 GGAGAAAGAATCGACCCATGTTG 59.625 47.826 0.00 0.00 0.00 3.33
397 403 9.464714 CAATCAATCAATCATGGAGAAAGAATC 57.535 33.333 0.00 0.00 0.00 2.52
412 418 3.355378 TCGGCCTCAACAATCAATCAAT 58.645 40.909 0.00 0.00 0.00 2.57
453 460 2.810852 GCTGGCTCCTGCAATATAAGTC 59.189 50.000 12.12 0.00 41.91 3.01
504 511 7.382898 ACACGCACCTCCATAATTTTATTTTT 58.617 30.769 0.00 0.00 0.00 1.94
505 512 6.930731 ACACGCACCTCCATAATTTTATTTT 58.069 32.000 0.00 0.00 0.00 1.82
506 513 6.524101 ACACGCACCTCCATAATTTTATTT 57.476 33.333 0.00 0.00 0.00 1.40
507 514 6.238266 CGTACACGCACCTCCATAATTTTATT 60.238 38.462 0.00 0.00 0.00 1.40
508 515 5.235616 CGTACACGCACCTCCATAATTTTAT 59.764 40.000 0.00 0.00 0.00 1.40
509 516 4.567558 CGTACACGCACCTCCATAATTTTA 59.432 41.667 0.00 0.00 0.00 1.52
630 637 3.057876 GCACTAGAGATCGATGGTACCAG 60.058 52.174 21.41 7.83 0.00 4.00
632 639 2.095668 CGCACTAGAGATCGATGGTACC 60.096 54.545 0.54 4.43 0.00 3.34
656 663 0.602905 GGGAATCGCTACCGGAATGG 60.603 60.000 9.46 0.00 46.41 3.16
657 664 0.602905 GGGGAATCGCTACCGGAATG 60.603 60.000 9.46 0.00 34.56 2.67
658 665 1.752833 GGGGAATCGCTACCGGAAT 59.247 57.895 9.46 0.00 34.56 3.01
659 666 2.437396 GGGGGAATCGCTACCGGAA 61.437 63.158 9.46 0.00 34.56 4.30
660 667 2.841044 GGGGGAATCGCTACCGGA 60.841 66.667 9.46 0.00 34.56 5.14
661 668 3.158648 TGGGGGAATCGCTACCGG 61.159 66.667 0.00 0.00 34.56 5.28
662 669 2.108362 GTGGGGGAATCGCTACCG 59.892 66.667 0.00 0.00 32.53 4.02
663 670 1.146263 CTGTGGGGGAATCGCTACC 59.854 63.158 0.00 0.00 36.68 3.18
664 671 1.146263 CCTGTGGGGGAATCGCTAC 59.854 63.158 0.00 0.00 37.72 3.58
665 672 3.642078 CCTGTGGGGGAATCGCTA 58.358 61.111 0.00 0.00 0.00 4.26
676 683 0.613260 TCGATTGAGTTCCCCTGTGG 59.387 55.000 0.00 0.00 0.00 4.17
677 684 2.679837 CAATCGATTGAGTTCCCCTGTG 59.320 50.000 30.12 1.31 40.14 3.66
678 685 2.571653 TCAATCGATTGAGTTCCCCTGT 59.428 45.455 31.83 0.00 41.51 4.00
679 686 3.266510 TCAATCGATTGAGTTCCCCTG 57.733 47.619 31.83 8.27 41.51 4.45
690 697 3.574396 TCGGAGAAGGCTATCAATCGATT 59.426 43.478 4.39 4.39 32.73 3.34
702 709 2.413453 GCATATCGATTTCGGAGAAGGC 59.587 50.000 1.71 0.00 45.90 4.35
716 723 7.946768 CGTAAGATGATTAAGTTGTGCATATCG 59.053 37.037 0.00 0.00 43.02 2.92
827 901 0.109226 GTCTCGTTTCCTGTCCTCGG 60.109 60.000 0.00 0.00 0.00 4.63
835 909 9.892130 ATTAAAGATAAAGATGTCTCGTTTCCT 57.108 29.630 0.00 0.00 0.00 3.36
898 972 2.044650 CCTCCATGGTGCAGTGGG 60.045 66.667 12.58 0.57 36.15 4.61
900 974 1.180456 TTTGCCTCCATGGTGCAGTG 61.180 55.000 23.93 7.41 36.21 3.66
901 975 0.469705 TTTTGCCTCCATGGTGCAGT 60.470 50.000 23.93 0.00 36.21 4.40
902 976 0.037975 GTTTTGCCTCCATGGTGCAG 60.038 55.000 23.93 10.97 36.21 4.41
903 977 0.469705 AGTTTTGCCTCCATGGTGCA 60.470 50.000 22.29 22.29 38.35 4.57
904 978 0.681175 AAGTTTTGCCTCCATGGTGC 59.319 50.000 12.58 16.10 38.35 5.01
914 988 0.936297 CGTGCTGCAGAAGTTTTGCC 60.936 55.000 20.43 2.24 40.81 4.52
934 1008 3.774702 GTTGTTCGTCGCTCCGGC 61.775 66.667 0.00 0.00 0.00 6.13
969 1043 0.466555 TACCCGTTTGGCTGCTTGTT 60.467 50.000 0.00 0.00 37.83 2.83
971 1045 1.579429 GTACCCGTTTGGCTGCTTG 59.421 57.895 0.00 0.00 37.83 4.01
980 1054 1.301165 GCAGTCACCGTACCCGTTT 60.301 57.895 0.00 0.00 0.00 3.60
1056 1130 1.216710 GACGAGACCCAGAGCAAGG 59.783 63.158 0.00 0.00 0.00 3.61
1125 1199 1.975407 GTGGTCCTCGAGGTCGGAA 60.975 63.158 30.17 8.66 40.29 4.30
1168 1242 1.535462 CCCGAAGTTGTTGATGACCAC 59.465 52.381 0.00 0.00 0.00 4.16
1257 1331 2.046988 CACAGATCCTGCACGCCA 60.047 61.111 0.00 0.00 34.37 5.69
1362 1436 2.811317 CCAGCGTGCTTCTCGTCC 60.811 66.667 0.00 0.00 0.00 4.79
1425 1499 3.467119 ATGCACGACGCGAACGAC 61.467 61.111 28.40 21.19 46.97 4.34
1543 1617 2.289320 TGCTCTCTCAGAACAGAAAGCC 60.289 50.000 0.00 0.00 0.00 4.35
1564 1645 3.447229 GGTAAACTGGCAAAGGCATACAT 59.553 43.478 0.00 0.00 43.71 2.29
1584 1665 6.237901 GGGAAAATAAAAGGAAAATGCAGGT 58.762 36.000 0.00 0.00 0.00 4.00
1585 1666 5.351189 CGGGAAAATAAAAGGAAAATGCAGG 59.649 40.000 0.00 0.00 0.00 4.85
1650 1731 5.018809 AGGCCAGAGCATATTTTCAGAAAA 58.981 37.500 10.80 10.80 42.56 2.29
1654 1735 5.068636 ACATAGGCCAGAGCATATTTTCAG 58.931 41.667 5.01 0.00 43.17 3.02
1655 1736 5.052693 ACATAGGCCAGAGCATATTTTCA 57.947 39.130 5.01 0.00 43.17 2.69
1656 1737 6.234177 AGTACATAGGCCAGAGCATATTTTC 58.766 40.000 5.01 0.00 43.17 2.29
1691 1774 3.431725 CGAAACTTCAGGCCCGGC 61.432 66.667 0.00 0.00 0.00 6.13
1692 1775 2.746277 CCGAAACTTCAGGCCCGG 60.746 66.667 0.00 0.00 0.00 5.73
1693 1776 1.741770 CTCCGAAACTTCAGGCCCG 60.742 63.158 0.00 0.00 0.00 6.13
1694 1777 1.377333 CCTCCGAAACTTCAGGCCC 60.377 63.158 0.00 0.00 0.00 5.80
1695 1778 2.041115 GCCTCCGAAACTTCAGGCC 61.041 63.158 8.85 0.00 45.04 5.19
1696 1779 3.579685 GCCTCCGAAACTTCAGGC 58.420 61.111 5.37 5.37 44.63 4.85
1697 1780 1.377333 GGGCCTCCGAAACTTCAGG 60.377 63.158 0.84 0.00 0.00 3.86
1698 1781 0.902531 TAGGGCCTCCGAAACTTCAG 59.097 55.000 10.74 0.00 38.33 3.02
1699 1782 0.902531 CTAGGGCCTCCGAAACTTCA 59.097 55.000 10.74 0.00 38.33 3.02
1700 1783 0.178301 CCTAGGGCCTCCGAAACTTC 59.822 60.000 10.74 0.00 38.33 3.01
1701 1784 1.272554 CCCTAGGGCCTCCGAAACTT 61.273 60.000 16.90 0.00 38.33 2.66
1702 1785 1.689582 CCCTAGGGCCTCCGAAACT 60.690 63.158 16.90 0.00 38.33 2.66
1703 1786 2.908796 CCCTAGGGCCTCCGAAAC 59.091 66.667 16.90 0.00 38.33 2.78
1713 1796 4.342092 CCATTTATTGAGTTTGCCCTAGGG 59.658 45.833 24.89 24.89 38.57 3.53
1714 1797 4.342092 CCCATTTATTGAGTTTGCCCTAGG 59.658 45.833 0.06 0.06 0.00 3.02
1715 1798 4.202151 GCCCATTTATTGAGTTTGCCCTAG 60.202 45.833 0.00 0.00 0.00 3.02
1716 1799 3.704061 GCCCATTTATTGAGTTTGCCCTA 59.296 43.478 0.00 0.00 0.00 3.53
1717 1800 2.501316 GCCCATTTATTGAGTTTGCCCT 59.499 45.455 0.00 0.00 0.00 5.19
1718 1801 2.419990 GGCCCATTTATTGAGTTTGCCC 60.420 50.000 0.00 0.00 0.00 5.36
1719 1802 2.419990 GGGCCCATTTATTGAGTTTGCC 60.420 50.000 19.95 0.00 35.65 4.52
1720 1803 2.235898 TGGGCCCATTTATTGAGTTTGC 59.764 45.455 24.45 0.00 0.00 3.68
1721 1804 3.515104 ACTGGGCCCATTTATTGAGTTTG 59.485 43.478 28.82 11.42 0.00 2.93
1722 1805 3.515104 CACTGGGCCCATTTATTGAGTTT 59.485 43.478 28.82 0.00 0.00 2.66
1723 1806 3.099141 CACTGGGCCCATTTATTGAGTT 58.901 45.455 28.82 0.00 0.00 3.01
1724 1807 2.624029 CCACTGGGCCCATTTATTGAGT 60.624 50.000 28.82 14.70 0.00 3.41
1725 1808 2.034124 CCACTGGGCCCATTTATTGAG 58.966 52.381 28.82 13.93 0.00 3.02
1726 1809 1.360852 ACCACTGGGCCCATTTATTGA 59.639 47.619 28.82 0.00 37.90 2.57
1727 1810 1.756538 GACCACTGGGCCCATTTATTG 59.243 52.381 28.82 15.63 37.90 1.90
1728 1811 1.684869 CGACCACTGGGCCCATTTATT 60.685 52.381 28.82 9.06 37.90 1.40
1729 1812 0.106719 CGACCACTGGGCCCATTTAT 60.107 55.000 28.82 12.16 37.90 1.40
1730 1813 1.202099 TCGACCACTGGGCCCATTTA 61.202 55.000 28.82 0.83 37.90 1.40
1731 1814 2.035626 CGACCACTGGGCCCATTT 59.964 61.111 28.82 13.37 37.90 2.32
1732 1815 2.484287 CTTCGACCACTGGGCCCATT 62.484 60.000 28.82 19.03 37.90 3.16
1733 1816 2.933287 TTCGACCACTGGGCCCAT 60.933 61.111 28.82 11.04 37.90 4.00
1734 1817 3.636231 CTTCGACCACTGGGCCCA 61.636 66.667 26.67 26.67 37.90 5.36
1735 1818 3.637273 ACTTCGACCACTGGGCCC 61.637 66.667 17.59 17.59 37.90 5.80
1736 1819 2.358737 CACTTCGACCACTGGGCC 60.359 66.667 0.00 0.00 37.90 5.80
1737 1820 1.227853 AACACTTCGACCACTGGGC 60.228 57.895 0.00 0.00 37.90 5.36
1738 1821 0.393077 AGAACACTTCGACCACTGGG 59.607 55.000 0.00 0.00 35.81 4.45
1739 1822 1.341531 AGAGAACACTTCGACCACTGG 59.658 52.381 0.00 0.00 34.02 4.00
1740 1823 2.802787 AGAGAACACTTCGACCACTG 57.197 50.000 0.00 0.00 34.02 3.66
1741 1824 3.821421 AAAGAGAACACTTCGACCACT 57.179 42.857 0.00 0.00 34.02 4.00
1742 1825 4.877323 AAAAAGAGAACACTTCGACCAC 57.123 40.909 0.00 0.00 34.02 4.16
1743 1826 5.909477 TCTAAAAAGAGAACACTTCGACCA 58.091 37.500 0.00 0.00 34.02 4.02
1744 1827 7.360185 GGAATCTAAAAAGAGAACACTTCGACC 60.360 40.741 0.00 0.00 34.02 4.79
1745 1828 7.170998 TGGAATCTAAAAAGAGAACACTTCGAC 59.829 37.037 0.00 0.00 34.02 4.20
1746 1829 7.214381 TGGAATCTAAAAAGAGAACACTTCGA 58.786 34.615 0.00 0.00 34.02 3.71
1747 1830 7.421530 TGGAATCTAAAAAGAGAACACTTCG 57.578 36.000 0.00 0.00 34.02 3.79
1749 1832 9.793259 TGTATGGAATCTAAAAAGAGAACACTT 57.207 29.630 0.00 0.00 0.00 3.16
1750 1833 9.965902 ATGTATGGAATCTAAAAAGAGAACACT 57.034 29.630 0.00 0.00 0.00 3.55
1842 1925 9.748708 ACGTAAAAGTACAACATTGTTACTAGA 57.251 29.630 1.98 0.00 42.35 2.43
1845 1928 9.101655 AGAACGTAAAAGTACAACATTGTTACT 57.898 29.630 1.98 0.42 42.35 2.24
1848 1931 9.316730 TCTAGAACGTAAAAGTACAACATTGTT 57.683 29.630 1.98 0.00 42.35 2.83
1849 1932 8.876275 TCTAGAACGTAAAAGTACAACATTGT 57.124 30.769 2.32 2.32 44.86 2.71
1850 1933 9.953825 GATCTAGAACGTAAAAGTACAACATTG 57.046 33.333 0.00 0.00 0.00 2.82
1851 1934 9.701098 TGATCTAGAACGTAAAAGTACAACATT 57.299 29.630 0.00 0.00 0.00 2.71
1852 1935 9.701098 TTGATCTAGAACGTAAAAGTACAACAT 57.299 29.630 0.00 0.00 0.00 2.71
1853 1936 9.531942 TTTGATCTAGAACGTAAAAGTACAACA 57.468 29.630 0.00 0.00 0.00 3.33
1875 1958 9.665719 TGTGCTCTGTAACTTATTGATATTTGA 57.334 29.630 0.00 0.00 0.00 2.69
1878 1961 9.448438 TGTTGTGCTCTGTAACTTATTGATATT 57.552 29.630 0.00 0.00 0.00 1.28
1879 1962 9.448438 TTGTTGTGCTCTGTAACTTATTGATAT 57.552 29.630 0.00 0.00 0.00 1.63
1880 1963 8.840833 TTGTTGTGCTCTGTAACTTATTGATA 57.159 30.769 0.00 0.00 0.00 2.15
1881 1964 7.744087 TTGTTGTGCTCTGTAACTTATTGAT 57.256 32.000 0.00 0.00 0.00 2.57
1882 1965 7.561021 TTTGTTGTGCTCTGTAACTTATTGA 57.439 32.000 0.00 0.00 0.00 2.57
1883 1966 8.627487 TTTTTGTTGTGCTCTGTAACTTATTG 57.373 30.769 0.00 0.00 0.00 1.90
1912 1995 9.868277 TCGTTTTTCATGATTATTAAAGGCATT 57.132 25.926 0.00 0.00 0.00 3.56
1913 1996 9.301153 GTCGTTTTTCATGATTATTAAAGGCAT 57.699 29.630 0.00 0.00 0.00 4.40
1914 1997 8.519526 AGTCGTTTTTCATGATTATTAAAGGCA 58.480 29.630 0.00 0.00 0.00 4.75
1915 1998 8.911247 AGTCGTTTTTCATGATTATTAAAGGC 57.089 30.769 0.00 0.00 0.00 4.35
1916 1999 9.503427 GGAGTCGTTTTTCATGATTATTAAAGG 57.497 33.333 0.00 0.00 0.00 3.11
1917 2000 9.210426 CGGAGTCGTTTTTCATGATTATTAAAG 57.790 33.333 0.00 0.00 0.00 1.85
1936 2019 4.092821 TGAATAGAAAAATGCACGGAGTCG 59.907 41.667 0.00 0.00 41.61 4.18
1937 2020 5.545658 TGAATAGAAAAATGCACGGAGTC 57.454 39.130 0.00 0.00 41.61 3.36
1938 2021 7.206687 TTTTTGAATAGAAAAATGCACGGAGT 58.793 30.769 0.00 0.00 33.37 3.85
1939 2022 7.636259 TTTTTGAATAGAAAAATGCACGGAG 57.364 32.000 0.00 0.00 31.39 4.63
1940 2023 7.869937 TGATTTTTGAATAGAAAAATGCACGGA 59.130 29.630 8.33 0.00 42.76 4.69
1941 2024 8.016497 TGATTTTTGAATAGAAAAATGCACGG 57.984 30.769 8.33 0.00 42.76 4.94
1942 2025 9.679596 GATGATTTTTGAATAGAAAAATGCACG 57.320 29.630 8.33 0.00 42.76 5.34
1955 2038 8.805175 TGACACTACCATTGATGATTTTTGAAT 58.195 29.630 0.00 0.00 0.00 2.57
1956 2039 8.175925 TGACACTACCATTGATGATTTTTGAA 57.824 30.769 0.00 0.00 0.00 2.69
1957 2040 7.757941 TGACACTACCATTGATGATTTTTGA 57.242 32.000 0.00 0.00 0.00 2.69
1958 2041 8.298854 TCTTGACACTACCATTGATGATTTTTG 58.701 33.333 0.00 0.00 0.00 2.44
1959 2042 8.408043 TCTTGACACTACCATTGATGATTTTT 57.592 30.769 0.00 0.00 0.00 1.94
1960 2043 8.585471 ATCTTGACACTACCATTGATGATTTT 57.415 30.769 0.00 0.00 0.00 1.82
1961 2044 8.585471 AATCTTGACACTACCATTGATGATTT 57.415 30.769 0.00 0.00 0.00 2.17
1962 2045 9.685276 TTAATCTTGACACTACCATTGATGATT 57.315 29.630 0.00 0.00 0.00 2.57
1963 2046 9.857656 ATTAATCTTGACACTACCATTGATGAT 57.142 29.630 0.00 0.00 0.00 2.45
1964 2047 9.112725 CATTAATCTTGACACTACCATTGATGA 57.887 33.333 0.00 0.00 0.00 2.92
1965 2048 9.112725 TCATTAATCTTGACACTACCATTGATG 57.887 33.333 0.00 0.00 0.00 3.07
1966 2049 9.857656 ATCATTAATCTTGACACTACCATTGAT 57.142 29.630 0.00 0.00 0.00 2.57
1993 2076 9.088512 CGACAGTAAAAGAGCAGATAAATTACT 57.911 33.333 0.00 0.00 33.66 2.24
1994 2077 9.084164 TCGACAGTAAAAGAGCAGATAAATTAC 57.916 33.333 0.00 0.00 0.00 1.89
1995 2078 9.647797 TTCGACAGTAAAAGAGCAGATAAATTA 57.352 29.630 0.00 0.00 0.00 1.40
1996 2079 8.547967 TTCGACAGTAAAAGAGCAGATAAATT 57.452 30.769 0.00 0.00 0.00 1.82
1997 2080 7.278868 CCTTCGACAGTAAAAGAGCAGATAAAT 59.721 37.037 0.00 0.00 0.00 1.40
1998 2081 6.590292 CCTTCGACAGTAAAAGAGCAGATAAA 59.410 38.462 0.00 0.00 0.00 1.40
1999 2082 6.100004 CCTTCGACAGTAAAAGAGCAGATAA 58.900 40.000 0.00 0.00 0.00 1.75
2000 2083 5.394224 CCCTTCGACAGTAAAAGAGCAGATA 60.394 44.000 0.00 0.00 0.00 1.98
2001 2084 4.499183 CCTTCGACAGTAAAAGAGCAGAT 58.501 43.478 0.00 0.00 0.00 2.90
2002 2085 3.306088 CCCTTCGACAGTAAAAGAGCAGA 60.306 47.826 0.00 0.00 0.00 4.26
2003 2086 2.996621 CCCTTCGACAGTAAAAGAGCAG 59.003 50.000 0.00 0.00 0.00 4.24
2004 2087 2.870435 GCCCTTCGACAGTAAAAGAGCA 60.870 50.000 0.00 0.00 0.00 4.26
2005 2088 1.732809 GCCCTTCGACAGTAAAAGAGC 59.267 52.381 0.00 0.00 0.00 4.09
2006 2089 2.289444 TGGCCCTTCGACAGTAAAAGAG 60.289 50.000 0.00 0.00 0.00 2.85
2007 2090 1.695242 TGGCCCTTCGACAGTAAAAGA 59.305 47.619 0.00 0.00 0.00 2.52
2008 2091 2.178912 TGGCCCTTCGACAGTAAAAG 57.821 50.000 0.00 0.00 0.00 2.27
2009 2092 2.817258 CAATGGCCCTTCGACAGTAAAA 59.183 45.455 0.00 0.00 0.00 1.52
2010 2093 2.432444 CAATGGCCCTTCGACAGTAAA 58.568 47.619 0.00 0.00 0.00 2.01
2011 2094 1.339631 CCAATGGCCCTTCGACAGTAA 60.340 52.381 0.00 0.00 0.00 2.24
2012 2095 0.251916 CCAATGGCCCTTCGACAGTA 59.748 55.000 0.00 0.00 0.00 2.74
2013 2096 1.002134 CCAATGGCCCTTCGACAGT 60.002 57.895 0.00 0.00 0.00 3.55
2014 2097 2.409870 GCCAATGGCCCTTCGACAG 61.410 63.158 14.47 0.00 44.06 3.51
2015 2098 2.361104 GCCAATGGCCCTTCGACA 60.361 61.111 14.47 0.00 44.06 4.35
2025 2108 6.701400 CCTTTCTAATAAAATTCGGCCAATGG 59.299 38.462 2.24 0.00 0.00 3.16
2026 2109 6.701400 CCCTTTCTAATAAAATTCGGCCAATG 59.299 38.462 2.24 0.00 0.00 2.82
2027 2110 6.609616 TCCCTTTCTAATAAAATTCGGCCAAT 59.390 34.615 2.24 0.00 0.00 3.16
2028 2111 5.952947 TCCCTTTCTAATAAAATTCGGCCAA 59.047 36.000 2.24 0.00 0.00 4.52
2029 2112 5.511363 TCCCTTTCTAATAAAATTCGGCCA 58.489 37.500 2.24 0.00 0.00 5.36
2030 2113 6.459670 TTCCCTTTCTAATAAAATTCGGCC 57.540 37.500 0.00 0.00 0.00 6.13
2031 2114 7.768240 TCTTTCCCTTTCTAATAAAATTCGGC 58.232 34.615 0.00 0.00 0.00 5.54
2069 2152 5.686650 GCTCTAGCTCTCCTAGACTGTAACT 60.687 48.000 0.00 0.00 45.87 2.24
2425 2508 1.868498 CTTCGTTTTAAGGCACGGACA 59.132 47.619 4.64 0.00 37.02 4.02
2449 2532 3.891366 ACTGCAATTTCACCAAGCTAGTT 59.109 39.130 0.00 0.00 0.00 2.24
2489 2572 0.108233 GCTTCTGAGCCTGAGTCCTG 60.108 60.000 0.00 0.00 43.29 3.86
2527 2610 0.681243 GGAGGAACTGGCCATCCAAC 60.681 60.000 24.32 17.41 42.91 3.77


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

AutoCloner maintained by Alex Coulton.