Multiple sequence alignment - TraesCS7A01G201400

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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 TraesCS7A01G201400 chr7A 100.000 2692 0 0 1 2692 163352121 163354812 0.000000e+00 4972.0
1 TraesCS7A01G201400 chr7A 95.132 719 29 5 9 724 669859410 669860125 0.000000e+00 1129.0
2 TraesCS7A01G201400 chr7A 94.110 730 35 7 1 728 130235031 130235754 0.000000e+00 1103.0
3 TraesCS7A01G201400 chr7A 84.379 877 92 30 907 1752 163299563 163300425 0.000000e+00 819.0
4 TraesCS7A01G201400 chr7A 83.529 935 82 33 779 1645 163360659 163361589 0.000000e+00 808.0
5 TraesCS7A01G201400 chr7A 90.258 503 46 2 1083 1582 163229775 163230277 0.000000e+00 654.0
6 TraesCS7A01G201400 chr7A 86.705 519 52 15 2184 2692 416509730 416509219 6.510000e-156 560.0
7 TraesCS7A01G201400 chr7A 98.655 223 2 1 2158 2380 163359232 163359453 6.990000e-106 394.0
8 TraesCS7A01G201400 chr7A 94.268 157 9 0 1807 1963 163300445 163300601 9.630000e-60 241.0
9 TraesCS7A01G201400 chr7A 82.639 144 15 10 2022 2157 706293263 706293122 4.710000e-23 119.0
10 TraesCS7A01G201400 chr7A 80.272 147 22 4 2018 2157 634957120 634956974 1.320000e-18 104.0
11 TraesCS7A01G201400 chr3A 94.944 712 30 4 20 728 38419093 38419801 0.000000e+00 1110.0
12 TraesCS7A01G201400 chr3A 94.538 714 32 5 17 726 81661284 81661994 0.000000e+00 1096.0
13 TraesCS7A01G201400 chr3A 94.150 718 30 8 17 727 467776534 467777246 0.000000e+00 1083.0
14 TraesCS7A01G201400 chr3A 87.918 538 55 7 2158 2692 26815966 26816496 2.280000e-175 625.0
15 TraesCS7A01G201400 chr2A 94.437 719 34 4 9 724 738268389 738267674 0.000000e+00 1101.0
16 TraesCS7A01G201400 chr2A 93.906 722 38 4 9 727 688226264 688225546 0.000000e+00 1085.0
17 TraesCS7A01G201400 chr6A 94.298 719 37 4 9 724 116954872 116955589 0.000000e+00 1098.0
18 TraesCS7A01G201400 chr5A 94.561 717 28 9 17 727 132905228 132905939 0.000000e+00 1098.0
19 TraesCS7A01G201400 chr5A 83.784 148 16 8 2018 2158 464212545 464212691 1.680000e-27 134.0
20 TraesCS7A01G201400 chr5A 82.877 146 18 6 2018 2157 9393770 9393914 1.010000e-24 124.0
21 TraesCS7A01G201400 chr7D 90.105 859 44 18 748 1588 162214296 162215131 0.000000e+00 1077.0
22 TraesCS7A01G201400 chr7D 84.260 1169 75 38 836 1967 162201119 162202215 0.000000e+00 1038.0
23 TraesCS7A01G201400 chr7D 89.881 504 48 2 1083 1583 162115164 162115667 0.000000e+00 645.0
24 TraesCS7A01G201400 chr7D 86.325 234 21 6 1790 2016 162193150 162193379 7.440000e-61 244.0
25 TraesCS7A01G201400 chr7D 93.407 91 6 0 748 838 162200724 162200814 4.670000e-28 135.0
26 TraesCS7A01G201400 chr7D 97.143 35 1 0 1644 1678 162193094 162193060 2.890000e-05 60.2
27 TraesCS7A01G201400 chr7B 86.957 989 71 27 748 1698 124257083 124258051 0.000000e+00 1059.0
28 TraesCS7A01G201400 chr7B 84.864 806 59 27 748 1522 124531260 124532033 0.000000e+00 754.0
29 TraesCS7A01G201400 chr7B 88.390 646 41 14 961 1576 124360198 124360839 0.000000e+00 747.0
30 TraesCS7A01G201400 chr7B 82.595 925 70 42 826 1705 124536332 124537210 0.000000e+00 732.0
31 TraesCS7A01G201400 chr7B 90.476 504 45 3 1083 1583 124129446 124129949 0.000000e+00 662.0
32 TraesCS7A01G201400 chr7B 85.233 386 29 7 1580 1961 124236906 124237267 3.270000e-99 372.0
33 TraesCS7A01G201400 chr7B 86.029 136 5 1 1631 1752 124363987 124364122 1.680000e-27 134.0
34 TraesCS7A01G201400 chr7B 100.000 29 0 0 1724 1752 124653687 124653715 1.000000e-03 54.7
35 TraesCS7A01G201400 chr1A 93.866 538 25 7 2158 2692 563247611 563248143 0.000000e+00 804.0
36 TraesCS7A01G201400 chr2B 91.682 541 33 10 2158 2692 632164836 632164302 0.000000e+00 739.0
37 TraesCS7A01G201400 chr2B 88.168 524 37 10 2173 2692 14534132 14534634 3.830000e-168 601.0
38 TraesCS7A01G201400 chr3B 87.906 554 55 9 2145 2692 760340512 760339965 2.260000e-180 641.0
39 TraesCS7A01G201400 chr3B 87.308 520 49 16 2184 2692 171715330 171714817 1.800000e-161 579.0
40 TraesCS7A01G201400 chr3B 88.525 488 36 16 2153 2630 751840151 751840628 8.360000e-160 573.0
41 TraesCS7A01G201400 chr1B 85.531 546 58 19 2158 2692 604097199 604097734 3.920000e-153 551.0
42 TraesCS7A01G201400 chr3D 81.967 122 14 6 2017 2136 31950846 31950961 2.210000e-16 97.1
43 TraesCS7A01G201400 chr4B 78.906 128 14 10 2018 2135 273233246 273233370 1.030000e-09 75.0


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 TraesCS7A01G201400 chr7A 163352121 163354812 2691 False 4972.0 4972 100.0000 1 2692 1 chr7A.!!$F3 2691
1 TraesCS7A01G201400 chr7A 669859410 669860125 715 False 1129.0 1129 95.1320 9 724 1 chr7A.!!$F4 715
2 TraesCS7A01G201400 chr7A 130235031 130235754 723 False 1103.0 1103 94.1100 1 728 1 chr7A.!!$F1 727
3 TraesCS7A01G201400 chr7A 163229775 163230277 502 False 654.0 654 90.2580 1083 1582 1 chr7A.!!$F2 499
4 TraesCS7A01G201400 chr7A 163359232 163361589 2357 False 601.0 808 91.0920 779 2380 2 chr7A.!!$F6 1601
5 TraesCS7A01G201400 chr7A 416509219 416509730 511 True 560.0 560 86.7050 2184 2692 1 chr7A.!!$R1 508
6 TraesCS7A01G201400 chr7A 163299563 163300601 1038 False 530.0 819 89.3235 907 1963 2 chr7A.!!$F5 1056
7 TraesCS7A01G201400 chr3A 38419093 38419801 708 False 1110.0 1110 94.9440 20 728 1 chr3A.!!$F2 708
8 TraesCS7A01G201400 chr3A 81661284 81661994 710 False 1096.0 1096 94.5380 17 726 1 chr3A.!!$F3 709
9 TraesCS7A01G201400 chr3A 467776534 467777246 712 False 1083.0 1083 94.1500 17 727 1 chr3A.!!$F4 710
10 TraesCS7A01G201400 chr3A 26815966 26816496 530 False 625.0 625 87.9180 2158 2692 1 chr3A.!!$F1 534
11 TraesCS7A01G201400 chr2A 738267674 738268389 715 True 1101.0 1101 94.4370 9 724 1 chr2A.!!$R2 715
12 TraesCS7A01G201400 chr2A 688225546 688226264 718 True 1085.0 1085 93.9060 9 727 1 chr2A.!!$R1 718
13 TraesCS7A01G201400 chr6A 116954872 116955589 717 False 1098.0 1098 94.2980 9 724 1 chr6A.!!$F1 715
14 TraesCS7A01G201400 chr5A 132905228 132905939 711 False 1098.0 1098 94.5610 17 727 1 chr5A.!!$F2 710
15 TraesCS7A01G201400 chr7D 162214296 162215131 835 False 1077.0 1077 90.1050 748 1588 1 chr7D.!!$F3 840
16 TraesCS7A01G201400 chr7D 162115164 162115667 503 False 645.0 645 89.8810 1083 1583 1 chr7D.!!$F1 500
17 TraesCS7A01G201400 chr7D 162200724 162202215 1491 False 586.5 1038 88.8335 748 1967 2 chr7D.!!$F4 1219
18 TraesCS7A01G201400 chr7B 124257083 124258051 968 False 1059.0 1059 86.9570 748 1698 1 chr7B.!!$F3 950
19 TraesCS7A01G201400 chr7B 124531260 124532033 773 False 754.0 754 84.8640 748 1522 1 chr7B.!!$F4 774
20 TraesCS7A01G201400 chr7B 124536332 124537210 878 False 732.0 732 82.5950 826 1705 1 chr7B.!!$F5 879
21 TraesCS7A01G201400 chr7B 124129446 124129949 503 False 662.0 662 90.4760 1083 1583 1 chr7B.!!$F1 500
22 TraesCS7A01G201400 chr7B 124360198 124364122 3924 False 440.5 747 87.2095 961 1752 2 chr7B.!!$F7 791
23 TraesCS7A01G201400 chr1A 563247611 563248143 532 False 804.0 804 93.8660 2158 2692 1 chr1A.!!$F1 534
24 TraesCS7A01G201400 chr2B 632164302 632164836 534 True 739.0 739 91.6820 2158 2692 1 chr2B.!!$R1 534
25 TraesCS7A01G201400 chr2B 14534132 14534634 502 False 601.0 601 88.1680 2173 2692 1 chr2B.!!$F1 519
26 TraesCS7A01G201400 chr3B 760339965 760340512 547 True 641.0 641 87.9060 2145 2692 1 chr3B.!!$R2 547
27 TraesCS7A01G201400 chr3B 171714817 171715330 513 True 579.0 579 87.3080 2184 2692 1 chr3B.!!$R1 508
28 TraesCS7A01G201400 chr1B 604097199 604097734 535 False 551.0 551 85.5310 2158 2692 1 chr1B.!!$F1 534

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
664 670 0.17915 GCGTGCAAAACCAGTCACAA 60.179 50.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 6334 0.036306 GTGAGTTCCGGTGGTGGATT 59.964 55.0 0.0 0.0 38.0 3.01 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
122 126 1.001268 GAGCATCTTCCGACGCTATGA 60.001 52.381 0.00 0.00 39.06 2.15
553 557 8.205512 TCCAAAACATCATATATGCAAAATGCT 58.794 29.630 7.92 0.00 45.31 3.79
659 665 3.591835 CGGGCGTGCAAAACCAGT 61.592 61.111 0.00 0.00 0.00 4.00
664 670 0.179150 GCGTGCAAAACCAGTCACAA 60.179 50.000 0.00 0.00 0.00 3.33
665 671 1.535860 GCGTGCAAAACCAGTCACAAT 60.536 47.619 0.00 0.00 0.00 2.71
673 679 2.316867 CCAGTCACAATGCGCGTGA 61.317 57.895 16.89 14.34 41.00 4.35
720 726 0.681733 AGCACGACTGTTGGAGATGT 59.318 50.000 0.00 0.00 0.00 3.06
728 734 3.935828 GACTGTTGGAGATGTTCTAAGGC 59.064 47.826 0.00 0.00 0.00 4.35
729 735 3.327757 ACTGTTGGAGATGTTCTAAGGCA 59.672 43.478 0.00 0.00 0.00 4.75
730 736 3.674997 TGTTGGAGATGTTCTAAGGCAC 58.325 45.455 0.00 0.00 0.00 5.01
731 737 3.010420 GTTGGAGATGTTCTAAGGCACC 58.990 50.000 0.00 0.00 0.00 5.01
732 738 2.265367 TGGAGATGTTCTAAGGCACCA 58.735 47.619 0.00 0.00 0.00 4.17
733 739 2.642311 TGGAGATGTTCTAAGGCACCAA 59.358 45.455 0.00 0.00 0.00 3.67
734 740 3.073798 TGGAGATGTTCTAAGGCACCAAA 59.926 43.478 0.00 0.00 0.00 3.28
735 741 3.691609 GGAGATGTTCTAAGGCACCAAAG 59.308 47.826 0.00 0.00 0.00 2.77
736 742 3.084786 AGATGTTCTAAGGCACCAAAGC 58.915 45.455 0.00 0.00 0.00 3.51
737 743 2.356665 TGTTCTAAGGCACCAAAGCA 57.643 45.000 0.00 0.00 35.83 3.91
738 744 2.875296 TGTTCTAAGGCACCAAAGCAT 58.125 42.857 0.00 0.00 35.83 3.79
739 745 2.819608 TGTTCTAAGGCACCAAAGCATC 59.180 45.455 0.00 0.00 35.83 3.91
740 746 1.737838 TCTAAGGCACCAAAGCATCG 58.262 50.000 0.00 0.00 35.83 3.84
741 747 1.003118 TCTAAGGCACCAAAGCATCGT 59.997 47.619 0.00 0.00 35.83 3.73
742 748 1.398390 CTAAGGCACCAAAGCATCGTC 59.602 52.381 0.00 0.00 35.83 4.20
743 749 1.244019 AAGGCACCAAAGCATCGTCC 61.244 55.000 0.00 0.00 35.83 4.79
744 750 2.480555 GCACCAAAGCATCGTCCG 59.519 61.111 0.00 0.00 0.00 4.79
745 751 2.325082 GCACCAAAGCATCGTCCGT 61.325 57.895 0.00 0.00 0.00 4.69
746 752 1.787847 CACCAAAGCATCGTCCGTC 59.212 57.895 0.00 0.00 0.00 4.79
829 1480 1.123928 CCACTAGGACCCTTAGCCAG 58.876 60.000 0.00 0.00 36.89 4.85
903 1861 2.999185 TTCCTTCCTCCAAAAGCCAT 57.001 45.000 0.00 0.00 0.00 4.40
925 1887 2.775219 AAACACCCCACGTCCCCT 60.775 61.111 0.00 0.00 0.00 4.79
943 1905 1.884579 CCTCATTTGACAGCAACAGCT 59.115 47.619 0.00 0.00 39.75 4.24
949 1911 1.229428 TGACAGCAACAGCTAACAGC 58.771 50.000 0.00 0.00 42.84 4.40
981 1944 7.084486 GCGATTCTTATAAATCAAACCCATCC 58.916 38.462 0.00 0.00 35.75 3.51
1276 2311 1.591863 GACCATCTTCTACGGCGGC 60.592 63.158 13.24 0.00 0.00 6.53
1423 2474 2.117156 CATGGAGAAGCGCAAGGGG 61.117 63.158 11.47 0.00 38.28 4.79
1540 2619 5.239087 GCGTAGTAGAGTAGCCTGAGTAATT 59.761 44.000 0.00 0.00 0.00 1.40
1541 2620 6.238703 GCGTAGTAGAGTAGCCTGAGTAATTT 60.239 42.308 0.00 0.00 0.00 1.82
1542 2621 7.041508 GCGTAGTAGAGTAGCCTGAGTAATTTA 60.042 40.741 0.00 0.00 0.00 1.40
1543 2622 8.281893 CGTAGTAGAGTAGCCTGAGTAATTTAC 58.718 40.741 0.00 0.00 0.00 2.01
1544 2623 7.261829 AGTAGAGTAGCCTGAGTAATTTACG 57.738 40.000 1.03 0.00 0.00 3.18
1545 2624 5.517322 AGAGTAGCCTGAGTAATTTACGG 57.483 43.478 1.03 0.00 0.00 4.02
1546 2625 4.954826 AGAGTAGCCTGAGTAATTTACGGT 59.045 41.667 1.03 0.00 0.00 4.83
1547 2626 5.067544 AGAGTAGCCTGAGTAATTTACGGTC 59.932 44.000 1.03 0.00 0.00 4.79
1548 2627 3.538634 AGCCTGAGTAATTTACGGTCC 57.461 47.619 1.03 0.00 0.00 4.46
1549 2628 2.835764 AGCCTGAGTAATTTACGGTCCA 59.164 45.455 1.03 0.00 0.00 4.02
1550 2629 2.934553 GCCTGAGTAATTTACGGTCCAC 59.065 50.000 1.03 0.00 0.00 4.02
1589 2668 4.019858 TGTTGGAGTCCAAATTGTTGACA 58.980 39.130 26.19 14.92 45.73 3.58
1597 2676 2.033299 CCAAATTGTTGACACACTCGCT 59.967 45.455 0.00 0.00 36.83 4.93
1601 2680 1.286501 TGTTGACACACTCGCTTGTC 58.713 50.000 0.00 0.00 42.18 3.18
1615 2694 1.949847 CTTGTCCCCGTCGCTCTGAT 61.950 60.000 0.00 0.00 0.00 2.90
1627 2706 5.003872 CCGTCGCTCTGATTTATTATGATCG 59.996 44.000 0.00 0.00 0.00 3.69
1678 5868 1.933181 TGATCATGGCGAATTGACGAC 59.067 47.619 0.00 0.00 42.12 4.34
1712 5917 0.865111 TTATACATCATGCGCACGCC 59.135 50.000 14.90 0.00 41.09 5.68
1752 5957 2.032071 GTGTTGGCGGTAGCTGGT 59.968 61.111 0.00 0.00 44.37 4.00
1753 5958 1.294138 GTGTTGGCGGTAGCTGGTA 59.706 57.895 0.00 0.00 44.37 3.25
1755 5960 0.397187 TGTTGGCGGTAGCTGGTAAA 59.603 50.000 0.00 0.00 44.37 2.01
1756 5961 0.800631 GTTGGCGGTAGCTGGTAAAC 59.199 55.000 0.00 0.00 44.37 2.01
1757 5962 0.397187 TTGGCGGTAGCTGGTAAACA 59.603 50.000 0.00 0.00 44.37 2.83
1758 5963 0.320946 TGGCGGTAGCTGGTAAACAC 60.321 55.000 0.00 0.00 44.37 3.32
1759 5964 1.022982 GGCGGTAGCTGGTAAACACC 61.023 60.000 0.00 0.00 44.37 4.16
1802 6007 1.872952 TGAAAATGTCGACACCTGCAG 59.127 47.619 22.71 6.78 0.00 4.41
1803 6008 1.873591 GAAAATGTCGACACCTGCAGT 59.126 47.619 22.71 0.00 0.00 4.40
1806 6011 0.603707 ATGTCGACACCTGCAGTTGG 60.604 55.000 22.71 2.18 0.00 3.77
1872 6077 2.203280 CCCACTTGGCCGTGTTGA 60.203 61.111 9.57 0.00 33.07 3.18
1884 6089 0.809636 CGTGTTGACAGCTGGACACA 60.810 55.000 31.39 22.43 41.77 3.72
1996 6201 8.555166 TTTAGCAAACAACTTATTTTGAGACG 57.445 30.769 0.00 0.00 35.13 4.18
1997 6202 6.371809 AGCAAACAACTTATTTTGAGACGA 57.628 33.333 0.00 0.00 35.13 4.20
1998 6203 6.791303 AGCAAACAACTTATTTTGAGACGAA 58.209 32.000 0.00 0.00 35.13 3.85
1999 6204 6.912591 AGCAAACAACTTATTTTGAGACGAAG 59.087 34.615 0.00 0.00 35.13 3.79
2000 6205 6.142320 GCAAACAACTTATTTTGAGACGAAGG 59.858 38.462 0.00 0.00 35.13 3.46
2001 6206 7.414436 CAAACAACTTATTTTGAGACGAAGGA 58.586 34.615 0.00 0.00 35.13 3.36
2002 6207 7.562454 AACAACTTATTTTGAGACGAAGGAA 57.438 32.000 0.00 0.00 0.00 3.36
2003 6208 7.190920 ACAACTTATTTTGAGACGAAGGAAG 57.809 36.000 0.00 0.00 0.00 3.46
2004 6209 6.766467 ACAACTTATTTTGAGACGAAGGAAGT 59.234 34.615 0.00 0.00 0.00 3.01
2005 6210 7.929785 ACAACTTATTTTGAGACGAAGGAAGTA 59.070 33.333 0.00 0.00 0.00 2.24
2006 6211 8.770828 CAACTTATTTTGAGACGAAGGAAGTAA 58.229 33.333 0.00 0.00 0.00 2.24
2007 6212 9.503399 AACTTATTTTGAGACGAAGGAAGTAAT 57.497 29.630 0.00 0.00 0.00 1.89
2008 6213 9.152595 ACTTATTTTGAGACGAAGGAAGTAATC 57.847 33.333 0.00 0.00 0.00 1.75
2009 6214 9.372369 CTTATTTTGAGACGAAGGAAGTAATCT 57.628 33.333 0.00 0.00 0.00 2.40
2012 6217 9.892130 ATTTTGAGACGAAGGAAGTAATCTAAT 57.108 29.630 0.00 0.00 0.00 1.73
2014 6219 9.798994 TTTGAGACGAAGGAAGTAATCTAATAC 57.201 33.333 0.00 0.00 0.00 1.89
2015 6220 7.637229 TGAGACGAAGGAAGTAATCTAATACG 58.363 38.462 0.00 0.00 0.00 3.06
2016 6221 6.968250 AGACGAAGGAAGTAATCTAATACGG 58.032 40.000 0.00 0.00 0.00 4.02
2017 6222 6.545298 AGACGAAGGAAGTAATCTAATACGGT 59.455 38.462 0.00 0.00 0.00 4.83
2018 6223 7.067981 AGACGAAGGAAGTAATCTAATACGGTT 59.932 37.037 0.00 0.00 0.00 4.44
2019 6224 7.550712 ACGAAGGAAGTAATCTAATACGGTTT 58.449 34.615 0.00 0.00 0.00 3.27
2020 6225 7.490402 ACGAAGGAAGTAATCTAATACGGTTTG 59.510 37.037 0.00 0.00 0.00 2.93
2021 6226 7.490402 CGAAGGAAGTAATCTAATACGGTTTGT 59.510 37.037 0.00 0.00 0.00 2.83
2022 6227 9.159364 GAAGGAAGTAATCTAATACGGTTTGTT 57.841 33.333 0.00 0.00 0.00 2.83
2023 6228 9.511272 AAGGAAGTAATCTAATACGGTTTGTTT 57.489 29.630 0.00 0.00 0.00 2.83
2024 6229 9.511272 AGGAAGTAATCTAATACGGTTTGTTTT 57.489 29.630 0.00 0.00 0.00 2.43
2025 6230 9.550811 GGAAGTAATCTAATACGGTTTGTTTTG 57.449 33.333 0.00 0.00 0.00 2.44
2031 6236 6.961576 TCTAATACGGTTTGTTTTGAACTGG 58.038 36.000 0.00 0.00 37.63 4.00
2032 6237 2.951457 ACGGTTTGTTTTGAACTGGG 57.049 45.000 0.00 0.00 37.63 4.45
2033 6238 2.448453 ACGGTTTGTTTTGAACTGGGA 58.552 42.857 0.00 0.00 37.63 4.37
2034 6239 2.826725 ACGGTTTGTTTTGAACTGGGAA 59.173 40.909 0.00 0.00 37.63 3.97
2035 6240 3.449377 ACGGTTTGTTTTGAACTGGGAAT 59.551 39.130 0.00 0.00 37.63 3.01
2036 6241 4.645588 ACGGTTTGTTTTGAACTGGGAATA 59.354 37.500 0.00 0.00 37.63 1.75
2037 6242 5.127356 ACGGTTTGTTTTGAACTGGGAATAA 59.873 36.000 0.00 0.00 37.63 1.40
2038 6243 5.460748 CGGTTTGTTTTGAACTGGGAATAAC 59.539 40.000 0.00 0.00 31.30 1.89
2039 6244 5.756347 GGTTTGTTTTGAACTGGGAATAACC 59.244 40.000 0.00 0.00 38.08 2.85
2053 6258 5.188988 GGAATAACCCCTTTCCACTAACT 57.811 43.478 0.00 0.00 40.93 2.24
2054 6259 4.948004 GGAATAACCCCTTTCCACTAACTG 59.052 45.833 0.00 0.00 40.93 3.16
2055 6260 5.280830 GGAATAACCCCTTTCCACTAACTGA 60.281 44.000 0.00 0.00 40.93 3.41
2056 6261 5.853572 ATAACCCCTTTCCACTAACTGAA 57.146 39.130 0.00 0.00 0.00 3.02
2057 6262 4.741928 AACCCCTTTCCACTAACTGAAT 57.258 40.909 0.00 0.00 0.00 2.57
2058 6263 5.853572 AACCCCTTTCCACTAACTGAATA 57.146 39.130 0.00 0.00 0.00 1.75
2059 6264 5.853572 ACCCCTTTCCACTAACTGAATAA 57.146 39.130 0.00 0.00 0.00 1.40
2060 6265 5.567430 ACCCCTTTCCACTAACTGAATAAC 58.433 41.667 0.00 0.00 0.00 1.89
2061 6266 4.634443 CCCCTTTCCACTAACTGAATAACG 59.366 45.833 0.00 0.00 0.00 3.18
2062 6267 5.484715 CCCTTTCCACTAACTGAATAACGA 58.515 41.667 0.00 0.00 0.00 3.85
2063 6268 5.935789 CCCTTTCCACTAACTGAATAACGAA 59.064 40.000 0.00 0.00 0.00 3.85
2064 6269 6.428771 CCCTTTCCACTAACTGAATAACGAAA 59.571 38.462 0.00 0.00 0.00 3.46
2065 6270 7.040961 CCCTTTCCACTAACTGAATAACGAAAA 60.041 37.037 0.00 0.00 0.00 2.29
2066 6271 8.512138 CCTTTCCACTAACTGAATAACGAAAAT 58.488 33.333 0.00 0.00 0.00 1.82
2069 6274 9.491675 TTCCACTAACTGAATAACGAAAATACA 57.508 29.630 0.00 0.00 0.00 2.29
2070 6275 9.661563 TCCACTAACTGAATAACGAAAATACAT 57.338 29.630 0.00 0.00 0.00 2.29
2071 6276 9.916397 CCACTAACTGAATAACGAAAATACATC 57.084 33.333 0.00 0.00 0.00 3.06
2077 6282 9.988350 ACTGAATAACGAAAATACATCATGAAC 57.012 29.630 0.00 0.00 0.00 3.18
2078 6283 9.438291 CTGAATAACGAAAATACATCATGAACC 57.562 33.333 0.00 0.00 0.00 3.62
2079 6284 8.951243 TGAATAACGAAAATACATCATGAACCA 58.049 29.630 0.00 0.00 0.00 3.67
2080 6285 9.781834 GAATAACGAAAATACATCATGAACCAA 57.218 29.630 0.00 0.00 0.00 3.67
2082 6287 9.950680 ATAACGAAAATACATCATGAACCAATC 57.049 29.630 0.00 0.00 0.00 2.67
2083 6288 7.389803 ACGAAAATACATCATGAACCAATCA 57.610 32.000 0.00 0.00 43.67 2.57
2084 6289 7.475015 ACGAAAATACATCATGAACCAATCAG 58.525 34.615 0.00 0.00 42.53 2.90
2085 6290 7.336679 ACGAAAATACATCATGAACCAATCAGA 59.663 33.333 0.00 0.00 42.53 3.27
2086 6291 8.183536 CGAAAATACATCATGAACCAATCAGAA 58.816 33.333 0.00 0.00 42.53 3.02
2087 6292 9.294030 GAAAATACATCATGAACCAATCAGAAC 57.706 33.333 0.00 0.00 42.53 3.01
2088 6293 4.952262 ACATCATGAACCAATCAGAACG 57.048 40.909 0.00 0.00 42.53 3.95
2089 6294 3.691118 ACATCATGAACCAATCAGAACGG 59.309 43.478 0.00 0.00 42.53 4.44
2090 6295 2.710377 TCATGAACCAATCAGAACGGG 58.290 47.619 0.00 0.00 42.53 5.28
2091 6296 2.304470 TCATGAACCAATCAGAACGGGA 59.696 45.455 0.00 0.00 42.53 5.14
2092 6297 2.178912 TGAACCAATCAGAACGGGAC 57.821 50.000 0.00 0.00 33.04 4.46
2093 6298 1.606994 TGAACCAATCAGAACGGGACG 60.607 52.381 0.00 0.00 46.24 4.79
2094 6299 4.813219 TGAACCAATCAGAACGGGACGG 62.813 54.545 0.00 0.00 45.49 4.79
2105 6310 3.173323 GGGACGGGAAAGGGGAAA 58.827 61.111 0.00 0.00 0.00 3.13
2106 6311 1.001269 GGGACGGGAAAGGGGAAAG 60.001 63.158 0.00 0.00 0.00 2.62
2107 6312 1.677966 GGACGGGAAAGGGGAAAGC 60.678 63.158 0.00 0.00 0.00 3.51
2108 6313 2.033602 ACGGGAAAGGGGAAAGCG 59.966 61.111 0.00 0.00 0.00 4.68
2109 6314 2.349755 CGGGAAAGGGGAAAGCGA 59.650 61.111 0.00 0.00 0.00 4.93
2110 6315 1.745489 CGGGAAAGGGGAAAGCGAG 60.745 63.158 0.00 0.00 0.00 5.03
2111 6316 1.379146 GGGAAAGGGGAAAGCGAGT 59.621 57.895 0.00 0.00 0.00 4.18
2112 6317 0.251209 GGGAAAGGGGAAAGCGAGTT 60.251 55.000 0.00 0.00 0.00 3.01
2113 6318 1.166129 GGAAAGGGGAAAGCGAGTTC 58.834 55.000 0.00 0.00 0.00 3.01
2114 6319 1.544759 GGAAAGGGGAAAGCGAGTTCA 60.545 52.381 0.00 0.00 0.00 3.18
2115 6320 2.227194 GAAAGGGGAAAGCGAGTTCAA 58.773 47.619 0.00 0.00 0.00 2.69
2116 6321 2.358322 AAGGGGAAAGCGAGTTCAAA 57.642 45.000 0.00 0.00 0.00 2.69
2117 6322 1.897560 AGGGGAAAGCGAGTTCAAAG 58.102 50.000 0.00 0.00 0.00 2.77
2118 6323 0.241213 GGGGAAAGCGAGTTCAAAGC 59.759 55.000 0.00 0.00 0.00 3.51
2119 6324 0.951558 GGGAAAGCGAGTTCAAAGCA 59.048 50.000 0.00 0.00 0.00 3.91
2120 6325 1.541588 GGGAAAGCGAGTTCAAAGCAT 59.458 47.619 0.00 0.00 0.00 3.79
2121 6326 2.414691 GGGAAAGCGAGTTCAAAGCATC 60.415 50.000 0.00 0.00 0.00 3.91
2122 6327 2.499896 GAAAGCGAGTTCAAAGCATCG 58.500 47.619 0.00 0.00 38.19 3.84
2125 6330 1.059369 CGAGTTCAAAGCATCGCCG 59.941 57.895 0.00 0.00 0.00 6.46
2126 6331 1.425428 GAGTTCAAAGCATCGCCGG 59.575 57.895 0.00 0.00 0.00 6.13
2127 6332 1.982073 GAGTTCAAAGCATCGCCGGG 61.982 60.000 2.18 0.00 0.00 5.73
2128 6333 2.038269 GTTCAAAGCATCGCCGGGA 61.038 57.895 2.18 0.00 0.00 5.14
2129 6334 1.302913 TTCAAAGCATCGCCGGGAA 60.303 52.632 2.18 0.00 0.00 3.97
2130 6335 0.891449 TTCAAAGCATCGCCGGGAAA 60.891 50.000 2.18 0.00 0.00 3.13
2131 6336 0.679640 TCAAAGCATCGCCGGGAAAT 60.680 50.000 2.18 0.00 0.00 2.17
2132 6337 0.248621 CAAAGCATCGCCGGGAAATC 60.249 55.000 2.18 0.00 0.00 2.17
2133 6338 1.384222 AAAGCATCGCCGGGAAATCC 61.384 55.000 2.18 0.00 0.00 3.01
2134 6339 2.515991 GCATCGCCGGGAAATCCA 60.516 61.111 2.18 0.00 37.91 3.41
2135 6340 2.834618 GCATCGCCGGGAAATCCAC 61.835 63.158 2.18 0.00 37.91 4.02
2136 6341 2.186826 CATCGCCGGGAAATCCACC 61.187 63.158 2.18 0.00 37.91 4.61
2137 6342 2.675242 ATCGCCGGGAAATCCACCA 61.675 57.895 2.18 0.00 37.91 4.17
2138 6343 2.886730 ATCGCCGGGAAATCCACCAC 62.887 60.000 2.18 0.00 37.91 4.16
2139 6344 2.754254 GCCGGGAAATCCACCACC 60.754 66.667 2.18 0.00 37.91 4.61
2140 6345 2.437716 CCGGGAAATCCACCACCG 60.438 66.667 0.00 0.00 43.89 4.94
2141 6346 2.437716 CGGGAAATCCACCACCGG 60.438 66.667 0.00 0.00 40.79 5.28
2142 6347 2.961893 CGGGAAATCCACCACCGGA 61.962 63.158 9.46 0.00 40.79 5.14
2143 6348 1.381076 GGGAAATCCACCACCGGAA 59.619 57.895 9.46 0.00 38.95 4.30
2144 6349 0.963856 GGGAAATCCACCACCGGAAC 60.964 60.000 9.46 0.00 38.95 3.62
2145 6350 0.037734 GGAAATCCACCACCGGAACT 59.962 55.000 9.46 0.00 38.95 3.01
2146 6351 1.450025 GAAATCCACCACCGGAACTC 58.550 55.000 9.46 0.00 38.95 3.01
2147 6352 0.768622 AAATCCACCACCGGAACTCA 59.231 50.000 9.46 0.00 38.95 3.41
2148 6353 0.036306 AATCCACCACCGGAACTCAC 59.964 55.000 9.46 0.00 38.95 3.51
2149 6354 2.167398 ATCCACCACCGGAACTCACG 62.167 60.000 9.46 0.00 38.95 4.35
2150 6355 2.420043 CACCACCGGAACTCACGT 59.580 61.111 9.46 0.00 0.00 4.49
2151 6356 1.661480 CACCACCGGAACTCACGTA 59.339 57.895 9.46 0.00 0.00 3.57
2152 6357 0.665369 CACCACCGGAACTCACGTAC 60.665 60.000 9.46 0.00 0.00 3.67
2153 6358 1.443194 CCACCGGAACTCACGTACG 60.443 63.158 15.01 15.01 0.00 3.67
2154 6359 1.575922 CACCGGAACTCACGTACGA 59.424 57.895 24.41 0.00 0.00 3.43
2155 6360 0.453950 CACCGGAACTCACGTACGAG 60.454 60.000 24.41 15.18 39.05 4.18
2156 6361 0.603707 ACCGGAACTCACGTACGAGA 60.604 55.000 24.41 19.05 36.47 4.04
2169 6374 7.441760 ACTCACGTACGAGATGTTAGAATAGAT 59.558 37.037 24.41 0.00 36.47 1.98
2171 6376 6.797513 CACGTACGAGATGTTAGAATAGATGG 59.202 42.308 24.41 0.00 0.00 3.51
2242 6454 6.786843 ATCTCTATCTCCTCTTCTCTCCTT 57.213 41.667 0.00 0.00 0.00 3.36
2243 6455 7.888514 ATCTCTATCTCCTCTTCTCTCCTTA 57.111 40.000 0.00 0.00 0.00 2.69
2297 6509 3.980646 ATCGTTCTCTCGATCTTCCTG 57.019 47.619 0.00 0.00 45.57 3.86
2299 6511 3.870274 TCGTTCTCTCGATCTTCCTGTA 58.130 45.455 0.00 0.00 34.85 2.74
2449 6667 2.355126 CCGCGACCGAGATCATGG 60.355 66.667 8.23 0.00 36.29 3.66
2493 6711 2.044650 AGCATCATGGGTGCGCTT 60.045 55.556 9.73 0.10 46.86 4.68
2580 6798 2.394563 GCCACCGCAAGAGAAGCTC 61.395 63.158 0.00 0.00 43.02 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 111 1.725665 CGGTCATAGCGTCGGAAGA 59.274 57.895 0.00 0.00 33.95 2.87
109 113 2.103538 GCGGTCATAGCGTCGGAA 59.896 61.111 0.00 0.00 41.74 4.30
192 196 4.832248 AGAAGGCACATCGAAAGACATTA 58.168 39.130 0.00 0.00 46.97 1.90
526 530 8.828644 GCATTTTGCATATATGATGTTTTGGAA 58.171 29.630 17.10 0.00 44.26 3.53
600 604 2.943345 GCTATAATGCAGCGCGCGT 61.943 57.895 32.35 15.53 46.97 6.01
641 647 3.591835 CTGGTTTTGCACGCCCGT 61.592 61.111 0.00 0.00 0.00 5.28
648 654 1.535649 CGCATTGTGACTGGTTTTGCA 60.536 47.619 0.00 0.00 0.00 4.08
664 670 1.448985 AACCTGTTTATCACGCGCAT 58.551 45.000 5.73 0.04 0.00 4.73
665 671 1.231221 AAACCTGTTTATCACGCGCA 58.769 45.000 5.73 0.00 0.00 6.09
707 713 3.327757 TGCCTTAGAACATCTCCAACAGT 59.672 43.478 0.00 0.00 0.00 3.55
720 726 2.083774 CGATGCTTTGGTGCCTTAGAA 58.916 47.619 0.00 0.00 0.00 2.10
728 734 1.635663 GGACGGACGATGCTTTGGTG 61.636 60.000 0.00 0.00 0.00 4.17
729 735 1.375523 GGACGGACGATGCTTTGGT 60.376 57.895 0.00 0.00 0.00 3.67
730 736 0.174845 TAGGACGGACGATGCTTTGG 59.825 55.000 0.00 0.00 0.00 3.28
731 737 1.860950 CATAGGACGGACGATGCTTTG 59.139 52.381 0.00 0.00 0.00 2.77
732 738 1.806623 GCATAGGACGGACGATGCTTT 60.807 52.381 15.65 0.00 41.19 3.51
733 739 0.249489 GCATAGGACGGACGATGCTT 60.249 55.000 15.65 0.00 41.19 3.91
734 740 1.364171 GCATAGGACGGACGATGCT 59.636 57.895 15.65 0.00 41.19 3.79
735 741 1.664965 GGCATAGGACGGACGATGC 60.665 63.158 14.94 14.94 43.19 3.91
736 742 0.319040 CAGGCATAGGACGGACGATG 60.319 60.000 0.00 0.00 0.00 3.84
737 743 2.041976 CAGGCATAGGACGGACGAT 58.958 57.895 0.00 0.00 0.00 3.73
738 744 2.782222 GCAGGCATAGGACGGACGA 61.782 63.158 0.00 0.00 0.00 4.20
739 745 2.279517 GCAGGCATAGGACGGACG 60.280 66.667 0.00 0.00 0.00 4.79
740 746 1.227380 CAGCAGGCATAGGACGGAC 60.227 63.158 0.00 0.00 0.00 4.79
741 747 3.094062 GCAGCAGGCATAGGACGGA 62.094 63.158 0.00 0.00 43.97 4.69
742 748 2.590007 GCAGCAGGCATAGGACGG 60.590 66.667 0.00 0.00 43.97 4.79
829 1480 1.786579 GCAAAGATGGTTTCAACGTGC 59.213 47.619 0.00 0.00 0.00 5.34
903 1861 0.971386 GGACGTGGGGTGTTTCTCTA 59.029 55.000 0.00 0.00 0.00 2.43
943 1905 1.951181 GAATCGCGCGTGTGCTGTTA 61.951 55.000 30.98 7.17 39.65 2.41
949 1911 3.562781 TTTATAAGAATCGCGCGTGTG 57.437 42.857 30.98 2.36 0.00 3.82
981 1944 3.354948 TTGATGGACTGGAGATGGTTG 57.645 47.619 0.00 0.00 0.00 3.77
1255 2290 1.491670 CGCCGTAGAAGATGGTCATG 58.508 55.000 0.00 0.00 36.46 3.07
1276 2311 2.031012 TCGAGCAACAGCACCTGG 59.969 61.111 0.00 0.00 35.51 4.45
1286 2321 3.744719 CGGGACCTCGTCGAGCAA 61.745 66.667 17.02 0.00 32.65 3.91
1404 2455 2.117156 CCCTTGCGCTTCTCCATGG 61.117 63.158 9.73 4.97 0.00 3.66
1540 2619 0.869068 CACATTTGCGTGGACCGTAA 59.131 50.000 0.00 0.00 39.47 3.18
1541 2620 0.249953 ACACATTTGCGTGGACCGTA 60.250 50.000 0.00 0.00 41.38 4.02
1542 2621 1.525077 ACACATTTGCGTGGACCGT 60.525 52.632 0.00 0.00 41.38 4.83
1543 2622 1.082169 CACACATTTGCGTGGACCG 60.082 57.895 0.00 0.00 41.38 4.79
1544 2623 4.942090 CACACATTTGCGTGGACC 57.058 55.556 0.00 0.00 41.38 4.46
1548 2627 2.017783 GCAGCCACACATTTGCGTG 61.018 57.895 0.00 0.00 42.81 5.34
1549 2628 2.195567 AGCAGCCACACATTTGCGT 61.196 52.632 0.00 0.00 41.27 5.24
1550 2629 1.731613 CAGCAGCCACACATTTGCG 60.732 57.895 0.00 0.00 41.27 4.85
1589 2668 3.222354 GACGGGGACAAGCGAGTGT 62.222 63.158 0.00 0.00 0.00 3.55
1597 2676 1.541310 AATCAGAGCGACGGGGACAA 61.541 55.000 0.00 0.00 0.00 3.18
1601 2680 2.240493 AATAAATCAGAGCGACGGGG 57.760 50.000 0.00 0.00 0.00 5.73
1627 2706 7.370383 TCAGAAGAACAACAGCAATAATTTCC 58.630 34.615 0.00 0.00 0.00 3.13
1712 5917 1.547372 CCAAGTGGGAATCAAAGGCAG 59.453 52.381 0.00 0.00 40.01 4.85
1721 5926 1.152830 AACACGGCCAAGTGGGAAT 59.847 52.632 14.36 0.00 45.80 3.01
1772 5977 9.541143 AGGTGTCGACATTTTCAAAAATAAAAT 57.459 25.926 23.12 0.00 36.52 1.82
1773 5978 8.812329 CAGGTGTCGACATTTTCAAAAATAAAA 58.188 29.630 23.12 0.00 36.52 1.52
1774 5979 7.043059 GCAGGTGTCGACATTTTCAAAAATAAA 60.043 33.333 23.12 0.00 36.52 1.40
1775 5980 6.419413 GCAGGTGTCGACATTTTCAAAAATAA 59.581 34.615 23.12 0.00 36.52 1.40
1776 5981 5.918011 GCAGGTGTCGACATTTTCAAAAATA 59.082 36.000 23.12 0.00 36.52 1.40
1777 5982 4.744631 GCAGGTGTCGACATTTTCAAAAAT 59.255 37.500 23.12 0.00 39.07 1.82
1778 5983 4.109050 GCAGGTGTCGACATTTTCAAAAA 58.891 39.130 23.12 0.00 0.00 1.94
1779 5984 3.129462 TGCAGGTGTCGACATTTTCAAAA 59.871 39.130 23.12 0.37 0.00 2.44
1780 5985 2.685388 TGCAGGTGTCGACATTTTCAAA 59.315 40.909 23.12 1.92 0.00 2.69
1781 5986 2.290367 CTGCAGGTGTCGACATTTTCAA 59.710 45.455 23.12 5.63 0.00 2.69
1782 5987 1.872952 CTGCAGGTGTCGACATTTTCA 59.127 47.619 23.12 15.76 0.00 2.69
1783 5988 1.873591 ACTGCAGGTGTCGACATTTTC 59.126 47.619 23.12 8.52 0.00 2.29
1784 5989 1.967319 ACTGCAGGTGTCGACATTTT 58.033 45.000 23.12 7.56 0.00 1.82
1785 5990 1.603802 CAACTGCAGGTGTCGACATTT 59.396 47.619 24.08 10.26 0.00 2.32
1786 5991 1.229428 CAACTGCAGGTGTCGACATT 58.771 50.000 24.08 10.65 0.00 2.71
1787 5992 0.603707 CCAACTGCAGGTGTCGACAT 60.604 55.000 29.22 3.16 0.00 3.06
1788 5993 1.227527 CCAACTGCAGGTGTCGACA 60.228 57.895 29.22 15.76 0.00 4.35
1802 6007 1.300853 ACGCTTGCCAATTGCCAAC 60.301 52.632 0.00 0.00 40.16 3.77
1803 6008 1.300775 CACGCTTGCCAATTGCCAA 60.301 52.632 1.45 1.45 40.16 4.52
1872 6077 0.107017 AGCAAAGTGTGTCCAGCTGT 60.107 50.000 13.81 0.00 0.00 4.40
1970 6175 9.180678 CGTCTCAAAATAAGTTGTTTGCTAAAT 57.819 29.630 0.00 0.00 35.21 1.40
1971 6176 8.399425 TCGTCTCAAAATAAGTTGTTTGCTAAA 58.601 29.630 0.00 0.00 35.21 1.85
1972 6177 7.921787 TCGTCTCAAAATAAGTTGTTTGCTAA 58.078 30.769 0.00 0.00 35.21 3.09
1973 6178 7.485418 TCGTCTCAAAATAAGTTGTTTGCTA 57.515 32.000 0.00 0.00 35.21 3.49
1974 6179 6.371809 TCGTCTCAAAATAAGTTGTTTGCT 57.628 33.333 0.00 0.00 35.21 3.91
1975 6180 6.142320 CCTTCGTCTCAAAATAAGTTGTTTGC 59.858 38.462 0.00 0.00 35.21 3.68
1976 6181 7.414436 TCCTTCGTCTCAAAATAAGTTGTTTG 58.586 34.615 0.00 3.39 36.30 2.93
1977 6182 7.562454 TCCTTCGTCTCAAAATAAGTTGTTT 57.438 32.000 0.00 0.00 0.00 2.83
1978 6183 7.282450 ACTTCCTTCGTCTCAAAATAAGTTGTT 59.718 33.333 0.00 0.00 0.00 2.83
1979 6184 6.766467 ACTTCCTTCGTCTCAAAATAAGTTGT 59.234 34.615 0.00 0.00 0.00 3.32
1980 6185 7.190920 ACTTCCTTCGTCTCAAAATAAGTTG 57.809 36.000 0.00 0.00 0.00 3.16
1981 6186 8.897872 TTACTTCCTTCGTCTCAAAATAAGTT 57.102 30.769 0.00 0.00 0.00 2.66
1982 6187 9.152595 GATTACTTCCTTCGTCTCAAAATAAGT 57.847 33.333 0.00 0.00 0.00 2.24
1983 6188 9.372369 AGATTACTTCCTTCGTCTCAAAATAAG 57.628 33.333 0.00 0.00 0.00 1.73
1986 6191 9.892130 ATTAGATTACTTCCTTCGTCTCAAAAT 57.108 29.630 0.00 0.00 0.00 1.82
1988 6193 9.798994 GTATTAGATTACTTCCTTCGTCTCAAA 57.201 33.333 0.00 0.00 0.00 2.69
1989 6194 8.127327 CGTATTAGATTACTTCCTTCGTCTCAA 58.873 37.037 0.00 0.00 0.00 3.02
1990 6195 7.255035 CCGTATTAGATTACTTCCTTCGTCTCA 60.255 40.741 0.00 0.00 0.00 3.27
1991 6196 7.076983 CCGTATTAGATTACTTCCTTCGTCTC 58.923 42.308 0.00 0.00 0.00 3.36
1992 6197 6.545298 ACCGTATTAGATTACTTCCTTCGTCT 59.455 38.462 0.00 0.00 0.00 4.18
1993 6198 6.733145 ACCGTATTAGATTACTTCCTTCGTC 58.267 40.000 0.00 0.00 0.00 4.20
1994 6199 6.705863 ACCGTATTAGATTACTTCCTTCGT 57.294 37.500 0.00 0.00 0.00 3.85
1995 6200 7.490402 ACAAACCGTATTAGATTACTTCCTTCG 59.510 37.037 0.00 0.00 0.00 3.79
1996 6201 8.713737 ACAAACCGTATTAGATTACTTCCTTC 57.286 34.615 0.00 0.00 0.00 3.46
1997 6202 9.511272 AAACAAACCGTATTAGATTACTTCCTT 57.489 29.630 0.00 0.00 0.00 3.36
1998 6203 9.511272 AAAACAAACCGTATTAGATTACTTCCT 57.489 29.630 0.00 0.00 0.00 3.36
1999 6204 9.550811 CAAAACAAACCGTATTAGATTACTTCC 57.449 33.333 0.00 0.00 0.00 3.46
2005 6210 8.079809 CCAGTTCAAAACAAACCGTATTAGATT 58.920 33.333 0.00 0.00 0.00 2.40
2006 6211 7.308951 CCCAGTTCAAAACAAACCGTATTAGAT 60.309 37.037 0.00 0.00 0.00 1.98
2007 6212 6.016943 CCCAGTTCAAAACAAACCGTATTAGA 60.017 38.462 0.00 0.00 0.00 2.10
2008 6213 6.016943 TCCCAGTTCAAAACAAACCGTATTAG 60.017 38.462 0.00 0.00 0.00 1.73
2009 6214 5.826737 TCCCAGTTCAAAACAAACCGTATTA 59.173 36.000 0.00 0.00 0.00 0.98
2010 6215 4.645588 TCCCAGTTCAAAACAAACCGTATT 59.354 37.500 0.00 0.00 0.00 1.89
2011 6216 4.208746 TCCCAGTTCAAAACAAACCGTAT 58.791 39.130 0.00 0.00 0.00 3.06
2012 6217 3.618351 TCCCAGTTCAAAACAAACCGTA 58.382 40.909 0.00 0.00 0.00 4.02
2013 6218 2.448453 TCCCAGTTCAAAACAAACCGT 58.552 42.857 0.00 0.00 0.00 4.83
2014 6219 3.512033 TTCCCAGTTCAAAACAAACCG 57.488 42.857 0.00 0.00 0.00 4.44
2015 6220 5.756347 GGTTATTCCCAGTTCAAAACAAACC 59.244 40.000 0.00 0.00 0.00 3.27
2016 6221 6.838198 GGTTATTCCCAGTTCAAAACAAAC 57.162 37.500 0.00 0.00 0.00 2.93
2031 6236 4.948004 CAGTTAGTGGAAAGGGGTTATTCC 59.052 45.833 0.00 0.00 44.38 3.01
2032 6237 5.812286 TCAGTTAGTGGAAAGGGGTTATTC 58.188 41.667 0.00 0.00 0.00 1.75
2033 6238 5.853572 TCAGTTAGTGGAAAGGGGTTATT 57.146 39.130 0.00 0.00 0.00 1.40
2034 6239 5.853572 TTCAGTTAGTGGAAAGGGGTTAT 57.146 39.130 0.00 0.00 0.00 1.89
2035 6240 5.853572 ATTCAGTTAGTGGAAAGGGGTTA 57.146 39.130 0.00 0.00 0.00 2.85
2036 6241 4.741928 ATTCAGTTAGTGGAAAGGGGTT 57.258 40.909 0.00 0.00 0.00 4.11
2037 6242 5.567430 GTTATTCAGTTAGTGGAAAGGGGT 58.433 41.667 0.00 0.00 0.00 4.95
2038 6243 4.634443 CGTTATTCAGTTAGTGGAAAGGGG 59.366 45.833 0.00 0.00 0.00 4.79
2039 6244 5.484715 TCGTTATTCAGTTAGTGGAAAGGG 58.515 41.667 0.00 0.00 0.00 3.95
2040 6245 7.429636 TTTCGTTATTCAGTTAGTGGAAAGG 57.570 36.000 0.00 0.00 0.00 3.11
2043 6248 9.491675 TGTATTTTCGTTATTCAGTTAGTGGAA 57.508 29.630 0.00 0.00 0.00 3.53
2044 6249 9.661563 ATGTATTTTCGTTATTCAGTTAGTGGA 57.338 29.630 0.00 0.00 0.00 4.02
2045 6250 9.916397 GATGTATTTTCGTTATTCAGTTAGTGG 57.084 33.333 0.00 0.00 0.00 4.00
2051 6256 9.988350 GTTCATGATGTATTTTCGTTATTCAGT 57.012 29.630 0.00 0.00 0.00 3.41
2052 6257 9.438291 GGTTCATGATGTATTTTCGTTATTCAG 57.562 33.333 0.00 0.00 0.00 3.02
2053 6258 8.951243 TGGTTCATGATGTATTTTCGTTATTCA 58.049 29.630 0.00 0.00 0.00 2.57
2054 6259 9.781834 TTGGTTCATGATGTATTTTCGTTATTC 57.218 29.630 0.00 0.00 0.00 1.75
2056 6261 9.950680 GATTGGTTCATGATGTATTTTCGTTAT 57.049 29.630 0.00 0.00 0.00 1.89
2057 6262 8.951243 TGATTGGTTCATGATGTATTTTCGTTA 58.049 29.630 0.00 0.00 0.00 3.18
2058 6263 7.825681 TGATTGGTTCATGATGTATTTTCGTT 58.174 30.769 0.00 0.00 0.00 3.85
2059 6264 7.336679 TCTGATTGGTTCATGATGTATTTTCGT 59.663 33.333 0.00 0.00 32.72 3.85
2060 6265 7.696755 TCTGATTGGTTCATGATGTATTTTCG 58.303 34.615 0.00 0.00 32.72 3.46
2061 6266 9.294030 GTTCTGATTGGTTCATGATGTATTTTC 57.706 33.333 0.00 0.00 32.72 2.29
2062 6267 7.970061 CGTTCTGATTGGTTCATGATGTATTTT 59.030 33.333 0.00 0.00 32.72 1.82
2063 6268 7.415541 CCGTTCTGATTGGTTCATGATGTATTT 60.416 37.037 0.00 0.00 32.72 1.40
2064 6269 6.038603 CCGTTCTGATTGGTTCATGATGTATT 59.961 38.462 0.00 0.00 32.72 1.89
2065 6270 5.528690 CCGTTCTGATTGGTTCATGATGTAT 59.471 40.000 0.00 0.00 32.72 2.29
2066 6271 4.875536 CCGTTCTGATTGGTTCATGATGTA 59.124 41.667 0.00 0.00 32.72 2.29
2067 6272 3.691118 CCGTTCTGATTGGTTCATGATGT 59.309 43.478 0.00 0.00 32.72 3.06
2068 6273 3.065786 CCCGTTCTGATTGGTTCATGATG 59.934 47.826 0.00 0.00 32.72 3.07
2069 6274 3.054434 TCCCGTTCTGATTGGTTCATGAT 60.054 43.478 0.00 0.00 32.72 2.45
2070 6275 2.304470 TCCCGTTCTGATTGGTTCATGA 59.696 45.455 0.00 0.00 32.72 3.07
2071 6276 2.420022 GTCCCGTTCTGATTGGTTCATG 59.580 50.000 0.00 0.00 32.72 3.07
2072 6277 2.711542 GTCCCGTTCTGATTGGTTCAT 58.288 47.619 0.00 0.00 32.72 2.57
2073 6278 1.606994 CGTCCCGTTCTGATTGGTTCA 60.607 52.381 0.00 0.00 0.00 3.18
2074 6279 1.076332 CGTCCCGTTCTGATTGGTTC 58.924 55.000 0.00 0.00 0.00 3.62
2075 6280 0.321298 CCGTCCCGTTCTGATTGGTT 60.321 55.000 0.00 0.00 0.00 3.67
2076 6281 1.295423 CCGTCCCGTTCTGATTGGT 59.705 57.895 0.00 0.00 0.00 3.67
2077 6282 1.449601 CCCGTCCCGTTCTGATTGG 60.450 63.158 0.00 0.00 0.00 3.16
2078 6283 0.036765 TTCCCGTCCCGTTCTGATTG 60.037 55.000 0.00 0.00 0.00 2.67
2079 6284 0.688487 TTTCCCGTCCCGTTCTGATT 59.312 50.000 0.00 0.00 0.00 2.57
2080 6285 0.249398 CTTTCCCGTCCCGTTCTGAT 59.751 55.000 0.00 0.00 0.00 2.90
2081 6286 1.669440 CTTTCCCGTCCCGTTCTGA 59.331 57.895 0.00 0.00 0.00 3.27
2082 6287 1.375523 CCTTTCCCGTCCCGTTCTG 60.376 63.158 0.00 0.00 0.00 3.02
2083 6288 2.590114 CCCTTTCCCGTCCCGTTCT 61.590 63.158 0.00 0.00 0.00 3.01
2084 6289 2.046604 CCCTTTCCCGTCCCGTTC 60.047 66.667 0.00 0.00 0.00 3.95
2085 6290 3.643554 CCCCTTTCCCGTCCCGTT 61.644 66.667 0.00 0.00 0.00 4.44
2086 6291 4.644288 TCCCCTTTCCCGTCCCGT 62.644 66.667 0.00 0.00 0.00 5.28
2087 6292 2.814913 CTTTCCCCTTTCCCGTCCCG 62.815 65.000 0.00 0.00 0.00 5.14
2088 6293 1.001269 CTTTCCCCTTTCCCGTCCC 60.001 63.158 0.00 0.00 0.00 4.46
2089 6294 1.677966 GCTTTCCCCTTTCCCGTCC 60.678 63.158 0.00 0.00 0.00 4.79
2090 6295 2.038837 CGCTTTCCCCTTTCCCGTC 61.039 63.158 0.00 0.00 0.00 4.79
2091 6296 2.033602 CGCTTTCCCCTTTCCCGT 59.966 61.111 0.00 0.00 0.00 5.28
2092 6297 1.745489 CTCGCTTTCCCCTTTCCCG 60.745 63.158 0.00 0.00 0.00 5.14
2093 6298 0.251209 AACTCGCTTTCCCCTTTCCC 60.251 55.000 0.00 0.00 0.00 3.97
2094 6299 1.166129 GAACTCGCTTTCCCCTTTCC 58.834 55.000 0.00 0.00 0.00 3.13
2095 6300 1.892209 TGAACTCGCTTTCCCCTTTC 58.108 50.000 0.00 0.00 0.00 2.62
2096 6301 2.358322 TTGAACTCGCTTTCCCCTTT 57.642 45.000 0.00 0.00 0.00 3.11
2097 6302 2.230660 CTTTGAACTCGCTTTCCCCTT 58.769 47.619 0.00 0.00 0.00 3.95
2098 6303 1.897560 CTTTGAACTCGCTTTCCCCT 58.102 50.000 0.00 0.00 0.00 4.79
2099 6304 0.241213 GCTTTGAACTCGCTTTCCCC 59.759 55.000 0.00 0.00 0.00 4.81
2100 6305 0.951558 TGCTTTGAACTCGCTTTCCC 59.048 50.000 0.00 0.00 0.00 3.97
2101 6306 2.726066 CGATGCTTTGAACTCGCTTTCC 60.726 50.000 0.00 0.00 0.00 3.13
2102 6307 2.499896 CGATGCTTTGAACTCGCTTTC 58.500 47.619 0.00 0.00 0.00 2.62
2103 6308 2.601481 CGATGCTTTGAACTCGCTTT 57.399 45.000 0.00 0.00 0.00 3.51
2107 6312 1.059369 CGGCGATGCTTTGAACTCG 59.941 57.895 0.00 0.00 0.00 4.18
2108 6313 1.425428 CCGGCGATGCTTTGAACTC 59.575 57.895 9.30 0.00 0.00 3.01
2109 6314 2.040544 CCCGGCGATGCTTTGAACT 61.041 57.895 9.30 0.00 0.00 3.01
2110 6315 1.582610 TTCCCGGCGATGCTTTGAAC 61.583 55.000 9.30 0.00 0.00 3.18
2111 6316 0.891449 TTTCCCGGCGATGCTTTGAA 60.891 50.000 9.30 0.00 0.00 2.69
2112 6317 0.679640 ATTTCCCGGCGATGCTTTGA 60.680 50.000 9.30 0.00 0.00 2.69
2113 6318 0.248621 GATTTCCCGGCGATGCTTTG 60.249 55.000 9.30 0.00 0.00 2.77
2114 6319 1.384222 GGATTTCCCGGCGATGCTTT 61.384 55.000 9.30 0.00 0.00 3.51
2115 6320 1.823899 GGATTTCCCGGCGATGCTT 60.824 57.895 9.30 0.00 0.00 3.91
2116 6321 2.203209 GGATTTCCCGGCGATGCT 60.203 61.111 9.30 0.00 0.00 3.79
2117 6322 2.515991 TGGATTTCCCGGCGATGC 60.516 61.111 9.30 0.00 37.93 3.91
2118 6323 2.186826 GGTGGATTTCCCGGCGATG 61.187 63.158 9.30 0.00 37.93 3.84
2119 6324 2.192175 GGTGGATTTCCCGGCGAT 59.808 61.111 9.30 0.00 37.93 4.58
2120 6325 3.323286 TGGTGGATTTCCCGGCGA 61.323 61.111 9.30 0.00 37.93 5.54
2121 6326 3.131478 GTGGTGGATTTCCCGGCG 61.131 66.667 0.00 0.00 37.93 6.46
2122 6327 2.754254 GGTGGTGGATTTCCCGGC 60.754 66.667 0.00 0.00 37.93 6.13
2123 6328 2.437716 CGGTGGTGGATTTCCCGG 60.438 66.667 0.00 0.00 37.93 5.73
2124 6329 2.437716 CCGGTGGTGGATTTCCCG 60.438 66.667 0.00 0.00 37.93 5.14
2125 6330 0.963856 GTTCCGGTGGTGGATTTCCC 60.964 60.000 0.00 0.00 38.00 3.97
2126 6331 0.037734 AGTTCCGGTGGTGGATTTCC 59.962 55.000 0.00 0.00 38.00 3.13
2127 6332 1.271163 TGAGTTCCGGTGGTGGATTTC 60.271 52.381 0.00 0.00 38.00 2.17
2128 6333 0.768622 TGAGTTCCGGTGGTGGATTT 59.231 50.000 0.00 0.00 38.00 2.17
2129 6334 0.036306 GTGAGTTCCGGTGGTGGATT 59.964 55.000 0.00 0.00 38.00 3.01
2130 6335 1.677552 GTGAGTTCCGGTGGTGGAT 59.322 57.895 0.00 0.00 38.00 3.41
2131 6336 2.863346 CGTGAGTTCCGGTGGTGGA 61.863 63.158 0.00 0.00 35.83 4.02
2132 6337 1.808531 TACGTGAGTTCCGGTGGTGG 61.809 60.000 0.00 0.00 46.40 4.61
2133 6338 0.665369 GTACGTGAGTTCCGGTGGTG 60.665 60.000 0.00 0.00 46.40 4.17
2134 6339 1.662044 GTACGTGAGTTCCGGTGGT 59.338 57.895 0.00 0.00 46.40 4.16
2135 6340 1.443194 CGTACGTGAGTTCCGGTGG 60.443 63.158 7.22 0.00 46.40 4.61
2136 6341 0.453950 CTCGTACGTGAGTTCCGGTG 60.454 60.000 16.05 0.00 46.40 4.94
2137 6342 0.603707 TCTCGTACGTGAGTTCCGGT 60.604 55.000 16.05 0.00 46.40 5.28
2138 6343 0.731417 ATCTCGTACGTGAGTTCCGG 59.269 55.000 22.60 0.00 46.40 5.14
2139 6344 1.129998 ACATCTCGTACGTGAGTTCCG 59.870 52.381 22.60 12.06 46.40 4.30
2140 6345 2.915738 ACATCTCGTACGTGAGTTCC 57.084 50.000 22.60 0.00 46.40 3.62
2141 6346 5.213913 TCTAACATCTCGTACGTGAGTTC 57.786 43.478 24.56 0.00 46.40 3.01
2142 6347 5.618056 TTCTAACATCTCGTACGTGAGTT 57.382 39.130 22.60 23.70 46.40 3.01
2144 6349 7.175073 TCTATTCTAACATCTCGTACGTGAG 57.825 40.000 22.60 16.80 37.33 3.51
2145 6350 7.307811 CCATCTATTCTAACATCTCGTACGTGA 60.308 40.741 20.89 20.89 0.00 4.35
2146 6351 6.797513 CCATCTATTCTAACATCTCGTACGTG 59.202 42.308 16.05 13.38 0.00 4.49
2147 6352 6.072618 CCCATCTATTCTAACATCTCGTACGT 60.073 42.308 16.05 0.00 0.00 3.57
2148 6353 6.072618 ACCCATCTATTCTAACATCTCGTACG 60.073 42.308 9.53 9.53 0.00 3.67
2149 6354 7.216973 ACCCATCTATTCTAACATCTCGTAC 57.783 40.000 0.00 0.00 0.00 3.67
2151 6356 9.179909 CTATACCCATCTATTCTAACATCTCGT 57.820 37.037 0.00 0.00 0.00 4.18
2152 6357 8.625651 CCTATACCCATCTATTCTAACATCTCG 58.374 40.741 0.00 0.00 0.00 4.04
2153 6358 9.702253 TCCTATACCCATCTATTCTAACATCTC 57.298 37.037 0.00 0.00 0.00 2.75
2154 6359 9.707957 CTCCTATACCCATCTATTCTAACATCT 57.292 37.037 0.00 0.00 0.00 2.90
2155 6360 9.482175 ACTCCTATACCCATCTATTCTAACATC 57.518 37.037 0.00 0.00 0.00 3.06
2156 6361 9.845214 AACTCCTATACCCATCTATTCTAACAT 57.155 33.333 0.00 0.00 0.00 2.71
2169 6374 8.908095 TCTATCCTTATACAACTCCTATACCCA 58.092 37.037 0.00 0.00 0.00 4.51
2242 6454 1.027357 GGCGGTCGTTACAGAGGATA 58.973 55.000 0.00 0.00 0.00 2.59
2243 6455 1.673808 GGGCGGTCGTTACAGAGGAT 61.674 60.000 0.00 0.00 0.00 3.24
2319 6533 2.752354 GCCGCATGTATATATTGGGCAA 59.248 45.455 12.89 0.00 39.10 4.52
2493 6711 0.178876 TGGAGGATGAGGTGGTGGAA 60.179 55.000 0.00 0.00 0.00 3.53
2568 6786 0.739112 CCCTCGTGAGCTTCTCTTGC 60.739 60.000 0.00 0.00 0.00 4.01
2580 6798 1.672356 CAGGAAGTTGCCCCTCGTG 60.672 63.158 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.