Multiple sequence alignment - TraesCS3A01G409200

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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 TraesCS3A01G409200 chr3A 100.000 5910 0 0 621 6530 653856883 653850974 0.000000e+00 10914.0
1 TraesCS3A01G409200 chr3A 100.000 177 0 0 1 177 653857503 653857327 1.760000e-85 327.0
2 TraesCS3A01G409200 chr3A 92.361 144 6 4 2649 2792 653854768 653854630 3.990000e-47 200.0
3 TraesCS3A01G409200 chr3A 92.361 144 6 4 2736 2874 653854855 653854712 3.990000e-47 200.0
4 TraesCS3A01G409200 chr3A 75.304 247 55 3 5138 5378 631615666 631615912 5.350000e-21 113.0
5 TraesCS3A01G409200 chr3D 95.018 3693 114 49 2736 6405 518154822 518151177 0.000000e+00 5736.0
6 TraesCS3A01G409200 chr3D 91.164 1460 78 24 624 2067 518156885 518155461 0.000000e+00 1934.0
7 TraesCS3A01G409200 chr3D 93.139 787 32 13 2020 2792 518155457 518154679 0.000000e+00 1134.0
8 TraesCS3A01G409200 chr3D 93.333 180 7 4 1 177 518157322 518157145 1.810000e-65 261.0
9 TraesCS3A01G409200 chr3B 94.365 3727 108 59 2736 6405 682789332 682785651 0.000000e+00 5626.0
10 TraesCS3A01G409200 chr3B 92.249 2219 110 36 624 2792 682791393 682789187 0.000000e+00 3088.0
11 TraesCS3A01G409200 chr3B 92.737 179 7 4 1 177 682791849 682791675 3.020000e-63 254.0
12 TraesCS3A01G409200 chr1D 85.759 962 135 2 4503 5463 362489985 362489025 0.000000e+00 1016.0
13 TraesCS3A01G409200 chr1A 85.151 963 141 2 4503 5464 462002135 462001174 0.000000e+00 985.0
14 TraesCS3A01G409200 chr1B 85.135 962 141 2 4503 5463 485289705 485288745 0.000000e+00 983.0
15 TraesCS3A01G409200 chr5A 87.805 123 14 1 6408 6530 641053662 641053783 6.830000e-30 143.0
16 TraesCS3A01G409200 chr4D 83.333 102 13 3 6402 6502 7138064 7137966 2.510000e-14 91.6
17 TraesCS3A01G409200 chr4D 96.970 33 0 1 5081 5112 105587469 105587437 3.000000e-03 54.7


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 TraesCS3A01G409200 chr3A 653850974 653857503 6529 True 2910.250000 10914 96.1805 1 6530 4 chr3A.!!$R1 6529
1 TraesCS3A01G409200 chr3D 518151177 518157322 6145 True 2266.250000 5736 93.1635 1 6405 4 chr3D.!!$R1 6404
2 TraesCS3A01G409200 chr3B 682785651 682791849 6198 True 2989.333333 5626 93.1170 1 6405 3 chr3B.!!$R1 6404
3 TraesCS3A01G409200 chr1D 362489025 362489985 960 True 1016.000000 1016 85.7590 4503 5463 1 chr1D.!!$R1 960
4 TraesCS3A01G409200 chr1A 462001174 462002135 961 True 985.000000 985 85.1510 4503 5464 1 chr1A.!!$R1 961
5 TraesCS3A01G409200 chr1B 485288745 485289705 960 True 983.000000 983 85.1350 4503 5463 1 chr1B.!!$R1 960

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
865 899 0.246635 CGAATCCTCCCGTGTTCTGT 59.753 55.000 0.00 0.0 0.00 3.41 F
978 1012 0.469070 CCAGAGGAGGCTTCATCCAG 59.531 60.000 6.89 0.4 39.47 3.86 F
1634 1682 0.543410 TTCGGTAACCCAGCTCCAGA 60.543 55.000 0.00 0.0 0.00 3.86 F
2357 2462 0.596082 CTGTTAAAAGTGGTGCGGGG 59.404 55.000 0.00 0.0 0.00 5.73 F
2358 2463 0.824182 TGTTAAAAGTGGTGCGGGGG 60.824 55.000 0.00 0.0 0.00 5.40 F
2359 2464 0.824595 GTTAAAAGTGGTGCGGGGGT 60.825 55.000 0.00 0.0 0.00 4.95 F
2485 2591 1.282157 ACCATCACCTAGGAAAGCACC 59.718 52.381 17.98 0.0 0.00 5.01 F
2547 2653 1.536073 GGAAAGGAAAGCACCAGGGC 61.536 60.000 0.00 0.0 0.00 5.19 F
2937 3054 1.755179 TTCATCTGCCTAGCCAAAGC 58.245 50.000 0.00 0.0 40.32 3.51 F
4399 4518 2.292828 AGGGAACATCACCACCTTTG 57.707 50.000 0.00 0.0 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 2506 0.402121 AAGGTTCAGAAGACCAGCCC 59.598 55.000 0.00 0.00 0.00 5.19 R
2547 2653 1.237285 AAGCCTACAAGCAAGCCACG 61.237 55.000 0.00 0.00 34.23 4.94 R
2937 3054 1.556911 ACACTCAATAGGCACTGGGAG 59.443 52.381 0.00 0.00 41.52 4.30 R
3713 3832 0.240945 GCAATTGTGTCCAAGACCCG 59.759 55.000 7.40 0.00 33.17 5.28 R
3785 3904 0.320771 GGTACAGTGTCTGCCAGGTG 60.321 60.000 0.00 0.00 34.37 4.00 R
4309 4428 0.322816 GCTCTTCCAGGCATTGTGGA 60.323 55.000 0.00 0.00 42.62 4.02 R
4381 4500 1.256812 CCAAAGGTGGTGATGTTCCC 58.743 55.000 0.00 0.00 40.42 3.97 R
4435 4554 2.955660 CAGGGACAACACTAAAAAGGCA 59.044 45.455 0.00 0.00 0.00 4.75 R
4581 4701 0.665068 TTTGAGCTGCTGCAATTGCG 60.665 50.000 24.58 19.32 45.83 4.85 R
6061 6211 0.252197 GGAACCACTTCCCATACGCT 59.748 55.000 0.00 0.00 40.38 5.07 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
85 89 6.607019 TCTCCCTCTCTATAAAACTCTCTCC 58.393 44.000 0.00 0.00 0.00 3.71
86 90 6.391649 TCTCCCTCTCTATAAAACTCTCTCCT 59.608 42.308 0.00 0.00 0.00 3.69
690 696 0.899717 TTGGGGCTGTCAGATTTGGC 60.900 55.000 3.32 0.00 0.00 4.52
724 730 3.111853 TCGCATTGCTCTCCGATATTT 57.888 42.857 7.12 0.00 0.00 1.40
725 731 3.466836 TCGCATTGCTCTCCGATATTTT 58.533 40.909 7.12 0.00 0.00 1.82
727 733 3.248363 CGCATTGCTCTCCGATATTTTCA 59.752 43.478 7.12 0.00 0.00 2.69
728 734 4.083643 CGCATTGCTCTCCGATATTTTCAT 60.084 41.667 7.12 0.00 0.00 2.57
729 735 5.388944 GCATTGCTCTCCGATATTTTCATC 58.611 41.667 0.16 0.00 0.00 2.92
738 745 8.792830 TCTCCGATATTTTCATCTTTTTCTGT 57.207 30.769 0.00 0.00 0.00 3.41
759 766 1.559682 TCTTATTTTCTCCCCTGCGCT 59.440 47.619 9.73 0.00 0.00 5.92
780 787 1.340405 ACTGTTCATCCCCACATGCTC 60.340 52.381 0.00 0.00 0.00 4.26
835 869 4.020839 AGCATTATTTGGCTTGCTGAACTT 60.021 37.500 0.00 0.00 43.44 2.66
837 871 5.472148 CATTATTTGGCTTGCTGAACTTCA 58.528 37.500 0.00 0.00 0.00 3.02
838 872 5.528043 TTATTTGGCTTGCTGAACTTCAA 57.472 34.783 0.00 0.00 0.00 2.69
839 873 3.441496 TTTGGCTTGCTGAACTTCAAG 57.559 42.857 0.00 0.00 41.79 3.02
844 878 3.265070 CTTGCTGAACTTCAAGCTCAC 57.735 47.619 11.87 0.00 34.12 3.51
845 879 2.330440 TGCTGAACTTCAAGCTCACA 57.670 45.000 11.87 0.00 0.00 3.58
846 880 1.942657 TGCTGAACTTCAAGCTCACAC 59.057 47.619 11.87 0.00 0.00 3.82
847 881 1.070309 GCTGAACTTCAAGCTCACACG 60.070 52.381 0.00 0.00 0.00 4.49
848 882 2.473816 CTGAACTTCAAGCTCACACGA 58.526 47.619 0.00 0.00 0.00 4.35
849 883 2.866156 CTGAACTTCAAGCTCACACGAA 59.134 45.455 0.00 0.00 0.00 3.85
850 884 3.466836 TGAACTTCAAGCTCACACGAAT 58.533 40.909 0.00 0.00 0.00 3.34
851 885 3.494626 TGAACTTCAAGCTCACACGAATC 59.505 43.478 0.00 0.00 0.00 2.52
852 886 2.417719 ACTTCAAGCTCACACGAATCC 58.582 47.619 0.00 0.00 0.00 3.01
853 887 2.037772 ACTTCAAGCTCACACGAATCCT 59.962 45.455 0.00 0.00 0.00 3.24
854 888 2.370281 TCAAGCTCACACGAATCCTC 57.630 50.000 0.00 0.00 0.00 3.71
855 889 1.066858 TCAAGCTCACACGAATCCTCC 60.067 52.381 0.00 0.00 0.00 4.30
856 890 0.250513 AAGCTCACACGAATCCTCCC 59.749 55.000 0.00 0.00 0.00 4.30
857 891 1.519455 GCTCACACGAATCCTCCCG 60.519 63.158 0.00 0.00 0.00 5.14
865 899 0.246635 CGAATCCTCCCGTGTTCTGT 59.753 55.000 0.00 0.00 0.00 3.41
978 1012 0.469070 CCAGAGGAGGCTTCATCCAG 59.531 60.000 6.89 0.40 39.47 3.86
984 1018 1.138661 GGAGGCTTCATCCAGACAGAG 59.861 57.143 0.00 0.00 36.79 3.35
1078 1112 4.410400 GCAGAACCCACCCCTCGG 62.410 72.222 0.00 0.00 0.00 4.63
1326 1366 3.755628 CGTCCGTCCGTCCATGGT 61.756 66.667 12.58 0.00 0.00 3.55
1331 1375 2.351276 GTCCGTCCATGGTGCCTT 59.649 61.111 12.58 0.00 0.00 4.35
1340 1384 1.229951 ATGGTGCCTTCCTCCTCCA 60.230 57.895 0.00 0.00 0.00 3.86
1408 1453 2.885135 TATGGCATCCATCCATCCAC 57.115 50.000 1.65 0.00 40.74 4.02
1412 1457 0.825010 GCATCCATCCATCCACCCAC 60.825 60.000 0.00 0.00 0.00 4.61
1421 1466 2.371841 TCCATCCACCCACATATGCTAC 59.628 50.000 1.58 0.00 0.00 3.58
1422 1467 2.553028 CCATCCACCCACATATGCTACC 60.553 54.545 1.58 0.00 0.00 3.18
1487 1535 1.083489 TTTCCGTTGCTAAGATGCCG 58.917 50.000 0.00 0.00 0.00 5.69
1505 1553 1.679944 CCGGAACTGCCATGAATCTGT 60.680 52.381 0.00 0.00 35.94 3.41
1506 1554 2.086869 CGGAACTGCCATGAATCTGTT 58.913 47.619 0.00 0.00 35.94 3.16
1516 1564 3.495193 CATGAATCTGTTGGTTCTTGCG 58.505 45.455 0.00 0.00 0.00 4.85
1520 1568 1.898574 CTGTTGGTTCTTGCGCCCT 60.899 57.895 4.18 0.00 0.00 5.19
1612 1660 8.270030 TGATCCCATATTTAGGAGATGCTAATG 58.730 37.037 0.00 0.00 35.08 1.90
1617 1665 8.734386 CCATATTTAGGAGATGCTAATGGTTTC 58.266 37.037 4.81 0.00 0.00 2.78
1634 1682 0.543410 TTCGGTAACCCAGCTCCAGA 60.543 55.000 0.00 0.00 0.00 3.86
1635 1683 1.218316 CGGTAACCCAGCTCCAGAC 59.782 63.158 0.00 0.00 0.00 3.51
1787 1836 2.186826 GCAGTGGGCACGTTGAGTT 61.187 57.895 0.00 0.00 43.97 3.01
1804 1853 0.669625 GTTGGTCAGCTCCGGTACAC 60.670 60.000 0.00 0.00 0.00 2.90
1850 1899 3.132824 GGTGACAATTGGGGATCATTTCC 59.867 47.826 10.83 0.00 44.62 3.13
1871 1920 5.393866 TCCTCTAGAAAATGCCAGGTTTTT 58.606 37.500 0.00 2.79 0.00 1.94
1915 1964 2.799540 GCGGCGAACGGAGTGAATC 61.800 63.158 12.98 0.00 45.00 2.52
1973 2022 1.635844 TAACGGCATTGACGCTACTG 58.364 50.000 12.82 0.00 37.73 2.74
1983 2032 2.833794 TGACGCTACTGCAAAGTTTCT 58.166 42.857 0.00 0.00 39.64 2.52
1984 2033 3.985008 TGACGCTACTGCAAAGTTTCTA 58.015 40.909 0.00 0.00 39.64 2.10
1985 2034 4.566004 TGACGCTACTGCAAAGTTTCTAT 58.434 39.130 0.00 0.00 39.64 1.98
2050 2099 2.657848 GCGTGTTTGCCGGTATTAAAAC 59.342 45.455 1.90 7.51 33.98 2.43
2094 2195 4.455533 CGATTTGAGACCAAGAAACATGGA 59.544 41.667 0.00 0.00 40.56 3.41
2156 2261 5.392487 GGTGCTCTCCTTTTCTAAAAGATGC 60.392 44.000 15.16 12.77 46.39 3.91
2158 2263 4.201861 GCTCTCCTTTTCTAAAAGATGCGG 60.202 45.833 15.16 1.35 46.39 5.69
2212 2317 1.611006 TGCGCTGGTTTTCATTTGCTA 59.389 42.857 9.73 0.00 0.00 3.49
2213 2318 2.035193 TGCGCTGGTTTTCATTTGCTAA 59.965 40.909 9.73 0.00 0.00 3.09
2248 2353 4.072088 GTGCGGAGAAACGTGCGG 62.072 66.667 0.00 0.00 35.98 5.69
2270 2375 2.632996 GCTTTTGTTCCCCTTAGCCTTT 59.367 45.455 0.00 0.00 0.00 3.11
2320 2425 5.819991 AGTGTGTGATCACTTCCCAATATT 58.180 37.500 25.55 0.00 44.92 1.28
2321 2426 5.649395 AGTGTGTGATCACTTCCCAATATTG 59.351 40.000 25.55 8.58 44.92 1.90
2324 2429 5.829924 GTGTGATCACTTCCCAATATTGGAT 59.170 40.000 32.11 17.97 44.46 3.41
2355 2460 1.535462 CTCCTGTTAAAAGTGGTGCGG 59.465 52.381 0.00 0.00 0.00 5.69
2357 2462 0.596082 CTGTTAAAAGTGGTGCGGGG 59.404 55.000 0.00 0.00 0.00 5.73
2358 2463 0.824182 TGTTAAAAGTGGTGCGGGGG 60.824 55.000 0.00 0.00 0.00 5.40
2359 2464 0.824595 GTTAAAAGTGGTGCGGGGGT 60.825 55.000 0.00 0.00 0.00 4.95
2395 2500 1.314534 TGCAATGCATGTTAGCCGCT 61.315 50.000 2.72 0.00 31.71 5.52
2401 2506 1.789078 GCATGTTAGCCGCTCATGGG 61.789 60.000 18.72 0.00 39.20 4.00
2485 2591 1.282157 ACCATCACCTAGGAAAGCACC 59.718 52.381 17.98 0.00 0.00 5.01
2547 2653 1.536073 GGAAAGGAAAGCACCAGGGC 61.536 60.000 0.00 0.00 0.00 5.19
2726 2840 6.205464 CAGAAGTGCCTATTTCAGAGTTTTGA 59.795 38.462 0.00 0.00 0.00 2.69
2780 2897 9.745018 ATCTGTTATATTGGGAAATCATACCTG 57.255 33.333 0.00 0.00 0.00 4.00
2781 2898 7.665559 TCTGTTATATTGGGAAATCATACCTGC 59.334 37.037 0.00 0.00 0.00 4.85
2782 2899 7.526041 TGTTATATTGGGAAATCATACCTGCT 58.474 34.615 0.00 0.00 0.00 4.24
2783 2900 8.004215 TGTTATATTGGGAAATCATACCTGCTT 58.996 33.333 0.00 0.00 0.00 3.91
2784 2901 8.515414 GTTATATTGGGAAATCATACCTGCTTC 58.485 37.037 0.00 0.00 0.00 3.86
2785 2902 4.591321 TTGGGAAATCATACCTGCTTCT 57.409 40.909 0.00 0.00 0.00 2.85
2786 2903 4.591321 TGGGAAATCATACCTGCTTCTT 57.409 40.909 0.00 0.00 0.00 2.52
2787 2904 4.526970 TGGGAAATCATACCTGCTTCTTC 58.473 43.478 0.00 0.00 0.00 2.87
2788 2905 4.018506 TGGGAAATCATACCTGCTTCTTCA 60.019 41.667 0.00 0.00 0.00 3.02
2789 2906 4.578105 GGGAAATCATACCTGCTTCTTCAG 59.422 45.833 0.00 0.00 0.00 3.02
2790 2907 5.431765 GGAAATCATACCTGCTTCTTCAGA 58.568 41.667 0.00 0.00 36.19 3.27
2791 2908 5.882557 GGAAATCATACCTGCTTCTTCAGAA 59.117 40.000 0.00 0.00 36.19 3.02
2804 2921 6.419980 CTTCTTCAGAAGTGCCTATTTCAG 57.580 41.667 10.09 0.00 44.80 3.02
2805 2922 5.745312 TCTTCAGAAGTGCCTATTTCAGA 57.255 39.130 10.09 0.00 0.00 3.27
2806 2923 5.728471 TCTTCAGAAGTGCCTATTTCAGAG 58.272 41.667 10.09 0.00 0.00 3.35
2807 2924 5.247110 TCTTCAGAAGTGCCTATTTCAGAGT 59.753 40.000 10.09 0.00 0.00 3.24
2808 2925 5.489792 TCAGAAGTGCCTATTTCAGAGTT 57.510 39.130 0.00 0.00 0.00 3.01
2809 2926 5.869579 TCAGAAGTGCCTATTTCAGAGTTT 58.130 37.500 0.00 0.00 0.00 2.66
2810 2927 6.299141 TCAGAAGTGCCTATTTCAGAGTTTT 58.701 36.000 0.00 0.00 0.00 2.43
2811 2928 6.205464 TCAGAAGTGCCTATTTCAGAGTTTTG 59.795 38.462 0.00 0.00 0.00 2.44
2812 2929 6.205464 CAGAAGTGCCTATTTCAGAGTTTTGA 59.795 38.462 0.00 0.00 0.00 2.69
2813 2930 6.944862 AGAAGTGCCTATTTCAGAGTTTTGAT 59.055 34.615 0.00 0.00 0.00 2.57
2814 2931 7.449704 AGAAGTGCCTATTTCAGAGTTTTGATT 59.550 33.333 0.00 0.00 0.00 2.57
2815 2932 7.530426 AGTGCCTATTTCAGAGTTTTGATTT 57.470 32.000 0.00 0.00 0.00 2.17
2816 2933 7.955918 AGTGCCTATTTCAGAGTTTTGATTTT 58.044 30.769 0.00 0.00 0.00 1.82
2817 2934 7.869429 AGTGCCTATTTCAGAGTTTTGATTTTG 59.131 33.333 0.00 0.00 0.00 2.44
2818 2935 7.116805 GTGCCTATTTCAGAGTTTTGATTTTGG 59.883 37.037 0.00 0.00 0.00 3.28
2819 2936 7.015098 TGCCTATTTCAGAGTTTTGATTTTGGA 59.985 33.333 0.00 0.00 0.00 3.53
2820 2937 7.329471 GCCTATTTCAGAGTTTTGATTTTGGAC 59.671 37.037 0.00 0.00 0.00 4.02
2821 2938 8.579863 CCTATTTCAGAGTTTTGATTTTGGACT 58.420 33.333 0.00 0.00 0.00 3.85
2824 2941 9.750125 ATTTCAGAGTTTTGATTTTGGACTAAC 57.250 29.630 0.00 0.00 0.00 2.34
2825 2942 7.873719 TCAGAGTTTTGATTTTGGACTAACA 57.126 32.000 0.00 0.00 0.00 2.41
2826 2943 8.287439 TCAGAGTTTTGATTTTGGACTAACAA 57.713 30.769 0.00 0.00 0.00 2.83
2827 2944 8.744652 TCAGAGTTTTGATTTTGGACTAACAAA 58.255 29.630 0.00 0.00 38.48 2.83
2828 2945 9.533253 CAGAGTTTTGATTTTGGACTAACAAAT 57.467 29.630 0.00 0.00 39.80 2.32
2916 3033 9.396022 TCTATAAATCTTAGGCAGAGTTTTTGG 57.604 33.333 0.00 0.00 40.37 3.28
2937 3054 1.755179 TTCATCTGCCTAGCCAAAGC 58.245 50.000 0.00 0.00 40.32 3.51
3000 3118 9.453325 GTGATATTGACAAAAGTAAAACGGAAA 57.547 29.630 0.00 0.00 0.00 3.13
3031 3149 6.158598 TCTTCCTGCATAACAAAATGAAAGC 58.841 36.000 0.00 0.00 0.00 3.51
3063 3181 3.207778 ACTCTACTGCTCTCGTGGTATC 58.792 50.000 0.00 0.00 0.00 2.24
3136 3254 5.652891 AGATAGCTTCTGAGTTCCGACTTTA 59.347 40.000 0.00 0.00 35.88 1.85
3480 3599 8.961294 ACACGTAGAACATTACTTTACACTAG 57.039 34.615 0.00 0.00 0.00 2.57
3482 3601 7.008992 CACGTAGAACATTACTTTACACTAGGC 59.991 40.741 0.00 0.00 0.00 3.93
3485 3604 9.733219 GTAGAACATTACTTTACACTAGGCTAG 57.267 37.037 19.83 19.83 0.00 3.42
3490 3609 4.820894 ACTTTACACTAGGCTAGGTTGG 57.179 45.455 24.57 13.38 0.00 3.77
3713 3832 7.417612 TCTTGAATTTTAACAGCACTGAGTTC 58.582 34.615 4.31 0.00 0.00 3.01
4360 4479 6.707608 TCTGTGGCAGTTGAAATATATAGCAG 59.292 38.462 0.00 0.00 32.61 4.24
4399 4518 2.292828 AGGGAACATCACCACCTTTG 57.707 50.000 0.00 0.00 0.00 2.77
4416 4535 6.029607 CACCTTTGGTTCGAATATTGTCATG 58.970 40.000 0.00 0.00 31.02 3.07
4467 4586 4.007659 GTGTTGTCCCTGTATTACTTGGG 58.992 47.826 15.06 15.06 40.95 4.12
4468 4587 3.911260 TGTTGTCCCTGTATTACTTGGGA 59.089 43.478 18.07 18.07 45.58 4.37
4494 4614 3.616956 TGATGAGTGACACCAATCCTC 57.383 47.619 13.01 4.42 36.63 3.71
4581 4701 1.002366 CAAGCGAGTATGTCTGTGGC 58.998 55.000 0.00 0.00 0.00 5.01
5283 5403 1.471684 GACAAGATGCCCAAGAAGCTG 59.528 52.381 0.00 0.00 0.00 4.24
5319 5439 3.708220 GAGGTCGAGGCTGAAGGCG 62.708 68.421 0.00 0.00 46.23 5.52
5555 5675 1.502039 TGTGTAGATATCCTCCCCCGT 59.498 52.381 0.00 0.00 0.00 5.28
5566 5686 2.645797 TCCTCCCCCGTGAAATTTTAGT 59.354 45.455 0.00 0.00 0.00 2.24
5591 5711 3.070734 ACCAGATGATGATACAGCAGACC 59.929 47.826 0.00 0.00 31.88 3.85
5592 5712 3.324268 CCAGATGATGATACAGCAGACCT 59.676 47.826 0.00 0.00 31.88 3.85
5797 5945 0.033208 TGGGTTCATCTTGGATGGGC 60.033 55.000 7.54 2.04 0.00 5.36
5821 5969 6.637365 CAATAATTCGTCGCTTGTAGGTAAG 58.363 40.000 0.00 0.00 0.00 2.34
5822 5970 3.863142 ATTCGTCGCTTGTAGGTAAGT 57.137 42.857 0.00 0.00 0.00 2.24
5826 5974 3.983344 TCGTCGCTTGTAGGTAAGTTTTC 59.017 43.478 0.00 0.00 0.00 2.29
5827 5975 3.985925 CGTCGCTTGTAGGTAAGTTTTCT 59.014 43.478 0.00 0.00 0.00 2.52
5828 5976 4.446719 CGTCGCTTGTAGGTAAGTTTTCTT 59.553 41.667 0.00 0.00 43.24 2.52
5861 6009 1.660560 CTATGGCTGGCTGTGTTGGC 61.661 60.000 2.00 0.00 0.00 4.52
5890 6039 8.996271 AGTGGTAGTTAGCTTTTGTAATGTAAC 58.004 33.333 0.00 0.00 0.00 2.50
5951 6100 1.379044 GTCTGGGGTGATGCAAGGG 60.379 63.158 0.00 0.00 0.00 3.95
6061 6211 0.320334 TTCAACTGCTCGGCGATTCA 60.320 50.000 11.27 10.93 0.00 2.57
6063 6213 2.103042 AACTGCTCGGCGATTCAGC 61.103 57.895 27.78 20.92 0.00 4.26
6064 6214 3.624300 CTGCTCGGCGATTCAGCG 61.624 66.667 20.77 6.77 35.81 5.18
6066 6216 2.278596 GCTCGGCGATTCAGCGTA 60.279 61.111 11.27 0.00 38.18 4.42
6067 6217 1.661821 GCTCGGCGATTCAGCGTAT 60.662 57.895 11.27 0.00 38.18 3.06
6072 6222 0.531974 GGCGATTCAGCGTATGGGAA 60.532 55.000 0.00 0.00 38.18 3.97
6073 6223 0.861837 GCGATTCAGCGTATGGGAAG 59.138 55.000 0.00 0.00 0.00 3.46
6077 6227 0.981183 TTCAGCGTATGGGAAGTGGT 59.019 50.000 0.00 0.00 0.00 4.16
6078 6228 0.981183 TCAGCGTATGGGAAGTGGTT 59.019 50.000 0.00 0.00 0.00 3.67
6079 6229 1.066430 TCAGCGTATGGGAAGTGGTTC 60.066 52.381 0.00 0.00 0.00 3.62
6101 6251 3.815401 CCCTGAGTCGTCTGAAATTGTTT 59.185 43.478 0.00 0.00 0.00 2.83
6102 6252 4.319766 CCCTGAGTCGTCTGAAATTGTTTG 60.320 45.833 0.00 0.00 0.00 2.93
6103 6253 4.209452 TGAGTCGTCTGAAATTGTTTGC 57.791 40.909 0.00 0.00 0.00 3.68
6111 6261 4.268405 GTCTGAAATTGTTTGCCTGTGTTG 59.732 41.667 0.00 0.00 0.00 3.33
6112 6262 2.935201 TGAAATTGTTTGCCTGTGTTGC 59.065 40.909 0.00 0.00 0.00 4.17
6113 6263 2.985957 AATTGTTTGCCTGTGTTGCT 57.014 40.000 0.00 0.00 0.00 3.91
6114 6264 2.228138 ATTGTTTGCCTGTGTTGCTG 57.772 45.000 0.00 0.00 0.00 4.41
6115 6265 0.894141 TTGTTTGCCTGTGTTGCTGT 59.106 45.000 0.00 0.00 0.00 4.40
6116 6266 1.756430 TGTTTGCCTGTGTTGCTGTA 58.244 45.000 0.00 0.00 0.00 2.74
6126 6282 3.348119 TGTGTTGCTGTAGAACAAACCA 58.652 40.909 0.00 0.00 35.15 3.67
6148 6304 2.983592 CGGCTGTGGGGTTGGTTC 60.984 66.667 0.00 0.00 0.00 3.62
6158 6314 1.372872 GGTTGGTTCGGTTGCATGC 60.373 57.895 11.82 11.82 0.00 4.06
6159 6315 1.361993 GTTGGTTCGGTTGCATGCA 59.638 52.632 18.46 18.46 0.00 3.96
6166 6322 1.171549 TCGGTTGCATGCATGTGTGT 61.172 50.000 26.79 0.00 0.00 3.72
6328 6494 1.751349 GACATGGCCCCATCATTGCC 61.751 60.000 0.00 0.00 45.56 4.52
6333 6499 1.152398 GCCCCATCATTGCCAGGAT 60.152 57.895 0.00 0.00 0.00 3.24
6334 6500 1.183676 GCCCCATCATTGCCAGGATC 61.184 60.000 0.00 0.00 0.00 3.36
6364 6530 3.353836 CCGTGCTCCGTTGGGTTG 61.354 66.667 0.00 0.00 33.66 3.77
6365 6531 3.353836 CGTGCTCCGTTGGGTTGG 61.354 66.667 0.00 0.00 33.83 3.77
6366 6532 2.983592 GTGCTCCGTTGGGTTGGG 60.984 66.667 0.00 0.00 33.83 4.12
6367 6533 3.494254 TGCTCCGTTGGGTTGGGT 61.494 61.111 0.00 0.00 33.83 4.51
6368 6534 2.203437 GCTCCGTTGGGTTGGGTT 60.203 61.111 0.00 0.00 33.83 4.11
6369 6535 2.265904 GCTCCGTTGGGTTGGGTTC 61.266 63.158 0.00 0.00 33.83 3.62
6370 6536 1.602605 CTCCGTTGGGTTGGGTTCC 60.603 63.158 0.00 0.00 33.83 3.62
6373 6539 1.460273 CCGTTGGGTTGGGTTCCTTG 61.460 60.000 0.00 0.00 0.00 3.61
6405 6571 1.021390 ATCTTTGTTGAGGCCGCTCG 61.021 55.000 8.34 0.00 0.00 5.03
6406 6572 1.667830 CTTTGTTGAGGCCGCTCGA 60.668 57.895 8.34 0.00 0.00 4.04
6407 6573 1.630244 CTTTGTTGAGGCCGCTCGAG 61.630 60.000 8.45 8.45 0.00 4.04
6408 6574 3.589654 TTGTTGAGGCCGCTCGAGG 62.590 63.158 15.58 0.00 0.00 4.63
6417 6583 3.312709 CCGCTCGAGGCAAATTTTC 57.687 52.632 15.58 0.00 41.91 2.29
6418 6584 0.521242 CCGCTCGAGGCAAATTTTCG 60.521 55.000 15.58 5.45 41.91 3.46
6419 6585 0.165944 CGCTCGAGGCAAATTTTCGT 59.834 50.000 15.58 0.00 41.91 3.85
6420 6586 1.606606 GCTCGAGGCAAATTTTCGTG 58.393 50.000 15.58 8.83 41.35 4.35
6421 6587 1.069227 GCTCGAGGCAAATTTTCGTGT 60.069 47.619 15.58 0.00 41.35 4.49
6422 6588 2.604614 GCTCGAGGCAAATTTTCGTGTT 60.605 45.455 15.58 0.00 41.35 3.32
6423 6589 3.628017 CTCGAGGCAAATTTTCGTGTTT 58.372 40.909 3.91 0.00 35.90 2.83
6424 6590 4.035278 TCGAGGCAAATTTTCGTGTTTT 57.965 36.364 9.81 0.00 35.90 2.43
6425 6591 3.794028 TCGAGGCAAATTTTCGTGTTTTG 59.206 39.130 9.81 0.00 35.90 2.44
6426 6592 3.794028 CGAGGCAAATTTTCGTGTTTTGA 59.206 39.130 3.17 0.00 33.24 2.69
6427 6593 4.317069 CGAGGCAAATTTTCGTGTTTTGAC 60.317 41.667 3.17 0.00 38.40 3.18
6428 6594 3.868661 AGGCAAATTTTCGTGTTTTGACC 59.131 39.130 0.00 0.00 38.81 4.02
6429 6595 3.868661 GGCAAATTTTCGTGTTTTGACCT 59.131 39.130 0.00 0.00 33.22 3.85
6430 6596 4.331443 GGCAAATTTTCGTGTTTTGACCTT 59.669 37.500 0.00 0.00 33.22 3.50
6431 6597 5.163804 GGCAAATTTTCGTGTTTTGACCTTT 60.164 36.000 0.00 0.00 33.22 3.11
6432 6598 6.310960 GCAAATTTTCGTGTTTTGACCTTTT 58.689 32.000 0.00 0.00 33.24 2.27
6433 6599 6.799441 GCAAATTTTCGTGTTTTGACCTTTTT 59.201 30.769 0.00 0.00 33.24 1.94
6482 6648 9.620259 ACCTAGTTTGAATTATCTTTGAGATCC 57.380 33.333 0.00 0.00 36.20 3.36
6483 6649 8.768955 CCTAGTTTGAATTATCTTTGAGATCCG 58.231 37.037 0.00 0.00 36.20 4.18
6484 6650 9.534565 CTAGTTTGAATTATCTTTGAGATCCGA 57.465 33.333 0.00 0.00 36.20 4.55
6485 6651 8.202745 AGTTTGAATTATCTTTGAGATCCGAC 57.797 34.615 0.00 0.00 36.20 4.79
6486 6652 7.281100 AGTTTGAATTATCTTTGAGATCCGACC 59.719 37.037 0.00 0.00 36.20 4.79
6487 6653 5.611374 TGAATTATCTTTGAGATCCGACCC 58.389 41.667 0.00 0.00 36.20 4.46
6488 6654 5.366768 TGAATTATCTTTGAGATCCGACCCT 59.633 40.000 0.00 0.00 36.20 4.34
6489 6655 5.896073 ATTATCTTTGAGATCCGACCCTT 57.104 39.130 0.00 0.00 36.20 3.95
6490 6656 5.693769 TTATCTTTGAGATCCGACCCTTT 57.306 39.130 0.00 0.00 36.20 3.11
6491 6657 4.576330 ATCTTTGAGATCCGACCCTTTT 57.424 40.909 0.00 0.00 25.75 2.27
6492 6658 3.674997 TCTTTGAGATCCGACCCTTTTG 58.325 45.455 0.00 0.00 0.00 2.44
6493 6659 1.821216 TTGAGATCCGACCCTTTTGC 58.179 50.000 0.00 0.00 0.00 3.68
6494 6660 0.984230 TGAGATCCGACCCTTTTGCT 59.016 50.000 0.00 0.00 0.00 3.91
6495 6661 2.184533 TGAGATCCGACCCTTTTGCTA 58.815 47.619 0.00 0.00 0.00 3.49
6496 6662 2.093658 TGAGATCCGACCCTTTTGCTAC 60.094 50.000 0.00 0.00 0.00 3.58
6497 6663 1.209747 AGATCCGACCCTTTTGCTACC 59.790 52.381 0.00 0.00 0.00 3.18
6498 6664 0.107848 ATCCGACCCTTTTGCTACCG 60.108 55.000 0.00 0.00 0.00 4.02
6499 6665 2.396157 CCGACCCTTTTGCTACCGC 61.396 63.158 0.00 0.00 0.00 5.68
6500 6666 2.396157 CGACCCTTTTGCTACCGCC 61.396 63.158 0.00 0.00 34.43 6.13
6501 6667 1.302993 GACCCTTTTGCTACCGCCA 60.303 57.895 0.00 0.00 34.43 5.69
6502 6668 1.303317 ACCCTTTTGCTACCGCCAG 60.303 57.895 0.00 0.00 34.43 4.85
6503 6669 1.002624 CCCTTTTGCTACCGCCAGA 60.003 57.895 0.00 0.00 34.43 3.86
6504 6670 0.608035 CCCTTTTGCTACCGCCAGAA 60.608 55.000 0.00 0.00 34.43 3.02
6505 6671 1.463674 CCTTTTGCTACCGCCAGAAT 58.536 50.000 0.00 0.00 34.43 2.40
6506 6672 1.401905 CCTTTTGCTACCGCCAGAATC 59.598 52.381 0.00 0.00 34.43 2.52
6507 6673 1.401905 CTTTTGCTACCGCCAGAATCC 59.598 52.381 0.00 0.00 34.43 3.01
6508 6674 0.326595 TTTGCTACCGCCAGAATCCA 59.673 50.000 0.00 0.00 34.43 3.41
6509 6675 0.546122 TTGCTACCGCCAGAATCCAT 59.454 50.000 0.00 0.00 34.43 3.41
6510 6676 0.179048 TGCTACCGCCAGAATCCATG 60.179 55.000 0.00 0.00 34.43 3.66
6511 6677 0.886490 GCTACCGCCAGAATCCATGG 60.886 60.000 4.97 4.97 41.04 3.66
6512 6678 0.469917 CTACCGCCAGAATCCATGGT 59.530 55.000 12.58 0.00 40.17 3.55
6513 6679 0.180171 TACCGCCAGAATCCATGGTG 59.820 55.000 12.58 1.95 45.94 4.17
6518 6684 2.787994 GCCAGAATCCATGGTGATAGG 58.212 52.381 12.58 10.89 40.17 2.57
6519 6685 2.553904 GCCAGAATCCATGGTGATAGGG 60.554 54.545 12.58 8.97 40.17 3.53
6520 6686 2.713167 CCAGAATCCATGGTGATAGGGT 59.287 50.000 12.58 0.00 32.85 4.34
6521 6687 3.244700 CCAGAATCCATGGTGATAGGGTC 60.245 52.174 12.58 0.00 32.85 4.46
6522 6688 3.649981 CAGAATCCATGGTGATAGGGTCT 59.350 47.826 12.58 1.55 0.00 3.85
6523 6689 4.840680 CAGAATCCATGGTGATAGGGTCTA 59.159 45.833 12.58 0.00 0.00 2.59
6524 6690 5.307976 CAGAATCCATGGTGATAGGGTCTAA 59.692 44.000 12.58 0.00 0.00 2.10
6525 6691 5.911178 AGAATCCATGGTGATAGGGTCTAAA 59.089 40.000 12.58 0.00 0.00 1.85
6526 6692 5.568620 ATCCATGGTGATAGGGTCTAAAC 57.431 43.478 12.58 0.00 0.00 2.01
6527 6693 4.367166 TCCATGGTGATAGGGTCTAAACA 58.633 43.478 12.58 0.00 0.00 2.83
6528 6694 4.408921 TCCATGGTGATAGGGTCTAAACAG 59.591 45.833 12.58 0.00 0.00 3.16
6529 6695 3.906720 TGGTGATAGGGTCTAAACAGC 57.093 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 62 7.518188 AGAGAGTTTTATAGAGAGGGAGAGAG 58.482 42.308 0.00 0.00 0.00 3.20
65 69 6.490040 CAGGAGGAGAGAGTTTTATAGAGAGG 59.510 46.154 0.00 0.00 0.00 3.69
620 626 8.689972 AGCATCTGAGAAAGAAAAGAAAAAGAA 58.310 29.630 0.00 0.00 38.79 2.52
621 627 8.230472 AGCATCTGAGAAAGAAAAGAAAAAGA 57.770 30.769 0.00 0.00 38.79 2.52
622 628 8.868635 AAGCATCTGAGAAAGAAAAGAAAAAG 57.131 30.769 0.00 0.00 38.79 2.27
690 696 2.193306 ATGCGAAATAAAGCGGCAAG 57.807 45.000 1.45 0.00 37.15 4.01
727 733 8.807118 GGGGAGAAAATAAGAACAGAAAAAGAT 58.193 33.333 0.00 0.00 0.00 2.40
728 734 8.004801 AGGGGAGAAAATAAGAACAGAAAAAGA 58.995 33.333 0.00 0.00 0.00 2.52
729 735 8.084684 CAGGGGAGAAAATAAGAACAGAAAAAG 58.915 37.037 0.00 0.00 0.00 2.27
738 745 2.026262 AGCGCAGGGGAGAAAATAAGAA 60.026 45.455 11.47 0.00 0.00 2.52
759 766 1.915489 AGCATGTGGGGATGAACAGTA 59.085 47.619 0.00 0.00 0.00 2.74
780 787 3.126831 GGGATAAGCAGATGAACAGACG 58.873 50.000 0.00 0.00 0.00 4.18
826 845 1.942657 GTGTGAGCTTGAAGTTCAGCA 59.057 47.619 12.09 10.28 36.12 4.41
828 847 2.473816 TCGTGTGAGCTTGAAGTTCAG 58.526 47.619 12.09 1.53 36.12 3.02
835 869 1.066858 GGAGGATTCGTGTGAGCTTGA 60.067 52.381 0.00 0.00 0.00 3.02
837 871 0.250513 GGGAGGATTCGTGTGAGCTT 59.749 55.000 0.00 0.00 0.00 3.74
838 872 1.901085 GGGAGGATTCGTGTGAGCT 59.099 57.895 0.00 0.00 0.00 4.09
839 873 1.519455 CGGGAGGATTCGTGTGAGC 60.519 63.158 0.00 0.00 0.00 4.26
841 875 4.107029 ACGGGAGGATTCGTGTGA 57.893 55.556 0.00 0.00 38.25 3.58
845 879 0.246635 CAGAACACGGGAGGATTCGT 59.753 55.000 0.00 0.00 40.49 3.85
846 880 0.246635 ACAGAACACGGGAGGATTCG 59.753 55.000 0.00 0.00 34.27 3.34
847 881 2.474410 AACAGAACACGGGAGGATTC 57.526 50.000 0.00 0.00 0.00 2.52
848 882 2.951229 AAACAGAACACGGGAGGATT 57.049 45.000 0.00 0.00 0.00 3.01
849 883 2.105821 TGAAAACAGAACACGGGAGGAT 59.894 45.455 0.00 0.00 0.00 3.24
850 884 1.487142 TGAAAACAGAACACGGGAGGA 59.513 47.619 0.00 0.00 0.00 3.71
851 885 1.873591 CTGAAAACAGAACACGGGAGG 59.126 52.381 0.00 0.00 0.00 4.30
852 886 2.833794 TCTGAAAACAGAACACGGGAG 58.166 47.619 0.00 0.00 0.00 4.30
853 887 2.992124 TCTGAAAACAGAACACGGGA 57.008 45.000 0.00 0.00 0.00 5.14
854 888 3.138304 TCATCTGAAAACAGAACACGGG 58.862 45.455 4.09 0.00 34.56 5.28
855 889 4.058124 TCTCATCTGAAAACAGAACACGG 58.942 43.478 4.09 0.00 34.56 4.94
856 890 5.657470 TTCTCATCTGAAAACAGAACACG 57.343 39.130 4.09 0.00 34.56 4.49
857 891 5.447573 GCTTCTCATCTGAAAACAGAACAC 58.552 41.667 4.09 0.00 34.56 3.32
865 899 1.078709 CGCCGCTTCTCATCTGAAAA 58.921 50.000 0.00 0.00 0.00 2.29
978 1012 1.016653 GGGCTCGCTTTCACTCTGTC 61.017 60.000 0.00 0.00 0.00 3.51
984 1018 2.044946 ATGGGGGCTCGCTTTCAC 60.045 61.111 0.97 0.00 0.00 3.18
1078 1112 4.209495 GGTATTTTTCTCTTCGGATCGAGC 59.791 45.833 0.00 0.00 37.14 5.03
1087 1121 7.941919 ACAGAAAAGTGGGTATTTTTCTCTTC 58.058 34.615 8.73 0.00 44.58 2.87
1326 1366 2.270434 AGTTATGGAGGAGGAAGGCA 57.730 50.000 0.00 0.00 0.00 4.75
1331 1375 2.317900 TCAGGGAAGTTATGGAGGAGGA 59.682 50.000 0.00 0.00 0.00 3.71
1340 1384 5.131142 CCACCTACAAGATCAGGGAAGTTAT 59.869 44.000 0.00 0.00 36.15 1.89
1400 1445 1.521764 AGCATATGTGGGTGGATGGA 58.478 50.000 4.29 0.00 0.00 3.41
1408 1453 1.490490 ACTGGTGGTAGCATATGTGGG 59.510 52.381 4.29 0.00 0.00 4.61
1421 1466 1.295423 CGGGAAGTGGTACTGGTGG 59.705 63.158 0.00 0.00 0.00 4.61
1422 1467 0.395312 AACGGGAAGTGGTACTGGTG 59.605 55.000 0.00 0.00 0.00 4.17
1487 1535 2.165030 CCAACAGATTCATGGCAGTTCC 59.835 50.000 0.00 0.00 0.00 3.62
1505 1553 0.467290 AAAGAGGGCGCAAGAACCAA 60.467 50.000 10.83 0.00 43.02 3.67
1506 1554 0.467290 AAAAGAGGGCGCAAGAACCA 60.467 50.000 10.83 0.00 43.02 3.67
1516 1564 5.853936 ACAAAATCAGGTTAAAAAGAGGGC 58.146 37.500 0.00 0.00 0.00 5.19
1617 1665 1.218316 GTCTGGAGCTGGGTTACCG 59.782 63.158 0.00 0.00 40.75 4.02
1634 1682 4.278310 GCCCCACCATAATAACAGAAAGT 58.722 43.478 0.00 0.00 0.00 2.66
1635 1683 3.636764 GGCCCCACCATAATAACAGAAAG 59.363 47.826 0.00 0.00 38.86 2.62
1660 1708 1.225855 GAACACATGAGCACCGACAA 58.774 50.000 0.00 0.00 0.00 3.18
1787 1836 1.228769 AGTGTACCGGAGCTGACCA 60.229 57.895 9.46 0.00 0.00 4.02
1804 1853 4.528674 CCACCGGCATGAAGAGAG 57.471 61.111 0.00 0.00 0.00 3.20
1850 1899 5.473039 CCAAAAACCTGGCATTTTCTAGAG 58.527 41.667 7.59 0.00 0.00 2.43
1871 1920 2.650322 GAAGAGTCAAACACAACCCCA 58.350 47.619 0.00 0.00 0.00 4.96
1915 1964 2.359975 GGAGACCAAGGTTGCCGG 60.360 66.667 0.00 0.00 0.00 6.13
1973 2022 7.439655 CCAGGTGTAGAGATATAGAAACTTTGC 59.560 40.741 0.00 0.00 0.00 3.68
1983 2032 5.655394 AGCAATCCCAGGTGTAGAGATATA 58.345 41.667 0.00 0.00 0.00 0.86
1984 2033 4.497516 AGCAATCCCAGGTGTAGAGATAT 58.502 43.478 0.00 0.00 0.00 1.63
1985 2034 3.898123 GAGCAATCCCAGGTGTAGAGATA 59.102 47.826 0.00 0.00 0.00 1.98
2050 2099 1.227089 AGCACGCTCCGATTAGCAG 60.227 57.895 5.45 1.65 42.91 4.24
2226 2331 1.597027 ACGTTTCTCCGCACCAAGG 60.597 57.895 0.00 0.00 0.00 3.61
2227 2332 1.569493 CACGTTTCTCCGCACCAAG 59.431 57.895 0.00 0.00 0.00 3.61
2229 2334 2.970324 GCACGTTTCTCCGCACCA 60.970 61.111 0.00 0.00 0.00 4.17
2248 2353 0.895530 GGCTAAGGGGAACAAAAGCC 59.104 55.000 0.00 0.00 40.87 4.35
2270 2375 4.876107 GTGATTTGGCTATCGAGGAGAAAA 59.124 41.667 1.39 2.22 0.00 2.29
2320 2425 0.694771 AGGAGAAACTGCAGCATCCA 59.305 50.000 22.01 0.00 0.00 3.41
2321 2426 1.093159 CAGGAGAAACTGCAGCATCC 58.907 55.000 15.27 15.50 0.00 3.51
2324 2429 2.928801 TAACAGGAGAAACTGCAGCA 57.071 45.000 15.27 0.00 42.21 4.41
2355 2460 5.532032 TGCAACACTAAAACTAAAGTACCCC 59.468 40.000 0.00 0.00 0.00 4.95
2357 2462 7.114388 GCATTGCAACACTAAAACTAAAGTACC 59.886 37.037 0.00 0.00 0.00 3.34
2358 2463 7.646130 TGCATTGCAACACTAAAACTAAAGTAC 59.354 33.333 9.33 0.00 34.76 2.73
2359 2464 7.708051 TGCATTGCAACACTAAAACTAAAGTA 58.292 30.769 9.33 0.00 34.76 2.24
2395 2500 1.229951 AGAAGACCAGCCCCCATGA 60.230 57.895 0.00 0.00 0.00 3.07
2401 2506 0.402121 AAGGTTCAGAAGACCAGCCC 59.598 55.000 0.00 0.00 0.00 5.19
2406 2511 2.037772 TGCTCAGAAGGTTCAGAAGACC 59.962 50.000 0.00 0.00 0.00 3.85
2485 2591 6.017400 ACAACCACAAAGATAGCTTTCATG 57.983 37.500 2.25 5.24 42.27 3.07
2547 2653 1.237285 AAGCCTACAAGCAAGCCACG 61.237 55.000 0.00 0.00 34.23 4.94
2759 2876 8.448008 AGAAGCAGGTATGATTTCCCAATATAA 58.552 33.333 0.00 0.00 34.53 0.98
2760 2877 7.988937 AGAAGCAGGTATGATTTCCCAATATA 58.011 34.615 0.00 0.00 34.53 0.86
2761 2878 6.856757 AGAAGCAGGTATGATTTCCCAATAT 58.143 36.000 0.00 0.00 34.53 1.28
2762 2879 6.266131 AGAAGCAGGTATGATTTCCCAATA 57.734 37.500 0.00 0.00 34.53 1.90
2763 2880 5.134725 AGAAGCAGGTATGATTTCCCAAT 57.865 39.130 0.00 0.00 34.53 3.16
2764 2881 4.591321 AGAAGCAGGTATGATTTCCCAA 57.409 40.909 0.00 0.00 34.53 4.12
2765 2882 4.018506 TGAAGAAGCAGGTATGATTTCCCA 60.019 41.667 0.00 0.00 34.53 4.37
2766 2883 4.526970 TGAAGAAGCAGGTATGATTTCCC 58.473 43.478 0.00 0.00 34.53 3.97
2767 2884 5.431765 TCTGAAGAAGCAGGTATGATTTCC 58.568 41.667 0.00 0.00 34.53 3.13
2768 2885 6.992063 TTCTGAAGAAGCAGGTATGATTTC 57.008 37.500 0.00 0.00 34.53 2.17
2769 2886 6.998968 CTTCTGAAGAAGCAGGTATGATTT 57.001 37.500 12.01 0.00 44.10 2.17
2782 2899 6.114187 TCTGAAATAGGCACTTCTGAAGAA 57.886 37.500 23.36 0.00 41.75 2.52
2783 2900 5.247110 ACTCTGAAATAGGCACTTCTGAAGA 59.753 40.000 23.36 1.29 41.75 2.87
2784 2901 5.486526 ACTCTGAAATAGGCACTTCTGAAG 58.513 41.667 15.59 15.59 41.75 3.02
2785 2902 5.489792 ACTCTGAAATAGGCACTTCTGAA 57.510 39.130 0.00 0.00 41.75 3.02
2786 2903 5.489792 AACTCTGAAATAGGCACTTCTGA 57.510 39.130 0.00 0.00 41.75 3.27
2787 2904 6.205464 TCAAAACTCTGAAATAGGCACTTCTG 59.795 38.462 0.00 0.00 41.75 3.02
2788 2905 6.299141 TCAAAACTCTGAAATAGGCACTTCT 58.701 36.000 0.00 0.00 41.75 2.85
2789 2906 6.560253 TCAAAACTCTGAAATAGGCACTTC 57.440 37.500 0.00 0.00 41.75 3.01
2790 2907 7.530426 AATCAAAACTCTGAAATAGGCACTT 57.470 32.000 0.00 0.00 41.75 3.16
2791 2908 7.530426 AAATCAAAACTCTGAAATAGGCACT 57.470 32.000 0.00 0.00 46.37 4.40
2792 2909 7.116805 CCAAAATCAAAACTCTGAAATAGGCAC 59.883 37.037 0.00 0.00 0.00 5.01
2793 2910 7.015098 TCCAAAATCAAAACTCTGAAATAGGCA 59.985 33.333 0.00 0.00 0.00 4.75
2794 2911 7.329471 GTCCAAAATCAAAACTCTGAAATAGGC 59.671 37.037 0.00 0.00 0.00 3.93
2795 2912 8.579863 AGTCCAAAATCAAAACTCTGAAATAGG 58.420 33.333 0.00 0.00 0.00 2.57
2798 2915 9.750125 GTTAGTCCAAAATCAAAACTCTGAAAT 57.250 29.630 0.00 0.00 0.00 2.17
2799 2916 8.744652 TGTTAGTCCAAAATCAAAACTCTGAAA 58.255 29.630 0.00 0.00 0.00 2.69
2800 2917 8.287439 TGTTAGTCCAAAATCAAAACTCTGAA 57.713 30.769 0.00 0.00 0.00 3.02
2801 2918 7.873719 TGTTAGTCCAAAATCAAAACTCTGA 57.126 32.000 0.00 0.00 0.00 3.27
2802 2919 8.925161 TTTGTTAGTCCAAAATCAAAACTCTG 57.075 30.769 0.00 0.00 31.66 3.35
2916 3033 2.159324 GCTTTGGCTAGGCAGATGAAAC 60.159 50.000 19.32 2.74 35.22 2.78
2937 3054 1.556911 ACACTCAATAGGCACTGGGAG 59.443 52.381 0.00 0.00 41.52 4.30
3000 3118 9.158233 CATTTTGTTATGCAGGAAGATGAATTT 57.842 29.630 0.00 0.00 0.00 1.82
3003 3121 7.465353 TCATTTTGTTATGCAGGAAGATGAA 57.535 32.000 0.00 0.00 0.00 2.57
3136 3254 5.360591 CGAAGTACTAATTCTGGCCAAGAT 58.639 41.667 7.01 0.00 33.93 2.40
3474 3593 3.961408 CAGATACCAACCTAGCCTAGTGT 59.039 47.826 0.00 0.00 0.00 3.55
3480 3599 5.484290 ACCATATACAGATACCAACCTAGCC 59.516 44.000 0.00 0.00 0.00 3.93
3482 3601 8.251721 GCTTACCATATACAGATACCAACCTAG 58.748 40.741 0.00 0.00 0.00 3.02
3485 3604 6.874134 CAGCTTACCATATACAGATACCAACC 59.126 42.308 0.00 0.00 0.00 3.77
3490 3609 9.823647 AATATGCAGCTTACCATATACAGATAC 57.176 33.333 10.20 0.00 34.47 2.24
3713 3832 0.240945 GCAATTGTGTCCAAGACCCG 59.759 55.000 7.40 0.00 33.17 5.28
3785 3904 0.320771 GGTACAGTGTCTGCCAGGTG 60.321 60.000 0.00 0.00 34.37 4.00
4309 4428 0.322816 GCTCTTCCAGGCATTGTGGA 60.323 55.000 0.00 0.00 42.62 4.02
4360 4479 7.710676 TCCCTATATGATAAAGCAGAGAGAC 57.289 40.000 0.00 0.00 0.00 3.36
4374 4493 4.566837 AGGTGGTGATGTTCCCTATATGA 58.433 43.478 0.00 0.00 0.00 2.15
4381 4500 1.256812 CCAAAGGTGGTGATGTTCCC 58.743 55.000 0.00 0.00 40.42 3.97
4399 4518 8.909708 TTTTCAATCATGACAATATTCGAACC 57.090 30.769 0.00 0.00 34.61 3.62
4416 4535 9.681692 AAAAGGCATAAAAGCAAATTTTCAATC 57.318 25.926 0.00 0.00 41.40 2.67
4435 4554 2.955660 CAGGGACAACACTAAAAAGGCA 59.044 45.455 0.00 0.00 0.00 4.75
4443 4562 5.046159 CCCAAGTAATACAGGGACAACACTA 60.046 44.000 13.62 0.00 44.30 2.74
4444 4563 4.263331 CCCAAGTAATACAGGGACAACACT 60.263 45.833 13.62 0.00 44.30 3.55
4445 4564 4.007659 CCCAAGTAATACAGGGACAACAC 58.992 47.826 13.62 0.00 44.30 3.32
4494 4614 5.797934 CGAGTAAAGTCTTGCTGTAAGAGAG 59.202 44.000 8.50 0.00 45.71 3.20
4581 4701 0.665068 TTTGAGCTGCTGCAATTGCG 60.665 50.000 24.58 19.32 45.83 4.85
5566 5686 6.153510 GGTCTGCTGTATCATCATCTGGTATA 59.846 42.308 0.00 0.00 0.00 1.47
5781 5929 5.796424 ATTATTGCCCATCCAAGATGAAC 57.204 39.130 6.15 0.00 0.00 3.18
5788 5936 2.616376 CGACGAATTATTGCCCATCCAA 59.384 45.455 0.00 0.00 0.00 3.53
5797 5945 6.255020 ACTTACCTACAAGCGACGAATTATTG 59.745 38.462 0.00 0.00 0.00 1.90
5826 5974 3.012518 CCATAGACAAGTCTTGCCCAAG 58.987 50.000 12.66 1.62 40.93 3.61
5827 5975 2.879756 GCCATAGACAAGTCTTGCCCAA 60.880 50.000 12.66 0.00 40.93 4.12
5828 5976 1.340017 GCCATAGACAAGTCTTGCCCA 60.340 52.381 12.66 0.00 40.93 5.36
5861 6009 2.806244 ACAAAAGCTAACTACCACTGCG 59.194 45.455 0.00 0.00 0.00 5.18
5890 6039 0.787787 CAACGACCACCATACACACG 59.212 55.000 0.00 0.00 0.00 4.49
5951 6100 1.429148 CCGCCGGTCAGCAATCTAAC 61.429 60.000 1.90 0.00 0.00 2.34
6015 6165 6.872585 ACCCAAATTCCATTACAACATCAT 57.127 33.333 0.00 0.00 0.00 2.45
6016 6166 6.462500 CAACCCAAATTCCATTACAACATCA 58.538 36.000 0.00 0.00 0.00 3.07
6061 6211 0.252197 GGAACCACTTCCCATACGCT 59.748 55.000 0.00 0.00 40.38 5.07
6077 6227 3.071023 ACAATTTCAGACGACTCAGGGAA 59.929 43.478 0.00 0.00 0.00 3.97
6078 6228 2.632996 ACAATTTCAGACGACTCAGGGA 59.367 45.455 0.00 0.00 0.00 4.20
6079 6229 3.045601 ACAATTTCAGACGACTCAGGG 57.954 47.619 0.00 0.00 0.00 4.45
6080 6230 4.776743 CAAACAATTTCAGACGACTCAGG 58.223 43.478 0.00 0.00 0.00 3.86
6081 6231 4.214437 GCAAACAATTTCAGACGACTCAG 58.786 43.478 0.00 0.00 0.00 3.35
6082 6232 3.003275 GGCAAACAATTTCAGACGACTCA 59.997 43.478 0.00 0.00 0.00 3.41
6084 6234 3.003689 CAGGCAAACAATTTCAGACGACT 59.996 43.478 0.00 0.00 0.00 4.18
6101 6251 1.134250 TGTTCTACAGCAACACAGGCA 60.134 47.619 0.00 0.00 0.00 4.75
6102 6252 1.593196 TGTTCTACAGCAACACAGGC 58.407 50.000 0.00 0.00 0.00 4.85
6103 6253 3.243068 GGTTTGTTCTACAGCAACACAGG 60.243 47.826 0.00 0.00 33.42 4.00
6111 6261 1.529865 GACCGTGGTTTGTTCTACAGC 59.470 52.381 0.00 0.00 0.00 4.40
6112 6262 1.790623 CGACCGTGGTTTGTTCTACAG 59.209 52.381 0.00 0.00 0.00 2.74
6113 6263 1.538634 CCGACCGTGGTTTGTTCTACA 60.539 52.381 0.00 0.00 0.00 2.74
6114 6264 1.142474 CCGACCGTGGTTTGTTCTAC 58.858 55.000 0.00 0.00 0.00 2.59
6115 6265 0.600782 GCCGACCGTGGTTTGTTCTA 60.601 55.000 0.00 0.00 0.00 2.10
6116 6266 1.890510 GCCGACCGTGGTTTGTTCT 60.891 57.895 0.00 0.00 0.00 3.01
6148 6304 1.004785 CACACACATGCATGCAACCG 61.005 55.000 26.68 18.18 0.00 4.44
6158 6314 1.268625 AGCTCAATGCACACACACATG 59.731 47.619 0.00 0.00 45.94 3.21
6159 6315 1.538512 GAGCTCAATGCACACACACAT 59.461 47.619 9.40 0.00 45.94 3.21
6166 6322 2.036571 CCGCTGAGCTCAATGCACA 61.037 57.895 23.16 0.00 45.94 4.57
6242 6399 2.160205 TGTGTGTCCTCCTCTTCTACG 58.840 52.381 0.00 0.00 0.00 3.51
6328 6494 2.738846 CGGCGAAATAATGGAGATCCTG 59.261 50.000 0.00 0.00 36.82 3.86
6333 6499 1.134521 AGCACGGCGAAATAATGGAGA 60.135 47.619 16.62 0.00 0.00 3.71
6334 6500 1.261619 GAGCACGGCGAAATAATGGAG 59.738 52.381 16.62 0.00 0.00 3.86
6364 6530 3.741476 CGCAGCTGCAAGGAACCC 61.741 66.667 36.03 5.81 42.21 4.11
6365 6531 3.741476 CCGCAGCTGCAAGGAACC 61.741 66.667 36.03 6.57 42.21 3.62
6366 6532 3.741476 CCCGCAGCTGCAAGGAAC 61.741 66.667 36.03 7.35 42.21 3.62
6405 6571 4.026062 GGTCAAAACACGAAAATTTGCCTC 60.026 41.667 0.00 0.00 34.77 4.70
6406 6572 3.868661 GGTCAAAACACGAAAATTTGCCT 59.131 39.130 0.00 0.00 34.77 4.75
6407 6573 3.868661 AGGTCAAAACACGAAAATTTGCC 59.131 39.130 0.00 2.01 34.77 4.52
6408 6574 5.463499 AAGGTCAAAACACGAAAATTTGC 57.537 34.783 0.00 0.00 34.77 3.68
6456 6622 9.620259 GGATCTCAAAGATAATTCAAACTAGGT 57.380 33.333 0.00 0.00 34.53 3.08
6457 6623 8.768955 CGGATCTCAAAGATAATTCAAACTAGG 58.231 37.037 0.00 0.00 34.53 3.02
6458 6624 9.534565 TCGGATCTCAAAGATAATTCAAACTAG 57.465 33.333 0.00 0.00 34.53 2.57
6459 6625 9.314321 GTCGGATCTCAAAGATAATTCAAACTA 57.686 33.333 0.00 0.00 34.53 2.24
6460 6626 7.281100 GGTCGGATCTCAAAGATAATTCAAACT 59.719 37.037 0.00 0.00 34.53 2.66
6461 6627 7.410485 GGTCGGATCTCAAAGATAATTCAAAC 58.590 38.462 0.00 0.00 34.53 2.93
6462 6628 6.542370 GGGTCGGATCTCAAAGATAATTCAAA 59.458 38.462 0.00 0.00 34.53 2.69
6463 6629 6.055588 GGGTCGGATCTCAAAGATAATTCAA 58.944 40.000 0.00 0.00 34.53 2.69
6464 6630 5.366768 AGGGTCGGATCTCAAAGATAATTCA 59.633 40.000 0.00 0.00 34.53 2.57
6465 6631 5.859495 AGGGTCGGATCTCAAAGATAATTC 58.141 41.667 0.00 0.00 34.53 2.17
6466 6632 5.896073 AGGGTCGGATCTCAAAGATAATT 57.104 39.130 0.00 0.00 34.53 1.40
6467 6633 5.896073 AAGGGTCGGATCTCAAAGATAAT 57.104 39.130 0.00 0.00 34.53 1.28
6468 6634 5.693769 AAAGGGTCGGATCTCAAAGATAA 57.306 39.130 0.00 0.00 34.53 1.75
6469 6635 5.428253 CAAAAGGGTCGGATCTCAAAGATA 58.572 41.667 0.00 0.00 34.53 1.98
6470 6636 4.265073 CAAAAGGGTCGGATCTCAAAGAT 58.735 43.478 0.00 0.00 37.73 2.40
6471 6637 3.674997 CAAAAGGGTCGGATCTCAAAGA 58.325 45.455 0.00 0.00 0.00 2.52
6472 6638 2.162408 GCAAAAGGGTCGGATCTCAAAG 59.838 50.000 0.00 0.00 0.00 2.77
6473 6639 2.159382 GCAAAAGGGTCGGATCTCAAA 58.841 47.619 0.00 0.00 0.00 2.69
6474 6640 1.351017 AGCAAAAGGGTCGGATCTCAA 59.649 47.619 0.00 0.00 0.00 3.02
6475 6641 0.984230 AGCAAAAGGGTCGGATCTCA 59.016 50.000 0.00 0.00 0.00 3.27
6476 6642 2.552031 GTAGCAAAAGGGTCGGATCTC 58.448 52.381 0.00 0.00 0.00 2.75
6477 6643 1.209747 GGTAGCAAAAGGGTCGGATCT 59.790 52.381 0.00 0.00 0.00 2.75
6478 6644 1.664873 GGTAGCAAAAGGGTCGGATC 58.335 55.000 0.00 0.00 0.00 3.36
6479 6645 0.107848 CGGTAGCAAAAGGGTCGGAT 60.108 55.000 0.00 0.00 0.00 4.18
6480 6646 1.294138 CGGTAGCAAAAGGGTCGGA 59.706 57.895 0.00 0.00 0.00 4.55
6481 6647 2.396157 GCGGTAGCAAAAGGGTCGG 61.396 63.158 0.00 0.00 44.35 4.79
6482 6648 3.174788 GCGGTAGCAAAAGGGTCG 58.825 61.111 0.00 0.00 44.35 4.79
6492 6658 0.886490 CCATGGATTCTGGCGGTAGC 60.886 60.000 5.56 0.00 44.18 3.58
6493 6659 0.469917 ACCATGGATTCTGGCGGTAG 59.530 55.000 21.47 0.00 37.27 3.18
6494 6660 0.180171 CACCATGGATTCTGGCGGTA 59.820 55.000 21.47 0.00 37.27 4.02
6495 6661 1.077501 CACCATGGATTCTGGCGGT 60.078 57.895 21.47 0.00 37.27 5.68
6496 6662 0.179009 ATCACCATGGATTCTGGCGG 60.179 55.000 21.47 0.00 37.27 6.13
6497 6663 2.420642 CTATCACCATGGATTCTGGCG 58.579 52.381 21.47 0.00 37.27 5.69
6498 6664 2.553904 CCCTATCACCATGGATTCTGGC 60.554 54.545 21.47 0.00 37.27 4.85
6499 6665 2.713167 ACCCTATCACCATGGATTCTGG 59.287 50.000 21.47 14.03 39.80 3.86
6500 6666 3.649981 AGACCCTATCACCATGGATTCTG 59.350 47.826 21.47 6.20 0.00 3.02
6501 6667 3.946824 AGACCCTATCACCATGGATTCT 58.053 45.455 21.47 4.71 0.00 2.40
6502 6668 5.825593 TTAGACCCTATCACCATGGATTC 57.174 43.478 21.47 2.42 0.00 2.52
6503 6669 5.431731 TGTTTAGACCCTATCACCATGGATT 59.568 40.000 21.47 4.85 0.00 3.01
6504 6670 4.975147 TGTTTAGACCCTATCACCATGGAT 59.025 41.667 21.47 4.75 0.00 3.41
6505 6671 4.367166 TGTTTAGACCCTATCACCATGGA 58.633 43.478 21.47 0.00 0.00 3.41
6506 6672 4.708177 CTGTTTAGACCCTATCACCATGG 58.292 47.826 11.19 11.19 0.00 3.66
6507 6673 4.130118 GCTGTTTAGACCCTATCACCATG 58.870 47.826 0.00 0.00 0.00 3.66
6508 6674 4.423625 GCTGTTTAGACCCTATCACCAT 57.576 45.455 0.00 0.00 0.00 3.55
6509 6675 3.906720 GCTGTTTAGACCCTATCACCA 57.093 47.619 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.