Multiple sequence alignment - TraesCS6A01G389200

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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 TraesCS6A01G389200 chr6A 100.000 3641 0 0 1 3641 604880022 604883662 0.000000e+00 6724
1 TraesCS6A01G389200 chr6A 93.578 218 8 2 3379 3596 616824974 616825185 1.630000e-83 320
2 TraesCS6A01G389200 chr6B 91.224 1413 82 20 1 1378 697761268 697759863 0.000000e+00 1884
3 TraesCS6A01G389200 chr6B 94.549 477 19 4 1423 1898 697759723 697759253 0.000000e+00 730
4 TraesCS6A01G389200 chr6B 84.667 600 52 19 1898 2471 697759062 697758477 2.450000e-156 562
5 TraesCS6A01G389200 chr6B 78.209 748 80 39 2509 3193 697758403 697757676 5.660000e-108 401
6 TraesCS6A01G389200 chr6D 89.862 1085 79 14 295 1358 458766669 458765595 0.000000e+00 1365
7 TraesCS6A01G389200 chr6D 88.972 535 30 3 1378 1888 458765531 458765002 5.130000e-178 634
8 TraesCS6A01G389200 chr6D 95.909 220 9 0 3377 3596 458762728 458762509 1.240000e-94 357
9 TraesCS6A01G389200 chr6D 89.062 256 17 7 2538 2787 458764226 458763976 1.270000e-79 307
10 TraesCS6A01G389200 chr6D 93.671 79 5 0 3108 3186 458763042 458762964 6.390000e-23 119
11 TraesCS6A01G389200 chr1A 82.538 922 101 29 1893 2766 389228289 389229198 0.000000e+00 756
12 TraesCS6A01G389200 chr1A 92.627 217 10 2 3380 3596 574279312 574279522 1.270000e-79 307
13 TraesCS6A01G389200 chr1A 92.202 218 11 2 3379 3596 592563370 592563581 1.640000e-78 303
14 TraesCS6A01G389200 chrUn 92.661 218 10 2 3379 3596 341585037 341585248 3.530000e-80 309
15 TraesCS6A01G389200 chr7A 92.661 218 10 2 3379 3596 103125673 103125884 3.530000e-80 309
16 TraesCS6A01G389200 chr4A 92.661 218 10 2 3379 3596 714758925 714759136 3.530000e-80 309
17 TraesCS6A01G389200 chr3A 92.661 218 10 2 3379 3596 739547519 739547730 3.530000e-80 309
18 TraesCS6A01G389200 chr3B 92.202 218 11 2 3379 3596 262587919 262587708 1.640000e-78 303


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 TraesCS6A01G389200 chr6A 604880022 604883662 3640 False 6724.00 6724 100.00000 1 3641 1 chr6A.!!$F1 3640
1 TraesCS6A01G389200 chr6B 697757676 697761268 3592 True 894.25 1884 87.16225 1 3193 4 chr6B.!!$R1 3192
2 TraesCS6A01G389200 chr6D 458762509 458766669 4160 True 556.40 1365 91.49520 295 3596 5 chr6D.!!$R1 3301
3 TraesCS6A01G389200 chr1A 389228289 389229198 909 False 756.00 756 82.53800 1893 2766 1 chr1A.!!$F1 873

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
179 184 0.106167 ACCTCTCTACTATGGCCGCA 60.106 55.0 0.0 0.0 0.0 5.69 F
953 970 0.174617 GTCCGCTTCCTCCTCTTCTG 59.825 60.0 0.0 0.0 0.0 3.02 F
956 973 0.174617 CGCTTCCTCCTCTTCTGGTC 59.825 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1204 1238 0.107654 GACCGGATTTCTCCACCCTG 60.108 60.0 9.46 0.0 42.19 4.45 R
2067 2548 0.175760 ATCGTTGTCCTGTGGATCCG 59.824 55.0 7.39 0.0 32.73 4.18 R
2817 3442 0.880278 TTCGTCTCCAACACAGCAGC 60.880 55.0 0.00 0.0 0.00 5.25 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
28 29 3.876274 AGATGTCGAGTTGCACAGTAT 57.124 42.857 0.00 0.00 0.00 2.12
41 42 2.739932 GCACAGTATGACCAGTAGGCAG 60.740 54.545 0.00 0.00 39.69 4.85
55 56 0.250640 AGGCAGGGCATCGATCATTC 60.251 55.000 0.00 0.00 0.00 2.67
179 184 0.106167 ACCTCTCTACTATGGCCGCA 60.106 55.000 0.00 0.00 0.00 5.69
230 235 5.175491 CCAACAAACACAGAAATGAAATCGG 59.825 40.000 0.00 0.00 0.00 4.18
285 290 3.951680 CCAGTACAACAATGGAATACCCC 59.048 47.826 0.00 0.00 36.09 4.95
326 331 2.939103 CCGAGGAGAAATGGTTAAGCTG 59.061 50.000 6.19 0.00 0.00 4.24
480 487 3.543536 GAGATCCGCCCTCCCATGC 62.544 68.421 0.00 0.00 0.00 4.06
553 560 2.335011 CATCTCGGCCGATGCGTA 59.665 61.111 31.19 12.40 38.85 4.42
554 561 2.016704 CATCTCGGCCGATGCGTAC 61.017 63.158 31.19 0.00 38.85 3.67
555 562 3.538028 ATCTCGGCCGATGCGTACG 62.538 63.158 31.19 15.53 38.85 3.67
567 576 2.185093 CGTACGTACCTTGGGGCC 59.815 66.667 19.67 0.00 35.63 5.80
715 724 3.052082 TGGTCGTCGGAGTCGGAC 61.052 66.667 18.32 18.32 39.90 4.79
727 736 3.664888 TCGGACGAGGGGAGGGAA 61.665 66.667 0.00 0.00 0.00 3.97
728 737 3.148279 CGGACGAGGGGAGGGAAG 61.148 72.222 0.00 0.00 0.00 3.46
729 738 2.363361 GGACGAGGGGAGGGAAGA 59.637 66.667 0.00 0.00 0.00 2.87
732 741 2.226149 GACGAGGGGAGGGAAGAGGA 62.226 65.000 0.00 0.00 0.00 3.71
734 743 1.074850 GAGGGGAGGGAAGAGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
735 744 2.770475 GGGGAGGGAAGAGGAGGC 60.770 72.222 0.00 0.00 0.00 4.70
736 745 2.770475 GGGAGGGAAGAGGAGGCC 60.770 72.222 0.00 0.00 0.00 5.19
737 746 3.157949 GGAGGGAAGAGGAGGCCG 61.158 72.222 0.00 0.00 0.00 6.13
738 747 2.042843 GAGGGAAGAGGAGGCCGA 60.043 66.667 0.00 0.00 0.00 5.54
739 748 2.042435 AGGGAAGAGGAGGCCGAG 60.042 66.667 0.00 0.00 0.00 4.63
740 749 2.042843 GGGAAGAGGAGGCCGAGA 60.043 66.667 0.00 0.00 0.00 4.04
741 750 2.428085 GGGAAGAGGAGGCCGAGAC 61.428 68.421 0.00 0.00 0.00 3.36
819 833 1.073897 GGCCCAACTGAGCTCAACT 59.926 57.895 18.85 4.52 0.00 3.16
820 834 0.538287 GGCCCAACTGAGCTCAACTT 60.538 55.000 18.85 9.11 0.00 2.66
822 836 2.619074 GGCCCAACTGAGCTCAACTTAT 60.619 50.000 18.85 0.00 0.00 1.73
823 837 3.370527 GGCCCAACTGAGCTCAACTTATA 60.371 47.826 18.85 0.00 0.00 0.98
830 844 2.777114 TGAGCTCAACTTATATGGGCCA 59.223 45.455 15.67 9.61 45.61 5.36
833 847 3.459598 AGCTCAACTTATATGGGCCAGAA 59.540 43.478 13.78 2.48 45.61 3.02
866 880 0.254747 TTGGATCTTTACTGGGCCGG 59.745 55.000 11.83 11.83 0.00 6.13
867 881 0.619255 TGGATCTTTACTGGGCCGGA 60.619 55.000 21.81 0.00 0.00 5.14
881 895 1.076777 CCGGAGCCCATTTGGTGAT 60.077 57.895 0.00 0.00 36.04 3.06
945 962 2.776913 CCTCCTCGTCCGCTTCCTC 61.777 68.421 0.00 0.00 0.00 3.71
949 966 1.751162 CTCGTCCGCTTCCTCCTCT 60.751 63.158 0.00 0.00 0.00 3.69
952 969 1.316706 CGTCCGCTTCCTCCTCTTCT 61.317 60.000 0.00 0.00 0.00 2.85
953 970 0.174617 GTCCGCTTCCTCCTCTTCTG 59.825 60.000 0.00 0.00 0.00 3.02
954 971 0.972983 TCCGCTTCCTCCTCTTCTGG 60.973 60.000 0.00 0.00 0.00 3.86
955 972 1.261238 CCGCTTCCTCCTCTTCTGGT 61.261 60.000 0.00 0.00 0.00 4.00
956 973 0.174617 CGCTTCCTCCTCTTCTGGTC 59.825 60.000 0.00 0.00 0.00 4.02
1059 1093 3.142838 GCCCTGTGCGCCATCAAT 61.143 61.111 4.18 0.00 0.00 2.57
1145 1179 0.526954 CGGTTCGATTCAGGTACGGG 60.527 60.000 0.00 0.00 0.00 5.28
1146 1180 0.533951 GGTTCGATTCAGGTACGGGT 59.466 55.000 0.00 0.00 0.00 5.28
1162 1196 1.299976 GGTTCGTGATCCCCAGCTT 59.700 57.895 0.00 0.00 0.00 3.74
1167 1201 3.194005 TCGTGATCCCCAGCTTATTTC 57.806 47.619 0.00 0.00 0.00 2.17
1194 1228 4.452733 GAGAACCTGGTCCGCCGG 62.453 72.222 0.00 0.00 40.89 6.13
1249 1283 2.610374 TGGTACCAAATTTAGCGCGATC 59.390 45.455 13.60 0.00 0.00 3.69
1276 1310 3.269347 CCCGGCGCGGTAAATCTG 61.269 66.667 8.83 0.00 46.80 2.90
1277 1311 2.510691 CCGGCGCGGTAAATCTGT 60.511 61.111 8.83 0.00 42.73 3.41
1344 1379 7.279313 GGTATGAACTTTGGATTAACGCTAAGA 59.721 37.037 0.00 0.00 0.00 2.10
1428 1602 9.152595 GGTGATAACTTCCTTTGTACTAGAAAG 57.847 37.037 0.00 0.00 0.00 2.62
1438 1612 8.198109 TCCTTTGTACTAGAAAGTAGATCATGC 58.802 37.037 0.00 0.00 38.89 4.06
1604 1799 9.269453 AGTAAGTAAATGTACAGTTTGTTCCTC 57.731 33.333 14.46 3.74 32.12 3.71
1657 1852 2.102084 TGCACTGCATTGCTAAACCAAA 59.898 40.909 26.72 4.13 43.41 3.28
1658 1853 3.129871 GCACTGCATTGCTAAACCAAAA 58.870 40.909 20.72 0.00 39.59 2.44
1659 1854 3.184986 GCACTGCATTGCTAAACCAAAAG 59.815 43.478 20.72 0.00 39.59 2.27
1660 1855 4.619973 CACTGCATTGCTAAACCAAAAGA 58.380 39.130 10.49 0.00 0.00 2.52
1661 1856 5.049167 CACTGCATTGCTAAACCAAAAGAA 58.951 37.500 10.49 0.00 0.00 2.52
1698 1893 7.655328 AGACTCGATTGGTAATTCTCATTGATC 59.345 37.037 0.00 0.00 0.00 2.92
1761 1956 1.300963 GGAGAGCCTGGCATGTCAA 59.699 57.895 22.65 0.00 0.00 3.18
1861 2056 4.096382 CCAAAGAGGTTATTTGACCCATCG 59.904 45.833 0.18 0.00 40.73 3.84
1862 2057 4.837093 AAGAGGTTATTTGACCCATCGA 57.163 40.909 0.00 0.00 40.73 3.59
1882 2077 2.627515 AGTCTCTTGTCTTTGCTGCA 57.372 45.000 0.00 0.00 0.00 4.41
1949 2428 2.158871 TGAACCTTGACGCTTTGGTACT 60.159 45.455 0.00 0.00 31.82 2.73
1960 2439 4.581409 ACGCTTTGGTACTTGGTTTTACAT 59.419 37.500 0.00 0.00 0.00 2.29
2007 2488 5.746990 ATAGCTGTCTACCCATATTGGTC 57.253 43.478 0.83 0.00 39.91 4.02
2017 2498 1.679680 CCATATTGGTCCAGCAGCTTG 59.320 52.381 0.00 0.00 31.35 4.01
2067 2548 5.715434 TCTTGTTTATTTACCAAGGCACC 57.285 39.130 0.00 0.00 36.94 5.01
2080 2561 2.125106 GCACCGGATCCACAGGAC 60.125 66.667 9.46 0.00 37.30 3.85
2207 2716 4.768968 AGCCAAACTGAATCTGCAAATACT 59.231 37.500 0.00 0.00 0.00 2.12
2208 2717 5.244626 AGCCAAACTGAATCTGCAAATACTT 59.755 36.000 0.00 0.00 0.00 2.24
2209 2718 6.434028 AGCCAAACTGAATCTGCAAATACTTA 59.566 34.615 0.00 0.00 0.00 2.24
2210 2719 6.749118 GCCAAACTGAATCTGCAAATACTTAG 59.251 38.462 0.00 0.00 0.00 2.18
2211 2720 7.362056 GCCAAACTGAATCTGCAAATACTTAGA 60.362 37.037 0.00 0.00 0.00 2.10
2212 2721 8.180267 CCAAACTGAATCTGCAAATACTTAGAG 58.820 37.037 0.00 0.00 0.00 2.43
2213 2722 7.856145 AACTGAATCTGCAAATACTTAGAGG 57.144 36.000 0.00 0.00 0.00 3.69
2236 2745 1.975363 GAGCGCTTCATCACAGCACC 61.975 60.000 13.26 0.00 37.07 5.01
2237 2746 3.044059 GCGCTTCATCACAGCACCC 62.044 63.158 0.00 0.00 37.07 4.61
2242 2751 2.165167 CTTCATCACAGCACCCACAAT 58.835 47.619 0.00 0.00 0.00 2.71
2275 2787 8.875803 CATTGTAATTAACATCTGCAATGCTTT 58.124 29.630 6.82 0.00 38.10 3.51
2302 2814 5.296151 TCATTAATCCTAGGCTGGTCTTG 57.704 43.478 2.96 0.00 0.00 3.02
2338 2861 0.948678 GTCAACGGCTGTAAAGGCAA 59.051 50.000 7.33 0.00 0.00 4.52
2348 2871 2.979813 CTGTAAAGGCAAACGCATGAAC 59.020 45.455 0.00 0.00 0.00 3.18
2355 2878 2.598589 GCAAACGCATGAACACATGAT 58.401 42.857 13.30 0.00 42.56 2.45
2455 2992 5.351465 CACTACTGCTATGTGGTTTGTAAGG 59.649 44.000 0.00 0.00 29.14 2.69
2501 3079 7.004555 TGACATCATCTTGTGTACCTTACTT 57.995 36.000 0.00 0.00 0.00 2.24
2502 3080 6.873605 TGACATCATCTTGTGTACCTTACTTG 59.126 38.462 0.00 0.00 0.00 3.16
2503 3081 6.173339 ACATCATCTTGTGTACCTTACTTGG 58.827 40.000 0.00 0.00 0.00 3.61
2505 3083 6.921486 TCATCTTGTGTACCTTACTTGGTA 57.079 37.500 0.00 0.00 41.22 3.25
2506 3084 7.490657 TCATCTTGTGTACCTTACTTGGTAT 57.509 36.000 0.00 0.00 43.54 2.73
2550 3136 0.109781 CCGTACAAACATGTGCAGCC 60.110 55.000 0.00 0.00 0.00 4.85
2647 3237 3.067461 TGCAAAAACACCTTGAAGCGTAT 59.933 39.130 0.00 0.00 0.00 3.06
2648 3238 4.276183 TGCAAAAACACCTTGAAGCGTATA 59.724 37.500 0.00 0.00 0.00 1.47
2656 3246 2.259618 CTTGAAGCGTATACGTGTGCT 58.740 47.619 25.04 11.67 42.22 4.40
2680 3280 2.671963 GTTCCAGAACACGGGGGC 60.672 66.667 5.66 0.00 40.84 5.80
2740 3348 3.271142 CCGCGGCGGTAAATAACTA 57.729 52.632 32.14 0.00 42.73 2.24
2741 3349 0.854705 CCGCGGCGGTAAATAACTAC 59.145 55.000 32.14 0.00 42.73 2.73
2783 3394 1.433879 GACAGTAGCCGCACGATCT 59.566 57.895 0.00 0.00 0.00 2.75
2787 3398 0.101399 AGTAGCCGCACGATCTTCTG 59.899 55.000 0.00 0.00 0.00 3.02
2788 3399 0.179134 GTAGCCGCACGATCTTCTGT 60.179 55.000 0.00 0.00 0.00 3.41
2791 3402 0.807667 GCCGCACGATCTTCTGTCAT 60.808 55.000 0.00 0.00 0.00 3.06
2793 3404 1.203928 CGCACGATCTTCTGTCATCC 58.796 55.000 0.00 0.00 0.00 3.51
2816 3441 6.205853 TCCATGTAAAATCACCTGTAACACAC 59.794 38.462 0.00 0.00 0.00 3.82
2817 3442 5.660629 TGTAAAATCACCTGTAACACACG 57.339 39.130 0.00 0.00 0.00 4.49
2842 4039 3.607078 GCTGTGTTGGAGACGAAATGAAC 60.607 47.826 0.00 0.00 0.00 3.18
2865 4062 7.778470 ACGAAGTTTAGCTAGTACGTACTAT 57.222 36.000 30.29 20.99 37.78 2.12
2868 4070 9.574401 CGAAGTTTAGCTAGTACGTACTATAAC 57.426 37.037 30.29 26.71 38.06 1.89
2897 4099 1.654220 GCAAATCGCTGTGTGGTGT 59.346 52.632 0.00 0.00 37.77 4.16
2902 4104 3.952675 CGCTGTGTGGTGTGGTGC 61.953 66.667 0.00 0.00 0.00 5.01
2906 4108 1.717791 CTGTGTGGTGTGGTGCTGTG 61.718 60.000 0.00 0.00 0.00 3.66
2907 4109 1.748879 GTGTGGTGTGGTGCTGTGT 60.749 57.895 0.00 0.00 0.00 3.72
2908 4110 1.001517 TGTGGTGTGGTGCTGTGTT 60.002 52.632 0.00 0.00 0.00 3.32
2909 4111 1.311651 TGTGGTGTGGTGCTGTGTTG 61.312 55.000 0.00 0.00 0.00 3.33
2912 4114 1.340114 TGGTGTGGTGCTGTGTTGTTA 60.340 47.619 0.00 0.00 0.00 2.41
2922 4124 4.155826 GTGCTGTGTTGTTAGATTATGGCA 59.844 41.667 0.00 0.00 0.00 4.92
2923 4125 4.395854 TGCTGTGTTGTTAGATTATGGCAG 59.604 41.667 0.00 0.00 0.00 4.85
2929 4131 5.647658 TGTTGTTAGATTATGGCAGTGGAAG 59.352 40.000 0.00 0.00 0.00 3.46
2931 4133 5.674525 TGTTAGATTATGGCAGTGGAAGAG 58.325 41.667 0.00 0.00 0.00 2.85
2935 4137 4.472833 AGATTATGGCAGTGGAAGAGAAGT 59.527 41.667 0.00 0.00 0.00 3.01
2939 4141 1.346068 GGCAGTGGAAGAGAAGTGACT 59.654 52.381 0.00 0.00 0.00 3.41
2940 4142 2.563179 GGCAGTGGAAGAGAAGTGACTA 59.437 50.000 0.00 0.00 0.00 2.59
2998 4227 1.840650 AGCCTCTGTGTGGAGCAGT 60.841 57.895 0.00 0.00 35.60 4.40
2999 4228 1.670406 GCCTCTGTGTGGAGCAGTG 60.670 63.158 0.00 0.00 35.60 3.66
3004 4233 0.892358 CTGTGTGGAGCAGTGGCATT 60.892 55.000 0.00 0.00 44.61 3.56
3016 4245 1.001764 TGGCATTGTCCTCTGCTGG 60.002 57.895 0.00 0.00 38.45 4.85
3017 4246 1.001641 GGCATTGTCCTCTGCTGGT 60.002 57.895 0.00 0.00 38.45 4.00
3019 4248 1.930908 GCATTGTCCTCTGCTGGTGC 61.931 60.000 0.00 0.00 35.49 5.01
3020 4249 0.322277 CATTGTCCTCTGCTGGTGCT 60.322 55.000 0.00 0.00 40.48 4.40
3021 4250 0.403271 ATTGTCCTCTGCTGGTGCTT 59.597 50.000 0.00 0.00 40.48 3.91
3022 4251 0.535780 TTGTCCTCTGCTGGTGCTTG 60.536 55.000 0.00 0.00 40.48 4.01
3023 4252 1.673665 GTCCTCTGCTGGTGCTTGG 60.674 63.158 0.00 0.00 40.48 3.61
3024 4253 3.060615 CCTCTGCTGGTGCTTGGC 61.061 66.667 0.00 0.00 40.48 4.52
3025 4254 2.033757 CTCTGCTGGTGCTTGGCT 59.966 61.111 0.00 0.00 40.48 4.75
3026 4255 1.602888 CTCTGCTGGTGCTTGGCTT 60.603 57.895 0.00 0.00 40.48 4.35
3029 4258 2.341176 GCTGGTGCTTGGCTTTGG 59.659 61.111 0.00 0.00 36.03 3.28
3030 4259 2.341176 CTGGTGCTTGGCTTTGGC 59.659 61.111 0.00 0.00 37.82 4.52
3031 4260 2.443577 TGGTGCTTGGCTTTGGCA 60.444 55.556 0.00 0.00 40.87 4.92
3032 4261 2.341176 GGTGCTTGGCTTTGGCAG 59.659 61.111 0.00 0.00 39.75 4.85
3033 4262 2.341176 GTGCTTGGCTTTGGCAGG 59.659 61.111 0.00 0.00 39.75 4.85
3039 4268 2.985847 GGCTTTGGCAGGCGAGTT 60.986 61.111 8.09 0.00 38.54 3.01
3040 4269 2.256461 GCTTTGGCAGGCGAGTTG 59.744 61.111 0.00 0.00 38.54 3.16
3041 4270 2.555547 GCTTTGGCAGGCGAGTTGT 61.556 57.895 0.00 0.00 38.54 3.32
3042 4271 1.283793 CTTTGGCAGGCGAGTTGTG 59.716 57.895 0.00 0.00 0.00 3.33
3043 4272 2.133742 CTTTGGCAGGCGAGTTGTGG 62.134 60.000 0.00 0.00 0.00 4.17
3044 4273 2.902423 TTTGGCAGGCGAGTTGTGGT 62.902 55.000 0.00 0.00 0.00 4.16
3045 4274 2.594592 GGCAGGCGAGTTGTGGTT 60.595 61.111 0.00 0.00 0.00 3.67
3046 4275 2.639286 GCAGGCGAGTTGTGGTTG 59.361 61.111 0.00 0.00 0.00 3.77
3047 4276 2.908073 GCAGGCGAGTTGTGGTTGG 61.908 63.158 0.00 0.00 0.00 3.77
3048 4277 2.113139 AGGCGAGTTGTGGTTGGG 59.887 61.111 0.00 0.00 0.00 4.12
3058 4287 2.856494 TGGTTGGGTGCCTGCCTA 60.856 61.111 0.00 0.00 0.00 3.93
3148 4467 2.358737 GGACGGGACAGCCACAAG 60.359 66.667 0.00 0.00 35.15 3.16
3211 4532 4.323477 CTCCCCGTCACCCGCAAA 62.323 66.667 0.00 0.00 34.38 3.68
3212 4533 4.323477 TCCCCGTCACCCGCAAAG 62.323 66.667 0.00 0.00 34.38 2.77
3223 4544 1.172180 CCCGCAAAGGCACAAAGAGA 61.172 55.000 0.00 0.00 41.24 3.10
3229 4550 0.695347 AAGGCACAAAGAGAGGAGGG 59.305 55.000 0.00 0.00 0.00 4.30
3231 4552 1.201429 GGCACAAAGAGAGGAGGGGA 61.201 60.000 0.00 0.00 0.00 4.81
3232 4553 0.251634 GCACAAAGAGAGGAGGGGAG 59.748 60.000 0.00 0.00 0.00 4.30
3233 4554 0.908198 CACAAAGAGAGGAGGGGAGG 59.092 60.000 0.00 0.00 0.00 4.30
3234 4555 0.252927 ACAAAGAGAGGAGGGGAGGG 60.253 60.000 0.00 0.00 0.00 4.30
3235 4556 0.985490 CAAAGAGAGGAGGGGAGGGG 60.985 65.000 0.00 0.00 0.00 4.79
3241 4562 3.695825 GGAGGGGAGGGGACTGGA 61.696 72.222 0.00 0.00 44.43 3.86
3242 4563 2.041405 GAGGGGAGGGGACTGGAG 60.041 72.222 0.00 0.00 44.43 3.86
3243 4564 3.700350 AGGGGAGGGGACTGGAGG 61.700 72.222 0.00 0.00 44.43 4.30
3244 4565 3.695825 GGGGAGGGGACTGGAGGA 61.696 72.222 0.00 0.00 44.43 3.71
3245 4566 2.041405 GGGAGGGGACTGGAGGAG 60.041 72.222 0.00 0.00 44.43 3.69
3246 4567 2.766229 GGAGGGGACTGGAGGAGC 60.766 72.222 0.00 0.00 44.43 4.70
3247 4568 3.151022 GAGGGGACTGGAGGAGCG 61.151 72.222 0.00 0.00 44.43 5.03
3248 4569 3.663815 GAGGGGACTGGAGGAGCGA 62.664 68.421 0.00 0.00 44.43 4.93
3249 4570 3.462678 GGGGACTGGAGGAGCGAC 61.463 72.222 0.00 0.00 0.00 5.19
3250 4571 3.827898 GGGACTGGAGGAGCGACG 61.828 72.222 0.00 0.00 0.00 5.12
3251 4572 2.750637 GGACTGGAGGAGCGACGA 60.751 66.667 0.00 0.00 0.00 4.20
3252 4573 2.486042 GACTGGAGGAGCGACGAC 59.514 66.667 0.00 0.00 0.00 4.34
3253 4574 3.053849 GACTGGAGGAGCGACGACC 62.054 68.421 0.00 0.61 0.00 4.79
3254 4575 4.180946 CTGGAGGAGCGACGACCG 62.181 72.222 0.00 0.00 42.21 4.79
3272 4593 3.669344 CCTGCCGCGCTTTTTCCA 61.669 61.111 5.56 0.00 0.00 3.53
3273 4594 2.429069 CTGCCGCGCTTTTTCCAC 60.429 61.111 5.56 0.00 0.00 4.02
3274 4595 3.896863 CTGCCGCGCTTTTTCCACC 62.897 63.158 5.56 0.00 0.00 4.61
3277 4598 4.025401 CGCGCTTTTTCCACCGCT 62.025 61.111 5.56 0.00 43.84 5.52
3278 4599 2.126850 GCGCTTTTTCCACCGCTC 60.127 61.111 0.00 0.00 42.83 5.03
3279 4600 2.561373 CGCTTTTTCCACCGCTCC 59.439 61.111 0.00 0.00 0.00 4.70
3280 4601 2.258013 CGCTTTTTCCACCGCTCCA 61.258 57.895 0.00 0.00 0.00 3.86
3281 4602 1.586154 CGCTTTTTCCACCGCTCCAT 61.586 55.000 0.00 0.00 0.00 3.41
3282 4603 0.171231 GCTTTTTCCACCGCTCCATC 59.829 55.000 0.00 0.00 0.00 3.51
3283 4604 0.447801 CTTTTTCCACCGCTCCATCG 59.552 55.000 0.00 0.00 0.00 3.84
3290 4611 2.897207 CCGCTCCATCGGTTACCA 59.103 61.111 1.13 0.00 44.18 3.25
3291 4612 1.520787 CCGCTCCATCGGTTACCAC 60.521 63.158 1.13 0.00 44.18 4.16
3292 4613 1.515954 CGCTCCATCGGTTACCACT 59.484 57.895 1.13 0.00 0.00 4.00
3293 4614 0.108329 CGCTCCATCGGTTACCACTT 60.108 55.000 1.13 0.00 0.00 3.16
3294 4615 1.135527 CGCTCCATCGGTTACCACTTA 59.864 52.381 1.13 0.00 0.00 2.24
3295 4616 2.547826 GCTCCATCGGTTACCACTTAC 58.452 52.381 1.13 0.00 0.00 2.34
3296 4617 2.740904 GCTCCATCGGTTACCACTTACC 60.741 54.545 1.13 0.00 0.00 2.85
3297 4618 2.764572 CTCCATCGGTTACCACTTACCT 59.235 50.000 1.13 0.00 32.08 3.08
3298 4619 2.762327 TCCATCGGTTACCACTTACCTC 59.238 50.000 1.13 0.00 32.08 3.85
3299 4620 2.159000 CCATCGGTTACCACTTACCTCC 60.159 54.545 1.13 0.00 32.08 4.30
3300 4621 2.307496 TCGGTTACCACTTACCTCCA 57.693 50.000 1.13 0.00 32.08 3.86
3301 4622 1.895131 TCGGTTACCACTTACCTCCAC 59.105 52.381 1.13 0.00 32.08 4.02
3302 4623 1.897802 CGGTTACCACTTACCTCCACT 59.102 52.381 1.13 0.00 32.08 4.00
3303 4624 2.353406 CGGTTACCACTTACCTCCACTG 60.353 54.545 1.13 0.00 32.08 3.66
3304 4625 2.614734 GGTTACCACTTACCTCCACTGC 60.615 54.545 0.00 0.00 0.00 4.40
3305 4626 2.302157 GTTACCACTTACCTCCACTGCT 59.698 50.000 0.00 0.00 0.00 4.24
3310 4631 3.093057 CACTTACCTCCACTGCTACTCT 58.907 50.000 0.00 0.00 0.00 3.24
3313 4634 2.137810 ACCTCCACTGCTACTCTCTC 57.862 55.000 0.00 0.00 0.00 3.20
3322 4643 1.063567 TGCTACTCTCTCCCCTCTTCC 60.064 57.143 0.00 0.00 0.00 3.46
3327 4648 2.024369 ACTCTCTCCCCTCTTCCTTCTC 60.024 54.545 0.00 0.00 0.00 2.87
3328 4649 2.244769 CTCTCTCCCCTCTTCCTTCTCT 59.755 54.545 0.00 0.00 0.00 3.10
3329 4650 2.657459 TCTCTCCCCTCTTCCTTCTCTT 59.343 50.000 0.00 0.00 0.00 2.85
3338 4724 3.622630 TCTTCCTTCTCTTCTACCTCCG 58.377 50.000 0.00 0.00 0.00 4.63
3345 4731 1.088340 TCTTCTACCTCCGCGTCTCG 61.088 60.000 4.92 0.00 38.08 4.04
3354 4740 4.477975 CGCGTCTCGGGGTCTCAC 62.478 72.222 0.00 0.00 36.19 3.51
3356 4742 3.053849 GCGTCTCGGGGTCTCACTC 62.054 68.421 0.00 0.00 0.00 3.51
3596 5036 1.686800 GTCCACCGTAAGCCCCCTA 60.687 63.158 0.00 0.00 0.00 3.53
3597 5037 1.686800 TCCACCGTAAGCCCCCTAC 60.687 63.158 0.00 0.00 0.00 3.18
3598 5038 1.688187 CCACCGTAAGCCCCCTACT 60.688 63.158 0.00 0.00 0.00 2.57
3599 5039 1.520666 CACCGTAAGCCCCCTACTG 59.479 63.158 0.00 0.00 0.00 2.74
3600 5040 2.364780 ACCGTAAGCCCCCTACTGC 61.365 63.158 0.00 0.00 0.00 4.40
3601 5041 2.504519 CGTAAGCCCCCTACTGCC 59.495 66.667 0.00 0.00 0.00 4.85
3602 5042 2.363975 CGTAAGCCCCCTACTGCCA 61.364 63.158 0.00 0.00 0.00 4.92
3603 5043 1.223763 GTAAGCCCCCTACTGCCAC 59.776 63.158 0.00 0.00 0.00 5.01
3604 5044 1.229690 TAAGCCCCCTACTGCCACA 60.230 57.895 0.00 0.00 0.00 4.17
3605 5045 1.271840 TAAGCCCCCTACTGCCACAG 61.272 60.000 0.00 0.00 37.52 3.66
3606 5046 4.115199 GCCCCCTACTGCCACAGG 62.115 72.222 0.00 0.00 35.51 4.00
3609 5049 2.990479 CCCTACTGCCACAGGGTC 59.010 66.667 5.62 0.00 45.70 4.46
3610 5050 1.613630 CCCTACTGCCACAGGGTCT 60.614 63.158 5.62 0.00 45.70 3.85
3611 5051 1.617947 CCCTACTGCCACAGGGTCTC 61.618 65.000 5.62 0.00 45.70 3.36
3612 5052 1.617947 CCTACTGCCACAGGGTCTCC 61.618 65.000 0.00 0.00 35.51 3.71
3613 5053 0.616111 CTACTGCCACAGGGTCTCCT 60.616 60.000 0.00 0.00 46.26 3.69
3614 5054 0.614979 TACTGCCACAGGGTCTCCTC 60.615 60.000 0.00 0.00 42.67 3.71
3615 5055 1.915266 CTGCCACAGGGTCTCCTCA 60.915 63.158 0.00 0.00 42.67 3.86
3616 5056 1.897225 CTGCCACAGGGTCTCCTCAG 61.897 65.000 0.00 0.00 42.67 3.35
3617 5057 2.985456 CCACAGGGTCTCCTCAGC 59.015 66.667 0.00 0.00 42.67 4.26
3618 5058 2.664081 CCACAGGGTCTCCTCAGCC 61.664 68.421 0.00 0.00 42.67 4.85
3619 5059 2.681778 ACAGGGTCTCCTCAGCCG 60.682 66.667 0.00 0.00 42.67 5.52
3620 5060 4.154347 CAGGGTCTCCTCAGCCGC 62.154 72.222 0.00 0.00 42.67 6.53
3628 5068 4.767255 CCTCAGCCGCGCCTTCTT 62.767 66.667 0.00 0.00 0.00 2.52
3629 5069 2.184322 CTCAGCCGCGCCTTCTTA 59.816 61.111 0.00 0.00 0.00 2.10
3630 5070 1.447838 CTCAGCCGCGCCTTCTTAA 60.448 57.895 0.00 0.00 0.00 1.85
3631 5071 0.811616 CTCAGCCGCGCCTTCTTAAT 60.812 55.000 0.00 0.00 0.00 1.40
3632 5072 0.392461 TCAGCCGCGCCTTCTTAATT 60.392 50.000 0.00 0.00 0.00 1.40
3633 5073 1.134640 TCAGCCGCGCCTTCTTAATTA 60.135 47.619 0.00 0.00 0.00 1.40
3634 5074 1.003866 CAGCCGCGCCTTCTTAATTAC 60.004 52.381 0.00 0.00 0.00 1.89
3635 5075 1.134491 AGCCGCGCCTTCTTAATTACT 60.134 47.619 0.00 0.00 0.00 2.24
3636 5076 1.669265 GCCGCGCCTTCTTAATTACTT 59.331 47.619 0.00 0.00 0.00 2.24
3637 5077 2.867975 GCCGCGCCTTCTTAATTACTTA 59.132 45.455 0.00 0.00 0.00 2.24
3638 5078 3.302935 GCCGCGCCTTCTTAATTACTTAC 60.303 47.826 0.00 0.00 0.00 2.34
3639 5079 4.117685 CCGCGCCTTCTTAATTACTTACT 58.882 43.478 0.00 0.00 0.00 2.24
3640 5080 4.569564 CCGCGCCTTCTTAATTACTTACTT 59.430 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.609491 GGTCATACTGTGCAACTCGACA 60.609 50.000 0.00 0.00 38.04 4.35
28 29 1.616327 ATGCCCTGCCTACTGGTCA 60.616 57.895 0.00 0.00 35.27 4.02
55 56 5.235516 ACTGGTGTCTAATTAAGTTGTCCG 58.764 41.667 0.00 0.00 0.00 4.79
190 195 5.351233 TTGTTGGATTACGTTGATGTGTC 57.649 39.130 0.00 0.00 0.00 3.67
191 196 5.066634 TGTTTGTTGGATTACGTTGATGTGT 59.933 36.000 0.00 0.00 0.00 3.72
192 197 5.398122 GTGTTTGTTGGATTACGTTGATGTG 59.602 40.000 0.00 0.00 0.00 3.21
193 198 5.066634 TGTGTTTGTTGGATTACGTTGATGT 59.933 36.000 0.00 0.00 0.00 3.06
285 290 3.725895 CGGAACTCTGATTGAATGCGTTG 60.726 47.826 0.00 0.00 0.00 4.10
398 405 2.954868 CGAGGTACATGTCCGCGC 60.955 66.667 20.56 0.00 40.70 6.86
552 559 3.076278 CGGGCCCCAAGGTACGTA 61.076 66.667 18.66 0.00 34.57 3.57
554 561 4.157120 CTCGGGCCCCAAGGTACG 62.157 72.222 18.66 0.95 36.24 3.67
555 562 4.484872 GCTCGGGCCCCAAGGTAC 62.485 72.222 18.66 0.00 34.57 3.34
715 724 1.456705 CTCCTCTTCCCTCCCCTCG 60.457 68.421 0.00 0.00 0.00 4.63
727 736 4.824515 CGGGTCTCGGCCTCCTCT 62.825 72.222 0.00 0.00 34.75 3.69
728 737 4.816984 TCGGGTCTCGGCCTCCTC 62.817 72.222 0.00 0.00 39.77 3.71
729 738 4.824515 CTCGGGTCTCGGCCTCCT 62.825 72.222 0.00 0.00 39.77 3.69
734 743 4.200283 CAGCTCTCGGGTCTCGGC 62.200 72.222 0.00 0.00 39.77 5.54
735 744 2.752238 ACAGCTCTCGGGTCTCGG 60.752 66.667 0.00 0.00 39.77 4.63
736 745 2.487428 CACAGCTCTCGGGTCTCG 59.513 66.667 0.00 0.00 40.90 4.04
737 746 1.979693 ACCACAGCTCTCGGGTCTC 60.980 63.158 0.00 0.00 0.00 3.36
738 747 2.118513 ACCACAGCTCTCGGGTCT 59.881 61.111 0.00 0.00 0.00 3.85
739 748 2.262915 CACCACAGCTCTCGGGTC 59.737 66.667 0.00 0.00 0.00 4.46
740 749 2.524394 ACACCACAGCTCTCGGGT 60.524 61.111 0.00 0.00 0.00 5.28
741 750 2.047844 CACACCACAGCTCTCGGG 60.048 66.667 0.00 0.00 0.00 5.14
845 859 2.222027 CGGCCCAGTAAAGATCCAATC 58.778 52.381 0.00 0.00 0.00 2.67
846 860 1.133792 CCGGCCCAGTAAAGATCCAAT 60.134 52.381 0.00 0.00 0.00 3.16
866 880 1.434696 CGCATCACCAAATGGGCTC 59.565 57.895 4.17 0.00 42.05 4.70
867 881 3.607163 CGCATCACCAAATGGGCT 58.393 55.556 4.17 0.00 42.05 5.19
937 954 0.174617 GACCAGAAGAGGAGGAAGCG 59.825 60.000 0.00 0.00 0.00 4.68
941 958 1.719378 AGAAGGACCAGAAGAGGAGGA 59.281 52.381 0.00 0.00 0.00 3.71
945 962 2.499693 GGAGAAGAAGGACCAGAAGAGG 59.500 54.545 0.00 0.00 0.00 3.69
949 966 1.267121 CCGGAGAAGAAGGACCAGAA 58.733 55.000 0.00 0.00 0.00 3.02
952 969 2.646175 CGCCGGAGAAGAAGGACCA 61.646 63.158 5.05 0.00 0.00 4.02
953 970 2.184579 CGCCGGAGAAGAAGGACC 59.815 66.667 5.05 0.00 0.00 4.46
954 971 1.139947 CTCGCCGGAGAAGAAGGAC 59.860 63.158 9.83 0.00 43.27 3.85
955 972 2.711922 GCTCGCCGGAGAAGAAGGA 61.712 63.158 9.83 0.00 43.27 3.36
956 973 2.202810 GCTCGCCGGAGAAGAAGG 60.203 66.667 9.83 0.00 43.27 3.46
1145 1179 2.622064 ATAAGCTGGGGATCACGAAC 57.378 50.000 0.00 0.00 0.00 3.95
1146 1180 3.054728 TGAAATAAGCTGGGGATCACGAA 60.055 43.478 0.00 0.00 0.00 3.85
1162 1196 4.081862 CAGGTTCTCCTACGGTGTGAAATA 60.082 45.833 0.00 0.00 43.07 1.40
1167 1201 0.246635 CCAGGTTCTCCTACGGTGTG 59.753 60.000 0.00 0.00 43.07 3.82
1204 1238 0.107654 GACCGGATTTCTCCACCCTG 60.108 60.000 9.46 0.00 42.19 4.45
1261 1295 2.701006 CACAGATTTACCGCGCCG 59.299 61.111 0.00 0.00 0.00 6.46
1267 1301 2.095213 TCGCGATTTGCACAGATTTACC 59.905 45.455 3.71 0.00 46.97 2.85
1276 1310 0.909843 GAAATGCTCGCGATTTGCAC 59.090 50.000 21.71 7.74 46.97 4.57
1277 1311 0.804364 AGAAATGCTCGCGATTTGCA 59.196 45.000 21.56 21.56 46.97 4.08
1344 1379 2.693074 AGCAGACCCACATTTCGTTTTT 59.307 40.909 0.00 0.00 0.00 1.94
1438 1612 4.274459 GGGATAGTGAAGTATTTGCAGCTG 59.726 45.833 10.11 10.11 0.00 4.24
1604 1799 7.776933 TCTTTCTTCATATCATGAGAAACGG 57.223 36.000 0.09 0.00 40.94 4.44
1637 1832 2.437200 TTGGTTTAGCAATGCAGTGC 57.563 45.000 30.52 30.52 45.28 4.40
1657 1852 8.940952 CCAATCGAGTCTATTTCTTCTTTTCTT 58.059 33.333 0.00 0.00 0.00 2.52
1658 1853 8.097662 ACCAATCGAGTCTATTTCTTCTTTTCT 58.902 33.333 0.00 0.00 0.00 2.52
1659 1854 8.257830 ACCAATCGAGTCTATTTCTTCTTTTC 57.742 34.615 0.00 0.00 0.00 2.29
1660 1855 9.720769 TTACCAATCGAGTCTATTTCTTCTTTT 57.279 29.630 0.00 0.00 0.00 2.27
1661 1856 9.892130 ATTACCAATCGAGTCTATTTCTTCTTT 57.108 29.630 0.00 0.00 0.00 2.52
1673 1868 7.439356 TGATCAATGAGAATTACCAATCGAGTC 59.561 37.037 0.00 0.00 0.00 3.36
1698 1893 6.823182 TCCTTCACCTATGTCATAATGTTGTG 59.177 38.462 0.00 0.00 0.00 3.33
1761 1956 1.597027 CCGTCCCTTCTTGCGTTGT 60.597 57.895 0.00 0.00 0.00 3.32
1861 2056 2.874701 TGCAGCAAAGACAAGAGACTTC 59.125 45.455 0.00 0.00 0.00 3.01
1862 2057 2.923121 TGCAGCAAAGACAAGAGACTT 58.077 42.857 0.00 0.00 0.00 3.01
1882 2077 4.018415 ACTGTTCAGTGTGCCCCTAAATAT 60.018 41.667 4.58 0.00 0.00 1.28
1949 2428 7.101652 TCAAAGCAGTTACATGTAAAACCAA 57.898 32.000 19.63 0.00 0.00 3.67
1960 2439 4.870123 ATGCCATTTCAAAGCAGTTACA 57.130 36.364 0.00 0.00 40.40 2.41
2017 2498 2.144482 AAAACATGTGAGCTTGCAGC 57.856 45.000 0.00 0.47 42.84 5.25
2052 2533 2.158726 GGATCCGGTGCCTTGGTAAATA 60.159 50.000 0.00 0.00 0.00 1.40
2067 2548 0.175760 ATCGTTGTCCTGTGGATCCG 59.824 55.000 7.39 0.00 32.73 4.18
2080 2561 7.998212 GCAAATGTAAACAGAGAAAAATCGTTG 59.002 33.333 0.00 0.00 0.00 4.10
2207 2716 3.699538 TGATGAAGCGCTCTAACCTCTAA 59.300 43.478 12.06 0.00 0.00 2.10
2208 2717 3.066900 GTGATGAAGCGCTCTAACCTCTA 59.933 47.826 12.06 0.00 0.00 2.43
2209 2718 2.103373 TGATGAAGCGCTCTAACCTCT 58.897 47.619 12.06 0.00 0.00 3.69
2210 2719 2.197577 GTGATGAAGCGCTCTAACCTC 58.802 52.381 12.06 3.48 0.00 3.85
2211 2720 1.550524 TGTGATGAAGCGCTCTAACCT 59.449 47.619 12.06 0.00 0.00 3.50
2212 2721 1.929836 CTGTGATGAAGCGCTCTAACC 59.070 52.381 12.06 0.00 0.00 2.85
2213 2722 1.325943 GCTGTGATGAAGCGCTCTAAC 59.674 52.381 12.06 6.04 0.00 2.34
2242 2751 7.040132 TGCAGATGTTAATTACAATGTTCCACA 60.040 33.333 0.00 0.00 40.89 4.17
2246 2758 8.323140 GCATTGCAGATGTTAATTACAATGTTC 58.677 33.333 17.22 5.35 42.89 3.18
2260 2772 7.578310 AATGATAGTAAAGCATTGCAGATGT 57.422 32.000 11.91 0.00 31.55 3.06
2264 2776 8.790718 AGGATTAATGATAGTAAAGCATTGCAG 58.209 33.333 11.91 0.00 34.41 4.41
2275 2787 7.479579 AGACCAGCCTAGGATTAATGATAGTA 58.520 38.462 14.75 0.00 0.00 1.82
2302 2814 2.923121 TGACAGGCTAGAATGGAATGC 58.077 47.619 0.00 0.00 0.00 3.56
2330 2853 2.359214 TGTGTTCATGCGTTTGCCTTTA 59.641 40.909 0.00 0.00 41.78 1.85
2420 2951 2.990066 GCAGTAGTGCCCAAGAGTAT 57.010 50.000 11.74 0.00 44.72 2.12
2471 3008 6.545666 AGGTACACAAGATGATGTCAAAACAA 59.454 34.615 0.00 0.00 39.30 2.83
2473 3010 6.560253 AGGTACACAAGATGATGTCAAAAC 57.440 37.500 0.00 0.00 0.00 2.43
2475 3012 7.450074 AGTAAGGTACACAAGATGATGTCAAA 58.550 34.615 0.00 0.00 0.00 2.69
2476 3013 7.004555 AGTAAGGTACACAAGATGATGTCAA 57.995 36.000 0.00 0.00 0.00 3.18
2477 3014 6.605471 AGTAAGGTACACAAGATGATGTCA 57.395 37.500 0.00 0.00 0.00 3.58
2479 3016 6.173339 CCAAGTAAGGTACACAAGATGATGT 58.827 40.000 0.00 0.00 0.00 3.06
2480 3017 6.173339 ACCAAGTAAGGTACACAAGATGATG 58.827 40.000 0.00 0.00 40.98 3.07
2481 3018 6.374417 ACCAAGTAAGGTACACAAGATGAT 57.626 37.500 0.00 0.00 40.98 2.45
2482 3019 5.818678 ACCAAGTAAGGTACACAAGATGA 57.181 39.130 0.00 0.00 40.98 2.92
2485 3022 9.705103 ACTATATACCAAGTAAGGTACACAAGA 57.295 33.333 0.00 0.00 46.29 3.02
2489 3067 9.129532 ACAGACTATATACCAAGTAAGGTACAC 57.870 37.037 0.00 0.00 46.29 2.90
2525 3103 5.690997 TGCACATGTTTGTACGGAAATAA 57.309 34.783 0.00 0.00 33.76 1.40
2550 3136 3.965539 CTTGCGCCACTCCTCCAGG 62.966 68.421 4.18 0.00 0.00 4.45
2637 3223 2.357327 AGCACACGTATACGCTTCAA 57.643 45.000 24.64 0.00 44.43 2.69
2647 3237 1.411394 GAACGCTTGTAGCACACGTA 58.589 50.000 0.00 0.00 42.58 3.57
2648 3238 1.219522 GGAACGCTTGTAGCACACGT 61.220 55.000 0.00 0.00 42.58 4.49
2656 3246 1.493772 CGTGTTCTGGAACGCTTGTA 58.506 50.000 20.00 0.00 46.44 2.41
2680 3280 3.190874 GAGAAGAAGAATACCAGTGCCG 58.809 50.000 0.00 0.00 0.00 5.69
2783 3394 6.375174 CAGGTGATTTTACATGGATGACAGAA 59.625 38.462 0.00 0.00 0.00 3.02
2787 3398 7.120579 TGTTACAGGTGATTTTACATGGATGAC 59.879 37.037 0.00 0.00 36.72 3.06
2788 3399 7.120579 GTGTTACAGGTGATTTTACATGGATGA 59.879 37.037 0.00 0.00 36.72 2.92
2791 3402 6.205853 GTGTGTTACAGGTGATTTTACATGGA 59.794 38.462 0.00 0.00 36.72 3.41
2793 3404 6.077197 CGTGTGTTACAGGTGATTTTACATG 58.923 40.000 0.00 0.00 38.25 3.21
2816 3441 2.661566 CGTCTCCAACACAGCAGCG 61.662 63.158 0.00 0.00 0.00 5.18
2817 3442 0.880278 TTCGTCTCCAACACAGCAGC 60.880 55.000 0.00 0.00 0.00 5.25
2842 4039 9.574401 GTTATAGTACGTACTAGCTAAACTTCG 57.426 37.037 32.35 0.00 41.62 3.79
2851 4048 9.994432 TTCTTTTCTGTTATAGTACGTACTAGC 57.006 33.333 32.35 25.18 41.62 3.42
2855 4052 7.756722 TGCCTTCTTTTCTGTTATAGTACGTAC 59.243 37.037 18.10 18.10 0.00 3.67
2856 4053 7.829725 TGCCTTCTTTTCTGTTATAGTACGTA 58.170 34.615 0.00 0.00 0.00 3.57
2859 4056 9.989869 GATTTGCCTTCTTTTCTGTTATAGTAC 57.010 33.333 0.00 0.00 0.00 2.73
2860 4057 8.879759 CGATTTGCCTTCTTTTCTGTTATAGTA 58.120 33.333 0.00 0.00 0.00 1.82
2862 4059 6.688813 GCGATTTGCCTTCTTTTCTGTTATAG 59.311 38.462 0.00 0.00 37.76 1.31
2863 4060 6.551736 GCGATTTGCCTTCTTTTCTGTTATA 58.448 36.000 0.00 0.00 37.76 0.98
2865 4062 4.794169 GCGATTTGCCTTCTTTTCTGTTA 58.206 39.130 0.00 0.00 37.76 2.41
2897 4099 4.699735 CCATAATCTAACAACACAGCACCA 59.300 41.667 0.00 0.00 0.00 4.17
2902 4104 5.163723 CCACTGCCATAATCTAACAACACAG 60.164 44.000 0.00 0.00 0.00 3.66
2906 4108 5.880332 TCTTCCACTGCCATAATCTAACAAC 59.120 40.000 0.00 0.00 0.00 3.32
2907 4109 6.061022 TCTTCCACTGCCATAATCTAACAA 57.939 37.500 0.00 0.00 0.00 2.83
2908 4110 5.425217 TCTCTTCCACTGCCATAATCTAACA 59.575 40.000 0.00 0.00 0.00 2.41
2909 4111 5.918608 TCTCTTCCACTGCCATAATCTAAC 58.081 41.667 0.00 0.00 0.00 2.34
2912 4114 4.472833 ACTTCTCTTCCACTGCCATAATCT 59.527 41.667 0.00 0.00 0.00 2.40
2922 4124 4.896482 ACAACTAGTCACTTCTCTTCCACT 59.104 41.667 0.00 0.00 0.00 4.00
2923 4125 5.203060 ACAACTAGTCACTTCTCTTCCAC 57.797 43.478 0.00 0.00 0.00 4.02
2929 4131 4.932200 CCCATGAACAACTAGTCACTTCTC 59.068 45.833 0.00 0.00 0.00 2.87
2931 4133 4.894784 TCCCATGAACAACTAGTCACTTC 58.105 43.478 0.00 0.00 0.00 3.01
2935 4137 4.072131 GCTTTCCCATGAACAACTAGTCA 58.928 43.478 0.00 0.00 0.00 3.41
2939 4141 4.250464 CGTAGCTTTCCCATGAACAACTA 58.750 43.478 0.00 0.00 0.00 2.24
2940 4142 3.074412 CGTAGCTTTCCCATGAACAACT 58.926 45.455 0.00 0.00 0.00 3.16
2969 4186 1.067354 CACAGAGGCTGCCAAAAATCC 60.067 52.381 22.65 0.68 34.37 3.01
2998 4227 1.001764 CCAGCAGAGGACAATGCCA 60.002 57.895 0.00 0.00 43.60 4.92
2999 4228 1.001641 ACCAGCAGAGGACAATGCC 60.002 57.895 0.00 0.00 43.60 4.40
3004 4233 1.071987 CAAGCACCAGCAGAGGACA 59.928 57.895 0.00 0.00 45.49 4.02
3016 4245 2.341176 CCTGCCAAAGCCAAGCAC 59.659 61.111 0.00 0.00 38.69 4.40
3017 4246 3.618750 GCCTGCCAAAGCCAAGCA 61.619 61.111 0.00 0.00 38.69 3.91
3019 4248 2.985282 TCGCCTGCCAAAGCCAAG 60.985 61.111 0.00 0.00 38.69 3.61
3020 4249 2.985282 CTCGCCTGCCAAAGCCAA 60.985 61.111 0.00 0.00 38.69 4.52
3021 4250 3.790416 AACTCGCCTGCCAAAGCCA 62.790 57.895 0.00 0.00 38.69 4.75
3022 4251 2.985847 AACTCGCCTGCCAAAGCC 60.986 61.111 0.00 0.00 38.69 4.35
3023 4252 2.256461 CAACTCGCCTGCCAAAGC 59.744 61.111 0.00 0.00 40.48 3.51
3024 4253 1.283793 CACAACTCGCCTGCCAAAG 59.716 57.895 0.00 0.00 0.00 2.77
3025 4254 2.192861 CCACAACTCGCCTGCCAAA 61.193 57.895 0.00 0.00 0.00 3.28
3026 4255 2.594303 CCACAACTCGCCTGCCAA 60.594 61.111 0.00 0.00 0.00 4.52
3029 4258 2.639286 CAACCACAACTCGCCTGC 59.361 61.111 0.00 0.00 0.00 4.85
3030 4259 2.260869 CCCAACCACAACTCGCCTG 61.261 63.158 0.00 0.00 0.00 4.85
3031 4260 2.113139 CCCAACCACAACTCGCCT 59.887 61.111 0.00 0.00 0.00 5.52
3032 4261 2.203294 ACCCAACCACAACTCGCC 60.203 61.111 0.00 0.00 0.00 5.54
3033 4262 3.030652 CACCCAACCACAACTCGC 58.969 61.111 0.00 0.00 0.00 5.03
3034 4263 2.551912 GGCACCCAACCACAACTCG 61.552 63.158 0.00 0.00 0.00 4.18
3035 4264 1.152756 AGGCACCCAACCACAACTC 60.153 57.895 0.00 0.00 0.00 3.01
3036 4265 1.455587 CAGGCACCCAACCACAACT 60.456 57.895 0.00 0.00 0.00 3.16
3037 4266 3.128375 CAGGCACCCAACCACAAC 58.872 61.111 0.00 0.00 0.00 3.32
3038 4267 2.837291 GCAGGCACCCAACCACAA 60.837 61.111 0.00 0.00 0.00 3.33
3039 4268 4.912395 GGCAGGCACCCAACCACA 62.912 66.667 0.00 0.00 0.00 4.17
3040 4269 2.706952 TTAGGCAGGCACCCAACCAC 62.707 60.000 0.00 0.00 0.00 4.16
3041 4270 2.012824 TTTAGGCAGGCACCCAACCA 62.013 55.000 0.00 0.00 0.00 3.67
3042 4271 0.830023 TTTTAGGCAGGCACCCAACC 60.830 55.000 0.00 0.00 0.00 3.77
3043 4272 0.317160 GTTTTAGGCAGGCACCCAAC 59.683 55.000 0.00 0.00 0.00 3.77
3044 4273 1.175983 CGTTTTAGGCAGGCACCCAA 61.176 55.000 0.00 0.00 0.00 4.12
3045 4274 1.602323 CGTTTTAGGCAGGCACCCA 60.602 57.895 0.00 0.00 0.00 4.51
3046 4275 1.176619 AACGTTTTAGGCAGGCACCC 61.177 55.000 0.00 0.00 0.00 4.61
3047 4276 0.240145 GAACGTTTTAGGCAGGCACC 59.760 55.000 0.46 0.00 0.00 5.01
3048 4277 0.110373 CGAACGTTTTAGGCAGGCAC 60.110 55.000 0.46 0.00 0.00 5.01
3058 4287 0.110373 GCGCCTGATTCGAACGTTTT 60.110 50.000 0.46 0.00 0.00 2.43
3195 4516 4.323477 CTTTGCGGGTGACGGGGA 62.323 66.667 0.00 0.00 44.51 4.81
3200 4521 2.010582 TTTGTGCCTTTGCGGGTGAC 62.011 55.000 0.00 0.00 41.78 3.67
3201 4522 1.733402 CTTTGTGCCTTTGCGGGTGA 61.733 55.000 0.00 0.00 41.78 4.02
3204 4525 1.172180 TCTCTTTGTGCCTTTGCGGG 61.172 55.000 0.00 0.00 41.78 6.13
3205 4526 0.239347 CTCTCTTTGTGCCTTTGCGG 59.761 55.000 0.00 0.00 41.78 5.69
3206 4527 0.239347 CCTCTCTTTGTGCCTTTGCG 59.761 55.000 0.00 0.00 41.78 4.85
3207 4528 1.538950 CTCCTCTCTTTGTGCCTTTGC 59.461 52.381 0.00 0.00 38.26 3.68
3208 4529 2.157738 CCTCCTCTCTTTGTGCCTTTG 58.842 52.381 0.00 0.00 0.00 2.77
3209 4530 1.074566 CCCTCCTCTCTTTGTGCCTTT 59.925 52.381 0.00 0.00 0.00 3.11
3210 4531 0.695347 CCCTCCTCTCTTTGTGCCTT 59.305 55.000 0.00 0.00 0.00 4.35
3211 4532 1.204113 CCCCTCCTCTCTTTGTGCCT 61.204 60.000 0.00 0.00 0.00 4.75
3212 4533 1.201429 TCCCCTCCTCTCTTTGTGCC 61.201 60.000 0.00 0.00 0.00 5.01
3223 4544 3.700350 CCAGTCCCCTCCCCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
3229 4550 2.766229 GCTCCTCCAGTCCCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
3231 4552 3.673597 TCGCTCCTCCAGTCCCCT 61.674 66.667 0.00 0.00 0.00 4.79
3232 4553 3.462678 GTCGCTCCTCCAGTCCCC 61.463 72.222 0.00 0.00 0.00 4.81
3233 4554 3.827898 CGTCGCTCCTCCAGTCCC 61.828 72.222 0.00 0.00 0.00 4.46
3234 4555 2.750637 TCGTCGCTCCTCCAGTCC 60.751 66.667 0.00 0.00 0.00 3.85
3235 4556 2.486042 GTCGTCGCTCCTCCAGTC 59.514 66.667 0.00 0.00 0.00 3.51
3255 4576 3.669344 TGGAAAAAGCGCGGCAGG 61.669 61.111 8.83 0.00 0.00 4.85
3256 4577 2.429069 GTGGAAAAAGCGCGGCAG 60.429 61.111 8.83 0.00 0.00 4.85
3257 4578 3.972276 GGTGGAAAAAGCGCGGCA 61.972 61.111 8.83 0.00 0.00 5.69
3262 4583 1.586154 ATGGAGCGGTGGAAAAAGCG 61.586 55.000 0.00 0.00 43.66 4.68
3263 4584 0.171231 GATGGAGCGGTGGAAAAAGC 59.829 55.000 0.00 0.00 0.00 3.51
3264 4585 0.447801 CGATGGAGCGGTGGAAAAAG 59.552 55.000 0.00 0.00 0.00 2.27
3265 4586 0.958382 CCGATGGAGCGGTGGAAAAA 60.958 55.000 0.00 0.00 46.07 1.94
3266 4587 1.376683 CCGATGGAGCGGTGGAAAA 60.377 57.895 0.00 0.00 46.07 2.29
3267 4588 2.267642 CCGATGGAGCGGTGGAAA 59.732 61.111 0.00 0.00 46.07 3.13
3274 4595 0.108329 AAGTGGTAACCGATGGAGCG 60.108 55.000 0.00 0.00 0.00 5.03
3275 4596 2.547826 GTAAGTGGTAACCGATGGAGC 58.452 52.381 0.00 0.00 0.00 4.70
3276 4597 2.764572 AGGTAAGTGGTAACCGATGGAG 59.235 50.000 0.00 0.00 40.88 3.86
3277 4598 2.762327 GAGGTAAGTGGTAACCGATGGA 59.238 50.000 0.00 0.00 40.88 3.41
3278 4599 2.159000 GGAGGTAAGTGGTAACCGATGG 60.159 54.545 0.00 0.00 40.88 3.51
3279 4600 2.498481 TGGAGGTAAGTGGTAACCGATG 59.502 50.000 0.00 0.00 40.88 3.84
3280 4601 2.498885 GTGGAGGTAAGTGGTAACCGAT 59.501 50.000 0.00 0.00 40.88 4.18
3281 4602 1.895131 GTGGAGGTAAGTGGTAACCGA 59.105 52.381 0.00 0.00 40.88 4.69
3282 4603 1.897802 AGTGGAGGTAAGTGGTAACCG 59.102 52.381 0.00 0.00 40.88 4.44
3283 4604 2.614734 GCAGTGGAGGTAAGTGGTAACC 60.615 54.545 0.00 0.00 35.91 2.85
3284 4605 2.302157 AGCAGTGGAGGTAAGTGGTAAC 59.698 50.000 0.00 0.00 0.00 2.50
3285 4606 2.616524 AGCAGTGGAGGTAAGTGGTAA 58.383 47.619 0.00 0.00 0.00 2.85
3286 4607 2.320681 AGCAGTGGAGGTAAGTGGTA 57.679 50.000 0.00 0.00 0.00 3.25
3287 4608 1.900486 GTAGCAGTGGAGGTAAGTGGT 59.100 52.381 0.00 0.00 33.48 4.16
3288 4609 2.166664 GAGTAGCAGTGGAGGTAAGTGG 59.833 54.545 0.00 0.00 0.00 4.00
3289 4610 3.093057 AGAGTAGCAGTGGAGGTAAGTG 58.907 50.000 0.00 0.00 0.00 3.16
3290 4611 3.010808 AGAGAGTAGCAGTGGAGGTAAGT 59.989 47.826 0.00 0.00 0.00 2.24
3291 4612 3.626930 AGAGAGTAGCAGTGGAGGTAAG 58.373 50.000 0.00 0.00 0.00 2.34
3292 4613 3.622630 GAGAGAGTAGCAGTGGAGGTAA 58.377 50.000 0.00 0.00 0.00 2.85
3293 4614 2.092321 GGAGAGAGTAGCAGTGGAGGTA 60.092 54.545 0.00 0.00 0.00 3.08
3294 4615 1.341581 GGAGAGAGTAGCAGTGGAGGT 60.342 57.143 0.00 0.00 0.00 3.85
3295 4616 1.398692 GGAGAGAGTAGCAGTGGAGG 58.601 60.000 0.00 0.00 0.00 4.30
3296 4617 1.398692 GGGAGAGAGTAGCAGTGGAG 58.601 60.000 0.00 0.00 0.00 3.86
3297 4618 0.033011 GGGGAGAGAGTAGCAGTGGA 60.033 60.000 0.00 0.00 0.00 4.02
3298 4619 0.032615 AGGGGAGAGAGTAGCAGTGG 60.033 60.000 0.00 0.00 0.00 4.00
3299 4620 1.064017 AGAGGGGAGAGAGTAGCAGTG 60.064 57.143 0.00 0.00 0.00 3.66
3300 4621 1.304891 AGAGGGGAGAGAGTAGCAGT 58.695 55.000 0.00 0.00 0.00 4.40
3301 4622 2.306847 GAAGAGGGGAGAGAGTAGCAG 58.693 57.143 0.00 0.00 0.00 4.24
3302 4623 1.063567 GGAAGAGGGGAGAGAGTAGCA 60.064 57.143 0.00 0.00 0.00 3.49
3303 4624 1.216930 AGGAAGAGGGGAGAGAGTAGC 59.783 57.143 0.00 0.00 0.00 3.58
3304 4625 3.204382 AGAAGGAAGAGGGGAGAGAGTAG 59.796 52.174 0.00 0.00 0.00 2.57
3305 4626 3.203059 AGAAGGAAGAGGGGAGAGAGTA 58.797 50.000 0.00 0.00 0.00 2.59
3310 4631 2.657459 AGAAGAGAAGGAAGAGGGGAGA 59.343 50.000 0.00 0.00 0.00 3.71
3313 4634 3.035363 GGTAGAAGAGAAGGAAGAGGGG 58.965 54.545 0.00 0.00 0.00 4.79
3322 4643 1.064357 GACGCGGAGGTAGAAGAGAAG 59.936 57.143 12.47 0.00 0.00 2.85
3327 4648 1.352404 CGAGACGCGGAGGTAGAAG 59.648 63.158 12.47 0.00 36.03 2.85
3328 4649 3.494378 CGAGACGCGGAGGTAGAA 58.506 61.111 12.47 0.00 36.03 2.10
3338 4724 3.053849 GAGTGAGACCCCGAGACGC 62.054 68.421 0.00 0.00 0.00 5.19
3347 4733 3.083997 ATGGGCGGGAGTGAGACC 61.084 66.667 0.00 0.00 0.00 3.85
3349 4735 3.083349 CCATGGGCGGGAGTGAGA 61.083 66.667 2.85 0.00 0.00 3.27
3566 5006 0.611200 CGGTGGACTGGATGGTGTTA 59.389 55.000 0.00 0.00 0.00 2.41
3596 5036 1.915769 GAGGAGACCCTGTGGCAGT 60.916 63.158 0.00 0.00 44.53 4.40
3597 5037 1.897225 CTGAGGAGACCCTGTGGCAG 61.897 65.000 0.00 0.00 44.53 4.85
3598 5038 1.915266 CTGAGGAGACCCTGTGGCA 60.915 63.158 0.00 0.00 44.53 4.92
3599 5039 2.985456 CTGAGGAGACCCTGTGGC 59.015 66.667 0.00 0.00 44.53 5.01
3600 5040 2.664081 GGCTGAGGAGACCCTGTGG 61.664 68.421 0.00 0.00 44.53 4.17
3601 5041 2.985456 GGCTGAGGAGACCCTGTG 59.015 66.667 0.00 0.00 44.53 3.66
3602 5042 2.681778 CGGCTGAGGAGACCCTGT 60.682 66.667 0.00 0.00 44.53 4.00
3603 5043 4.154347 GCGGCTGAGGAGACCCTG 62.154 72.222 0.00 0.00 44.53 4.45
3611 5051 2.852495 TTAAGAAGGCGCGGCTGAGG 62.852 60.000 36.94 0.00 0.00 3.86
3612 5052 0.811616 ATTAAGAAGGCGCGGCTGAG 60.812 55.000 36.94 0.00 0.00 3.35
3613 5053 0.392461 AATTAAGAAGGCGCGGCTGA 60.392 50.000 36.94 18.66 0.00 4.26
3614 5054 1.003866 GTAATTAAGAAGGCGCGGCTG 60.004 52.381 36.94 0.00 0.00 4.85
3615 5055 1.134491 AGTAATTAAGAAGGCGCGGCT 60.134 47.619 31.39 31.39 0.00 5.52
3616 5056 1.296727 AGTAATTAAGAAGGCGCGGC 58.703 50.000 27.06 27.06 0.00 6.53
3617 5057 4.117685 AGTAAGTAATTAAGAAGGCGCGG 58.882 43.478 8.83 0.00 0.00 6.46
3618 5058 5.713822 AAGTAAGTAATTAAGAAGGCGCG 57.286 39.130 0.00 0.00 0.00 6.86


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

AutoCloner maintained by Alex Coulton.