Multiple sequence alignment - TraesCS6B01G309100

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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 TraesCS6B01G309100 chr6B 100.000 4091 0 0 1 4091 553379154 553375064 0.000000e+00 7555.0
1 TraesCS6B01G309100 chr6B 89.896 673 40 15 1 649 666778131 666777463 0.000000e+00 841.0
2 TraesCS6B01G309100 chr6B 81.492 362 48 10 1378 1734 553377313 553376966 3.110000e-71 279.0
3 TraesCS6B01G309100 chr6B 81.492 362 48 9 1842 2189 553377777 553377421 3.110000e-71 279.0
4 TraesCS6B01G309100 chr6D 95.400 1413 53 6 2685 4088 368302763 368304172 0.000000e+00 2239.0
5 TraesCS6B01G309100 chr6D 90.963 1173 58 15 894 2018 368300980 368302152 0.000000e+00 1535.0
6 TraesCS6B01G309100 chr6D 90.641 577 36 7 2015 2591 368302181 368302739 0.000000e+00 750.0
7 TraesCS6B01G309100 chr6D 91.405 477 29 8 945 1410 368212650 368213125 0.000000e+00 643.0
8 TraesCS6B01G309100 chr6D 89.130 92 8 2 1452 1541 368298652 368298743 3.340000e-21 113.0
9 TraesCS6B01G309100 chr6D 89.873 79 7 1 769 847 368300912 368300989 2.600000e-17 100.0
10 TraesCS6B01G309100 chr6A 90.373 1475 86 20 894 2313 508846717 508848190 0.000000e+00 1886.0
11 TraesCS6B01G309100 chr6A 95.186 1101 48 4 2685 3782 508848596 508849694 0.000000e+00 1735.0
12 TraesCS6B01G309100 chr6A 93.590 312 13 3 3785 4089 508849737 508850048 3.730000e-125 459.0
13 TraesCS6B01G309100 chr6A 92.000 300 17 4 2318 2617 508848295 508848587 8.180000e-112 414.0
14 TraesCS6B01G309100 chr2B 97.535 649 13 2 1 647 697137678 697137031 0.000000e+00 1107.0
15 TraesCS6B01G309100 chr2B 90.462 671 38 14 1 649 204918740 204919406 0.000000e+00 861.0
16 TraesCS6B01G309100 chr2B 92.220 527 38 3 124 650 96147766 96147243 0.000000e+00 743.0
17 TraesCS6B01G309100 chr1B 90.812 653 34 12 1 630 660690064 660690713 0.000000e+00 850.0
18 TraesCS6B01G309100 chr1B 89.728 662 45 14 1 642 527381906 527381248 0.000000e+00 824.0
19 TraesCS6B01G309100 chr1B 88.872 647 62 10 1 642 108553235 108552594 0.000000e+00 787.0
20 TraesCS6B01G309100 chr7B 89.339 666 44 15 1 642 403411351 403410689 0.000000e+00 811.0
21 TraesCS6B01G309100 chr7B 88.722 665 41 12 1 642 567571364 567570711 0.000000e+00 782.0
22 TraesCS6B01G309100 chr7B 87.112 419 30 10 1 397 567571826 567571410 1.730000e-123 453.0
23 TraesCS6B01G309100 chr5B 89.785 558 48 7 90 642 92841628 92842181 0.000000e+00 706.0
24 TraesCS6B01G309100 chr5B 87.342 79 9 1 3 80 92841512 92841590 5.630000e-14 89.8


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 TraesCS6B01G309100 chr6B 553375064 553379154 4090 True 2704.333333 7555 87.661333 1 4091 3 chr6B.!!$R2 4090
1 TraesCS6B01G309100 chr6B 666777463 666778131 668 True 841.000000 841 89.896000 1 649 1 chr6B.!!$R1 648
2 TraesCS6B01G309100 chr6D 368298652 368304172 5520 False 947.400000 2239 91.201400 769 4088 5 chr6D.!!$F2 3319
3 TraesCS6B01G309100 chr6A 508846717 508850048 3331 False 1123.500000 1886 92.787250 894 4089 4 chr6A.!!$F1 3195
4 TraesCS6B01G309100 chr2B 697137031 697137678 647 True 1107.000000 1107 97.535000 1 647 1 chr2B.!!$R2 646
5 TraesCS6B01G309100 chr2B 204918740 204919406 666 False 861.000000 861 90.462000 1 649 1 chr2B.!!$F1 648
6 TraesCS6B01G309100 chr2B 96147243 96147766 523 True 743.000000 743 92.220000 124 650 1 chr2B.!!$R1 526
7 TraesCS6B01G309100 chr1B 660690064 660690713 649 False 850.000000 850 90.812000 1 630 1 chr1B.!!$F1 629
8 TraesCS6B01G309100 chr1B 527381248 527381906 658 True 824.000000 824 89.728000 1 642 1 chr1B.!!$R2 641
9 TraesCS6B01G309100 chr1B 108552594 108553235 641 True 787.000000 787 88.872000 1 642 1 chr1B.!!$R1 641
10 TraesCS6B01G309100 chr7B 403410689 403411351 662 True 811.000000 811 89.339000 1 642 1 chr7B.!!$R1 641
11 TraesCS6B01G309100 chr7B 567570711 567571826 1115 True 617.500000 782 87.917000 1 642 2 chr7B.!!$R2 641
12 TraesCS6B01G309100 chr5B 92841512 92842181 669 False 397.900000 706 88.563500 3 642 2 chr5B.!!$F1 639

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
690 1192 0.603707 AATCATCCGGCCTGTATGCG 60.604 55.0 0.00 0.00 0.00 4.73 F
1481 2986 0.027586 GGCATACGCAATTGACGACC 59.972 55.0 22.87 15.65 41.24 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 3529 0.316196 GCAACGCATCGCCTATTCAC 60.316 55.0 0.0 0.0 0.0 3.18 R
3111 4803 0.387565 TCACTACACGCTCTGCACAA 59.612 50.0 0.0 0.0 0.0 3.33 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
102 118 2.431454 CTTCCAGGGCTTTCACTCTTC 58.569 52.381 0.00 0.00 0.00 2.87
116 132 3.875134 TCACTCTTCTGTTCCGGTTTTTC 59.125 43.478 0.00 0.00 0.00 2.29
313 348 7.558137 GCCTTGCATTATAAAAATGTTCATCG 58.442 34.615 0.00 0.00 0.00 3.84
654 1156 3.983741 CGTGAGGTCTCAAGTTTTCTCT 58.016 45.455 1.86 0.00 41.85 3.10
657 1159 4.926832 GTGAGGTCTCAAGTTTTCTCTAGC 59.073 45.833 1.86 0.00 41.85 3.42
658 1160 4.021016 TGAGGTCTCAAGTTTTCTCTAGCC 60.021 45.833 0.00 0.00 36.53 3.93
660 1162 3.056749 GGTCTCAAGTTTTCTCTAGCCGA 60.057 47.826 0.00 0.00 0.00 5.54
661 1163 4.557205 GTCTCAAGTTTTCTCTAGCCGAA 58.443 43.478 0.00 0.00 0.00 4.30
662 1164 4.989168 GTCTCAAGTTTTCTCTAGCCGAAA 59.011 41.667 3.75 3.75 0.00 3.46
664 1166 5.696724 TCTCAAGTTTTCTCTAGCCGAAAAG 59.303 40.000 15.59 7.72 40.02 2.27
665 1167 5.607477 TCAAGTTTTCTCTAGCCGAAAAGA 58.393 37.500 15.59 9.81 40.02 2.52
667 1169 4.957296 AGTTTTCTCTAGCCGAAAAGACA 58.043 39.130 15.59 0.00 40.02 3.41
668 1170 5.365619 AGTTTTCTCTAGCCGAAAAGACAA 58.634 37.500 15.59 0.00 40.02 3.18
669 1171 5.467063 AGTTTTCTCTAGCCGAAAAGACAAG 59.533 40.000 15.59 0.00 40.02 3.16
670 1172 4.866508 TTCTCTAGCCGAAAAGACAAGA 57.133 40.909 0.00 0.00 0.00 3.02
672 1174 5.209818 TCTCTAGCCGAAAAGACAAGAAA 57.790 39.130 0.00 0.00 0.00 2.52
673 1175 5.794894 TCTCTAGCCGAAAAGACAAGAAAT 58.205 37.500 0.00 0.00 0.00 2.17
674 1176 5.869888 TCTCTAGCCGAAAAGACAAGAAATC 59.130 40.000 0.00 0.00 0.00 2.17
676 1178 6.173339 TCTAGCCGAAAAGACAAGAAATCAT 58.827 36.000 0.00 0.00 0.00 2.45
678 1180 4.156739 AGCCGAAAAGACAAGAAATCATCC 59.843 41.667 0.00 0.00 0.00 3.51
679 1181 4.651994 CCGAAAAGACAAGAAATCATCCG 58.348 43.478 0.00 0.00 0.00 4.18
681 1183 4.415735 GAAAAGACAAGAAATCATCCGGC 58.584 43.478 0.00 0.00 0.00 6.13
682 1184 2.044123 AGACAAGAAATCATCCGGCC 57.956 50.000 0.00 0.00 0.00 6.13
683 1185 1.561542 AGACAAGAAATCATCCGGCCT 59.438 47.619 0.00 0.00 0.00 5.19
684 1186 1.672881 GACAAGAAATCATCCGGCCTG 59.327 52.381 0.00 0.00 0.00 4.85
686 1188 2.238646 ACAAGAAATCATCCGGCCTGTA 59.761 45.455 0.00 0.00 0.00 2.74
687 1189 3.117888 ACAAGAAATCATCCGGCCTGTAT 60.118 43.478 0.00 0.00 0.00 2.29
688 1190 3.131709 AGAAATCATCCGGCCTGTATG 57.868 47.619 0.00 1.53 0.00 2.39
689 1191 1.537202 GAAATCATCCGGCCTGTATGC 59.463 52.381 0.00 0.00 0.00 3.14
690 1192 0.603707 AATCATCCGGCCTGTATGCG 60.604 55.000 0.00 0.00 0.00 4.73
691 1193 3.349006 CATCCGGCCTGTATGCGC 61.349 66.667 0.00 0.00 0.00 6.09
696 1198 4.794648 GGCCTGTATGCGCCCACA 62.795 66.667 4.18 8.07 39.39 4.17
697 1199 2.749839 GCCTGTATGCGCCCACAA 60.750 61.111 4.18 0.00 0.00 3.33
698 1200 2.339556 GCCTGTATGCGCCCACAAA 61.340 57.895 4.18 0.00 0.00 2.83
699 1201 1.666209 GCCTGTATGCGCCCACAAAT 61.666 55.000 4.18 0.00 0.00 2.32
700 1202 1.674359 CCTGTATGCGCCCACAAATA 58.326 50.000 4.18 0.00 0.00 1.40
701 1203 1.603802 CCTGTATGCGCCCACAAATAG 59.396 52.381 4.18 0.00 0.00 1.73
702 1204 1.002468 CTGTATGCGCCCACAAATAGC 60.002 52.381 4.18 0.00 0.00 2.97
703 1205 1.021202 GTATGCGCCCACAAATAGCA 58.979 50.000 4.18 0.00 42.28 3.49
705 1207 2.008268 ATGCGCCCACAAATAGCAGC 62.008 55.000 4.18 0.00 41.34 5.25
706 1208 2.800736 CGCCCACAAATAGCAGCC 59.199 61.111 0.00 0.00 0.00 4.85
707 1209 2.774799 CGCCCACAAATAGCAGCCC 61.775 63.158 0.00 0.00 0.00 5.19
709 1211 1.044790 GCCCACAAATAGCAGCCCAT 61.045 55.000 0.00 0.00 0.00 4.00
710 1212 1.753847 GCCCACAAATAGCAGCCCATA 60.754 52.381 0.00 0.00 0.00 2.74
711 1213 2.665165 CCCACAAATAGCAGCCCATAA 58.335 47.619 0.00 0.00 0.00 1.90
712 1214 2.362077 CCCACAAATAGCAGCCCATAAC 59.638 50.000 0.00 0.00 0.00 1.89
714 1216 3.316308 CCACAAATAGCAGCCCATAACTC 59.684 47.826 0.00 0.00 0.00 3.01
715 1217 3.002656 CACAAATAGCAGCCCATAACTCG 59.997 47.826 0.00 0.00 0.00 4.18
718 1220 1.407656 TAGCAGCCCATAACTCGGGG 61.408 60.000 0.00 0.00 44.67 5.73
727 1229 4.819105 CCATAACTCGGGGAGCATATAA 57.181 45.455 0.00 0.00 32.04 0.98
729 1231 4.504858 CATAACTCGGGGAGCATATAACC 58.495 47.826 0.00 0.00 32.04 2.85
730 1232 1.349067 ACTCGGGGAGCATATAACCC 58.651 55.000 0.00 0.00 42.58 4.11
731 1233 1.132817 ACTCGGGGAGCATATAACCCT 60.133 52.381 0.00 0.00 42.86 4.34
732 1234 2.111255 ACTCGGGGAGCATATAACCCTA 59.889 50.000 0.00 0.00 42.86 3.53
733 1235 2.761208 CTCGGGGAGCATATAACCCTAG 59.239 54.545 0.00 0.00 42.86 3.02
734 1236 1.207329 CGGGGAGCATATAACCCTAGC 59.793 57.143 0.00 0.00 42.86 3.42
735 1237 1.560146 GGGGAGCATATAACCCTAGCC 59.440 57.143 0.00 0.00 42.86 3.93
736 1238 1.560146 GGGAGCATATAACCCTAGCCC 59.440 57.143 0.00 0.00 40.39 5.19
737 1239 2.266279 GGAGCATATAACCCTAGCCCA 58.734 52.381 0.00 0.00 0.00 5.36
738 1240 2.237392 GGAGCATATAACCCTAGCCCAG 59.763 54.545 0.00 0.00 0.00 4.45
740 1242 3.583086 GAGCATATAACCCTAGCCCAGAA 59.417 47.826 0.00 0.00 0.00 3.02
742 1244 3.870299 GCATATAACCCTAGCCCAGAAGC 60.870 52.174 0.00 0.00 0.00 3.86
743 1245 0.759346 ATAACCCTAGCCCAGAAGCG 59.241 55.000 0.00 0.00 38.01 4.68
744 1246 1.968050 TAACCCTAGCCCAGAAGCGC 61.968 60.000 0.00 0.00 38.01 5.92
745 1247 4.554036 CCCTAGCCCAGAAGCGCC 62.554 72.222 2.29 0.00 38.01 6.53
746 1248 4.899239 CCTAGCCCAGAAGCGCCG 62.899 72.222 2.29 0.00 38.01 6.46
747 1249 4.899239 CTAGCCCAGAAGCGCCGG 62.899 72.222 2.29 0.00 38.01 6.13
754 1256 4.408821 AGAAGCGCCGGCCATGAA 62.409 61.111 23.46 0.00 41.24 2.57
755 1257 3.211963 GAAGCGCCGGCCATGAAT 61.212 61.111 23.46 0.44 41.24 2.57
756 1258 3.474230 GAAGCGCCGGCCATGAATG 62.474 63.158 23.46 5.76 41.24 2.67
759 1261 2.848858 GCGCCGGCCATGAATGAAT 61.849 57.895 23.46 0.00 0.00 2.57
777 2270 2.332063 ATTCAGTTACCTGGATGCGG 57.668 50.000 0.00 0.00 35.47 5.69
803 2296 1.520787 CACGGGCTTACGGGCTTAG 60.521 63.158 0.00 0.00 40.65 2.18
845 2338 3.861276 GGCAACTAACCCAATACCAAC 57.139 47.619 0.00 0.00 0.00 3.77
846 2339 2.494471 GGCAACTAACCCAATACCAACC 59.506 50.000 0.00 0.00 0.00 3.77
847 2340 3.427573 GCAACTAACCCAATACCAACCT 58.572 45.455 0.00 0.00 0.00 3.50
848 2341 3.442625 GCAACTAACCCAATACCAACCTC 59.557 47.826 0.00 0.00 0.00 3.85
849 2342 4.809691 GCAACTAACCCAATACCAACCTCT 60.810 45.833 0.00 0.00 0.00 3.69
850 2343 4.838904 ACTAACCCAATACCAACCTCTC 57.161 45.455 0.00 0.00 0.00 3.20
851 2344 3.522343 ACTAACCCAATACCAACCTCTCC 59.478 47.826 0.00 0.00 0.00 3.71
852 2345 2.361085 ACCCAATACCAACCTCTCCT 57.639 50.000 0.00 0.00 0.00 3.69
853 2346 3.502051 ACCCAATACCAACCTCTCCTA 57.498 47.619 0.00 0.00 0.00 2.94
854 2347 3.810623 ACCCAATACCAACCTCTCCTAA 58.189 45.455 0.00 0.00 0.00 2.69
855 2348 4.180723 ACCCAATACCAACCTCTCCTAAA 58.819 43.478 0.00 0.00 0.00 1.85
856 2349 4.604490 ACCCAATACCAACCTCTCCTAAAA 59.396 41.667 0.00 0.00 0.00 1.52
857 2350 5.075344 ACCCAATACCAACCTCTCCTAAAAA 59.925 40.000 0.00 0.00 0.00 1.94
879 2372 5.447624 AAAAACTCCAATACCAACCGAAG 57.552 39.130 0.00 0.00 0.00 3.79
880 2373 3.782656 AACTCCAATACCAACCGAAGT 57.217 42.857 0.00 0.00 0.00 3.01
881 2374 3.782656 ACTCCAATACCAACCGAAGTT 57.217 42.857 0.00 0.00 36.33 2.66
882 2375 4.895668 ACTCCAATACCAACCGAAGTTA 57.104 40.909 0.00 0.00 33.27 2.24
883 2376 5.231702 ACTCCAATACCAACCGAAGTTAA 57.768 39.130 0.00 0.00 33.27 2.01
884 2377 5.243207 ACTCCAATACCAACCGAAGTTAAG 58.757 41.667 0.00 0.00 33.27 1.85
885 2378 4.581868 TCCAATACCAACCGAAGTTAAGG 58.418 43.478 0.00 0.00 33.27 2.69
886 2379 4.041938 TCCAATACCAACCGAAGTTAAGGT 59.958 41.667 0.00 0.00 43.68 3.50
887 2380 5.248020 TCCAATACCAACCGAAGTTAAGGTA 59.752 40.000 3.24 0.00 40.37 3.08
888 2381 5.939296 CCAATACCAACCGAAGTTAAGGTAA 59.061 40.000 3.24 0.00 37.79 2.85
889 2382 6.600427 CCAATACCAACCGAAGTTAAGGTAAT 59.400 38.462 3.24 0.00 37.79 1.89
891 2384 5.494390 ACCAACCGAAGTTAAGGTAATCT 57.506 39.130 3.24 0.00 40.37 2.40
892 2385 5.872963 ACCAACCGAAGTTAAGGTAATCTT 58.127 37.500 3.24 0.00 40.37 2.40
943 2438 1.884235 CTACGGGGCAGATCAAATCC 58.116 55.000 0.00 0.00 0.00 3.01
963 2458 0.615850 GGGCAGGAAGTAGCTCAACT 59.384 55.000 0.00 0.00 0.00 3.16
1107 2603 4.367023 GTGGCGGTGGTGCTCGTA 62.367 66.667 0.00 0.00 34.52 3.43
1344 2840 3.072468 TCCTCCGCCGGTAGGTTG 61.072 66.667 17.42 10.84 40.50 3.77
1347 2843 3.366739 CTCCGCCGGTAGGTTGACC 62.367 68.421 15.97 0.00 40.50 4.02
1449 2950 7.068348 TCGACCAAACTAGTAGCTATTCTGAAT 59.932 37.037 8.14 8.14 0.00 2.57
1450 2951 7.168302 CGACCAAACTAGTAGCTATTCTGAATG 59.832 40.741 13.01 4.63 0.00 2.67
1480 2985 0.724549 TGGCATACGCAATTGACGAC 59.275 50.000 22.87 12.06 41.24 4.34
1481 2986 0.027586 GGCATACGCAATTGACGACC 59.972 55.000 22.87 15.65 41.24 4.79
1482 2987 0.315059 GCATACGCAATTGACGACCG 60.315 55.000 22.87 13.30 38.36 4.79
1504 3017 1.941209 GCACTCATCTTGACCTGCGAA 60.941 52.381 0.00 0.00 0.00 4.70
1540 3054 1.587547 TGCGTTGTACTGTTGCATCA 58.412 45.000 0.00 0.00 0.00 3.07
1591 3106 7.398618 TGTCCTGATGGAATTTGCCTTAAAATA 59.601 33.333 0.00 0.00 45.18 1.40
1637 3152 0.107831 TTCAGTGTCCCCAAAGTCCG 59.892 55.000 0.00 0.00 0.00 4.79
1657 3172 4.021456 TCCGAAGATCAAACTAACAGCTGA 60.021 41.667 23.35 0.00 0.00 4.26
1735 3250 1.342474 CCCCTAAGACTCAGAGGCTCA 60.342 57.143 18.26 0.00 27.04 4.26
1736 3251 2.031120 CCCTAAGACTCAGAGGCTCAG 58.969 57.143 18.26 9.22 27.04 3.35
1737 3252 1.408702 CCTAAGACTCAGAGGCTCAGC 59.591 57.143 18.26 0.00 27.04 4.26
1738 3253 1.065401 CTAAGACTCAGAGGCTCAGCG 59.935 57.143 18.26 6.29 27.04 5.18
1740 3255 3.714871 GACTCAGAGGCTCAGCGGC 62.715 68.421 18.26 1.29 38.75 6.53
1809 3351 7.400052 ACCACTATTTTTCAGCCAATCCTTAAT 59.600 33.333 0.00 0.00 0.00 1.40
1833 3375 2.119495 GGATACCCTGCTCTTCTCCAA 58.881 52.381 0.00 0.00 0.00 3.53
1861 3411 0.310543 GTTCAGTTTGCCATGACGCA 59.689 50.000 0.00 0.00 36.85 5.24
1883 3434 4.414337 AGATTCAGTGAGGCCAGTAATC 57.586 45.455 5.01 5.40 0.00 1.75
1928 3479 7.467267 GCTCTTCTGAAACTGTATGTCAACAAA 60.467 37.037 0.00 0.00 0.00 2.83
1948 3499 2.917701 TGGCATACGCAATTGACAAG 57.082 45.000 10.34 0.00 41.24 3.16
1967 3521 6.437477 TGACAAGTATACACTCATCTTGACCT 59.563 38.462 5.50 0.00 38.82 3.85
1969 3523 6.211584 ACAAGTATACACTCATCTTGACCTGT 59.788 38.462 5.50 0.00 38.82 4.00
1975 3529 4.219507 ACACTCATCTTGACCTGTGACTAG 59.780 45.833 0.00 0.00 0.00 2.57
1989 3543 3.053455 GTGACTAGTGAATAGGCGATGC 58.947 50.000 0.00 0.00 43.24 3.91
2026 3612 6.089150 GCATCAGAATTGAAAGCTCAAACTTC 59.911 38.462 0.00 0.00 44.64 3.01
2092 3678 5.934402 TCTCTTACTATTTCAGTGACCCC 57.066 43.478 0.00 0.00 38.24 4.95
2103 3689 2.176798 TCAGTGACCCCAAAGTCCAAAT 59.823 45.455 0.00 0.00 35.83 2.32
2136 3722 4.471386 ACAGCTGGGTATTACTCACTGAAT 59.529 41.667 19.93 7.75 33.99 2.57
2143 3729 7.001674 TGGGTATTACTCACTGAATTGTGTTT 58.998 34.615 0.00 0.00 38.90 2.83
2144 3730 7.040755 TGGGTATTACTCACTGAATTGTGTTTG 60.041 37.037 0.00 0.00 38.90 2.93
2149 3735 0.673437 ACTGAATTGTGTTTGGGGCG 59.327 50.000 0.00 0.00 0.00 6.13
2189 3775 2.211353 GCCGTAAGACTAAGAGGCTG 57.789 55.000 0.00 0.00 41.21 4.85
2313 3899 7.561722 TGCAGGACACTAGACTAAGAAGATTAT 59.438 37.037 0.00 0.00 0.00 1.28
2314 3900 9.069082 GCAGGACACTAGACTAAGAAGATTATA 57.931 37.037 0.00 0.00 0.00 0.98
2340 4026 2.276732 TTTCTCAGAAGCAACCTGGG 57.723 50.000 0.00 0.00 33.51 4.45
2350 4036 0.811281 GCAACCTGGGCATTAGACAC 59.189 55.000 0.00 0.00 0.00 3.67
2358 4044 2.304470 TGGGCATTAGACACTTGTGCTA 59.696 45.455 0.10 1.53 36.15 3.49
2364 4050 5.817816 GCATTAGACACTTGTGCTATACCTT 59.182 40.000 0.10 0.00 33.25 3.50
2385 4071 1.522668 TTTTGGCCACTCATCTGTCG 58.477 50.000 3.88 0.00 0.00 4.35
2488 4174 3.093814 TGCTCCTAACTGGATTGACGTA 58.906 45.455 0.00 0.00 45.16 3.57
2497 4183 2.233922 CTGGATTGACGTACAAGGGTCT 59.766 50.000 0.00 0.00 42.02 3.85
2498 4184 2.635915 TGGATTGACGTACAAGGGTCTT 59.364 45.455 0.00 0.00 42.02 3.01
2499 4185 3.833650 TGGATTGACGTACAAGGGTCTTA 59.166 43.478 0.00 0.00 42.02 2.10
2500 4186 4.283978 TGGATTGACGTACAAGGGTCTTAA 59.716 41.667 0.00 0.00 42.02 1.85
2501 4187 4.868734 GGATTGACGTACAAGGGTCTTAAG 59.131 45.833 0.00 0.00 42.02 1.85
2502 4188 5.337009 GGATTGACGTACAAGGGTCTTAAGA 60.337 44.000 0.00 0.00 42.02 2.10
2506 4198 6.527423 TGACGTACAAGGGTCTTAAGATTTT 58.473 36.000 8.75 1.17 34.31 1.82
2509 4201 6.769341 ACGTACAAGGGTCTTAAGATTTTGTT 59.231 34.615 24.50 12.84 31.81 2.83
2527 4219 8.709386 ATTTTGTTATGTTAACACAGTGCAAA 57.291 26.923 11.22 14.01 35.94 3.68
2528 4220 7.513190 TTTGTTATGTTAACACAGTGCAAAC 57.487 32.000 11.22 6.09 35.94 2.93
2529 4221 6.443934 TGTTATGTTAACACAGTGCAAACT 57.556 33.333 11.22 0.00 35.94 2.66
2530 4222 6.261859 TGTTATGTTAACACAGTGCAAACTG 58.738 36.000 11.22 4.36 43.03 3.16
2531 4223 3.143807 TGTTAACACAGTGCAAACTGC 57.856 42.857 3.59 0.00 45.29 4.40
2532 4224 3.130164 ATGTTAACACAGTGCAAACTGCA 59.870 39.130 11.22 0.00 43.70 4.41
2533 4225 4.381398 ATGTTAACACAGTGCAAACTGCAA 60.381 37.500 11.22 1.37 44.87 4.08
2551 4243 2.658325 GCAAAGCAGTCGCAACTAATTG 59.342 45.455 0.00 0.00 42.27 2.32
2576 4268 6.885922 AGTACAGGTAAGAGAACTTGTGTTT 58.114 36.000 0.00 0.00 39.69 2.83
2603 4295 6.883756 TGCACAAAATACAATAGTGGATCAGA 59.116 34.615 0.00 0.00 0.00 3.27
2628 4320 9.688592 GAATGATGATGAAATACAATTTCTCCC 57.311 33.333 12.25 4.15 0.00 4.30
2629 4321 9.430399 AATGATGATGAAATACAATTTCTCCCT 57.570 29.630 12.25 0.39 0.00 4.20
2630 4322 8.455903 TGATGATGAAATACAATTTCTCCCTC 57.544 34.615 12.25 7.77 0.00 4.30
2631 4323 6.925610 TGATGAAATACAATTTCTCCCTCG 57.074 37.500 12.25 0.00 0.00 4.63
2632 4324 5.296780 TGATGAAATACAATTTCTCCCTCGC 59.703 40.000 12.25 0.00 0.00 5.03
2633 4325 4.843728 TGAAATACAATTTCTCCCTCGCT 58.156 39.130 12.25 0.00 0.00 4.93
2634 4326 5.253330 TGAAATACAATTTCTCCCTCGCTT 58.747 37.500 12.25 0.00 0.00 4.68
2635 4327 5.710099 TGAAATACAATTTCTCCCTCGCTTT 59.290 36.000 12.25 0.00 0.00 3.51
2636 4328 6.882140 TGAAATACAATTTCTCCCTCGCTTTA 59.118 34.615 12.25 0.00 0.00 1.85
2637 4329 7.556275 TGAAATACAATTTCTCCCTCGCTTTAT 59.444 33.333 12.25 0.00 0.00 1.40
2638 4330 7.881775 AATACAATTTCTCCCTCGCTTTATT 57.118 32.000 0.00 0.00 0.00 1.40
2639 4331 7.881775 ATACAATTTCTCCCTCGCTTTATTT 57.118 32.000 0.00 0.00 0.00 1.40
2640 4332 6.590234 ACAATTTCTCCCTCGCTTTATTTT 57.410 33.333 0.00 0.00 0.00 1.82
2641 4333 6.389906 ACAATTTCTCCCTCGCTTTATTTTG 58.610 36.000 0.00 0.00 0.00 2.44
2642 4334 6.015434 ACAATTTCTCCCTCGCTTTATTTTGT 60.015 34.615 0.00 0.00 0.00 2.83
2643 4335 7.175990 ACAATTTCTCCCTCGCTTTATTTTGTA 59.824 33.333 0.00 0.00 0.00 2.41
2644 4336 7.696992 ATTTCTCCCTCGCTTTATTTTGTAA 57.303 32.000 0.00 0.00 0.00 2.41
2645 4337 7.513371 TTTCTCCCTCGCTTTATTTTGTAAA 57.487 32.000 0.00 0.00 0.00 2.01
2646 4338 7.696992 TTCTCCCTCGCTTTATTTTGTAAAT 57.303 32.000 0.00 0.00 0.00 1.40
2647 4339 8.795842 TTCTCCCTCGCTTTATTTTGTAAATA 57.204 30.769 0.00 0.00 0.00 1.40
2648 4340 8.205131 TCTCCCTCGCTTTATTTTGTAAATAC 57.795 34.615 0.00 0.00 0.00 1.89
2649 4341 7.825270 TCTCCCTCGCTTTATTTTGTAAATACA 59.175 33.333 0.00 0.00 0.00 2.29
2650 4342 8.338072 TCCCTCGCTTTATTTTGTAAATACAA 57.662 30.769 1.96 1.96 43.80 2.41
2651 4343 8.962679 TCCCTCGCTTTATTTTGTAAATACAAT 58.037 29.630 6.82 0.00 44.72 2.71
2673 4365 9.813446 ACAATAGTGCCTACTAGTTAACATAAC 57.187 33.333 8.61 0.00 42.36 1.89
2674 4366 8.965172 CAATAGTGCCTACTAGTTAACATAACG 58.035 37.037 8.61 0.00 42.36 3.18
2675 4367 6.521151 AGTGCCTACTAGTTAACATAACGT 57.479 37.500 8.61 0.05 34.74 3.99
2676 4368 7.630242 AGTGCCTACTAGTTAACATAACGTA 57.370 36.000 8.61 1.19 34.74 3.57
2677 4369 8.230472 AGTGCCTACTAGTTAACATAACGTAT 57.770 34.615 8.61 0.00 34.74 3.06
2678 4370 8.348507 AGTGCCTACTAGTTAACATAACGTATC 58.651 37.037 8.61 0.00 34.74 2.24
2679 4371 8.348507 GTGCCTACTAGTTAACATAACGTATCT 58.651 37.037 8.61 0.00 0.00 1.98
2680 4372 8.562892 TGCCTACTAGTTAACATAACGTATCTC 58.437 37.037 8.61 0.00 0.00 2.75
2681 4373 8.562892 GCCTACTAGTTAACATAACGTATCTCA 58.437 37.037 8.61 0.00 0.00 3.27
2682 4374 9.875675 CCTACTAGTTAACATAACGTATCTCAC 57.124 37.037 8.61 0.00 0.00 3.51
2703 4395 5.828859 TCACTCTACTAGTTATCTTCAGCCC 59.171 44.000 0.00 0.00 35.76 5.19
2712 4404 5.923204 AGTTATCTTCAGCCCTTCATGTAG 58.077 41.667 0.00 0.00 0.00 2.74
2716 4408 3.969976 TCTTCAGCCCTTCATGTAGCTAT 59.030 43.478 0.00 0.00 33.33 2.97
2726 4418 7.533426 CCCTTCATGTAGCTATTGAATTATGC 58.467 38.462 17.45 0.00 0.00 3.14
2743 4435 7.227314 TGAATTATGCTTGGTCATGTATCTCAC 59.773 37.037 0.00 0.00 0.00 3.51
2781 4473 3.602103 GCACCAATTGCGGGATCA 58.398 55.556 0.00 0.00 42.79 2.92
2919 4611 6.256053 ACCAAAGTTATTCATCATGGGAACT 58.744 36.000 3.34 0.00 0.00 3.01
2959 4651 2.965572 AAAGCAGCTGCAAAACAAGA 57.034 40.000 38.24 0.00 45.16 3.02
2991 4683 1.406887 GCTGGACGGGTTGATACACAT 60.407 52.381 0.00 0.00 0.00 3.21
3040 4732 4.591321 ATGGAAGGTCCTGCTTTTGATA 57.409 40.909 0.00 0.00 37.46 2.15
3094 4786 6.271488 TCAAATCTTTGCCCAAATAGAGTG 57.729 37.500 0.00 0.00 38.05 3.51
3111 4803 4.708177 AGAGTGCTGTAACTGTGTGAAAT 58.292 39.130 0.00 0.00 0.00 2.17
3114 4806 4.640201 AGTGCTGTAACTGTGTGAAATTGT 59.360 37.500 0.00 0.00 0.00 2.71
3118 4810 4.919206 TGTAACTGTGTGAAATTGTGCAG 58.081 39.130 0.00 0.00 0.00 4.41
3314 5007 2.679336 TCATCACGACATTGCAATCCAG 59.321 45.455 9.53 6.00 0.00 3.86
3561 5255 1.511850 TGACGACGAACCGAGACTAA 58.488 50.000 0.00 0.00 0.00 2.24
3642 5336 3.175710 AAGGGTGGCCTTCACGGT 61.176 61.111 3.32 0.00 46.96 4.83
3662 5356 2.348666 GTGACGAATGCACGCTAGAAAT 59.651 45.455 0.00 0.00 36.70 2.17
3689 5383 1.803922 CACGTAACGCGGCTGATCA 60.804 57.895 12.47 0.00 46.52 2.92
3883 5625 4.517285 TGGTCTGCACCTAGATCATTTTC 58.483 43.478 0.00 0.00 44.17 2.29
4019 5761 2.105930 CCAGCTGACGCCTCTAGC 59.894 66.667 17.39 0.00 36.60 3.42
4082 5826 4.259770 CGAAACACAATCTTTTGTTGCACC 60.260 41.667 0.00 0.00 43.57 5.01
4089 5833 3.955771 TCTTTTGTTGCACCGAGTTAC 57.044 42.857 0.00 0.00 0.00 2.50
4090 5834 3.537580 TCTTTTGTTGCACCGAGTTACT 58.462 40.909 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 107 3.113260 ACCGGAACAGAAGAGTGAAAG 57.887 47.619 9.46 0.00 0.00 2.62
102 118 8.095937 ACTAAGAATAAGAAAAACCGGAACAG 57.904 34.615 9.46 0.00 0.00 3.16
643 1145 5.236478 TGTCTTTTCGGCTAGAGAAAACTTG 59.764 40.000 17.20 11.17 41.10 3.16
650 1152 4.866508 TTCTTGTCTTTTCGGCTAGAGA 57.133 40.909 0.00 0.00 0.00 3.10
651 1153 5.639506 TGATTTCTTGTCTTTTCGGCTAGAG 59.360 40.000 0.00 0.00 0.00 2.43
652 1154 5.547465 TGATTTCTTGTCTTTTCGGCTAGA 58.453 37.500 0.00 0.00 0.00 2.43
653 1155 5.862924 TGATTTCTTGTCTTTTCGGCTAG 57.137 39.130 0.00 0.00 0.00 3.42
654 1156 5.354234 GGATGATTTCTTGTCTTTTCGGCTA 59.646 40.000 0.00 0.00 0.00 3.93
657 1159 4.437390 CCGGATGATTTCTTGTCTTTTCGG 60.437 45.833 0.00 0.00 0.00 4.30
658 1160 4.651994 CCGGATGATTTCTTGTCTTTTCG 58.348 43.478 0.00 0.00 0.00 3.46
660 1162 3.193479 GGCCGGATGATTTCTTGTCTTTT 59.807 43.478 5.05 0.00 0.00 2.27
661 1163 2.755103 GGCCGGATGATTTCTTGTCTTT 59.245 45.455 5.05 0.00 0.00 2.52
662 1164 2.025887 AGGCCGGATGATTTCTTGTCTT 60.026 45.455 5.05 0.00 0.00 3.01
664 1166 1.672881 CAGGCCGGATGATTTCTTGTC 59.327 52.381 5.05 0.00 0.00 3.18
665 1167 1.004745 ACAGGCCGGATGATTTCTTGT 59.995 47.619 10.86 0.00 0.00 3.16
667 1169 3.480470 CATACAGGCCGGATGATTTCTT 58.520 45.455 10.86 0.00 0.00 2.52
668 1170 2.811873 GCATACAGGCCGGATGATTTCT 60.812 50.000 19.93 0.00 0.00 2.52
669 1171 1.537202 GCATACAGGCCGGATGATTTC 59.463 52.381 19.93 2.74 0.00 2.17
670 1172 1.609208 GCATACAGGCCGGATGATTT 58.391 50.000 19.93 0.00 0.00 2.17
672 1174 1.004560 CGCATACAGGCCGGATGAT 60.005 57.895 19.93 4.35 0.00 2.45
673 1175 2.421314 CGCATACAGGCCGGATGA 59.579 61.111 19.93 2.23 0.00 2.92
674 1176 3.349006 GCGCATACAGGCCGGATG 61.349 66.667 10.86 12.53 0.00 3.51
681 1183 1.603802 CTATTTGTGGGCGCATACAGG 59.396 52.381 10.83 2.12 0.00 4.00
682 1184 1.002468 GCTATTTGTGGGCGCATACAG 60.002 52.381 10.83 2.85 0.00 2.74
683 1185 1.021202 GCTATTTGTGGGCGCATACA 58.979 50.000 10.83 11.12 0.00 2.29
684 1186 1.002468 CTGCTATTTGTGGGCGCATAC 60.002 52.381 10.83 8.16 0.00 2.39
686 1188 2.008268 GCTGCTATTTGTGGGCGCAT 62.008 55.000 10.83 0.00 0.00 4.73
687 1189 2.699768 GCTGCTATTTGTGGGCGCA 61.700 57.895 10.83 0.00 0.00 6.09
688 1190 2.102946 GCTGCTATTTGTGGGCGC 59.897 61.111 0.00 0.00 0.00 6.53
689 1191 2.774799 GGGCTGCTATTTGTGGGCG 61.775 63.158 0.00 0.00 0.00 6.13
690 1192 1.044790 ATGGGCTGCTATTTGTGGGC 61.045 55.000 0.00 0.00 0.00 5.36
691 1193 2.362077 GTTATGGGCTGCTATTTGTGGG 59.638 50.000 0.00 0.00 0.00 4.61
693 1195 3.002656 CGAGTTATGGGCTGCTATTTGTG 59.997 47.826 0.00 0.00 0.00 3.33
694 1196 3.206150 CGAGTTATGGGCTGCTATTTGT 58.794 45.455 0.00 0.00 0.00 2.83
695 1197 2.549754 CCGAGTTATGGGCTGCTATTTG 59.450 50.000 0.00 0.00 0.00 2.32
696 1198 2.487265 CCCGAGTTATGGGCTGCTATTT 60.487 50.000 0.00 0.00 40.47 1.40
697 1199 1.072331 CCCGAGTTATGGGCTGCTATT 59.928 52.381 0.00 0.00 40.47 1.73
698 1200 0.687354 CCCGAGTTATGGGCTGCTAT 59.313 55.000 0.00 0.00 40.47 2.97
699 1201 1.407656 CCCCGAGTTATGGGCTGCTA 61.408 60.000 0.00 0.00 45.95 3.49
700 1202 2.746375 CCCCGAGTTATGGGCTGCT 61.746 63.158 0.00 0.00 45.95 4.24
701 1203 2.203209 CCCCGAGTTATGGGCTGC 60.203 66.667 0.00 0.00 45.95 5.25
702 1204 1.447643 CTCCCCGAGTTATGGGCTG 59.552 63.158 0.00 0.00 45.95 4.85
703 1205 2.444256 GCTCCCCGAGTTATGGGCT 61.444 63.158 0.00 0.00 45.95 5.19
705 1207 1.348064 TATGCTCCCCGAGTTATGGG 58.652 55.000 0.00 0.00 46.93 4.00
706 1208 4.504858 GTTATATGCTCCCCGAGTTATGG 58.495 47.826 0.00 0.00 31.39 2.74
707 1209 4.504858 GGTTATATGCTCCCCGAGTTATG 58.495 47.826 0.00 0.00 31.39 1.90
709 1211 2.901839 GGGTTATATGCTCCCCGAGTTA 59.098 50.000 0.00 0.00 35.52 2.24
710 1212 1.697982 GGGTTATATGCTCCCCGAGTT 59.302 52.381 0.00 0.00 35.52 3.01
711 1213 1.132817 AGGGTTATATGCTCCCCGAGT 60.133 52.381 7.70 0.00 42.26 4.18
712 1214 1.645710 AGGGTTATATGCTCCCCGAG 58.354 55.000 7.70 0.00 42.26 4.63
714 1216 1.207329 GCTAGGGTTATATGCTCCCCG 59.793 57.143 7.70 2.83 42.26 5.73
715 1217 1.560146 GGCTAGGGTTATATGCTCCCC 59.440 57.143 7.70 0.00 41.95 4.81
717 1219 2.237392 CTGGGCTAGGGTTATATGCTCC 59.763 54.545 0.00 0.00 0.00 4.70
718 1220 3.173965 TCTGGGCTAGGGTTATATGCTC 58.826 50.000 0.00 0.00 0.00 4.26
720 1222 3.870299 GCTTCTGGGCTAGGGTTATATGC 60.870 52.174 0.00 0.00 0.00 3.14
721 1223 3.617531 CGCTTCTGGGCTAGGGTTATATG 60.618 52.174 0.00 0.00 0.00 1.78
723 1225 1.968493 CGCTTCTGGGCTAGGGTTATA 59.032 52.381 0.00 0.00 0.00 0.98
724 1226 0.759346 CGCTTCTGGGCTAGGGTTAT 59.241 55.000 0.00 0.00 0.00 1.89
725 1227 1.968050 GCGCTTCTGGGCTAGGGTTA 61.968 60.000 0.00 0.00 46.81 2.85
727 1229 3.787001 GCGCTTCTGGGCTAGGGT 61.787 66.667 0.00 0.00 46.81 4.34
737 1239 3.704231 ATTCATGGCCGGCGCTTCT 62.704 57.895 22.54 0.00 34.44 2.85
738 1240 3.211963 ATTCATGGCCGGCGCTTC 61.212 61.111 22.54 6.95 34.44 3.86
740 1242 3.993614 TTCATTCATGGCCGGCGCT 62.994 57.895 22.54 7.01 34.44 5.92
742 1244 0.318107 GAATTCATTCATGGCCGGCG 60.318 55.000 22.54 6.96 36.80 6.46
743 1245 0.746063 TGAATTCATTCATGGCCGGC 59.254 50.000 21.18 21.18 41.51 6.13
744 1246 2.026641 ACTGAATTCATTCATGGCCGG 58.973 47.619 8.96 0.00 44.92 6.13
745 1247 3.788333 AACTGAATTCATTCATGGCCG 57.212 42.857 8.96 0.00 44.92 6.13
746 1248 4.936891 GGTAACTGAATTCATTCATGGCC 58.063 43.478 8.96 0.00 44.92 5.36
763 1265 2.516225 GGCCCGCATCCAGGTAAC 60.516 66.667 0.00 0.00 0.00 2.50
764 1266 4.169696 CGGCCCGCATCCAGGTAA 62.170 66.667 0.00 0.00 0.00 2.85
767 1269 4.910585 GTACGGCCCGCATCCAGG 62.911 72.222 1.23 0.00 0.00 4.45
768 1270 4.910585 GGTACGGCCCGCATCCAG 62.911 72.222 1.23 0.00 0.00 3.86
803 2296 1.095807 GGTTAATGCTCGGTGGGCTC 61.096 60.000 0.00 0.00 0.00 4.70
833 2326 2.361085 AGGAGAGGTTGGTATTGGGT 57.639 50.000 0.00 0.00 0.00 4.51
834 2327 4.855298 TTTAGGAGAGGTTGGTATTGGG 57.145 45.455 0.00 0.00 0.00 4.12
857 2350 4.891168 ACTTCGGTTGGTATTGGAGTTTTT 59.109 37.500 0.00 0.00 0.00 1.94
858 2351 4.466827 ACTTCGGTTGGTATTGGAGTTTT 58.533 39.130 0.00 0.00 0.00 2.43
859 2352 4.094830 ACTTCGGTTGGTATTGGAGTTT 57.905 40.909 0.00 0.00 0.00 2.66
860 2353 3.782656 ACTTCGGTTGGTATTGGAGTT 57.217 42.857 0.00 0.00 0.00 3.01
861 2354 3.782656 AACTTCGGTTGGTATTGGAGT 57.217 42.857 0.00 0.00 36.72 3.85
862 2355 4.634443 CCTTAACTTCGGTTGGTATTGGAG 59.366 45.833 0.00 0.00 38.76 3.86
863 2356 4.041938 ACCTTAACTTCGGTTGGTATTGGA 59.958 41.667 0.00 0.00 38.76 3.53
864 2357 4.329392 ACCTTAACTTCGGTTGGTATTGG 58.671 43.478 0.00 0.00 38.76 3.16
865 2358 7.551617 AGATTACCTTAACTTCGGTTGGTATTG 59.448 37.037 0.00 0.00 36.78 1.90
866 2359 7.627311 AGATTACCTTAACTTCGGTTGGTATT 58.373 34.615 0.00 0.00 36.78 1.89
867 2360 7.191593 AGATTACCTTAACTTCGGTTGGTAT 57.808 36.000 0.00 0.00 36.78 2.73
868 2361 6.610075 AGATTACCTTAACTTCGGTTGGTA 57.390 37.500 0.00 0.00 38.76 3.25
869 2362 5.494390 AGATTACCTTAACTTCGGTTGGT 57.506 39.130 0.00 0.00 38.76 3.67
870 2363 7.910441 TTAAGATTACCTTAACTTCGGTTGG 57.090 36.000 0.00 0.00 41.15 3.77
897 2390 6.778834 TTTCCCTTCCTTAACTTCGTTTTT 57.221 33.333 0.00 0.00 0.00 1.94
898 2391 6.778834 TTTTCCCTTCCTTAACTTCGTTTT 57.221 33.333 0.00 0.00 0.00 2.43
901 2394 4.217767 GCATTTTCCCTTCCTTAACTTCGT 59.782 41.667 0.00 0.00 0.00 3.85
917 2410 1.604278 GATCTGCCCCGTAGCATTTTC 59.396 52.381 0.00 0.00 43.09 2.29
943 2438 0.741221 GTTGAGCTACTTCCTGCCCG 60.741 60.000 0.00 0.00 0.00 6.13
1107 2603 2.897699 GAGGATCGTGTAGGGGTGT 58.102 57.895 0.00 0.00 0.00 4.16
1233 2729 4.803426 CTGGAGCCCGTGAGCGAC 62.803 72.222 0.00 0.00 41.33 5.19
1344 2840 3.225061 GAGGGGATCGTCGGGGTC 61.225 72.222 0.00 0.00 0.00 4.46
1422 2918 6.376299 TCAGAATAGCTACTAGTTTGGTCGAA 59.624 38.462 0.00 0.00 0.00 3.71
1424 2920 6.132791 TCAGAATAGCTACTAGTTTGGTCG 57.867 41.667 0.00 0.00 0.00 4.79
1449 2950 2.290367 GCGTATGCCATTTGCTGATACA 59.710 45.455 0.00 0.00 42.00 2.29
1450 2951 2.290367 TGCGTATGCCATTTGCTGATAC 59.710 45.455 4.05 0.00 41.78 2.24
1480 2985 0.534412 AGGTCAAGATGAGTGCTCGG 59.466 55.000 0.00 0.00 0.00 4.63
1481 2986 1.638133 CAGGTCAAGATGAGTGCTCG 58.362 55.000 0.00 0.00 0.00 5.03
1482 2987 1.367659 GCAGGTCAAGATGAGTGCTC 58.632 55.000 7.17 0.00 35.64 4.26
1504 3017 2.138320 CGCATCGCCTATTCATTCTGT 58.862 47.619 0.00 0.00 0.00 3.41
1540 3054 5.859205 AGGTTGTTTGAGCTTTCAATTCT 57.141 34.783 0.00 0.00 0.00 2.40
1637 3152 8.485976 AATACTCAGCTGTTAGTTTGATCTTC 57.514 34.615 14.67 0.00 0.00 2.87
1657 3172 7.710676 AATCAGTGAGACAGTGAGTAATACT 57.289 36.000 13.37 0.00 45.31 2.12
1718 3233 1.065401 CGCTGAGCCTCTGAGTCTTAG 59.935 57.143 0.00 3.42 0.00 2.18
1737 3252 3.672295 GAGAAGACTGGGGCAGCCG 62.672 68.421 5.00 0.00 34.37 5.52
1738 3253 2.270527 GAGAAGACTGGGGCAGCC 59.729 66.667 1.26 1.26 34.37 4.85
1740 3255 0.979665 TTCTGAGAAGACTGGGGCAG 59.020 55.000 0.00 0.00 37.52 4.85
1741 3256 0.979665 CTTCTGAGAAGACTGGGGCA 59.020 55.000 17.02 0.00 0.00 5.36
1742 3257 0.392327 GCTTCTGAGAAGACTGGGGC 60.392 60.000 25.34 5.51 0.00 5.80
1782 3321 5.826643 AGGATTGGCTGAAAAATAGTGGTA 58.173 37.500 0.00 0.00 0.00 3.25
1809 3351 3.567397 GAGAAGAGCAGGGTATCCTACA 58.433 50.000 0.00 0.00 42.67 2.74
1823 3365 2.625737 ACATGCATCGTTGGAGAAGAG 58.374 47.619 0.00 0.00 0.00 2.85
1833 3375 1.068333 GGCAAACTGAACATGCATCGT 60.068 47.619 0.00 0.00 41.80 3.73
1861 3411 4.225942 TGATTACTGGCCTCACTGAATCTT 59.774 41.667 3.32 0.00 0.00 2.40
1883 3434 6.076981 AGAGCTACTTGTTTGGTCAATTTG 57.923 37.500 0.00 0.00 30.73 2.32
1928 3479 2.754552 ACTTGTCAATTGCGTATGCCAT 59.245 40.909 4.05 0.00 41.78 4.40
1936 3487 5.778161 TGAGTGTATACTTGTCAATTGCG 57.222 39.130 4.17 0.00 37.25 4.85
1948 3499 6.037098 GTCACAGGTCAAGATGAGTGTATAC 58.963 44.000 0.00 0.00 0.00 1.47
1967 3521 3.490933 GCATCGCCTATTCACTAGTCACA 60.491 47.826 0.00 0.00 0.00 3.58
1969 3523 2.287608 CGCATCGCCTATTCACTAGTCA 60.288 50.000 0.00 0.00 0.00 3.41
1975 3529 0.316196 GCAACGCATCGCCTATTCAC 60.316 55.000 0.00 0.00 0.00 3.18
2026 3612 5.477984 TGAAGGAAAATTCAATGAGGACAGG 59.522 40.000 0.00 0.00 36.28 4.00
2092 3678 9.167311 AGCTGTTAGTTAGATATTTGGACTTTG 57.833 33.333 0.00 0.00 0.00 2.77
2103 3689 9.075678 GAGTAATACCCAGCTGTTAGTTAGATA 57.924 37.037 13.81 0.00 0.00 1.98
2136 3722 1.379977 TCAACCGCCCCAAACACAA 60.380 52.632 0.00 0.00 0.00 3.33
2167 3753 2.166664 AGCCTCTTAGTCTTACGGCTTG 59.833 50.000 0.00 0.00 44.90 4.01
2170 3756 1.803252 GCAGCCTCTTAGTCTTACGGC 60.803 57.143 0.00 0.00 37.80 5.68
2189 3775 1.117150 TAGGATAAGGTCACCACGGC 58.883 55.000 0.00 0.00 0.00 5.68
2226 3812 6.606768 CAAGAAAGGTTGCTTATGAGAAGAC 58.393 40.000 0.00 0.00 0.00 3.01
2276 3862 6.763135 GTCTAGTGTCCTGCATTAATGATCAA 59.237 38.462 19.73 0.52 0.00 2.57
2277 3863 6.098838 AGTCTAGTGTCCTGCATTAATGATCA 59.901 38.462 19.73 7.53 0.00 2.92
2313 3899 7.363880 CCAGGTTGCTTCTGAGAAATACTACTA 60.364 40.741 0.00 0.00 34.36 1.82
2314 3900 6.402222 CAGGTTGCTTCTGAGAAATACTACT 58.598 40.000 0.00 0.00 34.36 2.57
2315 3901 5.582665 CCAGGTTGCTTCTGAGAAATACTAC 59.417 44.000 0.00 0.00 34.36 2.73
2316 3902 5.338381 CCCAGGTTGCTTCTGAGAAATACTA 60.338 44.000 0.00 0.00 34.36 1.82
2340 4026 5.360591 AGGTATAGCACAAGTGTCTAATGC 58.639 41.667 4.48 0.00 36.52 3.56
2488 4174 8.706322 ACATAACAAAATCTTAAGACCCTTGT 57.294 30.769 7.48 13.75 0.00 3.16
2498 4184 9.672086 GCACTGTGTTAACATAACAAAATCTTA 57.328 29.630 12.26 0.00 35.22 2.10
2499 4185 8.194104 TGCACTGTGTTAACATAACAAAATCTT 58.806 29.630 12.26 0.00 35.22 2.40
2500 4186 7.711846 TGCACTGTGTTAACATAACAAAATCT 58.288 30.769 12.26 0.00 35.22 2.40
2501 4187 7.922505 TGCACTGTGTTAACATAACAAAATC 57.077 32.000 12.26 0.00 35.22 2.17
2502 4188 8.599774 GTTTGCACTGTGTTAACATAACAAAAT 58.400 29.630 19.82 1.90 35.02 1.82
2506 4198 6.261859 CAGTTTGCACTGTGTTAACATAACA 58.738 36.000 12.26 4.41 44.96 2.41
2528 4220 7.760058 TCAATTAGTTGCGACTGCTTTGCAG 62.760 44.000 17.36 16.77 45.90 4.41
2529 4221 1.304254 TTAGTTGCGACTGCTTTGCA 58.696 45.000 17.36 0.00 43.50 4.08
2530 4222 2.619013 ATTAGTTGCGACTGCTTTGC 57.381 45.000 17.36 0.00 43.34 3.68
2531 4223 4.145876 TCAATTAGTTGCGACTGCTTTG 57.854 40.909 17.36 15.66 43.34 2.77
2532 4224 3.815401 ACTCAATTAGTTGCGACTGCTTT 59.185 39.130 17.36 4.68 43.34 3.51
2533 4225 3.403038 ACTCAATTAGTTGCGACTGCTT 58.597 40.909 17.36 6.98 43.34 3.91
2540 4232 6.097356 TCTTACCTGTACTCAATTAGTTGCG 58.903 40.000 0.00 0.00 39.80 4.85
2551 4243 6.086785 ACACAAGTTCTCTTACCTGTACTC 57.913 41.667 0.00 0.00 32.07 2.59
2576 4268 7.890515 TGATCCACTATTGTATTTTGTGCAAA 58.109 30.769 0.00 0.00 36.00 3.68
2594 4286 8.387190 TGTATTTCATCATCATTCTGATCCAC 57.613 34.615 0.00 0.00 34.28 4.02
2603 4295 9.430399 AGGGAGAAATTGTATTTCATCATCATT 57.570 29.630 13.00 0.00 0.00 2.57
2611 4303 4.843728 AGCGAGGGAGAAATTGTATTTCA 58.156 39.130 13.00 0.00 0.00 2.69
2617 4309 6.015434 ACAAAATAAAGCGAGGGAGAAATTGT 60.015 34.615 0.00 0.00 0.00 2.71
2618 4310 6.389906 ACAAAATAAAGCGAGGGAGAAATTG 58.610 36.000 0.00 0.00 0.00 2.32
2619 4311 6.590234 ACAAAATAAAGCGAGGGAGAAATT 57.410 33.333 0.00 0.00 0.00 1.82
2620 4312 7.696992 TTACAAAATAAAGCGAGGGAGAAAT 57.303 32.000 0.00 0.00 0.00 2.17
2621 4313 7.513371 TTTACAAAATAAAGCGAGGGAGAAA 57.487 32.000 0.00 0.00 0.00 2.52
2623 4315 7.825270 TGTATTTACAAAATAAAGCGAGGGAGA 59.175 33.333 0.00 0.00 32.40 3.71
2625 4317 7.925043 TGTATTTACAAAATAAAGCGAGGGA 57.075 32.000 0.00 0.00 32.40 4.20
2647 4339 9.813446 GTTATGTTAACTAGTAGGCACTATTGT 57.187 33.333 7.22 0.00 45.60 2.71
2648 4340 8.965172 CGTTATGTTAACTAGTAGGCACTATTG 58.035 37.037 7.22 0.00 45.60 1.90
2649 4341 8.689972 ACGTTATGTTAACTAGTAGGCACTATT 58.310 33.333 7.22 0.00 45.60 1.73
2650 4342 8.230472 ACGTTATGTTAACTAGTAGGCACTAT 57.770 34.615 7.22 0.00 45.60 2.12
2651 4343 7.630242 ACGTTATGTTAACTAGTAGGCACTA 57.370 36.000 7.22 0.00 41.75 2.74
2652 4344 6.521151 ACGTTATGTTAACTAGTAGGCACT 57.479 37.500 7.22 0.00 46.37 4.40
2653 4345 8.348507 AGATACGTTATGTTAACTAGTAGGCAC 58.651 37.037 7.22 0.00 0.00 5.01
2654 4346 8.455903 AGATACGTTATGTTAACTAGTAGGCA 57.544 34.615 7.22 0.00 0.00 4.75
2655 4347 8.562892 TGAGATACGTTATGTTAACTAGTAGGC 58.437 37.037 7.22 0.00 0.00 3.93
2656 4348 9.875675 GTGAGATACGTTATGTTAACTAGTAGG 57.124 37.037 7.22 0.00 0.00 3.18
2659 4351 9.393512 AGAGTGAGATACGTTATGTTAACTAGT 57.606 33.333 7.22 0.00 0.00 2.57
2662 4354 9.393512 AGTAGAGTGAGATACGTTATGTTAACT 57.606 33.333 7.22 0.00 0.00 2.24
2666 4358 8.961294 ACTAGTAGAGTGAGATACGTTATGTT 57.039 34.615 3.59 0.00 36.87 2.71
2667 4359 8.961294 AACTAGTAGAGTGAGATACGTTATGT 57.039 34.615 3.59 0.00 38.87 2.29
2671 4363 9.835389 AAGATAACTAGTAGAGTGAGATACGTT 57.165 33.333 3.59 0.00 38.87 3.99
2672 4364 9.480053 GAAGATAACTAGTAGAGTGAGATACGT 57.520 37.037 3.59 0.00 38.87 3.57
2673 4365 9.478768 TGAAGATAACTAGTAGAGTGAGATACG 57.521 37.037 3.59 0.00 38.87 3.06
2675 4367 9.496873 GCTGAAGATAACTAGTAGAGTGAGATA 57.503 37.037 3.59 0.00 38.87 1.98
2676 4368 7.447238 GGCTGAAGATAACTAGTAGAGTGAGAT 59.553 40.741 3.59 0.00 38.87 2.75
2677 4369 6.768861 GGCTGAAGATAACTAGTAGAGTGAGA 59.231 42.308 3.59 0.00 38.87 3.27
2678 4370 6.016610 GGGCTGAAGATAACTAGTAGAGTGAG 60.017 46.154 3.59 0.00 38.87 3.51
2679 4371 5.828859 GGGCTGAAGATAACTAGTAGAGTGA 59.171 44.000 3.59 0.00 38.87 3.41
2680 4372 5.830991 AGGGCTGAAGATAACTAGTAGAGTG 59.169 44.000 3.59 0.00 38.87 3.51
2681 4373 6.020881 AGGGCTGAAGATAACTAGTAGAGT 57.979 41.667 3.59 0.00 41.56 3.24
2682 4374 6.547880 TGAAGGGCTGAAGATAACTAGTAGAG 59.452 42.308 3.59 0.00 0.00 2.43
2683 4375 6.432581 TGAAGGGCTGAAGATAACTAGTAGA 58.567 40.000 3.59 0.00 0.00 2.59
2693 4385 2.776536 AGCTACATGAAGGGCTGAAGAT 59.223 45.455 0.00 0.00 33.50 2.40
2700 4392 7.533426 CATAATTCAATAGCTACATGAAGGGC 58.467 38.462 21.62 0.00 36.59 5.19
2703 4395 9.608617 CAAGCATAATTCAATAGCTACATGAAG 57.391 33.333 21.62 13.11 36.59 3.02
2712 4404 6.742109 ACATGACCAAGCATAATTCAATAGC 58.258 36.000 0.00 0.00 0.00 2.97
2716 4408 7.774625 TGAGATACATGACCAAGCATAATTCAA 59.225 33.333 0.00 0.00 0.00 2.69
2726 4418 6.707440 ACTAGAGTGAGATACATGACCAAG 57.293 41.667 0.00 0.00 0.00 3.61
2781 4473 3.560025 CCTGGTCAACCTTATCAACTGCT 60.560 47.826 0.10 0.00 36.82 4.24
2959 4651 1.078848 GTCCAGCAGCCGACTTGAT 60.079 57.895 3.42 0.00 0.00 2.57
2991 4683 1.073125 TGACCGGCTCCTTCAATCAAA 59.927 47.619 0.00 0.00 0.00 2.69
3091 4783 4.640201 ACAATTTCACACAGTTACAGCACT 59.360 37.500 0.00 0.00 0.00 4.40
3094 4786 3.730715 GCACAATTTCACACAGTTACAGC 59.269 43.478 0.00 0.00 0.00 4.40
3111 4803 0.387565 TCACTACACGCTCTGCACAA 59.612 50.000 0.00 0.00 0.00 3.33
3114 4806 0.887933 TCATCACTACACGCTCTGCA 59.112 50.000 0.00 0.00 0.00 4.41
3118 4810 2.531912 CGATGTTCATCACTACACGCTC 59.468 50.000 12.34 0.00 0.00 5.03
3414 5108 7.504403 TCAGAAAGACAGAAAGAGACAGAAAT 58.496 34.615 0.00 0.00 0.00 2.17
3561 5255 7.878127 CACCGATCATATATAACCTCAGGTTTT 59.122 37.037 16.22 9.88 44.33 2.43
3582 5276 3.961480 AAGACATGAGATCAACACCGA 57.039 42.857 0.00 0.00 0.00 4.69
3642 5336 2.073117 TTTCTAGCGTGCATTCGTCA 57.927 45.000 0.00 0.00 0.00 4.35
3651 5345 4.337763 GTGCATCTCAAATTTCTAGCGTG 58.662 43.478 0.00 0.00 0.00 5.34
3662 5356 0.436913 CGCGTTACGTGCATCTCAAA 59.563 50.000 5.13 0.00 36.87 2.69
3719 5413 4.261572 CCTCGAAGCCAAATCTGTTGAAAA 60.262 41.667 0.00 0.00 0.00 2.29
3782 5478 4.047822 TCAAATCAAATCCAACACGTTGC 58.952 39.130 4.34 0.00 39.16 4.17
3883 5625 0.865769 CTGACACGAAAAAGGACGGG 59.134 55.000 0.00 0.00 38.94 5.28
3930 5672 3.379865 TACGGCCCTTGATGACGCC 62.380 63.158 0.00 0.00 38.07 5.68


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

AutoCloner maintained by Alex Coulton.