Multiple sequence alignment - TraesCS1B01G313200

Loading Multiple Alignment...

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 TraesCS1B01G313200 chr1B 100.000 1422 0 0 1 1422 536769672 536771093 0.000000e+00 2627.0
1 TraesCS1B01G313200 chr1B 100.000 662 0 0 1639 2300 536771310 536771971 0.000000e+00 1223.0
2 TraesCS1B01G313200 chr1A 87.593 669 36 14 772 1422 496476621 496477260 0.000000e+00 732.0
3 TraesCS1B01G313200 chr1A 92.342 444 18 9 111 545 496476067 496476503 3.250000e-173 617.0
4 TraesCS1B01G313200 chr1A 82.153 678 82 29 1639 2300 496477306 496477960 1.550000e-151 545.0
5 TraesCS1B01G313200 chr1D 93.991 466 21 5 80 543 400060286 400060746 0.000000e+00 699.0
6 TraesCS1B01G313200 chr1D 85.693 678 35 25 762 1421 400060877 400061510 0.000000e+00 658.0
7 TraesCS1B01G313200 chr7D 100.000 32 0 0 547 578 161284377 161284346 2.470000e-05 60.2
8 TraesCS1B01G313200 chr5D 94.737 38 2 0 541 578 37660859 37660896 2.470000e-05 60.2
9 TraesCS1B01G313200 chr2B 100.000 32 0 0 547 578 609286114 609286083 2.470000e-05 60.2
10 TraesCS1B01G313200 chr3D 90.698 43 3 1 535 577 67055277 67055318 3.190000e-04 56.5


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 TraesCS1B01G313200 chr1B 536769672 536771971 2299 False 1925.000000 2627 100.000000 1 2300 2 chr1B.!!$F1 2299
1 TraesCS1B01G313200 chr1A 496476067 496477960 1893 False 631.333333 732 87.362667 111 2300 3 chr1A.!!$F1 2189
2 TraesCS1B01G313200 chr1D 400060286 400061510 1224 False 678.500000 699 89.842000 80 1421 2 chr1D.!!$F1 1341

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
44 45 0.394565 CGCTATCCTTTCAGGGAGGG 59.605 60.0 0.0 0.0 38.92 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1437 0.392706 TTTCGTCTCAGAGCCAAGCA 59.607 50.0 0.0 0.0 0.0 3.91 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
20 21 3.738830 TTTACGTGTTGGAGCAGTAGT 57.261 42.857 0.00 0.00 0.00 2.73
21 22 4.852134 TTTACGTGTTGGAGCAGTAGTA 57.148 40.909 0.00 0.00 0.00 1.82
22 23 4.430137 TTACGTGTTGGAGCAGTAGTAG 57.570 45.455 0.00 0.00 0.00 2.57
23 24 2.236766 ACGTGTTGGAGCAGTAGTAGT 58.763 47.619 0.00 0.00 0.00 2.73
24 25 3.415212 ACGTGTTGGAGCAGTAGTAGTA 58.585 45.455 0.00 0.00 0.00 1.82
25 26 3.190118 ACGTGTTGGAGCAGTAGTAGTAC 59.810 47.826 0.00 0.00 0.00 2.73
26 27 3.727079 CGTGTTGGAGCAGTAGTAGTACG 60.727 52.174 2.04 0.00 33.97 3.67
27 28 2.163010 TGTTGGAGCAGTAGTAGTACGC 59.837 50.000 13.34 13.34 33.97 4.42
28 29 2.414994 TGGAGCAGTAGTAGTACGCT 57.585 50.000 19.92 19.92 39.86 5.07
29 30 3.548745 TGGAGCAGTAGTAGTACGCTA 57.451 47.619 19.87 8.86 38.38 4.26
30 31 4.082665 TGGAGCAGTAGTAGTACGCTAT 57.917 45.455 19.87 6.56 38.38 2.97
31 32 4.063689 TGGAGCAGTAGTAGTACGCTATC 58.936 47.826 19.87 16.42 38.38 2.08
32 33 3.436359 GGAGCAGTAGTAGTACGCTATCC 59.564 52.174 19.87 15.94 38.38 2.59
33 34 4.317488 GAGCAGTAGTAGTACGCTATCCT 58.683 47.826 19.87 6.05 38.38 3.24
34 35 4.716794 AGCAGTAGTAGTACGCTATCCTT 58.283 43.478 18.99 2.42 37.30 3.36
35 36 5.131784 AGCAGTAGTAGTACGCTATCCTTT 58.868 41.667 18.99 1.90 37.30 3.11
36 37 5.239087 AGCAGTAGTAGTACGCTATCCTTTC 59.761 44.000 18.99 0.00 37.30 2.62
37 38 5.008415 GCAGTAGTAGTACGCTATCCTTTCA 59.992 44.000 13.72 0.00 33.97 2.69
38 39 6.660722 CAGTAGTAGTACGCTATCCTTTCAG 58.339 44.000 2.04 0.00 33.97 3.02
39 40 5.764192 AGTAGTAGTACGCTATCCTTTCAGG 59.236 44.000 2.04 0.00 33.49 3.86
40 41 3.890147 AGTAGTACGCTATCCTTTCAGGG 59.110 47.826 0.00 0.00 35.59 4.45
41 42 3.028094 AGTACGCTATCCTTTCAGGGA 57.972 47.619 0.00 0.00 39.95 4.20
42 43 2.959707 AGTACGCTATCCTTTCAGGGAG 59.040 50.000 0.00 0.00 38.92 4.30
43 44 1.123928 ACGCTATCCTTTCAGGGAGG 58.876 55.000 0.00 0.00 38.92 4.30
44 45 0.394565 CGCTATCCTTTCAGGGAGGG 59.605 60.000 0.00 0.00 38.92 4.30
45 46 1.807814 GCTATCCTTTCAGGGAGGGA 58.192 55.000 0.00 0.00 38.92 4.20
46 47 1.418264 GCTATCCTTTCAGGGAGGGAC 59.582 57.143 0.00 0.00 38.92 4.46
47 48 2.764269 CTATCCTTTCAGGGAGGGACA 58.236 52.381 0.00 0.00 38.92 4.02
48 49 2.059756 ATCCTTTCAGGGAGGGACAA 57.940 50.000 0.00 0.00 38.92 3.18
49 50 1.827792 TCCTTTCAGGGAGGGACAAA 58.172 50.000 0.00 0.00 35.59 2.83
50 51 1.423921 TCCTTTCAGGGAGGGACAAAC 59.576 52.381 0.00 0.00 35.59 2.93
51 52 1.144913 CCTTTCAGGGAGGGACAAACA 59.855 52.381 0.00 0.00 0.00 2.83
52 53 2.230660 CTTTCAGGGAGGGACAAACAC 58.769 52.381 0.00 0.00 0.00 3.32
53 54 1.518367 TTCAGGGAGGGACAAACACT 58.482 50.000 0.00 0.00 33.40 3.55
60 61 3.409026 GAGGGACAAACACTCTGATGT 57.591 47.619 0.00 0.00 44.90 3.06
61 62 3.070018 GAGGGACAAACACTCTGATGTG 58.930 50.000 0.00 5.93 44.90 3.21
72 73 5.947228 CACTCTGATGTGTAAATTGTGGT 57.053 39.130 0.00 0.00 33.61 4.16
73 74 5.692814 CACTCTGATGTGTAAATTGTGGTG 58.307 41.667 0.00 0.00 33.61 4.17
74 75 5.239306 CACTCTGATGTGTAAATTGTGGTGT 59.761 40.000 0.00 0.00 33.61 4.16
75 76 5.239306 ACTCTGATGTGTAAATTGTGGTGTG 59.761 40.000 0.00 0.00 0.00 3.82
76 77 4.518590 TCTGATGTGTAAATTGTGGTGTGG 59.481 41.667 0.00 0.00 0.00 4.17
77 78 3.571828 TGATGTGTAAATTGTGGTGTGGG 59.428 43.478 0.00 0.00 0.00 4.61
78 79 1.683917 TGTGTAAATTGTGGTGTGGGC 59.316 47.619 0.00 0.00 0.00 5.36
115 116 9.807649 GTACTACTACGATGGGAAAAGAAAATA 57.192 33.333 0.00 0.00 0.00 1.40
124 125 7.598493 CGATGGGAAAAGAAAATAAGCAGAAAA 59.402 33.333 0.00 0.00 0.00 2.29
125 126 9.271828 GATGGGAAAAGAAAATAAGCAGAAAAA 57.728 29.630 0.00 0.00 0.00 1.94
126 127 8.661352 TGGGAAAAGAAAATAAGCAGAAAAAG 57.339 30.769 0.00 0.00 0.00 2.27
248 253 1.097547 AAAAGCGCCATCTCCATCCG 61.098 55.000 2.29 0.00 0.00 4.18
363 368 1.628340 CCCTTGTCACCCACAGTATCA 59.372 52.381 0.00 0.00 35.97 2.15
405 413 7.416154 TGATCCTGTTTAGTGTAAAAGAACG 57.584 36.000 0.00 0.00 0.00 3.95
479 487 3.479370 GCTGATGAGCACGACCAC 58.521 61.111 0.00 0.00 45.46 4.16
530 539 2.482864 GGAGTGGCCAACAACATTTTG 58.517 47.619 7.24 0.00 36.21 2.44
531 540 1.866601 GAGTGGCCAACAACATTTTGC 59.133 47.619 7.24 0.00 36.00 3.68
533 542 2.158784 AGTGGCCAACAACATTTTGCAT 60.159 40.909 7.24 0.00 36.00 3.96
537 546 4.883585 TGGCCAACAACATTTTGCATAAAA 59.116 33.333 0.61 0.00 39.86 1.52
539 548 6.040166 TGGCCAACAACATTTTGCATAAAATT 59.960 30.769 0.61 0.00 42.33 1.82
540 549 6.362820 GGCCAACAACATTTTGCATAAAATTG 59.637 34.615 0.00 12.08 42.33 2.32
541 550 6.916932 GCCAACAACATTTTGCATAAAATTGT 59.083 30.769 13.01 13.01 42.33 2.71
542 551 8.072567 GCCAACAACATTTTGCATAAAATTGTA 58.927 29.630 16.77 0.00 42.33 2.41
551 560 8.472683 TTTTGCATAAAATTGTATTTCCTCCG 57.527 30.769 0.00 0.00 31.13 4.63
552 561 6.767524 TGCATAAAATTGTATTTCCTCCGT 57.232 33.333 0.00 0.00 0.00 4.69
553 562 7.867305 TGCATAAAATTGTATTTCCTCCGTA 57.133 32.000 0.00 0.00 0.00 4.02
554 563 8.282455 TGCATAAAATTGTATTTCCTCCGTAA 57.718 30.769 0.00 0.00 0.00 3.18
555 564 8.740906 TGCATAAAATTGTATTTCCTCCGTAAA 58.259 29.630 0.00 0.00 0.00 2.01
556 565 9.016623 GCATAAAATTGTATTTCCTCCGTAAAC 57.983 33.333 0.00 0.00 0.00 2.01
568 577 6.350629 TCCTCCGTAAACTAATATAAGGGC 57.649 41.667 0.00 0.00 0.00 5.19
569 578 5.840149 TCCTCCGTAAACTAATATAAGGGCA 59.160 40.000 0.00 0.00 0.00 5.36
570 579 6.499350 TCCTCCGTAAACTAATATAAGGGCAT 59.501 38.462 0.00 0.00 0.00 4.40
571 580 7.016858 TCCTCCGTAAACTAATATAAGGGCATT 59.983 37.037 0.00 0.00 0.00 3.56
572 581 7.664318 CCTCCGTAAACTAATATAAGGGCATTT 59.336 37.037 0.00 0.00 0.00 2.32
573 582 9.715121 CTCCGTAAACTAATATAAGGGCATTTA 57.285 33.333 0.00 0.00 0.00 1.40
574 583 9.715121 TCCGTAAACTAATATAAGGGCATTTAG 57.285 33.333 0.00 0.00 0.00 1.85
575 584 9.715121 CCGTAAACTAATATAAGGGCATTTAGA 57.285 33.333 0.00 0.00 0.00 2.10
662 671 5.650543 AGCGGAAAACACATTCATATTTCC 58.349 37.500 5.69 5.69 43.48 3.13
663 672 4.803613 GCGGAAAACACATTCATATTTCCC 59.196 41.667 9.33 0.91 43.84 3.97
683 713 0.685097 TCTATGACGCCATTAGCCCC 59.315 55.000 0.00 0.00 38.78 5.80
693 723 1.762370 CCATTAGCCCCAACCCATTTC 59.238 52.381 0.00 0.00 0.00 2.17
697 727 0.835971 AGCCCCAACCCATTTCCAAC 60.836 55.000 0.00 0.00 0.00 3.77
700 730 1.482177 CCCCAACCCATTTCCAACTGA 60.482 52.381 0.00 0.00 0.00 3.41
719 749 2.178984 TGAAGGAAACCCTGACCCATTT 59.821 45.455 0.00 0.00 33.44 2.32
720 750 3.239449 GAAGGAAACCCTGACCCATTTT 58.761 45.455 0.00 0.00 33.44 1.82
721 751 2.889512 AGGAAACCCTGACCCATTTTC 58.110 47.619 0.00 0.00 31.48 2.29
724 754 3.244078 GGAAACCCTGACCCATTTTCAAC 60.244 47.826 0.00 0.00 0.00 3.18
725 755 3.328535 AACCCTGACCCATTTTCAACT 57.671 42.857 0.00 0.00 0.00 3.16
726 756 2.597455 ACCCTGACCCATTTTCAACTG 58.403 47.619 0.00 0.00 0.00 3.16
727 757 2.176798 ACCCTGACCCATTTTCAACTGA 59.823 45.455 0.00 0.00 0.00 3.41
728 758 3.230134 CCCTGACCCATTTTCAACTGAA 58.770 45.455 0.00 0.00 0.00 3.02
729 759 3.256631 CCCTGACCCATTTTCAACTGAAG 59.743 47.826 0.00 0.00 35.21 3.02
730 760 4.144297 CCTGACCCATTTTCAACTGAAGA 58.856 43.478 0.00 0.00 35.21 2.87
731 761 4.584325 CCTGACCCATTTTCAACTGAAGAA 59.416 41.667 0.00 0.00 35.21 2.52
732 762 5.068987 CCTGACCCATTTTCAACTGAAGAAA 59.931 40.000 0.00 0.00 35.21 2.52
733 763 6.406849 CCTGACCCATTTTCAACTGAAGAAAA 60.407 38.462 11.92 11.92 45.68 2.29
734 764 6.337356 TGACCCATTTTCAACTGAAGAAAAC 58.663 36.000 11.82 3.64 44.78 2.43
735 765 5.670485 ACCCATTTTCAACTGAAGAAAACC 58.330 37.500 11.82 0.00 44.78 3.27
736 766 5.056480 CCCATTTTCAACTGAAGAAAACCC 58.944 41.667 11.82 0.00 44.78 4.11
737 767 5.163311 CCCATTTTCAACTGAAGAAAACCCT 60.163 40.000 11.82 0.00 44.78 4.34
738 768 5.754890 CCATTTTCAACTGAAGAAAACCCTG 59.245 40.000 11.82 8.29 44.78 4.45
739 769 6.406849 CCATTTTCAACTGAAGAAAACCCTGA 60.407 38.462 11.82 0.00 44.78 3.86
740 770 5.576447 TTTCAACTGAAGAAAACCCTGAC 57.424 39.130 0.00 0.00 35.21 3.51
741 771 3.551846 TCAACTGAAGAAAACCCTGACC 58.448 45.455 0.00 0.00 0.00 4.02
742 772 2.623416 CAACTGAAGAAAACCCTGACCC 59.377 50.000 0.00 0.00 0.00 4.46
743 773 1.850345 ACTGAAGAAAACCCTGACCCA 59.150 47.619 0.00 0.00 0.00 4.51
744 774 2.447047 ACTGAAGAAAACCCTGACCCAT 59.553 45.455 0.00 0.00 0.00 4.00
745 775 3.117131 ACTGAAGAAAACCCTGACCCATT 60.117 43.478 0.00 0.00 0.00 3.16
746 776 3.897505 CTGAAGAAAACCCTGACCCATTT 59.102 43.478 0.00 0.00 0.00 2.32
747 777 4.294347 TGAAGAAAACCCTGACCCATTTT 58.706 39.130 0.00 0.00 0.00 1.82
748 778 4.343814 TGAAGAAAACCCTGACCCATTTTC 59.656 41.667 0.00 0.00 40.01 2.29
749 779 3.922375 AGAAAACCCTGACCCATTTTCA 58.078 40.909 10.06 0.00 41.44 2.69
750 780 4.492646 AGAAAACCCTGACCCATTTTCAT 58.507 39.130 10.06 0.00 41.44 2.57
751 781 4.907269 AGAAAACCCTGACCCATTTTCATT 59.093 37.500 10.06 0.00 41.44 2.57
752 782 4.890158 AAACCCTGACCCATTTTCATTC 57.110 40.909 0.00 0.00 0.00 2.67
753 783 2.446435 ACCCTGACCCATTTTCATTCG 58.554 47.619 0.00 0.00 0.00 3.34
754 784 1.134946 CCCTGACCCATTTTCATTCGC 59.865 52.381 0.00 0.00 0.00 4.70
755 785 1.818060 CCTGACCCATTTTCATTCGCA 59.182 47.619 0.00 0.00 0.00 5.10
756 786 2.230992 CCTGACCCATTTTCATTCGCAA 59.769 45.455 0.00 0.00 0.00 4.85
757 787 3.305950 CCTGACCCATTTTCATTCGCAAA 60.306 43.478 0.00 0.00 0.00 3.68
758 788 4.305769 CTGACCCATTTTCATTCGCAAAA 58.694 39.130 0.00 0.00 0.00 2.44
759 789 4.697514 TGACCCATTTTCATTCGCAAAAA 58.302 34.783 0.00 0.00 0.00 1.94
817 849 3.701664 GGTCAAGGATCCAATTTCTGGT 58.298 45.455 15.82 0.00 46.51 4.00
818 850 4.089361 GGTCAAGGATCCAATTTCTGGTT 58.911 43.478 15.82 0.00 46.51 3.67
914 946 4.719369 GCCGTCGCGACCTCAGTT 62.719 66.667 31.84 0.00 0.00 3.16
915 947 2.504244 CCGTCGCGACCTCAGTTC 60.504 66.667 31.84 6.34 0.00 3.01
935 967 2.186903 CACCCGCAACCGCTAGAT 59.813 61.111 0.00 0.00 35.30 1.98
990 1047 2.436646 GTCCGTCGTCTCCCCGTA 60.437 66.667 0.00 0.00 0.00 4.02
1017 1074 1.814169 GATGGCGAGGTTCCGGTTC 60.814 63.158 0.00 0.00 0.00 3.62
1166 1226 2.651361 CCCGAATCCCGATCCGAG 59.349 66.667 0.00 0.00 41.76 4.63
1175 1235 0.107831 CCCGATCCGAGTCTCTCTCT 59.892 60.000 0.00 0.00 40.75 3.10
1176 1236 1.508632 CCGATCCGAGTCTCTCTCTC 58.491 60.000 0.00 0.00 40.75 3.20
1177 1237 1.070134 CCGATCCGAGTCTCTCTCTCT 59.930 57.143 0.00 0.00 40.75 3.10
1178 1238 2.484770 CCGATCCGAGTCTCTCTCTCTT 60.485 54.545 0.00 0.00 40.75 2.85
1179 1239 2.800544 CGATCCGAGTCTCTCTCTCTTC 59.199 54.545 0.00 0.00 40.75 2.87
1180 1240 3.492656 CGATCCGAGTCTCTCTCTCTTCT 60.493 52.174 0.00 0.00 40.75 2.85
1181 1241 3.536956 TCCGAGTCTCTCTCTCTTCTC 57.463 52.381 0.00 0.00 40.75 2.87
1184 1244 3.259064 CGAGTCTCTCTCTCTTCTCGTT 58.741 50.000 0.00 0.00 40.75 3.85
1189 1249 4.092968 GTCTCTCTCTCTTCTCGTTCTGAC 59.907 50.000 0.00 0.00 0.00 3.51
1324 1400 1.360185 GATCTGATCCCATGCCTCCT 58.640 55.000 6.37 0.00 0.00 3.69
1376 1452 1.376553 GGGTGCTTGGCTCTGAGAC 60.377 63.158 9.28 6.13 0.00 3.36
1394 1470 4.041198 TGAGACGAAATTCTAGGGTTTGGT 59.959 41.667 7.68 7.68 0.00 3.67
1408 1484 3.702548 GGGTTTGGTCTGGTGTTAAGTTT 59.297 43.478 0.00 0.00 0.00 2.66
1664 1740 3.254411 TCTGGTGTGAATTTGCGCATTTA 59.746 39.130 12.75 0.00 0.00 1.40
1676 1752 1.872237 GCGCATTTATCCGTAGCTGGA 60.872 52.381 0.30 0.00 43.58 3.86
1680 1756 3.815401 GCATTTATCCGTAGCTGGATTGT 59.185 43.478 10.65 0.00 46.74 2.71
1682 1758 4.746535 TTTATCCGTAGCTGGATTGTCA 57.253 40.909 10.65 0.00 46.74 3.58
1692 1769 4.084287 AGCTGGATTGTCATGTTGATTGT 58.916 39.130 0.00 0.00 0.00 2.71
1720 1797 3.406764 GTTGCAGATCACTGGAGACTTT 58.593 45.455 0.00 0.00 44.58 2.66
1721 1798 3.777106 TGCAGATCACTGGAGACTTTT 57.223 42.857 0.00 0.00 43.62 2.27
1722 1799 3.668447 TGCAGATCACTGGAGACTTTTC 58.332 45.455 0.00 0.00 43.62 2.29
1723 1800 3.326006 TGCAGATCACTGGAGACTTTTCT 59.674 43.478 0.00 0.00 43.62 2.52
1724 1801 3.683822 GCAGATCACTGGAGACTTTTCTG 59.316 47.826 0.00 0.00 43.62 3.02
1725 1802 4.562347 GCAGATCACTGGAGACTTTTCTGA 60.562 45.833 0.00 0.00 43.62 3.27
1726 1803 5.732633 CAGATCACTGGAGACTTTTCTGAT 58.267 41.667 0.00 0.00 40.14 2.90
1727 1804 5.581479 CAGATCACTGGAGACTTTTCTGATG 59.419 44.000 0.00 0.00 40.14 3.07
1728 1805 3.668447 TCACTGGAGACTTTTCTGATGC 58.332 45.455 0.00 0.00 29.47 3.91
1731 1808 2.419324 CTGGAGACTTTTCTGATGCTGC 59.581 50.000 0.00 0.00 29.47 5.25
1733 1810 2.419324 GGAGACTTTTCTGATGCTGCTG 59.581 50.000 0.00 0.00 29.47 4.41
1734 1811 1.811359 AGACTTTTCTGATGCTGCTGC 59.189 47.619 8.89 8.89 40.20 5.25
1735 1812 0.520404 ACTTTTCTGATGCTGCTGCG 59.480 50.000 11.21 0.00 43.34 5.18
1737 1814 1.239296 TTTTCTGATGCTGCTGCGCT 61.239 50.000 9.73 0.42 43.34 5.92
1753 1837 0.798159 CGCTGCTGTTATGCTTGACA 59.202 50.000 0.00 0.00 0.00 3.58
1767 1851 3.321396 TGCTTGACAGAATTGGATTGCAA 59.679 39.130 0.00 0.00 0.00 4.08
1803 1887 6.980593 TGTACTGAATTTCTGATTTGGTTGG 58.019 36.000 9.92 0.00 0.00 3.77
1808 1892 6.980593 TGAATTTCTGATTTGGTTGGTACTG 58.019 36.000 0.00 0.00 0.00 2.74
1809 1893 6.549364 TGAATTTCTGATTTGGTTGGTACTGT 59.451 34.615 0.00 0.00 0.00 3.55
1810 1894 7.721842 TGAATTTCTGATTTGGTTGGTACTGTA 59.278 33.333 0.00 0.00 0.00 2.74
1811 1895 8.650143 AATTTCTGATTTGGTTGGTACTGTAT 57.350 30.769 0.00 0.00 0.00 2.29
1812 1896 7.447374 TTTCTGATTTGGTTGGTACTGTATG 57.553 36.000 0.00 0.00 0.00 2.39
1830 1914 1.758122 GGTAGCCCCATTTGCCCTG 60.758 63.158 0.00 0.00 0.00 4.45
1833 1917 2.550699 TAGCCCCATTTGCCCTGTCG 62.551 60.000 0.00 0.00 0.00 4.35
1836 1920 1.595093 CCCCATTTGCCCTGTCGAAC 61.595 60.000 0.00 0.00 0.00 3.95
1844 1928 0.535335 GCCCTGTCGAACTGATGGTA 59.465 55.000 0.00 0.00 0.00 3.25
1858 1942 3.315765 TGGTACAGCTCGGGTTTTG 57.684 52.632 0.00 0.00 0.00 2.44
1859 1943 0.887387 TGGTACAGCTCGGGTTTTGC 60.887 55.000 0.00 0.00 0.00 3.68
1860 1944 1.495951 GTACAGCTCGGGTTTTGCG 59.504 57.895 0.00 0.00 0.00 4.85
1861 1945 1.070105 TACAGCTCGGGTTTTGCGT 59.930 52.632 0.00 0.00 0.00 5.24
1862 1946 0.947180 TACAGCTCGGGTTTTGCGTC 60.947 55.000 0.00 0.00 0.00 5.19
1901 1986 9.760077 GGCTAGTTTAGAAAATAGTATAGCACA 57.240 33.333 10.25 0.00 38.45 4.57
1907 1992 8.873215 TTAGAAAATAGTATAGCACAGTGAGC 57.127 34.615 4.15 4.14 0.00 4.26
1908 1993 7.118496 AGAAAATAGTATAGCACAGTGAGCT 57.882 36.000 19.17 19.17 45.77 4.09
1909 1994 7.206687 AGAAAATAGTATAGCACAGTGAGCTC 58.793 38.462 18.78 6.82 42.32 4.09
1910 1995 5.461032 AATAGTATAGCACAGTGAGCTCC 57.539 43.478 18.78 8.29 42.32 4.70
1911 1996 3.025322 AGTATAGCACAGTGAGCTCCT 57.975 47.619 18.78 10.34 42.32 3.69
1912 1997 3.370104 AGTATAGCACAGTGAGCTCCTT 58.630 45.455 18.78 7.89 42.32 3.36
1913 1998 3.772025 AGTATAGCACAGTGAGCTCCTTT 59.228 43.478 18.78 5.56 42.32 3.11
1929 2014 4.082026 GCTCCTTTGCAATGAGGTAAATGT 60.082 41.667 21.39 0.00 34.57 2.71
1932 2017 5.716228 TCCTTTGCAATGAGGTAAATGTCAT 59.284 36.000 15.29 0.00 34.79 3.06
1936 2021 5.499313 TGCAATGAGGTAAATGTCATCTGA 58.501 37.500 0.00 0.00 32.02 3.27
1962 2047 1.699634 TCTTTGAGGTGGGAGAAGTGG 59.300 52.381 0.00 0.00 0.00 4.00
1980 2065 1.295423 GTACTTCGGGCTTGGCAGA 59.705 57.895 0.00 0.00 0.00 4.26
1996 2081 2.125350 GAGCTTCCTCTGGCCGTG 60.125 66.667 0.00 0.00 35.16 4.94
2002 2087 1.827399 TTCCTCTGGCCGTGTTCTCC 61.827 60.000 0.00 0.00 0.00 3.71
2007 2092 2.432628 GGCCGTGTTCTCCAGTCG 60.433 66.667 0.00 0.00 0.00 4.18
2010 2095 1.658114 CCGTGTTCTCCAGTCGTCA 59.342 57.895 0.00 0.00 0.00 4.35
2015 2100 2.292569 GTGTTCTCCAGTCGTCACAGTA 59.707 50.000 0.00 0.00 0.00 2.74
2018 2103 2.701107 TCTCCAGTCGTCACAGTAGAG 58.299 52.381 0.00 0.00 0.00 2.43
2022 2107 4.079970 TCCAGTCGTCACAGTAGAGAATT 58.920 43.478 0.00 0.00 0.00 2.17
2032 2118 7.061210 CGTCACAGTAGAGAATTAAACTGACTG 59.939 40.741 9.20 12.96 41.47 3.51
2046 2132 2.092429 ACTGACTGCTTCTGTTTCCCAA 60.092 45.455 0.00 0.00 32.71 4.12
2051 2137 2.951642 CTGCTTCTGTTTCCCAACTTGA 59.048 45.455 0.00 0.00 33.58 3.02
2055 2141 5.596361 TGCTTCTGTTTCCCAACTTGATTTA 59.404 36.000 0.00 0.00 33.58 1.40
2056 2142 6.267471 TGCTTCTGTTTCCCAACTTGATTTAT 59.733 34.615 0.00 0.00 33.58 1.40
2057 2143 7.450014 TGCTTCTGTTTCCCAACTTGATTTATA 59.550 33.333 0.00 0.00 33.58 0.98
2089 2175 9.985730 TTTTGAAGAATGTTGATCTAAGCAATT 57.014 25.926 0.00 0.00 0.00 2.32
2090 2176 8.975410 TTGAAGAATGTTGATCTAAGCAATTG 57.025 30.769 0.00 0.00 0.00 2.32
2122 2208 3.186283 AGTAGACCTCTCTCCAGTCTCA 58.814 50.000 0.00 0.00 41.09 3.27
2123 2209 2.507407 AGACCTCTCTCCAGTCTCAC 57.493 55.000 0.00 0.00 36.06 3.51
2130 2216 2.750166 TCTCTCCAGTCTCACGTGAATC 59.250 50.000 20.49 14.70 0.00 2.52
2132 2218 0.895530 TCCAGTCTCACGTGAATCCC 59.104 55.000 20.49 7.45 0.00 3.85
2134 2220 2.100197 CCAGTCTCACGTGAATCCCTA 58.900 52.381 20.49 0.00 0.00 3.53
2136 2222 3.133003 CCAGTCTCACGTGAATCCCTATT 59.867 47.826 20.49 0.00 0.00 1.73
2145 2231 0.890996 GAATCCCTATTGGCTGGCCG 60.891 60.000 7.14 0.00 39.42 6.13
2146 2232 1.352622 AATCCCTATTGGCTGGCCGA 61.353 55.000 3.82 3.82 39.42 5.54
2165 2251 4.381932 GCCGAAGAATGGAAACCATGATTT 60.382 41.667 3.97 0.00 44.40 2.17
2166 2252 5.104374 CCGAAGAATGGAAACCATGATTTG 58.896 41.667 3.97 6.34 44.40 2.32
2170 2256 7.812191 CGAAGAATGGAAACCATGATTTGTTTA 59.188 33.333 3.97 0.00 44.40 2.01
2171 2257 8.831715 AAGAATGGAAACCATGATTTGTTTAC 57.168 30.769 3.97 0.00 44.40 2.01
2172 2258 7.961351 AGAATGGAAACCATGATTTGTTTACA 58.039 30.769 11.22 11.22 46.28 2.41
2187 2275 5.135508 TGTTTACACCTCTAGCAGACTTC 57.864 43.478 0.00 0.00 0.00 3.01
2188 2276 4.833380 TGTTTACACCTCTAGCAGACTTCT 59.167 41.667 0.00 0.00 0.00 2.85
2194 2283 2.356382 CCTCTAGCAGACTTCTACGTGG 59.644 54.545 0.00 0.00 0.00 4.94
2195 2284 1.743958 TCTAGCAGACTTCTACGTGGC 59.256 52.381 0.00 0.00 0.00 5.01
2199 2288 1.203994 GCAGACTTCTACGTGGCCTTA 59.796 52.381 3.32 0.00 0.00 2.69
2204 2293 3.858247 ACTTCTACGTGGCCTTAATGTC 58.142 45.455 3.32 0.00 0.00 3.06
2222 2311 9.927668 CTTAATGTCACATTGTTCCCTATTTTT 57.072 29.630 13.65 0.00 0.00 1.94
2231 2320 8.096414 ACATTGTTCCCTATTTTTCCTTTCATG 58.904 33.333 0.00 0.00 0.00 3.07
2239 2328 8.534496 CCCTATTTTTCCTTTCATGATCTTGTT 58.466 33.333 8.33 0.00 0.00 2.83
2247 2336 5.452356 CCTTTCATGATCTTGTTAATGCCCC 60.452 44.000 8.33 0.00 0.00 5.80
2248 2337 4.248174 TCATGATCTTGTTAATGCCCCA 57.752 40.909 8.33 0.00 0.00 4.96
2260 2349 2.555732 ATGCCCCATCCATTCTTGTT 57.444 45.000 0.00 0.00 0.00 2.83
2262 2351 2.178580 TGCCCCATCCATTCTTGTTTC 58.821 47.619 0.00 0.00 0.00 2.78
2270 2359 5.893255 CCATCCATTCTTGTTTCCCTCAATA 59.107 40.000 0.00 0.00 0.00 1.90
2276 2365 8.408601 CCATTCTTGTTTCCCTCAATAGTATTG 58.591 37.037 15.56 15.56 0.00 1.90
2277 2366 7.391148 TTCTTGTTTCCCTCAATAGTATTGC 57.609 36.000 16.68 3.34 0.00 3.56
2279 2368 5.186256 TGTTTCCCTCAATAGTATTGCCA 57.814 39.130 16.68 1.62 0.00 4.92
2285 2374 4.447616 CCCTCAATAGTATTGCCATTCCCA 60.448 45.833 16.68 0.00 0.00 4.37
2291 2380 2.895404 AGTATTGCCATTCCCATGCATC 59.105 45.455 0.00 0.00 0.00 3.91
2292 2381 2.097110 ATTGCCATTCCCATGCATCT 57.903 45.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.738830 ACTACTGCTCCAACACGTAAA 57.261 42.857 0.00 0.00 0.00 2.01
1 2 3.822735 ACTACTACTGCTCCAACACGTAA 59.177 43.478 0.00 0.00 0.00 3.18
2 3 3.415212 ACTACTACTGCTCCAACACGTA 58.585 45.455 0.00 0.00 0.00 3.57
3 4 2.236766 ACTACTACTGCTCCAACACGT 58.763 47.619 0.00 0.00 0.00 4.49
4 5 3.727079 CGTACTACTACTGCTCCAACACG 60.727 52.174 0.00 0.00 0.00 4.49
5 6 3.756069 CGTACTACTACTGCTCCAACAC 58.244 50.000 0.00 0.00 0.00 3.32
6 7 2.163010 GCGTACTACTACTGCTCCAACA 59.837 50.000 0.00 0.00 0.00 3.33
7 8 2.422832 AGCGTACTACTACTGCTCCAAC 59.577 50.000 0.00 0.00 31.34 3.77
8 9 2.719739 AGCGTACTACTACTGCTCCAA 58.280 47.619 0.00 0.00 31.34 3.53
9 10 2.414994 AGCGTACTACTACTGCTCCA 57.585 50.000 0.00 0.00 31.34 3.86
10 11 3.436359 GGATAGCGTACTACTACTGCTCC 59.564 52.174 0.00 0.00 35.62 4.70
11 12 4.317488 AGGATAGCGTACTACTACTGCTC 58.683 47.826 0.00 0.00 35.62 4.26
12 13 4.354893 AGGATAGCGTACTACTACTGCT 57.645 45.455 0.00 0.00 36.93 4.24
13 14 5.008415 TGAAAGGATAGCGTACTACTACTGC 59.992 44.000 0.00 0.00 0.00 4.40
14 15 6.615264 TGAAAGGATAGCGTACTACTACTG 57.385 41.667 0.00 0.00 0.00 2.74
15 16 6.864360 CTGAAAGGATAGCGTACTACTACT 57.136 41.667 0.00 0.00 0.00 2.57
32 33 2.158608 AGTGTTTGTCCCTCCCTGAAAG 60.159 50.000 0.00 0.00 0.00 2.62
33 34 1.850345 AGTGTTTGTCCCTCCCTGAAA 59.150 47.619 0.00 0.00 0.00 2.69
34 35 1.420138 GAGTGTTTGTCCCTCCCTGAA 59.580 52.381 0.00 0.00 0.00 3.02
35 36 1.056660 GAGTGTTTGTCCCTCCCTGA 58.943 55.000 0.00 0.00 0.00 3.86
36 37 1.059913 AGAGTGTTTGTCCCTCCCTG 58.940 55.000 0.00 0.00 0.00 4.45
37 38 1.059913 CAGAGTGTTTGTCCCTCCCT 58.940 55.000 0.00 0.00 0.00 4.20
38 39 1.056660 TCAGAGTGTTTGTCCCTCCC 58.943 55.000 0.00 0.00 0.00 4.30
39 40 2.039084 ACATCAGAGTGTTTGTCCCTCC 59.961 50.000 0.00 0.00 0.00 4.30
40 41 3.070018 CACATCAGAGTGTTTGTCCCTC 58.930 50.000 0.00 0.00 34.83 4.30
41 42 3.131709 CACATCAGAGTGTTTGTCCCT 57.868 47.619 0.00 0.00 34.83 4.20
50 51 5.239306 ACACCACAATTTACACATCAGAGTG 59.761 40.000 0.00 0.00 44.93 3.51
51 52 5.239306 CACACCACAATTTACACATCAGAGT 59.761 40.000 0.00 0.00 0.00 3.24
52 53 5.335113 CCACACCACAATTTACACATCAGAG 60.335 44.000 0.00 0.00 0.00 3.35
53 54 4.518590 CCACACCACAATTTACACATCAGA 59.481 41.667 0.00 0.00 0.00 3.27
54 55 4.321156 CCCACACCACAATTTACACATCAG 60.321 45.833 0.00 0.00 0.00 2.90
55 56 3.571828 CCCACACCACAATTTACACATCA 59.428 43.478 0.00 0.00 0.00 3.07
56 57 3.613910 GCCCACACCACAATTTACACATC 60.614 47.826 0.00 0.00 0.00 3.06
57 58 2.298729 GCCCACACCACAATTTACACAT 59.701 45.455 0.00 0.00 0.00 3.21
58 59 1.683917 GCCCACACCACAATTTACACA 59.316 47.619 0.00 0.00 0.00 3.72
59 60 1.335506 CGCCCACACCACAATTTACAC 60.336 52.381 0.00 0.00 0.00 2.90
60 61 0.955178 CGCCCACACCACAATTTACA 59.045 50.000 0.00 0.00 0.00 2.41
61 62 0.242555 CCGCCCACACCACAATTTAC 59.757 55.000 0.00 0.00 0.00 2.01
62 63 0.178987 ACCGCCCACACCACAATTTA 60.179 50.000 0.00 0.00 0.00 1.40
63 64 1.456705 ACCGCCCACACCACAATTT 60.457 52.632 0.00 0.00 0.00 1.82
64 65 1.901464 GACCGCCCACACCACAATT 60.901 57.895 0.00 0.00 0.00 2.32
65 66 2.282180 GACCGCCCACACCACAAT 60.282 61.111 0.00 0.00 0.00 2.71
66 67 3.765894 CTGACCGCCCACACCACAA 62.766 63.158 0.00 0.00 0.00 3.33
67 68 4.248842 CTGACCGCCCACACCACA 62.249 66.667 0.00 0.00 0.00 4.17
77 78 1.063811 GTAGTACGAGGCTGACCGC 59.936 63.158 0.00 0.00 42.76 5.68
78 79 1.596727 GTAGTAGTACGAGGCTGACCG 59.403 57.143 0.00 0.00 42.76 4.79
115 116 9.262358 CTGTAGTAGTAGTTTCTTTTTCTGCTT 57.738 33.333 0.00 0.00 0.00 3.91
124 125 5.593502 CGGGATCCTGTAGTAGTAGTTTCTT 59.406 44.000 12.93 0.00 0.00 2.52
125 126 5.131784 CGGGATCCTGTAGTAGTAGTTTCT 58.868 45.833 12.93 0.00 0.00 2.52
126 127 4.261530 GCGGGATCCTGTAGTAGTAGTTTC 60.262 50.000 21.88 0.00 0.00 2.78
363 368 1.002857 CATGGAAAAGGAGGAGGGGT 58.997 55.000 0.00 0.00 0.00 4.95
405 413 0.977395 AACCACTCCACTACTCCAGC 59.023 55.000 0.00 0.00 0.00 4.85
479 487 4.641645 TGGAGTTGGGCAGTGCGG 62.642 66.667 9.45 0.00 0.00 5.69
508 517 0.467290 AATGTTGTTGGCCACTCCGT 60.467 50.000 3.88 0.00 37.80 4.69
509 518 0.673437 AAATGTTGTTGGCCACTCCG 59.327 50.000 3.88 0.00 37.80 4.63
530 539 9.016623 GTTTACGGAGGAAATACAATTTTATGC 57.983 33.333 0.00 0.00 0.00 3.14
542 551 7.881751 GCCCTTATATTAGTTTACGGAGGAAAT 59.118 37.037 0.00 0.00 0.00 2.17
543 552 7.147514 TGCCCTTATATTAGTTTACGGAGGAAA 60.148 37.037 0.00 0.00 0.00 3.13
544 553 6.327104 TGCCCTTATATTAGTTTACGGAGGAA 59.673 38.462 0.00 0.00 0.00 3.36
545 554 5.840149 TGCCCTTATATTAGTTTACGGAGGA 59.160 40.000 0.00 0.00 0.00 3.71
546 555 6.105397 TGCCCTTATATTAGTTTACGGAGG 57.895 41.667 0.00 0.00 0.00 4.30
547 556 8.617290 AAATGCCCTTATATTAGTTTACGGAG 57.383 34.615 0.00 0.00 0.00 4.63
548 557 9.715121 CTAAATGCCCTTATATTAGTTTACGGA 57.285 33.333 0.00 0.00 0.00 4.69
549 558 9.715121 TCTAAATGCCCTTATATTAGTTTACGG 57.285 33.333 0.00 0.00 0.00 4.02
662 671 1.338200 GGGCTAATGGCGTCATAGAGG 60.338 57.143 1.27 0.00 42.94 3.69
663 672 1.338200 GGGGCTAATGGCGTCATAGAG 60.338 57.143 1.27 5.12 42.94 2.43
683 713 3.230134 TCCTTCAGTTGGAAATGGGTTG 58.770 45.455 0.00 0.00 34.44 3.77
693 723 2.230660 GTCAGGGTTTCCTTCAGTTGG 58.769 52.381 0.00 0.00 42.67 3.77
697 727 0.771127 TGGGTCAGGGTTTCCTTCAG 59.229 55.000 0.00 0.00 42.67 3.02
700 730 3.239449 GAAAATGGGTCAGGGTTTCCTT 58.761 45.455 0.00 0.00 42.67 3.36
719 749 3.951680 GGTCAGGGTTTTCTTCAGTTGAA 59.048 43.478 0.00 0.00 0.00 2.69
720 750 3.551846 GGTCAGGGTTTTCTTCAGTTGA 58.448 45.455 0.00 0.00 0.00 3.18
721 751 2.623416 GGGTCAGGGTTTTCTTCAGTTG 59.377 50.000 0.00 0.00 0.00 3.16
724 754 2.656947 TGGGTCAGGGTTTTCTTCAG 57.343 50.000 0.00 0.00 0.00 3.02
725 755 3.611025 AATGGGTCAGGGTTTTCTTCA 57.389 42.857 0.00 0.00 0.00 3.02
726 756 4.343814 TGAAAATGGGTCAGGGTTTTCTTC 59.656 41.667 9.83 0.00 39.84 2.87
727 757 4.294347 TGAAAATGGGTCAGGGTTTTCTT 58.706 39.130 9.83 0.00 39.84 2.52
728 758 3.922375 TGAAAATGGGTCAGGGTTTTCT 58.078 40.909 9.83 0.00 39.84 2.52
729 759 4.890158 ATGAAAATGGGTCAGGGTTTTC 57.110 40.909 0.00 0.00 39.67 2.29
730 760 4.262420 CGAATGAAAATGGGTCAGGGTTTT 60.262 41.667 0.00 0.00 0.00 2.43
731 761 3.258123 CGAATGAAAATGGGTCAGGGTTT 59.742 43.478 0.00 0.00 0.00 3.27
732 762 2.825532 CGAATGAAAATGGGTCAGGGTT 59.174 45.455 0.00 0.00 0.00 4.11
733 763 2.446435 CGAATGAAAATGGGTCAGGGT 58.554 47.619 0.00 0.00 0.00 4.34
734 764 1.134946 GCGAATGAAAATGGGTCAGGG 59.865 52.381 0.00 0.00 0.00 4.45
735 765 1.818060 TGCGAATGAAAATGGGTCAGG 59.182 47.619 0.00 0.00 0.00 3.86
736 766 3.574284 TTGCGAATGAAAATGGGTCAG 57.426 42.857 0.00 0.00 0.00 3.51
737 767 4.327982 TTTTGCGAATGAAAATGGGTCA 57.672 36.364 0.00 0.00 0.00 4.02
756 786 5.663456 GAAAACGGGTAAGGGTTTCTTTTT 58.337 37.500 0.00 0.00 35.44 1.94
757 787 4.202040 CGAAAACGGGTAAGGGTTTCTTTT 60.202 41.667 1.47 0.00 35.44 2.27
758 788 3.316029 CGAAAACGGGTAAGGGTTTCTTT 59.684 43.478 1.47 0.00 35.44 2.52
759 789 2.880268 CGAAAACGGGTAAGGGTTTCTT 59.120 45.455 1.47 0.00 35.44 2.52
760 790 2.158769 ACGAAAACGGGTAAGGGTTTCT 60.159 45.455 0.00 0.00 35.44 2.52
761 791 2.221169 ACGAAAACGGGTAAGGGTTTC 58.779 47.619 0.00 0.00 35.44 2.78
762 792 2.346766 ACGAAAACGGGTAAGGGTTT 57.653 45.000 0.00 0.00 37.94 3.27
763 793 3.483808 TTACGAAAACGGGTAAGGGTT 57.516 42.857 0.00 0.00 0.00 4.11
764 794 3.483808 TTTACGAAAACGGGTAAGGGT 57.516 42.857 0.00 0.00 30.96 4.34
765 795 4.827304 TTTTTACGAAAACGGGTAAGGG 57.173 40.909 0.00 0.00 30.96 3.95
844 876 3.536498 GAACGTTGGGCCAGTTGCG 62.536 63.158 15.14 15.79 42.61 4.85
850 882 2.112297 GTGGAGAACGTTGGGCCA 59.888 61.111 5.00 0.00 0.00 5.36
897 929 4.719369 AACTGAGGTCGCGACGGC 62.719 66.667 30.99 24.56 0.00 5.68
898 930 2.504244 GAACTGAGGTCGCGACGG 60.504 66.667 30.99 21.90 0.00 4.79
899 931 2.504244 GGAACTGAGGTCGCGACG 60.504 66.667 30.99 20.15 0.00 5.12
900 932 2.126031 GGGAACTGAGGTCGCGAC 60.126 66.667 30.67 30.67 0.00 5.19
901 933 3.379445 GGGGAACTGAGGTCGCGA 61.379 66.667 3.71 3.71 0.00 5.87
902 934 3.691342 TGGGGAACTGAGGTCGCG 61.691 66.667 8.52 0.00 0.00 5.87
903 935 2.047179 GTGGGGAACTGAGGTCGC 60.047 66.667 5.94 5.94 0.00 5.19
904 936 2.663196 GGTGGGGAACTGAGGTCG 59.337 66.667 0.00 0.00 0.00 4.79
905 937 2.955881 CGGGTGGGGAACTGAGGTC 61.956 68.421 0.00 0.00 0.00 3.85
906 938 2.928396 CGGGTGGGGAACTGAGGT 60.928 66.667 0.00 0.00 0.00 3.85
907 939 4.410400 GCGGGTGGGGAACTGAGG 62.410 72.222 0.00 0.00 0.00 3.86
908 940 3.190738 TTGCGGGTGGGGAACTGAG 62.191 63.158 0.00 0.00 0.00 3.35
909 941 3.172106 TTGCGGGTGGGGAACTGA 61.172 61.111 0.00 0.00 0.00 3.41
910 942 2.983592 GTTGCGGGTGGGGAACTG 60.984 66.667 0.00 0.00 35.62 3.16
911 943 4.280019 GGTTGCGGGTGGGGAACT 62.280 66.667 0.00 0.00 38.20 3.01
932 964 0.958091 AGCAGATTCGCGAGCTATCT 59.042 50.000 17.77 16.07 35.19 1.98
935 967 1.103987 AGGAGCAGATTCGCGAGCTA 61.104 55.000 19.01 0.44 37.48 3.32
1166 1226 4.092968 GTCAGAACGAGAAGAGAGAGAGAC 59.907 50.000 0.00 0.00 0.00 3.36
1204 1264 2.787249 CTTCGGCTGCATCCAACG 59.213 61.111 7.47 0.00 0.00 4.10
1361 1437 0.392706 TTTCGTCTCAGAGCCAAGCA 59.607 50.000 0.00 0.00 0.00 3.91
1376 1452 3.689649 CCAGACCAAACCCTAGAATTTCG 59.310 47.826 0.00 0.00 0.00 3.46
1394 1470 6.713450 GGGAACTATTCAAACTTAACACCAGA 59.287 38.462 0.00 0.00 0.00 3.86
1642 1718 1.246649 ATGCGCAAATTCACACCAGA 58.753 45.000 17.11 0.00 0.00 3.86
1649 1725 3.773860 ACGGATAAATGCGCAAATTCA 57.226 38.095 17.11 0.00 45.92 2.57
1676 1752 5.048782 ACGCACTAACAATCAACATGACAAT 60.049 36.000 0.00 0.00 0.00 2.71
1680 1756 4.782156 CAACGCACTAACAATCAACATGA 58.218 39.130 0.00 0.00 0.00 3.07
1682 1758 3.004210 TGCAACGCACTAACAATCAACAT 59.996 39.130 0.00 0.00 31.71 2.71
1692 1769 2.068519 CAGTGATCTGCAACGCACTAA 58.931 47.619 12.80 0.00 39.40 2.24
1731 1808 0.522705 CAAGCATAACAGCAGCGCAG 60.523 55.000 11.47 1.31 36.85 5.18
1733 1810 0.522076 GTCAAGCATAACAGCAGCGC 60.522 55.000 0.00 0.00 36.85 5.92
1734 1811 0.798159 TGTCAAGCATAACAGCAGCG 59.202 50.000 0.00 0.00 36.85 5.18
1735 1812 2.079158 TCTGTCAAGCATAACAGCAGC 58.921 47.619 7.33 0.00 42.10 5.25
1737 1814 4.082625 CCAATTCTGTCAAGCATAACAGCA 60.083 41.667 7.33 0.00 42.10 4.41
1767 1851 7.332926 CAGAAATTCAGTACAAGTCTAGCACAT 59.667 37.037 0.00 0.00 0.00 3.21
1798 1882 2.158856 GGGCTACCATACAGTACCAACC 60.159 54.545 0.00 0.00 36.50 3.77
1812 1896 1.758122 CAGGGCAAATGGGGCTACC 60.758 63.158 0.00 0.00 40.81 3.18
1825 1909 0.535335 TACCATCAGTTCGACAGGGC 59.465 55.000 0.00 0.00 0.00 5.19
1827 1911 2.881074 CTGTACCATCAGTTCGACAGG 58.119 52.381 0.00 0.00 31.53 4.00
1830 1914 2.531206 GAGCTGTACCATCAGTTCGAC 58.469 52.381 0.00 0.00 36.36 4.20
1833 1917 1.471676 CCCGAGCTGTACCATCAGTTC 60.472 57.143 0.00 0.00 40.53 3.01
1836 1920 0.537188 AACCCGAGCTGTACCATCAG 59.463 55.000 0.00 0.00 38.35 2.90
1844 1928 2.203153 ACGCAAAACCCGAGCTGT 60.203 55.556 0.00 0.00 0.00 4.40
1850 1934 2.126914 TTCAAATGACGCAAAACCCG 57.873 45.000 0.00 0.00 0.00 5.28
1854 1938 4.683781 GCCTTACATTCAAATGACGCAAAA 59.316 37.500 9.62 0.00 39.67 2.44
1856 1940 3.505680 AGCCTTACATTCAAATGACGCAA 59.494 39.130 9.62 0.00 39.67 4.85
1858 1942 3.764885 AGCCTTACATTCAAATGACGC 57.235 42.857 9.62 5.24 39.67 5.19
1859 1943 6.422776 AACTAGCCTTACATTCAAATGACG 57.577 37.500 9.62 0.00 39.67 4.35
1860 1944 9.162764 TCTAAACTAGCCTTACATTCAAATGAC 57.837 33.333 9.62 0.00 39.67 3.06
1861 1945 9.733556 TTCTAAACTAGCCTTACATTCAAATGA 57.266 29.630 9.62 0.00 39.67 2.57
1888 1973 5.144100 AGGAGCTCACTGTGCTATACTATT 58.856 41.667 17.19 0.00 41.30 1.73
1891 1976 3.025322 AGGAGCTCACTGTGCTATACT 57.975 47.619 17.19 2.86 41.30 2.12
1892 1977 3.810310 AAGGAGCTCACTGTGCTATAC 57.190 47.619 17.19 0.77 41.30 1.47
1895 1980 1.609061 GCAAAGGAGCTCACTGTGCTA 60.609 52.381 27.19 0.00 44.08 3.49
1901 1986 2.574006 TCATTGCAAAGGAGCTCACT 57.426 45.000 17.19 7.49 28.02 3.41
1908 1993 5.076182 TGACATTTACCTCATTGCAAAGGA 58.924 37.500 21.51 12.98 36.46 3.36
1909 1994 5.389859 TGACATTTACCTCATTGCAAAGG 57.610 39.130 14.48 14.48 38.70 3.11
1910 1995 6.750501 CAGATGACATTTACCTCATTGCAAAG 59.249 38.462 1.71 0.00 0.00 2.77
1911 1996 6.433716 TCAGATGACATTTACCTCATTGCAAA 59.566 34.615 1.71 0.00 0.00 3.68
1912 1997 5.945191 TCAGATGACATTTACCTCATTGCAA 59.055 36.000 0.00 0.00 0.00 4.08
1913 1998 5.499313 TCAGATGACATTTACCTCATTGCA 58.501 37.500 0.00 0.00 0.00 4.08
1929 2014 3.588842 ACCTCAAAGACCCAATCAGATGA 59.411 43.478 0.00 0.00 0.00 2.92
1932 2017 2.040278 CCACCTCAAAGACCCAATCAGA 59.960 50.000 0.00 0.00 0.00 3.27
1936 2021 1.355720 CTCCCACCTCAAAGACCCAAT 59.644 52.381 0.00 0.00 0.00 3.16
1962 2047 0.741221 CTCTGCCAAGCCCGAAGTAC 60.741 60.000 0.00 0.00 0.00 2.73
1972 2057 0.392729 CCAGAGGAAGCTCTGCCAAG 60.393 60.000 0.00 0.00 46.89 3.61
1980 2065 2.456287 GAACACGGCCAGAGGAAGCT 62.456 60.000 2.24 0.00 0.00 3.74
1992 2077 0.663568 GTGACGACTGGAGAACACGG 60.664 60.000 0.00 0.00 0.00 4.94
1996 2081 2.812591 TCTACTGTGACGACTGGAGAAC 59.187 50.000 0.00 0.00 37.89 3.01
2002 2087 7.061210 CAGTTTAATTCTCTACTGTGACGACTG 59.939 40.741 0.00 0.00 34.68 3.51
2007 2092 7.148722 GCAGTCAGTTTAATTCTCTACTGTGAC 60.149 40.741 0.00 0.00 39.16 3.67
2010 2095 6.998802 AGCAGTCAGTTTAATTCTCTACTGT 58.001 36.000 0.00 0.00 39.16 3.55
2015 2100 6.529220 ACAGAAGCAGTCAGTTTAATTCTCT 58.471 36.000 0.00 0.00 0.00 3.10
2018 2103 6.858478 GGAAACAGAAGCAGTCAGTTTAATTC 59.142 38.462 9.81 0.95 43.68 2.17
2022 2107 4.134563 GGGAAACAGAAGCAGTCAGTTTA 58.865 43.478 9.81 0.00 43.68 2.01
2032 2118 4.590850 AATCAAGTTGGGAAACAGAAGC 57.409 40.909 2.34 0.00 0.00 3.86
2062 2148 9.985730 ATTGCTTAGATCAACATTCTTCAAAAA 57.014 25.926 0.00 0.00 0.00 1.94
2083 2169 7.995488 AGGTCTACTTAGATAAATGCAATTGCT 59.005 33.333 29.37 13.50 36.98 3.91
2085 2171 9.553064 AGAGGTCTACTTAGATAAATGCAATTG 57.447 33.333 0.00 0.00 33.36 2.32
2087 2173 9.153479 AGAGAGGTCTACTTAGATAAATGCAAT 57.847 33.333 0.00 0.00 34.39 3.56
2089 2175 7.231722 GGAGAGAGGTCTACTTAGATAAATGCA 59.768 40.741 0.00 0.00 34.39 3.96
2090 2176 7.231722 TGGAGAGAGGTCTACTTAGATAAATGC 59.768 40.741 0.00 0.00 34.21 3.56
2106 2192 0.402504 ACGTGAGACTGGAGAGAGGT 59.597 55.000 0.00 0.00 0.00 3.85
2107 2193 0.808125 CACGTGAGACTGGAGAGAGG 59.192 60.000 10.90 0.00 0.00 3.69
2122 2208 1.134098 CCAGCCAATAGGGATTCACGT 60.134 52.381 0.00 0.00 40.01 4.49
2123 2209 1.597742 CCAGCCAATAGGGATTCACG 58.402 55.000 0.00 0.00 40.01 4.35
2130 2216 1.526917 CTTCGGCCAGCCAATAGGG 60.527 63.158 9.78 0.00 40.85 3.53
2132 2218 1.605710 CATTCTTCGGCCAGCCAATAG 59.394 52.381 9.78 2.61 35.37 1.73
2134 2220 1.039233 CCATTCTTCGGCCAGCCAAT 61.039 55.000 9.78 0.00 35.37 3.16
2136 2222 2.045045 CCATTCTTCGGCCAGCCA 60.045 61.111 9.78 0.00 35.37 4.75
2145 2231 7.967890 AAACAAATCATGGTTTCCATTCTTC 57.032 32.000 0.00 0.00 42.23 2.87
2146 2232 8.428063 TGTAAACAAATCATGGTTTCCATTCTT 58.572 29.630 0.00 0.00 42.23 2.52
2165 2251 4.833380 AGAAGTCTGCTAGAGGTGTAAACA 59.167 41.667 0.00 0.00 0.00 2.83
2166 2252 5.394224 AGAAGTCTGCTAGAGGTGTAAAC 57.606 43.478 0.00 0.00 0.00 2.01
2170 2256 3.011119 CGTAGAAGTCTGCTAGAGGTGT 58.989 50.000 0.00 0.00 0.00 4.16
2171 2257 3.011119 ACGTAGAAGTCTGCTAGAGGTG 58.989 50.000 0.00 0.00 0.00 4.00
2172 2258 3.011119 CACGTAGAAGTCTGCTAGAGGT 58.989 50.000 0.00 0.00 0.00 3.85
2187 2275 2.967362 TGTGACATTAAGGCCACGTAG 58.033 47.619 5.01 0.00 32.58 3.51
2188 2276 3.620427 ATGTGACATTAAGGCCACGTA 57.380 42.857 5.01 0.00 32.58 3.57
2194 2283 3.763897 AGGGAACAATGTGACATTAAGGC 59.236 43.478 10.89 1.31 0.00 4.35
2195 2284 7.645058 AATAGGGAACAATGTGACATTAAGG 57.355 36.000 10.89 1.53 0.00 2.69
2199 2288 7.235399 AGGAAAAATAGGGAACAATGTGACATT 59.765 33.333 4.72 4.72 0.00 2.71
2204 2293 7.441017 TGAAAGGAAAAATAGGGAACAATGTG 58.559 34.615 0.00 0.00 0.00 3.21
2222 2311 5.360714 GGGCATTAACAAGATCATGAAAGGA 59.639 40.000 4.68 0.00 0.00 3.36
2231 2320 3.565307 TGGATGGGGCATTAACAAGATC 58.435 45.455 0.00 0.00 0.00 2.75
2239 2328 3.686227 ACAAGAATGGATGGGGCATTA 57.314 42.857 0.00 0.00 0.00 1.90
2241 2330 2.555732 AACAAGAATGGATGGGGCAT 57.444 45.000 0.00 0.00 0.00 4.40
2247 2336 5.927281 ATTGAGGGAAACAAGAATGGATG 57.073 39.130 0.00 0.00 0.00 3.51
2248 2337 6.735556 ACTATTGAGGGAAACAAGAATGGAT 58.264 36.000 0.00 0.00 0.00 3.41
2260 2349 5.385198 GGAATGGCAATACTATTGAGGGAA 58.615 41.667 12.26 0.00 28.03 3.97
2262 2351 4.082125 GGGAATGGCAATACTATTGAGGG 58.918 47.826 12.26 0.00 28.03 4.30
2270 2359 2.457813 TGCATGGGAATGGCAATACT 57.542 45.000 0.00 0.00 34.05 2.12
2276 2365 1.544691 GATCAGATGCATGGGAATGGC 59.455 52.381 2.46 0.00 0.00 4.40
2277 2366 2.557056 GTGATCAGATGCATGGGAATGG 59.443 50.000 2.46 0.00 0.00 3.16
2279 2368 3.878237 AGTGATCAGATGCATGGGAAT 57.122 42.857 2.46 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.