Multiple sequence alignment - TraesCS2A01G447900

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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 TraesCS2A01G447900 chr2A 100.000 4827 0 0 1 4827 696917332 696922158 0.000000e+00 8914
1 TraesCS2A01G447900 chr2B 93.146 1707 87 14 1379 3079 664215267 664216949 0.000000e+00 2477
2 TraesCS2A01G447900 chr2B 93.175 967 39 13 3074 4019 664216978 664217938 0.000000e+00 1395
3 TraesCS2A01G447900 chr2B 95.197 458 19 3 1 457 664213777 664214232 0.000000e+00 721
4 TraesCS2A01G447900 chr2B 85.884 673 49 22 4180 4827 664218289 664218940 0.000000e+00 675
5 TraesCS2A01G447900 chr2B 84.895 523 40 19 885 1380 664214657 664215167 4.340000e-135 492
6 TraesCS2A01G447900 chr2B 76.426 263 49 9 1805 2059 214576338 214576081 3.920000e-26 130
7 TraesCS2A01G447900 chr2D 88.822 1825 116 34 1283 3079 556942205 556943969 0.000000e+00 2159
8 TraesCS2A01G447900 chr2D 93.796 951 35 12 3074 4019 556943998 556944929 0.000000e+00 1408
9 TraesCS2A01G447900 chr2D 89.712 729 36 19 4122 4827 556947733 556948445 0.000000e+00 894
10 TraesCS2A01G447900 chr2D 86.976 668 48 21 1 656 556941009 556941649 0.000000e+00 715
11 TraesCS2A01G447900 chr2D 82.353 425 32 20 830 1214 556941754 556942175 3.600000e-86 329
12 TraesCS2A01G447900 chr7D 90.426 94 9 0 1966 2059 46898103 46898196 1.820000e-24 124


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 TraesCS2A01G447900 chr2A 696917332 696922158 4826 False 8914 8914 100.0000 1 4827 1 chr2A.!!$F1 4826
1 TraesCS2A01G447900 chr2B 664213777 664218940 5163 False 1152 2477 90.4594 1 4827 5 chr2B.!!$F1 4826
2 TraesCS2A01G447900 chr2D 556941009 556948445 7436 False 1101 2159 88.3318 1 4827 5 chr2D.!!$F1 4826

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
500 502 0.453390 GCTGGATTTTTCTGAGCCCG 59.547 55.0 0.00 0.0 0.0 6.13 F
1097 1244 0.099791 CTGTTTTGTGTTCCGCCGTT 59.900 50.0 0.00 0.0 0.0 4.44 F
1529 1823 0.250989 TTGCCGAGGTAAGTTTGGGG 60.251 55.0 0.00 0.0 0.0 4.96 F
2481 2807 0.886490 AAGTTGCCACCAAGAGCTCG 60.886 55.0 8.37 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 1774 0.100682 TCTCGCTGCTTCGATGGTAC 59.899 55.0 0.00 0.0 37.87 3.34 R
2815 3151 0.035458 AGAAGCCTGGTACACACAGC 59.965 55.0 0.00 0.0 34.65 4.40 R
2825 3161 0.250640 AGCACAAGACAGAAGCCTGG 60.251 55.0 0.00 0.0 44.60 4.45 R
4021 4413 0.107897 ACACAAACTGGAGTGCACGA 60.108 50.0 12.01 0.0 39.30 4.35 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
59 60 0.903942 GCTTCATTGGATTTGGGCCA 59.096 50.000 0.00 0.00 0.00 5.36
149 150 4.410400 GGACCCCAAGTCTGCCCG 62.410 72.222 0.00 0.00 45.54 6.13
175 176 1.227205 CCTGCTGGAGATCTGCGTC 60.227 63.158 9.88 4.31 42.34 5.19
180 181 2.583593 GGAGATCTGCGTCGCCAC 60.584 66.667 15.88 3.45 37.91 5.01
290 292 3.777465 TCGGATGTGTAGACAAGTAGC 57.223 47.619 0.00 0.00 35.11 3.58
311 313 4.980805 TGTGCCGTTCGTCAGCCC 62.981 66.667 0.00 0.00 0.00 5.19
360 362 2.421424 GCAGCTAGTCCAAATCCTTGTG 59.579 50.000 0.00 0.00 0.00 3.33
445 447 1.379527 CCGTTCCCCTTCTTATGTGC 58.620 55.000 0.00 0.00 0.00 4.57
448 450 1.745653 GTTCCCCTTCTTATGTGCAGC 59.254 52.381 0.00 0.00 0.00 5.25
457 459 5.575606 CCTTCTTATGTGCAGCTTGATTTTG 59.424 40.000 0.00 0.00 0.00 2.44
458 460 4.487948 TCTTATGTGCAGCTTGATTTTGC 58.512 39.130 0.00 0.00 38.30 3.68
469 471 4.021981 AGCTTGATTTTGCTGTACCTTTCC 60.022 41.667 0.00 0.00 38.21 3.13
484 486 3.054361 ACCTTTCCCCTTATGTGTAGCTG 60.054 47.826 0.00 0.00 0.00 4.24
499 501 1.844687 AGCTGGATTTTTCTGAGCCC 58.155 50.000 0.00 0.00 0.00 5.19
500 502 0.453390 GCTGGATTTTTCTGAGCCCG 59.547 55.000 0.00 0.00 0.00 6.13
503 505 1.037579 GGATTTTTCTGAGCCCGGGG 61.038 60.000 25.28 9.31 0.00 5.73
515 521 0.540133 GCCCGGGGTTCAGGTTTTTA 60.540 55.000 25.28 0.00 0.00 1.52
521 527 4.820173 CCGGGGTTCAGGTTTTTATATCTC 59.180 45.833 0.00 0.00 0.00 2.75
525 531 5.299531 GGGTTCAGGTTTTTATATCTCAGCC 59.700 44.000 0.00 0.00 0.00 4.85
526 532 5.007724 GGTTCAGGTTTTTATATCTCAGCCG 59.992 44.000 0.00 0.00 0.00 5.52
550 562 1.068748 CAATCTGCTTGCCTGTCACAC 60.069 52.381 0.00 0.00 0.00 3.82
579 631 6.536582 ACCATCAGTACTCATGATCTTTTTCG 59.463 38.462 8.52 0.00 35.20 3.46
630 687 5.681639 TCTTTGAGATGACAGCATGATGAT 58.318 37.500 19.60 0.60 39.69 2.45
636 693 3.918294 TGACAGCATGATGATCCTGAA 57.082 42.857 19.60 0.00 39.69 3.02
637 694 4.224991 TGACAGCATGATGATCCTGAAA 57.775 40.909 19.60 0.00 39.69 2.69
638 695 4.196971 TGACAGCATGATGATCCTGAAAG 58.803 43.478 19.60 0.00 39.69 2.62
656 713 6.633500 TGAAAGGGATAGTGTCAAGTTTTG 57.367 37.500 0.00 0.00 0.00 2.44
657 714 5.534654 TGAAAGGGATAGTGTCAAGTTTTGG 59.465 40.000 0.00 0.00 0.00 3.28
658 715 4.034285 AGGGATAGTGTCAAGTTTTGGG 57.966 45.455 0.00 0.00 0.00 4.12
659 716 2.492088 GGGATAGTGTCAAGTTTTGGGC 59.508 50.000 0.00 0.00 0.00 5.36
660 717 2.492088 GGATAGTGTCAAGTTTTGGGCC 59.508 50.000 0.00 0.00 0.00 5.80
663 720 2.183679 AGTGTCAAGTTTTGGGCCAAA 58.816 42.857 27.28 27.28 0.00 3.28
666 723 3.312146 GTGTCAAGTTTTGGGCCAAATTG 59.688 43.478 30.82 29.07 33.19 2.32
667 724 3.054802 TGTCAAGTTTTGGGCCAAATTGT 60.055 39.130 30.20 18.71 33.19 2.71
668 725 3.944650 GTCAAGTTTTGGGCCAAATTGTT 59.055 39.130 30.20 22.12 33.19 2.83
670 727 5.012893 TCAAGTTTTGGGCCAAATTGTTTT 58.987 33.333 30.20 19.44 33.19 2.43
671 728 5.124617 TCAAGTTTTGGGCCAAATTGTTTTC 59.875 36.000 30.20 17.47 33.19 2.29
672 729 4.854173 AGTTTTGGGCCAAATTGTTTTCT 58.146 34.783 30.82 16.65 33.19 2.52
673 730 5.260424 AGTTTTGGGCCAAATTGTTTTCTT 58.740 33.333 30.82 7.50 33.19 2.52
674 731 6.418946 AGTTTTGGGCCAAATTGTTTTCTTA 58.581 32.000 30.82 10.39 33.19 2.10
675 732 6.542005 AGTTTTGGGCCAAATTGTTTTCTTAG 59.458 34.615 30.82 0.00 33.19 2.18
676 733 5.878406 TTGGGCCAAATTGTTTTCTTAGA 57.122 34.783 18.51 0.00 0.00 2.10
677 734 5.467035 TGGGCCAAATTGTTTTCTTAGAG 57.533 39.130 2.13 0.00 0.00 2.43
678 735 5.144100 TGGGCCAAATTGTTTTCTTAGAGA 58.856 37.500 2.13 0.00 0.00 3.10
679 736 5.243730 TGGGCCAAATTGTTTTCTTAGAGAG 59.756 40.000 2.13 0.00 0.00 3.20
680 737 5.243954 GGGCCAAATTGTTTTCTTAGAGAGT 59.756 40.000 4.39 0.00 0.00 3.24
681 738 6.433093 GGGCCAAATTGTTTTCTTAGAGAGTA 59.567 38.462 4.39 0.00 0.00 2.59
682 739 7.362142 GGGCCAAATTGTTTTCTTAGAGAGTAG 60.362 40.741 4.39 0.00 0.00 2.57
683 740 7.175119 GGCCAAATTGTTTTCTTAGAGAGTAGT 59.825 37.037 0.00 0.00 0.00 2.73
684 741 8.568794 GCCAAATTGTTTTCTTAGAGAGTAGTT 58.431 33.333 0.00 0.00 0.00 2.24
691 748 9.326413 TGTTTTCTTAGAGAGTAGTTTTTCAGG 57.674 33.333 0.00 0.00 0.00 3.86
692 749 9.327628 GTTTTCTTAGAGAGTAGTTTTTCAGGT 57.672 33.333 0.00 0.00 0.00 4.00
726 783 4.825085 GGATAGTGTCAAGTTTTGGACCAA 59.175 41.667 1.69 1.69 33.09 3.67
727 784 5.048713 GGATAGTGTCAAGTTTTGGACCAAG 60.049 44.000 7.07 0.00 33.09 3.61
728 785 2.427095 AGTGTCAAGTTTTGGACCAAGC 59.573 45.455 7.07 4.98 33.09 4.01
729 786 2.427095 GTGTCAAGTTTTGGACCAAGCT 59.573 45.455 7.07 7.24 33.09 3.74
730 787 2.426738 TGTCAAGTTTTGGACCAAGCTG 59.573 45.455 7.07 4.12 33.09 4.24
745 828 4.517075 ACCAAGCTGTTTTCTTAGAGAAGC 59.483 41.667 0.00 0.00 35.37 3.86
756 839 5.717078 TCTTAGAGAAGCGTTTTCAGGTA 57.283 39.130 4.94 0.00 32.21 3.08
759 842 6.987992 TCTTAGAGAAGCGTTTTCAGGTAAAA 59.012 34.615 4.94 0.00 32.13 1.52
767 850 6.452242 AGCGTTTTCAGGTAAAATTTTAGGG 58.548 36.000 10.92 4.37 39.22 3.53
768 851 5.119588 GCGTTTTCAGGTAAAATTTTAGGGC 59.880 40.000 10.92 0.18 39.22 5.19
770 853 6.364976 CGTTTTCAGGTAAAATTTTAGGGCAG 59.635 38.462 10.92 1.20 39.22 4.85
771 854 7.438564 GTTTTCAGGTAAAATTTTAGGGCAGA 58.561 34.615 10.92 3.34 39.22 4.26
773 856 8.887264 TTTCAGGTAAAATTTTAGGGCAGATA 57.113 30.769 10.92 0.00 0.00 1.98
775 858 8.463930 TCAGGTAAAATTTTAGGGCAGATATG 57.536 34.615 10.92 1.41 0.00 1.78
776 859 7.505585 TCAGGTAAAATTTTAGGGCAGATATGG 59.494 37.037 10.92 0.00 0.00 2.74
778 861 7.505923 AGGTAAAATTTTAGGGCAGATATGGTC 59.494 37.037 10.92 0.00 0.00 4.02
782 865 7.978099 AATTTTAGGGCAGATATGGTCTTTT 57.022 32.000 0.00 0.00 34.00 2.27
783 866 6.773976 TTTTAGGGCAGATATGGTCTTTTG 57.226 37.500 0.00 0.00 34.00 2.44
784 867 5.450818 TTAGGGCAGATATGGTCTTTTGT 57.549 39.130 0.00 0.00 34.00 2.83
786 869 4.677182 AGGGCAGATATGGTCTTTTGTTT 58.323 39.130 0.00 0.00 34.00 2.83
787 870 5.086621 AGGGCAGATATGGTCTTTTGTTTT 58.913 37.500 0.00 0.00 34.00 2.43
788 871 5.543790 AGGGCAGATATGGTCTTTTGTTTTT 59.456 36.000 0.00 0.00 34.00 1.94
840 936 6.959639 TTTTTGAGAATTGCTAAGGTCAGT 57.040 33.333 0.00 0.00 0.00 3.41
842 938 6.959639 TTTGAGAATTGCTAAGGTCAGTTT 57.040 33.333 0.00 0.00 0.00 2.66
868 964 1.319614 CGGGCCAAATTGGGGTAGTG 61.320 60.000 14.59 0.00 38.19 2.74
881 977 3.477210 GGGTAGTGAAGCCCAGATAAG 57.523 52.381 0.00 0.00 44.23 1.73
883 979 3.454812 GGGTAGTGAAGCCCAGATAAGAA 59.545 47.826 0.00 0.00 44.23 2.52
891 1012 7.554476 AGTGAAGCCCAGATAAGAATTTAAGAC 59.446 37.037 0.00 0.00 0.00 3.01
942 1067 4.779733 ACCATCCCGCCGTCTCCT 62.780 66.667 0.00 0.00 0.00 3.69
943 1068 3.917760 CCATCCCGCCGTCTCCTC 61.918 72.222 0.00 0.00 0.00 3.71
945 1070 4.458829 ATCCCGCCGTCTCCTCCA 62.459 66.667 0.00 0.00 0.00 3.86
948 1073 4.135153 CCGCCGTCTCCTCCACTG 62.135 72.222 0.00 0.00 0.00 3.66
949 1074 4.135153 CGCCGTCTCCTCCACTGG 62.135 72.222 0.00 0.00 0.00 4.00
951 1076 3.007973 GCCGTCTCCTCCACTGGTC 62.008 68.421 0.00 0.00 0.00 4.02
952 1077 1.606601 CCGTCTCCTCCACTGGTCA 60.607 63.158 0.00 0.00 0.00 4.02
953 1078 1.599606 CCGTCTCCTCCACTGGTCAG 61.600 65.000 0.00 0.00 0.00 3.51
995 1142 4.521062 CCCAAGCCGGAGAGCGAG 62.521 72.222 5.05 0.00 36.56 5.03
1073 1220 0.179124 CTAGTGAGTCCAGCTTCCGC 60.179 60.000 0.00 0.00 0.00 5.54
1081 1228 2.047465 CAGCTTCCGCTCTGCTGT 60.047 61.111 6.09 0.00 45.15 4.40
1094 1241 0.594796 CTGCTGTTTTGTGTTCCGCC 60.595 55.000 0.00 0.00 0.00 6.13
1097 1244 0.099791 CTGTTTTGTGTTCCGCCGTT 59.900 50.000 0.00 0.00 0.00 4.44
1101 1248 0.304098 TTTGTGTTCCGCCGTTTACG 59.696 50.000 0.00 0.00 39.44 3.18
1144 1319 1.379527 CGGATTGGGGAAGTAGTTGC 58.620 55.000 0.00 0.00 0.00 4.17
1166 1341 2.032178 CCGCGAGAAAAATCCAAGGATC 59.968 50.000 8.23 0.00 33.08 3.36
1167 1342 2.032178 CGCGAGAAAAATCCAAGGATCC 59.968 50.000 2.48 2.48 33.08 3.36
1168 1343 3.016736 GCGAGAAAAATCCAAGGATCCA 58.983 45.455 15.82 0.00 33.08 3.41
1173 1348 2.834638 AAATCCAAGGATCCACCAGG 57.165 50.000 15.82 9.85 42.04 4.45
1199 1380 0.685097 TTGCTTCGCTGTAGAACCCT 59.315 50.000 0.00 0.00 0.00 4.34
1208 1389 2.102757 GCTGTAGAACCCTAACCTAGGC 59.897 54.545 9.30 0.00 44.86 3.93
1258 1439 6.069331 AGAGAAATGGCTGATTTGCATATCT 58.931 36.000 16.62 0.00 34.18 1.98
1278 1459 2.974698 GCTCTGTGCTTGTGCGGT 60.975 61.111 0.00 0.00 43.34 5.68
1312 1493 1.617947 ATCGGACAGGGGTCAAGAGC 61.618 60.000 0.00 0.00 46.17 4.09
1348 1529 5.105063 GGAATTTTAATGAGGCTTCTGTGC 58.895 41.667 0.00 0.00 0.00 4.57
1359 1540 1.925946 GCTTCTGTGCAAAACGCGAAT 60.926 47.619 15.93 0.00 46.97 3.34
1360 1541 1.971962 CTTCTGTGCAAAACGCGAATC 59.028 47.619 15.93 0.00 46.97 2.52
1373 1554 1.860950 CGCGAATCTGTAGTTCATGGG 59.139 52.381 0.00 0.00 0.00 4.00
1409 1703 5.626543 CGATTGTTTTCTGGTTGAGATTGTG 59.373 40.000 0.00 0.00 0.00 3.33
1410 1704 6.513230 CGATTGTTTTCTGGTTGAGATTGTGA 60.513 38.462 0.00 0.00 0.00 3.58
1411 1705 6.522625 TTGTTTTCTGGTTGAGATTGTGAA 57.477 33.333 0.00 0.00 0.00 3.18
1412 1706 6.135290 TGTTTTCTGGTTGAGATTGTGAAG 57.865 37.500 0.00 0.00 0.00 3.02
1413 1707 5.652014 TGTTTTCTGGTTGAGATTGTGAAGT 59.348 36.000 0.00 0.00 0.00 3.01
1414 1708 5.756195 TTTCTGGTTGAGATTGTGAAGTG 57.244 39.130 0.00 0.00 0.00 3.16
1415 1709 3.743521 TCTGGTTGAGATTGTGAAGTGG 58.256 45.455 0.00 0.00 0.00 4.00
1416 1710 2.816087 CTGGTTGAGATTGTGAAGTGGG 59.184 50.000 0.00 0.00 0.00 4.61
1417 1711 2.441375 TGGTTGAGATTGTGAAGTGGGA 59.559 45.455 0.00 0.00 0.00 4.37
1418 1712 2.814336 GGTTGAGATTGTGAAGTGGGAC 59.186 50.000 0.00 0.00 0.00 4.46
1419 1713 3.476552 GTTGAGATTGTGAAGTGGGACA 58.523 45.455 0.00 0.00 0.00 4.02
1420 1714 3.407424 TGAGATTGTGAAGTGGGACAG 57.593 47.619 0.00 0.00 41.80 3.51
1424 1718 3.646162 AGATTGTGAAGTGGGACAGTACA 59.354 43.478 0.00 0.00 43.84 2.90
1529 1823 0.250989 TTGCCGAGGTAAGTTTGGGG 60.251 55.000 0.00 0.00 0.00 4.96
1594 1915 6.723298 TGGTGACCAGAAACACAAAATTAT 57.277 33.333 0.00 0.00 38.57 1.28
1595 1916 6.511416 TGGTGACCAGAAACACAAAATTATG 58.489 36.000 0.00 0.00 38.57 1.90
1596 1917 5.405269 GGTGACCAGAAACACAAAATTATGC 59.595 40.000 0.00 0.00 38.57 3.14
1597 1918 6.215845 GTGACCAGAAACACAAAATTATGCT 58.784 36.000 0.00 0.00 37.05 3.79
1598 1919 6.144402 GTGACCAGAAACACAAAATTATGCTG 59.856 38.462 0.00 0.00 37.05 4.41
1599 1920 6.160576 ACCAGAAACACAAAATTATGCTGT 57.839 33.333 0.00 0.00 0.00 4.40
1600 1921 5.984926 ACCAGAAACACAAAATTATGCTGTG 59.015 36.000 5.66 5.66 44.81 3.66
1601 1922 5.107375 CCAGAAACACAAAATTATGCTGTGC 60.107 40.000 6.79 0.00 43.42 4.57
1602 1923 5.462729 CAGAAACACAAAATTATGCTGTGCA 59.537 36.000 6.79 0.00 43.42 4.57
1617 1938 3.812262 CTGTGCAAGATCATACCATGGA 58.188 45.455 21.47 2.01 0.00 3.41
1624 1945 9.013229 GTGCAAGATCATACCATGGATTAATAA 57.987 33.333 21.47 0.00 0.00 1.40
1667 1989 5.471116 TGTTCATTCTCATTGGTTCAGTCAG 59.529 40.000 0.00 0.00 0.00 3.51
1674 1996 8.547967 TTCTCATTGGTTCAGTCAGTTATAAC 57.452 34.615 7.57 7.57 0.00 1.89
1762 2084 2.250237 GGCTATTGCTGCGAGAGGC 61.250 63.158 20.25 20.25 39.59 4.70
1799 2121 6.726764 AGACAAGGTCTTCTATAACTTGGAGT 59.273 38.462 5.91 0.00 40.28 3.85
1915 2237 4.101119 ACAGATGTATAACCTGGTACCTGC 59.899 45.833 14.36 0.00 32.52 4.85
1974 2296 8.090214 CCACTTCATGTTAAAGGAAATGTCATT 58.910 33.333 0.00 0.00 0.00 2.57
2128 2454 0.968405 TTGGCCTCATTTTGTCAGCC 59.032 50.000 3.32 0.00 40.87 4.85
2212 2538 3.402628 TGCTTCTGTTAGGTGACCTTC 57.597 47.619 10.53 4.40 34.61 3.46
2400 2726 5.048713 GCCCTTTGACTATATATGTTGCCAC 60.049 44.000 0.00 0.00 0.00 5.01
2481 2807 0.886490 AAGTTGCCACCAAGAGCTCG 60.886 55.000 8.37 0.00 0.00 5.03
2490 2816 1.137872 ACCAAGAGCTCGGAGCATTAG 59.862 52.381 29.88 18.94 45.56 1.73
2524 2850 4.074970 GGTTGGCCATATCATAAGACTGG 58.925 47.826 6.09 0.00 34.53 4.00
2525 2851 4.202461 GGTTGGCCATATCATAAGACTGGA 60.202 45.833 6.09 0.00 33.68 3.86
2526 2852 4.623932 TGGCCATATCATAAGACTGGAC 57.376 45.455 0.00 0.95 38.07 4.02
2528 2854 5.402630 TGGCCATATCATAAGACTGGACTA 58.597 41.667 0.00 0.00 38.30 2.59
2529 2855 5.843969 TGGCCATATCATAAGACTGGACTAA 59.156 40.000 0.00 0.00 38.30 2.24
2530 2856 6.501805 TGGCCATATCATAAGACTGGACTAAT 59.498 38.462 0.00 0.00 38.30 1.73
2531 2857 7.044798 GGCCATATCATAAGACTGGACTAATC 58.955 42.308 0.00 0.00 35.82 1.75
2532 2858 7.093112 GGCCATATCATAAGACTGGACTAATCT 60.093 40.741 0.00 0.00 35.82 2.40
2533 2859 8.972127 GCCATATCATAAGACTGGACTAATCTA 58.028 37.037 3.26 0.00 33.68 1.98
2688 3024 5.818136 TGCTGATTCCACTATGCTAAAAC 57.182 39.130 0.00 0.00 0.00 2.43
2693 3029 5.651576 TGATTCCACTATGCTAAAACATGCA 59.348 36.000 0.00 0.00 43.67 3.96
2699 3035 6.094048 CCACTATGCTAAAACATGCACTTACT 59.906 38.462 0.00 0.00 42.26 2.24
2769 3105 1.068434 GCTGGTAGAGTCTGCCTGATC 59.932 57.143 29.91 14.57 37.37 2.92
2798 3134 9.831682 TCTTTTTACCCTTTCCCTAAATATGTT 57.168 29.630 0.00 0.00 0.00 2.71
2825 3161 3.599343 TCATCTTCCATGCTGTGTGTAC 58.401 45.455 0.00 0.00 0.00 2.90
2840 3176 2.224281 TGTGTACCAGGCTTCTGTCTTG 60.224 50.000 0.00 0.00 36.81 3.02
2843 3179 0.536006 ACCAGGCTTCTGTCTTGTGC 60.536 55.000 0.00 0.00 36.81 4.57
2844 3180 0.250640 CCAGGCTTCTGTCTTGTGCT 60.251 55.000 0.00 0.00 36.81 4.40
2916 3252 4.695455 TCCGAAATTCAGGATGTTCTTGTC 59.305 41.667 3.18 0.00 37.40 3.18
2964 3300 6.203530 TCTCTTCAAAACAATCTAGTGTGCTG 59.796 38.462 0.00 0.00 0.00 4.41
3193 3563 3.325753 ACTCCAGGTCAGGCAGCC 61.326 66.667 1.84 1.84 0.00 4.85
3211 3581 1.950216 GCCTACCATTTCTTAGCTGGC 59.050 52.381 0.00 0.00 33.12 4.85
3324 3694 6.973229 ATGTTGCATAATTTCCTTGCTTTC 57.027 33.333 0.00 0.00 37.28 2.62
3332 3702 5.520748 AATTTCCTTGCTTTCCCTCTCTA 57.479 39.130 0.00 0.00 0.00 2.43
3336 3706 3.643792 TCCTTGCTTTCCCTCTCTATAGC 59.356 47.826 0.00 0.00 0.00 2.97
3338 3708 3.336509 TGCTTTCCCTCTCTATAGCCT 57.663 47.619 0.00 0.00 0.00 4.58
3434 3804 4.578928 TCTCTACCCTTGCAGTTGAAAAAC 59.421 41.667 0.00 0.00 0.00 2.43
3793 4167 2.552743 GGGCTTTATATCCGGCAAGTTC 59.447 50.000 0.00 0.00 0.00 3.01
3801 4175 1.175983 TCCGGCAAGTTCGGCAAATT 61.176 50.000 0.00 0.00 46.43 1.82
3823 4197 4.903045 TTTACCCGAGGAGTTCTCATTT 57.097 40.909 0.00 0.00 42.55 2.32
3833 4207 8.310382 CCGAGGAGTTCTCATTTTGATAGATAT 58.690 37.037 0.00 0.00 42.55 1.63
3862 4249 4.612264 AACCTAATTCAGTGTACGGTGT 57.388 40.909 0.00 0.00 0.00 4.16
3875 4262 2.956194 GGTGTTTTTACGCCGGGG 59.044 61.111 18.33 18.33 0.00 5.73
3900 4287 2.744202 AGATAGGCTTTGTTGCGTTCTG 59.256 45.455 0.00 0.00 32.99 3.02
3920 4307 7.268586 GTTCTGAATTGAACTGAGATAGGCTA 58.731 38.462 0.00 0.00 42.03 3.93
3932 4319 1.909986 GATAGGCTACCCCAATCTCCC 59.090 57.143 0.00 0.00 35.39 4.30
3945 4332 3.370315 CCAATCTCCCTCCTGAACAAGAG 60.370 52.174 0.00 0.00 0.00 2.85
4001 4389 2.047465 AGAGCTGCTGTGCCTTCG 60.047 61.111 7.01 0.00 0.00 3.79
4008 4400 2.614057 GCTGCTGTGCCTTCGTAATAAT 59.386 45.455 0.00 0.00 0.00 1.28
4019 4411 6.646653 TGCCTTCGTAATAATCTCATTAGCAG 59.353 38.462 0.00 0.00 0.00 4.24
4021 4413 7.155328 CCTTCGTAATAATCTCATTAGCAGGT 58.845 38.462 0.00 0.00 0.00 4.00
4022 4414 7.329717 CCTTCGTAATAATCTCATTAGCAGGTC 59.670 40.741 0.00 0.00 0.00 3.85
4038 4465 0.814010 GGTCGTGCACTCCAGTTTGT 60.814 55.000 16.19 0.00 0.00 2.83
4039 4466 0.304705 GTCGTGCACTCCAGTTTGTG 59.695 55.000 16.19 0.00 37.26 3.33
4042 4469 1.378531 GTGCACTCCAGTTTGTGTCA 58.621 50.000 10.32 0.00 36.63 3.58
4046 4473 1.331756 CACTCCAGTTTGTGTCACAGC 59.668 52.381 5.67 3.83 0.00 4.40
4047 4474 1.065491 ACTCCAGTTTGTGTCACAGCA 60.065 47.619 5.67 0.00 0.00 4.41
4048 4475 1.600957 CTCCAGTTTGTGTCACAGCAG 59.399 52.381 5.67 1.06 0.00 4.24
4049 4476 1.065491 TCCAGTTTGTGTCACAGCAGT 60.065 47.619 5.67 0.00 0.00 4.40
4050 4477 2.169561 TCCAGTTTGTGTCACAGCAGTA 59.830 45.455 5.67 0.00 0.00 2.74
4051 4478 2.545526 CCAGTTTGTGTCACAGCAGTAG 59.454 50.000 5.67 0.00 0.00 2.57
4096 5009 2.101750 TCGTGAGCTCCTGTTGTTACAA 59.898 45.455 12.15 0.00 32.92 2.41
4097 5010 2.221055 CGTGAGCTCCTGTTGTTACAAC 59.779 50.000 20.04 20.04 32.92 3.32
4111 5024 4.366586 TGTTACAACAAATACGACGGTGA 58.633 39.130 0.00 0.00 35.67 4.02
4112 5025 4.989797 TGTTACAACAAATACGACGGTGAT 59.010 37.500 0.00 0.00 35.67 3.06
4113 5026 5.107414 TGTTACAACAAATACGACGGTGATG 60.107 40.000 0.00 0.00 35.67 3.07
4115 5028 2.087501 ACAAATACGACGGTGATGCA 57.912 45.000 0.00 0.00 0.00 3.96
4116 5029 1.999735 ACAAATACGACGGTGATGCAG 59.000 47.619 0.00 0.00 0.00 4.41
4117 5030 2.267426 CAAATACGACGGTGATGCAGA 58.733 47.619 0.00 0.00 0.00 4.26
4118 5031 1.922570 AATACGACGGTGATGCAGAC 58.077 50.000 0.00 0.00 0.00 3.51
4119 5032 0.248498 ATACGACGGTGATGCAGACG 60.248 55.000 0.00 0.00 36.70 4.18
4177 7277 1.820906 CTCCGGGACACATGCCATG 60.821 63.158 0.00 2.40 35.61 3.66
4178 7278 2.045045 CCGGGACACATGCCATGT 60.045 61.111 4.03 4.03 46.22 3.21
4182 7390 1.382522 GGGACACATGCCATGTAGTG 58.617 55.000 10.53 0.89 42.70 2.74
4204 7412 2.228059 CAGGAATATTGAGCCCTGCTG 58.772 52.381 7.72 0.00 39.88 4.41
4238 7446 2.902523 GCAGATTGCAGAGATGTCAGA 58.097 47.619 0.00 0.00 44.26 3.27
4239 7447 3.468770 GCAGATTGCAGAGATGTCAGAT 58.531 45.455 0.00 0.00 44.26 2.90
4265 7476 0.036010 ATGGTTTCAGCGAGGACTGG 60.036 55.000 0.00 0.00 38.26 4.00
4317 7537 5.602978 TCCTCTTTATCTTACCTCCATCCAC 59.397 44.000 0.00 0.00 0.00 4.02
4318 7538 5.221742 CCTCTTTATCTTACCTCCATCCACC 60.222 48.000 0.00 0.00 0.00 4.61
4353 7573 4.082523 GGGCAGCAGTAGACGCCA 62.083 66.667 0.00 0.00 46.75 5.69
4408 7630 0.455464 GGACGCATTTGGCCGTTTAC 60.455 55.000 0.00 0.00 40.31 2.01
4410 7632 0.885196 ACGCATTTGGCCGTTTACAT 59.115 45.000 0.00 0.00 40.31 2.29
4411 7633 2.085320 ACGCATTTGGCCGTTTACATA 58.915 42.857 0.00 0.00 40.31 2.29
4430 7652 2.625695 AATTTTGGCATATGCTGGGC 57.374 45.000 26.12 10.88 41.70 5.36
4446 7668 1.611491 TGGGCGACTGAAAATCAAACC 59.389 47.619 0.00 0.00 0.00 3.27
4513 7741 1.269936 GCCTCATGTTTTTGTGCTGCT 60.270 47.619 0.00 0.00 0.00 4.24
4514 7742 2.400399 CCTCATGTTTTTGTGCTGCTG 58.600 47.619 0.00 0.00 0.00 4.41
4515 7743 1.790623 CTCATGTTTTTGTGCTGCTGC 59.209 47.619 8.89 8.89 40.20 5.25
4538 7776 1.000607 GTACACTCTGTCGCCTGTCAA 60.001 52.381 0.00 0.00 0.00 3.18
4568 7806 5.112686 GGCACACATTAACTGAACCAAAAA 58.887 37.500 0.00 0.00 0.00 1.94
4569 7807 5.234116 GGCACACATTAACTGAACCAAAAAG 59.766 40.000 0.00 0.00 0.00 2.27
4570 7808 5.276820 GCACACATTAACTGAACCAAAAAGC 60.277 40.000 0.00 0.00 0.00 3.51
4571 7809 5.809562 CACACATTAACTGAACCAAAAAGCA 59.190 36.000 0.00 0.00 0.00 3.91
4572 7810 5.810074 ACACATTAACTGAACCAAAAAGCAC 59.190 36.000 0.00 0.00 0.00 4.40
4573 7811 5.040635 ACATTAACTGAACCAAAAAGCACG 58.959 37.500 0.00 0.00 0.00 5.34
4574 7812 1.921243 AACTGAACCAAAAAGCACGC 58.079 45.000 0.00 0.00 0.00 5.34
4575 7813 1.102978 ACTGAACCAAAAAGCACGCT 58.897 45.000 0.00 0.00 0.00 5.07
4576 7814 1.202290 ACTGAACCAAAAAGCACGCTG 60.202 47.619 0.00 0.00 0.00 5.18
4577 7815 0.527385 TGAACCAAAAAGCACGCTGC 60.527 50.000 0.00 2.28 45.46 5.25
4620 7858 5.880054 ACACAACACATTGCCTACTAATC 57.120 39.130 0.00 0.00 39.66 1.75
4624 7862 3.545703 ACACATTGCCTACTAATCTGGC 58.454 45.455 0.00 0.00 46.26 4.85
4671 7909 0.393944 GCAGTAGGGGCCTTTGTACC 60.394 60.000 0.84 0.00 0.00 3.34
4681 7919 0.953960 CCTTTGTACCGAGTGGCCAC 60.954 60.000 29.22 29.22 39.70 5.01
4703 7941 0.978146 TTCAGAGACAGGCTAGCCCC 60.978 60.000 30.42 18.97 36.58 5.80
4704 7942 2.041405 AGAGACAGGCTAGCCCCC 60.041 66.667 30.42 18.61 36.58 5.40
4753 7991 2.023673 TCTGGAGCCAATAATTTGCGG 58.976 47.619 0.00 0.00 0.00 5.69
4768 8006 3.512978 GCGGGTGCATTTTGTCATT 57.487 47.368 0.00 0.00 42.15 2.57
4822 8063 6.223852 ACAGTAGAACTTCCAACATGTACTG 58.776 40.000 13.75 13.75 42.27 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 1.370051 TCGTCGTGTGAACTCGCAG 60.370 57.895 0.26 0.00 37.00 5.18
175 176 2.333926 TGAAATAGTGTTCTCGTGGCG 58.666 47.619 0.00 0.00 0.00 5.69
290 292 2.927618 CTGACGAACGGCACACACG 61.928 63.158 0.00 0.00 37.36 4.49
311 313 4.211164 TCCATCTAAATAAACAGCATCGCG 59.789 41.667 0.00 0.00 0.00 5.87
424 426 0.107848 ACATAAGAAGGGGAACGGCG 60.108 55.000 4.80 4.80 0.00 6.46
448 450 4.321974 GGGGAAAGGTACAGCAAAATCAAG 60.322 45.833 0.00 0.00 0.00 3.02
457 459 3.279434 CACATAAGGGGAAAGGTACAGC 58.721 50.000 0.00 0.00 0.00 4.40
458 460 4.569719 ACACATAAGGGGAAAGGTACAG 57.430 45.455 0.00 0.00 0.00 2.74
460 462 4.163649 AGCTACACATAAGGGGAAAGGTAC 59.836 45.833 0.00 0.00 0.00 3.34
462 464 3.054361 CAGCTACACATAAGGGGAAAGGT 60.054 47.826 0.00 0.00 0.00 3.50
464 466 3.199946 TCCAGCTACACATAAGGGGAAAG 59.800 47.826 0.00 0.00 0.00 2.62
469 471 5.888161 AGAAAAATCCAGCTACACATAAGGG 59.112 40.000 0.00 0.00 0.00 3.95
484 486 1.037579 CCCCGGGCTCAGAAAAATCC 61.038 60.000 17.73 0.00 0.00 3.01
499 501 5.433526 TGAGATATAAAAACCTGAACCCCG 58.566 41.667 0.00 0.00 0.00 5.73
500 502 5.299531 GCTGAGATATAAAAACCTGAACCCC 59.700 44.000 0.00 0.00 0.00 4.95
503 505 5.007724 CCGGCTGAGATATAAAAACCTGAAC 59.992 44.000 0.00 0.00 0.00 3.18
509 515 6.431198 TTGAACCGGCTGAGATATAAAAAC 57.569 37.500 0.00 0.00 0.00 2.43
515 521 3.805108 GCAGATTGAACCGGCTGAGATAT 60.805 47.826 0.00 0.00 0.00 1.63
521 527 0.169672 CAAGCAGATTGAACCGGCTG 59.830 55.000 0.00 0.00 41.83 4.85
525 531 0.169672 CAGGCAAGCAGATTGAACCG 59.830 55.000 1.54 0.00 41.83 4.44
526 532 1.200948 GACAGGCAAGCAGATTGAACC 59.799 52.381 1.54 0.00 41.83 3.62
550 562 6.159299 AGATCATGAGTACTGATGGTCAAG 57.841 41.667 29.67 7.26 32.90 3.02
559 571 4.572389 CCCCGAAAAAGATCATGAGTACTG 59.428 45.833 0.00 0.00 0.00 2.74
564 616 4.458989 TGTTTCCCCGAAAAAGATCATGAG 59.541 41.667 0.09 0.00 33.14 2.90
579 631 2.807676 AGTTCATCATGGTGTTTCCCC 58.192 47.619 5.73 0.00 34.77 4.81
630 687 4.168101 ACTTGACACTATCCCTTTCAGGA 58.832 43.478 0.00 0.00 37.67 3.86
636 693 4.407365 CCCAAAACTTGACACTATCCCTT 58.593 43.478 0.00 0.00 0.00 3.95
637 694 3.814316 GCCCAAAACTTGACACTATCCCT 60.814 47.826 0.00 0.00 0.00 4.20
638 695 2.492088 GCCCAAAACTTGACACTATCCC 59.508 50.000 0.00 0.00 0.00 3.85
651 708 5.574891 AAGAAAACAATTTGGCCCAAAAC 57.425 34.783 13.87 0.00 36.90 2.43
656 713 5.243954 ACTCTCTAAGAAAACAATTTGGCCC 59.756 40.000 0.00 0.00 0.00 5.80
657 714 6.332735 ACTCTCTAAGAAAACAATTTGGCC 57.667 37.500 0.00 0.00 0.00 5.36
658 715 8.100508 ACTACTCTCTAAGAAAACAATTTGGC 57.899 34.615 0.78 0.00 0.00 4.52
666 723 9.327628 ACCTGAAAAACTACTCTCTAAGAAAAC 57.672 33.333 0.00 0.00 0.00 2.43
685 742 9.362151 ACACTATCCTGAAAAATTTACCTGAAA 57.638 29.630 0.00 0.00 0.00 2.69
686 743 8.934023 ACACTATCCTGAAAAATTTACCTGAA 57.066 30.769 0.00 0.00 0.00 3.02
687 744 8.160765 TGACACTATCCTGAAAAATTTACCTGA 58.839 33.333 0.00 0.00 0.00 3.86
688 745 8.335532 TGACACTATCCTGAAAAATTTACCTG 57.664 34.615 0.00 0.00 0.00 4.00
689 746 8.934023 TTGACACTATCCTGAAAAATTTACCT 57.066 30.769 0.00 0.00 0.00 3.08
690 747 8.793592 ACTTGACACTATCCTGAAAAATTTACC 58.206 33.333 0.00 0.00 0.00 2.85
694 751 9.533253 CAAAACTTGACACTATCCTGAAAAATT 57.467 29.630 0.00 0.00 0.00 1.82
695 752 8.143835 CCAAAACTTGACACTATCCTGAAAAAT 58.856 33.333 0.00 0.00 0.00 1.82
696 753 7.340743 TCCAAAACTTGACACTATCCTGAAAAA 59.659 33.333 0.00 0.00 0.00 1.94
697 754 6.831353 TCCAAAACTTGACACTATCCTGAAAA 59.169 34.615 0.00 0.00 0.00 2.29
698 755 6.262273 GTCCAAAACTTGACACTATCCTGAAA 59.738 38.462 0.00 0.00 0.00 2.69
699 756 5.763204 GTCCAAAACTTGACACTATCCTGAA 59.237 40.000 0.00 0.00 0.00 3.02
700 757 5.305585 GTCCAAAACTTGACACTATCCTGA 58.694 41.667 0.00 0.00 0.00 3.86
701 758 4.455877 GGTCCAAAACTTGACACTATCCTG 59.544 45.833 0.00 0.00 0.00 3.86
702 759 4.104102 TGGTCCAAAACTTGACACTATCCT 59.896 41.667 0.00 0.00 0.00 3.24
703 760 4.394729 TGGTCCAAAACTTGACACTATCC 58.605 43.478 0.00 0.00 0.00 2.59
704 761 5.562890 GCTTGGTCCAAAACTTGACACTATC 60.563 44.000 5.64 0.00 0.00 2.08
705 762 4.278419 GCTTGGTCCAAAACTTGACACTAT 59.722 41.667 5.64 0.00 0.00 2.12
726 783 3.996480 ACGCTTCTCTAAGAAAACAGCT 58.004 40.909 0.00 0.00 33.19 4.24
727 784 4.733972 AACGCTTCTCTAAGAAAACAGC 57.266 40.909 0.00 0.00 33.19 4.40
728 785 6.715464 TGAAAACGCTTCTCTAAGAAAACAG 58.285 36.000 0.19 0.00 33.19 3.16
729 786 6.238374 CCTGAAAACGCTTCTCTAAGAAAACA 60.238 38.462 0.19 0.00 33.19 2.83
730 787 6.136743 CCTGAAAACGCTTCTCTAAGAAAAC 58.863 40.000 0.19 0.00 33.19 2.43
745 828 6.217294 TGCCCTAAAATTTTACCTGAAAACG 58.783 36.000 6.54 0.00 39.83 3.60
756 839 7.978099 AAGACCATATCTGCCCTAAAATTTT 57.022 32.000 8.75 8.75 37.88 1.82
759 842 6.897413 ACAAAAGACCATATCTGCCCTAAAAT 59.103 34.615 0.00 0.00 37.88 1.82
786 869 6.601332 ACTGACCTTAGTTGATCCTCAAAAA 58.399 36.000 0.00 0.00 38.22 1.94
787 870 6.187727 ACTGACCTTAGTTGATCCTCAAAA 57.812 37.500 0.00 0.00 38.22 2.44
788 871 5.825593 ACTGACCTTAGTTGATCCTCAAA 57.174 39.130 0.00 0.00 38.22 2.69
789 872 5.825593 AACTGACCTTAGTTGATCCTCAA 57.174 39.130 0.00 0.00 39.33 3.02
790 873 5.825593 AAACTGACCTTAGTTGATCCTCA 57.174 39.130 0.00 0.00 40.58 3.86
868 964 6.017852 CCGTCTTAAATTCTTATCTGGGCTTC 60.018 42.308 0.00 0.00 0.00 3.86
881 977 4.379499 CCAGTCAAAGCCCGTCTTAAATTC 60.379 45.833 0.00 0.00 33.88 2.17
883 979 3.081804 CCAGTCAAAGCCCGTCTTAAAT 58.918 45.455 0.00 0.00 33.88 1.40
937 1062 1.076438 TCTCTGACCAGTGGAGGAGA 58.924 55.000 18.40 19.93 0.00 3.71
942 1067 2.626780 CGCGTCTCTGACCAGTGGA 61.627 63.158 18.40 0.00 0.00 4.02
943 1068 2.126307 CGCGTCTCTGACCAGTGG 60.126 66.667 7.91 7.91 0.00 4.00
945 1070 4.057428 GGCGCGTCTCTGACCAGT 62.057 66.667 8.43 0.00 0.00 4.00
995 1142 3.455469 GAAGGCCCAGCATGTGCC 61.455 66.667 0.00 8.93 45.70 5.01
1073 1220 1.597937 GCGGAACACAAAACAGCAGAG 60.598 52.381 0.00 0.00 0.00 3.35
1081 1228 1.267932 CGTAAACGGCGGAACACAAAA 60.268 47.619 13.24 0.00 35.37 2.44
1094 1241 3.395671 CAAACAGAGCGATTCGTAAACG 58.604 45.455 8.03 0.00 41.45 3.60
1097 1244 2.411748 CAGCAAACAGAGCGATTCGTAA 59.588 45.455 8.03 0.00 37.01 3.18
1101 1248 0.801251 AGCAGCAAACAGAGCGATTC 59.199 50.000 0.00 0.00 37.01 2.52
1144 1319 0.451783 CCTTGGATTTTTCTCGCGGG 59.548 55.000 6.13 1.01 0.00 6.13
1166 1341 0.534203 AAGCAACGTGTACCTGGTGG 60.534 55.000 10.23 0.00 39.83 4.61
1167 1342 0.865769 GAAGCAACGTGTACCTGGTG 59.134 55.000 10.23 0.00 0.00 4.17
1168 1343 0.599204 CGAAGCAACGTGTACCTGGT 60.599 55.000 4.05 4.05 0.00 4.00
1199 1380 3.128848 TCTACTCCTCCTGCCTAGGTTA 58.871 50.000 11.31 0.00 44.88 2.85
1208 1389 2.243810 GCCCTACATCTACTCCTCCTG 58.756 57.143 0.00 0.00 0.00 3.86
1246 1427 4.319622 GCACAGAGCTCAGATATGCAAATC 60.320 45.833 17.77 0.00 41.15 2.17
1247 1428 3.564644 GCACAGAGCTCAGATATGCAAAT 59.435 43.478 17.77 0.00 41.15 2.32
1248 1429 2.941064 GCACAGAGCTCAGATATGCAAA 59.059 45.455 17.77 0.00 41.15 3.68
1278 1459 0.037697 CCGATCTTCCCAACGACACA 60.038 55.000 0.00 0.00 0.00 3.72
1312 1493 6.373216 TCATTAAAATTCCACACTAACCGAGG 59.627 38.462 0.00 0.00 0.00 4.63
1317 1498 7.158099 AGCCTCATTAAAATTCCACACTAAC 57.842 36.000 0.00 0.00 0.00 2.34
1348 1529 4.383774 TGAACTACAGATTCGCGTTTTG 57.616 40.909 5.77 3.34 0.00 2.44
1402 1696 3.646162 TGTACTGTCCCACTTCACAATCT 59.354 43.478 0.00 0.00 0.00 2.40
1409 1703 4.023193 CACCAAAATGTACTGTCCCACTTC 60.023 45.833 0.00 0.00 0.00 3.01
1410 1704 3.888930 CACCAAAATGTACTGTCCCACTT 59.111 43.478 0.00 0.00 0.00 3.16
1411 1705 3.137544 TCACCAAAATGTACTGTCCCACT 59.862 43.478 0.00 0.00 0.00 4.00
1412 1706 3.252458 GTCACCAAAATGTACTGTCCCAC 59.748 47.826 0.00 0.00 0.00 4.61
1413 1707 3.482436 GTCACCAAAATGTACTGTCCCA 58.518 45.455 0.00 0.00 0.00 4.37
1414 1708 2.817844 GGTCACCAAAATGTACTGTCCC 59.182 50.000 0.00 0.00 0.00 4.46
1415 1709 2.817844 GGGTCACCAAAATGTACTGTCC 59.182 50.000 0.00 0.00 36.50 4.02
1416 1710 3.502211 CAGGGTCACCAAAATGTACTGTC 59.498 47.826 0.00 0.00 40.13 3.51
1417 1711 3.117663 ACAGGGTCACCAAAATGTACTGT 60.118 43.478 0.00 0.00 40.13 3.55
1418 1712 3.486383 ACAGGGTCACCAAAATGTACTG 58.514 45.455 0.00 0.00 40.13 2.74
1419 1713 3.751518 GACAGGGTCACCAAAATGTACT 58.248 45.455 0.00 0.00 40.13 2.73
1420 1714 2.482721 CGACAGGGTCACCAAAATGTAC 59.517 50.000 0.00 0.00 40.13 2.90
1421 1715 2.105134 ACGACAGGGTCACCAAAATGTA 59.895 45.455 0.00 0.00 40.13 2.29
1424 1718 1.142060 TCACGACAGGGTCACCAAAAT 59.858 47.619 0.00 0.00 40.13 1.82
1480 1774 0.100682 TCTCGCTGCTTCGATGGTAC 59.899 55.000 0.00 0.00 37.87 3.34
1529 1823 2.813172 GAGGAGTACGGTATGGCTAGAC 59.187 54.545 0.00 0.00 0.00 2.59
1586 1907 7.168637 GGTATGATCTTGCACAGCATAATTTTG 59.831 37.037 4.72 0.00 38.76 2.44
1593 1914 3.286329 TGGTATGATCTTGCACAGCAT 57.714 42.857 1.48 1.48 38.76 3.79
1594 1915 2.785540 TGGTATGATCTTGCACAGCA 57.214 45.000 0.00 0.00 36.47 4.41
1595 1916 2.292569 CCATGGTATGATCTTGCACAGC 59.707 50.000 2.57 0.00 0.00 4.40
1596 1917 3.812262 TCCATGGTATGATCTTGCACAG 58.188 45.455 12.58 0.00 0.00 3.66
1597 1918 3.929955 TCCATGGTATGATCTTGCACA 57.070 42.857 12.58 0.00 0.00 4.57
1598 1919 6.882610 TTAATCCATGGTATGATCTTGCAC 57.117 37.500 12.58 0.00 0.00 4.57
1599 1920 9.013229 GTTATTAATCCATGGTATGATCTTGCA 57.987 33.333 12.58 0.00 0.00 4.08
1600 1921 9.236006 AGTTATTAATCCATGGTATGATCTTGC 57.764 33.333 12.58 0.00 0.00 4.01
1624 1945 7.639113 TGAACAACATAACTGAAAAGGAAGT 57.361 32.000 0.00 0.00 0.00 3.01
1631 1952 9.681692 CAATGAGAATGAACAACATAACTGAAA 57.318 29.630 0.00 0.00 38.38 2.69
1642 1964 5.827267 TGACTGAACCAATGAGAATGAACAA 59.173 36.000 0.00 0.00 0.00 2.83
1667 1989 6.086371 GCGAAAGAAGTGCAAACAGTTATAAC 59.914 38.462 7.57 7.57 39.60 1.89
1674 1996 1.334869 AGGCGAAAGAAGTGCAAACAG 59.665 47.619 0.00 0.00 0.00 3.16
1762 2084 2.388121 ACCTTGTCTTTTACGACGACG 58.612 47.619 5.58 5.58 45.75 5.12
1799 2121 3.384668 CACTTTTCTGAAGCTCTGACGA 58.615 45.455 0.00 0.00 0.00 4.20
1850 2172 9.851686 AATATACACACCATGACTAAATGACAT 57.148 29.630 0.00 0.00 0.00 3.06
1915 2237 1.429927 CGCTCTGCATGCTCCAGAAG 61.430 60.000 20.33 6.69 38.73 2.85
2212 2538 3.944015 GACTTGAGATGGATGAAAGGTGG 59.056 47.826 0.00 0.00 0.00 4.61
2440 2766 6.538021 ACTTGAATGCATGCACAAGTTAAAAA 59.462 30.769 34.03 16.72 46.69 1.94
2443 2769 5.199024 ACTTGAATGCATGCACAAGTTAA 57.801 34.783 34.03 18.97 46.69 2.01
2490 2816 2.978018 GCCAACCGCCAACTACAGC 61.978 63.158 0.00 0.00 0.00 4.40
2500 2826 2.484264 GTCTTATGATATGGCCAACCGC 59.516 50.000 10.96 0.00 39.70 5.68
2501 2827 3.748048 CAGTCTTATGATATGGCCAACCG 59.252 47.826 10.96 0.00 39.70 4.44
2502 2828 4.074970 CCAGTCTTATGATATGGCCAACC 58.925 47.826 10.96 1.89 0.00 3.77
2513 2839 7.510685 AGGCAATAGATTAGTCCAGTCTTATGA 59.489 37.037 0.00 0.00 0.00 2.15
2524 2850 8.268850 TCAACAAGAAAGGCAATAGATTAGTC 57.731 34.615 0.00 0.00 0.00 2.59
2525 2851 7.148171 GCTCAACAAGAAAGGCAATAGATTAGT 60.148 37.037 0.00 0.00 0.00 2.24
2526 2852 7.148188 TGCTCAACAAGAAAGGCAATAGATTAG 60.148 37.037 0.00 0.00 0.00 1.73
2528 2854 5.477984 TGCTCAACAAGAAAGGCAATAGATT 59.522 36.000 0.00 0.00 0.00 2.40
2529 2855 5.012239 TGCTCAACAAGAAAGGCAATAGAT 58.988 37.500 0.00 0.00 0.00 1.98
2530 2856 4.397420 TGCTCAACAAGAAAGGCAATAGA 58.603 39.130 0.00 0.00 0.00 1.98
2531 2857 4.771590 TGCTCAACAAGAAAGGCAATAG 57.228 40.909 0.00 0.00 0.00 1.73
2532 2858 5.472148 CAATGCTCAACAAGAAAGGCAATA 58.528 37.500 0.00 0.00 30.06 1.90
2533 2859 4.312443 CAATGCTCAACAAGAAAGGCAAT 58.688 39.130 0.00 0.00 30.06 3.56
2534 2860 3.719924 CAATGCTCAACAAGAAAGGCAA 58.280 40.909 0.00 0.00 30.06 4.52
2535 2861 2.546373 GCAATGCTCAACAAGAAAGGCA 60.546 45.455 0.00 0.00 30.71 4.75
2536 2862 2.064014 GCAATGCTCAACAAGAAAGGC 58.936 47.619 0.00 0.00 0.00 4.35
2537 2863 3.655276 AGCAATGCTCAACAAGAAAGG 57.345 42.857 0.00 0.00 30.62 3.11
2633 2969 4.262207 CCACATAGGATAAGTGATGAGCGT 60.262 45.833 0.00 0.00 42.47 5.07
2676 3012 7.076842 CAGTAAGTGCATGTTTTAGCATAGT 57.923 36.000 0.00 0.00 43.44 2.12
2693 3029 0.895559 GGGCAGCCAAAGCAGTAAGT 60.896 55.000 15.19 0.00 43.56 2.24
2699 3035 0.106719 GTATAGGGGCAGCCAAAGCA 60.107 55.000 15.19 0.00 43.56 3.91
2798 3134 7.056006 ACACACAGCATGGAAGATGAATAATA 58.944 34.615 0.00 0.00 43.62 0.98
2799 3135 5.889853 ACACACAGCATGGAAGATGAATAAT 59.110 36.000 0.00 0.00 43.62 1.28
2800 3136 5.255687 ACACACAGCATGGAAGATGAATAA 58.744 37.500 0.00 0.00 43.62 1.40
2815 3151 0.035458 AGAAGCCTGGTACACACAGC 59.965 55.000 0.00 0.00 34.65 4.40
2825 3161 0.250640 AGCACAAGACAGAAGCCTGG 60.251 55.000 0.00 0.00 44.60 4.45
2840 3176 3.372206 CAGCAGTACAATAGAACCAGCAC 59.628 47.826 0.00 0.00 0.00 4.40
2843 3179 5.617751 GCAAACAGCAGTACAATAGAACCAG 60.618 44.000 0.00 0.00 44.79 4.00
2844 3180 4.215399 GCAAACAGCAGTACAATAGAACCA 59.785 41.667 0.00 0.00 44.79 3.67
2964 3300 2.687935 TGCTCTTGACTTTGTTGGGAAC 59.312 45.455 0.00 0.00 0.00 3.62
3157 3527 3.019564 AGTGAGCTTTGATACCAATGGC 58.980 45.455 0.00 0.00 34.16 4.40
3193 3563 5.858381 TCATAGCCAGCTAAGAAATGGTAG 58.142 41.667 3.02 0.00 36.43 3.18
3211 3581 6.364701 TGGGACAAATTTACCATCCTCATAG 58.635 40.000 13.25 0.00 31.92 2.23
3324 3694 5.105513 GCTAGCTAAAAGGCTATAGAGAGGG 60.106 48.000 7.70 0.00 42.84 4.30
3336 3706 8.276252 TGTTGTAATAAAGGCTAGCTAAAAGG 57.724 34.615 15.72 0.00 0.00 3.11
3434 3804 4.556233 TCAGATAAGTTGGTGTCTTGTCG 58.444 43.478 0.00 0.00 37.83 4.35
3551 3921 6.536582 CCTGTAATTCATAGTGTCTGAAGTGG 59.463 42.308 0.00 0.00 36.16 4.00
3793 4167 1.813786 TCCTCGGGTAAAAATTTGCCG 59.186 47.619 6.88 0.00 42.95 5.69
3801 4175 4.903045 AATGAGAACTCCTCGGGTAAAA 57.097 40.909 0.00 0.00 44.92 1.52
3833 4207 7.814107 CCGTACACTGAATTAGGTTAACACTTA 59.186 37.037 8.10 0.00 0.00 2.24
3849 4236 2.539274 GCGTAAAAACACCGTACACTGA 59.461 45.455 0.00 0.00 0.00 3.41
3862 4249 1.078285 CTAGGCCCCGGCGTAAAAA 60.078 57.895 6.01 0.00 40.30 1.94
3900 4287 5.301555 GGGTAGCCTATCTCAGTTCAATTC 58.698 45.833 2.95 0.00 0.00 2.17
3920 4307 0.121197 TTCAGGAGGGAGATTGGGGT 59.879 55.000 0.00 0.00 0.00 4.95
3932 4319 3.049708 TGATGCACTCTTGTTCAGGAG 57.950 47.619 9.78 9.78 35.86 3.69
3945 4332 3.944015 AGGAGACAAAGCTAATGATGCAC 59.056 43.478 6.45 0.00 0.00 4.57
4001 4389 6.128795 GCACGACCTGCTAATGAGATTATTAC 60.129 42.308 0.00 0.00 43.33 1.89
4008 4400 3.741029 GCACGACCTGCTAATGAGA 57.259 52.632 0.00 0.00 43.33 3.27
4019 4411 0.814010 ACAAACTGGAGTGCACGACC 60.814 55.000 22.82 22.82 0.00 4.79
4021 4413 0.107897 ACACAAACTGGAGTGCACGA 60.108 50.000 12.01 0.00 39.30 4.35
4022 4414 0.304705 GACACAAACTGGAGTGCACG 59.695 55.000 12.01 0.00 39.30 5.34
4026 4418 1.331756 GCTGTGACACAAACTGGAGTG 59.668 52.381 10.02 0.00 41.40 3.51
4038 4465 3.227614 TGAACTACCTACTGCTGTGACA 58.772 45.455 6.48 0.00 0.00 3.58
4039 4466 3.936372 TGAACTACCTACTGCTGTGAC 57.064 47.619 6.48 0.00 0.00 3.67
4042 4469 2.093447 GCCATGAACTACCTACTGCTGT 60.093 50.000 0.66 0.66 0.00 4.40
4046 4473 1.141053 GGGGCCATGAACTACCTACTG 59.859 57.143 4.39 0.00 0.00 2.74
4047 4474 1.274184 TGGGGCCATGAACTACCTACT 60.274 52.381 4.39 0.00 0.00 2.57
4048 4475 1.141053 CTGGGGCCATGAACTACCTAC 59.859 57.143 4.39 0.00 0.00 3.18
4049 4476 1.274184 ACTGGGGCCATGAACTACCTA 60.274 52.381 4.39 0.00 0.00 3.08
4050 4477 0.550147 ACTGGGGCCATGAACTACCT 60.550 55.000 4.39 0.00 0.00 3.08
4051 4478 0.394352 CACTGGGGCCATGAACTACC 60.394 60.000 4.39 0.00 0.00 3.18
4096 5009 1.999735 CTGCATCACCGTCGTATTTGT 59.000 47.619 0.00 0.00 0.00 2.83
4097 5010 2.029244 GTCTGCATCACCGTCGTATTTG 59.971 50.000 0.00 0.00 0.00 2.32
4119 5032 3.782244 CTTGAGACGCCGCACTGC 61.782 66.667 0.00 0.00 0.00 4.40
4177 7277 3.142174 GGCTCAATATTCCTGCCACTAC 58.858 50.000 14.49 0.00 42.79 2.73
4178 7278 2.106511 GGGCTCAATATTCCTGCCACTA 59.893 50.000 18.70 0.00 44.85 2.74
4182 7390 1.613836 CAGGGCTCAATATTCCTGCC 58.386 55.000 7.72 10.07 40.04 4.85
4204 7412 4.288531 GCAATCTGCATGATAAACAGAGC 58.711 43.478 0.00 0.00 43.25 4.09
4238 7446 3.005554 CTCGCTGAAACCATGTGAAGAT 58.994 45.455 0.00 0.00 0.00 2.40
4239 7447 2.416747 CTCGCTGAAACCATGTGAAGA 58.583 47.619 0.00 0.00 0.00 2.87
4317 7537 1.654220 CCGCTTGTTGTCTTGTGGG 59.346 57.895 0.00 0.00 0.00 4.61
4318 7538 1.654220 CCCGCTTGTTGTCTTGTGG 59.346 57.895 0.00 0.00 0.00 4.17
4353 7573 1.338769 GGTGCACGTCTAATTGGGAGT 60.339 52.381 11.45 0.00 0.00 3.85
4408 7630 3.998341 GCCCAGCATATGCCAAAATTATG 59.002 43.478 23.96 12.54 43.38 1.90
4410 7632 2.035704 CGCCCAGCATATGCCAAAATTA 59.964 45.455 23.96 0.00 43.38 1.40
4411 7633 1.202557 CGCCCAGCATATGCCAAAATT 60.203 47.619 23.96 1.16 43.38 1.82
4430 7652 1.265635 TGCCGGTTTGATTTTCAGTCG 59.734 47.619 1.90 0.00 0.00 4.18
4513 7741 1.289066 GCGACAGAGTGTACCTGCA 59.711 57.895 0.00 0.00 35.14 4.41
4514 7742 1.446272 GGCGACAGAGTGTACCTGC 60.446 63.158 0.00 0.00 35.14 4.85
4515 7743 0.109086 CAGGCGACAGAGTGTACCTG 60.109 60.000 12.01 12.01 43.73 4.00
4516 7744 0.539901 ACAGGCGACAGAGTGTACCT 60.540 55.000 0.00 0.00 37.46 3.08
4517 7745 0.109226 GACAGGCGACAGAGTGTACC 60.109 60.000 0.00 0.00 0.00 3.34
4518 7746 0.596577 TGACAGGCGACAGAGTGTAC 59.403 55.000 0.00 0.00 0.00 2.90
4519 7747 1.324383 TTGACAGGCGACAGAGTGTA 58.676 50.000 0.00 0.00 0.00 2.90
4538 7776 4.406456 TCAGTTAATGTGTGCCAAAGGAT 58.594 39.130 0.00 0.00 0.00 3.24
4568 7806 0.652592 GAATTGATACGCAGCGTGCT 59.347 50.000 30.67 17.31 42.25 4.40
4569 7807 0.652592 AGAATTGATACGCAGCGTGC 59.347 50.000 30.67 21.27 41.39 5.34
4570 7808 1.593070 GCAGAATTGATACGCAGCGTG 60.593 52.381 30.67 11.20 41.39 5.34
4571 7809 0.652592 GCAGAATTGATACGCAGCGT 59.347 50.000 26.25 26.25 44.35 5.07
4572 7810 0.933097 AGCAGAATTGATACGCAGCG 59.067 50.000 14.82 14.82 0.00 5.18
4573 7811 1.667724 ACAGCAGAATTGATACGCAGC 59.332 47.619 0.00 0.00 0.00 5.25
4574 7812 3.865164 TGTACAGCAGAATTGATACGCAG 59.135 43.478 0.00 0.00 0.00 5.18
4575 7813 3.855858 TGTACAGCAGAATTGATACGCA 58.144 40.909 0.00 0.00 0.00 5.24
4576 7814 5.462068 TGTATGTACAGCAGAATTGATACGC 59.538 40.000 0.33 0.00 0.00 4.42
4577 7815 6.475402 TGTGTATGTACAGCAGAATTGATACG 59.525 38.462 0.33 0.00 36.78 3.06
4578 7816 7.770801 TGTGTATGTACAGCAGAATTGATAC 57.229 36.000 0.33 0.00 36.78 2.24
4620 7858 4.641645 TCAACACAGGCCCGCCAG 62.642 66.667 8.74 1.99 38.92 4.85
4624 7862 2.669569 CAGGTCAACACAGGCCCG 60.670 66.667 0.00 0.00 0.00 6.13
4652 7890 0.393944 GGTACAAAGGCCCCTACTGC 60.394 60.000 0.00 0.00 0.00 4.40
4671 7909 2.046892 CTGAAGGGTGGCCACTCG 60.047 66.667 33.91 14.91 36.76 4.18
4681 7919 0.463620 GCTAGCCTGTCTCTGAAGGG 59.536 60.000 2.29 0.00 33.87 3.95
4703 7941 4.419921 GTGGTACCTTGGGGCGGG 62.420 72.222 14.36 0.00 35.63 6.13
4704 7942 1.991167 TAGTGGTACCTTGGGGCGG 60.991 63.158 14.36 0.00 35.63 6.13
4706 7944 1.483827 GTAGTAGTGGTACCTTGGGGC 59.516 57.143 14.36 0.00 35.63 5.80
4753 7991 4.379652 ACTTTCCAATGACAAAATGCACC 58.620 39.130 0.00 0.00 0.00 5.01
4768 8006 1.610624 GGTGGAGCGATGAACTTTCCA 60.611 52.381 0.00 0.00 35.67 3.53


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

AutoCloner maintained by Alex Coulton.