Multiple sequence alignment - TraesCS1A01G079400

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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 TraesCS1A01G079400 chr1A 100.000 4568 0 0 1 4568 62025146 62020579 0.000000e+00 8436
1 TraesCS1A01G079400 chr1D 91.873 3765 207 31 331 4054 63371291 63374997 0.000000e+00 5166
2 TraesCS1A01G079400 chr1D 93.556 450 29 0 4060 4509 63375034 63375483 0.000000e+00 671
3 TraesCS1A01G079400 chr1D 85.769 260 25 5 80 327 63370788 63371047 9.740000e-67 265
4 TraesCS1A01G079400 chr1D 98.305 59 1 0 4510 4568 63375509 63375567 2.250000e-18 104
5 TraesCS1A01G079400 chr1B 89.677 1889 108 32 2175 4045 101221924 101223743 0.000000e+00 2327
6 TraesCS1A01G079400 chr1B 87.470 1245 80 24 114 1330 101220727 101221923 0.000000e+00 1365


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 TraesCS1A01G079400 chr1A 62020579 62025146 4567 True 8436.0 8436 100.00000 1 4568 1 chr1A.!!$R1 4567
1 TraesCS1A01G079400 chr1D 63370788 63375567 4779 False 1551.5 5166 92.37575 80 4568 4 chr1D.!!$F1 4488
2 TraesCS1A01G079400 chr1B 101220727 101223743 3016 False 1846.0 2327 88.57350 114 4045 2 chr1B.!!$F1 3931

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
941 1209 0.251634 AGCCAGCAAAGCTACTCTCC 59.748 55.0 0.0 0.0 39.29 3.71 F
1385 1656 0.534203 TCTGTGCCGTCCCTTTTCAC 60.534 55.0 0.0 0.0 0.00 3.18 F
2635 2943 0.539051 CTCGTGATGGAGCCTTCCTT 59.461 55.0 0.0 0.0 44.36 3.36 F
3281 3593 0.319641 AAGAAGAAGTGTCCGCCGTC 60.320 55.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2635 2943 1.528542 ATAGTCGAGCCCGCTAGCA 60.529 57.895 16.45 0.0 35.37 3.49 R
3252 3564 0.032130 ACTTCTTCTTGAGACGCGCA 59.968 50.000 5.73 0.0 33.02 6.09 R
3529 3841 0.253347 TTCAGCCTGATCTCCCCCTT 60.253 55.000 0.00 0.0 0.00 3.95 R
4346 4691 1.078848 GTCGCAAGCAGAGTGGGAT 60.079 57.895 0.00 0.0 39.74 3.85 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 2.105006 AGAGTGGCATAAGCACAGTG 57.895 50.000 0.00 0.00 44.61 3.66
21 22 1.089920 GAGTGGCATAAGCACAGTGG 58.910 55.000 1.84 0.00 44.61 4.00
22 23 0.692476 AGTGGCATAAGCACAGTGGA 59.308 50.000 1.84 0.00 44.61 4.02
23 24 0.804989 GTGGCATAAGCACAGTGGAC 59.195 55.000 1.84 0.00 44.61 4.02
24 25 0.399833 TGGCATAAGCACAGTGGACA 59.600 50.000 1.84 0.00 44.61 4.02
25 26 1.202867 TGGCATAAGCACAGTGGACAA 60.203 47.619 1.84 0.00 44.61 3.18
26 27 1.885887 GGCATAAGCACAGTGGACAAA 59.114 47.619 1.84 0.00 44.61 2.83
27 28 2.295909 GGCATAAGCACAGTGGACAAAA 59.704 45.455 1.84 0.00 44.61 2.44
28 29 3.568538 GCATAAGCACAGTGGACAAAAG 58.431 45.455 1.84 0.00 41.58 2.27
29 30 3.568538 CATAAGCACAGTGGACAAAAGC 58.431 45.455 1.84 0.00 0.00 3.51
30 31 1.767759 AAGCACAGTGGACAAAAGCT 58.232 45.000 1.84 0.00 0.00 3.74
31 32 2.638480 AGCACAGTGGACAAAAGCTA 57.362 45.000 1.84 0.00 0.00 3.32
32 33 2.930950 AGCACAGTGGACAAAAGCTAA 58.069 42.857 1.84 0.00 0.00 3.09
33 34 3.287222 AGCACAGTGGACAAAAGCTAAA 58.713 40.909 1.84 0.00 0.00 1.85
34 35 3.316308 AGCACAGTGGACAAAAGCTAAAG 59.684 43.478 1.84 0.00 0.00 1.85
35 36 3.066760 GCACAGTGGACAAAAGCTAAAGT 59.933 43.478 1.84 0.00 0.00 2.66
36 37 4.601019 CACAGTGGACAAAAGCTAAAGTG 58.399 43.478 0.00 0.00 0.00 3.16
37 38 3.632145 ACAGTGGACAAAAGCTAAAGTGG 59.368 43.478 0.00 0.00 0.00 4.00
38 39 2.623416 AGTGGACAAAAGCTAAAGTGGC 59.377 45.455 0.00 0.00 0.00 5.01
39 40 2.360801 GTGGACAAAAGCTAAAGTGGCA 59.639 45.455 0.00 0.00 0.00 4.92
40 41 2.622942 TGGACAAAAGCTAAAGTGGCAG 59.377 45.455 0.00 0.00 0.00 4.85
41 42 2.884639 GGACAAAAGCTAAAGTGGCAGA 59.115 45.455 0.00 0.00 0.00 4.26
42 43 3.317993 GGACAAAAGCTAAAGTGGCAGAA 59.682 43.478 0.00 0.00 0.00 3.02
43 44 4.202111 GGACAAAAGCTAAAGTGGCAGAAA 60.202 41.667 0.00 0.00 0.00 2.52
44 45 4.682787 ACAAAAGCTAAAGTGGCAGAAAC 58.317 39.130 0.00 0.00 0.00 2.78
45 46 4.159506 ACAAAAGCTAAAGTGGCAGAAACA 59.840 37.500 0.00 0.00 0.00 2.83
46 47 5.108517 CAAAAGCTAAAGTGGCAGAAACAA 58.891 37.500 0.00 0.00 0.00 2.83
47 48 5.337578 AAAGCTAAAGTGGCAGAAACAAA 57.662 34.783 0.00 0.00 0.00 2.83
48 49 4.574599 AGCTAAAGTGGCAGAAACAAAG 57.425 40.909 0.00 0.00 0.00 2.77
49 50 3.954258 AGCTAAAGTGGCAGAAACAAAGT 59.046 39.130 0.00 0.00 0.00 2.66
50 51 4.402474 AGCTAAAGTGGCAGAAACAAAGTT 59.598 37.500 0.00 0.00 0.00 2.66
51 52 5.105351 AGCTAAAGTGGCAGAAACAAAGTTT 60.105 36.000 0.00 0.00 0.00 2.66
52 53 5.580691 GCTAAAGTGGCAGAAACAAAGTTTT 59.419 36.000 0.00 0.00 0.00 2.43
53 54 6.237835 GCTAAAGTGGCAGAAACAAAGTTTTC 60.238 38.462 0.00 0.00 35.97 2.29
54 55 4.123497 AGTGGCAGAAACAAAGTTTTCC 57.877 40.909 0.00 0.89 36.31 3.13
55 56 3.118775 AGTGGCAGAAACAAAGTTTTCCC 60.119 43.478 0.00 0.00 36.31 3.97
56 57 3.103742 TGGCAGAAACAAAGTTTTCCCT 58.896 40.909 0.00 0.00 36.31 4.20
57 58 3.132111 TGGCAGAAACAAAGTTTTCCCTC 59.868 43.478 0.00 0.00 36.31 4.30
58 59 3.372060 GCAGAAACAAAGTTTTCCCTCG 58.628 45.455 0.00 0.00 36.31 4.63
59 60 3.066203 GCAGAAACAAAGTTTTCCCTCGA 59.934 43.478 0.00 0.00 36.31 4.04
60 61 4.261614 GCAGAAACAAAGTTTTCCCTCGAT 60.262 41.667 0.00 0.00 36.31 3.59
61 62 5.736207 GCAGAAACAAAGTTTTCCCTCGATT 60.736 40.000 0.00 0.00 36.31 3.34
62 63 5.687285 CAGAAACAAAGTTTTCCCTCGATTG 59.313 40.000 0.00 0.00 36.31 2.67
63 64 5.592688 AGAAACAAAGTTTTCCCTCGATTGA 59.407 36.000 0.00 0.00 36.31 2.57
64 65 5.438761 AACAAAGTTTTCCCTCGATTGAG 57.561 39.130 2.59 2.59 42.18 3.02
65 66 4.714632 ACAAAGTTTTCCCTCGATTGAGA 58.285 39.130 11.89 0.00 45.57 3.27
66 67 5.130350 ACAAAGTTTTCCCTCGATTGAGAA 58.870 37.500 11.89 0.00 45.57 2.87
67 68 5.008712 ACAAAGTTTTCCCTCGATTGAGAAC 59.991 40.000 11.89 7.71 45.57 3.01
68 69 4.625607 AGTTTTCCCTCGATTGAGAACT 57.374 40.909 11.89 9.80 45.57 3.01
69 70 4.319177 AGTTTTCCCTCGATTGAGAACTG 58.681 43.478 11.89 0.00 45.57 3.16
70 71 4.065789 GTTTTCCCTCGATTGAGAACTGT 58.934 43.478 11.89 0.00 45.57 3.55
71 72 4.351874 TTTCCCTCGATTGAGAACTGTT 57.648 40.909 11.89 0.00 45.57 3.16
72 73 4.351874 TTCCCTCGATTGAGAACTGTTT 57.648 40.909 11.89 0.00 45.57 2.83
73 74 4.351874 TCCCTCGATTGAGAACTGTTTT 57.648 40.909 11.89 0.00 45.57 2.43
74 75 4.315803 TCCCTCGATTGAGAACTGTTTTC 58.684 43.478 11.89 4.26 45.57 2.29
75 76 3.437049 CCCTCGATTGAGAACTGTTTTCC 59.563 47.826 11.89 0.00 45.57 3.13
76 77 3.437049 CCTCGATTGAGAACTGTTTTCCC 59.563 47.826 11.89 0.00 45.57 3.97
77 78 4.319177 CTCGATTGAGAACTGTTTTCCCT 58.681 43.478 3.60 0.00 45.57 4.20
78 79 4.315803 TCGATTGAGAACTGTTTTCCCTC 58.684 43.478 8.40 4.66 0.00 4.30
79 80 3.123621 CGATTGAGAACTGTTTTCCCTCG 59.876 47.826 13.74 13.74 0.00 4.63
80 81 3.830744 TTGAGAACTGTTTTCCCTCGA 57.169 42.857 8.40 1.54 0.00 4.04
81 82 4.351874 TTGAGAACTGTTTTCCCTCGAT 57.648 40.909 8.40 0.00 0.00 3.59
82 83 4.351874 TGAGAACTGTTTTCCCTCGATT 57.648 40.909 8.40 0.00 0.00 3.34
83 84 4.065088 TGAGAACTGTTTTCCCTCGATTG 58.935 43.478 8.40 0.00 0.00 2.67
84 85 4.202315 TGAGAACTGTTTTCCCTCGATTGA 60.202 41.667 8.40 0.00 0.00 2.57
85 86 4.319177 AGAACTGTTTTCCCTCGATTGAG 58.681 43.478 2.59 2.59 42.18 3.02
86 87 4.040461 AGAACTGTTTTCCCTCGATTGAGA 59.960 41.667 11.89 0.00 45.57 3.27
87 88 4.351874 ACTGTTTTCCCTCGATTGAGAA 57.648 40.909 11.89 0.00 45.57 2.87
88 89 4.065789 ACTGTTTTCCCTCGATTGAGAAC 58.934 43.478 11.89 8.21 45.57 3.01
89 90 4.202367 ACTGTTTTCCCTCGATTGAGAACT 60.202 41.667 11.89 0.00 45.57 3.01
90 91 4.714632 TGTTTTCCCTCGATTGAGAACTT 58.285 39.130 11.89 0.00 45.57 2.66
91 92 4.755123 TGTTTTCCCTCGATTGAGAACTTC 59.245 41.667 11.89 0.00 45.57 3.01
92 93 4.617253 TTTCCCTCGATTGAGAACTTCA 57.383 40.909 11.89 0.00 45.57 3.02
93 94 4.826274 TTCCCTCGATTGAGAACTTCAT 57.174 40.909 11.89 0.00 45.57 2.57
94 95 5.932619 TTCCCTCGATTGAGAACTTCATA 57.067 39.130 11.89 0.00 45.57 2.15
104 105 5.407407 TGAGAACTTCATAAGTCTGGGTC 57.593 43.478 0.00 0.00 41.91 4.46
128 129 6.531594 TCGATTTCTGTATACTGCAACTTCAG 59.468 38.462 4.17 0.00 39.86 3.02
137 139 8.531982 TGTATACTGCAACTTCAGAATAGTTCT 58.468 33.333 4.17 0.00 41.70 3.01
228 241 0.462759 GTGCATCCGCTTAAGGCTCT 60.463 55.000 4.29 0.00 39.64 4.09
248 262 9.143155 AGGCTCTACTGAAAATTTTTCCTTTTA 57.857 29.630 17.05 4.73 0.00 1.52
268 291 8.470002 CCTTTTATTTGAAGAGGGTTTCCTATG 58.530 37.037 0.00 0.00 45.05 2.23
309 332 7.148205 TGCTAGTACATATATCGGCGTAATTCA 60.148 37.037 6.85 0.00 0.00 2.57
316 339 9.302345 ACATATATCGGCGTAATTCAAGATAAG 57.698 33.333 6.85 0.00 0.00 1.73
319 342 4.049186 TCGGCGTAATTCAAGATAAGCTC 58.951 43.478 6.85 0.00 0.00 4.09
323 346 4.260212 GCGTAATTCAAGATAAGCTCGCAA 60.260 41.667 0.00 0.00 39.72 4.85
327 350 7.685712 CGTAATTCAAGATAAGCTCGCAATATG 59.314 37.037 0.00 0.00 0.00 1.78
392 655 2.819348 GCCAACCAGAAGAAAGGGACAT 60.819 50.000 0.00 0.00 0.00 3.06
396 661 5.514834 CCAACCAGAAGAAAGGGACATAAGA 60.515 44.000 0.00 0.00 0.00 2.10
397 662 5.843019 ACCAGAAGAAAGGGACATAAGAA 57.157 39.130 0.00 0.00 0.00 2.52
398 663 6.200878 ACCAGAAGAAAGGGACATAAGAAA 57.799 37.500 0.00 0.00 0.00 2.52
399 664 6.610830 ACCAGAAGAAAGGGACATAAGAAAA 58.389 36.000 0.00 0.00 0.00 2.29
400 665 6.717084 ACCAGAAGAAAGGGACATAAGAAAAG 59.283 38.462 0.00 0.00 0.00 2.27
401 666 6.942576 CCAGAAGAAAGGGACATAAGAAAAGA 59.057 38.462 0.00 0.00 0.00 2.52
402 667 7.094592 CCAGAAGAAAGGGACATAAGAAAAGAC 60.095 40.741 0.00 0.00 0.00 3.01
403 668 7.445402 CAGAAGAAAGGGACATAAGAAAAGACA 59.555 37.037 0.00 0.00 0.00 3.41
404 669 7.445707 AGAAGAAAGGGACATAAGAAAAGACAC 59.554 37.037 0.00 0.00 0.00 3.67
405 670 6.842676 AGAAAGGGACATAAGAAAAGACACT 58.157 36.000 0.00 0.00 0.00 3.55
406 671 7.974504 AGAAAGGGACATAAGAAAAGACACTA 58.025 34.615 0.00 0.00 0.00 2.74
407 672 8.606830 AGAAAGGGACATAAGAAAAGACACTAT 58.393 33.333 0.00 0.00 0.00 2.12
408 673 9.886132 GAAAGGGACATAAGAAAAGACACTATA 57.114 33.333 0.00 0.00 0.00 1.31
409 674 9.892130 AAAGGGACATAAGAAAAGACACTATAG 57.108 33.333 0.00 0.00 0.00 1.31
450 715 4.391523 GGCTCATCAAGAAAACAGTCTCTC 59.608 45.833 0.00 0.00 0.00 3.20
451 716 5.237048 GCTCATCAAGAAAACAGTCTCTCT 58.763 41.667 0.00 0.00 0.00 3.10
474 739 3.329386 GAGTCTTGAGCACTGCATTACA 58.671 45.455 3.30 0.00 0.00 2.41
492 757 8.789762 TGCATTACAATCCATCTATTCAATCAG 58.210 33.333 0.00 0.00 0.00 2.90
494 759 8.789762 CATTACAATCCATCTATTCAATCAGCA 58.210 33.333 0.00 0.00 0.00 4.41
503 768 6.149129 TCTATTCAATCAGCAGACGTACAT 57.851 37.500 0.00 0.00 0.00 2.29
512 777 6.880822 TCAGCAGACGTACATTACATTAAC 57.119 37.500 0.00 0.00 0.00 2.01
562 827 2.700897 CCTATCATGGACTTCGACCCTT 59.299 50.000 0.00 0.00 0.00 3.95
596 861 2.604614 GCAGTACGGGAACAAAAGCAAG 60.605 50.000 0.00 0.00 0.00 4.01
652 918 9.113838 AGGACAAATGAACATATGATTGAGTAC 57.886 33.333 10.38 3.27 0.00 2.73
664 930 8.715998 CATATGATTGAGTACTTAATCAGCCAC 58.284 37.037 33.32 14.90 44.86 5.01
668 934 5.854010 TGAGTACTTAATCAGCCACTAGG 57.146 43.478 0.00 0.00 38.23 3.02
767 1033 2.990066 AGGGCGAGACCTTAAATCAG 57.010 50.000 0.00 0.00 37.69 2.90
859 1125 2.268298 CGTACATTTCCGCTACAAGCT 58.732 47.619 0.00 0.00 39.60 3.74
916 1184 0.665835 CGTTTGTGGCTTGGCAGTAA 59.334 50.000 0.00 0.00 0.00 2.24
929 1197 0.391661 GCAGTAAGCACTAGCCAGCA 60.392 55.000 5.39 0.00 44.79 4.41
941 1209 0.251634 AGCCAGCAAAGCTACTCTCC 59.748 55.000 0.00 0.00 39.29 3.71
1025 1296 1.414897 GTTCGTCGACGTTCATGCC 59.585 57.895 34.40 13.53 40.80 4.40
1065 1336 1.775459 ACGGCTCTGATACTCCTCCTA 59.225 52.381 0.00 0.00 0.00 2.94
1149 1420 1.603739 GGAGTTGTGTCCCAAGGCC 60.604 63.158 0.00 0.00 32.51 5.19
1260 1531 2.879462 GTCCGTGTAAGCCGCTCG 60.879 66.667 0.00 0.00 0.00 5.03
1284 1555 6.366630 GCTGATGTTCACTAAGTTTGAGTTC 58.633 40.000 0.00 0.00 0.00 3.01
1312 1583 2.766970 TTGCACGGCAGTTTTTACTC 57.233 45.000 0.00 0.00 40.61 2.59
1326 1597 6.475402 CAGTTTTTACTCGATTTTTGCCACTT 59.525 34.615 0.00 0.00 0.00 3.16
1383 1654 2.396590 TATCTGTGCCGTCCCTTTTC 57.603 50.000 0.00 0.00 0.00 2.29
1385 1656 0.534203 TCTGTGCCGTCCCTTTTCAC 60.534 55.000 0.00 0.00 0.00 3.18
1488 1759 9.445786 ACAAGTTCTGAAATATTTTTACACACG 57.554 29.630 1.43 0.00 0.00 4.49
1491 1762 9.275398 AGTTCTGAAATATTTTTACACACGGTA 57.725 29.630 1.43 0.00 0.00 4.02
1505 1776 8.959734 TTACACACGGTAGATATAATGATTCG 57.040 34.615 0.00 0.00 32.49 3.34
1522 1793 4.878971 TGATTCGTTGACCTGAAAAGTTGA 59.121 37.500 0.00 0.00 0.00 3.18
1542 1836 8.452989 AGTTGATATTTTGTTTGCGAGAAATC 57.547 30.769 0.00 0.00 0.00 2.17
1559 1853 8.902735 GCGAGAAATCGAAAGTAAAAAGAAAAT 58.097 29.630 1.17 0.00 34.64 1.82
1567 1861 9.737427 TCGAAAGTAAAAAGAAAATAATGCACA 57.263 25.926 0.00 0.00 0.00 4.57
1568 1862 9.777843 CGAAAGTAAAAAGAAAATAATGCACAC 57.222 29.630 0.00 0.00 0.00 3.82
1569 1863 9.777843 GAAAGTAAAAAGAAAATAATGCACACG 57.222 29.630 0.00 0.00 0.00 4.49
1570 1864 9.522804 AAAGTAAAAAGAAAATAATGCACACGA 57.477 25.926 0.00 0.00 0.00 4.35
1586 1880 4.511454 GCACACGATATCTTGAGGCATAAA 59.489 41.667 15.55 0.00 0.00 1.40
1588 1882 6.596703 CACACGATATCTTGAGGCATAAATG 58.403 40.000 15.55 0.00 0.00 2.32
1589 1883 5.702670 ACACGATATCTTGAGGCATAAATGG 59.297 40.000 15.55 0.00 0.00 3.16
1601 1895 7.805163 TGAGGCATAAATGGATGGGTATATAG 58.195 38.462 0.00 0.00 0.00 1.31
1602 1896 7.627293 TGAGGCATAAATGGATGGGTATATAGA 59.373 37.037 0.00 0.00 0.00 1.98
1603 1897 8.038862 AGGCATAAATGGATGGGTATATAGAG 57.961 38.462 0.00 0.00 0.00 2.43
1613 1907 6.551601 GGATGGGTATATAGAGGATGTAGGTG 59.448 46.154 0.00 0.00 0.00 4.00
1666 1960 6.016360 TCAGGAACATGGTGTGTAATTTGAAG 60.016 38.462 0.00 0.00 41.14 3.02
1674 1968 4.083484 GGTGTGTAATTTGAAGGTCTTCCG 60.083 45.833 8.09 0.00 38.77 4.30
1704 1998 1.207329 GCTAGTCATGGGTCGGTCTTT 59.793 52.381 0.00 0.00 0.00 2.52
1749 2043 3.260128 TGCCACAAATATTTGCACCATCA 59.740 39.130 24.82 12.90 41.79 3.07
1785 2079 4.335315 TGGTCAAGCTTTCAAACAGTACAG 59.665 41.667 0.00 0.00 0.00 2.74
1797 2091 7.297936 TCAAACAGTACAGAGACTAATTGGA 57.702 36.000 0.00 0.00 30.67 3.53
1940 2234 2.281761 AAGTGCGGTGCCTCCAAG 60.282 61.111 0.00 0.00 35.57 3.61
1953 2247 2.757314 GCCTCCAAGGGAAAATTCTGAG 59.243 50.000 0.00 0.00 35.37 3.35
2050 2344 9.515020 CTTGTTAAGCTGTTTATTGACTTTTGA 57.485 29.630 0.00 0.00 0.00 2.69
2061 2355 8.752254 GTTTATTGACTTTTGAGGTTAACTTGC 58.248 33.333 5.42 0.00 0.00 4.01
2063 2357 3.314080 TGACTTTTGAGGTTAACTTGCCG 59.686 43.478 5.42 0.00 0.00 5.69
2065 2359 3.314357 ACTTTTGAGGTTAACTTGCCGTC 59.686 43.478 5.42 0.00 0.00 4.79
2075 2369 7.659186 AGGTTAACTTGCCGTCTATATTCTAG 58.341 38.462 5.42 0.00 0.00 2.43
2093 2387 4.307432 TCTAGGTTTTGTCTCGCAGAAAG 58.693 43.478 0.00 0.00 34.09 2.62
2098 2392 5.940470 AGGTTTTGTCTCGCAGAAAGATATT 59.060 36.000 0.00 0.00 34.09 1.28
2156 2451 6.749578 TGCAATAACAAGTACACAAAACACAG 59.250 34.615 0.00 0.00 0.00 3.66
2162 2457 7.151999 ACAAGTACACAAAACACAGAATGAA 57.848 32.000 0.00 0.00 39.69 2.57
2171 2466 7.216693 CACAAAACACAGAATGAAATGCAAAAC 59.783 33.333 0.00 0.00 39.69 2.43
2255 2550 8.637986 AGAAATGTTTTACAATTAGCTTGGACA 58.362 29.630 0.00 0.00 39.30 4.02
2563 2871 1.625818 AGTGACGCCAAGGAGATTCTT 59.374 47.619 0.00 0.00 0.00 2.52
2626 2934 2.121538 CCTCTCCGCTCGTGATGGA 61.122 63.158 0.00 0.00 0.00 3.41
2635 2943 0.539051 CTCGTGATGGAGCCTTCCTT 59.461 55.000 0.00 0.00 44.36 3.36
2694 3002 1.272480 TGATGGACTCGTCTCCAAGGA 60.272 52.381 7.73 0.00 43.79 3.36
2733 3041 3.771160 CCCTCACCCCGACTTCCG 61.771 72.222 0.00 0.00 38.18 4.30
2774 3082 5.652994 AAACTTCACTGCAAAAGGTAACA 57.347 34.783 7.75 0.00 41.41 2.41
2908 3216 7.870826 TGGCATCAACATAGAAAATATTACCG 58.129 34.615 0.00 0.00 0.00 4.02
2991 3299 9.155975 ACAATACTTACTTTCTAGTGAAGCATG 57.844 33.333 8.04 0.00 35.78 4.06
3044 3352 4.992951 GTGTAACCGTGAAGACCTTGTAAT 59.007 41.667 0.00 0.00 0.00 1.89
3045 3353 6.015180 AGTGTAACCGTGAAGACCTTGTAATA 60.015 38.462 0.00 0.00 37.80 0.98
3046 3354 6.815142 GTGTAACCGTGAAGACCTTGTAATAT 59.185 38.462 0.00 0.00 0.00 1.28
3047 3355 7.975616 GTGTAACCGTGAAGACCTTGTAATATA 59.024 37.037 0.00 0.00 0.00 0.86
3048 3356 8.530311 TGTAACCGTGAAGACCTTGTAATATAA 58.470 33.333 0.00 0.00 0.00 0.98
3089 3399 5.900339 TGTGACACTGAGAAAAATACGTC 57.100 39.130 7.20 0.00 0.00 4.34
3120 3432 5.048852 TGTTTAATGTACAGGTTTTACGGCC 60.049 40.000 0.33 0.00 0.00 6.13
3177 3489 1.357258 GCACCTCACACTGCTCATCG 61.357 60.000 0.00 0.00 0.00 3.84
3208 3520 5.659463 ACCGTTTGTACAAGTACTACAACA 58.341 37.500 8.56 4.92 34.53 3.33
3213 3525 5.261209 TGTACAAGTACTACAACAACGGT 57.739 39.130 11.27 0.00 37.00 4.83
3252 3564 4.235762 ATTCCGGCGGCGTATGCT 62.236 61.111 30.09 6.98 42.25 3.79
3273 3585 1.772182 CGCGTCTCAAGAAGAAGTGT 58.228 50.000 0.00 0.00 38.64 3.55
3276 3588 2.320367 CGTCTCAAGAAGAAGTGTCCG 58.680 52.381 0.00 0.00 35.21 4.79
3280 3592 0.600255 CAAGAAGAAGTGTCCGCCGT 60.600 55.000 0.00 0.00 0.00 5.68
3281 3593 0.319641 AAGAAGAAGTGTCCGCCGTC 60.320 55.000 0.00 0.00 0.00 4.79
3333 3645 2.635338 CTCGACGACGTGACACCA 59.365 61.111 4.58 0.00 40.69 4.17
3426 3738 4.131088 GACGACCCTGAGACGGCC 62.131 72.222 0.00 0.00 0.00 6.13
3472 3784 1.000019 CCCTCGGACTACTGGACCA 60.000 63.158 0.00 0.00 0.00 4.02
3522 3834 1.508545 CGAGATGGACGTGCTCACT 59.491 57.895 8.99 4.81 0.00 3.41
3529 3841 4.240103 ACGTGCTCACTGGCAGCA 62.240 61.111 15.89 4.45 44.80 4.41
3588 3900 9.686683 AACTAGTAATTGATTGAGCTATTGGTT 57.313 29.630 0.00 0.00 0.00 3.67
3589 3901 9.113838 ACTAGTAATTGATTGAGCTATTGGTTG 57.886 33.333 0.00 0.00 0.00 3.77
3590 3902 7.338800 AGTAATTGATTGAGCTATTGGTTGG 57.661 36.000 0.00 0.00 0.00 3.77
3591 3903 7.118723 AGTAATTGATTGAGCTATTGGTTGGA 58.881 34.615 0.00 0.00 0.00 3.53
3592 3904 6.855763 AATTGATTGAGCTATTGGTTGGAA 57.144 33.333 0.00 0.00 0.00 3.53
3640 3955 6.774673 TGCTTGGGGAAATTCACGATATATA 58.225 36.000 0.00 0.00 0.00 0.86
3726 4041 6.290294 AGCACATTTCCAAGAAAGCATATT 57.710 33.333 0.00 0.00 0.00 1.28
3762 4077 9.515020 GAGTTGTGAATTTGACAAGAAACAATA 57.485 29.630 1.45 0.00 34.02 1.90
3766 4081 9.814899 TGTGAATTTGACAAGAAACAATAATGT 57.185 25.926 0.00 0.00 43.14 2.71
3794 4109 5.709164 ACTAGTCCTACTACGTCATGTTTGT 59.291 40.000 0.00 0.00 0.00 2.83
3809 4124 8.026607 CGTCATGTTTGTACATTTCCCTTTTAT 58.973 33.333 0.00 0.00 42.29 1.40
3850 4165 7.595502 CGACTACTATCACTTTGTGAACTTCTT 59.404 37.037 4.46 0.00 45.96 2.52
3875 4190 9.527157 TTGATGAAATGGTTCAGATTTTAGGTA 57.473 29.630 0.00 0.00 46.75 3.08
3916 4231 4.038763 ACTGTGGTCGATCAAGTAAACAGA 59.961 41.667 16.09 0.00 37.73 3.41
3938 4253 4.606961 AGTTAACACAATCGCAACCAAAG 58.393 39.130 8.61 0.00 0.00 2.77
3942 4257 0.749649 ACAATCGCAACCAAAGGCAA 59.250 45.000 0.00 0.00 0.00 4.52
3979 4294 1.672356 CCCACGCCACCAGAAAGAG 60.672 63.158 0.00 0.00 0.00 2.85
4022 4337 7.506599 TGGATTATTGCTATCATGAACAATGGT 59.493 33.333 22.46 14.79 36.86 3.55
4045 4360 8.259411 TGGTAAATGATGCTTAAGAATTTGCAT 58.741 29.630 6.67 1.62 45.09 3.96
4046 4361 8.545420 GGTAAATGATGCTTAAGAATTTGCATG 58.455 33.333 6.67 0.00 43.45 4.06
4092 4437 3.134804 ACCGACAAATCCCTCCATCTTAG 59.865 47.826 0.00 0.00 0.00 2.18
4108 4453 5.988561 CCATCTTAGCCACTTTCAGATAGAC 59.011 44.000 0.00 0.00 0.00 2.59
4114 4459 5.574188 AGCCACTTTCAGATAGACCAAATT 58.426 37.500 0.00 0.00 0.00 1.82
4124 4469 3.295304 GACCAAATTGTGCCCGCCC 62.295 63.158 0.00 0.00 0.00 6.13
4130 4475 4.966787 TTGTGCCCGCCCACCTTC 62.967 66.667 1.93 0.00 34.85 3.46
4134 4479 4.660938 GCCCGCCCACCTTCTGTT 62.661 66.667 0.00 0.00 0.00 3.16
4137 4482 1.550130 CCCGCCCACCTTCTGTTAGA 61.550 60.000 0.00 0.00 0.00 2.10
4225 4570 6.320164 TGGCTACACAAAACAAGTGAAGTATT 59.680 34.615 0.00 0.00 40.16 1.89
4230 4575 8.460831 ACACAAAACAAGTGAAGTATTTTGTC 57.539 30.769 9.73 0.00 45.59 3.18
4271 4616 4.630644 AACAATTCCAGAGAAGCTCTCA 57.369 40.909 13.42 0.00 45.73 3.27
4286 4631 7.424001 AGAAGCTCTCAGTTTCATTTTTGAAG 58.576 34.615 3.36 0.00 37.82 3.02
4314 4659 4.321675 GGTGTCACCAAAAACCATCCATAC 60.322 45.833 17.59 0.00 38.42 2.39
4344 4689 4.197750 ACTCCAGAAATGATGCACTCATC 58.802 43.478 10.70 0.00 44.03 2.92
4346 4691 3.054213 TCCAGAAATGATGCACTCATCCA 60.054 43.478 10.70 0.00 46.60 3.41
4368 4713 0.882042 CCACTCTGCTTGCGACACTT 60.882 55.000 0.00 0.00 0.00 3.16
4382 4727 2.306847 GACACTTTGCTCTTTCCCCAA 58.693 47.619 0.00 0.00 0.00 4.12
4404 4749 4.027674 TGTCCAATGCAGGTAAAGCTTA 57.972 40.909 0.00 0.00 0.00 3.09
4416 4761 6.310467 GCAGGTAAAGCTTAAGGCAATTTTAC 59.690 38.462 0.00 7.75 44.79 2.01
4446 4791 6.840780 ATTTGGGCTTGCTATATTGGATAC 57.159 37.500 0.00 0.00 0.00 2.24
4491 4836 9.131791 AGATAAATATTTGGGCTTACGATTGTT 57.868 29.630 11.05 0.00 0.00 2.83
4559 4929 5.376854 AAAAGCAGTGGCACAAGTAATAG 57.623 39.130 21.41 0.14 44.16 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.093500 CCACTGTGCTTATGCCACTCTA 60.093 50.000 1.29 0.00 38.71 2.43
2 3 1.089920 CCACTGTGCTTATGCCACTC 58.910 55.000 1.29 0.00 38.71 3.51
3 4 0.692476 TCCACTGTGCTTATGCCACT 59.308 50.000 1.29 0.00 38.71 4.00
4 5 0.804989 GTCCACTGTGCTTATGCCAC 59.195 55.000 1.29 0.00 38.71 5.01
5 6 0.399833 TGTCCACTGTGCTTATGCCA 59.600 50.000 1.29 0.00 38.71 4.92
7 8 3.568538 CTTTTGTCCACTGTGCTTATGC 58.431 45.455 1.29 0.00 40.20 3.14
8 9 3.254166 AGCTTTTGTCCACTGTGCTTATG 59.746 43.478 1.29 0.00 0.00 1.90
9 10 3.490348 AGCTTTTGTCCACTGTGCTTAT 58.510 40.909 1.29 0.00 0.00 1.73
11 12 1.767759 AGCTTTTGTCCACTGTGCTT 58.232 45.000 1.29 0.00 0.00 3.91
12 13 2.638480 TAGCTTTTGTCCACTGTGCT 57.362 45.000 1.29 0.00 0.00 4.40
13 14 3.066760 ACTTTAGCTTTTGTCCACTGTGC 59.933 43.478 1.29 0.00 0.00 4.57
15 16 3.632145 CCACTTTAGCTTTTGTCCACTGT 59.368 43.478 0.00 0.00 0.00 3.55
16 17 3.550842 GCCACTTTAGCTTTTGTCCACTG 60.551 47.826 0.00 0.00 0.00 3.66
17 18 2.623416 GCCACTTTAGCTTTTGTCCACT 59.377 45.455 0.00 0.00 0.00 4.00
18 19 2.360801 TGCCACTTTAGCTTTTGTCCAC 59.639 45.455 0.00 0.00 0.00 4.02
19 20 2.622942 CTGCCACTTTAGCTTTTGTCCA 59.377 45.455 0.00 0.00 0.00 4.02
20 21 2.884639 TCTGCCACTTTAGCTTTTGTCC 59.115 45.455 0.00 0.00 0.00 4.02
21 22 4.568152 TTCTGCCACTTTAGCTTTTGTC 57.432 40.909 0.00 0.00 0.00 3.18
22 23 4.159506 TGTTTCTGCCACTTTAGCTTTTGT 59.840 37.500 0.00 0.00 0.00 2.83
23 24 4.681744 TGTTTCTGCCACTTTAGCTTTTG 58.318 39.130 0.00 0.00 0.00 2.44
24 25 5.337578 TTGTTTCTGCCACTTTAGCTTTT 57.662 34.783 0.00 0.00 0.00 2.27
25 26 5.105351 ACTTTGTTTCTGCCACTTTAGCTTT 60.105 36.000 0.00 0.00 0.00 3.51
26 27 4.402474 ACTTTGTTTCTGCCACTTTAGCTT 59.598 37.500 0.00 0.00 0.00 3.74
27 28 3.954258 ACTTTGTTTCTGCCACTTTAGCT 59.046 39.130 0.00 0.00 0.00 3.32
28 29 4.307443 ACTTTGTTTCTGCCACTTTAGC 57.693 40.909 0.00 0.00 0.00 3.09
29 30 6.255670 GGAAAACTTTGTTTCTGCCACTTTAG 59.744 38.462 0.00 0.00 37.60 1.85
30 31 6.103330 GGAAAACTTTGTTTCTGCCACTTTA 58.897 36.000 0.00 0.00 37.60 1.85
31 32 4.935205 GGAAAACTTTGTTTCTGCCACTTT 59.065 37.500 0.00 0.00 37.60 2.66
32 33 4.503910 GGAAAACTTTGTTTCTGCCACTT 58.496 39.130 0.00 0.00 37.60 3.16
33 34 3.118775 GGGAAAACTTTGTTTCTGCCACT 60.119 43.478 0.00 0.00 37.60 4.00
34 35 3.118775 AGGGAAAACTTTGTTTCTGCCAC 60.119 43.478 13.40 5.35 37.60 5.01
35 36 3.103742 AGGGAAAACTTTGTTTCTGCCA 58.896 40.909 13.40 0.00 37.60 4.92
36 37 3.717707 GAGGGAAAACTTTGTTTCTGCC 58.282 45.455 0.00 3.05 37.60 4.85
37 38 3.066203 TCGAGGGAAAACTTTGTTTCTGC 59.934 43.478 0.00 0.00 37.60 4.26
38 39 4.893424 TCGAGGGAAAACTTTGTTTCTG 57.107 40.909 0.00 0.00 37.60 3.02
39 40 5.592688 TCAATCGAGGGAAAACTTTGTTTCT 59.407 36.000 0.00 0.00 37.60 2.52
40 41 5.827666 TCAATCGAGGGAAAACTTTGTTTC 58.172 37.500 0.00 0.00 36.87 2.78
41 42 5.592688 TCTCAATCGAGGGAAAACTTTGTTT 59.407 36.000 0.00 0.00 39.95 2.83
42 43 5.130350 TCTCAATCGAGGGAAAACTTTGTT 58.870 37.500 0.00 0.00 39.95 2.83
43 44 4.714632 TCTCAATCGAGGGAAAACTTTGT 58.285 39.130 0.00 0.00 39.95 2.83
44 45 5.239525 AGTTCTCAATCGAGGGAAAACTTTG 59.760 40.000 2.86 0.00 39.95 2.77
45 46 5.239525 CAGTTCTCAATCGAGGGAAAACTTT 59.760 40.000 5.38 0.00 39.95 2.66
46 47 4.757149 CAGTTCTCAATCGAGGGAAAACTT 59.243 41.667 5.38 0.00 39.95 2.66
47 48 4.202367 ACAGTTCTCAATCGAGGGAAAACT 60.202 41.667 2.86 2.86 39.95 2.66
48 49 4.065789 ACAGTTCTCAATCGAGGGAAAAC 58.934 43.478 0.00 0.00 39.95 2.43
49 50 4.351874 ACAGTTCTCAATCGAGGGAAAA 57.648 40.909 0.00 0.00 39.95 2.29
50 51 4.351874 AACAGTTCTCAATCGAGGGAAA 57.648 40.909 0.00 0.00 39.95 3.13
51 52 4.351874 AAACAGTTCTCAATCGAGGGAA 57.648 40.909 0.00 0.00 39.95 3.97
52 53 4.315803 GAAAACAGTTCTCAATCGAGGGA 58.684 43.478 0.00 0.00 39.95 4.20
53 54 3.437049 GGAAAACAGTTCTCAATCGAGGG 59.563 47.826 0.00 0.00 39.95 4.30
54 55 3.437049 GGGAAAACAGTTCTCAATCGAGG 59.563 47.826 0.00 0.00 39.95 4.63
55 56 4.319177 AGGGAAAACAGTTCTCAATCGAG 58.681 43.478 0.00 0.00 40.98 4.04
56 57 4.315803 GAGGGAAAACAGTTCTCAATCGA 58.684 43.478 0.00 0.00 0.00 3.59
57 58 3.123621 CGAGGGAAAACAGTTCTCAATCG 59.876 47.826 0.02 0.02 0.00 3.34
58 59 4.315803 TCGAGGGAAAACAGTTCTCAATC 58.684 43.478 0.00 0.00 0.00 2.67
59 60 4.351874 TCGAGGGAAAACAGTTCTCAAT 57.648 40.909 0.00 0.00 0.00 2.57
60 61 3.830744 TCGAGGGAAAACAGTTCTCAA 57.169 42.857 0.00 0.00 0.00 3.02
61 62 4.065088 CAATCGAGGGAAAACAGTTCTCA 58.935 43.478 0.00 0.00 0.00 3.27
62 63 4.315803 TCAATCGAGGGAAAACAGTTCTC 58.684 43.478 0.00 0.00 0.00 2.87
63 64 4.040461 TCTCAATCGAGGGAAAACAGTTCT 59.960 41.667 0.00 0.00 39.95 3.01
64 65 4.315803 TCTCAATCGAGGGAAAACAGTTC 58.684 43.478 0.00 0.00 39.95 3.01
65 66 4.351874 TCTCAATCGAGGGAAAACAGTT 57.648 40.909 0.00 0.00 39.95 3.16
66 67 4.065789 GTTCTCAATCGAGGGAAAACAGT 58.934 43.478 0.00 0.00 39.95 3.55
67 68 4.319177 AGTTCTCAATCGAGGGAAAACAG 58.681 43.478 7.72 0.00 39.95 3.16
68 69 4.351874 AGTTCTCAATCGAGGGAAAACA 57.648 40.909 7.72 0.00 39.95 2.83
69 70 4.755123 TGAAGTTCTCAATCGAGGGAAAAC 59.245 41.667 4.17 0.00 39.95 2.43
70 71 4.968259 TGAAGTTCTCAATCGAGGGAAAA 58.032 39.130 4.17 0.00 39.95 2.29
71 72 4.617253 TGAAGTTCTCAATCGAGGGAAA 57.383 40.909 4.17 0.00 39.95 3.13
72 73 4.826274 ATGAAGTTCTCAATCGAGGGAA 57.174 40.909 4.17 0.00 39.95 3.97
73 74 5.422331 ACTTATGAAGTTCTCAATCGAGGGA 59.578 40.000 4.17 0.00 39.04 4.20
74 75 5.665459 ACTTATGAAGTTCTCAATCGAGGG 58.335 41.667 4.17 0.00 39.04 4.30
75 76 6.475076 CAGACTTATGAAGTTCTCAATCGAGG 59.525 42.308 4.17 0.00 43.03 4.63
76 77 6.475076 CCAGACTTATGAAGTTCTCAATCGAG 59.525 42.308 4.17 0.00 43.03 4.04
77 78 6.333416 CCAGACTTATGAAGTTCTCAATCGA 58.667 40.000 4.17 0.00 43.03 3.59
78 79 5.521735 CCCAGACTTATGAAGTTCTCAATCG 59.478 44.000 4.17 0.00 43.03 3.34
79 80 6.410540 ACCCAGACTTATGAAGTTCTCAATC 58.589 40.000 4.17 0.00 43.03 2.67
80 81 6.380079 ACCCAGACTTATGAAGTTCTCAAT 57.620 37.500 4.17 0.00 43.03 2.57
81 82 5.566826 CGACCCAGACTTATGAAGTTCTCAA 60.567 44.000 4.17 0.00 43.03 3.02
82 83 4.082190 CGACCCAGACTTATGAAGTTCTCA 60.082 45.833 4.17 0.00 43.03 3.27
83 84 4.158025 TCGACCCAGACTTATGAAGTTCTC 59.842 45.833 4.17 0.00 43.03 2.87
84 85 4.087182 TCGACCCAGACTTATGAAGTTCT 58.913 43.478 4.17 0.00 43.03 3.01
85 86 4.451629 TCGACCCAGACTTATGAAGTTC 57.548 45.455 0.00 0.00 43.03 3.01
86 87 5.422214 AATCGACCCAGACTTATGAAGTT 57.578 39.130 0.00 0.00 43.03 2.66
87 88 5.187967 AGAAATCGACCCAGACTTATGAAGT 59.812 40.000 0.00 0.00 46.38 3.01
88 89 5.521735 CAGAAATCGACCCAGACTTATGAAG 59.478 44.000 0.00 0.00 0.00 3.02
89 90 5.046591 ACAGAAATCGACCCAGACTTATGAA 60.047 40.000 0.00 0.00 0.00 2.57
90 91 4.466370 ACAGAAATCGACCCAGACTTATGA 59.534 41.667 0.00 0.00 0.00 2.15
91 92 4.759782 ACAGAAATCGACCCAGACTTATG 58.240 43.478 0.00 0.00 0.00 1.90
92 93 6.732896 ATACAGAAATCGACCCAGACTTAT 57.267 37.500 0.00 0.00 0.00 1.73
93 94 6.832384 AGTATACAGAAATCGACCCAGACTTA 59.168 38.462 5.50 0.00 0.00 2.24
94 95 5.657302 AGTATACAGAAATCGACCCAGACTT 59.343 40.000 5.50 0.00 0.00 3.01
104 105 6.531594 TCTGAAGTTGCAGTATACAGAAATCG 59.468 38.462 5.50 0.00 37.20 3.34
128 129 8.058915 CAGCGCATACTAGAAAAAGAACTATTC 58.941 37.037 11.47 0.00 0.00 1.75
189 202 5.729665 CACGTTTTGCACAAGATGATAAC 57.270 39.130 0.59 0.00 0.00 1.89
219 232 8.706322 AGGAAAAATTTTCAGTAGAGCCTTAA 57.294 30.769 18.70 0.00 0.00 1.85
248 262 5.254032 ACTCCATAGGAAACCCTCTTCAAAT 59.746 40.000 0.00 0.00 35.26 2.32
255 269 4.410555 AGATCAACTCCATAGGAAACCCTC 59.589 45.833 0.00 0.00 35.26 4.30
259 273 4.517285 TGCAGATCAACTCCATAGGAAAC 58.483 43.478 0.00 0.00 0.00 2.78
268 291 3.539604 ACTAGCATTGCAGATCAACTCC 58.460 45.455 11.91 0.00 37.53 3.85
323 346 4.820716 GCTCTCCTTTTCTGACATGCATAT 59.179 41.667 0.00 0.00 0.00 1.78
327 350 2.709213 AGCTCTCCTTTTCTGACATGC 58.291 47.619 0.00 0.00 0.00 4.06
392 655 9.216117 GTGCCTTTTCTATAGTGTCTTTTCTTA 57.784 33.333 0.00 0.00 0.00 2.10
396 661 6.998673 ACTGTGCCTTTTCTATAGTGTCTTTT 59.001 34.615 0.00 0.00 0.00 2.27
397 662 6.534634 ACTGTGCCTTTTCTATAGTGTCTTT 58.465 36.000 0.00 0.00 0.00 2.52
398 663 6.115448 ACTGTGCCTTTTCTATAGTGTCTT 57.885 37.500 0.00 0.00 0.00 3.01
399 664 5.746990 ACTGTGCCTTTTCTATAGTGTCT 57.253 39.130 0.00 0.00 0.00 3.41
400 665 6.034683 CGTAACTGTGCCTTTTCTATAGTGTC 59.965 42.308 0.00 0.00 0.00 3.67
401 666 5.867716 CGTAACTGTGCCTTTTCTATAGTGT 59.132 40.000 0.00 0.00 0.00 3.55
402 667 5.867716 ACGTAACTGTGCCTTTTCTATAGTG 59.132 40.000 0.00 0.00 0.00 2.74
403 668 5.867716 CACGTAACTGTGCCTTTTCTATAGT 59.132 40.000 0.00 0.00 32.31 2.12
404 669 5.291128 CCACGTAACTGTGCCTTTTCTATAG 59.709 44.000 0.00 0.00 38.55 1.31
405 670 5.172934 CCACGTAACTGTGCCTTTTCTATA 58.827 41.667 0.00 0.00 38.55 1.31
406 671 4.000988 CCACGTAACTGTGCCTTTTCTAT 58.999 43.478 0.00 0.00 38.55 1.98
407 672 3.395639 CCACGTAACTGTGCCTTTTCTA 58.604 45.455 0.00 0.00 38.55 2.10
408 673 2.218603 CCACGTAACTGTGCCTTTTCT 58.781 47.619 0.00 0.00 38.55 2.52
409 674 1.334689 GCCACGTAACTGTGCCTTTTC 60.335 52.381 0.00 0.00 38.55 2.29
450 715 0.038801 TGCAGTGCTCAAGACTCGAG 60.039 55.000 17.60 11.84 0.00 4.04
451 716 0.605083 ATGCAGTGCTCAAGACTCGA 59.395 50.000 17.60 0.00 0.00 4.04
474 739 5.699915 CGTCTGCTGATTGAATAGATGGATT 59.300 40.000 0.00 0.00 0.00 3.01
492 757 6.880822 TCAGTTAATGTAATGTACGTCTGC 57.119 37.500 0.00 0.00 0.00 4.26
494 759 6.198403 CGCATCAGTTAATGTAATGTACGTCT 59.802 38.462 0.00 0.00 0.00 4.18
503 768 5.635549 CGTGATCGCATCAGTTAATGTAA 57.364 39.130 7.12 0.00 40.53 2.41
562 827 1.270625 CGTACTGCAGGGGTTTCTCAA 60.271 52.381 19.93 0.00 0.00 3.02
596 861 0.468226 TGATCCATGGCCGTCCTAAC 59.532 55.000 6.96 0.00 0.00 2.34
652 918 3.133721 ACTGCTCCTAGTGGCTGATTAAG 59.866 47.826 14.53 3.14 0.00 1.85
664 930 2.685388 TCAACTGATCGACTGCTCCTAG 59.315 50.000 0.00 0.00 0.00 3.02
668 934 3.156511 TCATCAACTGATCGACTGCTC 57.843 47.619 0.00 0.00 31.21 4.26
916 1184 0.615331 TAGCTTTGCTGGCTAGTGCT 59.385 50.000 0.00 6.60 40.10 4.40
929 1197 5.338789 GGAATGAAGGAAGGAGAGTAGCTTT 60.339 44.000 0.00 0.00 0.00 3.51
941 1209 1.492599 GGGGAGGAGGAATGAAGGAAG 59.507 57.143 0.00 0.00 0.00 3.46
969 1240 0.682852 CCTGACCGACCAACTTACCA 59.317 55.000 0.00 0.00 0.00 3.25
975 1246 2.047179 GAGGCCTGACCGACCAAC 60.047 66.667 12.00 0.00 46.52 3.77
993 1264 1.748879 CGAACCGCCCATGGTGATT 60.749 57.895 11.73 0.00 42.89 2.57
1050 1321 5.357314 CGAAAACACTAGGAGGAGTATCAGA 59.643 44.000 0.00 0.00 36.25 3.27
1065 1336 1.213094 CTGGCGACGACGAAAACACT 61.213 55.000 12.29 0.00 42.66 3.55
1110 1381 4.079558 TCCTTATAGAACCCTACGGACAGT 60.080 45.833 0.00 0.00 0.00 3.55
1119 1390 4.470304 GGACACAACTCCTTATAGAACCCT 59.530 45.833 0.00 0.00 0.00 4.34
1128 1399 1.073284 GCCTTGGGACACAACTCCTTA 59.927 52.381 0.00 0.00 39.29 2.69
1130 1401 1.456287 GCCTTGGGACACAACTCCT 59.544 57.895 0.00 0.00 39.29 3.69
1221 1492 1.884235 AGCAGTCGTGGAAAAAGAGG 58.116 50.000 0.00 0.00 0.00 3.69
1260 1531 5.931441 ACTCAAACTTAGTGAACATCAGC 57.069 39.130 0.00 0.00 0.00 4.26
1284 1555 1.336148 ACTGCCGTGCAAAACATCATG 60.336 47.619 0.00 0.00 38.41 3.07
1326 1597 6.499350 ACACTGGGTTTATTAAGTCCACTCTA 59.501 38.462 0.00 0.00 0.00 2.43
1338 1609 3.418047 GTGCACCTACACTGGGTTTATT 58.582 45.455 5.22 0.00 37.58 1.40
1383 1654 0.604780 GCATCATGGATCTCCCCGTG 60.605 60.000 0.00 0.00 43.04 4.94
1385 1656 1.206610 CTAGCATCATGGATCTCCCCG 59.793 57.143 0.00 0.00 34.29 5.73
1463 1734 8.901748 CCGTGTGTAAAAATATTTCAGAACTTG 58.098 33.333 0.10 0.00 0.00 3.16
1487 1758 7.273598 CAGGTCAACGAATCATTATATCTACCG 59.726 40.741 0.00 0.00 0.00 4.02
1488 1759 8.304596 TCAGGTCAACGAATCATTATATCTACC 58.695 37.037 0.00 0.00 0.00 3.18
1491 1762 9.613428 TTTTCAGGTCAACGAATCATTATATCT 57.387 29.630 0.00 0.00 0.00 1.98
1505 1776 8.871686 ACAAAATATCAACTTTTCAGGTCAAC 57.128 30.769 0.00 0.00 0.00 3.18
1522 1793 7.807907 ACTTTCGATTTCTCGCAAACAAAATAT 59.192 29.630 0.00 0.00 44.65 1.28
1542 1836 9.777843 GTGTGCATTATTTTCTTTTTACTTTCG 57.222 29.630 0.00 0.00 0.00 3.46
1559 1853 4.058124 GCCTCAAGATATCGTGTGCATTA 58.942 43.478 21.17 4.11 0.00 1.90
1561 1855 2.158914 TGCCTCAAGATATCGTGTGCAT 60.159 45.455 23.24 0.00 33.03 3.96
1562 1856 1.206849 TGCCTCAAGATATCGTGTGCA 59.793 47.619 23.24 23.24 34.40 4.57
1563 1857 1.939974 TGCCTCAAGATATCGTGTGC 58.060 50.000 16.71 18.70 0.00 4.57
1564 1858 6.347969 CCATTTATGCCTCAAGATATCGTGTG 60.348 42.308 16.71 14.31 0.00 3.82
1565 1859 5.702670 CCATTTATGCCTCAAGATATCGTGT 59.297 40.000 16.71 1.96 0.00 4.49
1566 1860 5.934043 TCCATTTATGCCTCAAGATATCGTG 59.066 40.000 11.94 11.94 0.00 4.35
1567 1861 6.114187 TCCATTTATGCCTCAAGATATCGT 57.886 37.500 0.00 0.00 0.00 3.73
1568 1862 6.037940 CCATCCATTTATGCCTCAAGATATCG 59.962 42.308 0.00 0.00 0.00 2.92
1569 1863 6.320672 CCCATCCATTTATGCCTCAAGATATC 59.679 42.308 0.00 0.00 0.00 1.63
1570 1864 6.192773 CCCATCCATTTATGCCTCAAGATAT 58.807 40.000 0.00 0.00 0.00 1.63
1576 1870 6.656965 ATATACCCATCCATTTATGCCTCA 57.343 37.500 0.00 0.00 0.00 3.86
1586 1880 7.090845 ACCTACATCCTCTATATACCCATCCAT 60.091 40.741 0.00 0.00 0.00 3.41
1588 1882 6.551601 CACCTACATCCTCTATATACCCATCC 59.448 46.154 0.00 0.00 0.00 3.51
1589 1883 6.551601 CCACCTACATCCTCTATATACCCATC 59.448 46.154 0.00 0.00 0.00 3.51
1601 1895 3.477210 GATGAACCCACCTACATCCTC 57.523 52.381 0.00 0.00 34.81 3.71
1638 1932 4.632327 TTACACACCATGTTCCTGATCA 57.368 40.909 0.00 0.00 43.19 2.92
1650 1944 4.825085 GGAAGACCTTCAAATTACACACCA 59.175 41.667 11.38 0.00 41.20 4.17
1666 1960 0.169009 GCATGCTCAAACGGAAGACC 59.831 55.000 11.37 0.00 0.00 3.85
1708 2002 3.006752 GGCACTTTTCATGATGGTGGAAA 59.993 43.478 18.31 6.59 0.00 3.13
1721 2015 5.921004 TGCAAATATTTGTGGCACTTTTC 57.079 34.783 25.15 5.66 40.24 2.29
1749 2043 8.637986 TGAAAGCTTGACCAAAGTATAAATGTT 58.362 29.630 0.00 0.00 38.25 2.71
1785 2079 6.651225 GTGCCCAGTATATTCCAATTAGTCTC 59.349 42.308 0.00 0.00 0.00 3.36
1919 2213 2.401766 GGAGGCACCGCACTTCATG 61.402 63.158 0.00 0.00 0.00 3.07
1940 2234 5.995446 AGTGGTAGATCTCAGAATTTTCCC 58.005 41.667 0.00 0.00 0.00 3.97
1943 2237 6.656693 CCACAAGTGGTAGATCTCAGAATTTT 59.343 38.462 11.08 0.00 45.53 1.82
2012 2306 2.890945 GCTTAACAAGAAGCCTCCCAAA 59.109 45.455 0.00 0.00 45.08 3.28
2043 2337 3.284617 ACGGCAAGTTAACCTCAAAAGT 58.715 40.909 0.88 0.00 0.00 2.66
2050 2344 6.481434 AGAATATAGACGGCAAGTTAACCT 57.519 37.500 0.88 0.00 0.00 3.50
2061 2355 6.856938 CGAGACAAAACCTAGAATATAGACGG 59.143 42.308 0.00 0.00 0.00 4.79
2063 2357 7.201145 TGCGAGACAAAACCTAGAATATAGAC 58.799 38.462 0.00 0.00 0.00 2.59
2065 2359 7.426410 TCTGCGAGACAAAACCTAGAATATAG 58.574 38.462 0.00 0.00 0.00 1.31
2075 2369 5.803020 ATATCTTTCTGCGAGACAAAACC 57.197 39.130 0.00 0.00 0.00 3.27
2133 2427 8.903570 TTCTGTGTTTTGTGTACTTGTTATTG 57.096 30.769 0.00 0.00 0.00 1.90
2146 2441 6.981762 TTTGCATTTCATTCTGTGTTTTGT 57.018 29.167 0.00 0.00 0.00 2.83
2156 2451 6.064525 GCAACTTACGTTTTGCATTTCATTC 58.935 36.000 18.89 0.00 46.13 2.67
2171 2466 9.885743 GCTATTTTATTTTCAATGCAACTTACG 57.114 29.630 0.00 0.00 0.00 3.18
2198 2493 6.003950 AGGTTGCACATTTCTTGTATGTACT 58.996 36.000 0.00 0.00 36.57 2.73
2255 2550 8.709308 AGGATGTTATCTGAGTTGCTAGTTTAT 58.291 33.333 0.00 0.00 0.00 1.40
2394 2700 8.786937 TGAGTAAAGTTAAGTAGTTACACACG 57.213 34.615 7.36 0.00 0.00 4.49
2563 2871 2.167487 GGTTTGTGGGCAAAGTTTCTCA 59.833 45.455 0.00 0.00 44.27 3.27
2626 2934 2.586792 CCGCTAGCAAGGAAGGCT 59.413 61.111 16.45 0.00 45.18 4.58
2635 2943 1.528542 ATAGTCGAGCCCGCTAGCA 60.529 57.895 16.45 0.00 35.37 3.49
2733 3041 4.274459 AGTTTTCGATAAGCTGATCATGGC 59.726 41.667 11.79 0.00 0.00 4.40
2801 3109 2.472695 ATGTGGTTGTGCACGACTAT 57.527 45.000 31.23 21.26 35.21 2.12
2908 3216 7.218773 GTGTCATGCATTTGTGTTGTATATGTC 59.781 37.037 0.00 0.00 0.00 3.06
3044 3352 9.955208 CACAATATACGCCCGTTAGATATTATA 57.045 33.333 0.00 0.00 0.00 0.98
3045 3353 8.689061 TCACAATATACGCCCGTTAGATATTAT 58.311 33.333 0.00 0.00 0.00 1.28
3046 3354 7.970061 GTCACAATATACGCCCGTTAGATATTA 59.030 37.037 0.00 0.00 0.00 0.98
3047 3355 6.810182 GTCACAATATACGCCCGTTAGATATT 59.190 38.462 0.00 0.59 0.00 1.28
3048 3356 6.071784 TGTCACAATATACGCCCGTTAGATAT 60.072 38.462 0.00 0.00 0.00 1.63
3089 3399 5.705609 ACCTGTACATTAAACAAAGGCTG 57.294 39.130 0.00 0.00 0.00 4.85
3120 3432 1.080230 CAGTGTCACCAGCTCCTCG 60.080 63.158 0.00 0.00 0.00 4.63
3177 3489 1.569708 TGTACAAACGGTCCGTGAAC 58.430 50.000 19.67 13.78 39.99 3.18
3252 3564 0.032130 ACTTCTTCTTGAGACGCGCA 59.968 50.000 5.73 0.00 33.02 6.09
3258 3570 1.000955 GGCGGACACTTCTTCTTGAGA 59.999 52.381 0.00 0.00 0.00 3.27
3333 3645 2.859165 ACTGGTTGTCCATCACGAAT 57.141 45.000 0.00 0.00 43.43 3.34
3426 3738 2.513204 TAGAGGTCGACGAGGGCG 60.513 66.667 9.92 0.00 44.79 6.13
3459 3771 0.824759 ATCGCTTGGTCCAGTAGTCC 59.175 55.000 0.00 0.00 0.00 3.85
3499 3811 2.161486 GCACGTCCATCTCGCTGAC 61.161 63.158 0.00 0.00 0.00 3.51
3505 3817 0.459237 CCAGTGAGCACGTCCATCTC 60.459 60.000 0.00 0.00 36.20 2.75
3522 3834 2.614969 ATCTCCCCCTTGCTGCCA 60.615 61.111 0.00 0.00 0.00 4.92
3529 3841 0.253347 TTCAGCCTGATCTCCCCCTT 60.253 55.000 0.00 0.00 0.00 3.95
3588 3900 0.874390 GAGACAAACGCAGCATTCCA 59.126 50.000 0.00 0.00 0.00 3.53
3589 3901 1.135859 CAGAGACAAACGCAGCATTCC 60.136 52.381 0.00 0.00 0.00 3.01
3590 3902 1.532868 ACAGAGACAAACGCAGCATTC 59.467 47.619 0.00 0.00 0.00 2.67
3591 3903 1.597742 ACAGAGACAAACGCAGCATT 58.402 45.000 0.00 0.00 0.00 3.56
3592 3904 2.455674 TACAGAGACAAACGCAGCAT 57.544 45.000 0.00 0.00 0.00 3.79
3719 4034 8.437360 TCACAACTCAAATCGAATAATATGCT 57.563 30.769 0.00 0.00 0.00 3.79
3726 4041 8.563732 TGTCAAATTCACAACTCAAATCGAATA 58.436 29.630 0.00 0.00 0.00 1.75
3776 4091 7.201496 GGAAATGTACAAACATGACGTAGTAGG 60.201 40.741 0.00 0.00 44.12 3.18
3809 4124 9.541143 TGATAGTAGTCGAATCAAATGCATAAA 57.459 29.630 0.00 0.00 0.00 1.40
3831 4146 8.675705 TTCATCAAGAAGTTCACAAAGTGATA 57.324 30.769 5.50 0.00 42.40 2.15
3850 4165 9.699410 ATACCTAAAATCTGAACCATTTCATCA 57.301 29.630 0.00 0.00 41.05 3.07
3875 4190 6.208599 ACCACAGTTCAATAAAACATCCGAAT 59.791 34.615 0.00 0.00 0.00 3.34
3889 4204 3.469008 ACTTGATCGACCACAGTTCAA 57.531 42.857 0.00 0.00 0.00 2.69
3916 4231 4.499019 CCTTTGGTTGCGATTGTGTTAACT 60.499 41.667 7.22 0.00 0.00 2.24
3938 4253 0.254462 AGGAAGGCTCTAGCTTTGCC 59.746 55.000 13.39 14.11 46.64 4.52
3942 4257 1.557371 GGTTGAGGAAGGCTCTAGCTT 59.443 52.381 0.00 0.00 41.70 3.74
3979 4294 0.533951 CCATTGCCCTTCTTCTTGCC 59.466 55.000 0.00 0.00 0.00 4.52
3982 4297 6.475596 CAATAATCCATTGCCCTTCTTCTT 57.524 37.500 0.00 0.00 37.80 2.52
4022 4337 9.872721 TTCATGCAAATTCTTAAGCATCATTTA 57.127 25.926 0.00 0.00 45.14 1.40
4055 4370 9.198837 GGATTTGTCGGTATTGTATTTTTGTTT 57.801 29.630 0.00 0.00 0.00 2.83
4056 4371 7.815549 GGGATTTGTCGGTATTGTATTTTTGTT 59.184 33.333 0.00 0.00 0.00 2.83
4057 4372 7.177744 AGGGATTTGTCGGTATTGTATTTTTGT 59.822 33.333 0.00 0.00 0.00 2.83
4058 4373 7.543756 AGGGATTTGTCGGTATTGTATTTTTG 58.456 34.615 0.00 0.00 0.00 2.44
4071 4416 2.717639 AAGATGGAGGGATTTGTCGG 57.282 50.000 0.00 0.00 0.00 4.79
4072 4417 3.134458 GCTAAGATGGAGGGATTTGTCG 58.866 50.000 0.00 0.00 0.00 4.35
4092 4437 5.183904 ACAATTTGGTCTATCTGAAAGTGGC 59.816 40.000 0.78 0.00 33.76 5.01
4108 4453 3.309506 TGGGCGGGCACAATTTGG 61.310 61.111 3.27 0.00 0.00 3.28
4124 4469 4.641396 TGTGGTCAATCTAACAGAAGGTG 58.359 43.478 0.00 0.00 0.00 4.00
4130 4475 7.424803 TGTCAATTTTGTGGTCAATCTAACAG 58.575 34.615 0.00 0.00 33.32 3.16
4134 4479 7.581213 ACTTGTCAATTTTGTGGTCAATCTA 57.419 32.000 0.00 0.00 33.32 1.98
4137 4482 8.257306 AGTTTACTTGTCAATTTTGTGGTCAAT 58.743 29.630 0.00 0.00 33.32 2.57
4230 4575 5.406649 TGTTTGCCAGTTGTTTTCTGTAAG 58.593 37.500 0.00 0.00 0.00 2.34
4245 4590 2.297033 GCTTCTCTGGAATTGTTTGCCA 59.703 45.455 0.00 0.00 0.00 4.92
4260 4605 6.963796 TCAAAAATGAAACTGAGAGCTTCTC 58.036 36.000 6.31 6.31 43.65 2.87
4261 4606 6.949352 TCAAAAATGAAACTGAGAGCTTCT 57.051 33.333 0.00 0.00 0.00 2.85
4262 4607 7.199078 ACTTCAAAAATGAAACTGAGAGCTTC 58.801 34.615 0.00 0.00 0.00 3.86
4271 4616 8.527810 TGACACCTTAACTTCAAAAATGAAACT 58.472 29.630 0.00 0.00 0.00 2.66
4286 4631 4.722361 TGGTTTTTGGTGACACCTTAAC 57.278 40.909 24.81 21.81 42.67 2.01
4314 4659 4.437930 GCATCATTTCTGGAGTTTTCGAGG 60.438 45.833 0.00 0.00 30.80 4.63
4344 4689 2.110967 CGCAAGCAGAGTGGGATGG 61.111 63.158 0.00 0.00 0.00 3.51
4346 4691 1.078848 GTCGCAAGCAGAGTGGGAT 60.079 57.895 0.00 0.00 39.74 3.85
4368 4713 1.146774 TGGACATTGGGGAAAGAGCAA 59.853 47.619 0.00 0.00 0.00 3.91
4382 4727 3.091633 AGCTTTACCTGCATTGGACAT 57.908 42.857 0.00 0.00 0.00 3.06
4404 4749 9.119418 GCCCAAATATTTATGTAAAATTGCCTT 57.881 29.630 0.00 0.00 0.00 4.35
4416 4761 9.590451 CCAATATAGCAAGCCCAAATATTTATG 57.410 33.333 0.00 0.00 0.00 1.90
4429 4774 6.947464 TCTAAGGGTATCCAATATAGCAAGC 58.053 40.000 0.00 0.00 34.83 4.01
4483 4828 7.170998 AGTCGAGAAGATGTTTAAAACAATCGT 59.829 33.333 0.00 0.00 45.86 3.73
4491 4836 7.439955 TGCTTACAAGTCGAGAAGATGTTTAAA 59.560 33.333 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.