Multiple sequence alignment - TraesCS2A01G200600

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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 TraesCS2A01G200600 chr2A 100.000 1446 0 0 563 2008 173508888 173507443 0.000000e+00 2671.0
1 TraesCS2A01G200600 chr2A 100.000 1182 0 0 2308 3489 173507143 173505962 0.000000e+00 2183.0
2 TraesCS2A01G200600 chr2A 100.000 169 0 0 1 169 173509450 173509282 2.610000e-81 313.0
3 TraesCS2A01G200600 chr2A 74.009 227 45 12 1790 2006 61823549 61823771 2.890000e-11 80.5
4 TraesCS2A01G200600 chr2A 93.333 45 0 3 1791 1835 551228571 551228612 2.910000e-06 63.9
5 TraesCS2A01G200600 chr2D 95.481 1195 39 2 2310 3489 162506244 162505050 0.000000e+00 1893.0
6 TraesCS2A01G200600 chr2D 91.281 1101 58 22 712 1791 162507414 162506331 0.000000e+00 1467.0
7 TraesCS2A01G200600 chr2D 93.865 163 9 1 564 726 162507591 162507430 9.670000e-61 244.0
8 TraesCS2A01G200600 chr2B 93.579 1059 43 6 2311 3349 221925927 221924874 0.000000e+00 1555.0
9 TraesCS2A01G200600 chr2B 93.548 620 28 6 750 1365 221926560 221925949 0.000000e+00 913.0
10 TraesCS2A01G200600 chr2B 99.281 139 1 0 3351 3489 221924789 221924651 5.780000e-63 252.0
11 TraesCS2A01G200600 chr2B 93.805 113 6 1 582 694 221930556 221930445 5.990000e-38 169.0
12 TraesCS2A01G200600 chr7D 88.444 225 19 2 1791 2008 167576455 167576231 7.430000e-67 265.0
13 TraesCS2A01G200600 chr7D 89.091 55 6 0 1524 1578 85838715 85838661 6.250000e-08 69.4
14 TraesCS2A01G200600 chr3B 75.877 228 47 7 1788 2008 815183193 815183419 3.680000e-20 110.0
15 TraesCS2A01G200600 chr5A 92.453 53 4 0 1526 1578 159060320 159060372 3.730000e-10 76.8
16 TraesCS2A01G200600 chr5A 92.157 51 4 0 1528 1578 611651708 611651658 4.830000e-09 73.1
17 TraesCS2A01G200600 chr4D 93.878 49 3 0 1530 1578 484354669 484354717 1.340000e-09 75.0
18 TraesCS2A01G200600 chr1D 93.878 49 3 0 1530 1578 47644740 47644788 1.340000e-09 75.0
19 TraesCS2A01G200600 chr1D 93.878 49 3 0 1530 1578 423270281 423270233 1.340000e-09 75.0
20 TraesCS2A01G200600 chr4B 89.286 56 5 1 1523 1578 144029246 144029300 6.250000e-08 69.4
21 TraesCS2A01G200600 chr4B 89.286 56 5 1 1523 1578 144597369 144597423 6.250000e-08 69.4


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 TraesCS2A01G200600 chr2A 173505962 173509450 3488 True 1722.333333 2671 100.000000 1 3489 3 chr2A.!!$R1 3488
1 TraesCS2A01G200600 chr2D 162505050 162507591 2541 True 1201.333333 1893 93.542333 564 3489 3 chr2D.!!$R1 2925
2 TraesCS2A01G200600 chr2B 221924651 221930556 5905 True 722.250000 1555 95.053250 582 3489 4 chr2B.!!$R1 2907

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
26 27 0.029167 GAACCCTAGCGAGTACGAGC 59.971 60.0 7.40 7.4 42.66 5.03 F
1640 5488 0.028505 CAATGGAATTCTCGCCGCAG 59.971 55.0 5.23 0.0 31.22 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 5729 0.035739 GTTGGGTTAACGAGCCTCCA 59.964 55.000 0.0 0.0 46.39 3.86 R
2811 6690 1.674441 CCCGTCTTGTAGATGCGAGTA 59.326 52.381 0.0 0.0 29.93 2.59 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
18 19 3.212377 ATAACCCGAACCCTAGCGA 57.788 52.632 0.00 0.00 0.00 4.93
19 20 1.038280 ATAACCCGAACCCTAGCGAG 58.962 55.000 0.00 0.00 0.00 5.03
20 21 0.323725 TAACCCGAACCCTAGCGAGT 60.324 55.000 0.00 0.00 0.00 4.18
21 22 0.323725 AACCCGAACCCTAGCGAGTA 60.324 55.000 0.00 0.00 0.00 2.59
22 23 1.034292 ACCCGAACCCTAGCGAGTAC 61.034 60.000 0.00 0.00 0.00 2.73
23 24 1.354506 CCGAACCCTAGCGAGTACG 59.645 63.158 0.00 0.00 42.93 3.67
24 25 1.091771 CCGAACCCTAGCGAGTACGA 61.092 60.000 0.00 0.00 42.66 3.43
25 26 0.304098 CGAACCCTAGCGAGTACGAG 59.696 60.000 0.00 0.00 42.66 4.18
26 27 0.029167 GAACCCTAGCGAGTACGAGC 59.971 60.000 7.40 7.40 42.66 5.03
27 28 0.394080 AACCCTAGCGAGTACGAGCT 60.394 55.000 19.11 19.11 46.53 4.09
28 29 0.394080 ACCCTAGCGAGTACGAGCTT 60.394 55.000 20.06 7.73 44.15 3.74
29 30 0.029567 CCCTAGCGAGTACGAGCTTG 59.970 60.000 20.06 17.67 44.15 4.01
30 31 0.029567 CCTAGCGAGTACGAGCTTGG 59.970 60.000 22.75 22.75 46.27 3.61
31 32 0.733729 CTAGCGAGTACGAGCTTGGT 59.266 55.000 20.06 0.96 44.15 3.67
32 33 0.450583 TAGCGAGTACGAGCTTGGTG 59.549 55.000 20.06 0.00 44.15 4.17
33 34 1.211969 GCGAGTACGAGCTTGGTGA 59.788 57.895 5.79 0.00 42.66 4.02
34 35 0.798771 GCGAGTACGAGCTTGGTGAG 60.799 60.000 5.79 0.00 42.66 3.51
42 43 2.435059 GCTTGGTGAGCCGAGTCC 60.435 66.667 3.16 0.00 46.07 3.85
43 44 2.266055 CTTGGTGAGCCGAGTCCC 59.734 66.667 0.00 0.00 40.67 4.46
44 45 2.525629 TTGGTGAGCCGAGTCCCA 60.526 61.111 0.00 0.00 37.67 4.37
45 46 2.111999 CTTGGTGAGCCGAGTCCCAA 62.112 60.000 0.00 0.00 40.67 4.12
46 47 2.047179 GGTGAGCCGAGTCCCAAC 60.047 66.667 0.00 0.00 0.00 3.77
47 48 2.741092 GTGAGCCGAGTCCCAACA 59.259 61.111 0.00 0.00 0.00 3.33
48 49 1.070786 GTGAGCCGAGTCCCAACAA 59.929 57.895 0.00 0.00 0.00 2.83
49 50 1.070786 TGAGCCGAGTCCCAACAAC 59.929 57.895 0.00 0.00 0.00 3.32
50 51 1.671379 GAGCCGAGTCCCAACAACC 60.671 63.158 0.00 0.00 0.00 3.77
51 52 2.113243 GAGCCGAGTCCCAACAACCT 62.113 60.000 0.00 0.00 0.00 3.50
52 53 1.966451 GCCGAGTCCCAACAACCTG 60.966 63.158 0.00 0.00 0.00 4.00
53 54 1.752198 CCGAGTCCCAACAACCTGA 59.248 57.895 0.00 0.00 0.00 3.86
54 55 0.107831 CCGAGTCCCAACAACCTGAA 59.892 55.000 0.00 0.00 0.00 3.02
55 56 1.226746 CGAGTCCCAACAACCTGAAC 58.773 55.000 0.00 0.00 0.00 3.18
56 57 1.474320 CGAGTCCCAACAACCTGAACA 60.474 52.381 0.00 0.00 0.00 3.18
57 58 2.222027 GAGTCCCAACAACCTGAACAG 58.778 52.381 0.00 0.00 0.00 3.16
58 59 1.843851 AGTCCCAACAACCTGAACAGA 59.156 47.619 3.19 0.00 0.00 3.41
59 60 2.443255 AGTCCCAACAACCTGAACAGAT 59.557 45.455 3.19 0.00 0.00 2.90
60 61 3.117512 AGTCCCAACAACCTGAACAGATT 60.118 43.478 3.19 0.00 0.00 2.40
61 62 3.004734 GTCCCAACAACCTGAACAGATTG 59.995 47.826 7.30 7.30 0.00 2.67
62 63 2.958355 CCCAACAACCTGAACAGATTGT 59.042 45.455 8.56 8.56 36.86 2.71
63 64 3.384467 CCCAACAACCTGAACAGATTGTT 59.616 43.478 18.17 18.17 44.37 2.83
64 65 4.582656 CCCAACAACCTGAACAGATTGTTA 59.417 41.667 21.86 0.00 41.28 2.41
65 66 5.068460 CCCAACAACCTGAACAGATTGTTAA 59.932 40.000 21.86 0.00 41.28 2.01
66 67 6.239289 CCCAACAACCTGAACAGATTGTTAAT 60.239 38.462 21.86 3.55 41.28 1.40
67 68 6.863126 CCAACAACCTGAACAGATTGTTAATC 59.137 38.462 21.86 0.00 41.28 1.75
68 69 6.575162 ACAACCTGAACAGATTGTTAATCC 57.425 37.500 8.56 0.00 41.28 3.01
69 70 6.068010 ACAACCTGAACAGATTGTTAATCCA 58.932 36.000 8.56 0.00 41.28 3.41
70 71 6.016276 ACAACCTGAACAGATTGTTAATCCAC 60.016 38.462 8.56 0.00 41.28 4.02
71 72 5.880901 ACCTGAACAGATTGTTAATCCACT 58.119 37.500 3.19 0.00 41.28 4.00
72 73 7.016153 ACCTGAACAGATTGTTAATCCACTA 57.984 36.000 3.19 0.00 41.28 2.74
73 74 6.879458 ACCTGAACAGATTGTTAATCCACTAC 59.121 38.462 3.19 0.00 41.28 2.73
74 75 7.106239 CCTGAACAGATTGTTAATCCACTACT 58.894 38.462 3.19 0.00 41.28 2.57
75 76 7.278868 CCTGAACAGATTGTTAATCCACTACTC 59.721 40.741 3.19 0.00 41.28 2.59
76 77 7.907389 TGAACAGATTGTTAATCCACTACTCT 58.093 34.615 0.00 0.00 41.28 3.24
77 78 8.375506 TGAACAGATTGTTAATCCACTACTCTT 58.624 33.333 0.00 0.00 41.28 2.85
78 79 9.220767 GAACAGATTGTTAATCCACTACTCTTT 57.779 33.333 0.00 0.00 41.28 2.52
79 80 9.574516 AACAGATTGTTAATCCACTACTCTTTT 57.425 29.630 0.00 0.00 39.09 2.27
99 100 9.717892 CTCTTTTATCTTTTTAGAATTACCGCC 57.282 33.333 0.00 0.00 0.00 6.13
100 101 9.233649 TCTTTTATCTTTTTAGAATTACCGCCA 57.766 29.630 0.00 0.00 0.00 5.69
101 102 9.503427 CTTTTATCTTTTTAGAATTACCGCCAG 57.497 33.333 0.00 0.00 0.00 4.85
102 103 8.570068 TTTATCTTTTTAGAATTACCGCCAGT 57.430 30.769 0.00 0.00 0.00 4.00
103 104 8.570068 TTATCTTTTTAGAATTACCGCCAGTT 57.430 30.769 0.00 0.00 0.00 3.16
104 105 6.887626 TCTTTTTAGAATTACCGCCAGTTT 57.112 33.333 0.00 0.00 0.00 2.66
105 106 6.674066 TCTTTTTAGAATTACCGCCAGTTTG 58.326 36.000 0.00 0.00 0.00 2.93
106 107 6.263617 TCTTTTTAGAATTACCGCCAGTTTGT 59.736 34.615 0.00 0.00 0.00 2.83
107 108 5.365403 TTTAGAATTACCGCCAGTTTGTG 57.635 39.130 0.00 0.00 0.00 3.33
108 109 2.858745 AGAATTACCGCCAGTTTGTGT 58.141 42.857 0.00 0.00 0.00 3.72
109 110 3.219281 AGAATTACCGCCAGTTTGTGTT 58.781 40.909 0.00 0.00 0.00 3.32
110 111 3.634910 AGAATTACCGCCAGTTTGTGTTT 59.365 39.130 0.00 0.00 0.00 2.83
111 112 4.098807 AGAATTACCGCCAGTTTGTGTTTT 59.901 37.500 0.00 0.00 0.00 2.43
112 113 5.299782 AGAATTACCGCCAGTTTGTGTTTTA 59.700 36.000 0.00 0.00 0.00 1.52
113 114 4.555348 TTACCGCCAGTTTGTGTTTTAG 57.445 40.909 0.00 0.00 0.00 1.85
114 115 2.645802 ACCGCCAGTTTGTGTTTTAGA 58.354 42.857 0.00 0.00 0.00 2.10
115 116 3.018149 ACCGCCAGTTTGTGTTTTAGAA 58.982 40.909 0.00 0.00 0.00 2.10
116 117 3.181494 ACCGCCAGTTTGTGTTTTAGAAC 60.181 43.478 0.00 0.00 36.29 3.01
117 118 3.066203 CCGCCAGTTTGTGTTTTAGAACT 59.934 43.478 0.00 0.00 36.70 3.01
118 119 4.273969 CCGCCAGTTTGTGTTTTAGAACTA 59.726 41.667 0.00 0.00 36.70 2.24
119 120 5.202640 CGCCAGTTTGTGTTTTAGAACTAC 58.797 41.667 0.00 0.00 36.70 2.73
120 121 5.516996 GCCAGTTTGTGTTTTAGAACTACC 58.483 41.667 0.00 0.00 36.70 3.18
121 122 5.744490 CCAGTTTGTGTTTTAGAACTACCG 58.256 41.667 0.00 0.00 36.70 4.02
122 123 5.202640 CAGTTTGTGTTTTAGAACTACCGC 58.797 41.667 0.00 0.00 36.70 5.68
123 124 5.007332 CAGTTTGTGTTTTAGAACTACCGCT 59.993 40.000 0.00 0.00 36.70 5.52
124 125 5.587443 AGTTTGTGTTTTAGAACTACCGCTT 59.413 36.000 0.00 0.00 36.70 4.68
125 126 6.762661 AGTTTGTGTTTTAGAACTACCGCTTA 59.237 34.615 0.00 0.00 36.70 3.09
126 127 6.774354 TTGTGTTTTAGAACTACCGCTTAG 57.226 37.500 0.00 0.00 36.70 2.18
127 128 5.846203 TGTGTTTTAGAACTACCGCTTAGT 58.154 37.500 0.00 0.00 43.46 2.24
157 158 9.632807 TTTCGTTCTTTTTCTTTTGAGAAATGA 57.367 25.926 2.77 2.87 37.59 2.57
158 159 9.632807 TTCGTTCTTTTTCTTTTGAGAAATGAA 57.367 25.926 2.77 7.66 37.59 2.57
159 160 9.072294 TCGTTCTTTTTCTTTTGAGAAATGAAC 57.928 29.630 21.83 21.83 41.46 3.18
160 161 9.076596 CGTTCTTTTTCTTTTGAGAAATGAACT 57.923 29.630 24.81 0.00 41.93 3.01
594 595 6.475596 TTAGTAGTACTACTGAAATGGGCC 57.524 41.667 35.52 7.98 45.25 5.80
596 597 2.846950 AGTACTACTGAAATGGGCCCT 58.153 47.619 25.70 1.15 0.00 5.19
631 632 0.323725 AATGACTGCATCGGCCCTTT 60.324 50.000 0.00 0.00 40.13 3.11
708 4481 5.246307 CAATTCCTTTCTCGGTAGACCTTT 58.754 41.667 0.00 0.00 0.00 3.11
709 4482 3.955650 TCCTTTCTCGGTAGACCTTTG 57.044 47.619 0.00 0.00 0.00 2.77
710 4483 2.028385 TCCTTTCTCGGTAGACCTTTGC 60.028 50.000 0.00 0.00 0.00 3.68
711 4484 2.289444 CCTTTCTCGGTAGACCTTTGCA 60.289 50.000 0.00 0.00 0.00 4.08
712 4485 2.450609 TTCTCGGTAGACCTTTGCAC 57.549 50.000 0.00 0.00 0.00 4.57
713 4486 1.334160 TCTCGGTAGACCTTTGCACA 58.666 50.000 0.00 0.00 0.00 4.57
726 4528 2.686558 TTGCACAAATTCAGTCGAGC 57.313 45.000 0.00 0.00 0.00 5.03
727 4529 0.874390 TGCACAAATTCAGTCGAGCC 59.126 50.000 0.00 0.00 0.00 4.70
755 4557 1.270041 GCCGAGATCCTGTCTGAATCC 60.270 57.143 0.00 0.00 37.29 3.01
778 4608 1.016627 TATTTCTCCACGCTGCATGC 58.983 50.000 11.82 11.82 38.57 4.06
813 4643 0.809385 TTTGTTCGCAACCCAAACGA 59.191 45.000 0.00 0.00 36.74 3.85
816 4646 1.451567 TTCGCAACCCAAACGACCA 60.452 52.632 0.00 0.00 35.20 4.02
821 4651 4.636435 ACCCAAACGACCAGCCGG 62.636 66.667 0.00 0.00 38.77 6.13
871 4701 2.097918 CTCGAGTCGAACGTCCCG 59.902 66.667 17.27 0.00 34.74 5.14
913 4743 6.347806 CGTATCCTCTACATATATAGCCTGCG 60.348 46.154 0.00 0.00 0.00 5.18
931 4761 0.034059 CGTTTGCCTCTCAGACCACT 59.966 55.000 0.00 0.00 0.00 4.00
933 4763 1.346068 GTTTGCCTCTCAGACCACTCT 59.654 52.381 0.00 0.00 0.00 3.24
954 4787 1.229658 AGGTCCCTCCAGTTCCCAG 60.230 63.158 0.00 0.00 39.02 4.45
957 4790 1.463214 TCCCTCCAGTTCCCAGCAA 60.463 57.895 0.00 0.00 0.00 3.91
959 4792 1.455849 CCTCCAGTTCCCAGCAACA 59.544 57.895 0.00 0.00 0.00 3.33
960 4793 0.038744 CCTCCAGTTCCCAGCAACAT 59.961 55.000 0.00 0.00 0.00 2.71
961 4794 1.548582 CCTCCAGTTCCCAGCAACATT 60.549 52.381 0.00 0.00 0.00 2.71
1354 5192 3.462483 TGGTAAGCTTTCACGTCTCAA 57.538 42.857 3.20 0.00 0.00 3.02
1361 5199 2.821546 CTTTCACGTCTCAACTCACCA 58.178 47.619 0.00 0.00 0.00 4.17
1384 5231 4.087892 CCCGCCTCACCTCACCTG 62.088 72.222 0.00 0.00 0.00 4.00
1442 5290 1.408969 TCACGGGTGCTCATATGCTA 58.591 50.000 0.00 0.00 0.00 3.49
1443 5291 1.970640 TCACGGGTGCTCATATGCTAT 59.029 47.619 0.00 0.00 0.00 2.97
1484 5332 4.608058 GCAAATGTTTGTGCAAAAATAGCG 59.392 37.500 5.11 0.00 40.58 4.26
1496 5344 0.248289 AAATAGCGGTGTACGTGCCT 59.752 50.000 0.00 0.00 46.52 4.75
1500 5348 1.957186 GCGGTGTACGTGCCTGAAA 60.957 57.895 0.00 0.00 46.52 2.69
1540 5388 6.403878 TGCTAACTTTATGTTGTACTCCCTC 58.596 40.000 0.00 0.00 39.55 4.30
1541 5389 6.212791 TGCTAACTTTATGTTGTACTCCCTCT 59.787 38.462 0.00 0.00 39.55 3.69
1566 5414 6.929049 TGTCCCATAATATAAGAGCGTTTCTG 59.071 38.462 0.00 0.00 35.91 3.02
1595 5443 6.027025 AGTGTATAATCCCTGTCTAGTGGA 57.973 41.667 0.00 0.00 0.00 4.02
1596 5444 6.441222 AGTGTATAATCCCTGTCTAGTGGAA 58.559 40.000 0.00 0.00 30.40 3.53
1599 5447 2.254152 ATCCCTGTCTAGTGGAAGCA 57.746 50.000 0.00 0.00 30.40 3.91
1600 5448 1.561643 TCCCTGTCTAGTGGAAGCAG 58.438 55.000 0.00 0.00 0.00 4.24
1617 5465 3.871485 AGCAGATTGTCAGGAGTTGATC 58.129 45.455 0.00 0.00 38.29 2.92
1619 5467 4.005650 GCAGATTGTCAGGAGTTGATCAA 58.994 43.478 3.38 3.38 38.29 2.57
1637 5485 2.613595 TCAATCAATGGAATTCTCGCCG 59.386 45.455 5.23 0.00 31.22 6.46
1638 5486 0.947244 ATCAATGGAATTCTCGCCGC 59.053 50.000 5.23 0.00 31.22 6.53
1639 5487 0.392327 TCAATGGAATTCTCGCCGCA 60.392 50.000 5.23 0.00 31.22 5.69
1640 5488 0.028505 CAATGGAATTCTCGCCGCAG 59.971 55.000 5.23 0.00 31.22 5.18
1641 5489 1.718757 AATGGAATTCTCGCCGCAGC 61.719 55.000 5.23 0.00 0.00 5.25
1642 5490 2.512515 GGAATTCTCGCCGCAGCT 60.513 61.111 5.23 0.00 36.60 4.24
1643 5491 2.529619 GGAATTCTCGCCGCAGCTC 61.530 63.158 5.23 0.00 36.60 4.09
1644 5492 2.512515 AATTCTCGCCGCAGCTCC 60.513 61.111 0.00 0.00 36.60 4.70
1652 5500 2.982130 CCGCAGCTCCCTGTTAGT 59.018 61.111 0.00 0.00 41.26 2.24
1659 5507 0.250727 GCTCCCTGTTAGTTGTGGCA 60.251 55.000 0.00 0.00 0.00 4.92
1661 5509 1.072331 CTCCCTGTTAGTTGTGGCACT 59.928 52.381 19.83 0.54 0.00 4.40
1666 5522 3.557898 CCTGTTAGTTGTGGCACTGATCT 60.558 47.826 19.83 13.08 0.00 2.75
1708 5567 3.074412 GCCTCATCGTTTTCCTCTTTCA 58.926 45.455 0.00 0.00 0.00 2.69
1709 5568 3.691609 GCCTCATCGTTTTCCTCTTTCAT 59.308 43.478 0.00 0.00 0.00 2.57
1711 5570 5.354234 GCCTCATCGTTTTCCTCTTTCATAA 59.646 40.000 0.00 0.00 0.00 1.90
1715 5574 7.684670 TCATCGTTTTCCTCTTTCATAATTCG 58.315 34.615 0.00 0.00 0.00 3.34
1718 5577 5.952064 CGTTTTCCTCTTTCATAATTCGACG 59.048 40.000 0.00 0.00 0.00 5.12
1736 5596 3.121126 CGACGTGTTTACAGTCACCAATC 60.121 47.826 0.00 0.00 33.18 2.67
1791 5651 2.936498 CGCTGATGGTAATCGGAAGTTT 59.064 45.455 0.00 0.00 41.12 2.66
1792 5652 3.374058 CGCTGATGGTAATCGGAAGTTTT 59.626 43.478 0.00 0.00 41.12 2.43
1816 5676 5.708736 TTTAAGGAAGGCCATCATGACTA 57.291 39.130 10.67 0.00 36.29 2.59
1818 5678 1.419387 AGGAAGGCCATCATGACTAGC 59.581 52.381 10.67 0.63 36.29 3.42
1820 5680 2.158696 GGAAGGCCATCATGACTAGCTT 60.159 50.000 10.67 0.00 0.00 3.74
1821 5681 3.549794 GAAGGCCATCATGACTAGCTTT 58.450 45.455 5.01 3.93 0.00 3.51
1824 5684 5.316158 AGGCCATCATGACTAGCTTTATT 57.684 39.130 5.01 0.00 0.00 1.40
1826 5686 6.234177 AGGCCATCATGACTAGCTTTATTAC 58.766 40.000 5.01 0.00 0.00 1.89
1827 5687 5.997746 GGCCATCATGACTAGCTTTATTACA 59.002 40.000 0.00 0.00 0.00 2.41
1829 5689 7.355778 GCCATCATGACTAGCTTTATTACAAC 58.644 38.462 0.00 0.00 0.00 3.32
1830 5690 7.227512 GCCATCATGACTAGCTTTATTACAACT 59.772 37.037 0.00 0.00 0.00 3.16
1831 5691 9.113838 CCATCATGACTAGCTTTATTACAACTT 57.886 33.333 0.00 0.00 0.00 2.66
1872 5732 9.528489 AAAAGTTTAGGAATAATACAAGCTGGA 57.472 29.630 0.00 0.00 0.00 3.86
1873 5733 8.738645 AAGTTTAGGAATAATACAAGCTGGAG 57.261 34.615 0.00 0.00 0.00 3.86
1874 5734 7.283329 AGTTTAGGAATAATACAAGCTGGAGG 58.717 38.462 0.00 0.00 0.00 4.30
1875 5735 4.092116 AGGAATAATACAAGCTGGAGGC 57.908 45.455 0.00 0.00 42.19 4.70
1884 5744 4.203618 GCTGGAGGCTCGTTAACC 57.796 61.111 8.69 0.00 38.06 2.85
1885 5745 1.449778 GCTGGAGGCTCGTTAACCC 60.450 63.158 8.69 0.00 38.06 4.11
1886 5746 1.980052 CTGGAGGCTCGTTAACCCA 59.020 57.895 8.69 0.00 0.00 4.51
1887 5747 0.323629 CTGGAGGCTCGTTAACCCAA 59.676 55.000 8.69 0.00 0.00 4.12
1888 5748 0.035739 TGGAGGCTCGTTAACCCAAC 59.964 55.000 8.69 0.00 0.00 3.77
1889 5749 0.323957 GGAGGCTCGTTAACCCAACT 59.676 55.000 8.69 0.00 34.77 3.16
1890 5750 1.271217 GGAGGCTCGTTAACCCAACTT 60.271 52.381 8.69 0.00 34.77 2.66
1891 5751 1.804748 GAGGCTCGTTAACCCAACTTG 59.195 52.381 0.00 0.00 34.77 3.16
1892 5752 1.142262 AGGCTCGTTAACCCAACTTGT 59.858 47.619 0.00 0.00 34.77 3.16
1893 5753 1.951602 GGCTCGTTAACCCAACTTGTT 59.048 47.619 0.00 0.00 34.77 2.83
1894 5754 2.031420 GGCTCGTTAACCCAACTTGTTC 60.031 50.000 0.00 0.00 34.77 3.18
1895 5755 2.876550 GCTCGTTAACCCAACTTGTTCT 59.123 45.455 0.00 0.00 34.77 3.01
1896 5756 4.060205 GCTCGTTAACCCAACTTGTTCTA 58.940 43.478 0.00 0.00 34.77 2.10
1897 5757 4.512571 GCTCGTTAACCCAACTTGTTCTAA 59.487 41.667 0.00 0.00 34.77 2.10
1898 5758 5.180680 GCTCGTTAACCCAACTTGTTCTAAT 59.819 40.000 0.00 0.00 34.77 1.73
1899 5759 6.620089 GCTCGTTAACCCAACTTGTTCTAATC 60.620 42.308 0.00 0.00 34.77 1.75
1900 5760 6.527423 TCGTTAACCCAACTTGTTCTAATCT 58.473 36.000 0.00 0.00 34.77 2.40
1901 5761 6.993902 TCGTTAACCCAACTTGTTCTAATCTT 59.006 34.615 0.00 0.00 34.77 2.40
1902 5762 8.149647 TCGTTAACCCAACTTGTTCTAATCTTA 58.850 33.333 0.00 0.00 34.77 2.10
1903 5763 8.943002 CGTTAACCCAACTTGTTCTAATCTTAT 58.057 33.333 0.00 0.00 34.77 1.73
1907 5767 9.802039 AACCCAACTTGTTCTAATCTTATTACA 57.198 29.630 0.00 0.00 0.00 2.41
1908 5768 9.802039 ACCCAACTTGTTCTAATCTTATTACAA 57.198 29.630 0.00 0.00 0.00 2.41
1934 5794 7.721286 AACTATGATTAGTTAGCACATGAGC 57.279 36.000 7.07 7.07 44.90 4.26
1935 5795 7.060383 ACTATGATTAGTTAGCACATGAGCT 57.940 36.000 21.45 21.45 38.65 4.09
1936 5796 6.927936 ACTATGATTAGTTAGCACATGAGCTG 59.072 38.462 25.51 8.25 38.27 4.24
1937 5797 5.089970 TGATTAGTTAGCACATGAGCTGT 57.910 39.130 25.51 13.30 46.11 4.40
1938 5798 5.491070 TGATTAGTTAGCACATGAGCTGTT 58.509 37.500 25.51 13.70 46.11 3.16
1939 5799 5.939883 TGATTAGTTAGCACATGAGCTGTTT 59.060 36.000 25.51 13.39 46.11 2.83
1940 5800 5.611796 TTAGTTAGCACATGAGCTGTTTG 57.388 39.130 25.51 0.24 46.11 2.93
1941 5801 2.816087 AGTTAGCACATGAGCTGTTTGG 59.184 45.455 25.51 0.00 46.11 3.28
1942 5802 2.554032 GTTAGCACATGAGCTGTTTGGT 59.446 45.455 25.51 7.46 46.11 3.67
1943 5803 1.696063 AGCACATGAGCTGTTTGGTT 58.304 45.000 17.30 0.00 44.66 3.67
1944 5804 1.610522 AGCACATGAGCTGTTTGGTTC 59.389 47.619 17.30 0.00 44.66 3.62
1945 5805 1.337703 GCACATGAGCTGTTTGGTTCA 59.662 47.619 7.97 0.00 35.29 3.18
1946 5806 2.223782 GCACATGAGCTGTTTGGTTCAA 60.224 45.455 7.97 0.00 35.29 2.69
1947 5807 3.737663 GCACATGAGCTGTTTGGTTCAAA 60.738 43.478 7.97 0.00 35.29 2.69
1948 5808 4.046462 CACATGAGCTGTTTGGTTCAAAG 58.954 43.478 0.00 0.00 35.29 2.77
1949 5809 3.953612 ACATGAGCTGTTTGGTTCAAAGA 59.046 39.130 0.00 0.00 33.82 2.52
1950 5810 4.402155 ACATGAGCTGTTTGGTTCAAAGAA 59.598 37.500 0.00 0.00 33.82 2.52
1951 5811 4.370364 TGAGCTGTTTGGTTCAAAGAAC 57.630 40.909 0.00 1.37 33.82 3.01
1952 5812 3.181501 TGAGCTGTTTGGTTCAAAGAACG 60.182 43.478 0.00 0.00 33.82 3.95
1953 5813 3.013921 AGCTGTTTGGTTCAAAGAACGA 58.986 40.909 4.05 0.00 33.82 3.85
1954 5814 3.105937 GCTGTTTGGTTCAAAGAACGAC 58.894 45.455 4.05 4.04 33.82 4.34
1955 5815 3.691498 CTGTTTGGTTCAAAGAACGACC 58.309 45.455 4.05 0.00 33.82 4.79
1956 5816 3.082548 TGTTTGGTTCAAAGAACGACCA 58.917 40.909 4.05 0.00 40.23 4.02
1957 5817 3.119779 TGTTTGGTTCAAAGAACGACCAC 60.120 43.478 4.05 1.53 41.57 4.16
1958 5818 2.404923 TGGTTCAAAGAACGACCACA 57.595 45.000 4.05 0.00 37.26 4.17
1959 5819 2.712709 TGGTTCAAAGAACGACCACAA 58.287 42.857 4.05 0.00 37.26 3.33
1960 5820 3.283751 TGGTTCAAAGAACGACCACAAT 58.716 40.909 4.05 0.00 37.26 2.71
1961 5821 3.066064 TGGTTCAAAGAACGACCACAATG 59.934 43.478 4.05 0.00 37.26 2.82
1962 5822 3.042887 GTTCAAAGAACGACCACAATGC 58.957 45.455 0.00 0.00 0.00 3.56
1963 5823 2.571212 TCAAAGAACGACCACAATGCT 58.429 42.857 0.00 0.00 0.00 3.79
1964 5824 2.948979 TCAAAGAACGACCACAATGCTT 59.051 40.909 0.00 0.00 0.00 3.91
1970 5830 6.084326 AGAACGACCACAATGCTTAAAAAT 57.916 33.333 0.00 0.00 0.00 1.82
1977 5837 7.061789 CGACCACAATGCTTAAAAATAACCTTC 59.938 37.037 0.00 0.00 0.00 3.46
1978 5838 7.158697 ACCACAATGCTTAAAAATAACCTTCC 58.841 34.615 0.00 0.00 0.00 3.46
1979 5839 6.593770 CCACAATGCTTAAAAATAACCTTCCC 59.406 38.462 0.00 0.00 0.00 3.97
1981 5841 7.659390 CACAATGCTTAAAAATAACCTTCCCAA 59.341 33.333 0.00 0.00 0.00 4.12
1982 5842 8.382405 ACAATGCTTAAAAATAACCTTCCCAAT 58.618 29.630 0.00 0.00 0.00 3.16
1983 5843 9.883142 CAATGCTTAAAAATAACCTTCCCAATA 57.117 29.630 0.00 0.00 0.00 1.90
1987 5847 7.222031 GCTTAAAAATAACCTTCCCAATAAGCG 59.778 37.037 0.00 0.00 34.30 4.68
1988 5848 6.844097 AAAAATAACCTTCCCAATAAGCGA 57.156 33.333 0.00 0.00 0.00 4.93
1990 5850 6.391227 AAATAACCTTCCCAATAAGCGATG 57.609 37.500 0.00 0.00 0.00 3.84
1992 5852 3.644966 ACCTTCCCAATAAGCGATGAA 57.355 42.857 0.00 0.00 0.00 2.57
1993 5853 3.963129 ACCTTCCCAATAAGCGATGAAA 58.037 40.909 0.00 0.00 0.00 2.69
1994 5854 3.694566 ACCTTCCCAATAAGCGATGAAAC 59.305 43.478 0.00 0.00 0.00 2.78
1995 5855 3.242739 CCTTCCCAATAAGCGATGAAACG 60.243 47.826 0.00 0.00 0.00 3.60
1996 5856 2.980568 TCCCAATAAGCGATGAAACGT 58.019 42.857 0.00 0.00 35.59 3.99
1997 5857 2.933906 TCCCAATAAGCGATGAAACGTC 59.066 45.455 0.00 0.00 35.59 4.34
1998 5858 2.031683 CCCAATAAGCGATGAAACGTCC 59.968 50.000 0.00 0.00 35.59 4.79
1999 5859 2.675844 CCAATAAGCGATGAAACGTCCA 59.324 45.455 0.00 0.00 35.59 4.02
2000 5860 3.485216 CCAATAAGCGATGAAACGTCCAC 60.485 47.826 0.00 0.00 35.59 4.02
2001 5861 2.442212 TAAGCGATGAAACGTCCACA 57.558 45.000 0.00 0.00 35.59 4.17
2002 5862 0.865769 AAGCGATGAAACGTCCACAC 59.134 50.000 0.00 0.00 35.59 3.82
2003 5863 0.249699 AGCGATGAAACGTCCACACA 60.250 50.000 0.00 0.00 35.59 3.72
2004 5864 0.796312 GCGATGAAACGTCCACACAT 59.204 50.000 0.00 0.00 35.59 3.21
2005 5865 1.196808 GCGATGAAACGTCCACACATT 59.803 47.619 0.00 0.00 35.59 2.71
2006 5866 2.724839 GCGATGAAACGTCCACACATTC 60.725 50.000 0.00 0.00 35.59 2.67
2007 5867 2.159707 CGATGAAACGTCCACACATTCC 60.160 50.000 0.00 0.00 0.00 3.01
2401 6261 5.189928 TCTGAAACCTGCAAAAACACTAGA 58.810 37.500 0.00 0.00 0.00 2.43
2412 6287 8.256611 TGCAAAAACACTAGAACTGAGATATC 57.743 34.615 0.00 0.00 0.00 1.63
2686 6565 6.374333 TCGCCTAATAAAGAATTATCATGCCC 59.626 38.462 0.00 0.00 31.28 5.36
2714 6593 3.575687 AGGGAAAGCAACAATTTCAGGAG 59.424 43.478 1.37 0.00 38.21 3.69
2811 6690 9.003658 CAGGATAACCGAGCTTGAAATATTTAT 57.996 33.333 1.22 0.00 41.83 1.40
2919 6798 3.359950 AGCAAATGAATCTTCAGACCCC 58.640 45.455 0.00 0.00 41.08 4.95
2922 6801 4.441079 GCAAATGAATCTTCAGACCCCATG 60.441 45.833 0.00 0.00 41.08 3.66
3051 6930 1.241165 TGATTGCAGTCTTGGCAGTG 58.759 50.000 10.82 0.00 43.05 3.66
3107 6986 5.477984 TGAAAATTTCAGAGGAGGGAACATG 59.522 40.000 4.03 0.00 34.08 3.21
3133 7012 1.529865 GTTCAGCCGTAGACAAACACC 59.470 52.381 0.00 0.00 0.00 4.16
3154 7033 3.535561 CCAACGGATAGACTGAAGCAAT 58.464 45.455 0.00 0.00 0.00 3.56
3200 7080 2.081787 TGGGTCAACCTCCCTTGCA 61.082 57.895 0.00 0.00 44.84 4.08
3290 7170 0.043053 CGCATACGGCAATCTCAACG 60.043 55.000 0.00 0.00 45.17 4.10
3349 7312 4.789012 AGATTGGCACCTTTAACATGTG 57.211 40.909 0.00 0.00 0.00 3.21
3475 7438 0.904865 TGGAGCTGGATGGACTCGTT 60.905 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.038280 CTCGCTAGGGTTCGGGTTAT 58.962 55.000 6.70 0.00 0.00 1.89
1 2 0.323725 ACTCGCTAGGGTTCGGGTTA 60.324 55.000 6.70 0.00 35.67 2.85
2 3 0.323725 TACTCGCTAGGGTTCGGGTT 60.324 55.000 6.70 0.00 40.27 4.11
3 4 1.034292 GTACTCGCTAGGGTTCGGGT 61.034 60.000 6.70 2.47 42.61 5.28
4 5 1.732308 GTACTCGCTAGGGTTCGGG 59.268 63.158 6.70 0.00 30.72 5.14
5 6 1.091771 TCGTACTCGCTAGGGTTCGG 61.092 60.000 6.70 0.00 41.17 4.30
6 7 0.304098 CTCGTACTCGCTAGGGTTCG 59.696 60.000 6.70 7.74 42.01 3.95
7 8 0.029167 GCTCGTACTCGCTAGGGTTC 59.971 60.000 6.70 0.00 36.96 3.62
8 9 0.394080 AGCTCGTACTCGCTAGGGTT 60.394 55.000 6.70 0.00 34.11 4.11
9 10 0.394080 AAGCTCGTACTCGCTAGGGT 60.394 55.000 6.70 0.00 34.96 4.34
10 11 0.029567 CAAGCTCGTACTCGCTAGGG 59.970 60.000 0.00 0.00 34.96 3.53
11 12 0.029567 CCAAGCTCGTACTCGCTAGG 59.970 60.000 6.24 3.13 34.96 3.02
12 13 0.733729 ACCAAGCTCGTACTCGCTAG 59.266 55.000 6.24 4.58 34.96 3.42
13 14 0.450583 CACCAAGCTCGTACTCGCTA 59.549 55.000 6.24 0.00 34.96 4.26
14 15 1.213013 CACCAAGCTCGTACTCGCT 59.787 57.895 0.00 0.48 38.30 4.93
15 16 0.798771 CTCACCAAGCTCGTACTCGC 60.799 60.000 0.00 0.00 36.96 5.03
16 17 3.314339 CTCACCAAGCTCGTACTCG 57.686 57.895 0.00 0.00 38.55 4.18
26 27 2.111999 TTGGGACTCGGCTCACCAAG 62.112 60.000 0.00 0.00 36.37 3.61
27 28 2.144078 TTGGGACTCGGCTCACCAA 61.144 57.895 0.00 0.00 38.76 3.67
28 29 2.525629 TTGGGACTCGGCTCACCA 60.526 61.111 0.00 0.00 34.57 4.17
29 30 2.047179 GTTGGGACTCGGCTCACC 60.047 66.667 0.00 0.00 0.00 4.02
30 31 1.070786 TTGTTGGGACTCGGCTCAC 59.929 57.895 0.00 0.00 0.00 3.51
31 32 1.070786 GTTGTTGGGACTCGGCTCA 59.929 57.895 0.00 0.00 0.00 4.26
32 33 1.671379 GGTTGTTGGGACTCGGCTC 60.671 63.158 0.00 0.00 0.00 4.70
33 34 2.147387 AGGTTGTTGGGACTCGGCT 61.147 57.895 0.00 0.00 0.00 5.52
34 35 1.966451 CAGGTTGTTGGGACTCGGC 60.966 63.158 0.00 0.00 0.00 5.54
35 36 0.107831 TTCAGGTTGTTGGGACTCGG 59.892 55.000 0.00 0.00 0.00 4.63
36 37 1.226746 GTTCAGGTTGTTGGGACTCG 58.773 55.000 0.00 0.00 0.00 4.18
37 38 2.158813 TCTGTTCAGGTTGTTGGGACTC 60.159 50.000 0.00 0.00 0.00 3.36
38 39 1.843851 TCTGTTCAGGTTGTTGGGACT 59.156 47.619 0.00 0.00 0.00 3.85
39 40 2.341846 TCTGTTCAGGTTGTTGGGAC 57.658 50.000 0.00 0.00 0.00 4.46
40 41 3.221771 CAATCTGTTCAGGTTGTTGGGA 58.778 45.455 15.22 0.00 0.00 4.37
41 42 2.958355 ACAATCTGTTCAGGTTGTTGGG 59.042 45.455 21.16 2.94 31.20 4.12
42 43 4.654091 AACAATCTGTTCAGGTTGTTGG 57.346 40.909 30.63 10.15 41.64 3.77
43 44 6.863126 GGATTAACAATCTGTTCAGGTTGTTG 59.137 38.462 34.74 20.76 42.70 3.33
44 45 6.549364 TGGATTAACAATCTGTTCAGGTTGTT 59.451 34.615 32.24 32.24 44.33 2.83
45 46 6.016276 GTGGATTAACAATCTGTTCAGGTTGT 60.016 38.462 21.16 21.16 40.22 3.32
46 47 6.207417 AGTGGATTAACAATCTGTTCAGGTTG 59.793 38.462 20.03 20.03 40.22 3.77
47 48 6.306987 AGTGGATTAACAATCTGTTCAGGTT 58.693 36.000 0.00 0.00 40.22 3.50
48 49 5.880901 AGTGGATTAACAATCTGTTCAGGT 58.119 37.500 0.00 0.00 40.22 4.00
49 50 7.106239 AGTAGTGGATTAACAATCTGTTCAGG 58.894 38.462 0.00 0.00 40.22 3.86
50 51 8.037758 AGAGTAGTGGATTAACAATCTGTTCAG 58.962 37.037 0.00 0.00 40.22 3.02
51 52 7.907389 AGAGTAGTGGATTAACAATCTGTTCA 58.093 34.615 0.00 0.00 40.22 3.18
52 53 8.779354 AAGAGTAGTGGATTAACAATCTGTTC 57.221 34.615 0.00 0.00 40.22 3.18
53 54 9.574516 AAAAGAGTAGTGGATTAACAATCTGTT 57.425 29.630 0.00 0.00 43.88 3.16
73 74 9.717892 GGCGGTAATTCTAAAAAGATAAAAGAG 57.282 33.333 0.00 0.00 0.00 2.85
74 75 9.233649 TGGCGGTAATTCTAAAAAGATAAAAGA 57.766 29.630 0.00 0.00 0.00 2.52
75 76 9.503427 CTGGCGGTAATTCTAAAAAGATAAAAG 57.497 33.333 0.00 0.00 0.00 2.27
76 77 9.016438 ACTGGCGGTAATTCTAAAAAGATAAAA 57.984 29.630 0.00 0.00 0.00 1.52
77 78 8.570068 ACTGGCGGTAATTCTAAAAAGATAAA 57.430 30.769 0.00 0.00 0.00 1.40
78 79 8.570068 AACTGGCGGTAATTCTAAAAAGATAA 57.430 30.769 0.00 0.00 0.00 1.75
79 80 8.455682 CAAACTGGCGGTAATTCTAAAAAGATA 58.544 33.333 0.00 0.00 0.00 1.98
80 81 7.039993 ACAAACTGGCGGTAATTCTAAAAAGAT 60.040 33.333 0.00 0.00 0.00 2.40
81 82 6.263617 ACAAACTGGCGGTAATTCTAAAAAGA 59.736 34.615 0.00 0.00 0.00 2.52
82 83 6.362283 CACAAACTGGCGGTAATTCTAAAAAG 59.638 38.462 0.00 0.00 0.00 2.27
83 84 6.183360 ACACAAACTGGCGGTAATTCTAAAAA 60.183 34.615 0.00 0.00 0.00 1.94
84 85 5.299782 ACACAAACTGGCGGTAATTCTAAAA 59.700 36.000 0.00 0.00 0.00 1.52
85 86 4.822896 ACACAAACTGGCGGTAATTCTAAA 59.177 37.500 0.00 0.00 0.00 1.85
86 87 4.391155 ACACAAACTGGCGGTAATTCTAA 58.609 39.130 0.00 0.00 0.00 2.10
87 88 4.010667 ACACAAACTGGCGGTAATTCTA 57.989 40.909 0.00 0.00 0.00 2.10
88 89 2.858745 ACACAAACTGGCGGTAATTCT 58.141 42.857 0.00 0.00 0.00 2.40
89 90 3.636282 AACACAAACTGGCGGTAATTC 57.364 42.857 0.00 0.00 0.00 2.17
90 91 4.394439 AAAACACAAACTGGCGGTAATT 57.606 36.364 0.00 0.00 0.00 1.40
91 92 4.822896 TCTAAAACACAAACTGGCGGTAAT 59.177 37.500 0.00 0.00 0.00 1.89
92 93 4.197750 TCTAAAACACAAACTGGCGGTAA 58.802 39.130 0.00 0.00 0.00 2.85
93 94 3.806380 TCTAAAACACAAACTGGCGGTA 58.194 40.909 0.00 0.00 0.00 4.02
94 95 2.645802 TCTAAAACACAAACTGGCGGT 58.354 42.857 0.00 0.00 0.00 5.68
95 96 3.066203 AGTTCTAAAACACAAACTGGCGG 59.934 43.478 0.00 0.00 37.88 6.13
96 97 4.287238 AGTTCTAAAACACAAACTGGCG 57.713 40.909 0.00 0.00 37.88 5.69
97 98 5.516996 GGTAGTTCTAAAACACAAACTGGC 58.483 41.667 0.00 0.00 37.88 4.85
98 99 5.744490 CGGTAGTTCTAAAACACAAACTGG 58.256 41.667 0.00 0.00 37.88 4.00
99 100 5.007332 AGCGGTAGTTCTAAAACACAAACTG 59.993 40.000 0.00 0.00 37.88 3.16
100 101 5.121105 AGCGGTAGTTCTAAAACACAAACT 58.879 37.500 0.00 0.00 37.88 2.66
101 102 5.413969 AGCGGTAGTTCTAAAACACAAAC 57.586 39.130 0.00 0.00 37.88 2.93
102 103 6.762661 ACTAAGCGGTAGTTCTAAAACACAAA 59.237 34.615 0.00 0.00 40.33 2.83
103 104 6.282930 ACTAAGCGGTAGTTCTAAAACACAA 58.717 36.000 0.00 0.00 40.33 3.33
104 105 5.846203 ACTAAGCGGTAGTTCTAAAACACA 58.154 37.500 0.00 0.00 40.33 3.72
580 581 2.648059 CTTCAGGGCCCATTTCAGTAG 58.352 52.381 27.56 5.42 0.00 2.57
594 595 2.276732 TTTTCTGTGAGGCCTTCAGG 57.723 50.000 27.22 15.41 36.21 3.86
596 597 3.149196 GTCATTTTCTGTGAGGCCTTCA 58.851 45.455 6.77 9.16 0.00 3.02
605 606 2.730090 GCCGATGCAGTCATTTTCTGTG 60.730 50.000 0.00 0.00 37.47 3.66
708 4481 0.874390 GGCTCGACTGAATTTGTGCA 59.126 50.000 0.00 0.00 0.00 4.57
709 4482 0.169009 GGGCTCGACTGAATTTGTGC 59.831 55.000 0.00 0.00 0.00 4.57
710 4483 0.804989 GGGGCTCGACTGAATTTGTG 59.195 55.000 0.00 0.00 0.00 3.33
711 4484 0.693049 AGGGGCTCGACTGAATTTGT 59.307 50.000 0.00 0.00 0.00 2.83
712 4485 1.089920 CAGGGGCTCGACTGAATTTG 58.910 55.000 0.00 0.00 36.86 2.32
713 4486 0.678048 GCAGGGGCTCGACTGAATTT 60.678 55.000 5.04 0.00 36.86 1.82
755 4557 1.933181 TGCAGCGTGGAGAAATAATCG 59.067 47.619 0.00 0.00 0.00 3.34
816 4646 3.834056 TAGCTAGGAGGGCCGGCT 61.834 66.667 28.56 7.30 45.22 5.52
913 4743 1.346068 AGAGTGGTCTGAGAGGCAAAC 59.654 52.381 0.00 0.00 0.00 2.93
931 4761 1.645710 GAACTGGAGGGACCTGAAGA 58.354 55.000 0.00 0.00 40.23 2.87
933 4763 0.840722 GGGAACTGGAGGGACCTGAA 60.841 60.000 0.00 0.00 40.23 3.02
954 4787 2.099062 CAGCCGCTCGAATGTTGC 59.901 61.111 0.00 0.00 0.00 4.17
957 4790 2.510238 GCTCAGCCGCTCGAATGT 60.510 61.111 0.00 0.00 0.00 2.71
1127 4961 3.436359 GCCAGCAAGAAGAAGAAGAAGAG 59.564 47.826 0.00 0.00 0.00 2.85
1128 4962 3.406764 GCCAGCAAGAAGAAGAAGAAGA 58.593 45.455 0.00 0.00 0.00 2.87
1129 4963 2.159234 CGCCAGCAAGAAGAAGAAGAAG 59.841 50.000 0.00 0.00 0.00 2.85
1354 5192 1.303317 GGCGGGTGAAATGGTGAGT 60.303 57.895 0.00 0.00 0.00 3.41
1361 5199 1.299976 GAGGTGAGGCGGGTGAAAT 59.700 57.895 0.00 0.00 0.00 2.17
1384 5231 6.088824 GCACAACTGCTTGGCATATATAATC 58.911 40.000 0.00 0.00 40.63 1.75
1509 5357 9.191995 AGTACAACATAAAGTTAGCAAATTTGC 57.808 29.630 31.36 31.36 46.21 3.68
1513 5361 7.888546 AGGGAGTACAACATAAAGTTAGCAAAT 59.111 33.333 0.00 0.00 38.74 2.32
1514 5362 7.228590 AGGGAGTACAACATAAAGTTAGCAAA 58.771 34.615 0.00 0.00 38.74 3.68
1528 5376 1.640917 TGGGACAGAGGGAGTACAAC 58.359 55.000 0.00 0.00 0.00 3.32
1540 5388 7.116948 CAGAAACGCTCTTATATTATGGGACAG 59.883 40.741 0.00 0.00 34.24 3.51
1541 5389 6.929049 CAGAAACGCTCTTATATTATGGGACA 59.071 38.462 0.00 0.00 35.21 4.02
1566 5414 4.589374 AGACAGGGATTATACACTACTGCC 59.411 45.833 0.00 0.00 0.00 4.85
1595 5443 3.777106 TCAACTCCTGACAATCTGCTT 57.223 42.857 0.00 0.00 0.00 3.91
1596 5444 3.262660 TGATCAACTCCTGACAATCTGCT 59.737 43.478 0.00 0.00 36.69 4.24
1599 5447 6.058553 TGATTGATCAACTCCTGACAATCT 57.941 37.500 11.07 0.00 43.69 2.40
1600 5448 6.748333 TTGATTGATCAACTCCTGACAATC 57.252 37.500 11.07 0.00 43.65 2.67
1617 5465 2.855953 GCGGCGAGAATTCCATTGATTG 60.856 50.000 12.98 0.00 0.00 2.67
1619 5467 0.947244 GCGGCGAGAATTCCATTGAT 59.053 50.000 12.98 0.00 0.00 2.57
1637 5485 1.160137 CACAACTAACAGGGAGCTGC 58.840 55.000 0.00 0.00 0.00 5.25
1638 5486 1.813513 CCACAACTAACAGGGAGCTG 58.186 55.000 0.00 0.00 0.00 4.24
1639 5487 0.036875 GCCACAACTAACAGGGAGCT 59.963 55.000 0.00 0.00 0.00 4.09
1640 5488 0.250727 TGCCACAACTAACAGGGAGC 60.251 55.000 0.00 0.00 0.00 4.70
1641 5489 1.072331 AGTGCCACAACTAACAGGGAG 59.928 52.381 0.00 0.00 0.00 4.30
1642 5490 1.136828 AGTGCCACAACTAACAGGGA 58.863 50.000 0.00 0.00 0.00 4.20
1643 5491 1.202758 TCAGTGCCACAACTAACAGGG 60.203 52.381 0.00 0.00 0.00 4.45
1644 5492 2.254546 TCAGTGCCACAACTAACAGG 57.745 50.000 0.00 0.00 0.00 4.00
1652 5500 5.827797 ACTTCTAAAAAGATCAGTGCCACAA 59.172 36.000 0.00 0.00 0.00 3.33
1659 5507 7.967908 TCTCTCCAACTTCTAAAAAGATCAGT 58.032 34.615 0.00 0.00 0.00 3.41
1666 5522 7.038302 TGAGGCTATCTCTCCAACTTCTAAAAA 60.038 37.037 0.00 0.00 42.86 1.94
1708 5567 5.346822 GGTGACTGTAAACACGTCGAATTAT 59.653 40.000 0.00 0.00 37.82 1.28
1709 5568 4.681025 GGTGACTGTAAACACGTCGAATTA 59.319 41.667 0.00 0.00 37.82 1.40
1711 5570 3.054878 GGTGACTGTAAACACGTCGAAT 58.945 45.455 0.00 0.00 37.82 3.34
1715 5574 3.805422 TGATTGGTGACTGTAAACACGTC 59.195 43.478 0.00 6.03 37.82 4.34
1718 5577 4.553938 CGGTTGATTGGTGACTGTAAACAC 60.554 45.833 0.00 0.00 36.44 3.32
1736 5596 1.721487 CGCAAAGATAGGCCGGTTG 59.279 57.895 1.90 0.00 0.00 3.77
1792 5652 5.332743 AGTCATGATGGCCTTCCTTAAAAA 58.667 37.500 15.62 0.00 0.00 1.94
1794 5654 4.591321 AGTCATGATGGCCTTCCTTAAA 57.409 40.909 15.62 0.00 0.00 1.52
1795 5655 4.444876 GCTAGTCATGATGGCCTTCCTTAA 60.445 45.833 15.62 0.00 0.00 1.85
1796 5656 3.071602 GCTAGTCATGATGGCCTTCCTTA 59.928 47.826 15.62 0.00 0.00 2.69
1798 5658 1.419387 GCTAGTCATGATGGCCTTCCT 59.581 52.381 15.62 8.04 0.00 3.36
1799 5659 1.419387 AGCTAGTCATGATGGCCTTCC 59.581 52.381 15.62 0.71 0.00 3.46
1800 5660 2.926778 AGCTAGTCATGATGGCCTTC 57.073 50.000 11.69 11.69 0.00 3.46
1801 5661 3.659183 AAAGCTAGTCATGATGGCCTT 57.341 42.857 3.32 0.00 0.00 4.35
1803 5663 5.997746 TGTAATAAAGCTAGTCATGATGGCC 59.002 40.000 0.00 0.00 0.00 5.36
1804 5664 7.227512 AGTTGTAATAAAGCTAGTCATGATGGC 59.772 37.037 0.00 4.04 0.00 4.40
1846 5706 9.528489 TCCAGCTTGTATTATTCCTAAACTTTT 57.472 29.630 0.00 0.00 0.00 2.27
1847 5707 9.178758 CTCCAGCTTGTATTATTCCTAAACTTT 57.821 33.333 0.00 0.00 0.00 2.66
1849 5709 7.283329 CCTCCAGCTTGTATTATTCCTAAACT 58.717 38.462 0.00 0.00 0.00 2.66
1850 5710 6.017026 GCCTCCAGCTTGTATTATTCCTAAAC 60.017 42.308 0.00 0.00 38.99 2.01
1851 5711 6.062095 GCCTCCAGCTTGTATTATTCCTAAA 58.938 40.000 0.00 0.00 38.99 1.85
1852 5712 5.621193 GCCTCCAGCTTGTATTATTCCTAA 58.379 41.667 0.00 0.00 38.99 2.69
1853 5713 5.228945 GCCTCCAGCTTGTATTATTCCTA 57.771 43.478 0.00 0.00 38.99 2.94
1854 5714 4.092116 GCCTCCAGCTTGTATTATTCCT 57.908 45.455 0.00 0.00 38.99 3.36
1867 5727 1.449778 GGGTTAACGAGCCTCCAGC 60.450 63.158 0.00 0.00 42.81 4.85
1868 5728 0.323629 TTGGGTTAACGAGCCTCCAG 59.676 55.000 0.00 0.00 46.39 3.86
1869 5729 0.035739 GTTGGGTTAACGAGCCTCCA 59.964 55.000 0.00 0.00 46.39 3.86
1870 5730 0.323957 AGTTGGGTTAACGAGCCTCC 59.676 55.000 0.00 0.00 46.39 4.30
1871 5731 1.804748 CAAGTTGGGTTAACGAGCCTC 59.195 52.381 0.00 0.00 46.39 4.70
1872 5732 1.142262 ACAAGTTGGGTTAACGAGCCT 59.858 47.619 7.96 0.00 46.39 4.58
1873 5733 1.601166 ACAAGTTGGGTTAACGAGCC 58.399 50.000 7.96 0.00 44.15 4.70
1874 5734 2.876550 AGAACAAGTTGGGTTAACGAGC 59.123 45.455 7.96 0.00 44.15 5.03
1875 5735 6.649557 AGATTAGAACAAGTTGGGTTAACGAG 59.350 38.462 7.96 0.00 44.15 4.18
1876 5736 6.527423 AGATTAGAACAAGTTGGGTTAACGA 58.473 36.000 7.96 0.00 44.15 3.85
1877 5737 6.796705 AGATTAGAACAAGTTGGGTTAACG 57.203 37.500 7.96 0.00 44.15 3.18
1881 5741 9.802039 TGTAATAAGATTAGAACAAGTTGGGTT 57.198 29.630 7.96 0.00 0.00 4.11
1882 5742 9.802039 TTGTAATAAGATTAGAACAAGTTGGGT 57.198 29.630 7.96 0.00 0.00 4.51
1911 5771 6.927936 CAGCTCATGTGCTAACTAATCATAGT 59.072 38.462 21.05 0.00 41.76 2.12
1912 5772 6.927936 ACAGCTCATGTGCTAACTAATCATAG 59.072 38.462 21.05 7.68 41.91 2.23
1913 5773 6.820335 ACAGCTCATGTGCTAACTAATCATA 58.180 36.000 21.05 0.00 41.91 2.15
1914 5774 5.678583 ACAGCTCATGTGCTAACTAATCAT 58.321 37.500 21.05 0.00 41.91 2.45
1915 5775 5.089970 ACAGCTCATGTGCTAACTAATCA 57.910 39.130 21.05 0.00 41.91 2.57
1916 5776 6.253746 CAAACAGCTCATGTGCTAACTAATC 58.746 40.000 21.05 0.00 43.00 1.75
1917 5777 5.124457 CCAAACAGCTCATGTGCTAACTAAT 59.876 40.000 21.05 3.46 43.00 1.73
1918 5778 4.455533 CCAAACAGCTCATGTGCTAACTAA 59.544 41.667 21.05 0.00 43.00 2.24
1919 5779 4.002982 CCAAACAGCTCATGTGCTAACTA 58.997 43.478 21.05 0.00 43.00 2.24
1920 5780 2.816087 CCAAACAGCTCATGTGCTAACT 59.184 45.455 21.05 6.76 43.00 2.24
1921 5781 2.554032 ACCAAACAGCTCATGTGCTAAC 59.446 45.455 21.05 0.00 43.00 2.34
1922 5782 2.862541 ACCAAACAGCTCATGTGCTAA 58.137 42.857 21.05 0.00 43.00 3.09
1923 5783 2.566833 ACCAAACAGCTCATGTGCTA 57.433 45.000 21.05 0.00 43.00 3.49
1924 5784 1.610522 GAACCAAACAGCTCATGTGCT 59.389 47.619 16.33 16.33 43.00 4.40
1925 5785 1.337703 TGAACCAAACAGCTCATGTGC 59.662 47.619 11.79 11.79 43.00 4.57
1926 5786 3.713858 TTGAACCAAACAGCTCATGTG 57.286 42.857 0.00 0.00 43.00 3.21
1927 5787 3.953612 TCTTTGAACCAAACAGCTCATGT 59.046 39.130 0.00 0.00 46.97 3.21
1928 5788 4.572985 TCTTTGAACCAAACAGCTCATG 57.427 40.909 0.00 0.00 0.00 3.07
1929 5789 4.498009 CGTTCTTTGAACCAAACAGCTCAT 60.498 41.667 5.06 0.00 0.00 2.90
1930 5790 3.181501 CGTTCTTTGAACCAAACAGCTCA 60.182 43.478 5.06 0.00 0.00 4.26
1931 5791 3.064820 TCGTTCTTTGAACCAAACAGCTC 59.935 43.478 5.06 0.00 0.00 4.09
1932 5792 3.013921 TCGTTCTTTGAACCAAACAGCT 58.986 40.909 5.06 0.00 0.00 4.24
1933 5793 3.105937 GTCGTTCTTTGAACCAAACAGC 58.894 45.455 5.06 0.00 0.00 4.40
1934 5794 3.127895 TGGTCGTTCTTTGAACCAAACAG 59.872 43.478 5.06 0.00 0.00 3.16
1935 5795 3.082548 TGGTCGTTCTTTGAACCAAACA 58.917 40.909 5.06 0.77 0.00 2.83
1936 5796 3.119779 TGTGGTCGTTCTTTGAACCAAAC 60.120 43.478 5.06 2.15 0.00 2.93
1937 5797 3.082548 TGTGGTCGTTCTTTGAACCAAA 58.917 40.909 5.06 0.00 0.00 3.28
1938 5798 2.712709 TGTGGTCGTTCTTTGAACCAA 58.287 42.857 5.06 0.00 0.00 3.67
1939 5799 2.404923 TGTGGTCGTTCTTTGAACCA 57.595 45.000 5.06 0.00 0.00 3.67
1940 5800 3.628017 CATTGTGGTCGTTCTTTGAACC 58.372 45.455 5.06 0.00 0.00 3.62
1941 5801 3.042887 GCATTGTGGTCGTTCTTTGAAC 58.957 45.455 0.77 0.77 0.00 3.18
1942 5802 2.948979 AGCATTGTGGTCGTTCTTTGAA 59.051 40.909 0.00 0.00 0.00 2.69
1943 5803 2.571212 AGCATTGTGGTCGTTCTTTGA 58.429 42.857 0.00 0.00 0.00 2.69
1944 5804 3.354089 AAGCATTGTGGTCGTTCTTTG 57.646 42.857 0.00 0.00 0.00 2.77
1945 5805 5.508200 TTTAAGCATTGTGGTCGTTCTTT 57.492 34.783 0.00 0.00 0.00 2.52
1946 5806 5.508200 TTTTAAGCATTGTGGTCGTTCTT 57.492 34.783 0.00 0.00 0.00 2.52
1947 5807 5.508200 TTTTTAAGCATTGTGGTCGTTCT 57.492 34.783 0.00 0.00 0.00 3.01
1948 5808 7.148869 GGTTATTTTTAAGCATTGTGGTCGTTC 60.149 37.037 0.00 0.00 0.00 3.95
1949 5809 6.643360 GGTTATTTTTAAGCATTGTGGTCGTT 59.357 34.615 0.00 0.00 0.00 3.85
1950 5810 6.015772 AGGTTATTTTTAAGCATTGTGGTCGT 60.016 34.615 0.00 0.00 0.00 4.34
1951 5811 6.386654 AGGTTATTTTTAAGCATTGTGGTCG 58.613 36.000 0.00 0.00 0.00 4.79
1952 5812 7.330946 GGAAGGTTATTTTTAAGCATTGTGGTC 59.669 37.037 0.00 0.00 0.00 4.02
1953 5813 7.158697 GGAAGGTTATTTTTAAGCATTGTGGT 58.841 34.615 0.00 0.00 0.00 4.16
1954 5814 6.593770 GGGAAGGTTATTTTTAAGCATTGTGG 59.406 38.462 0.00 0.00 0.00 4.17
1955 5815 7.158021 TGGGAAGGTTATTTTTAAGCATTGTG 58.842 34.615 0.00 0.00 0.00 3.33
1956 5816 7.309770 TGGGAAGGTTATTTTTAAGCATTGT 57.690 32.000 0.00 0.00 0.00 2.71
1957 5817 8.791327 ATTGGGAAGGTTATTTTTAAGCATTG 57.209 30.769 0.00 0.00 0.00 2.82
1960 5820 8.038351 GCTTATTGGGAAGGTTATTTTTAAGCA 58.962 33.333 0.00 0.00 38.30 3.91
1961 5821 7.222031 CGCTTATTGGGAAGGTTATTTTTAAGC 59.778 37.037 0.00 0.00 36.24 3.09
1962 5822 8.463607 TCGCTTATTGGGAAGGTTATTTTTAAG 58.536 33.333 0.00 0.00 34.56 1.85
1963 5823 8.350852 TCGCTTATTGGGAAGGTTATTTTTAA 57.649 30.769 0.00 0.00 34.56 1.52
1964 5824 7.941431 TCGCTTATTGGGAAGGTTATTTTTA 57.059 32.000 0.00 0.00 34.56 1.52
1970 5830 4.764050 TCATCGCTTATTGGGAAGGTTA 57.236 40.909 0.00 0.00 41.04 2.85
1977 5837 2.031683 GGACGTTTCATCGCTTATTGGG 59.968 50.000 0.00 0.00 0.00 4.12
1978 5838 2.675844 TGGACGTTTCATCGCTTATTGG 59.324 45.455 0.00 0.00 0.00 3.16
1979 5839 3.124466 TGTGGACGTTTCATCGCTTATTG 59.876 43.478 0.00 0.00 0.00 1.90
1981 5841 2.671396 GTGTGGACGTTTCATCGCTTAT 59.329 45.455 0.00 0.00 0.00 1.73
1982 5842 2.063266 GTGTGGACGTTTCATCGCTTA 58.937 47.619 0.00 0.00 0.00 3.09
1983 5843 0.865769 GTGTGGACGTTTCATCGCTT 59.134 50.000 0.00 0.00 0.00 4.68
1987 5847 3.471495 GGAATGTGTGGACGTTTCATC 57.529 47.619 0.00 0.00 31.06 2.92
2307 6167 2.590073 CACAGCTTGAGTAGTGAGTCG 58.410 52.381 0.00 0.00 33.99 4.18
2308 6168 2.928731 GCCACAGCTTGAGTAGTGAGTC 60.929 54.545 1.41 0.00 33.99 3.36
2401 6261 6.990908 TCACAGATGATGGATATCTCAGTT 57.009 37.500 2.05 0.00 32.75 3.16
2412 6287 4.698780 ACAACACAGAATCACAGATGATGG 59.301 41.667 0.00 0.00 45.26 3.51
2590 6469 2.224305 ACACAGTTCTCTAGGCACAACC 60.224 50.000 0.00 0.00 39.61 3.77
2591 6470 2.802816 CACACAGTTCTCTAGGCACAAC 59.197 50.000 0.00 0.00 0.00 3.32
2661 6540 6.374333 GGGCATGATAATTCTTTATTAGGCGA 59.626 38.462 0.00 0.00 40.17 5.54
2695 6574 6.042143 TGTTTCTCCTGAAATTGTTGCTTTC 58.958 36.000 0.00 0.00 43.14 2.62
2714 6593 7.422399 TGGTAGCTGTCAAGTTTATTTGTTTC 58.578 34.615 0.00 0.00 0.00 2.78
2811 6690 1.674441 CCCGTCTTGTAGATGCGAGTA 59.326 52.381 0.00 0.00 29.93 2.59
2853 6732 2.538512 ACCCTGTTTACTTCACCGAC 57.461 50.000 0.00 0.00 0.00 4.79
2919 6798 3.787805 GCATTTCATGTCTGTCGAGCATG 60.788 47.826 10.92 10.92 40.76 4.06
2922 6801 2.005451 AGCATTTCATGTCTGTCGAGC 58.995 47.619 0.00 0.00 0.00 5.03
3051 6930 3.375299 CGGAGGATGAATGGTTTCTTGAC 59.625 47.826 0.00 0.00 32.78 3.18
3107 6986 3.165058 TGTCTACGGCTGAACATCATC 57.835 47.619 0.00 0.00 0.00 2.92
3133 7012 2.672961 TGCTTCAGTCTATCCGTTGG 57.327 50.000 0.00 0.00 0.00 3.77
3154 7033 8.477419 AAGGTCTGTAATCAAAATCTTTTCCA 57.523 30.769 0.00 0.00 0.00 3.53
3200 7080 2.792878 AGAGCAATTGCAGCTTTCTCT 58.207 42.857 30.89 19.58 43.58 3.10
3290 7170 6.709846 AGCTTATTCTTGATATGCACTTCCTC 59.290 38.462 0.00 0.00 41.47 3.71
3349 7312 6.223120 ACCAAATTTCCTGTTACTTTGATGC 58.777 36.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.