Multiple sequence alignment - TraesCS5B01G229500

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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 TraesCS5B01G229500 chr5B 100.000 2465 0 0 484 2948 406528970 406526506 0.000000e+00 4553.0
1 TraesCS5B01G229500 chr5B 100.000 205 0 0 1 205 406529453 406529249 2.140000e-101 379.0
2 TraesCS5B01G229500 chr5B 78.443 167 35 1 2290 2455 656725810 656725976 1.120000e-19 108.0
3 TraesCS5B01G229500 chr5B 78.107 169 32 4 2290 2455 470703033 470703199 5.200000e-18 102.0
4 TraesCS5B01G229500 chr5D 92.100 1886 92 26 599 2468 345082560 345084404 0.000000e+00 2604.0
5 TraesCS5B01G229500 chr5D 92.961 483 30 2 2467 2947 345084455 345084935 0.000000e+00 701.0
6 TraesCS5B01G229500 chr5A 92.663 1581 78 18 697 2249 446638063 446636493 0.000000e+00 2242.0
7 TraesCS5B01G229500 chr5A 91.000 100 9 0 602 701 446638253 446638154 5.130000e-28 135.0
8 TraesCS5B01G229500 chr5A 86.905 84 7 2 2467 2546 446635973 446635890 1.130000e-14 91.6
9 TraesCS5B01G229500 chr5A 81.538 65 10 2 523 585 299104429 299104365 5.000000e-03 52.8
10 TraesCS5B01G229500 chr2B 95.041 121 2 2 87 205 168118618 168118500 1.400000e-43 187.0
11 TraesCS5B01G229500 chr2D 95.041 121 1 2 87 205 492080591 492080474 5.020000e-43 185.0
12 TraesCS5B01G229500 chr2D 79.116 249 25 17 2715 2947 277682249 277682486 2.370000e-31 147.0
13 TraesCS5B01G229500 chr2D 86.777 121 11 2 87 205 585738597 585738714 2.380000e-26 130.0
14 TraesCS5B01G229500 chr6B 94.215 121 2 3 87 205 599887785 599887668 2.330000e-41 180.0
15 TraesCS5B01G229500 chr1A 94.068 118 2 2 87 202 555529562 555529676 1.090000e-39 174.0
16 TraesCS5B01G229500 chr4A 89.256 121 8 2 87 205 250709580 250709697 2.370000e-31 147.0
17 TraesCS5B01G229500 chr6A 88.462 130 2 3 87 205 574228728 574228855 8.520000e-31 145.0
18 TraesCS5B01G229500 chr6A 95.506 89 4 0 87 175 62962784 62962696 3.060000e-30 143.0
19 TraesCS5B01G229500 chr6A 78.286 175 31 6 2290 2461 564880250 564880420 4.020000e-19 106.0
20 TraesCS5B01G229500 chr6A 78.395 162 33 2 2296 2455 132178565 132178404 1.450000e-18 104.0
21 TraesCS5B01G229500 chr6A 77.841 176 30 8 2290 2461 547785483 547785653 1.870000e-17 100.0
22 TraesCS5B01G229500 chr2A 80.745 161 29 2 2296 2455 53289271 53289112 1.110000e-24 124.0
23 TraesCS5B01G229500 chr2A 84.298 121 13 5 87 204 134614890 134614773 2.400000e-21 113.0
24 TraesCS5B01G229500 chr4B 79.221 154 32 0 2290 2443 41774221 41774374 1.120000e-19 108.0
25 TraesCS5B01G229500 chr3A 78.698 169 30 5 2290 2455 648872771 648872936 1.120000e-19 108.0
26 TraesCS5B01G229500 chr7D 84.874 119 3 2 484 587 633070848 633070966 4.020000e-19 106.0
27 TraesCS5B01G229500 chr7D 95.349 43 2 0 484 526 633106091 633106133 5.270000e-08 69.4
28 TraesCS5B01G229500 chrUn 79.195 149 30 1 2293 2440 94859679 94859827 5.200000e-18 102.0
29 TraesCS5B01G229500 chr7B 89.091 55 6 0 531 585 696388943 696388997 5.270000e-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 TraesCS5B01G229500 chr5B 406526506 406529453 2947 True 2466.000000 4553 100.000000 1 2948 2 chr5B.!!$R1 2947
1 TraesCS5B01G229500 chr5D 345082560 345084935 2375 False 1652.500000 2604 92.530500 599 2947 2 chr5D.!!$F1 2348
2 TraesCS5B01G229500 chr5A 446635890 446638253 2363 True 822.866667 2242 90.189333 602 2546 3 chr5A.!!$R2 1944

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
83 84 0.178975 AATCAAAACCGGGTGGAGCA 60.179 50.0 6.32 0.0 39.21 4.26 F
568 569 0.258774 AGTGGCAAGTTCAGGGTTGT 59.741 50.0 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1348 1.058404 CGTCGAACGGAAGAAAGGTC 58.942 55.0 0.00 0.00 38.08 3.85 R
2456 2848 0.320771 AACTCAGATGACACCGGTGC 60.321 55.0 34.26 25.37 0.00 5.01 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
21 22 3.434309 AGGGGTCAAAAATCTGACATGG 58.566 45.455 0.00 0.00 46.31 3.66
22 23 2.094026 GGGGTCAAAAATCTGACATGGC 60.094 50.000 0.00 0.00 46.31 4.40
23 24 2.827921 GGGTCAAAAATCTGACATGGCT 59.172 45.455 0.00 0.00 46.31 4.75
24 25 3.119352 GGGTCAAAAATCTGACATGGCTC 60.119 47.826 0.00 0.00 46.31 4.70
25 26 3.760684 GGTCAAAAATCTGACATGGCTCT 59.239 43.478 0.00 0.00 46.31 4.09
26 27 4.380233 GGTCAAAAATCTGACATGGCTCTG 60.380 45.833 0.00 0.00 46.31 3.35
27 28 3.192001 TCAAAAATCTGACATGGCTCTGC 59.808 43.478 0.00 0.00 0.00 4.26
28 29 7.837163 GTCAAAAATCTGACATGGCTCTGCC 62.837 48.000 0.00 1.01 45.77 4.85
37 38 4.025858 GGCTCTGCCTGGTCAGCA 62.026 66.667 13.38 0.00 46.69 4.41
42 43 3.239464 TGCCTGGTCAGCAGACAA 58.761 55.556 11.67 0.00 46.80 3.18
43 44 1.531259 TGCCTGGTCAGCAGACAAA 59.469 52.632 11.67 0.00 46.80 2.83
44 45 0.819259 TGCCTGGTCAGCAGACAAAC 60.819 55.000 11.67 0.00 46.80 2.93
45 46 1.845809 GCCTGGTCAGCAGACAAACG 61.846 60.000 11.67 0.00 46.80 3.60
46 47 1.230635 CCTGGTCAGCAGACAAACGG 61.231 60.000 11.67 1.80 46.80 4.44
47 48 0.532862 CTGGTCAGCAGACAAACGGT 60.533 55.000 11.67 0.00 46.80 4.83
48 49 0.531974 TGGTCAGCAGACAAACGGTC 60.532 55.000 11.67 0.00 46.80 4.79
57 58 2.844122 GACAAACGGTCAAAACTGCT 57.156 45.000 0.00 0.00 46.19 4.24
58 59 2.716398 GACAAACGGTCAAAACTGCTC 58.284 47.619 0.00 0.00 46.19 4.26
59 60 2.354821 GACAAACGGTCAAAACTGCTCT 59.645 45.455 0.00 0.00 46.19 4.09
60 61 3.537580 ACAAACGGTCAAAACTGCTCTA 58.462 40.909 0.00 0.00 34.94 2.43
61 62 3.560068 ACAAACGGTCAAAACTGCTCTAG 59.440 43.478 0.00 0.00 34.94 2.43
62 63 2.457366 ACGGTCAAAACTGCTCTAGG 57.543 50.000 0.00 0.00 34.94 3.02
63 64 1.002087 ACGGTCAAAACTGCTCTAGGG 59.998 52.381 0.00 0.00 34.94 3.53
64 65 1.275291 CGGTCAAAACTGCTCTAGGGA 59.725 52.381 0.00 0.00 0.00 4.20
65 66 2.289444 CGGTCAAAACTGCTCTAGGGAA 60.289 50.000 0.00 0.00 0.00 3.97
66 67 3.619979 CGGTCAAAACTGCTCTAGGGAAT 60.620 47.826 0.00 0.00 0.00 3.01
67 68 3.942115 GGTCAAAACTGCTCTAGGGAATC 59.058 47.826 0.00 0.00 0.00 2.52
68 69 4.565652 GGTCAAAACTGCTCTAGGGAATCA 60.566 45.833 0.00 0.00 0.00 2.57
69 70 5.003804 GTCAAAACTGCTCTAGGGAATCAA 58.996 41.667 0.00 0.00 0.00 2.57
70 71 5.473504 GTCAAAACTGCTCTAGGGAATCAAA 59.526 40.000 0.00 0.00 0.00 2.69
71 72 6.016276 GTCAAAACTGCTCTAGGGAATCAAAA 60.016 38.462 0.00 0.00 0.00 2.44
72 73 5.966742 AAACTGCTCTAGGGAATCAAAAC 57.033 39.130 0.00 0.00 0.00 2.43
73 74 3.956744 ACTGCTCTAGGGAATCAAAACC 58.043 45.455 0.00 0.00 0.00 3.27
74 75 2.939103 CTGCTCTAGGGAATCAAAACCG 59.061 50.000 0.00 0.00 0.00 4.44
75 76 2.289565 GCTCTAGGGAATCAAAACCGG 58.710 52.381 0.00 0.00 0.00 5.28
76 77 2.919228 CTCTAGGGAATCAAAACCGGG 58.081 52.381 6.32 0.00 0.00 5.73
77 78 2.238898 CTCTAGGGAATCAAAACCGGGT 59.761 50.000 6.32 0.00 0.00 5.28
78 79 2.026636 TCTAGGGAATCAAAACCGGGTG 60.027 50.000 6.32 0.17 0.00 4.61
79 80 0.251608 AGGGAATCAAAACCGGGTGG 60.252 55.000 6.32 0.00 42.84 4.61
80 81 0.251430 GGGAATCAAAACCGGGTGGA 60.251 55.000 6.32 0.25 39.21 4.02
81 82 1.173913 GGAATCAAAACCGGGTGGAG 58.826 55.000 6.32 0.00 39.21 3.86
82 83 0.526211 GAATCAAAACCGGGTGGAGC 59.474 55.000 6.32 0.00 39.21 4.70
83 84 0.178975 AATCAAAACCGGGTGGAGCA 60.179 50.000 6.32 0.00 39.21 4.26
84 85 0.609131 ATCAAAACCGGGTGGAGCAG 60.609 55.000 6.32 0.00 39.21 4.24
85 86 1.528309 CAAAACCGGGTGGAGCAGT 60.528 57.895 6.32 0.00 39.21 4.40
86 87 1.528309 AAAACCGGGTGGAGCAGTG 60.528 57.895 6.32 0.00 39.21 3.66
87 88 2.279037 AAAACCGGGTGGAGCAGTGT 62.279 55.000 6.32 0.00 39.21 3.55
88 89 2.958578 AAACCGGGTGGAGCAGTGTG 62.959 60.000 6.32 0.00 39.21 3.82
89 90 4.704833 CCGGGTGGAGCAGTGTGG 62.705 72.222 0.00 0.00 37.49 4.17
93 94 4.314440 GTGGAGCAGTGTGGCGGA 62.314 66.667 0.00 0.00 39.27 5.54
94 95 4.007644 TGGAGCAGTGTGGCGGAG 62.008 66.667 0.00 0.00 39.27 4.63
109 110 4.299796 GAGCTTGGTGGGGGCCAA 62.300 66.667 4.39 0.00 45.37 4.52
110 111 4.621087 AGCTTGGTGGGGGCCAAC 62.621 66.667 4.39 2.38 42.98 3.77
112 113 3.914713 CTTGGTGGGGGCCAACCT 61.915 66.667 23.54 0.00 41.25 3.50
113 114 4.232061 TTGGTGGGGGCCAACCTG 62.232 66.667 23.54 0.00 41.25 4.00
179 180 8.984112 ACCTTAGTATTAGGCCTATTTATCCA 57.016 34.615 14.74 0.00 36.17 3.41
180 181 8.823794 ACCTTAGTATTAGGCCTATTTATCCAC 58.176 37.037 14.74 4.94 36.17 4.02
181 182 8.265764 CCTTAGTATTAGGCCTATTTATCCACC 58.734 40.741 14.74 0.00 0.00 4.61
182 183 8.745149 TTAGTATTAGGCCTATTTATCCACCA 57.255 34.615 14.74 0.00 0.00 4.17
183 184 7.642094 AGTATTAGGCCTATTTATCCACCAA 57.358 36.000 14.74 0.00 0.00 3.67
184 185 8.052621 AGTATTAGGCCTATTTATCCACCAAA 57.947 34.615 14.74 0.00 0.00 3.28
185 186 8.507761 AGTATTAGGCCTATTTATCCACCAAAA 58.492 33.333 14.74 0.00 0.00 2.44
186 187 9.138596 GTATTAGGCCTATTTATCCACCAAAAA 57.861 33.333 14.74 0.00 0.00 1.94
187 188 8.797436 ATTAGGCCTATTTATCCACCAAAAAT 57.203 30.769 14.74 0.00 0.00 1.82
188 189 6.731292 AGGCCTATTTATCCACCAAAAATC 57.269 37.500 1.29 0.00 0.00 2.17
189 190 6.201591 AGGCCTATTTATCCACCAAAAATCA 58.798 36.000 1.29 0.00 0.00 2.57
190 191 6.845975 AGGCCTATTTATCCACCAAAAATCAT 59.154 34.615 1.29 0.00 0.00 2.45
191 192 7.348011 AGGCCTATTTATCCACCAAAAATCATT 59.652 33.333 1.29 0.00 0.00 2.57
192 193 7.657354 GGCCTATTTATCCACCAAAAATCATTC 59.343 37.037 0.00 0.00 0.00 2.67
193 194 8.203485 GCCTATTTATCCACCAAAAATCATTCA 58.797 33.333 0.00 0.00 0.00 2.57
200 201 8.977267 ATCCACCAAAAATCATTCAAAAGAAA 57.023 26.923 0.00 0.00 0.00 2.52
201 202 8.977267 TCCACCAAAAATCATTCAAAAGAAAT 57.023 26.923 0.00 0.00 0.00 2.17
202 203 9.406113 TCCACCAAAAATCATTCAAAAGAAATT 57.594 25.926 0.00 0.00 0.00 1.82
503 504 2.084546 GGAGGGTTGATTCTTGAACCG 58.915 52.381 0.00 0.00 42.33 4.44
504 505 2.084546 GAGGGTTGATTCTTGAACCGG 58.915 52.381 0.00 0.00 42.33 5.28
505 506 1.702957 AGGGTTGATTCTTGAACCGGA 59.297 47.619 9.46 0.00 42.33 5.14
506 507 2.308866 AGGGTTGATTCTTGAACCGGAT 59.691 45.455 9.46 0.00 42.33 4.18
507 508 2.423538 GGGTTGATTCTTGAACCGGATG 59.576 50.000 9.46 0.00 42.33 3.51
508 509 2.423538 GGTTGATTCTTGAACCGGATGG 59.576 50.000 9.46 0.00 42.84 3.51
518 519 4.848685 CCGGATGGTTAGTTCGGG 57.151 61.111 0.00 0.00 37.35 5.14
519 520 1.145377 CCGGATGGTTAGTTCGGGG 59.855 63.158 0.00 0.00 37.35 5.73
520 521 1.619807 CCGGATGGTTAGTTCGGGGT 61.620 60.000 0.00 0.00 37.35 4.95
521 522 0.461339 CGGATGGTTAGTTCGGGGTG 60.461 60.000 0.00 0.00 0.00 4.61
522 523 0.616891 GGATGGTTAGTTCGGGGTGT 59.383 55.000 0.00 0.00 0.00 4.16
523 524 1.832998 GGATGGTTAGTTCGGGGTGTA 59.167 52.381 0.00 0.00 0.00 2.90
524 525 2.159000 GGATGGTTAGTTCGGGGTGTAG 60.159 54.545 0.00 0.00 0.00 2.74
525 526 2.307496 TGGTTAGTTCGGGGTGTAGA 57.693 50.000 0.00 0.00 0.00 2.59
526 527 2.173519 TGGTTAGTTCGGGGTGTAGAG 58.826 52.381 0.00 0.00 0.00 2.43
527 528 2.174360 GGTTAGTTCGGGGTGTAGAGT 58.826 52.381 0.00 0.00 0.00 3.24
528 529 2.564504 GGTTAGTTCGGGGTGTAGAGTT 59.435 50.000 0.00 0.00 0.00 3.01
529 530 3.582780 GTTAGTTCGGGGTGTAGAGTTG 58.417 50.000 0.00 0.00 0.00 3.16
530 531 2.005370 AGTTCGGGGTGTAGAGTTGA 57.995 50.000 0.00 0.00 0.00 3.18
531 532 1.893801 AGTTCGGGGTGTAGAGTTGAG 59.106 52.381 0.00 0.00 0.00 3.02
532 533 1.067071 GTTCGGGGTGTAGAGTTGAGG 60.067 57.143 0.00 0.00 0.00 3.86
533 534 0.613853 TCGGGGTGTAGAGTTGAGGG 60.614 60.000 0.00 0.00 0.00 4.30
534 535 0.903454 CGGGGTGTAGAGTTGAGGGT 60.903 60.000 0.00 0.00 0.00 4.34
535 536 1.359168 GGGGTGTAGAGTTGAGGGTT 58.641 55.000 0.00 0.00 0.00 4.11
536 537 1.003233 GGGGTGTAGAGTTGAGGGTTG 59.997 57.143 0.00 0.00 0.00 3.77
537 538 1.975680 GGGTGTAGAGTTGAGGGTTGA 59.024 52.381 0.00 0.00 0.00 3.18
538 539 2.370849 GGGTGTAGAGTTGAGGGTTGAA 59.629 50.000 0.00 0.00 0.00 2.69
539 540 3.009143 GGGTGTAGAGTTGAGGGTTGAAT 59.991 47.826 0.00 0.00 0.00 2.57
540 541 4.506802 GGGTGTAGAGTTGAGGGTTGAATT 60.507 45.833 0.00 0.00 0.00 2.17
541 542 5.070685 GGTGTAGAGTTGAGGGTTGAATTT 58.929 41.667 0.00 0.00 0.00 1.82
542 543 5.535030 GGTGTAGAGTTGAGGGTTGAATTTT 59.465 40.000 0.00 0.00 0.00 1.82
543 544 6.713450 GGTGTAGAGTTGAGGGTTGAATTTTA 59.287 38.462 0.00 0.00 0.00 1.52
544 545 7.229907 GGTGTAGAGTTGAGGGTTGAATTTTAA 59.770 37.037 0.00 0.00 0.00 1.52
545 546 8.626526 GTGTAGAGTTGAGGGTTGAATTTTAAA 58.373 33.333 0.00 0.00 0.00 1.52
546 547 8.626526 TGTAGAGTTGAGGGTTGAATTTTAAAC 58.373 33.333 0.00 0.00 0.00 2.01
547 548 7.050970 AGAGTTGAGGGTTGAATTTTAAACC 57.949 36.000 0.00 0.00 44.31 3.27
548 549 5.838529 AGTTGAGGGTTGAATTTTAAACCG 58.161 37.500 2.62 0.00 45.70 4.44
549 550 5.595133 AGTTGAGGGTTGAATTTTAAACCGA 59.405 36.000 2.62 0.00 45.70 4.69
550 551 5.699097 TGAGGGTTGAATTTTAAACCGAG 57.301 39.130 2.62 0.00 45.70 4.63
551 552 5.134661 TGAGGGTTGAATTTTAAACCGAGT 58.865 37.500 2.62 0.00 45.70 4.18
552 553 5.009210 TGAGGGTTGAATTTTAAACCGAGTG 59.991 40.000 2.62 0.00 45.70 3.51
553 554 4.279922 AGGGTTGAATTTTAAACCGAGTGG 59.720 41.667 2.62 0.00 45.70 4.00
554 555 3.985279 GGTTGAATTTTAAACCGAGTGGC 59.015 43.478 3.69 0.00 39.70 5.01
555 556 4.500035 GGTTGAATTTTAAACCGAGTGGCA 60.500 41.667 3.69 0.00 39.70 4.92
556 557 4.920640 TGAATTTTAAACCGAGTGGCAA 57.079 36.364 0.00 0.00 39.70 4.52
557 558 4.865776 TGAATTTTAAACCGAGTGGCAAG 58.134 39.130 0.00 0.00 39.70 4.01
558 559 4.339814 TGAATTTTAAACCGAGTGGCAAGT 59.660 37.500 0.00 0.00 39.70 3.16
559 560 4.929819 ATTTTAAACCGAGTGGCAAGTT 57.070 36.364 0.00 0.00 39.70 2.66
560 561 3.974871 TTTAAACCGAGTGGCAAGTTC 57.025 42.857 0.00 0.00 39.70 3.01
561 562 2.623878 TAAACCGAGTGGCAAGTTCA 57.376 45.000 0.00 0.00 39.70 3.18
562 563 1.308998 AAACCGAGTGGCAAGTTCAG 58.691 50.000 0.00 0.00 39.70 3.02
563 564 0.535102 AACCGAGTGGCAAGTTCAGG 60.535 55.000 0.00 0.00 39.70 3.86
564 565 1.672356 CCGAGTGGCAAGTTCAGGG 60.672 63.158 0.00 0.00 0.00 4.45
565 566 1.071471 CGAGTGGCAAGTTCAGGGT 59.929 57.895 0.00 0.00 0.00 4.34
566 567 0.535102 CGAGTGGCAAGTTCAGGGTT 60.535 55.000 0.00 0.00 0.00 4.11
567 568 0.954452 GAGTGGCAAGTTCAGGGTTG 59.046 55.000 0.00 0.00 0.00 3.77
568 569 0.258774 AGTGGCAAGTTCAGGGTTGT 59.741 50.000 0.00 0.00 0.00 3.32
569 570 1.493022 AGTGGCAAGTTCAGGGTTGTA 59.507 47.619 0.00 0.00 0.00 2.41
570 571 2.092103 AGTGGCAAGTTCAGGGTTGTAA 60.092 45.455 0.00 0.00 0.00 2.41
571 572 2.691011 GTGGCAAGTTCAGGGTTGTAAA 59.309 45.455 0.00 0.00 0.00 2.01
572 573 2.955660 TGGCAAGTTCAGGGTTGTAAAG 59.044 45.455 0.00 0.00 0.00 1.85
573 574 2.956333 GGCAAGTTCAGGGTTGTAAAGT 59.044 45.455 0.00 0.00 0.00 2.66
574 575 3.243401 GGCAAGTTCAGGGTTGTAAAGTG 60.243 47.826 0.00 0.00 0.00 3.16
575 576 3.243401 GCAAGTTCAGGGTTGTAAAGTGG 60.243 47.826 0.00 0.00 0.00 4.00
576 577 4.204012 CAAGTTCAGGGTTGTAAAGTGGA 58.796 43.478 0.00 0.00 0.00 4.02
577 578 4.724279 AGTTCAGGGTTGTAAAGTGGAT 57.276 40.909 0.00 0.00 0.00 3.41
578 579 5.061721 AGTTCAGGGTTGTAAAGTGGATT 57.938 39.130 0.00 0.00 0.00 3.01
579 580 5.454966 AGTTCAGGGTTGTAAAGTGGATTT 58.545 37.500 0.00 0.00 34.72 2.17
580 581 5.535030 AGTTCAGGGTTGTAAAGTGGATTTC 59.465 40.000 0.00 0.00 32.01 2.17
581 582 5.319043 TCAGGGTTGTAAAGTGGATTTCT 57.681 39.130 0.00 0.00 32.01 2.52
582 583 5.313712 TCAGGGTTGTAAAGTGGATTTCTC 58.686 41.667 0.00 0.00 32.01 2.87
583 584 5.073144 TCAGGGTTGTAAAGTGGATTTCTCT 59.927 40.000 0.00 0.00 32.01 3.10
584 585 5.412904 CAGGGTTGTAAAGTGGATTTCTCTC 59.587 44.000 0.00 0.00 32.01 3.20
585 586 5.310857 AGGGTTGTAAAGTGGATTTCTCTCT 59.689 40.000 0.00 0.00 32.01 3.10
586 587 6.500751 AGGGTTGTAAAGTGGATTTCTCTCTA 59.499 38.462 0.00 0.00 32.01 2.43
587 588 6.594547 GGGTTGTAAAGTGGATTTCTCTCTAC 59.405 42.308 0.00 0.00 32.01 2.59
588 589 6.594547 GGTTGTAAAGTGGATTTCTCTCTACC 59.405 42.308 0.00 0.00 32.01 3.18
589 590 6.928348 TGTAAAGTGGATTTCTCTCTACCA 57.072 37.500 0.00 0.00 32.01 3.25
590 591 7.496346 TGTAAAGTGGATTTCTCTCTACCAT 57.504 36.000 0.00 0.00 33.19 3.55
591 592 8.603898 TGTAAAGTGGATTTCTCTCTACCATA 57.396 34.615 0.00 0.00 33.19 2.74
592 593 9.213777 TGTAAAGTGGATTTCTCTCTACCATAT 57.786 33.333 0.00 0.00 33.19 1.78
599 600 9.702253 TGGATTTCTCTCTACCATATATAGTCC 57.298 37.037 0.00 0.00 0.00 3.85
600 601 9.138596 GGATTTCTCTCTACCATATATAGTCCC 57.861 40.741 0.00 0.00 0.00 4.46
678 679 3.490249 CCAATCGACGTGGCTATGTTAGA 60.490 47.826 0.00 0.27 0.00 2.10
681 682 2.946990 TCGACGTGGCTATGTTAGATCA 59.053 45.455 0.00 0.00 0.00 2.92
694 695 4.460263 TGTTAGATCAGGTGCAAAAGTGT 58.540 39.130 0.00 0.00 0.00 3.55
732 828 4.679373 TTGGCATGCAACCTTTTCTTAA 57.321 36.364 21.36 0.00 0.00 1.85
755 852 5.458041 AAGACATGTTTGGTCATCCTTTG 57.542 39.130 0.00 0.00 37.74 2.77
799 896 1.609208 ACTTGCCACATGAACAGGAC 58.391 50.000 0.00 0.00 0.00 3.85
951 1069 1.954146 GAGCGCACCACTCAAACGA 60.954 57.895 11.47 0.00 34.18 3.85
952 1070 1.495584 GAGCGCACCACTCAAACGAA 61.496 55.000 11.47 0.00 34.18 3.85
953 1071 1.092921 AGCGCACCACTCAAACGAAA 61.093 50.000 11.47 0.00 0.00 3.46
954 1072 0.928451 GCGCACCACTCAAACGAAAC 60.928 55.000 0.30 0.00 0.00 2.78
955 1073 0.653323 CGCACCACTCAAACGAAACG 60.653 55.000 0.00 0.00 0.00 3.60
1227 1348 0.243907 AGATGTTCGTGGACCACTCG 59.756 55.000 22.14 10.51 31.34 4.18
1233 1354 1.111116 TCGTGGACCACTCGACCTTT 61.111 55.000 22.14 0.00 31.34 3.11
1236 1357 1.070289 GTGGACCACTCGACCTTTCTT 59.930 52.381 17.84 0.00 0.00 2.52
1305 1426 1.227645 GCACGCCATCATCTGCCTA 60.228 57.895 0.00 0.00 0.00 3.93
1551 1672 3.941657 GAGCTTCGCCGTGAGCCTT 62.942 63.158 10.62 0.00 38.78 4.35
1755 1876 1.548719 TGGTACCTGTCCTTCATGACG 59.451 52.381 14.36 0.00 38.11 4.35
1779 1900 2.799371 GTCCTCGCGGTCTACCTG 59.201 66.667 6.13 0.00 0.00 4.00
1796 1917 0.717784 CTGTACGTGTGCAGCAGATG 59.282 55.000 10.20 10.20 36.56 2.90
1819 1940 4.796231 CCGAGCAAGCCTACGCGT 62.796 66.667 19.17 19.17 41.18 6.01
1913 2034 3.071459 GCGACAGCGACGTTCATGG 62.071 63.158 0.00 0.00 40.82 3.66
1984 2106 0.465824 TAGCTAGAGTCCCCGCAGAC 60.466 60.000 0.00 0.00 37.01 3.51
1985 2107 2.787567 GCTAGAGTCCCCGCAGACC 61.788 68.421 0.00 0.00 37.49 3.85
2007 2132 3.434641 CCATTGTACAGTGCTTGTCTGAG 59.565 47.826 12.62 0.00 41.29 3.35
2014 2139 3.070734 ACAGTGCTTGTCTGAGTCTGAAT 59.929 43.478 0.70 0.00 33.87 2.57
2022 2151 6.035866 GCTTGTCTGAGTCTGAATGTTATCTG 59.964 42.308 0.70 0.00 0.00 2.90
2041 2170 3.448660 TCTGCGAATATCCATGGATCGAT 59.551 43.478 30.98 19.23 36.17 3.59
2056 2185 3.124900 CGATCGGTTCGTACTCGTC 57.875 57.895 7.38 0.00 43.01 4.20
2092 2221 3.575965 CCTCGCTTTTTACAGGCATTT 57.424 42.857 0.00 0.00 0.00 2.32
2097 2226 3.674753 CGCTTTTTACAGGCATTTGAAGG 59.325 43.478 0.00 0.00 0.00 3.46
2128 2257 4.897140 TGCTTATCAAAAGGCAAAAGCAT 58.103 34.783 3.60 0.00 43.03 3.79
2154 2283 6.183360 GCATTGATTGGAGACGAAGACAAATA 60.183 38.462 0.00 0.00 0.00 1.40
2155 2284 6.968131 TTGATTGGAGACGAAGACAAATAG 57.032 37.500 0.00 0.00 0.00 1.73
2161 2290 3.933332 GAGACGAAGACAAATAGGTTGGG 59.067 47.826 0.00 0.00 41.97 4.12
2200 2329 3.313012 TGATCGAGTTCGGTGAAACAT 57.687 42.857 1.26 0.00 39.98 2.71
2231 2364 6.424032 ACTCCAAAGGTAAGTTTCTGTTTCT 58.576 36.000 0.00 0.00 0.00 2.52
2235 2368 7.394923 TCCAAAGGTAAGTTTCTGTTTCTCAAA 59.605 33.333 0.00 0.00 0.00 2.69
2270 2661 7.277760 AGGTAAGTTTTTGTGATGCTTTTTCAC 59.722 33.333 0.00 0.00 43.04 3.18
2275 2666 2.844946 TGTGATGCTTTTTCACGGAGA 58.155 42.857 0.00 0.00 45.14 3.71
2293 2684 2.275812 CGGACAATTCGCGCGAAC 60.276 61.111 43.50 30.51 36.91 3.95
2294 2685 2.275812 GGACAATTCGCGCGAACG 60.276 61.111 43.50 36.40 44.07 3.95
2315 2706 1.335132 ACGCACACCCTACCCCTATG 61.335 60.000 0.00 0.00 0.00 2.23
2317 2708 1.209621 GCACACCCTACCCCTATGAA 58.790 55.000 0.00 0.00 0.00 2.57
2326 2717 2.642171 ACCCCTATGAACACCTCTGA 57.358 50.000 0.00 0.00 0.00 3.27
2341 2732 2.293170 CTCTGAGATACTGAGCCGACA 58.707 52.381 0.00 0.00 37.65 4.35
2342 2733 2.884012 CTCTGAGATACTGAGCCGACAT 59.116 50.000 0.00 0.00 37.65 3.06
2350 2742 1.135915 ACTGAGCCGACATCACATCTC 59.864 52.381 0.00 0.00 0.00 2.75
2353 2745 1.592669 GCCGACATCACATCTCGGG 60.593 63.158 7.39 0.00 45.90 5.14
2354 2746 2.016393 GCCGACATCACATCTCGGGA 62.016 60.000 7.39 0.00 45.90 5.14
2355 2747 0.676184 CCGACATCACATCTCGGGAT 59.324 55.000 0.00 0.00 42.76 3.85
2356 2748 1.069204 CCGACATCACATCTCGGGATT 59.931 52.381 0.00 0.00 42.76 3.01
2357 2749 2.130395 CGACATCACATCTCGGGATTG 58.870 52.381 0.00 0.00 0.00 2.67
2358 2750 2.223805 CGACATCACATCTCGGGATTGA 60.224 50.000 11.05 11.05 0.00 2.57
2359 2751 3.126831 GACATCACATCTCGGGATTGAC 58.873 50.000 10.92 0.00 0.00 3.18
2374 2766 4.191544 GGATTGACGAAATCATCACAGGA 58.808 43.478 14.50 0.00 45.69 3.86
2379 2771 4.021104 TGACGAAATCATCACAGGAGTCTT 60.021 41.667 0.00 0.00 29.99 3.01
2394 2786 6.102663 CAGGAGTCTTGTAGTCGATGAAAAT 58.897 40.000 0.00 0.00 0.00 1.82
2396 2788 5.292101 GGAGTCTTGTAGTCGATGAAAATGG 59.708 44.000 0.00 0.00 0.00 3.16
2398 2790 4.391830 GTCTTGTAGTCGATGAAAATGGCA 59.608 41.667 0.00 0.00 0.00 4.92
2408 2800 4.464008 GATGAAAATGGCATCTCCCACTA 58.536 43.478 0.00 0.00 39.18 2.74
2420 2812 1.659098 CTCCCACTAAACGAACATCGC 59.341 52.381 0.00 0.00 45.12 4.58
2421 2813 1.274167 TCCCACTAAACGAACATCGCT 59.726 47.619 0.00 0.00 45.12 4.93
2428 2820 3.471495 AAACGAACATCGCTGGAAATC 57.529 42.857 0.00 0.00 45.12 2.17
2434 2826 2.359900 ACATCGCTGGAAATCCTGAAC 58.640 47.619 10.20 0.00 37.15 3.18
2440 2832 5.253330 TCGCTGGAAATCCTGAACTAAATT 58.747 37.500 10.20 0.00 37.15 1.82
2456 2848 9.151471 TGAACTAAATTCAGGAAAATACGAGAG 57.849 33.333 0.00 0.00 42.62 3.20
2458 2850 7.103641 ACTAAATTCAGGAAAATACGAGAGCA 58.896 34.615 0.00 0.00 0.00 4.26
2459 2851 5.803020 AATTCAGGAAAATACGAGAGCAC 57.197 39.130 0.00 0.00 0.00 4.40
2460 2852 3.247006 TCAGGAAAATACGAGAGCACC 57.753 47.619 0.00 0.00 0.00 5.01
2461 2853 1.927174 CAGGAAAATACGAGAGCACCG 59.073 52.381 0.00 0.00 0.00 4.94
2464 2856 1.659098 GAAAATACGAGAGCACCGGTG 59.341 52.381 30.66 30.66 0.00 4.94
2465 2857 0.606604 AAATACGAGAGCACCGGTGT 59.393 50.000 33.92 21.33 0.00 4.16
2525 2969 0.332632 AAATGGCAAGCCTCCTAGCA 59.667 50.000 12.96 0.00 36.94 3.49
2527 2971 1.438469 ATGGCAAGCCTCCTAGCATA 58.562 50.000 12.96 0.00 36.94 3.14
2581 3029 3.445096 AGACGGTAATAGTAACGCCAAGT 59.555 43.478 7.68 0.00 44.63 3.16
2629 3077 1.377333 GGGGGAAAAGAGGTGAGCG 60.377 63.158 0.00 0.00 0.00 5.03
2636 3084 3.119101 GGAAAAGAGGTGAGCGATAGACA 60.119 47.826 0.00 0.00 39.76 3.41
2643 3091 0.823460 TGAGCGATAGACATGGCACA 59.177 50.000 0.00 0.00 38.28 4.57
2702 3150 0.605319 TGTCAATTGCCGACAGGGAC 60.605 55.000 0.00 0.00 38.45 4.46
2725 3173 4.261572 CGTTGGAAGGACATCAAACACAAT 60.262 41.667 0.00 0.00 33.60 2.71
2732 3180 4.218417 AGGACATCAAACACAATAAGGTGC 59.782 41.667 0.00 0.00 42.55 5.01
2735 3183 2.577700 TCAAACACAATAAGGTGCGGT 58.422 42.857 0.00 0.00 42.55 5.68
2743 3191 0.107361 ATAAGGTGCGGTGTAAGGGC 60.107 55.000 0.00 0.00 0.00 5.19
2765 3213 3.120511 CGATCTCTCGCGATGTTCATCTA 60.121 47.826 10.36 0.00 38.20 1.98
2816 3264 2.115291 GGAGAAACGGATGCCCAGC 61.115 63.158 0.00 0.00 0.00 4.85
2904 3352 2.966732 GCGGTCTCCCCCACAATCA 61.967 63.158 0.00 0.00 0.00 2.57
2905 3353 1.078426 CGGTCTCCCCCACAATCAC 60.078 63.158 0.00 0.00 0.00 3.06
2911 3359 1.606313 CCCCCACAATCACCACCAC 60.606 63.158 0.00 0.00 0.00 4.16
2922 3370 0.535102 CACCACCACCACCACTTCTC 60.535 60.000 0.00 0.00 0.00 2.87
2925 3373 2.358737 CCACCACCACTTCTCGCC 60.359 66.667 0.00 0.00 0.00 5.54
2926 3374 2.743718 CACCACCACTTCTCGCCT 59.256 61.111 0.00 0.00 0.00 5.52
2947 3395 0.491823 TCTCCTCACCTTCTCCCCAA 59.508 55.000 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.434309 CCATGTCAGATTTTTGACCCCT 58.566 45.455 3.94 0.00 45.40 4.79
1 2 2.094026 GCCATGTCAGATTTTTGACCCC 60.094 50.000 3.94 0.00 45.40 4.95
2 3 2.827921 AGCCATGTCAGATTTTTGACCC 59.172 45.455 3.94 0.00 45.40 4.46
3 4 3.760684 AGAGCCATGTCAGATTTTTGACC 59.239 43.478 3.94 0.00 45.40 4.02
4 5 4.730657 CAGAGCCATGTCAGATTTTTGAC 58.269 43.478 0.00 0.00 46.02 3.18
5 6 3.192001 GCAGAGCCATGTCAGATTTTTGA 59.808 43.478 0.00 0.00 0.00 2.69
6 7 3.508762 GCAGAGCCATGTCAGATTTTTG 58.491 45.455 0.00 0.00 0.00 2.44
7 8 3.863142 GCAGAGCCATGTCAGATTTTT 57.137 42.857 0.00 0.00 0.00 1.94
26 27 1.845809 CGTTTGTCTGCTGACCAGGC 61.846 60.000 19.64 7.67 46.47 4.85
27 28 1.230635 CCGTTTGTCTGCTGACCAGG 61.231 60.000 19.64 13.39 42.28 4.45
28 29 0.532862 ACCGTTTGTCTGCTGACCAG 60.533 55.000 19.64 8.96 42.28 4.00
29 30 0.531974 GACCGTTTGTCTGCTGACCA 60.532 55.000 19.64 7.33 42.28 4.02
30 31 0.531974 TGACCGTTTGTCTGCTGACC 60.532 55.000 19.64 5.05 44.75 4.02
31 32 1.295792 TTGACCGTTTGTCTGCTGAC 58.704 50.000 16.18 16.18 44.75 3.51
32 33 2.031258 TTTGACCGTTTGTCTGCTGA 57.969 45.000 0.00 0.00 44.75 4.26
33 34 2.097466 AGTTTTGACCGTTTGTCTGCTG 59.903 45.455 0.00 0.00 44.75 4.41
34 35 2.097466 CAGTTTTGACCGTTTGTCTGCT 59.903 45.455 0.00 0.00 44.75 4.24
35 36 2.450160 CAGTTTTGACCGTTTGTCTGC 58.550 47.619 0.00 0.00 44.75 4.26
36 37 2.097466 AGCAGTTTTGACCGTTTGTCTG 59.903 45.455 0.00 0.00 44.75 3.51
37 38 2.354821 GAGCAGTTTTGACCGTTTGTCT 59.645 45.455 0.00 0.00 44.75 3.41
38 39 2.354821 AGAGCAGTTTTGACCGTTTGTC 59.645 45.455 0.00 0.00 44.72 3.18
39 40 2.365582 AGAGCAGTTTTGACCGTTTGT 58.634 42.857 0.00 0.00 0.00 2.83
40 41 3.058914 CCTAGAGCAGTTTTGACCGTTTG 60.059 47.826 0.00 0.00 0.00 2.93
41 42 3.139077 CCTAGAGCAGTTTTGACCGTTT 58.861 45.455 0.00 0.00 0.00 3.60
42 43 2.550208 CCCTAGAGCAGTTTTGACCGTT 60.550 50.000 0.00 0.00 0.00 4.44
43 44 1.002087 CCCTAGAGCAGTTTTGACCGT 59.998 52.381 0.00 0.00 0.00 4.83
44 45 1.275291 TCCCTAGAGCAGTTTTGACCG 59.725 52.381 0.00 0.00 0.00 4.79
45 46 3.418684 TTCCCTAGAGCAGTTTTGACC 57.581 47.619 0.00 0.00 0.00 4.02
46 47 4.579869 TGATTCCCTAGAGCAGTTTTGAC 58.420 43.478 0.00 0.00 0.00 3.18
47 48 4.908601 TGATTCCCTAGAGCAGTTTTGA 57.091 40.909 0.00 0.00 0.00 2.69
48 49 5.964958 TTTGATTCCCTAGAGCAGTTTTG 57.035 39.130 0.00 0.00 0.00 2.44
49 50 5.243954 GGTTTTGATTCCCTAGAGCAGTTTT 59.756 40.000 0.00 0.00 0.00 2.43
50 51 4.767409 GGTTTTGATTCCCTAGAGCAGTTT 59.233 41.667 0.00 0.00 0.00 2.66
51 52 4.336280 GGTTTTGATTCCCTAGAGCAGTT 58.664 43.478 0.00 0.00 0.00 3.16
52 53 3.619979 CGGTTTTGATTCCCTAGAGCAGT 60.620 47.826 0.00 0.00 0.00 4.40
53 54 2.939103 CGGTTTTGATTCCCTAGAGCAG 59.061 50.000 0.00 0.00 0.00 4.24
54 55 2.355716 CCGGTTTTGATTCCCTAGAGCA 60.356 50.000 0.00 0.00 0.00 4.26
55 56 2.289565 CCGGTTTTGATTCCCTAGAGC 58.710 52.381 0.00 0.00 0.00 4.09
56 57 2.238898 ACCCGGTTTTGATTCCCTAGAG 59.761 50.000 0.00 0.00 0.00 2.43
57 58 2.026636 CACCCGGTTTTGATTCCCTAGA 60.027 50.000 0.00 0.00 0.00 2.43
58 59 2.365582 CACCCGGTTTTGATTCCCTAG 58.634 52.381 0.00 0.00 0.00 3.02
59 60 1.004979 CCACCCGGTTTTGATTCCCTA 59.995 52.381 0.00 0.00 0.00 3.53
60 61 0.251608 CCACCCGGTTTTGATTCCCT 60.252 55.000 0.00 0.00 0.00 4.20
61 62 0.251430 TCCACCCGGTTTTGATTCCC 60.251 55.000 0.00 0.00 0.00 3.97
62 63 1.173913 CTCCACCCGGTTTTGATTCC 58.826 55.000 0.00 0.00 0.00 3.01
63 64 0.526211 GCTCCACCCGGTTTTGATTC 59.474 55.000 0.00 0.00 0.00 2.52
64 65 0.178975 TGCTCCACCCGGTTTTGATT 60.179 50.000 0.00 0.00 0.00 2.57
65 66 0.609131 CTGCTCCACCCGGTTTTGAT 60.609 55.000 0.00 0.00 0.00 2.57
66 67 1.228124 CTGCTCCACCCGGTTTTGA 60.228 57.895 0.00 0.00 0.00 2.69
67 68 1.528309 ACTGCTCCACCCGGTTTTG 60.528 57.895 0.00 0.00 0.00 2.44
68 69 1.528309 CACTGCTCCACCCGGTTTT 60.528 57.895 0.00 0.00 0.00 2.43
69 70 2.113139 CACTGCTCCACCCGGTTT 59.887 61.111 0.00 0.00 0.00 3.27
70 71 3.168528 ACACTGCTCCACCCGGTT 61.169 61.111 0.00 0.00 0.00 4.44
71 72 3.941188 CACACTGCTCCACCCGGT 61.941 66.667 0.00 0.00 0.00 5.28
72 73 4.704833 CCACACTGCTCCACCCGG 62.705 72.222 0.00 0.00 0.00 5.73
76 77 4.314440 TCCGCCACACTGCTCCAC 62.314 66.667 0.00 0.00 0.00 4.02
77 78 4.007644 CTCCGCCACACTGCTCCA 62.008 66.667 0.00 0.00 0.00 3.86
79 80 3.890936 AAGCTCCGCCACACTGCTC 62.891 63.158 0.00 0.00 33.10 4.26
80 81 3.946201 AAGCTCCGCCACACTGCT 61.946 61.111 0.00 0.00 35.30 4.24
81 82 3.730761 CAAGCTCCGCCACACTGC 61.731 66.667 0.00 0.00 0.00 4.40
82 83 3.052082 CCAAGCTCCGCCACACTG 61.052 66.667 0.00 0.00 0.00 3.66
83 84 3.560251 ACCAAGCTCCGCCACACT 61.560 61.111 0.00 0.00 0.00 3.55
84 85 3.357079 CACCAAGCTCCGCCACAC 61.357 66.667 0.00 0.00 0.00 3.82
85 86 4.641645 CCACCAAGCTCCGCCACA 62.642 66.667 0.00 0.00 0.00 4.17
92 93 4.299796 TTGGCCCCCACCAAGCTC 62.300 66.667 0.00 0.00 44.80 4.09
154 155 8.823794 GTGGATAAATAGGCCTAATACTAAGGT 58.176 37.037 18.42 0.00 36.43 3.50
155 156 8.265764 GGTGGATAAATAGGCCTAATACTAAGG 58.734 40.741 18.42 0.00 37.17 2.69
156 157 8.822805 TGGTGGATAAATAGGCCTAATACTAAG 58.177 37.037 18.42 0.00 0.00 2.18
157 158 8.745149 TGGTGGATAAATAGGCCTAATACTAA 57.255 34.615 18.42 0.00 0.00 2.24
158 159 8.745149 TTGGTGGATAAATAGGCCTAATACTA 57.255 34.615 18.42 6.27 0.00 1.82
159 160 7.642094 TTGGTGGATAAATAGGCCTAATACT 57.358 36.000 18.42 2.00 0.00 2.12
160 161 8.700439 TTTTGGTGGATAAATAGGCCTAATAC 57.300 34.615 18.42 7.42 0.00 1.89
161 162 9.890915 ATTTTTGGTGGATAAATAGGCCTAATA 57.109 29.630 18.42 13.51 0.00 0.98
162 163 8.797436 ATTTTTGGTGGATAAATAGGCCTAAT 57.203 30.769 18.42 5.27 0.00 1.73
163 164 7.841729 TGATTTTTGGTGGATAAATAGGCCTAA 59.158 33.333 18.42 0.00 0.00 2.69
164 165 7.358263 TGATTTTTGGTGGATAAATAGGCCTA 58.642 34.615 16.60 16.60 0.00 3.93
165 166 6.201591 TGATTTTTGGTGGATAAATAGGCCT 58.798 36.000 11.78 11.78 0.00 5.19
166 167 6.478512 TGATTTTTGGTGGATAAATAGGCC 57.521 37.500 0.00 0.00 0.00 5.19
167 168 8.203485 TGAATGATTTTTGGTGGATAAATAGGC 58.797 33.333 0.00 0.00 0.00 3.93
175 176 8.977267 TTTCTTTTGAATGATTTTTGGTGGAT 57.023 26.923 0.00 0.00 38.37 3.41
176 177 8.977267 ATTTCTTTTGAATGATTTTTGGTGGA 57.023 26.923 0.00 0.00 38.37 4.02
483 484 2.084546 CGGTTCAAGAATCAACCCTCC 58.915 52.381 0.00 0.00 39.22 4.30
484 485 2.084546 CCGGTTCAAGAATCAACCCTC 58.915 52.381 0.00 0.00 39.22 4.30
485 486 1.702957 TCCGGTTCAAGAATCAACCCT 59.297 47.619 0.00 0.00 39.22 4.34
486 487 2.194201 TCCGGTTCAAGAATCAACCC 57.806 50.000 0.00 0.00 39.22 4.11
487 488 2.423538 CCATCCGGTTCAAGAATCAACC 59.576 50.000 0.00 0.00 39.04 3.77
488 489 3.081804 ACCATCCGGTTCAAGAATCAAC 58.918 45.455 0.00 0.00 46.31 3.18
489 490 3.433306 ACCATCCGGTTCAAGAATCAA 57.567 42.857 0.00 0.00 46.31 2.57
501 502 1.145377 CCCCGAACTAACCATCCGG 59.855 63.158 0.00 0.00 39.85 5.14
502 503 0.461339 CACCCCGAACTAACCATCCG 60.461 60.000 0.00 0.00 0.00 4.18
503 504 0.616891 ACACCCCGAACTAACCATCC 59.383 55.000 0.00 0.00 0.00 3.51
504 505 2.762327 TCTACACCCCGAACTAACCATC 59.238 50.000 0.00 0.00 0.00 3.51
505 506 2.764572 CTCTACACCCCGAACTAACCAT 59.235 50.000 0.00 0.00 0.00 3.55
506 507 2.173519 CTCTACACCCCGAACTAACCA 58.826 52.381 0.00 0.00 0.00 3.67
507 508 2.174360 ACTCTACACCCCGAACTAACC 58.826 52.381 0.00 0.00 0.00 2.85
508 509 3.256631 TCAACTCTACACCCCGAACTAAC 59.743 47.826 0.00 0.00 0.00 2.34
509 510 3.499338 TCAACTCTACACCCCGAACTAA 58.501 45.455 0.00 0.00 0.00 2.24
510 511 3.087031 CTCAACTCTACACCCCGAACTA 58.913 50.000 0.00 0.00 0.00 2.24
511 512 1.893801 CTCAACTCTACACCCCGAACT 59.106 52.381 0.00 0.00 0.00 3.01
512 513 1.067071 CCTCAACTCTACACCCCGAAC 60.067 57.143 0.00 0.00 0.00 3.95
513 514 1.263356 CCTCAACTCTACACCCCGAA 58.737 55.000 0.00 0.00 0.00 4.30
514 515 0.613853 CCCTCAACTCTACACCCCGA 60.614 60.000 0.00 0.00 0.00 5.14
515 516 0.903454 ACCCTCAACTCTACACCCCG 60.903 60.000 0.00 0.00 0.00 5.73
516 517 1.003233 CAACCCTCAACTCTACACCCC 59.997 57.143 0.00 0.00 0.00 4.95
517 518 1.975680 TCAACCCTCAACTCTACACCC 59.024 52.381 0.00 0.00 0.00 4.61
518 519 3.764237 TTCAACCCTCAACTCTACACC 57.236 47.619 0.00 0.00 0.00 4.16
519 520 6.635030 AAAATTCAACCCTCAACTCTACAC 57.365 37.500 0.00 0.00 0.00 2.90
520 521 8.626526 GTTTAAAATTCAACCCTCAACTCTACA 58.373 33.333 0.00 0.00 0.00 2.74
521 522 8.080417 GGTTTAAAATTCAACCCTCAACTCTAC 58.920 37.037 0.00 0.00 37.11 2.59
522 523 7.040961 CGGTTTAAAATTCAACCCTCAACTCTA 60.041 37.037 4.18 0.00 39.58 2.43
523 524 6.238925 CGGTTTAAAATTCAACCCTCAACTCT 60.239 38.462 4.18 0.00 39.58 3.24
524 525 5.918576 CGGTTTAAAATTCAACCCTCAACTC 59.081 40.000 4.18 0.00 39.58 3.01
525 526 5.595133 TCGGTTTAAAATTCAACCCTCAACT 59.405 36.000 4.18 0.00 39.58 3.16
526 527 5.834169 TCGGTTTAAAATTCAACCCTCAAC 58.166 37.500 4.18 0.00 39.58 3.18
527 528 5.595133 ACTCGGTTTAAAATTCAACCCTCAA 59.405 36.000 4.18 0.00 39.58 3.02
528 529 5.009210 CACTCGGTTTAAAATTCAACCCTCA 59.991 40.000 4.18 0.00 39.58 3.86
529 530 5.458015 CACTCGGTTTAAAATTCAACCCTC 58.542 41.667 4.18 0.00 39.58 4.30
530 531 4.279922 CCACTCGGTTTAAAATTCAACCCT 59.720 41.667 4.18 0.00 39.58 4.34
531 532 4.552355 CCACTCGGTTTAAAATTCAACCC 58.448 43.478 4.18 0.00 39.58 4.11
532 533 3.985279 GCCACTCGGTTTAAAATTCAACC 59.015 43.478 0.00 0.13 39.38 3.77
533 534 4.612943 TGCCACTCGGTTTAAAATTCAAC 58.387 39.130 0.00 0.00 33.28 3.18
534 535 4.920640 TGCCACTCGGTTTAAAATTCAA 57.079 36.364 0.00 0.00 33.28 2.69
535 536 4.339814 ACTTGCCACTCGGTTTAAAATTCA 59.660 37.500 0.00 0.00 33.28 2.57
536 537 4.866921 ACTTGCCACTCGGTTTAAAATTC 58.133 39.130 0.00 0.00 33.28 2.17
537 538 4.929819 ACTTGCCACTCGGTTTAAAATT 57.070 36.364 0.00 0.00 33.28 1.82
538 539 4.339814 TGAACTTGCCACTCGGTTTAAAAT 59.660 37.500 0.00 0.00 33.28 1.82
539 540 3.695060 TGAACTTGCCACTCGGTTTAAAA 59.305 39.130 0.00 0.00 33.28 1.52
540 541 3.280295 TGAACTTGCCACTCGGTTTAAA 58.720 40.909 0.00 0.00 33.28 1.52
541 542 2.875933 CTGAACTTGCCACTCGGTTTAA 59.124 45.455 0.00 0.00 33.28 1.52
542 543 2.489971 CTGAACTTGCCACTCGGTTTA 58.510 47.619 0.00 0.00 33.28 2.01
543 544 1.308998 CTGAACTTGCCACTCGGTTT 58.691 50.000 0.00 0.00 33.28 3.27
544 545 0.535102 CCTGAACTTGCCACTCGGTT 60.535 55.000 0.00 0.00 33.28 4.44
545 546 1.071471 CCTGAACTTGCCACTCGGT 59.929 57.895 0.00 0.00 33.28 4.69
546 547 1.672356 CCCTGAACTTGCCACTCGG 60.672 63.158 0.00 0.00 0.00 4.63
547 548 0.535102 AACCCTGAACTTGCCACTCG 60.535 55.000 0.00 0.00 0.00 4.18
548 549 0.954452 CAACCCTGAACTTGCCACTC 59.046 55.000 0.00 0.00 0.00 3.51
549 550 0.258774 ACAACCCTGAACTTGCCACT 59.741 50.000 0.00 0.00 0.00 4.00
550 551 1.975660 TACAACCCTGAACTTGCCAC 58.024 50.000 0.00 0.00 0.00 5.01
551 552 2.738587 TTACAACCCTGAACTTGCCA 57.261 45.000 0.00 0.00 0.00 4.92
552 553 2.956333 ACTTTACAACCCTGAACTTGCC 59.044 45.455 0.00 0.00 0.00 4.52
553 554 3.243401 CCACTTTACAACCCTGAACTTGC 60.243 47.826 0.00 0.00 0.00 4.01
554 555 4.204012 TCCACTTTACAACCCTGAACTTG 58.796 43.478 0.00 0.00 0.00 3.16
555 556 4.513406 TCCACTTTACAACCCTGAACTT 57.487 40.909 0.00 0.00 0.00 2.66
556 557 4.724279 ATCCACTTTACAACCCTGAACT 57.276 40.909 0.00 0.00 0.00 3.01
557 558 5.535030 AGAAATCCACTTTACAACCCTGAAC 59.465 40.000 0.00 0.00 0.00 3.18
558 559 5.701224 AGAAATCCACTTTACAACCCTGAA 58.299 37.500 0.00 0.00 0.00 3.02
559 560 5.073144 AGAGAAATCCACTTTACAACCCTGA 59.927 40.000 0.00 0.00 0.00 3.86
560 561 5.316987 AGAGAAATCCACTTTACAACCCTG 58.683 41.667 0.00 0.00 0.00 4.45
561 562 5.310857 AGAGAGAAATCCACTTTACAACCCT 59.689 40.000 0.00 0.00 0.00 4.34
562 563 5.561679 AGAGAGAAATCCACTTTACAACCC 58.438 41.667 0.00 0.00 0.00 4.11
563 564 6.594547 GGTAGAGAGAAATCCACTTTACAACC 59.405 42.308 0.00 0.00 0.00 3.77
564 565 7.159372 TGGTAGAGAGAAATCCACTTTACAAC 58.841 38.462 0.00 0.00 0.00 3.32
565 566 7.311092 TGGTAGAGAGAAATCCACTTTACAA 57.689 36.000 0.00 0.00 0.00 2.41
566 567 6.928348 TGGTAGAGAGAAATCCACTTTACA 57.072 37.500 0.00 0.00 0.00 2.41
573 574 9.702253 GGACTATATATGGTAGAGAGAAATCCA 57.298 37.037 1.14 0.00 0.00 3.41
574 575 9.138596 GGGACTATATATGGTAGAGAGAAATCC 57.861 40.741 1.14 0.00 0.00 3.01
575 576 9.930158 AGGGACTATATATGGTAGAGAGAAATC 57.070 37.037 1.14 0.00 36.02 2.17
578 579 9.577337 ACTAGGGACTATATATGGTAGAGAGAA 57.423 37.037 1.14 0.00 41.70 2.87
579 580 9.216148 GACTAGGGACTATATATGGTAGAGAGA 57.784 40.741 1.14 0.00 41.70 3.10
580 581 9.220906 AGACTAGGGACTATATATGGTAGAGAG 57.779 40.741 1.14 1.36 41.70 3.20
581 582 9.216148 GAGACTAGGGACTATATATGGTAGAGA 57.784 40.741 1.14 0.00 41.70 3.10
582 583 8.994500 TGAGACTAGGGACTATATATGGTAGAG 58.006 40.741 1.14 0.72 41.70 2.43
583 584 8.928672 TGAGACTAGGGACTATATATGGTAGA 57.071 38.462 1.14 0.00 41.70 2.59
584 585 9.398538 GTTGAGACTAGGGACTATATATGGTAG 57.601 40.741 1.14 0.00 41.70 3.18
585 586 8.897692 TGTTGAGACTAGGGACTATATATGGTA 58.102 37.037 1.14 0.00 41.70 3.25
586 587 7.766628 TGTTGAGACTAGGGACTATATATGGT 58.233 38.462 0.66 0.66 41.70 3.55
587 588 8.690884 CATGTTGAGACTAGGGACTATATATGG 58.309 40.741 0.00 0.00 41.70 2.74
588 589 9.249053 ACATGTTGAGACTAGGGACTATATATG 57.751 37.037 0.00 0.00 41.70 1.78
589 590 9.830186 AACATGTTGAGACTAGGGACTATATAT 57.170 33.333 11.07 0.00 41.70 0.86
590 591 9.298250 GAACATGTTGAGACTAGGGACTATATA 57.702 37.037 17.58 0.00 41.70 0.86
591 592 7.785028 TGAACATGTTGAGACTAGGGACTATAT 59.215 37.037 17.58 0.00 41.70 0.86
592 593 7.068348 GTGAACATGTTGAGACTAGGGACTATA 59.932 40.741 17.58 0.00 41.70 1.31
593 594 5.958380 TGAACATGTTGAGACTAGGGACTAT 59.042 40.000 17.58 0.00 41.70 2.12
594 595 5.185249 GTGAACATGTTGAGACTAGGGACTA 59.815 44.000 17.58 0.00 41.75 2.59
595 596 4.021016 GTGAACATGTTGAGACTAGGGACT 60.021 45.833 17.58 0.00 46.37 3.85
596 597 4.246458 GTGAACATGTTGAGACTAGGGAC 58.754 47.826 17.58 0.00 0.00 4.46
597 598 3.056821 CGTGAACATGTTGAGACTAGGGA 60.057 47.826 17.58 0.00 0.00 4.20
598 599 3.254060 CGTGAACATGTTGAGACTAGGG 58.746 50.000 17.58 0.00 0.00 3.53
599 600 3.675225 CACGTGAACATGTTGAGACTAGG 59.325 47.826 17.58 3.74 0.00 3.02
600 601 3.675225 CCACGTGAACATGTTGAGACTAG 59.325 47.826 17.58 2.84 0.00 2.57
678 679 5.373222 TGTACTTACACTTTTGCACCTGAT 58.627 37.500 0.00 0.00 0.00 2.90
681 682 7.996098 ATATTGTACTTACACTTTTGCACCT 57.004 32.000 0.00 0.00 35.64 4.00
732 828 5.363580 ACAAAGGATGACCAAACATGTCTTT 59.636 36.000 0.00 0.00 38.94 2.52
755 852 2.140717 CCTCCGTTACTGTTTCCACAC 58.859 52.381 0.00 0.00 0.00 3.82
813 910 3.134458 GAGTTGCTTGTAAGTCAGCACT 58.866 45.455 0.00 0.00 36.98 4.40
951 1069 1.232119 GTTGGACCGATTGACCGTTT 58.768 50.000 0.00 0.00 0.00 3.60
952 1070 0.604511 GGTTGGACCGATTGACCGTT 60.605 55.000 0.00 0.00 0.00 4.44
953 1071 1.004200 GGTTGGACCGATTGACCGT 60.004 57.895 0.00 0.00 0.00 4.83
954 1072 1.019278 CAGGTTGGACCGATTGACCG 61.019 60.000 0.00 0.00 44.90 4.79
955 1073 1.305930 GCAGGTTGGACCGATTGACC 61.306 60.000 1.38 0.00 44.90 4.02
1227 1348 1.058404 CGTCGAACGGAAGAAAGGTC 58.942 55.000 0.00 0.00 38.08 3.85
1233 1354 3.356267 TCGGCGTCGAACGGAAGA 61.356 61.111 10.97 0.00 42.82 2.87
1305 1426 2.024871 GCGTAGACGATGAGCGCT 59.975 61.111 11.27 11.27 46.04 5.92
1386 1507 3.343421 GCGAACACCACGGACACC 61.343 66.667 0.00 0.00 0.00 4.16
1812 1933 4.208686 GGGAGGAGCCACGCGTAG 62.209 72.222 13.44 5.62 38.95 3.51
1898 2019 2.742372 GCCCATGAACGTCGCTGT 60.742 61.111 0.00 0.00 0.00 4.40
1984 2106 2.485426 CAGACAAGCACTGTACAATGGG 59.515 50.000 6.43 0.00 38.84 4.00
1985 2107 3.402110 TCAGACAAGCACTGTACAATGG 58.598 45.455 6.43 0.00 38.84 3.16
2007 2132 6.646653 TGGATATTCGCAGATAACATTCAGAC 59.353 38.462 0.00 0.00 35.04 3.51
2014 2139 5.482163 TCCATGGATATTCGCAGATAACA 57.518 39.130 11.44 0.00 35.04 2.41
2022 2151 2.791560 CGATCGATCCATGGATATTCGC 59.208 50.000 27.38 13.29 34.60 4.70
2092 2221 4.671831 TGATAAGCATGTTTTCCCCTTCA 58.328 39.130 0.00 0.00 0.00 3.02
2097 2226 4.631377 GCCTTTTGATAAGCATGTTTTCCC 59.369 41.667 0.00 0.00 0.00 3.97
2128 2257 3.002791 GTCTTCGTCTCCAATCAATGCA 58.997 45.455 0.00 0.00 0.00 3.96
2154 2283 3.081554 CAGCTGGCTACCCAACCT 58.918 61.111 5.57 0.00 41.58 3.50
2155 2284 2.751837 GCAGCTGGCTACCCAACC 60.752 66.667 17.12 0.00 41.58 3.77
2161 2290 2.650813 ATACGCTGGCAGCTGGCTAC 62.651 60.000 36.39 27.03 44.01 3.58
2244 2377 7.277760 GTGAAAAAGCATCACAAAAACTTACCT 59.722 33.333 2.01 0.00 45.13 3.08
2270 2661 2.505498 CGCGAATTGTCCGTCTCCG 61.505 63.158 0.00 0.00 0.00 4.63
2275 2666 2.735478 TTCGCGCGAATTGTCCGT 60.735 55.556 38.79 0.00 0.00 4.69
2277 2668 2.275812 CGTTCGCGCGAATTGTCC 60.276 61.111 42.96 29.45 36.45 4.02
2315 2706 3.181480 GGCTCAGTATCTCAGAGGTGTTC 60.181 52.174 0.00 0.00 31.57 3.18
2317 2708 2.383855 GGCTCAGTATCTCAGAGGTGT 58.616 52.381 0.00 0.00 31.57 4.16
2326 2717 2.379005 TGTGATGTCGGCTCAGTATCT 58.621 47.619 0.00 0.00 0.00 1.98
2341 2732 2.031870 TCGTCAATCCCGAGATGTGAT 58.968 47.619 0.00 0.00 31.29 3.06
2342 2733 1.470051 TCGTCAATCCCGAGATGTGA 58.530 50.000 0.00 0.00 31.29 3.58
2350 2742 2.935849 TGTGATGATTTCGTCAATCCCG 59.064 45.455 4.11 0.00 42.83 5.14
2353 2745 4.872691 ACTCCTGTGATGATTTCGTCAATC 59.127 41.667 4.11 3.88 42.83 2.67
2354 2746 4.836825 ACTCCTGTGATGATTTCGTCAAT 58.163 39.130 4.11 0.00 42.83 2.57
2355 2747 4.021104 AGACTCCTGTGATGATTTCGTCAA 60.021 41.667 4.11 0.00 42.83 3.18
2356 2748 3.511540 AGACTCCTGTGATGATTTCGTCA 59.488 43.478 0.00 0.00 42.06 4.35
2357 2749 4.116747 AGACTCCTGTGATGATTTCGTC 57.883 45.455 0.00 0.00 0.00 4.20
2358 2750 4.248859 CAAGACTCCTGTGATGATTTCGT 58.751 43.478 0.00 0.00 0.00 3.85
2359 2751 4.248859 ACAAGACTCCTGTGATGATTTCG 58.751 43.478 0.00 0.00 0.00 3.46
2374 2766 4.631813 GCCATTTTCATCGACTACAAGACT 59.368 41.667 0.00 0.00 0.00 3.24
2379 2771 4.769688 AGATGCCATTTTCATCGACTACA 58.230 39.130 0.00 0.00 43.68 2.74
2394 2786 1.271856 TCGTTTAGTGGGAGATGCCA 58.728 50.000 0.00 0.00 38.95 4.92
2396 2788 2.695359 TGTTCGTTTAGTGGGAGATGC 58.305 47.619 0.00 0.00 0.00 3.91
2398 2790 3.782046 CGATGTTCGTTTAGTGGGAGAT 58.218 45.455 0.00 0.00 34.72 2.75
2408 2800 2.161609 GGATTTCCAGCGATGTTCGTTT 59.838 45.455 0.00 0.00 37.88 3.60
2434 2826 7.402640 GTGCTCTCGTATTTTCCTGAATTTAG 58.597 38.462 0.00 0.00 0.00 1.85
2440 2832 2.416836 CGGTGCTCTCGTATTTTCCTGA 60.417 50.000 0.00 0.00 0.00 3.86
2449 2841 0.963856 ATGACACCGGTGCTCTCGTA 60.964 55.000 34.26 14.35 0.00 3.43
2455 2847 1.188219 ACTCAGATGACACCGGTGCT 61.188 55.000 34.26 19.96 0.00 4.40
2456 2848 0.320771 AACTCAGATGACACCGGTGC 60.321 55.000 34.26 25.37 0.00 5.01
2458 2850 2.418746 GCATAACTCAGATGACACCGGT 60.419 50.000 0.00 0.00 0.00 5.28
2459 2851 2.159043 AGCATAACTCAGATGACACCGG 60.159 50.000 0.00 0.00 0.00 5.28
2460 2852 3.119291 GAGCATAACTCAGATGACACCG 58.881 50.000 0.00 0.00 45.49 4.94
2483 2925 9.816354 ATTTTACACAACTAAACAAAGCTGAAT 57.184 25.926 0.00 0.00 0.00 2.57
2491 2933 6.256757 GCTTGCCATTTTACACAACTAAACAA 59.743 34.615 0.00 0.00 0.00 2.83
2527 2971 9.578576 AGATATGGTTATGTTTTGATAGTGCAT 57.421 29.630 0.00 0.00 0.00 3.96
2575 3023 1.065551 GGTTCGGCATTGATACTTGGC 59.934 52.381 0.00 0.00 35.25 4.52
2581 3029 2.174639 AGGGATTGGTTCGGCATTGATA 59.825 45.455 0.00 0.00 0.00 2.15
2617 3065 3.181471 CCATGTCTATCGCTCACCTCTTT 60.181 47.826 0.00 0.00 0.00 2.52
2629 3077 2.286294 CGAGCTTTGTGCCATGTCTATC 59.714 50.000 0.00 0.00 44.23 2.08
2636 3084 1.674441 CATGATCGAGCTTTGTGCCAT 59.326 47.619 0.90 0.00 44.23 4.40
2680 3128 0.888736 CCTGTCGGCAATTGACACCA 60.889 55.000 12.81 5.91 41.20 4.17
2702 3150 2.616376 TGTGTTTGATGTCCTTCCAACG 59.384 45.455 0.00 0.00 0.00 4.10
2725 3173 1.297364 GCCCTTACACCGCACCTTA 59.703 57.895 0.00 0.00 0.00 2.69
2732 3180 0.030908 GAGAGATCGCCCTTACACCG 59.969 60.000 0.00 0.00 0.00 4.94
2755 3203 8.873830 CGACACAGTAAAAAGATAGATGAACAT 58.126 33.333 0.00 0.00 0.00 2.71
2759 3207 7.093902 ACCTCGACACAGTAAAAAGATAGATGA 60.094 37.037 0.00 0.00 0.00 2.92
2765 3213 5.209818 TCACCTCGACACAGTAAAAAGAT 57.790 39.130 0.00 0.00 0.00 2.40
2829 3277 1.054231 GATAGGGTTAGGGAACGGGG 58.946 60.000 0.00 0.00 36.32 5.73
2832 3280 1.969208 GGGAGATAGGGTTAGGGAACG 59.031 57.143 0.00 0.00 36.32 3.95
2834 3282 2.181642 GAGGGGAGATAGGGTTAGGGAA 59.818 54.545 0.00 0.00 0.00 3.97
2835 3283 1.793902 GAGGGGAGATAGGGTTAGGGA 59.206 57.143 0.00 0.00 0.00 4.20
2904 3352 1.837090 GAGAAGTGGTGGTGGTGGT 59.163 57.895 0.00 0.00 0.00 4.16
2905 3353 1.301716 CGAGAAGTGGTGGTGGTGG 60.302 63.158 0.00 0.00 0.00 4.61
2911 3359 1.216710 GAGAGGCGAGAAGTGGTGG 59.783 63.158 0.00 0.00 0.00 4.61
2922 3370 0.682855 AGAAGGTGAGGAGAGAGGCG 60.683 60.000 0.00 0.00 0.00 5.52
2925 3373 1.687996 GGGGAGAAGGTGAGGAGAGAG 60.688 61.905 0.00 0.00 0.00 3.20
2926 3374 0.336737 GGGGAGAAGGTGAGGAGAGA 59.663 60.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.