Multiple sequence alignment - TraesCS3A01G153900

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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 TraesCS3A01G153900 chr3A 100.000 5172 0 0 1 5172 144547844 144542673 0.000000e+00 9551.0
1 TraesCS3A01G153900 chr3D 92.308 2925 152 33 2114 4983 131806024 131803118 0.000000e+00 4087.0
2 TraesCS3A01G153900 chr3D 97.330 824 20 2 765 1588 131807389 131806568 0.000000e+00 1399.0
3 TraesCS3A01G153900 chr3D 95.179 560 19 3 1626 2178 131806583 131806025 0.000000e+00 878.0
4 TraesCS3A01G153900 chr3D 93.367 196 13 0 4977 5172 131803240 131803045 1.820000e-74 291.0
5 TraesCS3A01G153900 chr3D 94.595 37 1 1 708 743 131807496 131807460 7.230000e-04 56.5
6 TraesCS3A01G153900 chr3B 95.403 2219 68 11 1626 3827 188247333 188245132 0.000000e+00 3502.0
7 TraesCS3A01G153900 chr3B 95.696 883 23 8 708 1588 188248187 188247318 0.000000e+00 1406.0
8 TraesCS3A01G153900 chr3B 92.708 672 29 7 4086 4750 188244482 188243824 0.000000e+00 952.0
9 TraesCS3A01G153900 chr3B 96.178 157 6 0 3890 4046 188245126 188244970 1.850000e-64 257.0
10 TraesCS3A01G153900 chr3B 91.860 86 4 1 4780 4865 188243829 188243747 3.270000e-22 117.0
11 TraesCS3A01G153900 chr3B 100.000 28 0 0 717 744 689335469 689335496 9.000000e-03 52.8
12 TraesCS3A01G153900 chr5B 80.865 601 86 12 121 705 19554448 19555035 3.670000e-121 446.0
13 TraesCS3A01G153900 chr5B 90.000 50 2 3 44 92 310222952 310222999 1.560000e-05 62.1
14 TraesCS3A01G153900 chr7D 79.323 532 81 15 140 665 548612992 548612484 3.830000e-91 346.0
15 TraesCS3A01G153900 chr7D 84.709 327 39 7 250 565 53579582 53579256 3.010000e-82 316.0
16 TraesCS3A01G153900 chr7A 76.250 480 86 13 208 679 632387822 632387363 4.030000e-56 230.0
17 TraesCS3A01G153900 chr1B 78.030 396 63 18 249 634 657498175 657498556 1.450000e-55 228.0
18 TraesCS3A01G153900 chr7B 85.938 64 8 1 713 776 125379545 125379607 3.340000e-07 67.6
19 TraesCS3A01G153900 chr4B 91.304 46 1 3 120 165 10580458 10580500 5.590000e-05 60.2
20 TraesCS3A01G153900 chr5D 100.000 30 0 0 720 749 446539378 446539349 7.230000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G153900 chr3A 144542673 144547844 5171 True 9551.0 9551 100.0000 1 5172 1 chr3A.!!$R1 5171
1 TraesCS3A01G153900 chr3D 131803045 131807496 4451 True 1342.3 4087 94.5558 708 5172 5 chr3D.!!$R1 4464
2 TraesCS3A01G153900 chr3B 188243747 188248187 4440 True 1246.8 3502 94.3690 708 4865 5 chr3B.!!$R1 4157
3 TraesCS3A01G153900 chr5B 19554448 19555035 587 False 446.0 446 80.8650 121 705 1 chr5B.!!$F1 584
4 TraesCS3A01G153900 chr7D 548612484 548612992 508 True 346.0 346 79.3230 140 665 1 chr7D.!!$R2 525

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
50 51 0.250901 AGGTCAGTGTGGTTGATGGC 60.251 55.000 0.00 0.0 0.00 4.40 F
1616 1694 0.106967 GGGCTAGCCTCCTTTTCCAG 60.107 60.000 32.18 0.0 36.10 3.86 F
2028 2113 0.804989 GCGCAGGTACAAAAGCATCT 59.195 50.000 0.30 0.0 0.00 2.90 F
3360 3523 1.723542 CTGTACGAAGTGAAGCAGCAG 59.276 52.381 0.00 0.0 45.73 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1714 0.040958 GCAGCAAAATCGCCGGATAG 60.041 55.000 5.05 0.00 31.01 2.08 R
3083 3241 0.321564 TTGCAACCGACATGCTAGCT 60.322 50.000 17.23 0.00 44.14 3.32 R
3638 3801 1.065854 AGCCACAGAAAGGAGAATCGG 60.066 52.381 0.00 0.00 34.37 4.18 R
4913 5585 0.109781 ATGAACAATGTTGCGGTCGC 60.110 50.000 2.20 8.54 42.35 5.19 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
24 25 7.216920 TGATTAAAGTGTCATCGACGTAATG 57.783 36.000 4.42 4.42 34.95 1.90
25 26 6.809689 TGATTAAAGTGTCATCGACGTAATGT 59.190 34.615 9.51 0.00 34.95 2.71
26 27 7.969508 TGATTAAAGTGTCATCGACGTAATGTA 59.030 33.333 9.51 0.23 34.95 2.29
27 28 8.692110 ATTAAAGTGTCATCGACGTAATGTAA 57.308 30.769 9.51 2.43 34.95 2.41
28 29 8.518151 TTAAAGTGTCATCGACGTAATGTAAA 57.482 30.769 9.51 0.00 34.95 2.01
29 30 7.410800 AAAGTGTCATCGACGTAATGTAAAA 57.589 32.000 9.51 0.00 34.95 1.52
30 31 7.591006 AAGTGTCATCGACGTAATGTAAAAT 57.409 32.000 9.51 0.00 34.95 1.82
31 32 8.692110 AAGTGTCATCGACGTAATGTAAAATA 57.308 30.769 9.51 0.00 34.95 1.40
32 33 8.336498 AGTGTCATCGACGTAATGTAAAATAG 57.664 34.615 9.51 0.00 34.95 1.73
33 34 7.434307 AGTGTCATCGACGTAATGTAAAATAGG 59.566 37.037 9.51 0.00 34.95 2.57
34 35 7.221452 GTGTCATCGACGTAATGTAAAATAGGT 59.779 37.037 9.51 0.00 34.95 3.08
35 36 7.433131 TGTCATCGACGTAATGTAAAATAGGTC 59.567 37.037 9.51 0.00 34.95 3.85
36 37 7.433131 GTCATCGACGTAATGTAAAATAGGTCA 59.567 37.037 9.51 0.00 36.97 4.02
37 38 7.646526 TCATCGACGTAATGTAAAATAGGTCAG 59.353 37.037 9.51 0.00 36.97 3.51
38 39 6.855836 TCGACGTAATGTAAAATAGGTCAGT 58.144 36.000 0.00 0.00 36.97 3.41
39 40 6.748658 TCGACGTAATGTAAAATAGGTCAGTG 59.251 38.462 0.00 0.00 36.97 3.66
40 41 6.529125 CGACGTAATGTAAAATAGGTCAGTGT 59.471 38.462 0.00 0.00 36.97 3.55
41 42 7.462331 CGACGTAATGTAAAATAGGTCAGTGTG 60.462 40.741 0.00 0.00 36.97 3.82
42 43 6.592607 ACGTAATGTAAAATAGGTCAGTGTGG 59.407 38.462 0.00 0.00 0.00 4.17
43 44 6.592607 CGTAATGTAAAATAGGTCAGTGTGGT 59.407 38.462 0.00 0.00 0.00 4.16
44 45 7.118680 CGTAATGTAAAATAGGTCAGTGTGGTT 59.881 37.037 0.00 0.00 0.00 3.67
45 46 6.817765 ATGTAAAATAGGTCAGTGTGGTTG 57.182 37.500 0.00 0.00 0.00 3.77
46 47 5.931294 TGTAAAATAGGTCAGTGTGGTTGA 58.069 37.500 0.00 0.00 0.00 3.18
47 48 6.539173 TGTAAAATAGGTCAGTGTGGTTGAT 58.461 36.000 0.00 0.00 0.00 2.57
48 49 5.964958 AAAATAGGTCAGTGTGGTTGATG 57.035 39.130 0.00 0.00 0.00 3.07
49 50 3.634397 ATAGGTCAGTGTGGTTGATGG 57.366 47.619 0.00 0.00 0.00 3.51
50 51 0.250901 AGGTCAGTGTGGTTGATGGC 60.251 55.000 0.00 0.00 0.00 4.40
51 52 0.250901 GGTCAGTGTGGTTGATGGCT 60.251 55.000 0.00 0.00 0.00 4.75
52 53 1.160137 GTCAGTGTGGTTGATGGCTC 58.840 55.000 0.00 0.00 0.00 4.70
53 54 0.320683 TCAGTGTGGTTGATGGCTCG 60.321 55.000 0.00 0.00 0.00 5.03
54 55 0.320683 CAGTGTGGTTGATGGCTCGA 60.321 55.000 0.00 0.00 0.00 4.04
55 56 0.615331 AGTGTGGTTGATGGCTCGAT 59.385 50.000 0.00 0.00 0.00 3.59
56 57 1.831106 AGTGTGGTTGATGGCTCGATA 59.169 47.619 0.00 0.00 0.00 2.92
57 58 2.435805 AGTGTGGTTGATGGCTCGATAT 59.564 45.455 0.00 0.00 0.00 1.63
58 59 3.118261 AGTGTGGTTGATGGCTCGATATT 60.118 43.478 0.00 0.00 0.00 1.28
59 60 3.627577 GTGTGGTTGATGGCTCGATATTT 59.372 43.478 0.00 0.00 0.00 1.40
60 61 4.096382 GTGTGGTTGATGGCTCGATATTTT 59.904 41.667 0.00 0.00 0.00 1.82
61 62 4.704540 TGTGGTTGATGGCTCGATATTTTT 59.295 37.500 0.00 0.00 0.00 1.94
88 89 8.808092 TCACTTTTACAAGGGTATTTTAATGGG 58.192 33.333 0.00 0.00 34.63 4.00
89 90 8.038351 CACTTTTACAAGGGTATTTTAATGGGG 58.962 37.037 0.00 0.00 33.82 4.96
90 91 7.735777 ACTTTTACAAGGGTATTTTAATGGGGT 59.264 33.333 0.00 0.00 33.82 4.95
91 92 8.507582 TTTTACAAGGGTATTTTAATGGGGTT 57.492 30.769 0.00 0.00 0.00 4.11
92 93 7.721409 TTACAAGGGTATTTTAATGGGGTTC 57.279 36.000 0.00 0.00 0.00 3.62
93 94 5.027460 ACAAGGGTATTTTAATGGGGTTCC 58.973 41.667 0.00 0.00 0.00 3.62
94 95 4.274794 AGGGTATTTTAATGGGGTTCCC 57.725 45.455 0.00 0.00 45.71 3.97
106 107 3.313012 GGGGTTCCCAAAAGATTTTCG 57.687 47.619 10.25 0.00 44.65 3.46
107 108 2.631062 GGGGTTCCCAAAAGATTTTCGT 59.369 45.455 10.25 0.00 44.65 3.85
108 109 3.070446 GGGGTTCCCAAAAGATTTTCGTT 59.930 43.478 10.25 0.00 44.65 3.85
109 110 4.281435 GGGGTTCCCAAAAGATTTTCGTTA 59.719 41.667 10.25 0.00 44.65 3.18
110 111 5.221481 GGGGTTCCCAAAAGATTTTCGTTAA 60.221 40.000 10.25 0.00 44.65 2.01
111 112 6.460781 GGGTTCCCAAAAGATTTTCGTTAAT 58.539 36.000 2.59 0.00 0.00 1.40
112 113 6.932400 GGGTTCCCAAAAGATTTTCGTTAATT 59.068 34.615 2.59 0.00 0.00 1.40
113 114 7.117236 GGGTTCCCAAAAGATTTTCGTTAATTC 59.883 37.037 2.59 0.00 0.00 2.17
114 115 7.870954 GGTTCCCAAAAGATTTTCGTTAATTCT 59.129 33.333 0.00 0.00 0.00 2.40
115 116 8.912658 GTTCCCAAAAGATTTTCGTTAATTCTC 58.087 33.333 0.00 0.00 0.00 2.87
116 117 7.302524 TCCCAAAAGATTTTCGTTAATTCTCG 58.697 34.615 0.00 0.00 0.00 4.04
117 118 7.040961 TCCCAAAAGATTTTCGTTAATTCTCGT 60.041 33.333 2.95 0.00 0.00 4.18
118 119 8.231837 CCCAAAAGATTTTCGTTAATTCTCGTA 58.768 33.333 2.95 0.00 0.00 3.43
119 120 9.769093 CCAAAAGATTTTCGTTAATTCTCGTAT 57.231 29.630 2.95 0.00 0.00 3.06
160 161 1.000145 GTCGGCCGACTGATCTTTTC 59.000 55.000 43.32 19.15 41.57 2.29
188 189 4.451150 CCGCCTCCGCAGCAGTAA 62.451 66.667 0.00 0.00 34.03 2.24
191 192 1.369091 CGCCTCCGCAGCAGTAAATT 61.369 55.000 0.00 0.00 34.03 1.82
214 215 3.943381 TGGCACAATTCATTGCAACAAAA 59.057 34.783 0.00 0.00 41.38 2.44
215 216 4.201891 TGGCACAATTCATTGCAACAAAAC 60.202 37.500 0.00 0.00 41.38 2.43
242 243 4.801516 GTGTTTCGTAACCTTTTGCAACAT 59.198 37.500 0.00 0.00 33.15 2.71
244 245 6.472808 GTGTTTCGTAACCTTTTGCAACATAA 59.527 34.615 0.00 0.00 33.15 1.90
245 246 6.472808 TGTTTCGTAACCTTTTGCAACATAAC 59.527 34.615 0.00 0.00 33.15 1.89
276 277 7.509141 TGCAGAAACAATTGAACAGAGATTA 57.491 32.000 13.59 0.00 0.00 1.75
292 299 8.345724 ACAGAGATTATGTTGCAGATTTTTCT 57.654 30.769 0.00 0.00 0.00 2.52
300 307 6.455360 TGTTGCAGATTTTTCTTCTTCACT 57.545 33.333 0.00 0.00 0.00 3.41
348 355 2.191128 AGGACTTCTGCAACATGGAC 57.809 50.000 0.00 0.00 0.00 4.02
363 370 5.759506 ACATGGACGTTGTTGTGAATTTA 57.240 34.783 0.00 0.00 0.00 1.40
388 395 3.181504 TGCAATGAAAGATGATGTCGCAG 60.182 43.478 0.00 0.00 0.00 5.18
410 417 2.184167 CACCGCCCTCGTTGTTGTT 61.184 57.895 0.00 0.00 0.00 2.83
411 418 1.452470 ACCGCCCTCGTTGTTGTTT 60.452 52.632 0.00 0.00 0.00 2.83
439 446 1.593933 GTAACTCCGTCGTTGTTGCAA 59.406 47.619 0.00 0.00 0.00 4.08
449 456 4.381983 GTCGTTGTTGCAAAAACTTGTTG 58.618 39.130 25.99 12.97 0.00 3.33
452 459 2.771089 TGTTGCAAAAACTTGTTGGCA 58.229 38.095 0.00 0.00 0.00 4.92
473 480 4.980805 GGCGGCACAGTCGGACAA 62.981 66.667 11.27 0.00 0.00 3.18
476 483 2.358737 GGCACAGTCGGACAAGGG 60.359 66.667 11.27 4.72 0.00 3.95
477 484 3.050275 GCACAGTCGGACAAGGGC 61.050 66.667 11.27 11.23 0.00 5.19
480 487 1.227853 ACAGTCGGACAAGGGCAAC 60.228 57.895 11.27 0.00 0.00 4.17
484 492 1.072505 TCGGACAAGGGCAACTTCC 59.927 57.895 0.00 0.00 37.29 3.46
486 494 2.626780 GGACAAGGGCAACTTCCGC 61.627 63.158 0.00 0.00 37.29 5.54
504 512 1.268032 CGCCGGTAATGTTGCAGATTC 60.268 52.381 1.90 0.00 0.00 2.52
514 522 7.806014 GGTAATGTTGCAGATTCTTTTCGTTTA 59.194 33.333 0.00 0.00 0.00 2.01
553 569 5.971202 TGAGAGTTGTTGCGAAAGAAATTTC 59.029 36.000 10.33 10.33 0.00 2.17
613 630 0.443869 GCACATGATCGCACGAAACT 59.556 50.000 0.00 0.00 0.00 2.66
621 638 1.415374 TCGCACGAAACTGCTAGAAC 58.585 50.000 0.00 0.00 34.77 3.01
638 656 5.409214 GCTAGAACTAGTACTAGATGACCCG 59.591 48.000 31.93 15.86 38.53 5.28
648 666 0.615331 AGATGACCCGTGCAAGACAT 59.385 50.000 0.00 4.10 0.00 3.06
684 702 2.272447 TGACGGACGCCTCACATGA 61.272 57.895 0.00 0.00 0.00 3.07
686 704 1.934220 GACGGACGCCTCACATGAGA 61.934 60.000 10.55 0.00 44.74 3.27
687 705 1.517257 CGGACGCCTCACATGAGAC 60.517 63.158 10.55 0.00 44.74 3.36
688 706 1.591703 GGACGCCTCACATGAGACA 59.408 57.895 10.55 0.00 44.74 3.41
691 709 1.080501 CGCCTCACATGAGACACGT 60.081 57.895 10.55 0.00 44.74 4.49
705 723 1.278637 CACGTCGGCAGAAACCAAC 59.721 57.895 0.00 0.00 0.00 3.77
706 724 1.890510 ACGTCGGCAGAAACCAACC 60.891 57.895 0.00 0.00 0.00 3.77
707 725 1.890041 CGTCGGCAGAAACCAACCA 60.890 57.895 0.00 0.00 0.00 3.67
708 726 1.234615 CGTCGGCAGAAACCAACCAT 61.235 55.000 0.00 0.00 0.00 3.55
709 727 0.958822 GTCGGCAGAAACCAACCATT 59.041 50.000 0.00 0.00 0.00 3.16
710 728 1.339929 GTCGGCAGAAACCAACCATTT 59.660 47.619 0.00 0.00 0.00 2.32
711 729 1.611491 TCGGCAGAAACCAACCATTTC 59.389 47.619 0.00 0.00 36.49 2.17
712 730 1.336795 CGGCAGAAACCAACCATTTCC 60.337 52.381 0.00 0.00 36.84 3.13
883 959 4.295051 CCGTAAAAACCCATCAACACAAG 58.705 43.478 0.00 0.00 0.00 3.16
1197 1274 2.759973 TTCCAGCGCCTCTCCGAT 60.760 61.111 2.29 0.00 0.00 4.18
1503 1580 2.447244 AGCTCAAGAACAAGACGGAG 57.553 50.000 0.00 0.00 0.00 4.63
1541 1618 5.770162 AGCTAAAGCAGTTTGACAAGGTAAT 59.230 36.000 4.54 0.00 45.16 1.89
1549 1627 9.908152 AGCAGTTTGACAAGGTAATAAATAAAC 57.092 29.630 0.00 0.00 0.00 2.01
1592 1670 9.890352 GCTTTGCTAGATTTAATTTATCAGAGG 57.110 33.333 0.00 0.00 0.00 3.69
1593 1671 9.890352 CTTTGCTAGATTTAATTTATCAGAGGC 57.110 33.333 0.00 0.00 0.00 4.70
1594 1672 7.986085 TGCTAGATTTAATTTATCAGAGGCC 57.014 36.000 0.00 0.00 0.00 5.19
1595 1673 6.650807 TGCTAGATTTAATTTATCAGAGGCCG 59.349 38.462 0.00 0.00 0.00 6.13
1596 1674 6.092807 GCTAGATTTAATTTATCAGAGGCCGG 59.907 42.308 0.00 0.00 0.00 6.13
1597 1675 5.316987 AGATTTAATTTATCAGAGGCCGGG 58.683 41.667 2.18 0.00 0.00 5.73
1598 1676 3.502123 TTAATTTATCAGAGGCCGGGG 57.498 47.619 2.18 0.00 0.00 5.73
1599 1677 0.478507 AATTTATCAGAGGCCGGGGG 59.521 55.000 2.18 0.00 0.00 5.40
1613 1691 4.988744 GGGGCTAGCCTCCTTTTC 57.011 61.111 32.18 14.17 36.10 2.29
1614 1692 1.227664 GGGGCTAGCCTCCTTTTCC 59.772 63.158 32.18 19.31 36.10 3.13
1615 1693 1.571773 GGGGCTAGCCTCCTTTTCCA 61.572 60.000 32.18 0.00 36.10 3.53
1616 1694 0.106967 GGGCTAGCCTCCTTTTCCAG 60.107 60.000 32.18 0.00 36.10 3.86
1617 1695 0.912486 GGCTAGCCTCCTTTTCCAGA 59.088 55.000 27.17 0.00 0.00 3.86
1618 1696 1.282157 GGCTAGCCTCCTTTTCCAGAA 59.718 52.381 27.17 0.00 0.00 3.02
1619 1697 2.290960 GGCTAGCCTCCTTTTCCAGAAA 60.291 50.000 27.17 0.00 0.00 2.52
1620 1698 3.421844 GCTAGCCTCCTTTTCCAGAAAA 58.578 45.455 2.29 5.51 37.90 2.29
1621 1699 3.826729 GCTAGCCTCCTTTTCCAGAAAAA 59.173 43.478 2.29 0.00 39.49 1.94
1649 1727 7.612677 ACTAGATTTAATCTATCCGGCGATTT 58.387 34.615 14.20 0.00 40.82 2.17
1659 1737 1.430632 CGGCGATTTTGCTGCTGAT 59.569 52.632 0.00 0.00 37.16 2.90
1674 1759 5.532406 TGCTGCTGATAAGTTCTTTCTGTTT 59.468 36.000 0.00 0.00 0.00 2.83
1793 1878 1.000955 CTGGAGTCGTTTACTGCCACT 59.999 52.381 0.00 0.00 45.50 4.00
1796 1881 2.353803 GGAGTCGTTTACTGCCACTGAT 60.354 50.000 0.00 0.00 40.51 2.90
2028 2113 0.804989 GCGCAGGTACAAAAGCATCT 59.195 50.000 0.30 0.00 0.00 2.90
2111 2196 5.759763 TCCATACACACATAAGCAGCATAAG 59.240 40.000 0.00 0.00 0.00 1.73
2145 2230 9.658799 GCTAGCATCTCTATAATTGTCCAATAA 57.341 33.333 10.63 0.00 0.00 1.40
2449 2599 3.567478 ATTTGCCTATCTCTGTGTCCC 57.433 47.619 0.00 0.00 0.00 4.46
2593 2743 1.754803 GCCTGCCCCAAGTTTATTACC 59.245 52.381 0.00 0.00 0.00 2.85
2707 2857 4.935808 AGTTTCTACAGGCAAATTCTACCG 59.064 41.667 0.00 0.00 0.00 4.02
2802 2952 7.509546 TCCATATTTCAGAGTCCTACAATTCC 58.490 38.462 0.00 0.00 0.00 3.01
2808 2958 2.840651 AGAGTCCTACAATTCCAGGGTG 59.159 50.000 2.68 0.00 32.40 4.61
2878 3029 5.953571 ACATCTAGGGTGAGGTTTTTCTTT 58.046 37.500 3.50 0.00 0.00 2.52
2880 3031 6.839134 ACATCTAGGGTGAGGTTTTTCTTTTT 59.161 34.615 3.50 0.00 0.00 1.94
3083 3241 7.394816 AGGCTAGTTTTCTTATCAGTTAAGCA 58.605 34.615 0.00 0.00 37.75 3.91
3168 3328 8.345565 ACAGATGTACTTCTGAACATTTTTGTC 58.654 33.333 33.61 0.00 44.88 3.18
3170 3330 6.912203 TGTACTTCTGAACATTTTTGTCGA 57.088 33.333 0.00 0.00 0.00 4.20
3171 3331 7.490962 TGTACTTCTGAACATTTTTGTCGAT 57.509 32.000 0.00 0.00 0.00 3.59
3172 3332 7.351981 TGTACTTCTGAACATTTTTGTCGATG 58.648 34.615 0.00 0.00 0.00 3.84
3173 3333 6.377327 ACTTCTGAACATTTTTGTCGATGT 57.623 33.333 0.00 0.00 38.08 3.06
3174 3334 6.201517 ACTTCTGAACATTTTTGTCGATGTG 58.798 36.000 0.00 0.00 36.65 3.21
3175 3335 4.536065 TCTGAACATTTTTGTCGATGTGC 58.464 39.130 0.00 0.00 36.65 4.57
3191 3351 4.631131 GATGTGCCTGTACTGCATATGTA 58.369 43.478 19.30 0.00 40.12 2.29
3207 3367 8.310406 TGCATATGTATTGAGGTTCTTATTCG 57.690 34.615 4.29 0.00 0.00 3.34
3360 3523 1.723542 CTGTACGAAGTGAAGCAGCAG 59.276 52.381 0.00 0.00 45.73 4.24
3696 3859 4.970003 GCATCCGCTTATTATGTTTGTGTC 59.030 41.667 0.00 0.00 34.30 3.67
3830 3993 2.174424 GGAGCTCCTTCCTGGAATGAAT 59.826 50.000 26.25 4.39 45.63 2.57
3885 4048 4.236935 CCATGATTGTGTTAACTTGTGCC 58.763 43.478 7.22 0.00 0.00 5.01
3910 4073 4.130118 CTCAAGTCTGTTGCCTACTTTGT 58.870 43.478 0.00 0.00 31.21 2.83
3971 4143 7.496747 TCATTCAGGATGTTATTCATGTCGTA 58.503 34.615 0.00 0.00 36.83 3.43
3977 4149 5.625721 GGATGTTATTCATGTCGTAGAGTCG 59.374 44.000 0.00 0.00 34.82 4.18
4030 4202 9.678941 CTTTTTGAGACAGATTTTAAAGGTACC 57.321 33.333 2.73 2.73 0.00 3.34
4035 4207 7.016268 TGAGACAGATTTTAAAGGTACCTGAGT 59.984 37.037 17.14 6.72 0.00 3.41
4083 4255 7.118390 CCCTTTCCTTTTATAGATAGCACATCG 59.882 40.741 0.00 0.00 0.00 3.84
4257 4877 2.462456 GTGAGAGGCACTTGTGATGA 57.538 50.000 4.79 0.00 44.27 2.92
4316 4936 4.142600 ACACTTTTTGACTCAGTGAAGCAC 60.143 41.667 5.57 0.00 34.86 4.40
4337 4957 5.297776 GCACTGGCAATTCACTGTATTATCT 59.702 40.000 0.00 0.00 40.72 1.98
4345 4965 8.391106 GCAATTCACTGTATTATCTCGTTTCTT 58.609 33.333 0.00 0.00 0.00 2.52
4374 4994 8.049117 TCCTGTTTGCTATTTGATGAGTAATCT 58.951 33.333 0.00 0.00 36.15 2.40
4408 5028 7.225734 GCTAATTGAGAACTTGAGATACCTTCC 59.774 40.741 0.00 0.00 0.00 3.46
4421 5041 5.425630 AGATACCTTCCGTGTTTATCCAAC 58.574 41.667 0.00 0.00 35.71 3.77
4474 5094 1.775459 AGATCTGGAGGCTGATTGCAT 59.225 47.619 0.00 0.00 45.15 3.96
4549 5169 1.478510 TCGCTCCTTCTGATCTTGACC 59.521 52.381 0.00 0.00 0.00 4.02
4550 5170 1.472376 CGCTCCTTCTGATCTTGACCC 60.472 57.143 0.00 0.00 0.00 4.46
4551 5171 1.836802 GCTCCTTCTGATCTTGACCCT 59.163 52.381 0.00 0.00 0.00 4.34
4671 5306 2.350895 CAACGATGAGGTGCCCCA 59.649 61.111 0.00 0.00 0.00 4.96
4680 5315 2.033448 GGTGCCCCAATGACGACA 59.967 61.111 0.00 0.00 0.00 4.35
4682 5317 1.302511 GTGCCCCAATGACGACAGT 60.303 57.895 0.00 0.00 0.00 3.55
4752 5394 1.739608 AAAGGGGTGGATGTTGCCCT 61.740 55.000 0.00 0.00 42.01 5.19
4753 5395 1.739608 AAGGGGTGGATGTTGCCCTT 61.740 55.000 0.00 0.00 42.01 3.95
4754 5396 1.984026 GGGGTGGATGTTGCCCTTG 60.984 63.158 0.00 0.00 42.01 3.61
4790 5432 0.608856 ATCGCCTGTGTTGCAATGGA 60.609 50.000 0.59 0.00 0.00 3.41
4870 5542 2.596346 TGGGTGATTGCAATGTTGTCT 58.404 42.857 18.59 0.00 0.00 3.41
4901 5573 0.871722 GGTGTGCGCAACATTACTCA 59.128 50.000 14.00 0.00 41.97 3.41
4902 5574 1.468520 GGTGTGCGCAACATTACTCAT 59.531 47.619 14.00 0.00 41.97 2.90
4903 5575 2.508867 GTGTGCGCAACATTACTCATG 58.491 47.619 14.00 0.00 41.97 3.07
4918 5590 1.662629 CTCATGTTGTGATGAGCGACC 59.337 52.381 0.00 0.00 42.18 4.79
4919 5591 0.371301 CATGTTGTGATGAGCGACCG 59.629 55.000 0.00 0.00 0.00 4.79
4920 5592 1.361668 ATGTTGTGATGAGCGACCGC 61.362 55.000 6.25 6.25 42.33 5.68
4921 5593 2.027073 GTTGTGATGAGCGACCGCA 61.027 57.895 16.97 0.00 44.88 5.69
4922 5594 1.301322 TTGTGATGAGCGACCGCAA 60.301 52.632 16.97 4.77 44.88 4.85
4923 5595 1.565156 TTGTGATGAGCGACCGCAAC 61.565 55.000 16.97 10.33 44.88 4.17
4924 5596 2.027073 GTGATGAGCGACCGCAACA 61.027 57.895 16.97 15.24 44.88 3.33
4925 5597 1.079197 TGATGAGCGACCGCAACAT 60.079 52.632 19.99 19.99 44.88 2.71
4926 5598 0.673333 TGATGAGCGACCGCAACATT 60.673 50.000 16.97 6.69 44.88 2.71
4927 5599 0.247814 GATGAGCGACCGCAACATTG 60.248 55.000 16.97 0.00 44.88 2.82
4928 5600 0.955428 ATGAGCGACCGCAACATTGT 60.955 50.000 16.97 0.00 44.88 2.71
4929 5601 1.163420 TGAGCGACCGCAACATTGTT 61.163 50.000 16.97 0.00 44.88 2.83
4930 5602 0.452784 GAGCGACCGCAACATTGTTC 60.453 55.000 16.97 0.00 44.88 3.18
4931 5603 1.163420 AGCGACCGCAACATTGTTCA 61.163 50.000 16.97 0.00 44.88 3.18
4932 5604 0.109781 GCGACCGCAACATTGTTCAT 60.110 50.000 9.73 0.00 41.49 2.57
4933 5605 1.605500 CGACCGCAACATTGTTCATG 58.394 50.000 0.00 0.00 39.07 3.07
4946 5618 5.406175 ACATTGTTCATGTTGCAATTGTAGC 59.594 36.000 0.59 5.30 44.40 3.58
4947 5619 3.911868 TGTTCATGTTGCAATTGTAGCC 58.088 40.909 0.59 0.00 0.00 3.93
4948 5620 3.573538 TGTTCATGTTGCAATTGTAGCCT 59.426 39.130 0.59 0.00 0.00 4.58
4949 5621 4.039004 TGTTCATGTTGCAATTGTAGCCTT 59.961 37.500 0.59 0.00 0.00 4.35
4950 5622 4.439305 TCATGTTGCAATTGTAGCCTTC 57.561 40.909 0.59 0.00 0.00 3.46
4951 5623 2.987413 TGTTGCAATTGTAGCCTTCG 57.013 45.000 0.59 0.00 0.00 3.79
4952 5624 1.068610 TGTTGCAATTGTAGCCTTCGC 60.069 47.619 0.59 0.00 0.00 4.70
4953 5625 0.525761 TTGCAATTGTAGCCTTCGCC 59.474 50.000 7.40 0.00 34.57 5.54
4954 5626 1.062525 GCAATTGTAGCCTTCGCCG 59.937 57.895 7.40 0.00 34.57 6.46
4955 5627 1.366111 GCAATTGTAGCCTTCGCCGA 61.366 55.000 7.40 0.00 34.57 5.54
4956 5628 1.299541 CAATTGTAGCCTTCGCCGAT 58.700 50.000 0.00 0.00 34.57 4.18
4957 5629 1.003545 CAATTGTAGCCTTCGCCGATG 60.004 52.381 0.00 0.00 34.57 3.84
4958 5630 0.464036 ATTGTAGCCTTCGCCGATGA 59.536 50.000 1.04 0.00 34.57 2.92
4959 5631 0.459585 TTGTAGCCTTCGCCGATGAC 60.460 55.000 1.04 0.00 34.57 3.06
4960 5632 1.320344 TGTAGCCTTCGCCGATGACT 61.320 55.000 1.04 0.00 34.57 3.41
4961 5633 0.666913 GTAGCCTTCGCCGATGACTA 59.333 55.000 1.04 0.00 34.57 2.59
4962 5634 1.269998 GTAGCCTTCGCCGATGACTAT 59.730 52.381 1.04 0.00 34.57 2.12
4963 5635 1.617322 AGCCTTCGCCGATGACTATA 58.383 50.000 1.04 0.00 34.57 1.31
4964 5636 2.171840 AGCCTTCGCCGATGACTATAT 58.828 47.619 1.04 0.00 34.57 0.86
4965 5637 2.094494 AGCCTTCGCCGATGACTATATG 60.094 50.000 1.04 0.00 34.57 1.78
4966 5638 2.881074 CCTTCGCCGATGACTATATGG 58.119 52.381 1.04 0.00 0.00 2.74
4967 5639 2.417379 CCTTCGCCGATGACTATATGGG 60.417 54.545 1.04 0.00 0.00 4.00
4968 5640 1.182667 TCGCCGATGACTATATGGGG 58.817 55.000 0.00 0.00 0.00 4.96
4969 5641 1.182667 CGCCGATGACTATATGGGGA 58.817 55.000 0.00 0.00 34.84 4.81
4970 5642 1.135083 CGCCGATGACTATATGGGGAC 60.135 57.143 0.00 0.00 34.84 4.46
4984 5656 4.519610 GGACAGGCCCAACATTGT 57.480 55.556 0.00 0.00 0.00 2.71
4985 5657 2.267045 GGACAGGCCCAACATTGTC 58.733 57.895 11.19 11.19 39.29 3.18
4986 5658 2.267045 GACAGGCCCAACATTGTCC 58.733 57.895 8.94 0.00 35.15 4.02
4987 5659 0.539438 GACAGGCCCAACATTGTCCA 60.539 55.000 8.94 0.00 35.15 4.02
4988 5660 0.114954 ACAGGCCCAACATTGTCCAT 59.885 50.000 0.00 0.00 0.00 3.41
4989 5661 0.533491 CAGGCCCAACATTGTCCATG 59.467 55.000 0.00 0.00 39.07 3.66
5000 5672 4.922206 ACATTGTCCATGTTGTGATAGGT 58.078 39.130 0.00 0.00 44.40 3.08
5001 5673 4.701651 ACATTGTCCATGTTGTGATAGGTG 59.298 41.667 0.00 0.00 44.40 4.00
5002 5674 4.632327 TTGTCCATGTTGTGATAGGTGA 57.368 40.909 0.00 0.00 0.00 4.02
5003 5675 4.206477 TGTCCATGTTGTGATAGGTGAG 57.794 45.455 0.00 0.00 0.00 3.51
5004 5676 2.939103 GTCCATGTTGTGATAGGTGAGC 59.061 50.000 0.00 0.00 0.00 4.26
5005 5677 2.571202 TCCATGTTGTGATAGGTGAGCA 59.429 45.455 0.00 0.00 0.00 4.26
5006 5678 2.679837 CCATGTTGTGATAGGTGAGCAC 59.320 50.000 0.00 0.00 45.09 4.40
5014 5686 5.470845 GTGATAGGTGAGCACAACATTAC 57.529 43.478 0.99 0.00 44.23 1.89
5015 5687 5.178797 GTGATAGGTGAGCACAACATTACT 58.821 41.667 0.99 0.00 44.23 2.24
5016 5688 5.292101 GTGATAGGTGAGCACAACATTACTC 59.708 44.000 0.99 0.00 44.23 2.59
5079 5751 1.944676 GCCTTCGCCGATGACTACG 60.945 63.158 1.04 0.00 0.00 3.51
5105 5777 2.354821 GACAGACCCAACAGTTCACAAC 59.645 50.000 0.00 0.00 0.00 3.32
5111 5783 1.334960 CCAACAGTTCACAACGATGCC 60.335 52.381 0.00 0.00 36.23 4.40
5112 5784 1.333308 CAACAGTTCACAACGATGCCA 59.667 47.619 0.00 0.00 36.23 4.92
5132 5804 3.490761 CCAACGTTTGCCAAAGATCAGTT 60.491 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.218145 ACATTACGTCGATGACACTTTAATC 57.782 36.000 12.58 0.00 32.09 1.75
2 3 8.692110 TTACATTACGTCGATGACACTTTAAT 57.308 30.769 12.58 1.01 32.09 1.40
8 9 7.221452 ACCTATTTTACATTACGTCGATGACAC 59.779 37.037 12.58 0.00 32.09 3.67
9 10 7.259882 ACCTATTTTACATTACGTCGATGACA 58.740 34.615 12.58 0.00 32.09 3.58
11 12 7.482474 TGACCTATTTTACATTACGTCGATGA 58.518 34.615 12.58 0.00 0.00 2.92
12 13 7.434307 ACTGACCTATTTTACATTACGTCGATG 59.566 37.037 2.26 2.26 0.00 3.84
13 14 7.434307 CACTGACCTATTTTACATTACGTCGAT 59.566 37.037 0.00 0.00 0.00 3.59
14 15 6.748658 CACTGACCTATTTTACATTACGTCGA 59.251 38.462 0.00 0.00 0.00 4.20
15 16 6.529125 ACACTGACCTATTTTACATTACGTCG 59.471 38.462 0.00 0.00 0.00 5.12
16 17 7.201496 CCACACTGACCTATTTTACATTACGTC 60.201 40.741 0.00 0.00 0.00 4.34
17 18 6.592607 CCACACTGACCTATTTTACATTACGT 59.407 38.462 0.00 0.00 0.00 3.57
18 19 6.592607 ACCACACTGACCTATTTTACATTACG 59.407 38.462 0.00 0.00 0.00 3.18
19 20 7.916914 ACCACACTGACCTATTTTACATTAC 57.083 36.000 0.00 0.00 0.00 1.89
20 21 8.158132 TCAACCACACTGACCTATTTTACATTA 58.842 33.333 0.00 0.00 0.00 1.90
21 22 7.001674 TCAACCACACTGACCTATTTTACATT 58.998 34.615 0.00 0.00 0.00 2.71
22 23 6.539173 TCAACCACACTGACCTATTTTACAT 58.461 36.000 0.00 0.00 0.00 2.29
23 24 5.931294 TCAACCACACTGACCTATTTTACA 58.069 37.500 0.00 0.00 0.00 2.41
24 25 6.128007 CCATCAACCACACTGACCTATTTTAC 60.128 42.308 0.00 0.00 0.00 2.01
25 26 5.943416 CCATCAACCACACTGACCTATTTTA 59.057 40.000 0.00 0.00 0.00 1.52
26 27 4.766891 CCATCAACCACACTGACCTATTTT 59.233 41.667 0.00 0.00 0.00 1.82
27 28 4.335416 CCATCAACCACACTGACCTATTT 58.665 43.478 0.00 0.00 0.00 1.40
28 29 3.873801 GCCATCAACCACACTGACCTATT 60.874 47.826 0.00 0.00 0.00 1.73
29 30 2.356125 GCCATCAACCACACTGACCTAT 60.356 50.000 0.00 0.00 0.00 2.57
30 31 1.003118 GCCATCAACCACACTGACCTA 59.997 52.381 0.00 0.00 0.00 3.08
31 32 0.250901 GCCATCAACCACACTGACCT 60.251 55.000 0.00 0.00 0.00 3.85
32 33 0.250901 AGCCATCAACCACACTGACC 60.251 55.000 0.00 0.00 0.00 4.02
33 34 1.160137 GAGCCATCAACCACACTGAC 58.840 55.000 0.00 0.00 0.00 3.51
34 35 0.320683 CGAGCCATCAACCACACTGA 60.321 55.000 0.00 0.00 0.00 3.41
35 36 0.320683 TCGAGCCATCAACCACACTG 60.321 55.000 0.00 0.00 0.00 3.66
36 37 0.615331 ATCGAGCCATCAACCACACT 59.385 50.000 0.00 0.00 0.00 3.55
37 38 2.309528 TATCGAGCCATCAACCACAC 57.690 50.000 0.00 0.00 0.00 3.82
38 39 3.558931 AATATCGAGCCATCAACCACA 57.441 42.857 0.00 0.00 0.00 4.17
39 40 4.900635 AAAATATCGAGCCATCAACCAC 57.099 40.909 0.00 0.00 0.00 4.16
62 63 8.808092 CCCATTAAAATACCCTTGTAAAAGTGA 58.192 33.333 0.00 0.00 0.00 3.41
63 64 8.038351 CCCCATTAAAATACCCTTGTAAAAGTG 58.962 37.037 0.00 0.00 0.00 3.16
64 65 7.735777 ACCCCATTAAAATACCCTTGTAAAAGT 59.264 33.333 0.00 0.00 0.00 2.66
65 66 8.141298 ACCCCATTAAAATACCCTTGTAAAAG 57.859 34.615 0.00 0.00 0.00 2.27
66 67 8.507582 AACCCCATTAAAATACCCTTGTAAAA 57.492 30.769 0.00 0.00 0.00 1.52
67 68 7.180587 GGAACCCCATTAAAATACCCTTGTAAA 59.819 37.037 0.00 0.00 0.00 2.01
68 69 6.668718 GGAACCCCATTAAAATACCCTTGTAA 59.331 38.462 0.00 0.00 0.00 2.41
69 70 6.196434 GGAACCCCATTAAAATACCCTTGTA 58.804 40.000 0.00 0.00 0.00 2.41
70 71 5.027460 GGAACCCCATTAAAATACCCTTGT 58.973 41.667 0.00 0.00 0.00 3.16
71 72 5.607939 GGAACCCCATTAAAATACCCTTG 57.392 43.478 0.00 0.00 0.00 3.61
89 90 8.812147 AGAATTAACGAAAATCTTTTGGGAAC 57.188 30.769 0.00 0.00 31.27 3.62
90 91 7.806014 CGAGAATTAACGAAAATCTTTTGGGAA 59.194 33.333 0.00 0.00 31.27 3.97
91 92 7.040961 ACGAGAATTAACGAAAATCTTTTGGGA 60.041 33.333 10.04 0.00 31.27 4.37
92 93 7.081976 ACGAGAATTAACGAAAATCTTTTGGG 58.918 34.615 10.04 0.00 31.27 4.12
93 94 9.769093 ATACGAGAATTAACGAAAATCTTTTGG 57.231 29.630 10.04 0.00 32.96 3.28
108 109 9.499585 CACGACTCTTAGAAAATACGAGAATTA 57.500 33.333 0.00 0.00 0.00 1.40
109 110 7.009357 GCACGACTCTTAGAAAATACGAGAATT 59.991 37.037 0.00 0.00 0.00 2.17
110 111 6.472808 GCACGACTCTTAGAAAATACGAGAAT 59.527 38.462 0.00 0.00 0.00 2.40
111 112 5.798934 GCACGACTCTTAGAAAATACGAGAA 59.201 40.000 0.00 0.00 0.00 2.87
112 113 5.123502 AGCACGACTCTTAGAAAATACGAGA 59.876 40.000 0.00 0.00 0.00 4.04
113 114 5.333513 AGCACGACTCTTAGAAAATACGAG 58.666 41.667 0.00 0.00 0.00 4.18
114 115 5.306532 AGCACGACTCTTAGAAAATACGA 57.693 39.130 0.00 0.00 0.00 3.43
115 116 5.169208 CGTAGCACGACTCTTAGAAAATACG 59.831 44.000 3.04 0.00 46.05 3.06
116 117 6.479654 CGTAGCACGACTCTTAGAAAATAC 57.520 41.667 3.04 0.00 46.05 1.89
149 150 3.253432 GCGGGTCTTTTGAAAAGATCAGT 59.747 43.478 26.68 0.00 39.77 3.41
151 152 2.556622 GGCGGGTCTTTTGAAAAGATCA 59.443 45.455 26.68 3.67 35.85 2.92
160 161 3.431725 GAGGCGGCGGGTCTTTTG 61.432 66.667 9.78 0.00 0.00 2.44
184 185 5.996513 TGCAATGAATTGTGCCAAATTTACT 59.003 32.000 5.02 0.00 40.14 2.24
188 189 4.579340 TGTTGCAATGAATTGTGCCAAATT 59.421 33.333 0.59 0.00 40.14 1.82
191 192 3.189618 TGTTGCAATGAATTGTGCCAA 57.810 38.095 0.59 0.00 40.14 4.52
201 202 2.425312 ACACTCCGTTTTGTTGCAATGA 59.575 40.909 0.59 0.00 0.00 2.57
214 215 2.896745 AAGGTTACGAAACACTCCGT 57.103 45.000 0.00 0.00 42.15 4.69
215 216 3.847105 GCAAAAGGTTACGAAACACTCCG 60.847 47.826 0.00 0.00 37.34 4.63
242 243 9.243637 GTTCAATTGTTTCTGCAACATAAGTTA 57.756 29.630 5.13 0.00 45.17 2.24
244 245 7.264221 TGTTCAATTGTTTCTGCAACATAAGT 58.736 30.769 5.13 0.00 45.17 2.24
245 246 7.648908 TCTGTTCAATTGTTTCTGCAACATAAG 59.351 33.333 5.13 0.00 45.17 1.73
262 263 7.876936 ATCTGCAACATAATCTCTGTTCAAT 57.123 32.000 0.00 0.00 34.69 2.57
276 277 7.047460 AGTGAAGAAGAAAAATCTGCAACAT 57.953 32.000 0.00 0.00 34.25 2.71
348 355 7.562412 TCATTGCAAATAAATTCACAACAACG 58.438 30.769 1.71 0.00 0.00 4.10
363 370 4.802039 GCGACATCATCTTTCATTGCAAAT 59.198 37.500 1.71 0.00 0.00 2.32
399 406 3.494232 ACAAAACGGAAACAACAACGAG 58.506 40.909 0.00 0.00 0.00 4.18
439 446 0.879839 GCCGCATGCCAACAAGTTTT 60.880 50.000 13.15 0.00 0.00 2.43
476 483 1.303091 ACATTACCGGCGGAAGTTGC 61.303 55.000 35.78 0.00 0.00 4.17
477 484 1.135803 CAACATTACCGGCGGAAGTTG 60.136 52.381 35.78 30.45 0.00 3.16
480 487 1.302383 TGCAACATTACCGGCGGAAG 61.302 55.000 35.78 20.21 0.00 3.46
484 492 0.732571 AATCTGCAACATTACCGGCG 59.267 50.000 0.00 0.00 0.00 6.46
486 494 4.701956 AAAGAATCTGCAACATTACCGG 57.298 40.909 0.00 0.00 0.00 5.28
487 495 4.788100 CGAAAAGAATCTGCAACATTACCG 59.212 41.667 0.00 0.00 0.00 4.02
491 499 7.920682 AGTTAAACGAAAAGAATCTGCAACATT 59.079 29.630 0.00 0.00 0.00 2.71
543 559 9.206870 ACATCATTTGTATTGCGAAATTTCTTT 57.793 25.926 15.92 1.30 36.57 2.52
553 569 4.413969 TCTGCAACATCATTTGTATTGCG 58.586 39.130 0.00 0.00 42.50 4.85
558 574 8.196771 AGAAAGTTTTCTGCAACATCATTTGTA 58.803 29.630 6.33 0.00 45.27 2.41
585 601 1.128611 GATCATGTGCGCGCGATAC 59.871 57.895 37.18 29.62 0.00 2.24
587 603 3.695409 CGATCATGTGCGCGCGAT 61.695 61.111 37.18 22.07 0.00 4.58
613 630 6.297582 GGGTCATCTAGTACTAGTTCTAGCA 58.702 44.000 25.58 16.45 35.13 3.49
621 638 3.211865 TGCACGGGTCATCTAGTACTAG 58.788 50.000 21.87 21.87 34.56 2.57
638 656 0.307453 TTGCGACACATGTCTTGCAC 59.693 50.000 14.87 0.00 39.75 4.57
648 666 0.317160 CACCTCCTACTTGCGACACA 59.683 55.000 0.00 0.00 0.00 3.72
659 677 2.753043 GGCGTCCGTCACCTCCTA 60.753 66.667 0.00 0.00 0.00 2.94
679 697 1.080501 CTGCCGACGTGTCTCATGT 60.081 57.895 0.00 0.00 36.19 3.21
684 702 1.300697 GGTTTCTGCCGACGTGTCT 60.301 57.895 0.00 0.00 0.00 3.41
686 704 1.153329 TTGGTTTCTGCCGACGTGT 60.153 52.632 0.00 0.00 0.00 4.49
687 705 1.278637 GTTGGTTTCTGCCGACGTG 59.721 57.895 0.00 0.00 33.65 4.49
688 706 1.890510 GGTTGGTTTCTGCCGACGT 60.891 57.895 0.00 0.00 42.52 4.34
691 709 1.611491 GAAATGGTTGGTTTCTGCCGA 59.389 47.619 0.00 0.00 33.79 5.54
709 727 9.273016 CGAAGGATTAGCATTAGAAAATAGGAA 57.727 33.333 0.00 0.00 0.00 3.36
710 728 8.647796 TCGAAGGATTAGCATTAGAAAATAGGA 58.352 33.333 0.00 0.00 0.00 2.94
711 729 8.833231 TCGAAGGATTAGCATTAGAAAATAGG 57.167 34.615 0.00 0.00 0.00 2.57
712 730 9.698309 TCTCGAAGGATTAGCATTAGAAAATAG 57.302 33.333 0.00 0.00 0.00 1.73
759 777 7.824704 ATTATACATTTCTGCAGATCGCTAG 57.175 36.000 19.04 7.34 43.06 3.42
777 849 9.817809 TTGAAGCGAGATCCCAATATATTATAC 57.182 33.333 0.00 0.00 0.00 1.47
779 851 8.543774 ACTTGAAGCGAGATCCCAATATATTAT 58.456 33.333 0.00 0.00 0.00 1.28
780 852 7.819415 CACTTGAAGCGAGATCCCAATATATTA 59.181 37.037 0.00 0.00 0.00 0.98
781 853 6.652481 CACTTGAAGCGAGATCCCAATATATT 59.348 38.462 0.00 0.00 0.00 1.28
883 959 2.626840 TGGCCTTTGTCTTTGTTTTGC 58.373 42.857 3.32 0.00 0.00 3.68
1338 1415 2.035155 TTCCAGGACTCGGAGCGA 59.965 61.111 4.58 0.00 33.01 4.93
1512 1589 2.291741 GTCAAACTGCTTTAGCTGCTGT 59.708 45.455 13.43 0.00 42.72 4.40
1549 1627 6.365050 AGCAAAGCAAAATAAAAATGAAGCG 58.635 32.000 0.00 0.00 0.00 4.68
1579 1657 1.702957 CCCCCGGCCTCTGATAAATTA 59.297 52.381 0.00 0.00 0.00 1.40
1581 1659 2.069165 GCCCCCGGCCTCTGATAAAT 62.069 60.000 0.00 0.00 44.06 1.40
1594 1672 2.610532 GAAAAGGAGGCTAGCCCCCG 62.611 65.000 30.42 0.00 36.58 5.73
1595 1673 1.227664 GAAAAGGAGGCTAGCCCCC 59.772 63.158 30.42 28.41 36.58 5.40
1596 1674 1.227664 GGAAAAGGAGGCTAGCCCC 59.772 63.158 30.42 27.73 36.58 5.80
1597 1675 0.106967 CTGGAAAAGGAGGCTAGCCC 60.107 60.000 30.42 20.50 36.58 5.19
1598 1676 0.912486 TCTGGAAAAGGAGGCTAGCC 59.088 55.000 27.19 27.19 0.00 3.93
1599 1677 2.789409 TTCTGGAAAAGGAGGCTAGC 57.211 50.000 6.04 6.04 0.00 3.42
1620 1698 7.929785 TCGCCGGATAGATTAAATCTAGTTTTT 59.070 33.333 5.05 2.10 44.44 1.94
1621 1699 7.439381 TCGCCGGATAGATTAAATCTAGTTTT 58.561 34.615 5.05 4.30 44.44 2.43
1622 1700 6.989659 TCGCCGGATAGATTAAATCTAGTTT 58.010 36.000 5.05 0.00 44.44 2.66
1623 1701 6.585695 TCGCCGGATAGATTAAATCTAGTT 57.414 37.500 5.05 0.00 44.44 2.24
1624 1702 6.777213 ATCGCCGGATAGATTAAATCTAGT 57.223 37.500 5.05 0.00 44.44 2.57
1625 1703 8.383619 CAAAATCGCCGGATAGATTAAATCTAG 58.616 37.037 5.05 0.00 44.44 2.43
1626 1704 7.148474 GCAAAATCGCCGGATAGATTAAATCTA 60.148 37.037 5.05 0.00 45.23 1.98
1627 1705 6.348540 GCAAAATCGCCGGATAGATTAAATCT 60.349 38.462 5.05 0.00 43.33 2.40
1628 1706 5.795441 GCAAAATCGCCGGATAGATTAAATC 59.205 40.000 5.05 0.49 36.20 2.17
1629 1707 5.473504 AGCAAAATCGCCGGATAGATTAAAT 59.526 36.000 5.05 0.75 36.20 1.40
1630 1708 4.819630 AGCAAAATCGCCGGATAGATTAAA 59.180 37.500 5.05 0.00 36.20 1.52
1631 1709 4.213270 CAGCAAAATCGCCGGATAGATTAA 59.787 41.667 5.05 0.00 36.20 1.40
1632 1710 3.745975 CAGCAAAATCGCCGGATAGATTA 59.254 43.478 5.05 0.00 36.20 1.75
1633 1711 2.549754 CAGCAAAATCGCCGGATAGATT 59.450 45.455 5.05 10.13 38.58 2.40
1634 1712 2.146342 CAGCAAAATCGCCGGATAGAT 58.854 47.619 5.05 3.24 31.01 1.98
1635 1713 1.581934 CAGCAAAATCGCCGGATAGA 58.418 50.000 5.05 0.25 31.01 1.98
1636 1714 0.040958 GCAGCAAAATCGCCGGATAG 60.041 55.000 5.05 0.00 31.01 2.08
1649 1727 5.065914 ACAGAAAGAACTTATCAGCAGCAA 58.934 37.500 0.00 0.00 0.00 3.91
1674 1759 2.633967 AGACATTCCATGCCTGCAAAAA 59.366 40.909 0.00 0.00 0.00 1.94
2449 2599 8.517878 ACATTTTCATCTATGAGTTTGTTCTGG 58.482 33.333 0.00 0.00 38.19 3.86
2593 2743 3.869623 CAGAACTGGAGGTGATGGG 57.130 57.895 0.00 0.00 0.00 4.00
2707 2857 7.658575 TGATGACTAAAACAAGTAGGGTTACAC 59.341 37.037 0.00 0.00 31.96 2.90
2755 2905 6.217481 GGATTTCCAACTACCAAAGGGTTGA 61.217 44.000 6.62 0.00 41.71 3.18
2802 2952 2.623416 GGACAAGAAAAACCTCACCCTG 59.377 50.000 0.00 0.00 0.00 4.45
2808 2958 7.272037 TGTTGAATAGGACAAGAAAAACCTC 57.728 36.000 0.00 0.00 34.42 3.85
2878 3029 9.691362 GCACTGAAACCTTTGAGAAAATATAAA 57.309 29.630 0.00 0.00 0.00 1.40
2880 3031 8.635765 AGCACTGAAACCTTTGAGAAAATATA 57.364 30.769 0.00 0.00 0.00 0.86
3004 3162 5.499139 TTTTAGCAACTGTCTTGTTCCTG 57.501 39.130 0.00 0.00 0.00 3.86
3083 3241 0.321564 TTGCAACCGACATGCTAGCT 60.322 50.000 17.23 0.00 44.14 3.32
3168 3328 2.223537 TATGCAGTACAGGCACATCG 57.776 50.000 13.53 0.00 45.23 3.84
3170 3330 3.565764 ACATATGCAGTACAGGCACAT 57.434 42.857 13.53 5.99 45.23 3.21
3171 3331 4.687901 ATACATATGCAGTACAGGCACA 57.312 40.909 13.53 3.80 45.23 4.57
3172 3332 5.056480 TCAATACATATGCAGTACAGGCAC 58.944 41.667 13.53 0.00 45.23 5.01
3173 3333 5.289083 TCAATACATATGCAGTACAGGCA 57.711 39.130 13.60 13.60 46.66 4.75
3174 3334 4.692625 CCTCAATACATATGCAGTACAGGC 59.307 45.833 1.58 0.00 0.00 4.85
3175 3335 5.858381 ACCTCAATACATATGCAGTACAGG 58.142 41.667 1.58 4.33 0.00 4.00
3191 3351 8.567285 AATTCTCAACGAATAAGAACCTCAAT 57.433 30.769 0.00 0.00 41.42 2.57
3360 3523 1.382692 GGATCCCAGAAAGCAGCTGC 61.383 60.000 31.53 31.53 42.49 5.25
3638 3801 1.065854 AGCCACAGAAAGGAGAATCGG 60.066 52.381 0.00 0.00 34.37 4.18
3679 3842 8.895932 AAGAAATCGACACAAACATAATAAGC 57.104 30.769 0.00 0.00 0.00 3.09
3696 3859 5.957796 GCACCAACTCGTAATAAAGAAATCG 59.042 40.000 0.00 0.00 0.00 3.34
3854 4017 8.458573 AGTTAACACAATCATGGTTGAACTTA 57.541 30.769 25.29 12.94 34.96 2.24
3885 4048 4.264460 AGTAGGCAACAGACTTGAGAAG 57.736 45.455 0.00 0.00 41.41 2.85
3977 4149 1.741770 ATGGCGCTTGGTCGACTTC 60.742 57.895 16.46 0.00 38.54 3.01
4030 4202 0.898320 ATCGTCAAGTGGGGACTCAG 59.102 55.000 0.00 0.00 33.11 3.35
4035 4207 1.481871 GAGGTATCGTCAAGTGGGGA 58.518 55.000 0.00 0.00 0.00 4.81
4076 4248 1.656652 ATGGTCTAGCAACGATGTGC 58.343 50.000 0.00 0.00 45.28 4.57
4257 4877 5.923733 ACTAATGCTCTGCTAACAGTAGT 57.076 39.130 0.00 0.00 44.77 2.73
4316 4936 5.755375 ACGAGATAATACAGTGAATTGCCAG 59.245 40.000 0.00 0.00 0.00 4.85
4337 4957 3.013921 AGCAAACAGGAACAAGAAACGA 58.986 40.909 0.00 0.00 0.00 3.85
4345 4965 5.769662 ACTCATCAAATAGCAAACAGGAACA 59.230 36.000 0.00 0.00 0.00 3.18
4374 4994 6.054941 TCAAGTTCTCAATTAGCAACTGACA 58.945 36.000 0.00 0.00 30.70 3.58
4408 5028 1.810151 CCACCCAGTTGGATAAACACG 59.190 52.381 0.00 0.00 41.61 4.49
4439 5059 5.953571 TCCAGATCTAATACCTGTGAGCTA 58.046 41.667 0.00 0.00 0.00 3.32
4440 5060 4.809193 TCCAGATCTAATACCTGTGAGCT 58.191 43.478 0.00 0.00 0.00 4.09
4474 5094 4.284123 GGCAACTGATGAGCGTCA 57.716 55.556 0.00 0.00 0.00 4.35
4549 5169 2.125106 GTTGGGCAGCGGACTAGG 60.125 66.667 0.00 0.00 0.00 3.02
4550 5170 1.003839 TTGTTGGGCAGCGGACTAG 60.004 57.895 0.00 0.00 0.00 2.57
4551 5171 1.302192 GTTGTTGGGCAGCGGACTA 60.302 57.895 0.00 0.00 0.00 2.59
4670 5305 2.390599 CGGCCCACTGTCGTCATTG 61.391 63.158 0.00 0.00 0.00 2.82
4671 5306 2.047274 CGGCCCACTGTCGTCATT 60.047 61.111 0.00 0.00 0.00 2.57
4680 5315 4.101448 GCAGATCCACGGCCCACT 62.101 66.667 0.00 0.00 33.80 4.00
4752 5394 1.671054 GCTACAAGCACCTCGCCAA 60.671 57.895 0.00 0.00 44.04 4.52
4753 5395 2.047274 GCTACAAGCACCTCGCCA 60.047 61.111 0.00 0.00 44.04 5.69
4765 5407 1.298157 GCAACACAGGCGATGCTACA 61.298 55.000 0.00 0.00 35.93 2.74
4790 5432 3.101437 ACACATGGGATGTTGCAATGAT 58.899 40.909 0.00 0.00 42.70 2.45
4865 5507 4.126437 CACACCTATCACAACACAGACAA 58.874 43.478 0.00 0.00 0.00 3.18
4866 5508 3.727726 CACACCTATCACAACACAGACA 58.272 45.455 0.00 0.00 0.00 3.41
4870 5542 1.507562 CGCACACCTATCACAACACA 58.492 50.000 0.00 0.00 0.00 3.72
4901 5573 1.361668 GCGGTCGCTCATCACAACAT 61.362 55.000 8.20 0.00 38.26 2.71
4902 5574 2.027073 GCGGTCGCTCATCACAACA 61.027 57.895 8.20 0.00 38.26 3.33
4903 5575 1.565156 TTGCGGTCGCTCATCACAAC 61.565 55.000 16.36 0.00 42.51 3.32
4904 5576 1.301322 TTGCGGTCGCTCATCACAA 60.301 52.632 16.36 0.00 42.51 3.33
4905 5577 2.027073 GTTGCGGTCGCTCATCACA 61.027 57.895 16.36 0.00 42.51 3.58
4906 5578 1.361668 ATGTTGCGGTCGCTCATCAC 61.362 55.000 16.36 6.18 42.51 3.06
4907 5579 0.673333 AATGTTGCGGTCGCTCATCA 60.673 50.000 16.36 9.95 42.51 3.07
4908 5580 0.247814 CAATGTTGCGGTCGCTCATC 60.248 55.000 16.36 5.14 42.51 2.92
4909 5581 0.955428 ACAATGTTGCGGTCGCTCAT 60.955 50.000 16.36 15.98 42.51 2.90
4910 5582 1.163420 AACAATGTTGCGGTCGCTCA 61.163 50.000 16.36 14.60 42.51 4.26
4911 5583 0.452784 GAACAATGTTGCGGTCGCTC 60.453 55.000 16.36 9.87 42.51 5.03
4912 5584 1.163420 TGAACAATGTTGCGGTCGCT 61.163 50.000 16.36 0.00 42.51 4.93
4913 5585 0.109781 ATGAACAATGTTGCGGTCGC 60.110 50.000 2.20 8.54 42.35 5.19
4914 5586 1.605500 CATGAACAATGTTGCGGTCG 58.394 50.000 2.20 0.00 0.00 4.79
4923 5595 5.163933 GGCTACAATTGCAACATGAACAATG 60.164 40.000 18.17 4.41 42.48 2.82
4924 5596 4.931002 GGCTACAATTGCAACATGAACAAT 59.069 37.500 18.17 3.24 35.59 2.71
4925 5597 4.039004 AGGCTACAATTGCAACATGAACAA 59.961 37.500 18.17 0.63 0.00 2.83
4926 5598 3.573538 AGGCTACAATTGCAACATGAACA 59.426 39.130 18.17 4.95 0.00 3.18
4927 5599 4.178545 AGGCTACAATTGCAACATGAAC 57.821 40.909 18.17 8.42 0.00 3.18
4928 5600 4.615682 CGAAGGCTACAATTGCAACATGAA 60.616 41.667 18.17 0.00 0.00 2.57
4929 5601 3.119884 CGAAGGCTACAATTGCAACATGA 60.120 43.478 18.17 4.33 0.00 3.07
4930 5602 3.173599 CGAAGGCTACAATTGCAACATG 58.826 45.455 0.00 6.92 0.00 3.21
4931 5603 2.415893 GCGAAGGCTACAATTGCAACAT 60.416 45.455 0.00 0.00 35.83 2.71
4932 5604 1.068610 GCGAAGGCTACAATTGCAACA 60.069 47.619 0.00 0.00 35.83 3.33
4933 5605 1.617740 GCGAAGGCTACAATTGCAAC 58.382 50.000 0.00 0.00 35.83 4.17
4946 5618 2.417379 CCCATATAGTCATCGGCGAAGG 60.417 54.545 15.93 9.89 0.00 3.46
4947 5619 2.417379 CCCCATATAGTCATCGGCGAAG 60.417 54.545 15.93 10.47 0.00 3.79
4948 5620 1.548719 CCCCATATAGTCATCGGCGAA 59.451 52.381 15.93 0.00 0.00 4.70
4949 5621 1.182667 CCCCATATAGTCATCGGCGA 58.817 55.000 13.87 13.87 0.00 5.54
4950 5622 1.135083 GTCCCCATATAGTCATCGGCG 60.135 57.143 0.00 0.00 0.00 6.46
4951 5623 1.899814 TGTCCCCATATAGTCATCGGC 59.100 52.381 0.00 0.00 0.00 5.54
4952 5624 2.497675 CCTGTCCCCATATAGTCATCGG 59.502 54.545 0.00 0.00 0.00 4.18
4953 5625 2.093973 GCCTGTCCCCATATAGTCATCG 60.094 54.545 0.00 0.00 0.00 3.84
4954 5626 2.237392 GGCCTGTCCCCATATAGTCATC 59.763 54.545 0.00 0.00 0.00 2.92
4955 5627 2.269940 GGCCTGTCCCCATATAGTCAT 58.730 52.381 0.00 0.00 0.00 3.06
4956 5628 1.729586 GGCCTGTCCCCATATAGTCA 58.270 55.000 0.00 0.00 0.00 3.41
4967 5639 2.267045 GACAATGTTGGGCCTGTCC 58.733 57.895 10.85 0.00 33.57 4.02
4968 5640 0.539438 TGGACAATGTTGGGCCTGTC 60.539 55.000 13.00 13.00 37.95 3.51
4969 5641 0.114954 ATGGACAATGTTGGGCCTGT 59.885 50.000 4.53 0.00 0.00 4.00
4970 5642 0.533491 CATGGACAATGTTGGGCCTG 59.467 55.000 4.53 0.00 0.00 4.85
4971 5643 2.980541 CATGGACAATGTTGGGCCT 58.019 52.632 4.53 0.00 0.00 5.19
4979 5651 4.943093 TCACCTATCACAACATGGACAATG 59.057 41.667 0.00 0.00 42.48 2.82
4980 5652 5.178096 TCACCTATCACAACATGGACAAT 57.822 39.130 0.00 0.00 0.00 2.71
4981 5653 4.578871 CTCACCTATCACAACATGGACAA 58.421 43.478 0.00 0.00 0.00 3.18
4982 5654 3.619733 GCTCACCTATCACAACATGGACA 60.620 47.826 0.00 0.00 0.00 4.02
4983 5655 2.939103 GCTCACCTATCACAACATGGAC 59.061 50.000 0.00 0.00 0.00 4.02
4984 5656 2.571202 TGCTCACCTATCACAACATGGA 59.429 45.455 0.00 0.00 0.00 3.41
4985 5657 2.679837 GTGCTCACCTATCACAACATGG 59.320 50.000 0.00 0.00 0.00 3.66
4986 5658 3.337358 TGTGCTCACCTATCACAACATG 58.663 45.455 0.00 0.00 37.73 3.21
4987 5659 3.701205 TGTGCTCACCTATCACAACAT 57.299 42.857 0.00 0.00 37.73 2.71
4988 5660 3.483808 TTGTGCTCACCTATCACAACA 57.516 42.857 3.27 0.00 43.30 3.33
4990 5662 3.483808 TGTTGTGCTCACCTATCACAA 57.516 42.857 3.27 3.27 45.16 3.33
4991 5663 3.701205 ATGTTGTGCTCACCTATCACA 57.299 42.857 0.00 0.00 38.76 3.58
4992 5664 5.178797 AGTAATGTTGTGCTCACCTATCAC 58.821 41.667 0.00 0.00 0.00 3.06
4993 5665 5.419542 GAGTAATGTTGTGCTCACCTATCA 58.580 41.667 0.00 0.00 0.00 2.15
4994 5666 4.504461 CGAGTAATGTTGTGCTCACCTATC 59.496 45.833 0.00 0.00 0.00 2.08
4995 5667 4.081642 ACGAGTAATGTTGTGCTCACCTAT 60.082 41.667 0.00 0.00 0.00 2.57
4996 5668 3.257375 ACGAGTAATGTTGTGCTCACCTA 59.743 43.478 0.00 0.00 0.00 3.08
4997 5669 2.037251 ACGAGTAATGTTGTGCTCACCT 59.963 45.455 0.00 0.00 0.00 4.00
4998 5670 2.157668 CACGAGTAATGTTGTGCTCACC 59.842 50.000 0.00 0.00 0.00 4.02
4999 5671 2.800544 ACACGAGTAATGTTGTGCTCAC 59.199 45.455 0.00 0.00 35.48 3.51
5000 5672 3.106242 ACACGAGTAATGTTGTGCTCA 57.894 42.857 0.00 0.00 35.48 4.26
5016 5688 2.391821 GTCGCTCATCGCAACACG 59.608 61.111 0.00 0.00 45.62 4.49
5096 5768 0.586319 CGTTGGCATCGTTGTGAACT 59.414 50.000 9.71 0.00 0.00 3.01
5097 5769 0.306533 ACGTTGGCATCGTTGTGAAC 59.693 50.000 17.21 0.00 38.38 3.18
5111 5783 3.354089 ACTGATCTTTGGCAAACGTTG 57.646 42.857 8.93 0.00 0.00 4.10
5112 5784 3.490761 CCAACTGATCTTTGGCAAACGTT 60.491 43.478 8.93 0.00 37.31 3.99
5132 5804 2.516906 ACACATGTTGCACATCATCCA 58.483 42.857 0.00 0.00 36.53 3.41


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

AutoCloner maintained by Alex Coulton.