Multiple sequence alignment - TraesCS5B01G214100

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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 TraesCS5B01G214100 chr5B 100.000 5378 0 0 1 5378 386837281 386842658 0.000000e+00 9932.0
1 TraesCS5B01G214100 chr5B 100.000 48 0 0 3628 3675 386840878 386840925 7.420000e-14 89.8
2 TraesCS5B01G214100 chr5B 100.000 48 0 0 3598 3645 386840908 386840955 7.420000e-14 89.8
3 TraesCS5B01G214100 chr5D 88.676 3391 211 55 57 3361 331255319 331258622 0.000000e+00 3975.0
4 TraesCS5B01G214100 chr5D 90.868 668 49 6 3965 4625 331259464 331260126 0.000000e+00 885.0
5 TraesCS5B01G214100 chr5D 82.961 358 39 11 3639 3981 331259096 331259446 2.430000e-78 303.0
6 TraesCS5B01G214100 chr5D 82.906 351 21 3 4631 4942 331260167 331260517 4.100000e-71 279.0
7 TraesCS5B01G214100 chr5D 88.360 189 16 4 3285 3468 331258445 331258632 7.010000e-54 222.0
8 TraesCS5B01G214100 chr5D 85.965 171 15 6 5177 5347 575444 575283 1.990000e-39 174.0
9 TraesCS5B01G214100 chr5D 84.239 184 12 7 4788 4958 331262557 331262736 4.310000e-36 163.0
10 TraesCS5B01G214100 chr5D 84.615 143 19 2 4623 4763 371874048 371874189 7.260000e-29 139.0
11 TraesCS5B01G214100 chr5D 80.488 123 8 7 3057 3166 98723798 98723917 4.470000e-11 80.5
12 TraesCS5B01G214100 chr5D 97.297 37 0 1 3609 3645 331259096 331259131 1.620000e-05 62.1
13 TraesCS5B01G214100 chr5D 100.000 31 0 0 13 43 331255289 331255319 2.090000e-04 58.4
14 TraesCS5B01G214100 chr5A 89.817 2573 141 41 991 3494 431891127 431893647 0.000000e+00 3188.0
15 TraesCS5B01G214100 chr5A 82.879 917 89 28 57 933 431890237 431891125 0.000000e+00 761.0
16 TraesCS5B01G214100 chr5A 88.397 655 40 19 3983 4625 431894551 431895181 0.000000e+00 756.0
17 TraesCS5B01G214100 chr5A 80.591 474 38 14 4628 5066 431895212 431895666 3.130000e-82 316.0
18 TraesCS5B01G214100 chr5A 87.018 285 28 3 3297 3574 431893547 431893829 4.040000e-81 313.0
19 TraesCS5B01G214100 chr5A 82.776 389 23 18 3646 3998 431894132 431894512 1.880000e-79 307.0
20 TraesCS5B01G214100 chr5A 85.714 77 6 3 4880 4956 431907078 431907149 5.780000e-10 76.8
21 TraesCS5B01G214100 chr2A 88.095 168 10 8 5181 5348 38921027 38920870 1.980000e-44 191.0
22 TraesCS5B01G214100 chr7D 86.517 178 14 6 5173 5350 134845032 134844865 2.560000e-43 187.0
23 TraesCS5B01G214100 chr7D 84.699 183 16 8 5174 5355 579762522 579762693 7.160000e-39 172.0
24 TraesCS5B01G214100 chr7D 86.029 136 16 2 4623 4755 60494764 60494629 5.610000e-30 143.0
25 TraesCS5B01G214100 chr2D 86.188 181 15 6 5166 5346 526525129 526524959 2.560000e-43 187.0
26 TraesCS5B01G214100 chr7A 87.135 171 12 6 5177 5347 694194962 694194802 9.200000e-43 185.0
27 TraesCS5B01G214100 chr7A 83.957 187 16 10 5165 5350 691723638 691723811 3.330000e-37 167.0
28 TraesCS5B01G214100 chr7A 90.426 94 7 1 5082 5175 55891499 55891408 7.310000e-24 122.0
29 TraesCS5B01G214100 chr2B 85.876 177 17 5 5171 5347 769078172 769078004 1.190000e-41 182.0
30 TraesCS5B01G214100 chr6A 85.246 183 17 6 5167 5349 48520210 48520038 4.280000e-41 180.0
31 TraesCS5B01G214100 chr4B 89.600 125 11 2 4633 4755 212948344 212948468 2.010000e-34 158.0
32 TraesCS5B01G214100 chr3A 81.443 194 29 5 4986 5175 741841453 741841643 9.330000e-33 152.0
33 TraesCS5B01G214100 chr3A 100.000 33 0 0 5004 5036 584030867 584030899 1.620000e-05 62.1
34 TraesCS5B01G214100 chrUn 88.333 120 13 1 4637 4755 28288802 28288683 5.610000e-30 143.0
35 TraesCS5B01G214100 chr4D 90.090 111 9 1 5066 5176 277233268 277233160 5.610000e-30 143.0
36 TraesCS5B01G214100 chr6B 87.395 119 13 2 4639 4755 470122546 470122428 9.400000e-28 135.0
37 TraesCS5B01G214100 chr6B 91.176 68 6 0 4888 4955 692573209 692573142 5.740000e-15 93.5
38 TraesCS5B01G214100 chr3B 86.992 123 13 2 4634 4755 547153737 547153617 9.400000e-28 135.0
39 TraesCS5B01G214100 chr1D 87.395 119 14 1 4634 4752 383158548 383158665 9.400000e-28 135.0
40 TraesCS5B01G214100 chr4A 80.925 173 17 5 5016 5175 668155760 668155591 7.310000e-24 122.0


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 TraesCS5B01G214100 chr5B 386837281 386842658 5377 False 3370.533333 9932 100.000000 1 5378 3 chr5B.!!$F1 5377
1 TraesCS5B01G214100 chr5D 331255289 331262736 7447 False 743.437500 3975 89.413375 13 4958 8 chr5D.!!$F3 4945
2 TraesCS5B01G214100 chr5A 431890237 431895666 5429 False 940.166667 3188 85.246333 57 5066 6 chr5A.!!$F2 5009

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
51 52 0.167251 CGGCGGCGTTTTAGAATTGT 59.833 50.0 24.74 0.0 0.0 2.71 F
88 90 0.178858 TTGTGGGGATGAGGGTGGTA 60.179 55.0 0.00 0.0 0.0 3.25 F
1428 1498 0.108138 CCGGAACCTTCGAGAGCATT 60.108 55.0 0.00 0.0 0.0 3.56 F
1566 1636 0.033601 AGACGCAGACCATCCTCTCT 60.034 55.0 0.00 0.0 0.0 3.10 F
3289 3417 0.238289 GTTCACATGCACACCTTCCG 59.762 55.0 0.00 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1409 1479 0.108138 AATGCTCTCGAAGGTTCCGG 60.108 55.0 0.00 0.00 0.0 5.14 R
1549 1619 0.323816 TGAGAGAGGATGGTCTGCGT 60.324 55.0 0.00 0.00 0.0 5.24 R
3046 3140 0.179045 ATGGCCGGCTTCTGTGTATC 60.179 55.0 28.56 5.64 0.0 2.24 R
3357 3560 0.458370 GCATGTGAACGGATTTGGCC 60.458 55.0 0.00 0.00 0.0 5.36 R
4389 5059 0.037326 TGCAGAGACACAACCGATCC 60.037 55.0 0.00 0.00 0.0 3.36 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
45 46 4.454717 GTGGCGGCGGCGTTTTAG 62.455 66.667 32.35 3.84 41.24 1.85
46 47 4.683721 TGGCGGCGGCGTTTTAGA 62.684 61.111 32.35 6.09 41.24 2.10
47 48 3.424859 GGCGGCGGCGTTTTAGAA 61.425 61.111 32.35 0.00 41.24 2.10
48 49 2.757056 GGCGGCGGCGTTTTAGAAT 61.757 57.895 32.35 0.00 41.24 2.40
49 50 1.135939 GCGGCGGCGTTTTAGAATT 59.864 52.632 32.35 0.00 0.00 2.17
50 51 1.131618 GCGGCGGCGTTTTAGAATTG 61.132 55.000 32.35 0.00 0.00 2.32
51 52 0.167251 CGGCGGCGTTTTAGAATTGT 59.833 50.000 24.74 0.00 0.00 2.71
52 53 1.613270 GGCGGCGTTTTAGAATTGTG 58.387 50.000 9.37 0.00 0.00 3.33
53 54 1.068816 GGCGGCGTTTTAGAATTGTGT 60.069 47.619 9.37 0.00 0.00 3.72
54 55 2.239201 GCGGCGTTTTAGAATTGTGTC 58.761 47.619 9.37 0.00 0.00 3.67
55 56 2.350007 GCGGCGTTTTAGAATTGTGTCA 60.350 45.455 9.37 0.00 0.00 3.58
58 59 3.608073 GGCGTTTTAGAATTGTGTCATGC 59.392 43.478 0.00 0.00 0.00 4.06
74 76 1.903877 ATGCGAGAGGGAGGTTGTGG 61.904 60.000 0.00 0.00 0.00 4.17
86 88 1.000896 GTTGTGGGGATGAGGGTGG 60.001 63.158 0.00 0.00 0.00 4.61
88 90 0.178858 TTGTGGGGATGAGGGTGGTA 60.179 55.000 0.00 0.00 0.00 3.25
109 111 8.019094 GTGGTATGGTGTTTAAGTTGTTGATAC 58.981 37.037 0.00 0.00 0.00 2.24
151 155 7.958053 TTTTCCTTCTCTTTACGGTTTAGAG 57.042 36.000 11.04 11.04 37.37 2.43
187 191 4.864704 TGGAAACAAAGTAGAATTGGGC 57.135 40.909 0.00 0.00 37.44 5.36
190 194 4.379499 GGAAACAAAGTAGAATTGGGCGAG 60.379 45.833 0.00 0.00 32.02 5.03
206 210 0.670546 CGAGAGGATTTGTGGCACGT 60.671 55.000 13.77 1.00 0.00 4.49
209 213 1.066143 AGAGGATTTGTGGCACGTAGG 60.066 52.381 13.77 0.00 0.00 3.18
244 248 1.379044 CCCTCGCCCATGCTCTTTT 60.379 57.895 0.00 0.00 34.43 2.27
292 299 9.672086 TCATATCGTTTCAACCAAAAGTTTAAG 57.328 29.630 0.00 0.00 36.18 1.85
297 304 9.688592 TCGTTTCAACCAAAAGTTTAAGTTAAA 57.311 25.926 3.88 3.88 36.18 1.52
326 333 5.437289 TTTCAGACTTATGTTGCTTGTGG 57.563 39.130 0.00 0.00 0.00 4.17
433 440 8.760103 AGTTTCGGAACTAGATCTTAGAAAAC 57.240 34.615 7.51 3.95 44.13 2.43
434 441 8.365647 AGTTTCGGAACTAGATCTTAGAAAACA 58.634 33.333 7.51 0.00 44.13 2.83
438 445 9.186837 TCGGAACTAGATCTTAGAAAACATACT 57.813 33.333 0.00 0.00 0.00 2.12
448 455 9.838339 ATCTTAGAAAACATACTCGGAATCAAT 57.162 29.630 0.00 0.00 0.00 2.57
454 461 6.668541 AACATACTCGGAATCAATGACTTG 57.331 37.500 0.00 0.00 0.00 3.16
462 469 3.209410 GAATCAATGACTTGGCGGATCT 58.791 45.455 0.00 0.00 32.95 2.75
463 470 4.380531 GAATCAATGACTTGGCGGATCTA 58.619 43.478 0.00 0.00 32.95 1.98
467 474 3.742433 ATGACTTGGCGGATCTAGAAG 57.258 47.619 0.00 0.00 0.00 2.85
473 480 2.042464 TGGCGGATCTAGAAGCAATCT 58.958 47.619 16.49 0.00 42.48 2.40
556 563 7.169591 TCCGGTAGAATTTGGTTAGATTTGAA 58.830 34.615 0.00 0.00 0.00 2.69
561 568 9.841880 GTAGAATTTGGTTAGATTTGAAACCTC 57.158 33.333 5.88 0.00 44.55 3.85
565 572 4.918588 TGGTTAGATTTGAAACCTCTCCC 58.081 43.478 5.88 0.00 44.55 4.30
574 581 4.034285 TGAAACCTCTCCCCTTTCATTC 57.966 45.455 0.00 0.00 30.66 2.67
575 582 3.657727 TGAAACCTCTCCCCTTTCATTCT 59.342 43.478 0.00 0.00 30.66 2.40
577 584 4.308526 AACCTCTCCCCTTTCATTCTTC 57.691 45.455 0.00 0.00 0.00 2.87
580 595 5.039645 ACCTCTCCCCTTTCATTCTTCATA 58.960 41.667 0.00 0.00 0.00 2.15
757 799 3.408851 GCGTTTGGTCGGTCGGTC 61.409 66.667 0.00 0.00 0.00 4.79
758 800 3.101428 CGTTTGGTCGGTCGGTCG 61.101 66.667 0.00 0.00 0.00 4.79
761 803 3.211564 TTTGGTCGGTCGGTCGGTC 62.212 63.158 0.00 0.00 0.00 4.79
762 804 4.953010 TGGTCGGTCGGTCGGTCA 62.953 66.667 0.00 0.00 0.00 4.02
763 805 3.673484 GGTCGGTCGGTCGGTCAA 61.673 66.667 0.00 0.00 0.00 3.18
764 806 2.570181 GTCGGTCGGTCGGTCAAT 59.430 61.111 0.00 0.00 0.00 2.57
766 808 0.668401 GTCGGTCGGTCGGTCAATTT 60.668 55.000 0.00 0.00 0.00 1.82
767 809 0.668096 TCGGTCGGTCGGTCAATTTG 60.668 55.000 0.00 0.00 0.00 2.32
768 810 0.947180 CGGTCGGTCGGTCAATTTGT 60.947 55.000 0.00 0.00 0.00 2.83
769 811 1.669502 CGGTCGGTCGGTCAATTTGTA 60.670 52.381 0.00 0.00 0.00 2.41
854 896 0.753867 TTCCCTTATATGCGCGTCCA 59.246 50.000 4.79 0.00 0.00 4.02
883 926 0.817229 TTGTGCAGGTCATGACGCAA 60.817 50.000 24.22 15.47 35.87 4.85
899 942 1.364721 GCAACGCCCAAACAAAACTT 58.635 45.000 0.00 0.00 0.00 2.66
932 975 2.721468 GCGCGTACGAGATCGACC 60.721 66.667 23.53 0.00 43.93 4.79
941 984 1.212616 CGAGATCGACCAAATCCAGC 58.787 55.000 0.00 0.00 43.02 4.85
942 985 1.587547 GAGATCGACCAAATCCAGCC 58.412 55.000 0.00 0.00 0.00 4.85
951 994 0.609957 CAAATCCAGCCTGCCTGTCA 60.610 55.000 0.00 0.00 40.06 3.58
1059 1108 2.266055 GAGGAACCAGAGCCCGTG 59.734 66.667 0.00 0.00 0.00 4.94
1283 1347 1.003355 ACATGCAAGACCTCGTGGG 60.003 57.895 8.63 2.00 41.89 4.61
1343 1407 3.766691 GCTCGGCGACTACCCCAA 61.767 66.667 4.99 0.00 0.00 4.12
1359 1423 4.658786 AACTCCTCCAGGGCCGGT 62.659 66.667 1.90 0.00 35.41 5.28
1409 1479 4.303282 GACAACTTCTTGGAGAGACAGAC 58.697 47.826 0.00 0.00 33.02 3.51
1413 1483 0.404426 TCTTGGAGAGACAGACCGGA 59.596 55.000 9.46 0.00 0.00 5.14
1428 1498 0.108138 CCGGAACCTTCGAGAGCATT 60.108 55.000 0.00 0.00 0.00 3.56
1551 1621 3.125573 TCTCCGGCGAGACAGACG 61.126 66.667 9.30 0.00 40.34 4.18
1566 1636 0.033601 AGACGCAGACCATCCTCTCT 60.034 55.000 0.00 0.00 0.00 3.10
2001 2074 1.376466 GCCCAAGTTCTGCCAGAGA 59.624 57.895 0.00 0.00 0.00 3.10
2085 2158 2.432628 CTGGCCGACAACGAGGTC 60.433 66.667 0.00 0.00 42.66 3.85
2125 2198 3.338250 GCATGGACACCCTCCCCA 61.338 66.667 0.00 0.00 38.49 4.96
2130 2203 1.207488 TGGACACCCTCCCCATCTTG 61.207 60.000 0.00 0.00 38.49 3.02
2186 2259 3.188100 CGCGACGTGCATGACCAT 61.188 61.111 14.17 0.00 46.97 3.55
2263 2336 4.500265 GCAAGGGCAAGGAGAACA 57.500 55.556 0.00 0.00 40.72 3.18
2654 2727 3.628032 TGCAGGTATTACTCTCAGTCTCG 59.372 47.826 0.00 0.00 0.00 4.04
2659 2732 5.129815 AGGTATTACTCTCAGTCTCGTCTCT 59.870 44.000 0.00 0.00 0.00 3.10
2672 2745 8.399425 TCAGTCTCGTCTCTATTGATTCTTTAC 58.601 37.037 0.00 0.00 0.00 2.01
2674 2747 7.066043 AGTCTCGTCTCTATTGATTCTTTACGT 59.934 37.037 0.00 0.00 0.00 3.57
2680 2753 9.141400 GTCTCTATTGATTCTTTACGTTCTGTT 57.859 33.333 0.00 0.00 0.00 3.16
2755 2828 8.336801 AGAGCCAAGTAAAACACTTAATTAGG 57.663 34.615 0.00 0.00 46.04 2.69
2758 2838 7.039993 AGCCAAGTAAAACACTTAATTAGGTGG 60.040 37.037 25.98 12.18 46.04 4.61
2769 2849 6.016777 CACTTAATTAGGTGGATTCATCAGGC 60.017 42.308 17.62 0.00 30.56 4.85
2770 2850 4.524802 AATTAGGTGGATTCATCAGGCA 57.475 40.909 0.00 0.00 0.00 4.75
2772 2852 2.905415 AGGTGGATTCATCAGGCAAA 57.095 45.000 0.00 0.00 0.00 3.68
2865 2952 6.673154 AAGTACTTTACCGTGCATATTTCC 57.327 37.500 1.12 0.00 0.00 3.13
2941 3035 7.961351 TCAAACCTCAAAATGATTTGGTACAT 58.039 30.769 0.00 0.00 44.88 2.29
2961 3055 1.383456 TTGGTTTGCTGCGCTCTTGT 61.383 50.000 9.73 0.00 0.00 3.16
2974 3068 1.689959 CTCTTGTGCGGCAATGTTTC 58.310 50.000 3.23 0.00 36.36 2.78
2978 3072 1.028130 TGTGCGGCAATGTTTCTTGA 58.972 45.000 3.23 0.00 0.00 3.02
2995 3089 7.173218 TGTTTCTTGACATGTTAAGGACATCTC 59.827 37.037 25.16 12.27 45.88 2.75
2997 3091 4.123497 TGACATGTTAAGGACATCTCCG 57.877 45.455 0.00 0.00 45.88 4.63
3019 3113 0.958876 GACGACCCGCAAATTCCCTT 60.959 55.000 0.00 0.00 0.00 3.95
3077 3196 2.580276 GGCCATCGAACCGTACCA 59.420 61.111 0.00 0.00 0.00 3.25
3096 3215 5.033589 ACCAGCATCCATTTGAAAACAAA 57.966 34.783 0.00 0.00 0.00 2.83
3222 3350 6.533819 TCCGTTCAATTGTGTGTTAGTAAG 57.466 37.500 5.13 0.00 0.00 2.34
3258 3386 2.093869 TCACTAATACACACCTTCCGCC 60.094 50.000 0.00 0.00 0.00 6.13
3269 3397 0.537371 CCTTCCGCCAAACACCTTCT 60.537 55.000 0.00 0.00 0.00 2.85
3275 3403 1.268539 CGCCAAACACCTTCTGTTCAC 60.269 52.381 0.00 0.00 42.70 3.18
3289 3417 0.238289 GTTCACATGCACACCTTCCG 59.762 55.000 0.00 0.00 0.00 4.30
3291 3419 3.049674 ACATGCACACCTTCCGCG 61.050 61.111 0.00 0.00 0.00 6.46
3304 3432 2.629051 CTTCCGCGAAAATACCTTCCT 58.371 47.619 8.23 0.00 0.00 3.36
3312 3440 5.286082 CGCGAAAATACCTTCCTTTCAATTG 59.714 40.000 0.00 0.00 0.00 2.32
3399 3607 2.560981 CACCTTCCGCCAAATTACCTTT 59.439 45.455 0.00 0.00 0.00 3.11
3417 3625 9.877178 ATTACCTTTTGTTCAATTGTGTGTTAA 57.123 25.926 5.13 0.00 0.00 2.01
3468 3676 0.040425 CCTTTCGCCAAACACCTTCG 60.040 55.000 0.00 0.00 0.00 3.79
3475 3683 1.675552 CCAAACACCTTCGGTTCACT 58.324 50.000 0.00 0.00 31.02 3.41
3480 3688 1.238439 CACCTTCGGTTCACTTGCAT 58.762 50.000 0.00 0.00 31.02 3.96
3486 3694 2.695359 TCGGTTCACTTGCATACCTTC 58.305 47.619 0.00 0.00 0.00 3.46
3487 3695 1.737793 CGGTTCACTTGCATACCTTCC 59.262 52.381 0.00 0.00 0.00 3.46
3494 3702 1.543802 CTTGCATACCTTCCGCCAAAA 59.456 47.619 0.00 0.00 0.00 2.44
3498 3706 2.029380 GCATACCTTCCGCCAAAAACTT 60.029 45.455 0.00 0.00 0.00 2.66
3499 3707 3.574614 CATACCTTCCGCCAAAAACTTG 58.425 45.455 0.00 0.00 0.00 3.16
3579 3873 0.247460 CTGGATGGAGAGCGAACACA 59.753 55.000 0.00 0.00 0.00 3.72
3598 3892 1.068434 CATGGTGGCTTTTGGTTCGTT 59.932 47.619 0.00 0.00 0.00 3.85
3599 3893 0.457851 TGGTGGCTTTTGGTTCGTTG 59.542 50.000 0.00 0.00 0.00 4.10
3600 3894 0.741915 GGTGGCTTTTGGTTCGTTGA 59.258 50.000 0.00 0.00 0.00 3.18
3601 3895 1.339929 GGTGGCTTTTGGTTCGTTGAT 59.660 47.619 0.00 0.00 0.00 2.57
3605 3899 2.223947 GGCTTTTGGTTCGTTGATTGGT 60.224 45.455 0.00 0.00 0.00 3.67
3607 3901 4.500035 GGCTTTTGGTTCGTTGATTGGTTA 60.500 41.667 0.00 0.00 0.00 2.85
3608 3902 4.443063 GCTTTTGGTTCGTTGATTGGTTAC 59.557 41.667 0.00 0.00 0.00 2.50
3609 3903 5.578005 TTTTGGTTCGTTGATTGGTTACA 57.422 34.783 0.00 0.00 0.00 2.41
3610 3904 5.578005 TTTGGTTCGTTGATTGGTTACAA 57.422 34.783 0.00 0.00 41.59 2.41
3611 3905 4.822036 TGGTTCGTTGATTGGTTACAAG 57.178 40.909 0.00 0.00 40.49 3.16
3612 3906 4.200874 TGGTTCGTTGATTGGTTACAAGT 58.799 39.130 0.00 0.00 40.49 3.16
3613 3907 4.641094 TGGTTCGTTGATTGGTTACAAGTT 59.359 37.500 0.00 0.00 40.49 2.66
3614 3908 4.973663 GGTTCGTTGATTGGTTACAAGTTG 59.026 41.667 0.00 0.00 40.49 3.16
3615 3909 5.220892 GGTTCGTTGATTGGTTACAAGTTGA 60.221 40.000 10.54 0.00 40.49 3.18
3616 3910 6.435428 GTTCGTTGATTGGTTACAAGTTGAT 58.565 36.000 10.54 0.00 40.49 2.57
3617 3911 6.627395 TCGTTGATTGGTTACAAGTTGATT 57.373 33.333 10.54 0.00 40.49 2.57
3618 3912 6.434596 TCGTTGATTGGTTACAAGTTGATTG 58.565 36.000 10.54 0.00 45.01 2.67
3631 3925 3.665745 GTTGATTGTGGCCAACTTGAT 57.334 42.857 7.24 0.00 39.47 2.57
3633 3927 3.663995 TGATTGTGGCCAACTTGATTG 57.336 42.857 7.24 0.00 38.12 2.67
3682 4216 0.318360 GGTTACAAGTTGCAACCGGC 60.318 55.000 25.62 10.20 34.43 6.13
3729 4263 1.337167 TGAGACAACCTGCAGTGATCG 60.337 52.381 13.81 0.00 0.00 3.69
3781 4319 8.011673 CACAAAGCTCATGATACATATAAACGG 58.988 37.037 0.00 0.00 0.00 4.44
3867 4412 3.369147 GCTGCACGCATTATATAGAGGTG 59.631 47.826 0.00 0.00 38.92 4.00
3909 4475 4.180817 CCGTTTGCTGATGTGTGTATCTA 58.819 43.478 0.00 0.00 0.00 1.98
3942 4508 2.096496 GCACATACATCACACTGCCTTC 59.904 50.000 0.00 0.00 0.00 3.46
4001 4661 1.155424 TTTCGAACGCCACACTGACC 61.155 55.000 0.00 0.00 0.00 4.02
4002 4662 2.023414 TTCGAACGCCACACTGACCT 62.023 55.000 0.00 0.00 0.00 3.85
4008 4669 0.171455 CGCCACACTGACCTACTCTC 59.829 60.000 0.00 0.00 0.00 3.20
4168 4829 2.124983 CCCACCACATCGAGCTGG 60.125 66.667 9.18 9.18 0.00 4.85
4238 4902 3.195002 CGCCGTCGCCATGAACAT 61.195 61.111 0.00 0.00 0.00 2.71
4389 5059 6.039382 ACTTCTTTTACTAGTTGGCTTGGTTG 59.961 38.462 0.00 0.00 0.00 3.77
4419 5089 2.439701 CTCTGCATGCACAGGGGG 60.440 66.667 18.46 6.11 38.26 5.40
4420 5090 2.934932 TCTGCATGCACAGGGGGA 60.935 61.111 18.46 8.77 38.26 4.81
4437 5107 1.374631 GACTGAGCGGTGACATGCA 60.375 57.895 0.00 0.00 0.00 3.96
4450 5120 1.138036 CATGCATGGCCGAGTGTTG 59.862 57.895 19.40 0.00 0.00 3.33
4457 5127 0.948623 TGGCCGAGTGTTGTTCATCG 60.949 55.000 0.00 0.00 35.02 3.84
4472 5145 4.233789 GTTCATCGCTCTGGTAGATGATC 58.766 47.826 7.99 4.57 46.65 2.92
4498 5171 0.536460 TCTGTTTCCTTCCCGGTTGC 60.536 55.000 0.00 0.00 0.00 4.17
4508 5181 1.029408 TCCCGGTTGCGATTTGATGG 61.029 55.000 0.00 0.00 0.00 3.51
4568 5241 7.374272 AGAATATCGGACTTCAGTATCACATG 58.626 38.462 0.00 0.00 0.00 3.21
4625 5303 8.414778 CCTTCCGTTCTACTAAAGTGATCTAAT 58.585 37.037 0.00 0.00 0.00 1.73
4669 5382 7.832503 AAAAGTCAAACTTCATGAACTTTGG 57.167 32.000 26.62 13.65 37.47 3.28
4780 5516 6.020281 CACACTAGATTATGAAACGCAGAGAC 60.020 42.308 0.00 0.00 0.00 3.36
4800 5543 6.595716 AGAGACTATTAAACAGGTGCATGTTC 59.404 38.462 6.17 0.00 42.49 3.18
4981 5809 5.480772 ACTCCCTCCGTTCCATATTATAGTG 59.519 44.000 0.00 0.00 0.00 2.74
4982 5810 5.399991 TCCCTCCGTTCCATATTATAGTGT 58.600 41.667 0.00 0.00 0.00 3.55
5126 5968 7.807433 CCATTCTGTCGATGTAAATGTTTTTCA 59.193 33.333 0.00 0.00 0.00 2.69
5127 5969 8.629986 CATTCTGTCGATGTAAATGTTTTTCAC 58.370 33.333 0.00 0.00 0.00 3.18
5129 5971 6.261158 TCTGTCGATGTAAATGTTTTTCACCA 59.739 34.615 0.00 0.00 0.00 4.17
5130 5972 6.976088 TGTCGATGTAAATGTTTTTCACCAT 58.024 32.000 0.00 0.00 0.00 3.55
5133 5975 9.061610 GTCGATGTAAATGTTTTTCACCATAAG 57.938 33.333 0.00 0.00 0.00 1.73
5145 5987 7.226523 GTTTTTCACCATAAGCTTGGTCAAAAT 59.773 33.333 17.00 0.00 45.35 1.82
5180 6022 8.477419 TTGACTTTTCAAAACATCTAATCCCT 57.523 30.769 0.00 0.00 38.87 4.20
5181 6023 8.110860 TGACTTTTCAAAACATCTAATCCCTC 57.889 34.615 0.00 0.00 0.00 4.30
5182 6024 7.176690 TGACTTTTCAAAACATCTAATCCCTCC 59.823 37.037 0.00 0.00 0.00 4.30
5183 6025 6.151144 ACTTTTCAAAACATCTAATCCCTCCG 59.849 38.462 0.00 0.00 0.00 4.63
5184 6026 4.837093 TCAAAACATCTAATCCCTCCGT 57.163 40.909 0.00 0.00 0.00 4.69
5185 6027 5.174037 TCAAAACATCTAATCCCTCCGTT 57.826 39.130 0.00 0.00 0.00 4.44
5186 6028 5.566469 TCAAAACATCTAATCCCTCCGTTT 58.434 37.500 0.00 0.00 0.00 3.60
5187 6029 5.646360 TCAAAACATCTAATCCCTCCGTTTC 59.354 40.000 0.00 0.00 0.00 2.78
5188 6030 5.437191 AAACATCTAATCCCTCCGTTTCT 57.563 39.130 0.00 0.00 0.00 2.52
5189 6031 6.555463 AAACATCTAATCCCTCCGTTTCTA 57.445 37.500 0.00 0.00 0.00 2.10
5190 6032 6.555463 AACATCTAATCCCTCCGTTTCTAA 57.445 37.500 0.00 0.00 0.00 2.10
5191 6033 6.555463 ACATCTAATCCCTCCGTTTCTAAA 57.445 37.500 0.00 0.00 0.00 1.85
5192 6034 7.138054 ACATCTAATCCCTCCGTTTCTAAAT 57.862 36.000 0.00 0.00 0.00 1.40
5193 6035 8.258850 ACATCTAATCCCTCCGTTTCTAAATA 57.741 34.615 0.00 0.00 0.00 1.40
5194 6036 8.881262 ACATCTAATCCCTCCGTTTCTAAATAT 58.119 33.333 0.00 0.00 0.00 1.28
5197 6039 9.370930 TCTAATCCCTCCGTTTCTAAATATACA 57.629 33.333 0.00 0.00 0.00 2.29
5198 6040 9.991906 CTAATCCCTCCGTTTCTAAATATACAA 57.008 33.333 0.00 0.00 0.00 2.41
5199 6041 8.904099 AATCCCTCCGTTTCTAAATATACAAG 57.096 34.615 0.00 0.00 0.00 3.16
5200 6042 7.427989 TCCCTCCGTTTCTAAATATACAAGT 57.572 36.000 0.00 0.00 0.00 3.16
5201 6043 7.495055 TCCCTCCGTTTCTAAATATACAAGTC 58.505 38.462 0.00 0.00 0.00 3.01
5202 6044 7.343833 TCCCTCCGTTTCTAAATATACAAGTCT 59.656 37.037 0.00 0.00 0.00 3.24
5203 6045 7.985752 CCCTCCGTTTCTAAATATACAAGTCTT 59.014 37.037 0.00 0.00 0.00 3.01
5204 6046 9.379791 CCTCCGTTTCTAAATATACAAGTCTTT 57.620 33.333 0.00 0.00 0.00 2.52
5237 6079 9.751542 AGATTCCACTATAAAGACTACATTTCG 57.248 33.333 0.00 0.00 0.00 3.46
5238 6080 9.745880 GATTCCACTATAAAGACTACATTTCGA 57.254 33.333 0.00 0.00 0.00 3.71
5240 6082 9.529325 TTCCACTATAAAGACTACATTTCGATG 57.471 33.333 0.00 0.00 0.00 3.84
5241 6083 8.909923 TCCACTATAAAGACTACATTTCGATGA 58.090 33.333 0.00 0.00 0.00 2.92
5242 6084 9.698309 CCACTATAAAGACTACATTTCGATGAT 57.302 33.333 0.00 0.00 0.00 2.45
5291 6133 8.732746 ATATAAGTTCACTTATTTTGCTCCGT 57.267 30.769 15.71 0.00 44.33 4.69
5292 6134 9.826574 ATATAAGTTCACTTATTTTGCTCCGTA 57.173 29.630 15.71 0.00 44.33 4.02
5293 6135 8.732746 ATAAGTTCACTTATTTTGCTCCGTAT 57.267 30.769 6.41 0.00 44.33 3.06
5294 6136 6.422776 AGTTCACTTATTTTGCTCCGTATG 57.577 37.500 0.00 0.00 0.00 2.39
5295 6137 5.938125 AGTTCACTTATTTTGCTCCGTATGT 59.062 36.000 0.00 0.00 0.00 2.29
5296 6138 7.101054 AGTTCACTTATTTTGCTCCGTATGTA 58.899 34.615 0.00 0.00 0.00 2.29
5297 6139 7.277981 AGTTCACTTATTTTGCTCCGTATGTAG 59.722 37.037 0.00 0.00 0.00 2.74
5298 6140 6.636705 TCACTTATTTTGCTCCGTATGTAGT 58.363 36.000 0.00 0.00 0.00 2.73
5299 6141 6.755141 TCACTTATTTTGCTCCGTATGTAGTC 59.245 38.462 0.00 0.00 0.00 2.59
5300 6142 6.757010 CACTTATTTTGCTCCGTATGTAGTCT 59.243 38.462 0.00 0.00 0.00 3.24
5301 6143 7.919091 CACTTATTTTGCTCCGTATGTAGTCTA 59.081 37.037 0.00 0.00 0.00 2.59
5302 6144 8.639761 ACTTATTTTGCTCCGTATGTAGTCTAT 58.360 33.333 0.00 0.00 0.00 1.98
5305 6147 7.578310 TTTTGCTCCGTATGTAGTCTATAGT 57.422 36.000 0.00 0.00 0.00 2.12
5306 6148 6.555812 TTGCTCCGTATGTAGTCTATAGTG 57.444 41.667 0.00 0.00 0.00 2.74
5307 6149 5.001874 TGCTCCGTATGTAGTCTATAGTGG 58.998 45.833 0.00 0.00 0.00 4.00
5308 6150 5.221783 TGCTCCGTATGTAGTCTATAGTGGA 60.222 44.000 0.00 0.00 0.00 4.02
5309 6151 5.704515 GCTCCGTATGTAGTCTATAGTGGAA 59.295 44.000 0.00 0.00 0.00 3.53
5310 6152 6.374894 GCTCCGTATGTAGTCTATAGTGGAAT 59.625 42.308 0.00 0.00 0.00 3.01
5311 6153 7.414319 GCTCCGTATGTAGTCTATAGTGGAATC 60.414 44.444 0.00 0.00 0.00 2.52
5312 6154 7.687388 TCCGTATGTAGTCTATAGTGGAATCT 58.313 38.462 0.00 0.00 0.00 2.40
5313 6155 7.823310 TCCGTATGTAGTCTATAGTGGAATCTC 59.177 40.741 0.00 0.00 0.00 2.75
5314 6156 7.825270 CCGTATGTAGTCTATAGTGGAATCTCT 59.175 40.741 0.00 0.00 0.00 3.10
5315 6157 9.221933 CGTATGTAGTCTATAGTGGAATCTCTT 57.778 37.037 0.00 0.00 0.00 2.85
5345 6187 7.639062 ACATATATTCAGAAATGGAGGGAGT 57.361 36.000 0.00 0.00 0.00 3.85
5353 6195 5.549228 TCAGAAATGGAGGGAGTATATGCAT 59.451 40.000 3.79 3.79 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.694856 GGCCACCCCTTTCCATGTA 59.305 57.895 0.00 0.00 0.00 2.29
1 2 2.445155 GGCCACCCCTTTCCATGT 59.555 61.111 0.00 0.00 0.00 3.21
2 3 2.755469 CGGCCACCCCTTTCCATG 60.755 66.667 2.24 0.00 0.00 3.66
3 4 4.060667 CCGGCCACCCCTTTCCAT 62.061 66.667 2.24 0.00 0.00 3.41
6 7 4.986708 TTGCCGGCCACCCCTTTC 62.987 66.667 26.77 0.00 0.00 2.62
7 8 4.994756 CTTGCCGGCCACCCCTTT 62.995 66.667 26.77 0.00 0.00 3.11
43 44 3.430790 CCCTCTCGCATGACACAATTCTA 60.431 47.826 0.00 0.00 0.00 2.10
44 45 2.625737 CCTCTCGCATGACACAATTCT 58.374 47.619 0.00 0.00 0.00 2.40
45 46 1.667724 CCCTCTCGCATGACACAATTC 59.332 52.381 0.00 0.00 0.00 2.17
46 47 1.278985 TCCCTCTCGCATGACACAATT 59.721 47.619 0.00 0.00 0.00 2.32
47 48 0.904649 TCCCTCTCGCATGACACAAT 59.095 50.000 0.00 0.00 0.00 2.71
48 49 0.247460 CTCCCTCTCGCATGACACAA 59.753 55.000 0.00 0.00 0.00 3.33
49 50 1.607801 CCTCCCTCTCGCATGACACA 61.608 60.000 0.00 0.00 0.00 3.72
50 51 1.142748 CCTCCCTCTCGCATGACAC 59.857 63.158 0.00 0.00 0.00 3.67
51 52 0.904865 AACCTCCCTCTCGCATGACA 60.905 55.000 0.00 0.00 0.00 3.58
52 53 0.460987 CAACCTCCCTCTCGCATGAC 60.461 60.000 0.00 0.00 0.00 3.06
53 54 0.904865 ACAACCTCCCTCTCGCATGA 60.905 55.000 0.00 0.00 0.00 3.07
54 55 0.742281 CACAACCTCCCTCTCGCATG 60.742 60.000 0.00 0.00 0.00 4.06
55 56 1.599047 CACAACCTCCCTCTCGCAT 59.401 57.895 0.00 0.00 0.00 4.73
58 59 2.660064 CCCCACAACCTCCCTCTCG 61.660 68.421 0.00 0.00 0.00 4.04
74 76 0.474184 CACCATACCACCCTCATCCC 59.526 60.000 0.00 0.00 0.00 3.85
86 88 8.780249 ACAGTATCAACAACTTAAACACCATAC 58.220 33.333 0.00 0.00 0.00 2.39
88 90 7.255451 CCACAGTATCAACAACTTAAACACCAT 60.255 37.037 0.00 0.00 0.00 3.55
129 131 5.046807 CCCTCTAAACCGTAAAGAGAAGGAA 60.047 44.000 10.33 0.00 39.29 3.36
135 137 6.278172 ACTAACCCTCTAAACCGTAAAGAG 57.722 41.667 3.93 3.93 37.17 2.85
142 145 7.012044 CCAATTATGAACTAACCCTCTAAACCG 59.988 40.741 0.00 0.00 0.00 4.44
147 150 8.607713 TGTTTCCAATTATGAACTAACCCTCTA 58.392 33.333 0.00 0.00 0.00 2.43
149 153 7.696992 TGTTTCCAATTATGAACTAACCCTC 57.303 36.000 0.00 0.00 0.00 4.30
151 155 8.364894 ACTTTGTTTCCAATTATGAACTAACCC 58.635 33.333 0.00 0.00 0.00 4.11
187 191 0.670546 ACGTGCCACAAATCCTCTCG 60.671 55.000 0.00 0.00 0.00 4.04
190 194 1.338769 ACCTACGTGCCACAAATCCTC 60.339 52.381 0.00 0.00 0.00 3.71
297 304 9.199982 CAAGCAACATAAGTCTGAAAATGAAAT 57.800 29.630 0.00 0.00 0.00 2.17
301 308 6.364165 CCACAAGCAACATAAGTCTGAAAATG 59.636 38.462 0.00 0.00 0.00 2.32
302 309 6.265196 TCCACAAGCAACATAAGTCTGAAAAT 59.735 34.615 0.00 0.00 0.00 1.82
311 318 6.753279 CCAAACATATCCACAAGCAACATAAG 59.247 38.462 0.00 0.00 0.00 1.73
313 320 5.714333 ACCAAACATATCCACAAGCAACATA 59.286 36.000 0.00 0.00 0.00 2.29
433 440 4.024556 GCCAAGTCATTGATTCCGAGTATG 60.025 45.833 0.00 0.00 38.83 2.39
434 441 4.130118 GCCAAGTCATTGATTCCGAGTAT 58.870 43.478 0.00 0.00 38.83 2.12
438 445 1.368641 CGCCAAGTCATTGATTCCGA 58.631 50.000 0.00 0.00 38.83 4.55
448 455 1.137086 GCTTCTAGATCCGCCAAGTCA 59.863 52.381 0.00 0.00 0.00 3.41
454 461 2.805099 CAAGATTGCTTCTAGATCCGCC 59.195 50.000 0.00 0.00 33.05 6.13
510 517 1.079819 CTCTCGACGGCACAATGGT 60.080 57.895 0.00 0.00 0.00 3.55
511 518 0.670546 AACTCTCGACGGCACAATGG 60.671 55.000 0.00 0.00 0.00 3.16
512 519 1.126846 GAAACTCTCGACGGCACAATG 59.873 52.381 0.00 0.00 0.00 2.82
513 520 1.429463 GAAACTCTCGACGGCACAAT 58.571 50.000 0.00 0.00 0.00 2.71
514 521 0.599204 GGAAACTCTCGACGGCACAA 60.599 55.000 0.00 0.00 0.00 3.33
515 522 1.006571 GGAAACTCTCGACGGCACA 60.007 57.895 0.00 0.00 0.00 4.57
521 528 3.779271 ATTCTACCGGAAACTCTCGAC 57.221 47.619 9.46 0.00 37.49 4.20
522 529 4.491676 CAAATTCTACCGGAAACTCTCGA 58.508 43.478 9.46 0.00 37.49 4.04
556 563 3.657727 TGAAGAATGAAAGGGGAGAGGTT 59.342 43.478 0.00 0.00 0.00 3.50
561 568 7.285566 TGAAGATATGAAGAATGAAAGGGGAG 58.714 38.462 0.00 0.00 0.00 4.30
649 691 4.578105 TCCCAAAAACAAATGCAAATGGAC 59.422 37.500 6.99 0.00 0.00 4.02
732 774 1.489824 CGACCAAACGCGGTGTAAG 59.510 57.895 12.47 0.00 40.22 2.34
745 787 4.953010 TGACCGACCGACCGACCA 62.953 66.667 0.00 0.00 0.00 4.02
753 795 1.591158 CGGATACAAATTGACCGACCG 59.409 52.381 18.97 13.07 45.31 4.79
754 796 2.624636 ACGGATACAAATTGACCGACC 58.375 47.619 25.68 11.31 45.31 4.79
755 797 4.673534 AAACGGATACAAATTGACCGAC 57.326 40.909 25.68 4.49 45.31 4.79
758 800 5.783100 TCGTAAACGGATACAAATTGACC 57.217 39.130 0.00 0.00 40.29 4.02
761 803 5.016985 CGGTTCGTAAACGGATACAAATTG 58.983 41.667 2.24 0.00 37.79 2.32
762 804 4.928615 TCGGTTCGTAAACGGATACAAATT 59.071 37.500 2.24 0.00 39.12 1.82
763 805 4.493547 TCGGTTCGTAAACGGATACAAAT 58.506 39.130 2.24 0.00 39.12 2.32
764 806 3.906998 TCGGTTCGTAAACGGATACAAA 58.093 40.909 2.24 0.00 39.12 2.83
766 808 3.057596 AGTTCGGTTCGTAAACGGATACA 60.058 43.478 2.24 0.00 42.26 2.29
767 809 3.501950 AGTTCGGTTCGTAAACGGATAC 58.498 45.455 2.24 0.00 42.26 2.24
768 810 3.727673 CGAGTTCGGTTCGTAAACGGATA 60.728 47.826 2.24 0.00 42.26 2.59
769 811 2.599659 GAGTTCGGTTCGTAAACGGAT 58.400 47.619 2.24 0.00 42.26 4.18
854 896 1.963515 GACCTGCACAATTGGAAAGGT 59.036 47.619 21.42 21.42 40.69 3.50
883 926 3.194755 AGAGAAAAGTTTTGTTTGGGCGT 59.805 39.130 5.36 0.00 0.00 5.68
899 942 2.261671 GCCGCTCCACGAGAGAAA 59.738 61.111 10.72 0.00 46.50 2.52
923 966 1.139853 AGGCTGGATTTGGTCGATCTC 59.860 52.381 0.00 0.00 0.00 2.75
932 975 0.609957 TGACAGGCAGGCTGGATTTG 60.610 55.000 26.71 2.99 0.00 2.32
941 984 2.357517 GTGACGGTGACAGGCAGG 60.358 66.667 0.00 0.00 0.00 4.85
942 985 2.734723 CGTGACGGTGACAGGCAG 60.735 66.667 0.00 0.00 0.00 4.85
985 1028 0.036732 TCCATTGCACCTGACCTCAC 59.963 55.000 0.00 0.00 0.00 3.51
986 1029 0.325933 CTCCATTGCACCTGACCTCA 59.674 55.000 0.00 0.00 0.00 3.86
987 1030 0.615331 TCTCCATTGCACCTGACCTC 59.385 55.000 0.00 0.00 0.00 3.85
988 1031 1.067295 TTCTCCATTGCACCTGACCT 58.933 50.000 0.00 0.00 0.00 3.85
989 1032 1.815003 CTTTCTCCATTGCACCTGACC 59.185 52.381 0.00 0.00 0.00 4.02
992 1035 3.129988 GGATTCTTTCTCCATTGCACCTG 59.870 47.826 0.00 0.00 32.72 4.00
1041 1087 2.120718 ACGGGCTCTGGTTCCTCT 59.879 61.111 0.00 0.00 0.00 3.69
1342 1406 4.658786 ACCGGCCCTGGAGGAGTT 62.659 66.667 0.00 0.00 38.24 3.01
1377 1441 4.250305 AAGTTGTCCGCGGTGGCT 62.250 61.111 27.15 15.94 37.80 4.75
1409 1479 0.108138 AATGCTCTCGAAGGTTCCGG 60.108 55.000 0.00 0.00 0.00 5.14
1413 1483 3.529533 CTCATGAATGCTCTCGAAGGTT 58.470 45.455 0.00 0.00 0.00 3.50
1428 1498 0.614697 TTCCGCTCTCCACCTCATGA 60.615 55.000 0.00 0.00 0.00 3.07
1548 1618 0.383949 GAGAGAGGATGGTCTGCGTC 59.616 60.000 0.00 0.00 0.00 5.19
1549 1619 0.323816 TGAGAGAGGATGGTCTGCGT 60.324 55.000 0.00 0.00 0.00 5.24
1550 1620 0.820226 TTGAGAGAGGATGGTCTGCG 59.180 55.000 0.00 0.00 0.00 5.18
1551 1621 2.106566 TCTTGAGAGAGGATGGTCTGC 58.893 52.381 0.00 0.00 0.00 4.26
1552 1622 2.098934 CGTCTTGAGAGAGGATGGTCTG 59.901 54.545 0.00 0.00 39.56 3.51
1553 1623 2.374184 CGTCTTGAGAGAGGATGGTCT 58.626 52.381 0.00 0.00 39.56 3.85
1662 1732 3.093278 CCGCATCTTCTTGCCGAC 58.907 61.111 0.00 0.00 39.52 4.79
1666 1736 3.446175 GAGCGCCGCATCTTCTTGC 62.446 63.158 13.36 0.00 39.29 4.01
1836 1906 1.994467 CTTGTCAGCATCGTCGAGC 59.006 57.895 0.00 4.89 0.00 5.03
1956 2026 0.833949 ATCCGCCCTCTTCTTCTTCC 59.166 55.000 0.00 0.00 0.00 3.46
2186 2259 0.755698 GATCCTGCCCTCCACGTAGA 60.756 60.000 0.00 0.00 0.00 2.59
2562 2635 2.590575 CACTGTTTCCACCGGCGT 60.591 61.111 6.01 0.00 0.00 5.68
2567 2640 1.966451 CTCGGGCACTGTTTCCACC 60.966 63.158 0.00 0.00 35.30 4.61
2654 2727 8.690680 ACAGAACGTAAAGAATCAATAGAGAC 57.309 34.615 0.00 0.00 0.00 3.36
2754 2827 3.259123 AGTTTTTGCCTGATGAATCCACC 59.741 43.478 0.00 0.00 0.00 4.61
2755 2828 4.525912 AGTTTTTGCCTGATGAATCCAC 57.474 40.909 0.00 0.00 0.00 4.02
2758 2838 7.977853 ACAATGATAGTTTTTGCCTGATGAATC 59.022 33.333 0.00 0.00 0.00 2.52
2828 2913 9.248291 CGGTAAAGTACTTTGAACTAAGTGTAA 57.752 33.333 27.40 3.11 38.72 2.41
2829 2914 8.413229 ACGGTAAAGTACTTTGAACTAAGTGTA 58.587 33.333 27.40 3.30 38.72 2.90
2961 3055 1.028130 TGTCAAGAAACATTGCCGCA 58.972 45.000 0.00 0.00 0.00 5.69
2997 3091 1.418755 GAATTTGCGGGTCGTCGTC 59.581 57.895 0.00 0.00 0.00 4.20
3037 3131 5.048013 CCGGCTTCTGTGTATCACTATATCA 60.048 44.000 0.00 0.00 35.11 2.15
3039 3133 4.322049 GCCGGCTTCTGTGTATCACTATAT 60.322 45.833 22.15 0.00 35.11 0.86
3045 3139 1.220749 GGCCGGCTTCTGTGTATCA 59.779 57.895 28.56 0.00 0.00 2.15
3046 3140 0.179045 ATGGCCGGCTTCTGTGTATC 60.179 55.000 28.56 5.64 0.00 2.24
3048 3142 1.220749 GATGGCCGGCTTCTGTGTA 59.779 57.895 28.56 3.08 0.00 2.90
3050 3144 3.197790 CGATGGCCGGCTTCTGTG 61.198 66.667 28.56 7.99 33.91 3.66
3133 3261 1.748493 ACCAACACAAGCAACACGAAT 59.252 42.857 0.00 0.00 0.00 3.34
3245 3373 1.077357 TGTTTGGCGGAAGGTGTGT 60.077 52.632 0.00 0.00 0.00 3.72
3269 3397 1.317613 GGAAGGTGTGCATGTGAACA 58.682 50.000 0.00 0.00 0.00 3.18
3275 3403 1.851021 TTTCGCGGAAGGTGTGCATG 61.851 55.000 6.13 0.00 0.00 4.06
3289 3417 6.089417 CACAATTGAAAGGAAGGTATTTTCGC 59.911 38.462 13.59 0.00 34.40 4.70
3291 3419 7.926018 ACACACAATTGAAAGGAAGGTATTTTC 59.074 33.333 13.59 0.00 0.00 2.29
3357 3560 0.458370 GCATGTGAACGGATTTGGCC 60.458 55.000 0.00 0.00 0.00 5.36
3468 3676 1.737793 CGGAAGGTATGCAAGTGAACC 59.262 52.381 0.00 0.00 0.00 3.62
3475 3683 1.621992 TTTTGGCGGAAGGTATGCAA 58.378 45.000 0.00 0.00 0.00 4.08
3480 3688 2.359531 CACAAGTTTTTGGCGGAAGGTA 59.640 45.455 0.00 0.00 38.66 3.08
3486 3694 3.634568 TCATACACAAGTTTTTGGCGG 57.365 42.857 0.00 0.00 38.66 6.13
3487 3695 7.810766 ATTAATCATACACAAGTTTTTGGCG 57.189 32.000 0.00 0.00 38.66 5.69
3498 3706 7.654520 GGCGGAAACTACTATTAATCATACACA 59.345 37.037 0.00 0.00 0.00 3.72
3499 3707 7.654520 TGGCGGAAACTACTATTAATCATACAC 59.345 37.037 0.00 0.00 0.00 2.90
3537 3831 4.067972 TGGAGGATAGTTGCGGTTAATC 57.932 45.455 0.00 0.00 0.00 1.75
3538 3832 4.348168 AGATGGAGGATAGTTGCGGTTAAT 59.652 41.667 0.00 0.00 0.00 1.40
3542 3836 1.414181 CAGATGGAGGATAGTTGCGGT 59.586 52.381 0.00 0.00 0.00 5.68
3574 3868 1.494960 ACCAAAAGCCACCATGTGTT 58.505 45.000 0.00 0.00 0.00 3.32
3579 3873 1.068434 CAACGAACCAAAAGCCACCAT 59.932 47.619 0.00 0.00 0.00 3.55
3598 3892 5.508825 GCCACAATCAACTTGTAACCAATCA 60.509 40.000 0.00 0.00 46.43 2.57
3599 3893 4.923281 GCCACAATCAACTTGTAACCAATC 59.077 41.667 0.00 0.00 46.43 2.67
3600 3894 4.262420 GGCCACAATCAACTTGTAACCAAT 60.262 41.667 0.00 0.00 46.43 3.16
3601 3895 3.068873 GGCCACAATCAACTTGTAACCAA 59.931 43.478 0.00 0.00 46.43 3.67
3605 3899 4.314740 GTTGGCCACAATCAACTTGTAA 57.685 40.909 3.88 0.00 46.43 2.41
3611 3905 3.665745 ATCAAGTTGGCCACAATCAAC 57.334 42.857 3.88 0.00 42.37 3.18
3612 3906 3.992643 CAATCAAGTTGGCCACAATCAA 58.007 40.909 3.88 0.00 39.13 2.57
3613 3907 3.663995 CAATCAAGTTGGCCACAATCA 57.336 42.857 3.88 0.00 39.13 2.57
3626 3920 6.642131 CCACAATCAACTTGTAACCAATCAAG 59.358 38.462 0.00 0.00 46.43 3.02
3628 3922 5.508825 GCCACAATCAACTTGTAACCAATCA 60.509 40.000 0.00 0.00 46.43 2.57
3629 3923 4.923281 GCCACAATCAACTTGTAACCAATC 59.077 41.667 0.00 0.00 46.43 2.67
3630 3924 4.262420 GGCCACAATCAACTTGTAACCAAT 60.262 41.667 0.00 0.00 46.43 3.16
3631 3925 3.068873 GGCCACAATCAACTTGTAACCAA 59.931 43.478 0.00 0.00 46.43 3.67
3633 3927 2.625790 TGGCCACAATCAACTTGTAACC 59.374 45.455 0.00 0.00 46.43 2.85
3634 3928 4.048504 GTTGGCCACAATCAACTTGTAAC 58.951 43.478 3.88 0.00 46.43 2.50
3641 3935 3.665745 ATCAAGTTGGCCACAATCAAC 57.334 42.857 3.88 0.00 42.37 3.18
3682 4216 2.547299 AAAATGGCATGTGTTGGTGG 57.453 45.000 0.00 0.00 0.00 4.61
3867 4412 2.423538 GGTGCAAACATGGGAGTGATAC 59.576 50.000 0.00 0.00 0.00 2.24
3994 4600 2.560542 AGCACAAGAGAGTAGGTCAGTG 59.439 50.000 0.00 0.00 0.00 3.66
4001 4661 3.583806 CACCTTCAGCACAAGAGAGTAG 58.416 50.000 0.00 0.00 0.00 2.57
4002 4662 2.289072 GCACCTTCAGCACAAGAGAGTA 60.289 50.000 0.00 0.00 0.00 2.59
4008 4669 2.949106 CCGCACCTTCAGCACAAG 59.051 61.111 0.00 0.00 0.00 3.16
4222 4886 2.404789 CATGTTCATGGCGACGGC 59.595 61.111 15.43 15.43 38.90 5.68
4223 4887 2.108514 AGCATGTTCATGGCGACGG 61.109 57.895 13.55 0.00 0.00 4.79
4224 4888 1.061411 CAGCATGTTCATGGCGACG 59.939 57.895 13.55 0.00 0.00 5.12
4225 4889 1.226491 GCAGCATGTTCATGGCGAC 60.226 57.895 13.55 0.00 39.31 5.19
4229 4893 2.048023 ACCGGCAGCATGTTCATGG 61.048 57.895 0.00 0.00 39.31 3.66
4389 5059 0.037326 TGCAGAGACACAACCGATCC 60.037 55.000 0.00 0.00 0.00 3.36
4419 5089 0.742281 ATGCATGTCACCGCTCAGTC 60.742 55.000 0.00 0.00 0.00 3.51
4420 5090 1.022982 CATGCATGTCACCGCTCAGT 61.023 55.000 18.91 0.00 0.00 3.41
4425 5095 4.197498 GGCCATGCATGTCACCGC 62.197 66.667 24.58 19.05 0.00 5.68
4437 5107 1.453155 GATGAACAACACTCGGCCAT 58.547 50.000 2.24 0.00 0.00 4.40
4450 5120 3.717400 TCATCTACCAGAGCGATGAAC 57.283 47.619 0.00 0.00 40.20 3.18
4457 5127 4.701765 ACATTGTGATCATCTACCAGAGC 58.298 43.478 0.00 0.00 0.00 4.09
4472 5145 2.226437 CGGGAAGGAAACAGACATTGTG 59.774 50.000 0.00 0.00 40.74 3.33
4568 5241 6.904498 TGTGGCATGTAATAGTTTAACACAC 58.096 36.000 0.00 0.00 31.08 3.82
4769 5504 5.408604 CACCTGTTTAATAGTCTCTGCGTTT 59.591 40.000 0.00 0.00 0.00 3.60
4774 5510 5.877012 ACATGCACCTGTTTAATAGTCTCTG 59.123 40.000 0.00 0.00 0.00 3.35
4780 5516 6.500684 ACTGAACATGCACCTGTTTAATAG 57.499 37.500 7.11 6.63 39.40 1.73
4800 5543 6.849502 TCTAGTTACGTGATCACCTAAACTG 58.150 40.000 28.30 21.71 31.18 3.16
4927 5680 9.832445 ATGAATATTTAACTCACAACGTATCCT 57.168 29.630 0.00 0.00 0.00 3.24
4956 5784 6.014499 CACTATAATATGGAACGGAGGGAGTT 60.014 42.308 0.00 0.00 34.07 3.01
5100 5942 7.807433 TGAAAAACATTTACATCGACAGAATGG 59.193 33.333 13.67 0.00 43.62 3.16
5107 5949 8.958175 TTATGGTGAAAAACATTTACATCGAC 57.042 30.769 0.00 0.00 0.00 4.20
5109 5951 7.754924 AGCTTATGGTGAAAAACATTTACATCG 59.245 33.333 0.00 0.00 0.00 3.84
5127 5969 7.331687 CCTTACAAATTTTGACCAAGCTTATGG 59.668 37.037 15.81 0.00 46.38 2.74
5129 5971 7.962441 ACCTTACAAATTTTGACCAAGCTTAT 58.038 30.769 15.81 0.00 0.00 1.73
5130 5972 7.354751 ACCTTACAAATTTTGACCAAGCTTA 57.645 32.000 15.81 0.00 0.00 3.09
5133 5975 6.536941 TCAAACCTTACAAATTTTGACCAAGC 59.463 34.615 15.81 0.00 33.96 4.01
5159 6001 6.151144 ACGGAGGGATTAGATGTTTTGAAAAG 59.849 38.462 0.00 0.00 0.00 2.27
5174 6016 8.491958 ACTTGTATATTTAGAAACGGAGGGATT 58.508 33.333 0.00 0.00 0.00 3.01
5175 6017 8.030913 ACTTGTATATTTAGAAACGGAGGGAT 57.969 34.615 0.00 0.00 0.00 3.85
5176 6018 7.343833 AGACTTGTATATTTAGAAACGGAGGGA 59.656 37.037 0.00 0.00 0.00 4.20
5177 6019 7.498443 AGACTTGTATATTTAGAAACGGAGGG 58.502 38.462 0.00 0.00 0.00 4.30
5178 6020 8.943909 AAGACTTGTATATTTAGAAACGGAGG 57.056 34.615 0.00 0.00 0.00 4.30
5211 6053 9.751542 CGAAATGTAGTCTTTATAGTGGAATCT 57.248 33.333 0.00 0.00 0.00 2.40
5212 6054 9.745880 TCGAAATGTAGTCTTTATAGTGGAATC 57.254 33.333 0.00 0.00 0.00 2.52
5214 6056 9.529325 CATCGAAATGTAGTCTTTATAGTGGAA 57.471 33.333 0.00 0.00 0.00 3.53
5215 6057 8.909923 TCATCGAAATGTAGTCTTTATAGTGGA 58.090 33.333 0.00 0.00 34.32 4.02
5216 6058 9.698309 ATCATCGAAATGTAGTCTTTATAGTGG 57.302 33.333 0.00 0.00 34.32 4.00
5265 6107 9.826574 ACGGAGCAAAATAAGTGAACTTATATA 57.173 29.630 14.48 0.00 45.55 0.86
5266 6108 8.732746 ACGGAGCAAAATAAGTGAACTTATAT 57.267 30.769 14.48 6.04 45.55 0.86
5267 6109 9.826574 ATACGGAGCAAAATAAGTGAACTTATA 57.173 29.630 14.48 0.00 45.55 0.98
5269 6111 7.604927 ACATACGGAGCAAAATAAGTGAACTTA 59.395 33.333 5.43 5.43 42.04 2.24
5270 6112 6.430000 ACATACGGAGCAAAATAAGTGAACTT 59.570 34.615 0.71 0.71 39.85 2.66
5271 6113 5.938125 ACATACGGAGCAAAATAAGTGAACT 59.062 36.000 0.00 0.00 0.00 3.01
5272 6114 6.178239 ACATACGGAGCAAAATAAGTGAAC 57.822 37.500 0.00 0.00 0.00 3.18
5273 6115 7.101054 ACTACATACGGAGCAAAATAAGTGAA 58.899 34.615 0.00 0.00 0.00 3.18
5274 6116 6.636705 ACTACATACGGAGCAAAATAAGTGA 58.363 36.000 0.00 0.00 0.00 3.41
5275 6117 6.757010 AGACTACATACGGAGCAAAATAAGTG 59.243 38.462 0.00 0.00 0.00 3.16
5276 6118 6.875076 AGACTACATACGGAGCAAAATAAGT 58.125 36.000 0.00 0.00 0.00 2.24
5279 6121 9.293404 ACTATAGACTACATACGGAGCAAAATA 57.707 33.333 6.78 0.00 0.00 1.40
5280 6122 8.082852 CACTATAGACTACATACGGAGCAAAAT 58.917 37.037 6.78 0.00 0.00 1.82
5281 6123 7.423199 CACTATAGACTACATACGGAGCAAAA 58.577 38.462 6.78 0.00 0.00 2.44
5282 6124 6.016527 CCACTATAGACTACATACGGAGCAAA 60.017 42.308 6.78 0.00 0.00 3.68
5283 6125 5.472478 CCACTATAGACTACATACGGAGCAA 59.528 44.000 6.78 0.00 0.00 3.91
5284 6126 5.001874 CCACTATAGACTACATACGGAGCA 58.998 45.833 6.78 0.00 0.00 4.26
5285 6127 5.243981 TCCACTATAGACTACATACGGAGC 58.756 45.833 6.78 0.00 0.00 4.70
5286 6128 7.825270 AGATTCCACTATAGACTACATACGGAG 59.175 40.741 6.78 0.00 0.00 4.63
5287 6129 7.687388 AGATTCCACTATAGACTACATACGGA 58.313 38.462 6.78 0.00 0.00 4.69
5288 6130 7.825270 AGAGATTCCACTATAGACTACATACGG 59.175 40.741 6.78 0.00 0.00 4.02
5289 6131 8.780846 AGAGATTCCACTATAGACTACATACG 57.219 38.462 6.78 0.00 0.00 3.06
5319 6161 9.343994 ACTCCCTCCATTTCTGAATATATGTAT 57.656 33.333 0.00 0.00 0.00 2.29
5320 6162 8.742125 ACTCCCTCCATTTCTGAATATATGTA 57.258 34.615 0.00 0.00 0.00 2.29
5321 6163 7.639062 ACTCCCTCCATTTCTGAATATATGT 57.361 36.000 0.00 0.00 0.00 2.29
5325 6167 8.270744 GCATATACTCCCTCCATTTCTGAATAT 58.729 37.037 0.00 0.00 0.00 1.28
5326 6168 7.237471 TGCATATACTCCCTCCATTTCTGAATA 59.763 37.037 0.00 0.00 0.00 1.75
5327 6169 6.044754 TGCATATACTCCCTCCATTTCTGAAT 59.955 38.462 0.00 0.00 0.00 2.57
5328 6170 5.369404 TGCATATACTCCCTCCATTTCTGAA 59.631 40.000 0.00 0.00 0.00 3.02
5329 6171 4.907269 TGCATATACTCCCTCCATTTCTGA 59.093 41.667 0.00 0.00 0.00 3.27
5330 6172 5.233083 TGCATATACTCCCTCCATTTCTG 57.767 43.478 0.00 0.00 0.00 3.02
5331 6173 6.460103 AATGCATATACTCCCTCCATTTCT 57.540 37.500 0.00 0.00 0.00 2.52
5332 6174 7.168219 TGTAATGCATATACTCCCTCCATTTC 58.832 38.462 0.00 0.00 0.00 2.17
5333 6175 7.090319 TGTAATGCATATACTCCCTCCATTT 57.910 36.000 0.00 0.00 0.00 2.32
5334 6176 6.702449 TGTAATGCATATACTCCCTCCATT 57.298 37.500 0.00 0.00 0.00 3.16
5335 6177 6.898171 ATGTAATGCATATACTCCCTCCAT 57.102 37.500 0.00 0.00 35.74 3.41
5336 6178 6.702449 AATGTAATGCATATACTCCCTCCA 57.298 37.500 0.00 0.00 36.67 3.86
5337 6179 7.716998 CCATAATGTAATGCATATACTCCCTCC 59.283 40.741 0.00 0.00 36.67 4.30
5338 6180 8.486210 TCCATAATGTAATGCATATACTCCCTC 58.514 37.037 0.00 0.00 36.67 4.30
5339 6181 8.392631 TCCATAATGTAATGCATATACTCCCT 57.607 34.615 0.00 0.00 36.67 4.20
5340 6182 9.632638 ATTCCATAATGTAATGCATATACTCCC 57.367 33.333 0.00 0.00 36.67 4.30


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

AutoCloner maintained by Alex Coulton.