Multiple sequence alignment - TraesCS3A01G179200

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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 TraesCS3A01G179200 chr3A 100.000 6639 0 0 1 6639 206622387 206629025 0.000000e+00 12261.0
1 TraesCS3A01G179200 chr3A 90.566 53 3 2 4738 4788 510299815 510299867 1.190000e-07 69.4
2 TraesCS3A01G179200 chr3D 95.867 6315 189 34 14 6289 164994529 164988248 0.000000e+00 10150.0
3 TraesCS3A01G179200 chr3D 87.625 501 54 3 1329 1829 55719999 55719507 5.770000e-160 575.0
4 TraesCS3A01G179200 chr3D 87.575 499 54 4 1329 1827 603818673 603819163 7.470000e-159 571.0
5 TraesCS3A01G179200 chr3D 89.796 196 13 5 6267 6461 164984736 164984547 1.850000e-60 244.0
6 TraesCS3A01G179200 chr3D 88.525 61 5 2 4738 4796 131489217 131489157 9.230000e-09 73.1
7 TraesCS3A01G179200 chr3D 90.566 53 3 2 4738 4788 389633166 389633218 1.190000e-07 69.4
8 TraesCS3A01G179200 chr3B 95.958 4800 121 34 229 4976 240597933 240593155 0.000000e+00 7721.0
9 TraesCS3A01G179200 chr3B 97.007 1370 30 6 5100 6461 240592343 240590977 0.000000e+00 2292.0
10 TraesCS3A01G179200 chr3B 95.238 126 6 0 4977 5102 240592561 240592436 4.060000e-47 200.0
11 TraesCS3A01G179200 chr1D 94.129 528 28 2 1629 2156 65740992 65741516 0.000000e+00 800.0
12 TraesCS3A01G179200 chr1D 84.483 812 77 12 2812 3599 455097809 455097023 0.000000e+00 756.0
13 TraesCS3A01G179200 chr1D 82.184 696 70 25 2395 3084 422880050 422880697 3.500000e-152 549.0
14 TraesCS3A01G179200 chr1D 91.667 132 8 1 3070 3201 422880711 422880839 5.290000e-41 180.0
15 TraesCS3A01G179200 chr1D 91.489 47 3 1 4741 4786 253525991 253525945 5.560000e-06 63.9
16 TraesCS3A01G179200 chr1D 89.796 49 4 1 4739 4786 372835999 372836047 2.000000e-05 62.1
17 TraesCS3A01G179200 chr1D 100.000 31 0 0 4759 4789 64895567 64895537 2.590000e-04 58.4
18 TraesCS3A01G179200 chr1D 82.353 68 6 6 4757 4823 159982182 159982120 3.000000e-03 54.7
19 TraesCS3A01G179200 chr1D 88.889 45 4 1 4745 4788 257183759 257183715 3.000000e-03 54.7
20 TraesCS3A01G179200 chr1D 86.275 51 5 2 4738 4786 403524326 403524376 3.000000e-03 54.7
21 TraesCS3A01G179200 chr7D 93.939 528 28 3 1629 2156 173527288 173527811 0.000000e+00 795.0
22 TraesCS3A01G179200 chr7D 88.577 499 49 4 1329 1827 578173934 578174424 3.430000e-167 599.0
23 TraesCS3A01G179200 chr7D 89.937 159 16 0 10 168 16419882 16420040 8.730000e-49 206.0
24 TraesCS3A01G179200 chr7D 89.937 159 16 0 10 168 153974131 153973973 8.730000e-49 206.0
25 TraesCS3A01G179200 chr7D 93.478 46 2 1 4741 4785 488790289 488790244 4.300000e-07 67.6
26 TraesCS3A01G179200 chr5D 93.182 528 33 2 1629 2156 221498624 221499148 0.000000e+00 773.0
27 TraesCS3A01G179200 chr5D 93.182 528 31 4 1629 2156 237989 237467 0.000000e+00 771.0
28 TraesCS3A01G179200 chr5D 88.166 169 17 3 6 173 76030741 76030575 1.460000e-46 198.0
29 TraesCS3A01G179200 chr5D 91.489 47 2 2 4742 4786 230024096 230024142 5.560000e-06 63.9
30 TraesCS3A01G179200 chr5D 93.023 43 2 1 4745 4786 177683459 177683501 2.000000e-05 62.1
31 TraesCS3A01G179200 chr5D 89.796 49 4 1 4738 4785 482103310 482103358 2.000000e-05 62.1
32 TraesCS3A01G179200 chrUn 92.979 527 34 2 1629 2155 144595951 144596474 0.000000e+00 765.0
33 TraesCS3A01G179200 chrUn 92.410 527 37 2 1629 2155 146572405 146571882 0.000000e+00 749.0
34 TraesCS3A01G179200 chrUn 87.976 499 52 4 1329 1827 260711791 260711301 3.450000e-162 582.0
35 TraesCS3A01G179200 chrUn 92.500 40 2 1 4756 4794 70193226 70193187 1.000000e-03 56.5
36 TraesCS3A01G179200 chrUn 87.755 49 5 1 4736 4783 308089933 308089981 1.000000e-03 56.5
37 TraesCS3A01G179200 chr5B 92.600 527 36 2 1629 2155 328373 327850 0.000000e+00 754.0
38 TraesCS3A01G179200 chr5B 89.308 159 17 0 10 168 646377737 646377895 4.060000e-47 200.0
39 TraesCS3A01G179200 chr6D 84.496 774 72 11 2850 3599 197299673 197300422 0.000000e+00 721.0
40 TraesCS3A01G179200 chr6D 100.000 34 0 0 4754 4787 383757370 383757337 5.560000e-06 63.9
41 TraesCS3A01G179200 chr6D 96.875 32 1 0 4757 4788 86855224 86855255 3.000000e-03 54.7
42 TraesCS3A01G179200 chr6D 100.000 29 0 0 4757 4785 338806224 338806196 3.000000e-03 54.7
43 TraesCS3A01G179200 chr6D 94.286 35 2 0 4751 4785 383757425 383757459 3.000000e-03 54.7
44 TraesCS3A01G179200 chr6D 90.476 42 3 1 4745 4785 445417004 445417045 3.000000e-03 54.7
45 TraesCS3A01G179200 chr6D 100.000 28 0 0 4757 4784 245267598 245267625 1.200000e-02 52.8
46 TraesCS3A01G179200 chr6D 96.875 32 0 1 4759 4789 413075596 413075627 1.200000e-02 52.8
47 TraesCS3A01G179200 chr2D 87.425 501 55 3 1329 1829 47826519 47826027 2.690000e-158 569.0
48 TraesCS3A01G179200 chr2D 87.226 501 56 3 1329 1829 399961974 399962466 1.250000e-156 564.0
49 TraesCS3A01G179200 chr4A 87.400 500 54 5 1329 1827 598469029 598468538 3.470000e-157 566.0
50 TraesCS3A01G179200 chr7B 88.953 172 18 1 6 176 592548124 592547953 1.880000e-50 211.0
51 TraesCS3A01G179200 chr1B 89.441 161 17 0 7 167 90310092 90310252 3.140000e-48 204.0
52 TraesCS3A01G179200 chr7A 89.308 159 17 0 10 168 437074592 437074434 4.060000e-47 200.0
53 TraesCS3A01G179200 chr7A 95.652 46 1 1 4741 4785 556168503 556168458 9.230000e-09 73.1
54 TraesCS3A01G179200 chr7A 87.719 57 4 3 4738 4792 85209351 85209296 5.560000e-06 63.9
55 TraesCS3A01G179200 chr7A 88.679 53 4 2 4739 4789 200040353 200040301 5.560000e-06 63.9
56 TraesCS3A01G179200 chr6A 86.857 175 23 0 6 180 582438649 582438475 5.250000e-46 196.0
57 TraesCS3A01G179200 chr6A 90.000 50 3 2 4738 4785 604890701 604890750 5.560000e-06 63.9
58 TraesCS3A01G179200 chr4D 95.349 43 1 1 4744 4785 107696566 107696524 4.300000e-07 67.6
59 TraesCS3A01G179200 chr4D 97.059 34 1 0 4756 4789 261053119 261053152 2.590000e-04 58.4
60 TraesCS3A01G179200 chr2B 89.091 55 5 1 4740 4793 358674745 358674799 4.300000e-07 67.6
61 TraesCS3A01G179200 chr2A 89.091 55 5 1 4740 4793 373869005 373868951 4.300000e-07 67.6
62 TraesCS3A01G179200 chr1A 90.000 50 3 2 4738 4785 7183394 7183443 5.560000e-06 63.9
63 TraesCS3A01G179200 chr4B 87.755 49 5 1 4736 4783 20277570 20277522 1.000000e-03 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 TraesCS3A01G179200 chr3A 206622387 206629025 6638 False 12261.000000 12261 100.000000 1 6639 1 chr3A.!!$F1 6638
1 TraesCS3A01G179200 chr3D 164984547 164994529 9982 True 5197.000000 10150 92.831500 14 6461 2 chr3D.!!$R3 6447
2 TraesCS3A01G179200 chr3B 240590977 240597933 6956 True 3404.333333 7721 96.067667 229 6461 3 chr3B.!!$R1 6232
3 TraesCS3A01G179200 chr1D 65740992 65741516 524 False 800.000000 800 94.129000 1629 2156 1 chr1D.!!$F1 527
4 TraesCS3A01G179200 chr1D 455097023 455097809 786 True 756.000000 756 84.483000 2812 3599 1 chr1D.!!$R5 787
5 TraesCS3A01G179200 chr1D 422880050 422880839 789 False 364.500000 549 86.925500 2395 3201 2 chr1D.!!$F4 806
6 TraesCS3A01G179200 chr7D 173527288 173527811 523 False 795.000000 795 93.939000 1629 2156 1 chr7D.!!$F2 527
7 TraesCS3A01G179200 chr5D 221498624 221499148 524 False 773.000000 773 93.182000 1629 2156 1 chr5D.!!$F2 527
8 TraesCS3A01G179200 chr5D 237467 237989 522 True 771.000000 771 93.182000 1629 2156 1 chr5D.!!$R1 527
9 TraesCS3A01G179200 chrUn 144595951 144596474 523 False 765.000000 765 92.979000 1629 2155 1 chrUn.!!$F1 526
10 TraesCS3A01G179200 chrUn 146571882 146572405 523 True 749.000000 749 92.410000 1629 2155 1 chrUn.!!$R2 526
11 TraesCS3A01G179200 chr5B 327850 328373 523 True 754.000000 754 92.600000 1629 2155 1 chr5B.!!$R1 526
12 TraesCS3A01G179200 chr6D 197299673 197300422 749 False 721.000000 721 84.496000 2850 3599 1 chr6D.!!$F2 749

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
70 71 0.181587 TTTTGTCCGGCTCCAGTGAA 59.818 50.0 0.00 0.0 0.00 3.18 F
1168 1190 0.185175 AAGGAGGGGTTTGTGTGTCC 59.815 55.0 0.00 0.0 0.00 4.02 F
1787 1810 0.321564 ACGCTGCCACTTGCTTATGA 60.322 50.0 0.00 0.0 42.00 2.15 F
2607 2678 0.251742 CCAGTTGGCAATTGGGGAGA 60.252 55.0 28.57 0.0 34.85 3.71 F
4152 4286 0.179124 GGTTTCTTTGCACCAACGCA 60.179 50.0 0.00 0.0 41.03 5.24 F
4713 4853 1.099689 GCCACCGCATTAGCCTAAAA 58.900 50.0 0.00 0.0 37.52 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1423 1445 0.684805 ATCGGGAGAAGAGAAGCGGT 60.685 55.000 0.00 0.00 45.37 5.68 R
2607 2678 1.280421 GATCCTGGCAGAACAGAAGGT 59.720 52.381 17.94 0.00 40.97 3.50 R
3624 3757 2.104792 AGCTGCACTACTTTCAAGTCCA 59.895 45.455 1.02 0.00 40.37 4.02 R
4537 4671 0.322546 CCAAGGAAGTACCCACCAGC 60.323 60.000 0.00 0.00 40.05 4.85 R
5362 6198 0.622665 ATGCTGAAGGGCTGTAGCTT 59.377 50.000 3.63 0.00 41.70 3.74 R
6531 10902 0.093026 GATTTCGTCACGGTTGAGCG 59.907 55.000 0.00 0.52 30.10 5.03 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
29 30 2.694109 AGGGCCTTAGTATGACGACTTC 59.306 50.000 0.00 0.00 0.00 3.01
33 34 2.947652 CCTTAGTATGACGACTTCCCGA 59.052 50.000 0.00 0.00 0.00 5.14
34 35 3.243002 CCTTAGTATGACGACTTCCCGAC 60.243 52.174 0.00 0.00 0.00 4.79
47 48 3.505293 ACTTCCCGACTGTCTACTACAAC 59.495 47.826 6.21 0.00 37.74 3.32
70 71 0.181587 TTTTGTCCGGCTCCAGTGAA 59.818 50.000 0.00 0.00 0.00 3.18
79 80 4.975490 TCCAGTGAAGGAGGAGCA 57.025 55.556 0.00 0.00 32.77 4.26
86 87 1.066858 GTGAAGGAGGAGCAATGACGA 60.067 52.381 0.00 0.00 0.00 4.20
87 88 1.833630 TGAAGGAGGAGCAATGACGAT 59.166 47.619 0.00 0.00 0.00 3.73
92 93 2.325857 GAGCAATGACGATGGCGC 59.674 61.111 0.00 0.00 42.48 6.53
93 94 2.436469 AGCAATGACGATGGCGCA 60.436 55.556 10.83 0.00 42.48 6.09
108 109 3.127533 GCACCTGCGGCTCGATTT 61.128 61.111 0.00 0.00 0.00 2.17
114 115 0.807667 CTGCGGCTCGATTTAGTGCT 60.808 55.000 0.00 0.00 0.00 4.40
118 119 2.536365 CGGCTCGATTTAGTGCTTGTA 58.464 47.619 0.00 0.00 0.00 2.41
123 124 4.413087 CTCGATTTAGTGCTTGTAGTCGT 58.587 43.478 0.00 0.00 0.00 4.34
138 139 2.216898 AGTCGTCGCTAGGTGGTATAC 58.783 52.381 0.00 0.00 0.00 1.47
140 141 0.385223 CGTCGCTAGGTGGTATACGC 60.385 60.000 0.00 0.00 0.00 4.42
151 152 3.257375 GGTGGTATACGCATCTGGATGTA 59.743 47.826 11.52 0.00 40.80 2.29
153 154 5.479306 GTGGTATACGCATCTGGATGTAAT 58.521 41.667 11.52 6.21 40.80 1.89
154 155 5.932303 GTGGTATACGCATCTGGATGTAATT 59.068 40.000 11.52 0.00 40.80 1.40
207 208 9.369904 GGGTTATTTCTAACACTATTTGTACGA 57.630 33.333 0.00 0.00 38.09 3.43
317 328 2.218454 CCGGACCACCACCTACCAA 61.218 63.158 0.00 0.00 35.59 3.67
634 646 4.958897 TTGCGTTTCCACCCCCGG 62.959 66.667 0.00 0.00 0.00 5.73
1168 1190 0.185175 AAGGAGGGGTTTGTGTGTCC 59.815 55.000 0.00 0.00 0.00 4.02
1479 1501 1.690893 TGCTCTGCTTCACTTCAGTCT 59.309 47.619 0.00 0.00 0.00 3.24
1482 1504 3.056891 GCTCTGCTTCACTTCAGTCTAGT 60.057 47.826 0.00 0.00 0.00 2.57
1483 1505 4.560513 GCTCTGCTTCACTTCAGTCTAGTT 60.561 45.833 0.00 0.00 0.00 2.24
1596 1618 3.417690 GCCTCTTGCTGTGATTGAATC 57.582 47.619 0.00 0.00 36.87 2.52
1698 1721 5.288472 TGTCGTTGATTATGTGATTGACTCG 59.712 40.000 0.00 0.00 0.00 4.18
1787 1810 0.321564 ACGCTGCCACTTGCTTATGA 60.322 50.000 0.00 0.00 42.00 2.15
1789 1812 2.212652 CGCTGCCACTTGCTTATGATA 58.787 47.619 0.00 0.00 42.00 2.15
1898 1921 5.065988 ACATGTTTCCAGTGAGTTGTTGTAC 59.934 40.000 0.00 0.00 0.00 2.90
2071 2094 6.017192 TGTGAGGTAATGAAACTAGTCCTCT 58.983 40.000 19.65 0.00 40.14 3.69
2100 2123 3.851976 ATAGTCGAAAACTCGCTCACT 57.148 42.857 0.00 0.00 39.55 3.41
2171 2194 5.874810 TGGTACTTGCTATTTCAGTCATCAC 59.125 40.000 0.00 0.00 0.00 3.06
2380 2447 4.289672 TGATCTAGTCTTGGCCCTTCTTTT 59.710 41.667 0.00 0.00 0.00 2.27
2540 2611 4.041567 AGAGACACCAAACATGTATCCACA 59.958 41.667 0.00 0.00 38.75 4.17
2577 2648 3.375699 TGTCTCTTCCCCTCTTCCATAC 58.624 50.000 0.00 0.00 0.00 2.39
2607 2678 0.251742 CCAGTTGGCAATTGGGGAGA 60.252 55.000 28.57 0.00 34.85 3.71
2785 2857 5.527214 TCATCGAGCAAGGGTGTTTTATATG 59.473 40.000 0.00 0.00 0.00 1.78
2910 2982 2.554032 AGCAGGAGCATTGTGTTGTAAC 59.446 45.455 0.00 0.00 45.49 2.50
2920 2992 8.165239 AGCATTGTGTTGTAACAGAAGATTAA 57.835 30.769 12.01 0.00 43.98 1.40
3014 3114 2.107204 ACTGAACTGCCCTGATGACTTT 59.893 45.455 0.00 0.00 0.00 2.66
3368 3497 2.711922 CGGCCGGTGAGTAGCTCTT 61.712 63.158 20.10 0.00 0.00 2.85
3373 3502 2.350580 GCCGGTGAGTAGCTCTTATACG 60.351 54.545 1.90 0.00 0.00 3.06
3374 3503 2.350580 CCGGTGAGTAGCTCTTATACGC 60.351 54.545 0.00 0.00 0.00 4.42
3599 3732 6.876257 AGTAGTGATCATTCAGTTTTCCAGTC 59.124 38.462 0.00 0.00 36.84 3.51
3624 3757 7.554835 TCATTACAGGTTTTGAGTGTTACTGTT 59.445 33.333 0.00 0.00 38.50 3.16
3826 3959 5.316167 TGTAATTGCACCTTCAAGTCTGAT 58.684 37.500 0.00 0.00 0.00 2.90
3881 4014 9.586435 GTGAAGCAAAGCCAACTATATAAAATT 57.414 29.630 0.00 0.00 0.00 1.82
4005 4139 5.295787 GTGTAGGACAGTGTTTTGTGAATCA 59.704 40.000 0.00 0.00 0.00 2.57
4010 4144 6.266103 AGGACAGTGTTTTGTGAATCATCAAT 59.734 34.615 0.00 0.00 37.30 2.57
4017 4151 8.767085 GTGTTTTGTGAATCATCAATCAAATGT 58.233 29.630 0.00 0.00 37.30 2.71
4152 4286 0.179124 GGTTTCTTTGCACCAACGCA 60.179 50.000 0.00 0.00 41.03 5.24
4288 4422 6.206634 CACTCTTCTGGGTTTTTGCATAACTA 59.793 38.462 10.82 2.54 0.00 2.24
4289 4423 6.775629 ACTCTTCTGGGTTTTTGCATAACTAA 59.224 34.615 10.82 1.64 0.00 2.24
4366 4500 6.000891 TCTGCATCTGTGTAAATTTGACAC 57.999 37.500 9.74 9.74 46.07 3.67
4623 4758 5.738370 CAAAACGAAACTACCTCTGACTTG 58.262 41.667 0.00 0.00 0.00 3.16
4713 4853 1.099689 GCCACCGCATTAGCCTAAAA 58.900 50.000 0.00 0.00 37.52 1.52
4721 4861 6.482308 CACCGCATTAGCCTAAAATACTAACT 59.518 38.462 0.00 0.00 37.52 2.24
4747 4887 9.142515 TCGTATAACATCACTCGTAAAATTTGT 57.857 29.630 0.00 0.00 0.00 2.83
4754 4894 9.528018 ACATCACTCGTAAAATTTGTCAAAATT 57.472 25.926 1.31 0.00 45.81 1.82
4796 4936 4.219288 TCGGAGGGAGTAGAAAGTTTGTAC 59.781 45.833 13.61 13.61 0.00 2.90
4855 4997 5.660460 TCAGGAAAACCTTTCTTTTGCTTC 58.340 37.500 0.00 0.00 39.12 3.86
4860 5002 4.391405 AACCTTTCTTTTGCTTCCACTG 57.609 40.909 0.00 0.00 0.00 3.66
4876 5018 6.151817 GCTTCCACTGGAGTTCATAGAAAAAT 59.848 38.462 0.00 0.00 31.21 1.82
5086 5822 5.098211 GGAAAGCACACTTCTCATAAATGC 58.902 41.667 0.00 0.00 34.05 3.56
5170 6001 7.648142 TCTGTTATTGAATTCCTTGTGACAAC 58.352 34.615 2.27 0.00 0.00 3.32
5172 6003 7.950512 TGTTATTGAATTCCTTGTGACAACAT 58.049 30.769 2.27 0.00 35.83 2.71
5173 6004 7.866898 TGTTATTGAATTCCTTGTGACAACATG 59.133 33.333 2.27 0.00 35.83 3.21
5174 6005 6.653526 ATTGAATTCCTTGTGACAACATGA 57.346 33.333 0.00 0.00 35.83 3.07
5293 6129 2.753043 GGTGCCCAGCCATGTCTG 60.753 66.667 0.00 0.00 0.00 3.51
5371 6207 0.537188 TGGGTGCTCTAAGCTACAGC 59.463 55.000 4.82 4.82 42.97 4.40
5404 6240 1.019278 CGCTTGGTGACGTGCCTATT 61.019 55.000 0.00 0.00 0.00 1.73
5454 6290 1.078955 CCTATGGCCCCATCTCCATT 58.921 55.000 0.00 0.00 42.62 3.16
5497 6333 1.366319 ACATTCTGGCCAAGGACTCT 58.634 50.000 7.01 0.00 0.00 3.24
5646 6482 3.539604 GTGGAGAGTTCTGATCCCATTG 58.460 50.000 0.00 0.00 31.73 2.82
5689 6526 7.498900 TGTTCAGAAAGCTTCTCAAGATGTTTA 59.501 33.333 0.00 0.00 38.11 2.01
5785 6624 1.202330 CCTCTCAGCATCTTCACCCT 58.798 55.000 0.00 0.00 0.00 4.34
5789 6628 2.842496 TCTCAGCATCTTCACCCTGAAT 59.158 45.455 0.00 0.00 35.59 2.57
5790 6629 3.265221 TCTCAGCATCTTCACCCTGAATT 59.735 43.478 0.00 0.00 35.59 2.17
6126 6965 8.053026 ACGAGTCTACAACTTCTGTAATATGT 57.947 34.615 0.00 0.00 40.06 2.29
6313 10684 5.560953 GCTGTGAATTTGTTCGCTAAGTTCT 60.561 40.000 3.75 0.00 32.95 3.01
6315 10686 5.525745 TGTGAATTTGTTCGCTAAGTTCTCA 59.474 36.000 3.75 0.00 32.95 3.27
6338 10709 1.079750 GACAAGTCCCCACGAGCTC 60.080 63.158 2.73 2.73 0.00 4.09
6419 10790 3.529533 CAGGAAAGTATCAGGTGCTGAG 58.470 50.000 0.00 0.00 44.08 3.35
6461 10832 6.564709 TTCTTGTTGAATGTTCATGAGAGG 57.435 37.500 0.00 0.00 37.00 3.69
6462 10833 4.456911 TCTTGTTGAATGTTCATGAGAGGC 59.543 41.667 0.00 0.00 37.00 4.70
6463 10834 3.753815 TGTTGAATGTTCATGAGAGGCA 58.246 40.909 0.00 0.00 37.00 4.75
6464 10835 4.143543 TGTTGAATGTTCATGAGAGGCAA 58.856 39.130 0.00 0.00 37.00 4.52
6465 10836 4.583907 TGTTGAATGTTCATGAGAGGCAAA 59.416 37.500 0.00 0.00 37.00 3.68
6466 10837 5.068855 TGTTGAATGTTCATGAGAGGCAAAA 59.931 36.000 0.00 0.00 37.00 2.44
6467 10838 5.787953 TGAATGTTCATGAGAGGCAAAAA 57.212 34.783 0.00 0.00 31.01 1.94
6468 10839 5.531634 TGAATGTTCATGAGAGGCAAAAAC 58.468 37.500 0.00 0.00 31.01 2.43
6469 10840 3.624326 TGTTCATGAGAGGCAAAAACG 57.376 42.857 0.00 0.00 31.33 3.60
6470 10841 3.210227 TGTTCATGAGAGGCAAAAACGA 58.790 40.909 0.00 0.00 31.33 3.85
6471 10842 3.003275 TGTTCATGAGAGGCAAAAACGAC 59.997 43.478 0.00 0.00 31.33 4.34
6472 10843 2.844946 TCATGAGAGGCAAAAACGACA 58.155 42.857 0.00 0.00 0.00 4.35
6473 10844 3.210227 TCATGAGAGGCAAAAACGACAA 58.790 40.909 0.00 0.00 0.00 3.18
6474 10845 3.629855 TCATGAGAGGCAAAAACGACAAA 59.370 39.130 0.00 0.00 0.00 2.83
6475 10846 4.097135 TCATGAGAGGCAAAAACGACAAAA 59.903 37.500 0.00 0.00 0.00 2.44
6476 10847 4.647424 TGAGAGGCAAAAACGACAAAAT 57.353 36.364 0.00 0.00 0.00 1.82
6477 10848 5.004922 TGAGAGGCAAAAACGACAAAATT 57.995 34.783 0.00 0.00 0.00 1.82
6478 10849 4.803088 TGAGAGGCAAAAACGACAAAATTG 59.197 37.500 0.00 0.00 0.00 2.32
6479 10850 5.004922 AGAGGCAAAAACGACAAAATTGA 57.995 34.783 0.00 0.00 0.00 2.57
6480 10851 4.803613 AGAGGCAAAAACGACAAAATTGAC 59.196 37.500 0.00 0.00 0.00 3.18
6481 10852 3.868661 AGGCAAAAACGACAAAATTGACC 59.131 39.130 0.00 0.00 29.07 4.02
6482 10853 3.868661 GGCAAAAACGACAAAATTGACCT 59.131 39.130 0.00 0.00 0.00 3.85
6483 10854 4.260172 GGCAAAAACGACAAAATTGACCTG 60.260 41.667 0.00 0.00 0.00 4.00
6484 10855 4.328712 GCAAAAACGACAAAATTGACCTGT 59.671 37.500 0.00 0.00 0.00 4.00
6485 10856 5.723678 GCAAAAACGACAAAATTGACCTGTG 60.724 40.000 0.00 0.00 0.00 3.66
6486 10857 3.708563 AACGACAAAATTGACCTGTGG 57.291 42.857 0.00 0.00 0.00 4.17
6487 10858 1.953686 ACGACAAAATTGACCTGTGGG 59.046 47.619 0.00 0.00 38.88 4.61
6488 10859 1.335872 CGACAAAATTGACCTGTGGGC 60.336 52.381 0.00 0.00 35.63 5.36
6489 10860 0.673437 ACAAAATTGACCTGTGGGCG 59.327 50.000 0.00 0.00 35.63 6.13
6490 10861 0.958091 CAAAATTGACCTGTGGGCGA 59.042 50.000 0.00 0.00 35.63 5.54
6491 10862 1.339610 CAAAATTGACCTGTGGGCGAA 59.660 47.619 0.00 0.00 35.63 4.70
6492 10863 1.698506 AAATTGACCTGTGGGCGAAA 58.301 45.000 0.00 0.00 35.63 3.46
6493 10864 1.923356 AATTGACCTGTGGGCGAAAT 58.077 45.000 0.00 0.00 35.63 2.17
6494 10865 1.463674 ATTGACCTGTGGGCGAAATC 58.536 50.000 0.00 0.00 35.63 2.17
6495 10866 0.109532 TTGACCTGTGGGCGAAATCA 59.890 50.000 0.00 0.00 35.63 2.57
6496 10867 0.109532 TGACCTGTGGGCGAAATCAA 59.890 50.000 0.00 0.00 35.63 2.57
6497 10868 1.271871 TGACCTGTGGGCGAAATCAAT 60.272 47.619 0.00 0.00 35.63 2.57
6498 10869 1.818674 GACCTGTGGGCGAAATCAATT 59.181 47.619 0.00 0.00 35.63 2.32
6499 10870 1.818674 ACCTGTGGGCGAAATCAATTC 59.181 47.619 0.00 0.00 35.63 2.17
6500 10871 1.818060 CCTGTGGGCGAAATCAATTCA 59.182 47.619 0.00 0.00 37.96 2.57
6501 10872 2.415893 CCTGTGGGCGAAATCAATTCAC 60.416 50.000 0.00 0.00 37.96 3.18
6502 10873 2.228582 CTGTGGGCGAAATCAATTCACA 59.771 45.455 0.00 0.00 37.96 3.58
6503 10874 2.625314 TGTGGGCGAAATCAATTCACAA 59.375 40.909 0.00 0.00 37.96 3.33
6504 10875 3.068732 TGTGGGCGAAATCAATTCACAAA 59.931 39.130 0.00 0.00 37.96 2.83
6505 10876 3.428534 GTGGGCGAAATCAATTCACAAAC 59.571 43.478 0.00 0.00 37.96 2.93
6506 10877 3.320541 TGGGCGAAATCAATTCACAAACT 59.679 39.130 0.00 0.00 37.96 2.66
6507 10878 3.674753 GGGCGAAATCAATTCACAAACTG 59.325 43.478 0.00 0.00 37.96 3.16
6508 10879 4.545610 GGCGAAATCAATTCACAAACTGA 58.454 39.130 0.00 0.00 37.96 3.41
6509 10880 4.981674 GGCGAAATCAATTCACAAACTGAA 59.018 37.500 0.00 0.00 43.28 3.02
6543 10914 4.815040 TTTTTAAATCGCTCAACCGTGA 57.185 36.364 0.00 0.00 0.00 4.35
6544 10915 3.799137 TTTAAATCGCTCAACCGTGAC 57.201 42.857 0.00 0.00 0.00 3.67
6545 10916 1.342555 TAAATCGCTCAACCGTGACG 58.657 50.000 0.00 0.00 32.81 4.35
6546 10917 0.319211 AAATCGCTCAACCGTGACGA 60.319 50.000 6.54 0.00 39.70 4.20
6547 10918 0.319211 AATCGCTCAACCGTGACGAA 60.319 50.000 6.54 0.00 39.23 3.85
6548 10919 0.319211 ATCGCTCAACCGTGACGAAA 60.319 50.000 6.54 0.00 39.23 3.46
6549 10920 0.319211 TCGCTCAACCGTGACGAAAT 60.319 50.000 6.54 0.00 35.68 2.17
6550 10921 0.093026 CGCTCAACCGTGACGAAATC 59.907 55.000 6.54 0.00 33.10 2.17
6551 10922 0.093026 GCTCAACCGTGACGAAATCG 59.907 55.000 6.54 0.48 46.33 3.34
6552 10923 1.693467 CTCAACCGTGACGAAATCGA 58.307 50.000 6.54 0.00 43.02 3.59
6553 10924 2.259618 CTCAACCGTGACGAAATCGAT 58.740 47.619 6.54 0.00 43.02 3.59
6554 10925 2.666508 CTCAACCGTGACGAAATCGATT 59.333 45.455 6.54 4.39 43.02 3.34
6555 10926 2.664568 TCAACCGTGACGAAATCGATTC 59.335 45.455 11.83 4.45 43.02 2.52
6556 10927 2.357327 ACCGTGACGAAATCGATTCA 57.643 45.000 11.83 1.89 43.02 2.57
6557 10928 1.990563 ACCGTGACGAAATCGATTCAC 59.009 47.619 11.83 13.80 43.02 3.18
6558 10929 1.989864 CCGTGACGAAATCGATTCACA 59.010 47.619 21.67 12.88 42.07 3.58
6559 10930 2.410392 CCGTGACGAAATCGATTCACAA 59.590 45.455 21.67 3.43 42.07 3.33
6560 10931 3.120820 CCGTGACGAAATCGATTCACAAA 60.121 43.478 21.67 4.33 42.07 2.83
6561 10932 3.833061 CGTGACGAAATCGATTCACAAAC 59.167 43.478 21.67 13.11 42.07 2.93
6562 10933 4.376008 CGTGACGAAATCGATTCACAAACT 60.376 41.667 21.67 2.88 42.07 2.66
6563 10934 4.840772 GTGACGAAATCGATTCACAAACTG 59.159 41.667 18.63 4.46 41.78 3.16
6564 10935 4.084066 TGACGAAATCGATTCACAAACTGG 60.084 41.667 11.83 0.00 43.02 4.00
6565 10936 4.062293 ACGAAATCGATTCACAAACTGGA 58.938 39.130 11.83 0.00 43.02 3.86
6566 10937 4.695455 ACGAAATCGATTCACAAACTGGAT 59.305 37.500 11.83 0.00 43.02 3.41
6567 10938 5.181245 ACGAAATCGATTCACAAACTGGATT 59.819 36.000 11.83 0.00 43.02 3.01
6568 10939 5.509272 CGAAATCGATTCACAAACTGGATTG 59.491 40.000 11.83 0.00 43.02 2.67
6569 10940 3.829886 TCGATTCACAAACTGGATTGC 57.170 42.857 0.00 0.00 33.52 3.56
6570 10941 3.411446 TCGATTCACAAACTGGATTGCT 58.589 40.909 0.00 0.00 33.52 3.91
6571 10942 3.820467 TCGATTCACAAACTGGATTGCTT 59.180 39.130 0.00 0.00 33.52 3.91
6572 10943 4.278170 TCGATTCACAAACTGGATTGCTTT 59.722 37.500 0.00 0.00 33.52 3.51
6573 10944 4.984161 CGATTCACAAACTGGATTGCTTTT 59.016 37.500 0.00 0.00 33.52 2.27
6574 10945 5.463061 CGATTCACAAACTGGATTGCTTTTT 59.537 36.000 0.00 0.00 33.52 1.94
6575 10946 6.640499 CGATTCACAAACTGGATTGCTTTTTA 59.360 34.615 0.00 0.00 33.52 1.52
6576 10947 7.168972 CGATTCACAAACTGGATTGCTTTTTAA 59.831 33.333 0.00 0.00 33.52 1.52
6577 10948 8.729805 ATTCACAAACTGGATTGCTTTTTAAA 57.270 26.923 0.00 0.00 33.52 1.52
6578 10949 8.553459 TTCACAAACTGGATTGCTTTTTAAAA 57.447 26.923 0.00 0.00 33.52 1.52
6579 10950 8.553459 TCACAAACTGGATTGCTTTTTAAAAA 57.447 26.923 12.62 12.62 33.52 1.94
6597 10968 3.643159 AAAATTTCGCTCAACTGACCC 57.357 42.857 0.00 0.00 0.00 4.46
6598 10969 2.568623 AATTTCGCTCAACTGACCCT 57.431 45.000 0.00 0.00 0.00 4.34
6599 10970 2.568623 ATTTCGCTCAACTGACCCTT 57.431 45.000 0.00 0.00 0.00 3.95
6600 10971 2.341846 TTTCGCTCAACTGACCCTTT 57.658 45.000 0.00 0.00 0.00 3.11
6601 10972 2.341846 TTCGCTCAACTGACCCTTTT 57.658 45.000 0.00 0.00 0.00 2.27
6602 10973 1.593196 TCGCTCAACTGACCCTTTTG 58.407 50.000 0.00 0.00 0.00 2.44
6603 10974 1.134220 TCGCTCAACTGACCCTTTTGT 60.134 47.619 0.00 0.00 0.00 2.83
6604 10975 1.002468 CGCTCAACTGACCCTTTTGTG 60.002 52.381 0.00 0.00 0.00 3.33
6605 10976 2.024414 GCTCAACTGACCCTTTTGTGT 58.976 47.619 0.00 0.00 0.00 3.72
6606 10977 3.211045 GCTCAACTGACCCTTTTGTGTA 58.789 45.455 0.00 0.00 0.00 2.90
6607 10978 3.251004 GCTCAACTGACCCTTTTGTGTAG 59.749 47.826 0.00 0.00 0.00 2.74
6608 10979 3.211045 TCAACTGACCCTTTTGTGTAGC 58.789 45.455 0.00 0.00 0.00 3.58
6609 10980 1.878953 ACTGACCCTTTTGTGTAGCG 58.121 50.000 0.00 0.00 0.00 4.26
6610 10981 0.517316 CTGACCCTTTTGTGTAGCGC 59.483 55.000 0.00 0.00 0.00 5.92
6611 10982 0.887387 TGACCCTTTTGTGTAGCGCC 60.887 55.000 2.29 0.00 0.00 6.53
6612 10983 0.605589 GACCCTTTTGTGTAGCGCCT 60.606 55.000 2.29 0.00 0.00 5.52
6613 10984 0.889186 ACCCTTTTGTGTAGCGCCTG 60.889 55.000 2.29 0.00 0.00 4.85
6614 10985 0.605319 CCCTTTTGTGTAGCGCCTGA 60.605 55.000 2.29 0.00 0.00 3.86
6615 10986 0.517316 CCTTTTGTGTAGCGCCTGAC 59.483 55.000 2.29 0.00 0.00 3.51
6616 10987 1.225855 CTTTTGTGTAGCGCCTGACA 58.774 50.000 2.29 3.02 0.00 3.58
6617 10988 1.195448 CTTTTGTGTAGCGCCTGACAG 59.805 52.381 2.29 0.00 0.00 3.51
6618 10989 1.227999 TTTGTGTAGCGCCTGACAGC 61.228 55.000 2.29 2.45 0.00 4.40
6619 10990 2.815647 GTGTAGCGCCTGACAGCC 60.816 66.667 2.29 0.00 0.00 4.85
6620 10991 3.310307 TGTAGCGCCTGACAGCCA 61.310 61.111 2.29 0.00 0.00 4.75
6621 10992 2.510238 GTAGCGCCTGACAGCCAG 60.510 66.667 2.29 0.00 42.55 4.85
6628 10999 2.345244 CTGACAGCCAGGCGTTCT 59.655 61.111 5.55 0.00 39.23 3.01
6629 11000 1.591703 CTGACAGCCAGGCGTTCTA 59.408 57.895 5.55 0.00 39.23 2.10
6630 11001 0.176680 CTGACAGCCAGGCGTTCTAT 59.823 55.000 5.55 0.00 39.23 1.98
6631 11002 1.409064 CTGACAGCCAGGCGTTCTATA 59.591 52.381 5.55 0.00 39.23 1.31
6632 11003 1.409064 TGACAGCCAGGCGTTCTATAG 59.591 52.381 5.55 0.00 0.00 1.31
6633 11004 1.409427 GACAGCCAGGCGTTCTATAGT 59.591 52.381 5.55 0.00 0.00 2.12
6634 11005 1.137086 ACAGCCAGGCGTTCTATAGTG 59.863 52.381 5.55 0.00 0.00 2.74
6635 11006 1.137086 CAGCCAGGCGTTCTATAGTGT 59.863 52.381 5.55 0.00 0.00 3.55
6636 11007 2.361119 CAGCCAGGCGTTCTATAGTGTA 59.639 50.000 5.55 0.00 0.00 2.90
6637 11008 2.623889 AGCCAGGCGTTCTATAGTGTAG 59.376 50.000 5.55 0.00 0.00 2.74
6638 11009 2.361438 GCCAGGCGTTCTATAGTGTAGT 59.639 50.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.105837 CGTCATACTAAGGCCCTATAAGGTC 60.106 48.000 0.00 0.00 31.93 3.85
1 2 4.771054 CGTCATACTAAGGCCCTATAAGGT 59.229 45.833 0.00 0.00 31.93 3.50
2 3 5.014858 TCGTCATACTAAGGCCCTATAAGG 58.985 45.833 0.00 0.00 34.30 2.69
3 4 5.711036 AGTCGTCATACTAAGGCCCTATAAG 59.289 44.000 0.00 0.00 0.00 1.73
4 5 5.638133 AGTCGTCATACTAAGGCCCTATAA 58.362 41.667 0.00 0.00 0.00 0.98
5 6 5.252586 AGTCGTCATACTAAGGCCCTATA 57.747 43.478 0.00 0.00 0.00 1.31
6 7 4.115398 AGTCGTCATACTAAGGCCCTAT 57.885 45.455 0.00 0.00 0.00 2.57
7 8 3.589951 AGTCGTCATACTAAGGCCCTA 57.410 47.619 0.00 0.00 0.00 3.53
8 9 2.456073 AGTCGTCATACTAAGGCCCT 57.544 50.000 0.00 0.00 0.00 5.19
9 10 2.223994 GGAAGTCGTCATACTAAGGCCC 60.224 54.545 0.00 0.00 0.00 5.80
10 11 2.223994 GGGAAGTCGTCATACTAAGGCC 60.224 54.545 0.00 0.00 0.00 5.19
11 12 2.543238 CGGGAAGTCGTCATACTAAGGC 60.543 54.545 0.00 0.00 0.00 4.35
12 13 2.947652 TCGGGAAGTCGTCATACTAAGG 59.052 50.000 0.00 0.00 0.00 2.69
18 19 1.741706 GACAGTCGGGAAGTCGTCATA 59.258 52.381 0.00 0.00 0.00 2.15
29 30 3.255149 ACTTGTTGTAGTAGACAGTCGGG 59.745 47.826 0.00 0.00 39.88 5.14
33 34 6.537660 GGACAAAACTTGTTGTAGTAGACAGT 59.462 38.462 0.00 0.00 45.52 3.55
34 35 6.292168 CGGACAAAACTTGTTGTAGTAGACAG 60.292 42.308 0.00 0.00 45.52 3.51
47 48 0.593128 CTGGAGCCGGACAAAACTTG 59.407 55.000 5.05 0.00 0.00 3.16
56 57 1.984570 CTCCTTCACTGGAGCCGGA 60.985 63.158 5.05 0.00 45.84 5.14
70 71 0.467384 CCATCGTCATTGCTCCTCCT 59.533 55.000 0.00 0.00 0.00 3.69
76 77 2.436469 TGCGCCATCGTCATTGCT 60.436 55.556 4.18 0.00 38.14 3.91
79 80 2.108514 CAGGTGCGCCATCGTCATT 61.109 57.895 20.59 0.00 38.14 2.57
108 109 1.162698 AGCGACGACTACAAGCACTA 58.837 50.000 0.00 0.00 0.00 2.74
114 115 0.806868 CCACCTAGCGACGACTACAA 59.193 55.000 0.00 0.00 0.00 2.41
118 119 2.216898 GTATACCACCTAGCGACGACT 58.783 52.381 0.00 0.00 0.00 4.18
123 124 1.538512 GATGCGTATACCACCTAGCGA 59.461 52.381 0.00 0.00 0.00 4.93
317 328 3.347216 GTGCATGGATAGTTTGGTGACT 58.653 45.455 0.00 0.00 0.00 3.41
454 466 2.032528 CACCGTCATGTGCCCACT 59.967 61.111 0.00 0.00 0.00 4.00
634 646 1.002011 GGTGAGACCAAGGGGAAGC 60.002 63.158 0.00 0.00 38.42 3.86
1168 1190 2.627699 TCCAAAACCCTAGCAAGCAAAG 59.372 45.455 0.00 0.00 0.00 2.77
1423 1445 0.684805 ATCGGGAGAAGAGAAGCGGT 60.685 55.000 0.00 0.00 45.37 5.68
1479 1501 5.010922 TCGTAAGTAGCAAGTCCCAAAACTA 59.989 40.000 0.00 0.00 39.48 2.24
1482 1504 4.060205 GTCGTAAGTAGCAAGTCCCAAAA 58.940 43.478 0.00 0.00 39.48 2.44
1483 1505 3.322828 AGTCGTAAGTAGCAAGTCCCAAA 59.677 43.478 0.00 0.00 39.48 3.28
1596 1618 9.542462 TCCTAAACCATAACTAGAATCAATTCG 57.458 33.333 0.00 0.00 41.56 3.34
1787 1810 3.761218 CGAGTGACTGATCAGGCCTATAT 59.239 47.826 25.94 6.94 34.90 0.86
1789 1812 1.959985 CGAGTGACTGATCAGGCCTAT 59.040 52.381 25.94 11.46 34.90 2.57
2022 2045 3.612247 CTGACCTGGGCGTTCTGGG 62.612 68.421 0.00 0.00 0.00 4.45
2071 2094 5.607119 GAGTTTTCGACTATTGGCAAGAA 57.393 39.130 5.96 0.07 39.19 2.52
2577 2648 1.604378 CCAACTGGCTAGAGGTGGG 59.396 63.158 3.17 0.00 0.00 4.61
2607 2678 1.280421 GATCCTGGCAGAACAGAAGGT 59.720 52.381 17.94 0.00 40.97 3.50
2785 2857 9.927668 TTTGGTCCAGATTAAAAGATTCATTTC 57.072 29.630 0.00 0.00 0.00 2.17
3413 3542 9.051679 GTATGCTTTTGGTTTAACTTCCATTTT 57.948 29.630 0.00 0.00 33.50 1.82
3599 3732 7.259290 ACAGTAACACTCAAAACCTGTAATG 57.741 36.000 0.00 0.00 0.00 1.90
3624 3757 2.104792 AGCTGCACTACTTTCAAGTCCA 59.895 45.455 1.02 0.00 40.37 4.02
3729 3862 3.128589 TGAACTAAAGCAATGGAATCCGC 59.871 43.478 0.00 0.00 0.00 5.54
3826 3959 6.229936 AGTCGACTATACAATGGGCTAAAA 57.770 37.500 18.46 0.00 0.00 1.52
3969 4103 8.948631 ACACTGTCCTACACATAATATTCTTG 57.051 34.615 0.00 0.00 33.23 3.02
4005 4139 8.667076 TGAACATCGATCTACATTTGATTGAT 57.333 30.769 0.00 0.00 42.59 2.57
4152 4286 6.324770 CCTACCCTTTGCCATCATTATTTTCT 59.675 38.462 0.00 0.00 0.00 2.52
4288 4422 8.261492 CTAGTGAGCAATAAACAGAAGACATT 57.739 34.615 0.00 0.00 0.00 2.71
4289 4423 7.840342 CTAGTGAGCAATAAACAGAAGACAT 57.160 36.000 0.00 0.00 0.00 3.06
4439 4573 7.497249 CCTCCATCTTCAAAGAATTACGAGATT 59.503 37.037 0.00 0.00 38.77 2.40
4440 4574 6.989169 CCTCCATCTTCAAAGAATTACGAGAT 59.011 38.462 0.00 0.00 38.77 2.75
4442 4576 5.007136 GCCTCCATCTTCAAAGAATTACGAG 59.993 44.000 0.00 0.00 38.77 4.18
4443 4577 4.876107 GCCTCCATCTTCAAAGAATTACGA 59.124 41.667 0.00 0.00 38.77 3.43
4444 4578 4.878397 AGCCTCCATCTTCAAAGAATTACG 59.122 41.667 0.00 0.00 38.77 3.18
4445 4579 6.765915 AAGCCTCCATCTTCAAAGAATTAC 57.234 37.500 0.00 0.00 38.77 1.89
4537 4671 0.322546 CCAAGGAAGTACCCACCAGC 60.323 60.000 0.00 0.00 40.05 4.85
4623 4758 4.870426 TCAAGAATCAAGATACTTGCGACC 59.130 41.667 6.62 0.00 39.33 4.79
4713 4853 8.375608 ACGAGTGATGTTATACGAGTTAGTAT 57.624 34.615 0.00 0.00 40.16 2.12
4721 4861 9.142515 ACAAATTTTACGAGTGATGTTATACGA 57.857 29.630 0.00 0.00 0.00 3.43
4736 4876 7.987486 TGTCGCTAATTTTGACAAATTTTACG 58.013 30.769 12.00 14.38 39.19 3.18
4754 4894 6.275494 TCCGATCCATATTAATTGTCGCTA 57.725 37.500 0.00 0.00 0.00 4.26
4796 4936 6.307776 TCATAGATAGGACAAGGTACTCCAG 58.692 44.000 2.07 0.00 38.49 3.86
4844 4986 3.297134 ACTCCAGTGGAAGCAAAAGAA 57.703 42.857 14.17 0.00 0.00 2.52
4845 4987 3.214328 GAACTCCAGTGGAAGCAAAAGA 58.786 45.455 14.17 0.00 0.00 2.52
4855 4997 5.358160 GGGATTTTTCTATGAACTCCAGTGG 59.642 44.000 1.40 1.40 0.00 4.00
4860 5002 4.777463 TCCGGGATTTTTCTATGAACTCC 58.223 43.478 0.00 0.00 0.00 3.85
4876 5018 0.834687 AGTAACCTGCACTTCCGGGA 60.835 55.000 0.00 0.00 35.17 5.14
5086 5822 8.023128 CCAAAATGAACTACTACAGGAACATTG 58.977 37.037 0.00 0.00 31.12 2.82
5293 6129 5.640732 CAAAACCCATGCTGTGAATAGTAC 58.359 41.667 0.00 0.00 0.00 2.73
5362 6198 0.622665 ATGCTGAAGGGCTGTAGCTT 59.377 50.000 3.63 0.00 41.70 3.74
5371 6207 0.661552 CAAGCGATGATGCTGAAGGG 59.338 55.000 0.00 0.00 46.60 3.95
5404 6240 3.495331 GAGACTGAGAGGATATGGAGCA 58.505 50.000 0.00 0.00 0.00 4.26
5454 6290 0.975556 TGGCCGCAGACCAGAAGATA 60.976 55.000 0.00 0.00 32.06 1.98
5497 6333 0.890542 ACGCTGGCTGATTTGCTGAA 60.891 50.000 0.00 0.00 0.00 3.02
5545 6381 5.695816 TGGAGCATAAATTTTTGACAACTGC 59.304 36.000 12.18 5.89 0.00 4.40
5646 6482 3.448301 TGAACATCCATTTTCATCCCAGC 59.552 43.478 0.00 0.00 0.00 4.85
5689 6526 5.282055 TCTCATCTCATCTACGCCAAAAT 57.718 39.130 0.00 0.00 0.00 1.82
5785 6624 3.251016 TTCACATTGGGTGGGAATTCA 57.749 42.857 7.93 0.00 45.13 2.57
6139 6978 5.972973 ACGACGTTCTTATGTTCGCATTATA 59.027 36.000 0.00 0.00 38.94 0.98
6175 7014 4.529897 CAGATGATTCCATTGAGGGTTCA 58.470 43.478 0.00 0.00 38.24 3.18
6313 10684 2.901192 TCGTGGGGACTTGTCTAAATGA 59.099 45.455 0.61 0.00 0.00 2.57
6315 10686 2.354805 GCTCGTGGGGACTTGTCTAAAT 60.355 50.000 0.61 0.00 0.00 1.40
6338 10709 2.096218 GGCTCAGTAAACGAACTTGCTG 60.096 50.000 0.00 0.00 39.56 4.41
6436 10807 7.428020 CCTCTCATGAACATTCAACAAGAAAA 58.572 34.615 0.00 0.00 41.13 2.29
6437 10808 6.515531 GCCTCTCATGAACATTCAACAAGAAA 60.516 38.462 0.00 0.00 41.13 2.52
6443 10814 4.771590 TTGCCTCTCATGAACATTCAAC 57.228 40.909 0.00 0.00 41.13 3.18
6445 10816 5.531634 GTTTTTGCCTCTCATGAACATTCA 58.468 37.500 0.00 0.00 42.14 2.57
6461 10832 4.328712 ACAGGTCAATTTTGTCGTTTTTGC 59.671 37.500 0.00 0.00 0.00 3.68
6462 10833 5.220378 CCACAGGTCAATTTTGTCGTTTTTG 60.220 40.000 0.00 0.00 0.00 2.44
6463 10834 4.867608 CCACAGGTCAATTTTGTCGTTTTT 59.132 37.500 0.00 0.00 0.00 1.94
6464 10835 4.429108 CCACAGGTCAATTTTGTCGTTTT 58.571 39.130 0.00 0.00 0.00 2.43
6465 10836 3.181480 CCCACAGGTCAATTTTGTCGTTT 60.181 43.478 0.00 0.00 0.00 3.60
6466 10837 2.360801 CCCACAGGTCAATTTTGTCGTT 59.639 45.455 0.00 0.00 0.00 3.85
6467 10838 1.953686 CCCACAGGTCAATTTTGTCGT 59.046 47.619 0.00 0.00 0.00 4.34
6468 10839 1.335872 GCCCACAGGTCAATTTTGTCG 60.336 52.381 0.00 0.00 34.57 4.35
6469 10840 1.335872 CGCCCACAGGTCAATTTTGTC 60.336 52.381 0.00 0.00 34.57 3.18
6470 10841 0.673437 CGCCCACAGGTCAATTTTGT 59.327 50.000 0.00 0.00 34.57 2.83
6471 10842 0.958091 TCGCCCACAGGTCAATTTTG 59.042 50.000 0.00 0.00 34.57 2.44
6472 10843 1.698506 TTCGCCCACAGGTCAATTTT 58.301 45.000 0.00 0.00 34.57 1.82
6473 10844 1.698506 TTTCGCCCACAGGTCAATTT 58.301 45.000 0.00 0.00 34.57 1.82
6474 10845 1.818674 GATTTCGCCCACAGGTCAATT 59.181 47.619 0.00 0.00 34.57 2.32
6475 10846 1.271871 TGATTTCGCCCACAGGTCAAT 60.272 47.619 0.00 0.00 34.57 2.57
6476 10847 0.109532 TGATTTCGCCCACAGGTCAA 59.890 50.000 0.00 0.00 34.57 3.18
6477 10848 0.109532 TTGATTTCGCCCACAGGTCA 59.890 50.000 0.00 0.00 34.57 4.02
6478 10849 1.463674 ATTGATTTCGCCCACAGGTC 58.536 50.000 0.00 0.00 34.57 3.85
6479 10850 1.818674 GAATTGATTTCGCCCACAGGT 59.181 47.619 0.00 0.00 34.57 4.00
6480 10851 1.818060 TGAATTGATTTCGCCCACAGG 59.182 47.619 0.00 0.00 37.13 4.00
6481 10852 2.228582 TGTGAATTGATTTCGCCCACAG 59.771 45.455 0.00 0.00 42.96 3.66
6482 10853 2.234143 TGTGAATTGATTTCGCCCACA 58.766 42.857 0.00 0.00 42.96 4.17
6483 10854 3.296322 TTGTGAATTGATTTCGCCCAC 57.704 42.857 0.00 0.00 42.96 4.61
6484 10855 3.320541 AGTTTGTGAATTGATTTCGCCCA 59.679 39.130 0.00 0.00 42.96 5.36
6485 10856 3.674753 CAGTTTGTGAATTGATTTCGCCC 59.325 43.478 0.00 0.00 42.96 6.13
6486 10857 4.545610 TCAGTTTGTGAATTGATTTCGCC 58.454 39.130 0.00 0.00 42.96 5.54
6522 10893 4.529446 GTCACGGTTGAGCGATTTAAAAA 58.471 39.130 9.76 0.00 30.10 1.94
6523 10894 3.363182 CGTCACGGTTGAGCGATTTAAAA 60.363 43.478 9.76 0.00 31.74 1.52
6524 10895 2.156117 CGTCACGGTTGAGCGATTTAAA 59.844 45.455 9.76 0.00 31.74 1.52
6525 10896 1.722464 CGTCACGGTTGAGCGATTTAA 59.278 47.619 9.76 0.00 31.74 1.52
6526 10897 1.068402 TCGTCACGGTTGAGCGATTTA 60.068 47.619 9.76 0.00 33.33 1.40
6527 10898 0.319211 TCGTCACGGTTGAGCGATTT 60.319 50.000 9.76 0.00 33.33 2.17
6528 10899 0.319211 TTCGTCACGGTTGAGCGATT 60.319 50.000 9.76 0.00 36.13 3.34
6529 10900 0.319211 TTTCGTCACGGTTGAGCGAT 60.319 50.000 9.76 0.00 36.13 4.58
6530 10901 0.319211 ATTTCGTCACGGTTGAGCGA 60.319 50.000 9.76 0.00 35.13 4.93
6531 10902 0.093026 GATTTCGTCACGGTTGAGCG 59.907 55.000 0.00 0.52 30.10 5.03
6532 10903 0.093026 CGATTTCGTCACGGTTGAGC 59.907 55.000 0.00 0.00 30.10 4.26
6533 10904 1.693467 TCGATTTCGTCACGGTTGAG 58.307 50.000 0.00 0.00 40.80 3.02
6534 10905 2.357327 ATCGATTTCGTCACGGTTGA 57.643 45.000 0.00 0.00 40.80 3.18
6535 10906 2.410392 TGAATCGATTTCGTCACGGTTG 59.590 45.455 12.81 0.00 40.80 3.77
6536 10907 2.410730 GTGAATCGATTTCGTCACGGTT 59.589 45.455 12.81 0.00 36.27 4.44
6537 10908 1.990563 GTGAATCGATTTCGTCACGGT 59.009 47.619 12.81 0.00 36.27 4.83
6538 10909 1.989864 TGTGAATCGATTTCGTCACGG 59.010 47.619 12.81 0.00 43.70 4.94
6539 10910 3.698420 TTGTGAATCGATTTCGTCACG 57.302 42.857 12.81 0.00 43.70 4.35
6540 10911 4.840772 CAGTTTGTGAATCGATTTCGTCAC 59.159 41.667 17.29 17.29 42.21 3.67
6541 10912 4.084066 CCAGTTTGTGAATCGATTTCGTCA 60.084 41.667 12.81 2.48 40.80 4.35
6542 10913 4.151689 TCCAGTTTGTGAATCGATTTCGTC 59.848 41.667 12.81 0.00 40.80 4.20
6543 10914 4.062293 TCCAGTTTGTGAATCGATTTCGT 58.938 39.130 12.81 0.00 40.80 3.85
6544 10915 4.661993 TCCAGTTTGTGAATCGATTTCG 57.338 40.909 12.81 0.00 37.13 3.46
6545 10916 5.287035 GCAATCCAGTTTGTGAATCGATTTC 59.713 40.000 12.81 9.40 34.72 2.17
6546 10917 5.047802 AGCAATCCAGTTTGTGAATCGATTT 60.048 36.000 12.81 0.00 0.00 2.17
6547 10918 4.460382 AGCAATCCAGTTTGTGAATCGATT 59.540 37.500 11.20 11.20 0.00 3.34
6548 10919 4.012374 AGCAATCCAGTTTGTGAATCGAT 58.988 39.130 0.00 0.00 0.00 3.59
6549 10920 3.411446 AGCAATCCAGTTTGTGAATCGA 58.589 40.909 0.00 0.00 0.00 3.59
6550 10921 3.837213 AGCAATCCAGTTTGTGAATCG 57.163 42.857 0.00 0.00 0.00 3.34
6551 10922 6.849588 AAAAAGCAATCCAGTTTGTGAATC 57.150 33.333 0.00 0.00 0.00 2.52
6552 10923 8.729805 TTTAAAAAGCAATCCAGTTTGTGAAT 57.270 26.923 0.00 0.00 0.00 2.57
6553 10924 8.553459 TTTTAAAAAGCAATCCAGTTTGTGAA 57.447 26.923 0.00 0.00 0.00 3.18
6554 10925 8.553459 TTTTTAAAAAGCAATCCAGTTTGTGA 57.447 26.923 9.31 0.00 0.00 3.58
6576 10947 3.636764 AGGGTCAGTTGAGCGAAATTTTT 59.363 39.130 5.36 0.00 43.03 1.94
6577 10948 3.222603 AGGGTCAGTTGAGCGAAATTTT 58.777 40.909 5.36 0.00 43.03 1.82
6578 10949 2.863809 AGGGTCAGTTGAGCGAAATTT 58.136 42.857 5.36 0.00 43.03 1.82
6579 10950 2.568623 AGGGTCAGTTGAGCGAAATT 57.431 45.000 5.36 0.00 43.03 1.82
6580 10951 2.568623 AAGGGTCAGTTGAGCGAAAT 57.431 45.000 5.36 0.00 43.03 2.17
6581 10952 2.341846 AAAGGGTCAGTTGAGCGAAA 57.658 45.000 5.36 0.00 43.03 3.46
6582 10953 1.946768 CAAAAGGGTCAGTTGAGCGAA 59.053 47.619 5.36 0.00 43.03 4.70
6583 10954 1.134220 ACAAAAGGGTCAGTTGAGCGA 60.134 47.619 5.36 0.00 43.03 4.93
6584 10955 1.002468 CACAAAAGGGTCAGTTGAGCG 60.002 52.381 5.36 0.00 43.03 5.03
6585 10956 2.024414 ACACAAAAGGGTCAGTTGAGC 58.976 47.619 2.80 2.80 41.50 4.26
6586 10957 3.251004 GCTACACAAAAGGGTCAGTTGAG 59.749 47.826 0.00 0.00 0.00 3.02
6587 10958 3.211045 GCTACACAAAAGGGTCAGTTGA 58.789 45.455 0.00 0.00 0.00 3.18
6588 10959 2.032030 CGCTACACAAAAGGGTCAGTTG 60.032 50.000 0.00 0.00 0.00 3.16
6589 10960 2.218603 CGCTACACAAAAGGGTCAGTT 58.781 47.619 0.00 0.00 0.00 3.16
6590 10961 1.878953 CGCTACACAAAAGGGTCAGT 58.121 50.000 0.00 0.00 0.00 3.41
6591 10962 0.517316 GCGCTACACAAAAGGGTCAG 59.483 55.000 0.00 0.00 0.00 3.51
6592 10963 0.887387 GGCGCTACACAAAAGGGTCA 60.887 55.000 7.64 0.00 32.25 4.02
6593 10964 0.605589 AGGCGCTACACAAAAGGGTC 60.606 55.000 7.64 0.00 0.00 4.46
6594 10965 0.889186 CAGGCGCTACACAAAAGGGT 60.889 55.000 7.64 0.00 0.00 4.34
6595 10966 0.605319 TCAGGCGCTACACAAAAGGG 60.605 55.000 7.64 0.00 0.00 3.95
6596 10967 0.517316 GTCAGGCGCTACACAAAAGG 59.483 55.000 7.64 0.00 0.00 3.11
6597 10968 1.195448 CTGTCAGGCGCTACACAAAAG 59.805 52.381 7.64 0.00 0.00 2.27
6598 10969 1.225855 CTGTCAGGCGCTACACAAAA 58.774 50.000 7.64 0.00 0.00 2.44
6599 10970 1.227999 GCTGTCAGGCGCTACACAAA 61.228 55.000 7.64 0.00 0.00 2.83
6600 10971 1.667830 GCTGTCAGGCGCTACACAA 60.668 57.895 7.64 0.00 0.00 3.33
6601 10972 2.048222 GCTGTCAGGCGCTACACA 60.048 61.111 7.64 6.51 0.00 3.72
6602 10973 2.815647 GGCTGTCAGGCGCTACAC 60.816 66.667 11.07 1.37 0.00 2.90
6603 10974 3.300934 CTGGCTGTCAGGCGCTACA 62.301 63.158 20.38 8.97 44.78 2.74
6604 10975 2.510238 CTGGCTGTCAGGCGCTAC 60.510 66.667 20.38 4.10 44.78 3.58
6611 10982 0.176680 ATAGAACGCCTGGCTGTCAG 59.823 55.000 17.92 1.37 43.00 3.51
6612 10983 1.409064 CTATAGAACGCCTGGCTGTCA 59.591 52.381 17.92 6.16 0.00 3.58
6613 10984 1.409427 ACTATAGAACGCCTGGCTGTC 59.591 52.381 17.92 13.28 0.00 3.51
6614 10985 1.137086 CACTATAGAACGCCTGGCTGT 59.863 52.381 17.92 13.35 0.00 4.40
6615 10986 1.137086 ACACTATAGAACGCCTGGCTG 59.863 52.381 17.92 12.68 0.00 4.85
6616 10987 1.486211 ACACTATAGAACGCCTGGCT 58.514 50.000 17.92 0.00 0.00 4.75
6617 10988 2.361438 ACTACACTATAGAACGCCTGGC 59.639 50.000 9.11 9.11 0.00 4.85


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

AutoCloner maintained by Alex Coulton.