Multiple sequence alignment - TraesCS7A01G457300

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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 TraesCS7A01G457300 chr7A 100.000 5659 0 0 1 5659 652722975 652717317 0.000000e+00 10451.0
1 TraesCS7A01G457300 chr7B 91.614 4138 219 53 824 4878 620659805 620663897 0.000000e+00 5602.0
2 TraesCS7A01G457300 chr7B 82.759 493 46 20 1 460 620658869 620659355 2.460000e-108 403.0
3 TraesCS7A01G457300 chr7D 89.254 2252 146 50 2900 5101 566550069 566547864 0.000000e+00 2730.0
4 TraesCS7A01G457300 chr7D 90.102 2152 128 30 766 2878 566552243 566550138 0.000000e+00 2715.0
5 TraesCS7A01G457300 chr7D 84.605 708 56 17 1 678 566552968 566552284 0.000000e+00 654.0
6 TraesCS7A01G457300 chr7D 91.748 206 7 6 5099 5297 566546749 566546547 1.550000e-70 278.0
7 TraesCS7A01G457300 chr7D 92.857 182 10 1 5480 5658 566546502 566546321 1.560000e-65 261.0
8 TraesCS7A01G457300 chr7D 92.857 168 12 0 5317 5484 235502571 235502404 1.570000e-60 244.0
9 TraesCS7A01G457300 chr6A 86.540 1471 157 29 2905 4352 115829587 115828135 0.000000e+00 1581.0
10 TraesCS7A01G457300 chr6A 85.832 974 72 24 948 1919 115831441 115830532 0.000000e+00 974.0
11 TraesCS7A01G457300 chr6A 85.792 915 82 30 1917 2799 115830481 115829583 0.000000e+00 926.0
12 TraesCS7A01G457300 chr6A 87.585 443 53 2 4377 4818 115827873 115827432 3.910000e-141 512.0
13 TraesCS7A01G457300 chr6B 86.458 1440 155 28 2936 4352 179989701 179988279 0.000000e+00 1543.0
14 TraesCS7A01G457300 chr6B 85.421 974 74 27 948 1919 179991768 179990861 0.000000e+00 950.0
15 TraesCS7A01G457300 chr6B 85.246 915 87 28 1917 2799 179990810 179989912 0.000000e+00 898.0
16 TraesCS7A01G457300 chr6B 88.496 226 22 4 2905 3127 179989916 179989692 2.600000e-68 270.0
17 TraesCS7A01G457300 chr6D 86.757 1329 139 20 3048 4352 96825409 96824094 0.000000e+00 1445.0
18 TraesCS7A01G457300 chr6D 85.700 979 66 27 948 1919 96827411 96826500 0.000000e+00 965.0
19 TraesCS7A01G457300 chr6D 87.966 698 57 17 1918 2599 96826448 96825762 0.000000e+00 798.0
20 TraesCS7A01G457300 chr6D 90.659 182 16 1 5302 5482 81746749 81746930 2.040000e-59 241.0
21 TraesCS7A01G457300 chr3B 87.625 299 21 12 4160 4451 797640606 797640895 3.270000e-87 333.0
22 TraesCS7A01G457300 chr3A 86.957 253 18 12 4160 4406 724897311 724897554 2.600000e-68 270.0
23 TraesCS7A01G457300 chr3A 90.476 63 6 0 261 323 532041326 532041264 3.630000e-12 84.2
24 TraesCS7A01G457300 chr3A 90.476 63 6 0 261 323 532066813 532066751 3.630000e-12 84.2
25 TraesCS7A01G457300 chr3A 90.476 63 6 0 261 323 532092617 532092555 3.630000e-12 84.2
26 TraesCS7A01G457300 chr1D 91.667 180 13 2 5318 5496 20054874 20055052 1.220000e-61 248.0
27 TraesCS7A01G457300 chr1D 93.413 167 10 1 5320 5485 311986774 311986608 4.380000e-61 246.0
28 TraesCS7A01G457300 chr1D 92.857 168 12 0 5316 5483 23004241 23004074 1.570000e-60 244.0
29 TraesCS7A01G457300 chr1D 91.573 178 14 1 5317 5493 450202218 450202041 1.570000e-60 244.0
30 TraesCS7A01G457300 chr5D 92.353 170 12 1 5317 5485 498721904 498722073 2.040000e-59 241.0
31 TraesCS7A01G457300 chr2D 87.383 214 18 9 5308 5516 592922214 592922005 2.640000e-58 237.0
32 TraesCS7A01G457300 chr5B 90.110 182 16 2 5319 5498 633177975 633177794 9.480000e-58 235.0


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 TraesCS7A01G457300 chr7A 652717317 652722975 5658 True 10451.000000 10451 100.000000 1 5659 1 chr7A.!!$R1 5658
1 TraesCS7A01G457300 chr7B 620658869 620663897 5028 False 3002.500000 5602 87.186500 1 4878 2 chr7B.!!$F1 4877
2 TraesCS7A01G457300 chr7D 566546321 566552968 6647 True 1327.600000 2730 89.713200 1 5658 5 chr7D.!!$R2 5657
3 TraesCS7A01G457300 chr6A 115827432 115831441 4009 True 998.250000 1581 86.437250 948 4818 4 chr6A.!!$R1 3870
4 TraesCS7A01G457300 chr6B 179988279 179991768 3489 True 915.250000 1543 86.405250 948 4352 4 chr6B.!!$R1 3404
5 TraesCS7A01G457300 chr6D 96824094 96827411 3317 True 1069.333333 1445 86.807667 948 4352 3 chr6D.!!$R1 3404

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
263 289 0.036164 TGTGTTCTTGGGGTCGATGG 59.964 55.0 0.00 0.00 0.00 3.51 F
1210 1456 0.034059 CCGACTGTTTGAGCTCAGGT 59.966 55.0 17.43 13.89 36.17 4.00 F
1494 1740 0.042131 TAAGGTGGTCTCCGGATGGT 59.958 55.0 3.57 0.00 36.30 3.55 F
1570 1817 0.670546 ATTCACTTCTGGTCGGTGCG 60.671 55.0 0.00 0.00 0.00 5.34 F
1751 2009 0.801067 GTAGAGTGCTAACCGCGTGG 60.801 60.0 14.93 14.93 43.27 4.94 F
3169 3845 0.647410 CGAGCAAGAAGGTACATGCG 59.353 55.0 0.00 0.00 43.39 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1818 0.035881 CTCTGCTCTCCCTGCAACAA 59.964 55.000 0.00 0.0 40.13 2.83 R
2721 3095 1.091771 CACGGGGACATGACTGATGC 61.092 60.000 0.00 0.0 35.15 3.91 R
2752 3126 1.369692 CCGGCGTATCCCTGCATTA 59.630 57.895 6.01 0.0 0.00 1.90 R
3059 3734 1.560866 CCCTGCCCAGAGCTTCTTCT 61.561 60.000 0.00 0.0 44.23 2.85 R
3598 4316 1.371635 GCCGTTGAACACACATGCC 60.372 57.895 0.00 0.0 0.00 4.40 R
4867 5859 0.031178 AAGCCAAGCAAGAAACGCAG 59.969 50.000 0.00 0.0 0.00 5.18 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
96 115 2.172505 AGTGAAATGTGTCCTGGTGTGA 59.827 45.455 0.00 0.00 0.00 3.58
102 122 3.080300 TGTGTCCTGGTGTGAGTTTTT 57.920 42.857 0.00 0.00 0.00 1.94
263 289 0.036164 TGTGTTCTTGGGGTCGATGG 59.964 55.000 0.00 0.00 0.00 3.51
342 368 2.111878 GGTCAGGGCCCATCATCG 59.888 66.667 27.56 4.67 0.00 3.84
345 371 2.194056 CAGGGCCCATCATCGCTT 59.806 61.111 27.56 0.00 0.00 4.68
350 376 0.947244 GGCCCATCATCGCTTGTTAG 59.053 55.000 0.00 0.00 0.00 2.34
360 386 5.938322 TCATCGCTTGTTAGTCCAATTTTC 58.062 37.500 0.00 0.00 0.00 2.29
529 719 8.437360 TCATCTATACAACATTTTTCGCTCAT 57.563 30.769 0.00 0.00 0.00 2.90
535 725 4.739716 ACAACATTTTTCGCTCATGAACAC 59.260 37.500 0.00 0.00 0.00 3.32
538 728 5.215160 ACATTTTTCGCTCATGAACACTTC 58.785 37.500 0.00 0.00 0.00 3.01
546 736 7.202016 TCGCTCATGAACACTTCTTAAAAAT 57.798 32.000 0.00 0.00 0.00 1.82
549 739 8.015087 CGCTCATGAACACTTCTTAAAAATACA 58.985 33.333 0.00 0.00 0.00 2.29
656 847 8.272866 GCGCAAACATTTTTCAGTATTTAAACT 58.727 29.630 0.30 0.00 0.00 2.66
818 1009 1.746615 CCAGAATCCAGCCCACGTG 60.747 63.158 9.08 9.08 0.00 4.49
894 1109 8.474577 CGAATGTGACAAATTTTCTCTCAAAAG 58.525 33.333 0.00 0.00 0.00 2.27
924 1151 1.343465 AGCTCCCGTCGAAAAGAAGAA 59.657 47.619 0.00 0.00 0.00 2.52
1103 1334 4.814294 CCGCCCCTTCGACTTCCG 62.814 72.222 0.00 0.00 40.25 4.30
1106 1337 4.468689 CCCCTTCGACTTCCGCCC 62.469 72.222 0.00 0.00 38.37 6.13
1107 1338 4.468689 CCCTTCGACTTCCGCCCC 62.469 72.222 0.00 0.00 38.37 5.80
1108 1339 3.391382 CCTTCGACTTCCGCCCCT 61.391 66.667 0.00 0.00 38.37 4.79
1109 1340 2.663196 CTTCGACTTCCGCCCCTT 59.337 61.111 0.00 0.00 38.37 3.95
1110 1341 1.448013 CTTCGACTTCCGCCCCTTC 60.448 63.158 0.00 0.00 38.37 3.46
1111 1342 3.291101 TTCGACTTCCGCCCCTTCG 62.291 63.158 0.00 0.00 38.37 3.79
1112 1343 3.755628 CGACTTCCGCCCCTTCGA 61.756 66.667 0.00 0.00 0.00 3.71
1113 1344 2.125633 GACTTCCGCCCCTTCGAC 60.126 66.667 0.00 0.00 0.00 4.20
1165 1411 1.149627 CTCGACTCGATCCCCTCCT 59.850 63.158 0.62 0.00 34.61 3.69
1167 1413 1.899534 CGACTCGATCCCCTCCTCC 60.900 68.421 0.00 0.00 0.00 4.30
1171 1417 3.851184 CGATCCCCTCCTCCCCCT 61.851 72.222 0.00 0.00 0.00 4.79
1190 1436 4.162690 CCCCTTCTCCTTCCGCGG 62.163 72.222 22.12 22.12 0.00 6.46
1210 1456 0.034059 CCGACTGTTTGAGCTCAGGT 59.966 55.000 17.43 13.89 36.17 4.00
1211 1457 1.143305 CGACTGTTTGAGCTCAGGTG 58.857 55.000 17.43 10.93 36.17 4.00
1219 1465 1.153667 GAGCTCAGGTGGCTTCTCG 60.154 63.158 9.40 0.00 40.40 4.04
1275 1521 0.620556 TTGGAATCTGCAGGGAGGAC 59.379 55.000 15.13 0.55 0.00 3.85
1494 1740 0.042131 TAAGGTGGTCTCCGGATGGT 59.958 55.000 3.57 0.00 36.30 3.55
1548 1795 7.442666 AGAGAGTTGAAGTGTGGAGTTTAATTC 59.557 37.037 0.00 0.00 0.00 2.17
1570 1817 0.670546 ATTCACTTCTGGTCGGTGCG 60.671 55.000 0.00 0.00 0.00 5.34
1571 1818 2.023414 TTCACTTCTGGTCGGTGCGT 62.023 55.000 0.00 0.00 0.00 5.24
1572 1819 1.594293 CACTTCTGGTCGGTGCGTT 60.594 57.895 0.00 0.00 0.00 4.84
1573 1820 1.594293 ACTTCTGGTCGGTGCGTTG 60.594 57.895 0.00 0.00 0.00 4.10
1574 1821 1.594293 CTTCTGGTCGGTGCGTTGT 60.594 57.895 0.00 0.00 0.00 3.32
1575 1822 1.153329 TTCTGGTCGGTGCGTTGTT 60.153 52.632 0.00 0.00 0.00 2.83
1622 1875 2.384382 GAATCCTTGTGTGTTGTTGCG 58.616 47.619 0.00 0.00 0.00 4.85
1703 1961 5.131977 TGGGTTGTATATTGCCTACTGATGT 59.868 40.000 0.00 0.00 0.00 3.06
1704 1962 6.327887 TGGGTTGTATATTGCCTACTGATGTA 59.672 38.462 0.00 0.00 0.00 2.29
1705 1963 7.147461 TGGGTTGTATATTGCCTACTGATGTAA 60.147 37.037 0.00 0.00 0.00 2.41
1706 1964 7.883311 GGGTTGTATATTGCCTACTGATGTAAT 59.117 37.037 0.00 0.00 0.00 1.89
1707 1965 8.721478 GGTTGTATATTGCCTACTGATGTAATG 58.279 37.037 0.00 0.00 0.00 1.90
1738 1996 3.177228 AGTGAATGCTTCTGGGTAGAGT 58.823 45.455 0.00 0.00 33.70 3.24
1751 2009 0.801067 GTAGAGTGCTAACCGCGTGG 60.801 60.000 14.93 14.93 43.27 4.94
1927 2244 8.850156 AGGTTATTGTATATGCTCCAATTTGTC 58.150 33.333 0.00 0.00 31.63 3.18
1940 2257 4.327898 TCCAATTTGTCGTGTCGCTATAAC 59.672 41.667 0.00 0.00 0.00 1.89
2064 2383 7.176515 ACACTGCCATGAAATTTGTCTTATGTA 59.823 33.333 0.00 0.00 0.00 2.29
2201 2530 1.877443 ACATGAAGGGCGTGTTGTTAC 59.123 47.619 0.00 0.00 44.17 2.50
2247 2576 3.262660 TCTCATGACAGTCTTTGGCTGAT 59.737 43.478 6.16 0.00 35.09 2.90
2248 2577 3.603532 TCATGACAGTCTTTGGCTGATC 58.396 45.455 6.16 1.44 35.09 2.92
2318 2647 1.067821 GAGGAAGGATGACAGCTACGG 59.932 57.143 0.00 0.00 0.00 4.02
2428 2757 4.319118 GCTTCGGTTAAAGCTGCTGATATC 60.319 45.833 1.35 0.00 46.51 1.63
2564 2899 4.288366 TGGGAATGTGGTTCATGAACTCTA 59.712 41.667 31.81 20.34 40.94 2.43
2565 2900 5.044919 TGGGAATGTGGTTCATGAACTCTAT 60.045 40.000 31.81 21.39 40.94 1.98
2566 2901 5.297776 GGGAATGTGGTTCATGAACTCTATG 59.702 44.000 31.81 0.00 40.94 2.23
2752 3126 0.966875 TCCCCGTGCAGTACATACGT 60.967 55.000 13.10 0.00 36.17 3.57
2756 3130 2.792674 CCCGTGCAGTACATACGTAATG 59.207 50.000 0.00 1.41 44.58 1.90
2801 3196 6.318900 GTGTATCCCCAAGTATCCTTTTTGAG 59.681 42.308 0.00 0.00 0.00 3.02
2833 3228 3.858247 AGTCCTAGGCGTTAATTGTGTC 58.142 45.455 2.96 0.00 0.00 3.67
3040 3692 1.002134 CAGGCGGGGATGAAGTTGT 60.002 57.895 0.00 0.00 0.00 3.32
3099 3775 1.856873 AAAGATGGGGACTGGGCCA 60.857 57.895 5.85 5.85 0.00 5.36
3169 3845 0.647410 CGAGCAAGAAGGTACATGCG 59.353 55.000 0.00 0.00 43.39 4.73
3174 3851 2.125269 GAAGGTACATGCGGCGGT 60.125 61.111 9.78 0.00 0.00 5.68
3231 3908 2.381941 GGAGCAAGGGGAGGCAGAT 61.382 63.158 0.00 0.00 0.00 2.90
3322 4001 4.142730 GCACTGCTCAAAGTCCTTCATTAG 60.143 45.833 0.00 0.00 0.00 1.73
3328 4007 6.716628 TGCTCAAAGTCCTTCATTAGTGAAAT 59.283 34.615 2.06 0.00 43.39 2.17
3332 4011 8.567948 TCAAAGTCCTTCATTAGTGAAATTGTC 58.432 33.333 2.06 0.00 43.39 3.18
3451 4157 3.588210 TCCCAGTGTCTGTATATCCGA 57.412 47.619 0.00 0.00 0.00 4.55
3452 4158 4.114015 TCCCAGTGTCTGTATATCCGAT 57.886 45.455 0.00 0.00 0.00 4.18
3453 4159 4.480115 TCCCAGTGTCTGTATATCCGATT 58.520 43.478 0.00 0.00 0.00 3.34
3454 4160 5.637127 TCCCAGTGTCTGTATATCCGATTA 58.363 41.667 0.00 0.00 0.00 1.75
3455 4161 6.253758 TCCCAGTGTCTGTATATCCGATTAT 58.746 40.000 0.00 0.00 0.00 1.28
3456 4162 6.377429 TCCCAGTGTCTGTATATCCGATTATC 59.623 42.308 0.00 0.00 0.00 1.75
3457 4163 6.378564 CCCAGTGTCTGTATATCCGATTATCT 59.621 42.308 0.00 0.00 0.00 1.98
3458 4164 7.254137 CCAGTGTCTGTATATCCGATTATCTG 58.746 42.308 0.00 0.00 0.00 2.90
3468 4174 4.521130 TCCGATTATCTGTATCTGTGCC 57.479 45.455 0.00 0.00 0.00 5.01
3485 4191 2.509336 CTCTTAGCGTGGCCGTGG 60.509 66.667 0.00 0.00 36.15 4.94
3725 4447 6.536224 GGATCAAAACCCATGCTATTCTTTTG 59.464 38.462 0.00 0.00 32.36 2.44
3820 4542 4.235360 AGAAGTTAACGTTCCTGATGTCG 58.765 43.478 2.82 0.00 0.00 4.35
3836 4558 2.034878 TGTCGCTATGAAGGAGAGCAT 58.965 47.619 0.00 0.00 39.00 3.79
3881 4603 0.617935 TCGAAGGCACCCAATGATGA 59.382 50.000 0.00 0.00 0.00 2.92
3953 4675 0.687354 ACCTTGACTGCAGACCGAAT 59.313 50.000 23.35 0.00 0.00 3.34
4001 4723 1.404047 CGTTGGTGGCCCATCAAATTC 60.404 52.381 11.86 0.00 41.49 2.17
4042 4764 4.260538 GCACTTCTCTAAATCCGAGCATTG 60.261 45.833 0.00 0.00 0.00 2.82
4049 4771 7.148641 TCTCTAAATCCGAGCATTGAATAGTC 58.851 38.462 0.00 0.00 0.00 2.59
4083 4806 1.337118 TTGCCAACCACCCTGATTTC 58.663 50.000 0.00 0.00 0.00 2.17
4183 4911 9.202273 GAATTGTGTTTGCCTGTTATATTTTCA 57.798 29.630 0.00 0.00 0.00 2.69
4295 5024 7.455953 AGTCCTCACTAGCCATGAAATATGATA 59.544 37.037 0.00 0.00 0.00 2.15
4296 5025 8.097038 GTCCTCACTAGCCATGAAATATGATAA 58.903 37.037 0.00 0.00 0.00 1.75
4329 5065 4.766373 TGCTGAAACATGTGTTCCATATGT 59.234 37.500 0.00 1.35 45.47 2.29
4366 5102 6.148811 CGGCTGAGTTAACTAATTCTGGAAAA 59.851 38.462 8.42 0.00 0.00 2.29
4367 5103 7.308348 CGGCTGAGTTAACTAATTCTGGAAAAA 60.308 37.037 8.42 0.00 0.00 1.94
4479 5452 2.153645 CACCAGCTGTAGCAAATGACA 58.846 47.619 13.81 0.00 45.16 3.58
4495 5468 5.733620 AATGACAAAAAGCATGAGGATGT 57.266 34.783 0.00 0.00 31.50 3.06
4503 5476 0.879400 GCATGAGGATGTCGAGCCAG 60.879 60.000 0.00 0.00 31.50 4.85
4510 5483 1.406069 GGATGTCGAGCCAGTGTTGAT 60.406 52.381 0.00 0.00 0.00 2.57
4673 5648 6.402222 CAAGAGTTAGATTGACTGTAGCCTT 58.598 40.000 0.00 0.00 0.00 4.35
4674 5649 7.548097 CAAGAGTTAGATTGACTGTAGCCTTA 58.452 38.462 0.00 0.00 0.00 2.69
4676 5651 8.135382 AGAGTTAGATTGACTGTAGCCTTAAA 57.865 34.615 0.00 0.00 0.00 1.52
4761 5745 7.011950 GCACATGCTACAGTGGTACATTATTAA 59.988 37.037 0.00 0.00 38.47 1.40
4790 5782 4.872664 AGCAACGAGTAATAGTGCTATCC 58.127 43.478 0.00 0.00 0.00 2.59
4830 5822 3.743396 CCTATAGTTTCTGATTGCGCCTC 59.257 47.826 4.18 1.89 0.00 4.70
4831 5823 2.024176 TAGTTTCTGATTGCGCCTCC 57.976 50.000 4.18 0.00 0.00 4.30
4850 5842 1.612156 CTCGTGCTGTCTTCTCTTCG 58.388 55.000 0.00 0.00 0.00 3.79
4867 5859 5.696724 TCTCTTCGTCATCTTTTTCTTGTCC 59.303 40.000 0.00 0.00 0.00 4.02
4881 5873 1.334869 CTTGTCCTGCGTTTCTTGCTT 59.665 47.619 0.00 0.00 0.00 3.91
4882 5874 0.662619 TGTCCTGCGTTTCTTGCTTG 59.337 50.000 0.00 0.00 0.00 4.01
4971 5963 6.715347 AAAACTAGATTCCATGCATAACCC 57.285 37.500 0.00 0.00 0.00 4.11
4977 5969 1.317613 TCCATGCATAACCCGATTGC 58.682 50.000 0.00 0.00 36.91 3.56
4978 5970 1.133823 TCCATGCATAACCCGATTGCT 60.134 47.619 0.00 0.00 37.28 3.91
4979 5971 1.682854 CCATGCATAACCCGATTGCTT 59.317 47.619 0.00 0.00 37.28 3.91
4980 5972 2.101249 CCATGCATAACCCGATTGCTTT 59.899 45.455 0.00 0.00 37.28 3.51
4981 5973 3.430651 CCATGCATAACCCGATTGCTTTT 60.431 43.478 0.00 0.00 37.28 2.27
5083 6075 8.787852 AGAAAGTCTCAACTGTTCCAATTATTC 58.212 33.333 0.00 0.00 35.36 1.75
5138 7248 7.632721 CAACACTTGGATTGGAAAAATGAAAG 58.367 34.615 0.00 0.00 0.00 2.62
5178 7288 5.579047 TGTCCATGATAGTTGTTCCCATTT 58.421 37.500 0.00 0.00 0.00 2.32
5179 7289 6.726379 TGTCCATGATAGTTGTTCCCATTTA 58.274 36.000 0.00 0.00 0.00 1.40
5184 7294 9.889128 CCATGATAGTTGTTCCCATTTATTTTT 57.111 29.630 0.00 0.00 0.00 1.94
5231 7346 7.205992 GCATTATTTCCCAATTCTTCCTCTTC 58.794 38.462 0.00 0.00 0.00 2.87
5234 7349 2.546899 TCCCAATTCTTCCTCTTCGGA 58.453 47.619 0.00 0.00 41.06 4.55
5260 7375 5.894298 AGACCATCAAAGATAGCATACCA 57.106 39.130 0.00 0.00 0.00 3.25
5265 7380 6.835488 ACCATCAAAGATAGCATACCAAATGT 59.165 34.615 0.00 0.00 0.00 2.71
5310 7448 3.402110 TGACAGTACAAGAGCAACCATG 58.598 45.455 0.00 0.00 0.00 3.66
5324 7462 4.361451 CAACCATGCAAAGATGTACTCC 57.639 45.455 0.00 0.00 0.00 3.85
5325 7463 3.004752 ACCATGCAAAGATGTACTCCC 57.995 47.619 0.00 0.00 0.00 4.30
5326 7464 2.578021 ACCATGCAAAGATGTACTCCCT 59.422 45.455 0.00 0.00 0.00 4.20
5327 7465 3.209410 CCATGCAAAGATGTACTCCCTC 58.791 50.000 0.00 0.00 0.00 4.30
5328 7466 3.209410 CATGCAAAGATGTACTCCCTCC 58.791 50.000 0.00 0.00 0.00 4.30
5329 7467 1.207089 TGCAAAGATGTACTCCCTCCG 59.793 52.381 0.00 0.00 0.00 4.63
5330 7468 1.207329 GCAAAGATGTACTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
5331 7469 2.354805 GCAAAGATGTACTCCCTCCGTT 60.355 50.000 0.00 0.00 0.00 4.44
5332 7470 3.868754 GCAAAGATGTACTCCCTCCGTTT 60.869 47.826 0.00 0.00 0.00 3.60
5333 7471 3.889520 AAGATGTACTCCCTCCGTTTC 57.110 47.619 0.00 0.00 0.00 2.78
5334 7472 3.103080 AGATGTACTCCCTCCGTTTCT 57.897 47.619 0.00 0.00 0.00 2.52
5335 7473 4.246712 AGATGTACTCCCTCCGTTTCTA 57.753 45.455 0.00 0.00 0.00 2.10
5336 7474 4.607239 AGATGTACTCCCTCCGTTTCTAA 58.393 43.478 0.00 0.00 0.00 2.10
5337 7475 5.021458 AGATGTACTCCCTCCGTTTCTAAA 58.979 41.667 0.00 0.00 0.00 1.85
5338 7476 5.661759 AGATGTACTCCCTCCGTTTCTAAAT 59.338 40.000 0.00 0.00 0.00 1.40
5339 7477 6.837568 AGATGTACTCCCTCCGTTTCTAAATA 59.162 38.462 0.00 0.00 0.00 1.40
5340 7478 7.509659 AGATGTACTCCCTCCGTTTCTAAATAT 59.490 37.037 0.00 0.00 0.00 1.28
5341 7479 8.716674 ATGTACTCCCTCCGTTTCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
5342 7480 8.537728 TGTACTCCCTCCGTTTCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
5343 7481 8.636213 TGTACTCCCTCCGTTTCTAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
5344 7482 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
5345 7483 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
5346 7484 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
5347 7485 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
5348 7486 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
5349 7487 9.043079 CCCTCCGTTTCTAAATATAAGTCTTTC 57.957 37.037 0.00 0.00 0.00 2.62
5350 7488 9.819267 CCTCCGTTTCTAAATATAAGTCTTTCT 57.181 33.333 0.00 0.00 0.00 2.52
5387 7525 6.834168 AATGGACTACATTCGGAACAAAAT 57.166 33.333 0.00 0.00 46.67 1.82
5388 7526 5.621197 TGGACTACATTCGGAACAAAATG 57.379 39.130 0.00 0.00 37.23 2.32
5389 7527 5.309638 TGGACTACATTCGGAACAAAATGA 58.690 37.500 0.00 0.00 35.51 2.57
5390 7528 5.765677 TGGACTACATTCGGAACAAAATGAA 59.234 36.000 0.00 0.00 35.51 2.57
5391 7529 6.432783 TGGACTACATTCGGAACAAAATGAAT 59.567 34.615 0.00 0.00 35.51 2.57
5392 7530 6.747280 GGACTACATTCGGAACAAAATGAATG 59.253 38.462 11.13 11.13 35.51 2.67
5393 7531 7.361713 GGACTACATTCGGAACAAAATGAATGA 60.362 37.037 17.70 4.17 35.51 2.57
5394 7532 7.881142 ACTACATTCGGAACAAAATGAATGAA 58.119 30.769 17.70 0.00 35.51 2.57
5395 7533 8.522830 ACTACATTCGGAACAAAATGAATGAAT 58.477 29.630 17.70 2.53 35.51 2.57
5396 7534 7.816945 ACATTCGGAACAAAATGAATGAATC 57.183 32.000 17.70 0.00 35.51 2.52
5397 7535 7.605449 ACATTCGGAACAAAATGAATGAATCT 58.395 30.769 17.70 0.00 35.51 2.40
5398 7536 8.739039 ACATTCGGAACAAAATGAATGAATCTA 58.261 29.630 17.70 0.00 35.51 1.98
5399 7537 9.013490 CATTCGGAACAAAATGAATGAATCTAC 57.987 33.333 7.79 0.00 34.34 2.59
5400 7538 7.680442 TCGGAACAAAATGAATGAATCTACA 57.320 32.000 0.00 0.00 0.00 2.74
5401 7539 7.526608 TCGGAACAAAATGAATGAATCTACAC 58.473 34.615 0.00 0.00 0.00 2.90
5402 7540 7.390440 TCGGAACAAAATGAATGAATCTACACT 59.610 33.333 0.00 0.00 0.00 3.55
5403 7541 8.023128 CGGAACAAAATGAATGAATCTACACTT 58.977 33.333 0.00 0.00 0.00 3.16
5426 7564 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
5431 7569 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
5432 7570 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
5433 7571 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
5434 7572 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
5435 7573 7.435488 GCATCTATATACATCCGTATGTGGTTC 59.565 40.741 3.56 0.00 45.99 3.62
5436 7574 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
5437 7575 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
5438 7576 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
5441 7579 7.905604 ATACATCCGTATGTGGTTCATAATG 57.094 36.000 3.56 0.00 45.99 1.90
5442 7580 5.063204 ACATCCGTATGTGGTTCATAATGG 58.937 41.667 0.00 0.00 44.79 3.16
5443 7581 5.163248 ACATCCGTATGTGGTTCATAATGGA 60.163 40.000 0.00 10.37 44.79 3.41
5444 7582 5.360649 TCCGTATGTGGTTCATAATGGAA 57.639 39.130 7.27 0.00 40.10 3.53
5445 7583 5.935945 TCCGTATGTGGTTCATAATGGAAT 58.064 37.500 7.27 0.00 40.10 3.01
5446 7584 5.995282 TCCGTATGTGGTTCATAATGGAATC 59.005 40.000 7.27 0.00 40.10 2.52
5447 7585 5.997746 CCGTATGTGGTTCATAATGGAATCT 59.002 40.000 0.00 0.00 40.21 2.40
5448 7586 6.147821 CCGTATGTGGTTCATAATGGAATCTC 59.852 42.308 0.00 0.00 40.21 2.75
5449 7587 6.931281 CGTATGTGGTTCATAATGGAATCTCT 59.069 38.462 0.00 0.00 40.21 3.10
5450 7588 8.088365 CGTATGTGGTTCATAATGGAATCTCTA 58.912 37.037 0.00 0.00 40.21 2.43
5451 7589 9.209175 GTATGTGGTTCATAATGGAATCTCTAC 57.791 37.037 0.00 0.00 40.21 2.59
5452 7590 7.194112 TGTGGTTCATAATGGAATCTCTACA 57.806 36.000 0.00 0.00 0.00 2.74
5453 7591 7.629157 TGTGGTTCATAATGGAATCTCTACAA 58.371 34.615 0.00 0.00 0.00 2.41
5454 7592 8.106462 TGTGGTTCATAATGGAATCTCTACAAA 58.894 33.333 0.00 0.00 0.00 2.83
5455 7593 8.616076 GTGGTTCATAATGGAATCTCTACAAAG 58.384 37.037 0.00 0.00 0.00 2.77
5456 7594 8.548025 TGGTTCATAATGGAATCTCTACAAAGA 58.452 33.333 0.00 0.00 0.00 2.52
5457 7595 8.831550 GGTTCATAATGGAATCTCTACAAAGAC 58.168 37.037 0.00 0.00 0.00 3.01
5458 7596 9.606631 GTTCATAATGGAATCTCTACAAAGACT 57.393 33.333 0.00 0.00 0.00 3.24
5480 7618 9.453830 AGACTTATATTTAGAAATGGAGGGAGT 57.546 33.333 0.00 0.00 0.00 3.85
5527 7665 9.287373 ACAACATGCATTCTTTTCCAAATAAAT 57.713 25.926 0.00 0.00 0.00 1.40
5561 7699 7.591795 GTGAAGTACCATGAGAACATACGATAG 59.408 40.741 0.00 0.00 36.97 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.756642 CACTTATCAGTCAAGCTTTCACCA 59.243 41.667 0.00 0.00 0.00 4.17
127 147 6.211986 ACAATGTTTCCAAAGGATCATGACAT 59.788 34.615 0.00 0.00 31.17 3.06
181 202 4.001652 ACTCACACTGATCATTGCTTCAG 58.998 43.478 12.62 12.28 43.97 3.02
225 251 1.212688 CATTAGGGACTCACATGGCCA 59.787 52.381 8.56 8.56 41.75 5.36
263 289 5.293324 TCGTTAGTCCAACATAATCACATGC 59.707 40.000 0.00 0.00 36.92 4.06
305 331 5.954752 TGACCCATTGGACTAAATATTTGCA 59.045 36.000 11.05 0.00 34.81 4.08
309 335 5.705400 CCCTGACCCATTGGACTAAATATT 58.295 41.667 3.62 0.00 34.81 1.28
338 364 5.942872 AGAAAATTGGACTAACAAGCGATG 58.057 37.500 0.00 0.00 33.23 3.84
342 368 8.648557 AAAGAAAGAAAATTGGACTAACAAGC 57.351 30.769 0.00 0.00 33.23 4.01
454 482 4.519213 TGGAAGAACCGAAAGACAAAGAA 58.481 39.130 0.00 0.00 42.61 2.52
500 528 9.559958 AGCGAAAAATGTTGTATAGATGAAAAG 57.440 29.630 0.00 0.00 0.00 2.27
502 530 8.726068 TGAGCGAAAAATGTTGTATAGATGAAA 58.274 29.630 0.00 0.00 0.00 2.69
503 531 8.262715 TGAGCGAAAAATGTTGTATAGATGAA 57.737 30.769 0.00 0.00 0.00 2.57
504 532 7.841915 TGAGCGAAAAATGTTGTATAGATGA 57.158 32.000 0.00 0.00 0.00 2.92
505 533 8.337532 TCATGAGCGAAAAATGTTGTATAGATG 58.662 33.333 0.00 0.00 0.00 2.90
506 534 8.437360 TCATGAGCGAAAAATGTTGTATAGAT 57.563 30.769 0.00 0.00 0.00 1.98
507 535 7.841915 TCATGAGCGAAAAATGTTGTATAGA 57.158 32.000 0.00 0.00 0.00 1.98
508 536 7.962373 TGTTCATGAGCGAAAAATGTTGTATAG 59.038 33.333 5.02 0.00 0.00 1.31
510 538 6.582295 GTGTTCATGAGCGAAAAATGTTGTAT 59.418 34.615 5.02 0.00 0.00 2.29
513 703 4.977963 AGTGTTCATGAGCGAAAAATGTTG 59.022 37.500 5.02 0.00 0.00 3.33
516 706 5.455392 AGAAGTGTTCATGAGCGAAAAATG 58.545 37.500 5.02 0.00 0.00 2.32
630 821 8.272866 AGTTTAAATACTGAAAAATGTTTGCGC 58.727 29.630 0.00 0.00 0.00 6.09
768 959 7.978975 CCCGAACACCACAATATTCATATTTTT 59.021 33.333 0.00 0.00 30.91 1.94
769 960 7.488322 CCCGAACACCACAATATTCATATTTT 58.512 34.615 0.00 0.00 30.91 1.82
770 961 6.460953 GCCCGAACACCACAATATTCATATTT 60.461 38.462 0.00 0.00 30.91 1.40
771 962 5.009610 GCCCGAACACCACAATATTCATATT 59.990 40.000 0.00 0.00 33.44 1.28
772 963 4.518970 GCCCGAACACCACAATATTCATAT 59.481 41.667 0.00 0.00 0.00 1.78
773 964 3.880490 GCCCGAACACCACAATATTCATA 59.120 43.478 0.00 0.00 0.00 2.15
774 965 2.687935 GCCCGAACACCACAATATTCAT 59.312 45.455 0.00 0.00 0.00 2.57
775 966 2.088423 GCCCGAACACCACAATATTCA 58.912 47.619 0.00 0.00 0.00 2.57
776 967 1.404035 GGCCCGAACACCACAATATTC 59.596 52.381 0.00 0.00 0.00 1.75
777 968 1.470051 GGCCCGAACACCACAATATT 58.530 50.000 0.00 0.00 0.00 1.28
778 969 0.746563 CGGCCCGAACACCACAATAT 60.747 55.000 0.00 0.00 0.00 1.28
779 970 1.376166 CGGCCCGAACACCACAATA 60.376 57.895 0.00 0.00 0.00 1.90
818 1009 3.712907 TGCGGGTTAGCTGTCCCC 61.713 66.667 18.34 13.03 40.54 4.81
850 1065 1.206115 CGTTGTGTTTTTGAGCGGCC 61.206 55.000 0.00 0.00 0.00 6.13
901 1116 0.677288 TCTTTTCGACGGGAGCTTGA 59.323 50.000 0.00 0.00 0.00 3.02
902 1117 1.461127 CTTCTTTTCGACGGGAGCTTG 59.539 52.381 0.00 0.00 0.00 4.01
1103 1334 3.894547 TTGCGGAAGTCGAAGGGGC 62.895 63.158 0.00 0.00 42.43 5.80
1104 1335 1.741770 CTTGCGGAAGTCGAAGGGG 60.742 63.158 8.74 0.00 42.43 4.79
1105 1336 2.391389 GCTTGCGGAAGTCGAAGGG 61.391 63.158 18.40 0.00 42.43 3.95
1106 1337 1.355066 GAGCTTGCGGAAGTCGAAGG 61.355 60.000 18.40 0.00 42.43 3.46
1107 1338 0.667487 TGAGCTTGCGGAAGTCGAAG 60.667 55.000 18.40 0.00 42.43 3.79
1108 1339 0.944311 GTGAGCTTGCGGAAGTCGAA 60.944 55.000 18.40 0.00 42.43 3.71
1109 1340 1.372997 GTGAGCTTGCGGAAGTCGA 60.373 57.895 18.40 0.00 42.43 4.20
1110 1341 1.221466 TTGTGAGCTTGCGGAAGTCG 61.221 55.000 18.40 0.00 42.76 4.18
1111 1342 1.129437 GATTGTGAGCTTGCGGAAGTC 59.871 52.381 18.40 13.93 0.00 3.01
1112 1343 1.160137 GATTGTGAGCTTGCGGAAGT 58.840 50.000 18.40 5.04 0.00 3.01
1113 1344 1.396301 GAGATTGTGAGCTTGCGGAAG 59.604 52.381 12.94 12.94 0.00 3.46
1165 1411 3.707189 GGAGAAGGGGGAGGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
1167 1413 1.694525 GAAGGAGAAGGGGGAGGGG 60.695 68.421 0.00 0.00 0.00 4.79
1171 1417 2.687566 GCGGAAGGAGAAGGGGGA 60.688 66.667 0.00 0.00 0.00 4.81
1190 1436 1.294659 CCTGAGCTCAAACAGTCGGC 61.295 60.000 18.85 0.00 32.93 5.54
1196 1442 0.183492 AAGCCACCTGAGCTCAAACA 59.817 50.000 18.85 0.00 40.49 2.83
1254 1500 0.745845 CCTCCCTGCAGATTCCAACG 60.746 60.000 17.39 0.00 0.00 4.10
1374 1620 2.128035 GAGAACTCGGTGAATATGGCG 58.872 52.381 0.00 0.00 0.00 5.69
1455 1701 1.226575 GCCACGATCGATGACACGA 60.227 57.895 24.34 0.00 46.04 4.35
1548 1795 0.246635 ACCGACCAGAAGTGAATCCG 59.753 55.000 0.00 0.00 0.00 4.18
1570 1817 0.250467 TCTGCTCTCCCTGCAACAAC 60.250 55.000 0.00 0.00 40.13 3.32
1571 1818 0.035881 CTCTGCTCTCCCTGCAACAA 59.964 55.000 0.00 0.00 40.13 2.83
1572 1819 1.675801 CTCTGCTCTCCCTGCAACA 59.324 57.895 0.00 0.00 40.13 3.33
1573 1820 1.744741 GCTCTGCTCTCCCTGCAAC 60.745 63.158 0.00 0.00 40.13 4.17
1574 1821 2.667418 GCTCTGCTCTCCCTGCAA 59.333 61.111 0.00 0.00 40.13 4.08
1575 1822 3.397439 GGCTCTGCTCTCCCTGCA 61.397 66.667 0.00 0.00 38.81 4.41
1622 1875 2.440980 GCCCAGACATGCTTCCCC 60.441 66.667 0.00 0.00 0.00 4.81
1751 2009 8.303780 TCCTGAGAGATACATCCATATCATTC 57.696 38.462 0.00 0.00 34.50 2.67
1915 2232 0.452784 GCGACACGACAAATTGGAGC 60.453 55.000 0.00 0.00 0.00 4.70
1921 2238 3.761657 TCGTTATAGCGACACGACAAAT 58.238 40.909 7.66 0.00 38.00 2.32
1927 2244 3.048942 ACTTCTCGTTATAGCGACACG 57.951 47.619 7.66 0.00 36.80 4.49
1940 2257 7.295952 AGTCATACAAATTTGCTACTTCTCG 57.704 36.000 18.12 0.00 0.00 4.04
2197 2526 5.412594 TGAGAGCAACAAGATGATTGGTAAC 59.587 40.000 0.00 0.00 36.70 2.50
2201 2530 4.882427 AGATGAGAGCAACAAGATGATTGG 59.118 41.667 0.00 0.00 0.00 3.16
2247 2576 6.103997 GGATCGATAACCTACACACAAAAGA 58.896 40.000 0.00 0.00 0.00 2.52
2248 2577 5.872617 TGGATCGATAACCTACACACAAAAG 59.127 40.000 0.00 0.00 0.00 2.27
2318 2647 4.929808 ACAGACATCACCATTCGAGTTAAC 59.070 41.667 0.00 0.00 0.00 2.01
2428 2757 5.463061 CACCTTGGTCTTTATTTTGCTTGTG 59.537 40.000 0.00 0.00 0.00 3.33
2721 3095 1.091771 CACGGGGACATGACTGATGC 61.092 60.000 0.00 0.00 35.15 3.91
2752 3126 1.369692 CCGGCGTATCCCTGCATTA 59.630 57.895 6.01 0.00 0.00 1.90
2756 3130 3.234630 TATGCCGGCGTATCCCTGC 62.235 63.158 24.54 0.00 0.00 4.85
2801 3196 4.774124 ACGCCTAGGACTTTTTATAACCC 58.226 43.478 14.75 0.00 0.00 4.11
2815 3210 5.390613 CAAAAGACACAATTAACGCCTAGG 58.609 41.667 3.67 3.67 0.00 3.02
2833 3228 2.031120 TGGTCAGAAAGGTGGCAAAAG 58.969 47.619 0.00 0.00 0.00 2.27
3059 3734 1.560866 CCCTGCCCAGAGCTTCTTCT 61.561 60.000 0.00 0.00 44.23 2.85
3099 3775 2.079925 GCTTGAATCTTCTTCGCTGGT 58.920 47.619 0.00 0.00 0.00 4.00
3169 3845 2.171489 GAGAAAACGACTGCACCGCC 62.171 60.000 3.89 0.00 0.00 6.13
3231 3908 3.053395 CCTCCATCCTTTCCCATTCTCAA 60.053 47.826 0.00 0.00 0.00 3.02
3328 4007 7.650890 TGAGTACTAAAGATACGTTGTGACAA 58.349 34.615 0.00 0.00 0.00 3.18
3332 4011 8.516811 AAGTTGAGTACTAAAGATACGTTGTG 57.483 34.615 0.00 0.00 35.54 3.33
3451 4157 6.571344 CGCTAAGAGGCACAGATACAGATAAT 60.571 42.308 0.00 0.00 0.00 1.28
3452 4158 5.278512 CGCTAAGAGGCACAGATACAGATAA 60.279 44.000 0.00 0.00 0.00 1.75
3453 4159 4.216472 CGCTAAGAGGCACAGATACAGATA 59.784 45.833 0.00 0.00 0.00 1.98
3454 4160 3.005261 CGCTAAGAGGCACAGATACAGAT 59.995 47.826 0.00 0.00 0.00 2.90
3455 4161 2.359214 CGCTAAGAGGCACAGATACAGA 59.641 50.000 0.00 0.00 0.00 3.41
3456 4162 2.099921 ACGCTAAGAGGCACAGATACAG 59.900 50.000 0.00 0.00 0.00 2.74
3457 4163 2.100197 ACGCTAAGAGGCACAGATACA 58.900 47.619 0.00 0.00 0.00 2.29
3458 4164 2.464865 CACGCTAAGAGGCACAGATAC 58.535 52.381 0.00 0.00 0.00 2.24
3468 4174 2.509336 CCACGGCCACGCTAAGAG 60.509 66.667 2.24 0.00 46.04 2.85
3497 4203 1.969589 GGTGTGTTAACCAGGGCCG 60.970 63.158 2.48 0.00 40.22 6.13
3598 4316 1.371635 GCCGTTGAACACACATGCC 60.372 57.895 0.00 0.00 0.00 4.40
3725 4447 5.056894 AGTGTACTTATCGACCTGAACAC 57.943 43.478 11.98 11.98 36.98 3.32
3820 4542 2.251409 TGCATGCTCTCCTTCATAGC 57.749 50.000 20.33 0.00 36.77 2.97
3836 4558 3.591196 GGTTTTCCATTGCACTATGCA 57.409 42.857 0.00 0.00 45.53 3.96
3881 4603 5.129980 TCATCACCTTCACTTATCTGCTGAT 59.870 40.000 11.14 11.14 36.74 2.90
4001 4723 0.526524 GCAGCACTCCAGTAGCTACG 60.527 60.000 17.99 12.54 36.73 3.51
4042 4764 7.798982 GGCAAAACTTATATCAAGCGACTATTC 59.201 37.037 0.00 0.00 0.00 1.75
4049 4771 4.798387 GGTTGGCAAAACTTATATCAAGCG 59.202 41.667 0.00 0.00 0.00 4.68
4083 4806 4.564406 GGAGTATGGATCCCTACATTGCAG 60.564 50.000 24.08 0.00 0.00 4.41
4202 4931 9.197306 TCATTATAGGTAGTAAGCACTCAGAAA 57.803 33.333 0.00 0.00 36.14 2.52
4203 4932 8.762481 TCATTATAGGTAGTAAGCACTCAGAA 57.238 34.615 0.00 0.00 36.14 3.02
4250 4979 6.538263 AGGACTAGAATTGAAAACTGAAGCT 58.462 36.000 0.00 0.00 0.00 3.74
4295 5024 7.940850 ACACATGTTTCAGCACTTTTACTATT 58.059 30.769 0.00 0.00 0.00 1.73
4296 5025 7.510549 ACACATGTTTCAGCACTTTTACTAT 57.489 32.000 0.00 0.00 0.00 2.12
4329 5065 1.339055 ACTCAGCCGAAGCATGCTTAA 60.339 47.619 32.02 12.68 43.56 1.85
4366 5102 8.311836 TCGTTCTTGTCCAGTTAAGAGATATTT 58.688 33.333 0.00 0.00 34.68 1.40
4367 5103 7.837863 TCGTTCTTGTCCAGTTAAGAGATATT 58.162 34.615 0.00 0.00 34.68 1.28
4368 5104 7.406031 TCGTTCTTGTCCAGTTAAGAGATAT 57.594 36.000 0.00 0.00 34.68 1.63
4369 5105 6.829229 TCGTTCTTGTCCAGTTAAGAGATA 57.171 37.500 0.00 0.00 34.68 1.98
4370 5106 5.723672 TCGTTCTTGTCCAGTTAAGAGAT 57.276 39.130 0.00 0.00 34.68 2.75
4479 5452 2.421424 GCTCGACATCCTCATGCTTTTT 59.579 45.455 0.00 0.00 32.57 1.94
4495 5468 2.542020 TTCAATCAACACTGGCTCGA 57.458 45.000 0.00 0.00 0.00 4.04
4503 5476 6.825721 ACCTCTGGATTAGATTCAATCAACAC 59.174 38.462 0.00 0.00 36.77 3.32
4510 5483 7.391554 CACTTTTCACCTCTGGATTAGATTCAA 59.608 37.037 0.00 0.00 34.21 2.69
4673 5648 6.349280 GCAACCATCATGCAGTTAAGACTTTA 60.349 38.462 0.00 0.00 43.29 1.85
4674 5649 5.565439 GCAACCATCATGCAGTTAAGACTTT 60.565 40.000 0.00 0.00 43.29 2.66
4676 5651 3.441572 GCAACCATCATGCAGTTAAGACT 59.558 43.478 0.00 0.00 43.29 3.24
4761 5745 8.040716 AGCACTATTACTCGTTGCTTAAAATT 57.959 30.769 0.00 0.00 0.00 1.82
4790 5782 6.883217 ACTATAGGAATGATGGCATAGCAAAG 59.117 38.462 0.00 0.00 33.44 2.77
4830 5822 1.730772 CGAAGAGAAGACAGCACGAGG 60.731 57.143 0.00 0.00 0.00 4.63
4831 5823 1.068885 ACGAAGAGAAGACAGCACGAG 60.069 52.381 0.00 0.00 0.00 4.18
4850 5842 3.251004 ACGCAGGACAAGAAAAAGATGAC 59.749 43.478 0.00 0.00 0.00 3.06
4867 5859 0.031178 AAGCCAAGCAAGAAACGCAG 59.969 50.000 0.00 0.00 0.00 5.18
4900 5892 5.163457 GGATCCAAAACTCAGTTGACCAAAA 60.163 40.000 6.95 0.00 0.00 2.44
4907 5899 4.916983 TTGTGGATCCAAAACTCAGTTG 57.083 40.909 18.20 0.00 0.00 3.16
4955 5947 3.612479 GCAATCGGGTTATGCATGGAATC 60.612 47.826 10.16 0.00 39.81 2.52
5013 6005 4.722279 TGGGACCCAAAATGTTAAAACCTT 59.278 37.500 12.05 0.00 0.00 3.50
5015 6007 4.691326 TGGGACCCAAAATGTTAAAACC 57.309 40.909 12.05 0.00 0.00 3.27
5034 6026 7.476667 TCTACAATACGGTTATGCAATTTTGG 58.523 34.615 0.00 0.00 0.00 3.28
5044 6036 8.529476 AGTTGAGACTTTCTACAATACGGTTAT 58.471 33.333 0.00 0.00 34.50 1.89
5083 6075 2.817258 TGGCTTCCCTATGTTTTCAACG 59.183 45.455 0.00 0.00 0.00 4.10
5186 7296 4.415596 TGCCAGAGTCCCATTGTATTTTT 58.584 39.130 0.00 0.00 0.00 1.94
5231 7346 4.509600 GCTATCTTTGATGGTCTTCTTCCG 59.490 45.833 0.00 0.00 0.00 4.30
5234 7349 6.995091 GGTATGCTATCTTTGATGGTCTTCTT 59.005 38.462 0.00 0.00 0.00 2.52
5265 7380 9.958180 TCATCATGATTTTCTACTAAACAGGAA 57.042 29.630 5.16 0.00 0.00 3.36
5310 7448 1.207329 ACGGAGGGAGTACATCTTTGC 59.793 52.381 0.00 0.00 0.00 3.68
5321 7459 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
5322 7460 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
5323 7461 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
5324 7462 9.819267 AGAAAGACTTATATTTAGAAACGGAGG 57.181 33.333 0.00 0.00 0.00 4.30
5352 7490 9.869844 CGAATGTAGTCCATTTAATGAAATCTC 57.130 33.333 6.50 0.00 43.87 2.75
5353 7491 8.840321 CCGAATGTAGTCCATTTAATGAAATCT 58.160 33.333 6.50 2.31 43.87 2.40
5354 7492 8.836413 TCCGAATGTAGTCCATTTAATGAAATC 58.164 33.333 6.50 0.00 43.87 2.17
5355 7493 8.746052 TCCGAATGTAGTCCATTTAATGAAAT 57.254 30.769 6.50 0.00 43.87 2.17
5356 7494 8.455682 GTTCCGAATGTAGTCCATTTAATGAAA 58.544 33.333 6.50 0.00 43.87 2.69
5357 7495 7.608376 TGTTCCGAATGTAGTCCATTTAATGAA 59.392 33.333 6.50 0.00 43.87 2.57
5358 7496 7.106890 TGTTCCGAATGTAGTCCATTTAATGA 58.893 34.615 6.50 0.00 43.87 2.57
5359 7497 7.315247 TGTTCCGAATGTAGTCCATTTAATG 57.685 36.000 0.00 0.00 43.87 1.90
5360 7498 7.931578 TTGTTCCGAATGTAGTCCATTTAAT 57.068 32.000 0.00 0.00 43.87 1.40
5361 7499 7.747155 TTTGTTCCGAATGTAGTCCATTTAA 57.253 32.000 0.00 0.00 43.87 1.52
5362 7500 7.747155 TTTTGTTCCGAATGTAGTCCATTTA 57.253 32.000 0.00 0.00 43.87 1.40
5363 7501 6.642707 TTTTGTTCCGAATGTAGTCCATTT 57.357 33.333 0.00 0.00 43.87 2.32
5364 7502 6.432783 TCATTTTGTTCCGAATGTAGTCCATT 59.567 34.615 0.00 0.00 46.51 3.16
5365 7503 5.943416 TCATTTTGTTCCGAATGTAGTCCAT 59.057 36.000 0.00 0.00 35.35 3.41
5366 7504 5.309638 TCATTTTGTTCCGAATGTAGTCCA 58.690 37.500 0.00 0.00 35.35 4.02
5367 7505 5.873179 TCATTTTGTTCCGAATGTAGTCC 57.127 39.130 0.00 0.00 35.35 3.85
5368 7506 7.526608 TCATTCATTTTGTTCCGAATGTAGTC 58.473 34.615 9.94 0.00 43.29 2.59
5369 7507 7.447374 TCATTCATTTTGTTCCGAATGTAGT 57.553 32.000 9.94 0.00 43.29 2.73
5370 7508 8.915871 ATTCATTCATTTTGTTCCGAATGTAG 57.084 30.769 9.94 0.00 43.29 2.74
5371 7509 8.739039 AGATTCATTCATTTTGTTCCGAATGTA 58.261 29.630 9.94 2.69 43.29 2.29
5372 7510 7.605449 AGATTCATTCATTTTGTTCCGAATGT 58.395 30.769 9.94 0.00 43.29 2.71
5373 7511 9.013490 GTAGATTCATTCATTTTGTTCCGAATG 57.987 33.333 0.00 0.00 43.87 2.67
5374 7512 8.739039 TGTAGATTCATTCATTTTGTTCCGAAT 58.261 29.630 0.00 0.00 0.00 3.34
5375 7513 8.020819 GTGTAGATTCATTCATTTTGTTCCGAA 58.979 33.333 0.00 0.00 0.00 4.30
5376 7514 7.390440 AGTGTAGATTCATTCATTTTGTTCCGA 59.610 33.333 0.00 0.00 0.00 4.55
5377 7515 7.530010 AGTGTAGATTCATTCATTTTGTTCCG 58.470 34.615 0.00 0.00 0.00 4.30
5400 7538 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
5404 7542 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
5405 7543 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
5406 7544 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
5407 7545 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
5408 7546 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
5409 7547 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
5410 7548 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
5411 7549 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
5412 7550 8.589701 ATGAACCACATACGGATGTATATAGA 57.410 34.615 14.23 0.00 44.82 1.98
5415 7553 9.599866 CATTATGAACCACATACGGATGTATAT 57.400 33.333 14.23 1.68 44.82 0.86
5416 7554 8.038351 CCATTATGAACCACATACGGATGTATA 58.962 37.037 14.23 4.47 44.82 1.47
5417 7555 6.878923 CCATTATGAACCACATACGGATGTAT 59.121 38.462 14.23 5.54 44.82 2.29
5418 7556 6.042208 TCCATTATGAACCACATACGGATGTA 59.958 38.462 14.23 0.00 44.82 2.29
5420 7558 5.304778 TCCATTATGAACCACATACGGATG 58.695 41.667 5.94 5.94 40.62 3.51
5421 7559 5.560722 TCCATTATGAACCACATACGGAT 57.439 39.130 0.00 0.00 40.62 4.18
5422 7560 5.360649 TTCCATTATGAACCACATACGGA 57.639 39.130 0.00 0.00 40.62 4.69
5423 7561 5.997746 AGATTCCATTATGAACCACATACGG 59.002 40.000 0.00 0.00 40.62 4.02
5424 7562 6.931281 AGAGATTCCATTATGAACCACATACG 59.069 38.462 0.00 0.00 40.62 3.06
5425 7563 9.209175 GTAGAGATTCCATTATGAACCACATAC 57.791 37.037 0.00 0.00 40.62 2.39
5426 7564 8.933653 TGTAGAGATTCCATTATGAACCACATA 58.066 33.333 0.00 0.00 40.07 2.29
5427 7565 7.805163 TGTAGAGATTCCATTATGAACCACAT 58.195 34.615 0.00 0.00 42.39 3.21
5428 7566 7.194112 TGTAGAGATTCCATTATGAACCACA 57.806 36.000 0.00 0.00 0.00 4.17
5429 7567 8.506168 TTTGTAGAGATTCCATTATGAACCAC 57.494 34.615 0.00 0.00 0.00 4.16
5430 7568 8.548025 TCTTTGTAGAGATTCCATTATGAACCA 58.452 33.333 0.00 0.00 0.00 3.67
5431 7569 8.831550 GTCTTTGTAGAGATTCCATTATGAACC 58.168 37.037 0.00 0.00 0.00 3.62
5432 7570 9.606631 AGTCTTTGTAGAGATTCCATTATGAAC 57.393 33.333 0.00 0.00 0.00 3.18
5454 7592 9.453830 ACTCCCTCCATTTCTAAATATAAGTCT 57.546 33.333 0.00 0.00 0.00 3.24
5466 7604 9.942526 AAATTAATCATTACTCCCTCCATTTCT 57.057 29.630 0.00 0.00 0.00 2.52
5527 7665 7.284261 TGTTCTCATGGTACTTCACATTTTCAA 59.716 33.333 0.00 0.00 0.00 2.69
5609 7747 5.049336 CCGAGGGAGTATATGCTATCGTATG 60.049 48.000 16.02 3.87 30.51 2.39
5611 7749 4.080695 ACCGAGGGAGTATATGCTATCGTA 60.081 45.833 16.02 0.00 30.51 3.43
5612 7750 3.280295 CCGAGGGAGTATATGCTATCGT 58.720 50.000 16.02 5.60 30.51 3.73
5613 7751 3.280295 ACCGAGGGAGTATATGCTATCG 58.720 50.000 12.58 12.58 0.00 2.92


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

AutoCloner maintained by Alex Coulton.