Multiple sequence alignment - TraesCS6D01G354800

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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 TraesCS6D01G354800 chr6D 100.000 2321 0 0 1 2321 450079917 450082237 0.000000e+00 4287.0
1 TraesCS6D01G354800 chr6B 88.060 603 54 7 1540 2138 682537880 682538468 0.000000e+00 699.0
2 TraesCS6D01G354800 chr6B 85.205 730 44 19 838 1509 682537002 682537725 0.000000e+00 691.0
3 TraesCS6D01G354800 chr6B 92.068 353 16 4 480 820 682536598 682536950 9.640000e-134 486.0
4 TraesCS6D01G354800 chr6B 93.333 255 17 0 36 290 682533504 682533758 6.050000e-101 377.0
5 TraesCS6D01G354800 chr6B 91.150 113 4 3 2132 2238 682538879 682538991 5.170000e-32 148.0
6 TraesCS6D01G354800 chr6B 100.000 34 0 0 5 38 682520640 682520673 1.930000e-06 63.9
7 TraesCS6D01G354800 chr6A 91.613 465 36 1 1 462 595562547 595563011 6.990000e-180 640.0
8 TraesCS6D01G354800 chr6A 94.461 343 13 2 489 825 595563112 595563454 7.350000e-145 523.0
9 TraesCS6D01G354800 chr6A 82.466 519 55 15 838 1327 595563504 595564015 2.760000e-114 422.0
10 TraesCS6D01G354800 chr6A 79.782 643 64 36 707 1321 595578476 595579080 7.720000e-110 407.0
11 TraesCS6D01G354800 chr3B 83.226 155 24 2 299 453 602283137 602283289 8.650000e-30 141.0
12 TraesCS6D01G354800 chr1D 79.592 147 28 2 308 453 391256029 391255884 1.130000e-18 104.0
13 TraesCS6D01G354800 chr7B 83.505 97 16 0 282 378 156687252 156687348 8.830000e-15 91.6


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 TraesCS6D01G354800 chr6D 450079917 450082237 2320 False 4287.000000 4287 100.000000 1 2321 1 chr6D.!!$F1 2320
1 TraesCS6D01G354800 chr6B 682533504 682538991 5487 False 480.200000 699 89.963200 36 2238 5 chr6B.!!$F2 2202
2 TraesCS6D01G354800 chr6A 595562547 595564015 1468 False 528.333333 640 89.513333 1 1327 3 chr6A.!!$F2 1326
3 TraesCS6D01G354800 chr6A 595578476 595579080 604 False 407.000000 407 79.782000 707 1321 1 chr6A.!!$F1 614

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
424 2964 0.179234 TGTGCGTTCAGTGGGAGAAA 59.821 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 4569 0.608582 AGAGGGTACTGACGCGTTCT 60.609 55.0 15.53 6.6 43.15 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.860930 ATCGCCTGCCCCGTTTTGT 62.861 57.895 0.00 0.00 0.00 2.83
82 83 4.860022 CCCACCTTCCATTGAGATAAACT 58.140 43.478 0.00 0.00 0.00 2.66
183 184 0.976641 AAGATGAAGAGGGCGTGTCA 59.023 50.000 0.00 0.00 0.00 3.58
306 2845 4.083802 GCGAACCAACCTATGATTAGATGC 60.084 45.833 0.00 0.00 0.00 3.91
316 2855 6.439058 ACCTATGATTAGATGCTTAGGAGGAC 59.561 42.308 0.00 0.00 36.16 3.85
329 2868 1.646447 AGGAGGACAGTGGTATCTCCA 59.354 52.381 18.73 0.00 44.02 3.86
371 2910 2.867624 ACACTTGACATTGGTGCTCAT 58.132 42.857 0.00 0.00 34.70 2.90
378 2918 7.062605 CACTTGACATTGGTGCTCATATTTTTC 59.937 37.037 0.00 0.00 0.00 2.29
400 2940 8.704849 TTTCTGAATTAATTCCAGGTCTTTCA 57.295 30.769 22.42 3.65 35.97 2.69
424 2964 0.179234 TGTGCGTTCAGTGGGAGAAA 59.821 50.000 0.00 0.00 0.00 2.52
426 2966 1.880027 GTGCGTTCAGTGGGAGAAAAT 59.120 47.619 0.00 0.00 0.00 1.82
462 3002 0.940126 AAGACGTCTGCAGCAACTTG 59.060 50.000 20.85 0.00 0.00 3.16
463 3003 1.082496 GACGTCTGCAGCAACTTGC 60.082 57.895 9.47 5.55 45.46 4.01
464 3004 2.253452 CGTCTGCAGCAACTTGCC 59.747 61.111 9.47 0.00 46.52 4.52
466 3006 2.979676 TCTGCAGCAACTTGCCCG 60.980 61.111 9.47 3.45 46.52 6.13
467 3007 4.047059 CTGCAGCAACTTGCCCGG 62.047 66.667 10.25 0.00 46.52 5.73
469 3009 2.671619 GCAGCAACTTGCCCGGTA 60.672 61.111 10.25 0.00 46.52 4.02
470 3010 2.690778 GCAGCAACTTGCCCGGTAG 61.691 63.158 10.25 0.00 46.52 3.18
471 3011 1.003839 CAGCAACTTGCCCGGTAGA 60.004 57.895 10.25 0.00 46.52 2.59
474 3014 0.240145 GCAACTTGCCCGGTAGAAAC 59.760 55.000 0.00 0.00 37.42 2.78
475 3015 0.879090 CAACTTGCCCGGTAGAAACC 59.121 55.000 0.00 0.00 42.95 3.27
504 3162 1.606668 GATGAAAACCACGGTTGAGCA 59.393 47.619 1.35 2.01 38.47 4.26
631 3295 3.071457 TGATCAGAGAGCTTCACCAAACA 59.929 43.478 0.00 0.00 0.00 2.83
669 3333 5.600908 TTATATTCCCTTAATTCGCGTGC 57.399 39.130 5.77 0.00 0.00 5.34
697 3361 2.971997 GCAAGCACATGCATGGATG 58.028 52.632 29.41 24.00 45.70 3.51
783 3447 4.692475 CGACCCGACAACCCCACC 62.692 72.222 0.00 0.00 0.00 4.61
804 3471 5.625311 CACCAATTAAGAAAACAAGAGACGC 59.375 40.000 0.00 0.00 0.00 5.19
821 3491 2.795297 CGAGAGGACAGAGGTCGC 59.205 66.667 0.00 0.00 45.28 5.19
825 3495 1.079750 GAGGACAGAGGTCGCAACC 60.080 63.158 0.00 0.00 45.28 3.77
852 3560 3.484547 GGTTCCGCCGCACGTTAG 61.485 66.667 0.00 0.00 41.42 2.34
866 3574 3.727258 TTAGCCCGCCACTGCCAT 61.727 61.111 0.00 0.00 0.00 4.40
867 3575 3.697439 TTAGCCCGCCACTGCCATC 62.697 63.158 0.00 0.00 0.00 3.51
870 3578 4.776322 CCCGCCACTGCCATCGAA 62.776 66.667 0.00 0.00 0.00 3.71
871 3579 3.197790 CCGCCACTGCCATCGAAG 61.198 66.667 0.00 0.00 0.00 3.79
873 3581 2.268920 GCCACTGCCATCGAAGGA 59.731 61.111 11.67 0.00 0.00 3.36
874 3582 1.817099 GCCACTGCCATCGAAGGAG 60.817 63.158 11.67 8.34 0.00 3.69
876 3584 1.153289 CACTGCCATCGAAGGAGGG 60.153 63.158 11.67 2.72 46.85 4.30
882 3590 1.301244 CATCGAAGGAGGGCATCGG 60.301 63.158 0.00 0.00 37.20 4.18
883 3591 2.511452 ATCGAAGGAGGGCATCGGG 61.511 63.158 0.00 0.00 37.20 5.14
893 3601 1.741770 GGCATCGGGCGCCTATAAG 60.742 63.158 28.56 13.88 46.56 1.73
898 3606 1.913778 TCGGGCGCCTATAAGATACA 58.086 50.000 28.56 0.00 0.00 2.29
1015 3742 1.613317 ATCCATGGCGTCCGTGAAGA 61.613 55.000 6.96 8.77 42.73 2.87
1143 3885 1.680651 CTGCCTCCTCCTCGTCAGT 60.681 63.158 0.00 0.00 0.00 3.41
1164 3906 2.108771 TGCGAGAAGTGCTGCACA 59.891 55.556 31.90 9.08 36.74 4.57
1206 3948 2.989253 TTCTGCGAGGTGGAGCGA 60.989 61.111 0.00 0.00 35.70 4.93
1212 3954 3.844090 GAGGTGGAGCGAGAGGCC 61.844 72.222 0.00 0.00 45.17 5.19
1270 4012 2.869192 GCCGACAAGAAGATCAAGATCC 59.131 50.000 6.45 0.00 38.58 3.36
1271 4013 3.679917 GCCGACAAGAAGATCAAGATCCA 60.680 47.826 6.45 0.00 38.58 3.41
1313 4055 0.947244 AAGAACCTCAAGTGCAAGCG 59.053 50.000 0.00 0.00 0.00 4.68
1331 4073 4.382320 TGCGTGAAGGCCGGTACC 62.382 66.667 1.90 0.16 0.00 3.34
1332 4074 4.078516 GCGTGAAGGCCGGTACCT 62.079 66.667 10.90 0.00 43.91 3.08
1376 4126 6.760298 AGTATATCTCGTCTCTCGTTTGTGTA 59.240 38.462 0.00 0.00 40.80 2.90
1398 4168 1.264288 CGACTTTGTGGTCTGGCTTTC 59.736 52.381 0.00 0.00 34.38 2.62
1403 4173 0.250295 TGTGGTCTGGCTTTCTTCCG 60.250 55.000 0.00 0.00 0.00 4.30
1413 4183 3.197766 TGGCTTTCTTCCGACTATGATGT 59.802 43.478 0.00 0.00 0.00 3.06
1416 4189 5.815740 GGCTTTCTTCCGACTATGATGTTTA 59.184 40.000 0.00 0.00 0.00 2.01
1433 4207 3.054878 GTTTATGTTGTGTCGTCGTCCT 58.945 45.455 0.00 0.00 0.00 3.85
1434 4208 2.624316 TATGTTGTGTCGTCGTCCTC 57.376 50.000 0.00 0.00 0.00 3.71
1462 4240 5.897377 AACTTTGGTATAACATGGTGCTC 57.103 39.130 0.00 0.00 0.00 4.26
1483 4261 5.343593 GCTCGATCTAAAACTATCCACATCG 59.656 44.000 0.00 0.00 34.55 3.84
1487 4265 4.357142 TCTAAAACTATCCACATCGTCGC 58.643 43.478 0.00 0.00 0.00 5.19
1513 4433 6.750501 TGTACGCTTCTATCATGTACTTTGTC 59.249 38.462 0.00 0.00 37.04 3.18
1520 4440 6.786207 TCTATCATGTACTTTGTCTGTCGAG 58.214 40.000 0.00 0.00 0.00 4.04
1524 4444 5.183140 TCATGTACTTTGTCTGTCGAGATCA 59.817 40.000 0.00 0.00 0.00 2.92
1525 4445 4.795268 TGTACTTTGTCTGTCGAGATCAC 58.205 43.478 0.00 0.00 0.00 3.06
1526 4446 4.519350 TGTACTTTGTCTGTCGAGATCACT 59.481 41.667 0.00 0.00 0.00 3.41
1527 4447 4.592485 ACTTTGTCTGTCGAGATCACTT 57.408 40.909 0.00 0.00 0.00 3.16
1528 4448 4.302455 ACTTTGTCTGTCGAGATCACTTG 58.698 43.478 0.00 0.00 0.00 3.16
1529 4449 4.038042 ACTTTGTCTGTCGAGATCACTTGA 59.962 41.667 0.00 0.00 34.50 3.02
1530 4450 4.790765 TTGTCTGTCGAGATCACTTGAT 57.209 40.909 0.00 0.00 38.60 2.57
1531 4451 4.102035 TGTCTGTCGAGATCACTTGATG 57.898 45.455 0.00 0.00 38.60 3.07
1532 4452 2.857152 GTCTGTCGAGATCACTTGATGC 59.143 50.000 0.00 0.00 38.60 3.91
1533 4453 2.493278 TCTGTCGAGATCACTTGATGCA 59.507 45.455 0.00 0.00 38.60 3.96
1534 4454 3.131755 TCTGTCGAGATCACTTGATGCAT 59.868 43.478 0.00 0.00 38.60 3.96
1535 4455 3.192466 TGTCGAGATCACTTGATGCATG 58.808 45.455 2.46 0.00 38.60 4.06
1536 4456 2.033065 GTCGAGATCACTTGATGCATGC 60.033 50.000 11.82 11.82 38.60 4.06
1537 4457 1.937899 CGAGATCACTTGATGCATGCA 59.062 47.619 25.04 25.04 34.37 3.96
1538 4458 2.548480 CGAGATCACTTGATGCATGCAT 59.452 45.455 32.66 32.66 39.69 3.96
1564 4484 7.048629 TGCATCTCTACTATTCTTCTTCAGG 57.951 40.000 0.00 0.00 0.00 3.86
1572 4495 8.061920 TCTACTATTCTTCTTCAGGGATCAAGA 58.938 37.037 0.00 0.00 0.00 3.02
1581 4504 5.488919 TCTTCAGGGATCAAGACATTTACCT 59.511 40.000 0.00 0.00 0.00 3.08
1583 4506 4.122776 CAGGGATCAAGACATTTACCTCG 58.877 47.826 0.00 0.00 0.00 4.63
1595 4518 3.955771 TTTACCTCGACAAAAGTGTGC 57.044 42.857 0.00 0.00 38.41 4.57
1598 4521 1.400494 ACCTCGACAAAAGTGTGCAAC 59.600 47.619 0.00 0.00 38.41 4.17
1608 4531 5.746539 CAAAAGTGTGCAACTGTTGTTTTT 58.253 33.333 20.57 15.23 45.63 1.94
1609 4532 6.882072 CAAAAGTGTGCAACTGTTGTTTTTA 58.118 32.000 20.57 2.43 45.63 1.52
1659 4582 8.130469 TCACATTTATATTAGAACGCGTCAGTA 58.870 33.333 14.44 0.96 0.00 2.74
1697 4620 4.806342 TTTTCTCGGTTGACAACTTAGC 57.194 40.909 17.52 0.60 0.00 3.09
1699 4622 2.750948 TCTCGGTTGACAACTTAGCAC 58.249 47.619 17.52 0.00 0.00 4.40
1700 4623 1.798813 CTCGGTTGACAACTTAGCACC 59.201 52.381 17.52 0.00 0.00 5.01
1730 4653 2.736144 TCCAAATTCGTACGTCAGCT 57.264 45.000 16.05 0.00 0.00 4.24
1732 4655 3.395639 TCCAAATTCGTACGTCAGCTTT 58.604 40.909 16.05 6.35 0.00 3.51
1735 4658 5.077424 CCAAATTCGTACGTCAGCTTTTAC 58.923 41.667 16.05 0.00 0.00 2.01
1785 4708 8.135382 ACACATGGTACTCTAAAACTATCAGT 57.865 34.615 0.00 0.00 0.00 3.41
1850 4773 9.601217 AACTGTATCCTGTAATATTGTCTGTTC 57.399 33.333 0.00 0.00 0.00 3.18
1851 4774 8.982723 ACTGTATCCTGTAATATTGTCTGTTCT 58.017 33.333 0.00 0.00 0.00 3.01
1877 4800 6.406692 TGTATTCTAGTACTGGCTTCCATC 57.593 41.667 5.39 0.00 30.82 3.51
1878 4801 4.592485 ATTCTAGTACTGGCTTCCATCG 57.408 45.455 5.39 0.00 30.82 3.84
1903 4827 3.384146 TGATGTTGTGTGCATCTTTTGGT 59.616 39.130 0.00 0.00 42.21 3.67
1904 4828 3.162202 TGTTGTGTGCATCTTTTGGTG 57.838 42.857 0.00 0.00 0.00 4.17
1905 4829 1.860326 GTTGTGTGCATCTTTTGGTGC 59.140 47.619 0.00 0.00 41.61 5.01
1906 4830 1.401761 TGTGTGCATCTTTTGGTGCT 58.598 45.000 2.95 0.00 41.78 4.40
1907 4831 2.580962 TGTGTGCATCTTTTGGTGCTA 58.419 42.857 2.95 0.00 41.78 3.49
1927 4851 7.345192 GTGCTATGACAACAATAATTCCTACG 58.655 38.462 0.00 0.00 0.00 3.51
1935 4859 7.250569 ACAACAATAATTCCTACGCATTCTTG 58.749 34.615 0.00 0.00 0.00 3.02
1946 4870 4.737855 ACGCATTCTTGGTACTATGAGT 57.262 40.909 0.00 0.00 0.00 3.41
1959 4883 5.864474 GGTACTATGAGTTAATGATCCTGCG 59.136 44.000 0.00 0.00 0.00 5.18
1961 4885 5.533482 ACTATGAGTTAATGATCCTGCGAC 58.467 41.667 0.00 0.00 0.00 5.19
1968 4892 5.361285 AGTTAATGATCCTGCGACTCTAACT 59.639 40.000 0.00 0.00 0.00 2.24
1974 4898 4.330944 TCCTGCGACTCTAACTTTTTGA 57.669 40.909 0.00 0.00 0.00 2.69
1997 4921 2.444140 CTAGGGCCAGGGCGTACT 60.444 66.667 11.30 8.51 43.06 2.73
1999 4923 2.029307 CTAGGGCCAGGGCGTACTTC 62.029 65.000 11.30 0.00 43.06 3.01
2006 4930 1.066143 CCAGGGCGTACTTCATCAACT 60.066 52.381 0.00 0.00 0.00 3.16
2021 4945 6.245115 TCATCAACTCAAAATGTAGCACTG 57.755 37.500 0.00 0.00 0.00 3.66
2026 4950 5.474578 ACTCAAAATGTAGCACTGAGAGA 57.525 39.130 4.49 0.00 37.53 3.10
2034 4958 8.798859 AAATGTAGCACTGAGAGAAAATGTAT 57.201 30.769 0.00 0.00 0.00 2.29
2070 4994 2.778299 TCCTTGGTGTTACAGTGCATC 58.222 47.619 0.00 0.00 0.00 3.91
2071 4995 2.371841 TCCTTGGTGTTACAGTGCATCT 59.628 45.455 0.00 0.00 0.00 2.90
2112 5036 4.468510 AGATTTTGATACCCGTGTACAGGA 59.531 41.667 16.93 0.00 0.00 3.86
2130 5054 8.468399 TGTACAGGACGTGTATCAATAACATAA 58.532 33.333 10.94 0.00 43.70 1.90
2134 5058 9.208022 CAGGACGTGTATCAATAACATAATGAT 57.792 33.333 0.00 0.00 37.54 2.45
2185 5532 9.161629 TCATGTTTGTGTATGAGTATCGATTTT 57.838 29.630 1.71 0.00 38.61 1.82
2187 5534 8.541133 TGTTTGTGTATGAGTATCGATTTTCA 57.459 30.769 1.71 8.60 38.61 2.69
2238 5585 6.363473 GTTTGTTTAGACTGATGTGTACTGC 58.637 40.000 0.00 0.00 0.00 4.40
2239 5586 5.468540 TGTTTAGACTGATGTGTACTGCT 57.531 39.130 0.00 0.00 0.00 4.24
2240 5587 5.853936 TGTTTAGACTGATGTGTACTGCTT 58.146 37.500 0.00 0.00 0.00 3.91
2241 5588 6.288294 TGTTTAGACTGATGTGTACTGCTTT 58.712 36.000 0.00 0.00 0.00 3.51
2242 5589 6.765989 TGTTTAGACTGATGTGTACTGCTTTT 59.234 34.615 0.00 0.00 0.00 2.27
2243 5590 7.282224 TGTTTAGACTGATGTGTACTGCTTTTT 59.718 33.333 0.00 0.00 0.00 1.94
2272 5619 6.822073 AAAAACTACAAAATTGACGAAGGC 57.178 33.333 0.00 0.00 0.00 4.35
2273 5620 5.767816 AAACTACAAAATTGACGAAGGCT 57.232 34.783 0.00 0.00 0.00 4.58
2274 5621 6.870971 AAACTACAAAATTGACGAAGGCTA 57.129 33.333 0.00 0.00 0.00 3.93
2275 5622 6.481954 AACTACAAAATTGACGAAGGCTAG 57.518 37.500 0.00 0.00 0.00 3.42
2276 5623 5.548406 ACTACAAAATTGACGAAGGCTAGT 58.452 37.500 0.00 0.00 0.00 2.57
2277 5624 5.638234 ACTACAAAATTGACGAAGGCTAGTC 59.362 40.000 13.97 13.97 37.85 2.59
2278 5625 4.642429 ACAAAATTGACGAAGGCTAGTCT 58.358 39.130 19.31 0.00 38.16 3.24
2279 5626 5.790593 ACAAAATTGACGAAGGCTAGTCTA 58.209 37.500 19.31 14.26 38.16 2.59
2280 5627 6.407202 ACAAAATTGACGAAGGCTAGTCTAT 58.593 36.000 19.31 15.53 38.16 1.98
2281 5628 6.535508 ACAAAATTGACGAAGGCTAGTCTATC 59.464 38.462 19.31 0.00 38.16 2.08
2282 5629 5.854010 AATTGACGAAGGCTAGTCTATCA 57.146 39.130 19.31 0.00 38.16 2.15
2283 5630 5.854010 ATTGACGAAGGCTAGTCTATCAA 57.146 39.130 16.54 16.54 38.16 2.57
2284 5631 4.902443 TGACGAAGGCTAGTCTATCAAG 57.098 45.455 19.31 0.00 38.16 3.02
2285 5632 4.524053 TGACGAAGGCTAGTCTATCAAGA 58.476 43.478 19.31 0.51 38.16 3.02
2286 5633 4.948004 TGACGAAGGCTAGTCTATCAAGAA 59.052 41.667 19.31 0.00 38.16 2.52
2287 5634 5.163642 TGACGAAGGCTAGTCTATCAAGAAC 60.164 44.000 19.31 0.00 38.16 3.01
2288 5635 4.705507 ACGAAGGCTAGTCTATCAAGAACA 59.294 41.667 0.00 0.00 32.16 3.18
2289 5636 5.038033 CGAAGGCTAGTCTATCAAGAACAC 58.962 45.833 0.00 0.00 32.16 3.32
2290 5637 5.393135 CGAAGGCTAGTCTATCAAGAACACA 60.393 44.000 0.00 0.00 32.16 3.72
2291 5638 6.360370 AAGGCTAGTCTATCAAGAACACAA 57.640 37.500 0.00 0.00 32.16 3.33
2292 5639 6.360370 AGGCTAGTCTATCAAGAACACAAA 57.640 37.500 0.00 0.00 32.16 2.83
2293 5640 6.951971 AGGCTAGTCTATCAAGAACACAAAT 58.048 36.000 0.00 0.00 32.16 2.32
2294 5641 8.079211 AGGCTAGTCTATCAAGAACACAAATA 57.921 34.615 0.00 0.00 32.16 1.40
2295 5642 8.709308 AGGCTAGTCTATCAAGAACACAAATAT 58.291 33.333 0.00 0.00 32.16 1.28
2296 5643 8.768955 GGCTAGTCTATCAAGAACACAAATATG 58.231 37.037 0.00 0.00 32.16 1.78
2297 5644 8.768955 GCTAGTCTATCAAGAACACAAATATGG 58.231 37.037 0.00 0.00 32.16 2.74
2300 5647 9.911788 AGTCTATCAAGAACACAAATATGGATT 57.088 29.630 0.00 0.00 32.16 3.01
2311 5658 9.806203 AACACAAATATGGATTAATGTCATGTG 57.194 29.630 13.06 13.06 0.00 3.21
2312 5659 8.970020 ACACAAATATGGATTAATGTCATGTGT 58.030 29.630 13.85 13.85 0.00 3.72
2313 5660 9.240159 CACAAATATGGATTAATGTCATGTGTG 57.760 33.333 16.38 16.38 0.00 3.82
2314 5661 8.970020 ACAAATATGGATTAATGTCATGTGTGT 58.030 29.630 11.72 11.72 29.53 3.72
2318 5665 6.375945 TGGATTAATGTCATGTGTGTATGC 57.624 37.500 0.00 0.00 0.00 3.14
2319 5666 5.884792 TGGATTAATGTCATGTGTGTATGCA 59.115 36.000 0.00 0.00 0.00 3.96
2320 5667 6.546772 TGGATTAATGTCATGTGTGTATGCAT 59.453 34.615 3.79 3.79 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.363473 GCGATTAAATCTTTCACCTAATCGG 58.637 40.000 18.65 0.00 45.69 4.18
7 8 5.065988 GCAGGCGATTAAATCTTTCACCTAA 59.934 40.000 0.00 0.00 0.00 2.69
30 31 1.029681 AGTGAGAAACAAAACGGGGC 58.970 50.000 0.00 0.00 0.00 5.80
41 42 2.555227 GGGCCCAGATCAAAGTGAGAAA 60.555 50.000 19.95 0.00 0.00 2.52
82 83 5.652014 CCTTGTAGTTTGATCATTTGCCCTA 59.348 40.000 0.00 0.00 0.00 3.53
266 270 2.897436 TCGCCTCAATCATGTCTTCTG 58.103 47.619 0.00 0.00 0.00 3.02
306 2845 3.892588 GGAGATACCACTGTCCTCCTAAG 59.107 52.174 0.00 0.00 39.50 2.18
316 2855 2.969628 GTGGACTGGAGATACCACTG 57.030 55.000 0.00 0.00 46.14 3.66
329 2868 1.341531 CGACTTGAACTCTGGTGGACT 59.658 52.381 0.00 0.00 0.00 3.85
378 2918 7.391554 TCACTGAAAGACCTGGAATTAATTCAG 59.608 37.037 25.55 19.75 44.87 3.02
400 2940 0.603707 CCCACTGAACGCACATCACT 60.604 55.000 0.00 0.00 0.00 3.41
424 2964 5.004440 CGTCTTCGTAATCGACATGAACATT 59.996 40.000 0.00 0.00 46.03 2.71
426 2966 3.849708 CGTCTTCGTAATCGACATGAACA 59.150 43.478 0.00 0.00 46.03 3.18
453 2993 0.605319 TTCTACCGGGCAAGTTGCTG 60.605 55.000 26.16 18.42 44.28 4.41
466 3006 4.824289 TCATCTTAACCGTGGTTTCTACC 58.176 43.478 9.96 0.00 45.26 3.18
467 3007 6.790285 TTTCATCTTAACCGTGGTTTCTAC 57.210 37.500 9.96 0.00 39.31 2.59
469 3009 5.009310 GGTTTTCATCTTAACCGTGGTTTCT 59.991 40.000 9.96 0.00 39.31 2.52
470 3010 5.217393 GGTTTTCATCTTAACCGTGGTTTC 58.783 41.667 9.96 0.00 39.31 2.78
471 3011 4.645588 TGGTTTTCATCTTAACCGTGGTTT 59.354 37.500 9.96 0.00 45.40 3.27
474 3014 3.364565 CGTGGTTTTCATCTTAACCGTGG 60.365 47.826 0.00 0.00 45.40 4.94
475 3015 3.364565 CCGTGGTTTTCATCTTAACCGTG 60.365 47.826 0.00 0.00 45.40 4.94
476 3016 2.809696 CCGTGGTTTTCATCTTAACCGT 59.190 45.455 0.00 0.00 45.40 4.83
477 3017 2.809696 ACCGTGGTTTTCATCTTAACCG 59.190 45.455 0.00 0.00 45.40 4.44
478 3018 4.276431 TCAACCGTGGTTTTCATCTTAACC 59.724 41.667 0.44 0.00 43.28 2.85
484 3142 1.606668 TGCTCAACCGTGGTTTTCATC 59.393 47.619 0.44 0.00 36.00 2.92
487 3145 1.335872 CCATGCTCAACCGTGGTTTTC 60.336 52.381 0.44 0.00 37.17 2.29
504 3162 1.077716 GCAAGTTCTACCGGGCCAT 60.078 57.895 6.32 0.00 0.00 4.40
631 3295 9.461734 AGGGAATATAATCTTAGTTAACTGGGT 57.538 33.333 18.56 4.48 0.00 4.51
783 3447 5.675970 TCGCGTCTCTTGTTTTCTTAATTG 58.324 37.500 5.77 0.00 0.00 2.32
804 3471 1.587043 TTGCGACCTCTGTCCTCTCG 61.587 60.000 0.00 0.00 38.32 4.04
821 3491 3.562732 GAACCCCCGGTCCTGGTTG 62.563 68.421 16.72 0.00 42.27 3.77
836 3506 4.143363 GCTAACGTGCGGCGGAAC 62.143 66.667 9.78 0.00 46.52 3.62
859 3567 3.036429 GCCCTCCTTCGATGGCAGT 62.036 63.158 12.42 0.00 46.16 4.40
864 3572 1.301244 CCGATGCCCTCCTTCGATG 60.301 63.158 0.00 0.00 41.96 3.84
866 3574 3.154473 CCCGATGCCCTCCTTCGA 61.154 66.667 0.00 0.00 41.96 3.71
867 3575 4.918201 GCCCGATGCCCTCCTTCG 62.918 72.222 0.00 0.00 39.88 3.79
876 3584 0.108138 ATCTTATAGGCGCCCGATGC 60.108 55.000 26.15 0.00 0.00 3.91
882 3590 3.006537 TCTTGGTGTATCTTATAGGCGCC 59.993 47.826 21.89 21.89 0.00 6.53
883 3591 3.988517 GTCTTGGTGTATCTTATAGGCGC 59.011 47.826 0.00 0.00 0.00 6.53
893 3601 0.389426 ACACGGCGTCTTGGTGTATC 60.389 55.000 10.85 0.00 42.65 2.24
1015 3742 2.490217 CAAGAGGACGACGGCGAT 59.510 61.111 22.49 1.35 41.64 4.58
1143 3885 1.665916 GCAGCACTTCTCGCACTCA 60.666 57.895 0.00 0.00 0.00 3.41
1206 3948 2.430610 GCACTGGATCTCGGCCTCT 61.431 63.158 0.00 0.00 0.00 3.69
1271 4013 0.820871 GCAGGAGAGGTTCATCTCGT 59.179 55.000 8.09 6.21 45.60 4.18
1313 4055 3.116531 GTACCGGCCTTCACGCAC 61.117 66.667 0.00 0.00 0.00 5.34
1321 4063 2.732619 GCAGCTAAGGTACCGGCCT 61.733 63.158 18.90 0.00 41.41 5.19
1331 4073 5.331876 ACTTGTAGTAGGAAGCAGCTAAG 57.668 43.478 0.00 0.00 0.00 2.18
1332 4074 8.707796 ATATACTTGTAGTAGGAAGCAGCTAA 57.292 34.615 0.00 0.00 33.66 3.09
1335 4077 7.222000 AGATATACTTGTAGTAGGAAGCAGC 57.778 40.000 0.00 0.00 33.66 5.25
1376 4126 0.687354 AGCCAGACCACAAAGTCGAT 59.313 50.000 0.00 0.00 41.83 3.59
1398 4168 7.064609 ACACAACATAAACATCATAGTCGGAAG 59.935 37.037 0.00 0.00 0.00 3.46
1403 4173 7.290857 ACGACACAACATAAACATCATAGTC 57.709 36.000 0.00 0.00 0.00 2.59
1413 4183 3.243468 TGAGGACGACGACACAACATAAA 60.243 43.478 0.00 0.00 0.00 1.40
1416 4189 0.671796 TGAGGACGACGACACAACAT 59.328 50.000 0.00 0.00 0.00 2.71
1433 4207 8.735315 CACCATGTTATACCAAAGTTTACATGA 58.265 33.333 20.80 0.00 38.62 3.07
1434 4208 7.487829 GCACCATGTTATACCAAAGTTTACATG 59.512 37.037 15.45 15.45 37.45 3.21
1462 4240 5.339875 CGACGATGTGGATAGTTTTAGATCG 59.660 44.000 0.00 0.00 37.92 3.69
1487 4265 6.752351 ACAAAGTACATGATAGAAGCGTACAG 59.248 38.462 0.00 0.00 35.89 2.74
1513 4433 2.884827 TGCATCAAGTGATCTCGACAG 58.115 47.619 0.00 0.00 31.21 3.51
1535 4455 9.086336 GAAGAAGAATAGTAGAGATGCATATGC 57.914 37.037 21.09 21.09 42.50 3.14
1538 4458 8.801299 CCTGAAGAAGAATAGTAGAGATGCATA 58.199 37.037 0.00 0.00 0.00 3.14
1545 4465 7.831691 TGATCCCTGAAGAAGAATAGTAGAG 57.168 40.000 0.00 0.00 0.00 2.43
1557 4477 5.488919 AGGTAAATGTCTTGATCCCTGAAGA 59.511 40.000 0.00 0.00 0.00 2.87
1562 4482 4.030913 TCGAGGTAAATGTCTTGATCCCT 58.969 43.478 0.00 0.00 0.00 4.20
1563 4483 4.120589 GTCGAGGTAAATGTCTTGATCCC 58.879 47.826 0.00 0.00 0.00 3.85
1564 4484 4.755411 TGTCGAGGTAAATGTCTTGATCC 58.245 43.478 0.00 0.00 0.00 3.36
1572 4495 4.261031 GCACACTTTTGTCGAGGTAAATGT 60.261 41.667 0.00 0.00 31.66 2.71
1581 4504 2.080693 ACAGTTGCACACTTTTGTCGA 58.919 42.857 0.00 0.00 31.66 4.20
1642 4565 3.282021 AGGGTACTGACGCGTTCTAATA 58.718 45.455 15.53 0.00 43.15 0.98
1643 4566 2.097825 AGGGTACTGACGCGTTCTAAT 58.902 47.619 15.53 0.00 43.15 1.73
1644 4567 1.470098 GAGGGTACTGACGCGTTCTAA 59.530 52.381 15.53 0.00 43.15 2.10
1645 4568 1.089920 GAGGGTACTGACGCGTTCTA 58.910 55.000 15.53 1.94 43.15 2.10
1646 4569 0.608582 AGAGGGTACTGACGCGTTCT 60.609 55.000 15.53 6.60 43.15 3.01
1659 4582 0.889186 AAATGCACGCGAAAGAGGGT 60.889 50.000 15.93 0.00 36.35 4.34
1697 4620 4.568956 GAATTTGGAAACCATCTTGGGTG 58.431 43.478 0.00 0.00 35.52 4.61
1699 4622 3.258123 ACGAATTTGGAAACCATCTTGGG 59.742 43.478 0.00 0.00 43.37 4.12
1700 4623 4.519540 ACGAATTTGGAAACCATCTTGG 57.480 40.909 0.00 0.00 45.02 3.61
1730 4653 5.127356 ACAAGTTTGGATCCGGTTTGTAAAA 59.873 36.000 17.12 4.29 0.00 1.52
1732 4655 4.208746 ACAAGTTTGGATCCGGTTTGTAA 58.791 39.130 17.12 0.00 0.00 2.41
1735 4658 6.693315 ATATACAAGTTTGGATCCGGTTTG 57.307 37.500 7.39 11.21 32.88 2.93
1776 4699 6.877611 AAAACGTGATTTGGACTGATAGTT 57.122 33.333 0.00 0.00 0.00 2.24
1785 4708 8.112016 TCAAACCATATAAAACGTGATTTGGA 57.888 30.769 16.51 0.00 30.99 3.53
1844 4767 7.817962 GCCAGTACTAGAATACAAAAGAACAGA 59.182 37.037 0.00 0.00 0.00 3.41
1845 4768 7.819900 AGCCAGTACTAGAATACAAAAGAACAG 59.180 37.037 0.00 0.00 0.00 3.16
1850 4773 7.103641 TGGAAGCCAGTACTAGAATACAAAAG 58.896 38.462 0.00 0.00 0.00 2.27
1851 4774 7.011499 TGGAAGCCAGTACTAGAATACAAAA 57.989 36.000 0.00 0.00 0.00 2.44
1865 4788 3.117491 CATCATACGATGGAAGCCAGT 57.883 47.619 0.00 0.00 44.59 4.00
1877 4800 4.604843 AAGATGCACACAACATCATACG 57.395 40.909 6.53 0.00 45.19 3.06
1878 4801 5.574055 CCAAAAGATGCACACAACATCATAC 59.426 40.000 6.53 0.00 45.19 2.39
1887 4811 1.401761 AGCACCAAAAGATGCACACA 58.598 45.000 0.00 0.00 44.59 3.72
1892 4816 4.168760 GTTGTCATAGCACCAAAAGATGC 58.831 43.478 0.00 0.00 42.39 3.91
1903 4827 6.018262 GCGTAGGAATTATTGTTGTCATAGCA 60.018 38.462 0.00 0.00 0.00 3.49
1904 4828 6.018262 TGCGTAGGAATTATTGTTGTCATAGC 60.018 38.462 0.00 0.00 0.00 2.97
1905 4829 7.477144 TGCGTAGGAATTATTGTTGTCATAG 57.523 36.000 0.00 0.00 0.00 2.23
1906 4830 8.445275 AATGCGTAGGAATTATTGTTGTCATA 57.555 30.769 0.00 0.00 0.00 2.15
1907 4831 6.942532 ATGCGTAGGAATTATTGTTGTCAT 57.057 33.333 0.00 0.00 0.00 3.06
1927 4851 8.662781 TCATTAACTCATAGTACCAAGAATGC 57.337 34.615 0.00 0.00 0.00 3.56
1935 4859 5.864474 CGCAGGATCATTAACTCATAGTACC 59.136 44.000 0.00 0.00 0.00 3.34
1946 4870 5.854010 AGTTAGAGTCGCAGGATCATTAA 57.146 39.130 0.00 0.00 0.00 1.40
1959 4883 8.884726 CCCTAGCTTTATCAAAAAGTTAGAGTC 58.115 37.037 17.62 0.00 40.95 3.36
1961 4885 7.201741 GGCCCTAGCTTTATCAAAAAGTTAGAG 60.202 40.741 17.62 9.52 40.95 2.43
1968 4892 4.023291 CCTGGCCCTAGCTTTATCAAAAA 58.977 43.478 0.00 0.00 39.73 1.94
1974 4898 1.846973 GCCCTGGCCCTAGCTTTAT 59.153 57.895 0.00 0.00 39.73 1.40
1997 4921 6.486320 TCAGTGCTACATTTTGAGTTGATGAA 59.514 34.615 0.00 0.00 0.00 2.57
1999 4923 6.148315 TCTCAGTGCTACATTTTGAGTTGATG 59.852 38.462 0.00 0.00 37.23 3.07
2006 4930 7.229306 ACATTTTCTCTCAGTGCTACATTTTGA 59.771 33.333 0.00 0.00 0.00 2.69
2034 4958 9.747898 AACACCAAGGATACATACTTTTATTGA 57.252 29.630 0.00 0.00 41.41 2.57
2047 4971 3.670625 TGCACTGTAACACCAAGGATAC 58.329 45.455 0.00 0.00 0.00 2.24
2050 4974 2.371841 AGATGCACTGTAACACCAAGGA 59.628 45.455 0.00 0.00 0.00 3.36
2051 4975 2.485426 CAGATGCACTGTAACACCAAGG 59.515 50.000 0.00 0.00 41.30 3.61
2094 5018 1.473677 CGTCCTGTACACGGGTATCAA 59.526 52.381 0.00 0.00 43.01 2.57
2097 5021 0.813184 CACGTCCTGTACACGGGTAT 59.187 55.000 0.00 0.00 43.01 2.73
2101 5025 1.469703 TGATACACGTCCTGTACACGG 59.530 52.381 8.91 7.07 41.73 4.94
2138 5062 9.889128 ACATGAATATCAAAATGTTTTTAGGGG 57.111 29.630 0.00 0.00 28.99 4.79
2158 5500 8.716646 AATCGATACTCATACACAAACATGAA 57.283 30.769 0.00 0.00 31.04 2.57
2173 5515 5.051641 CCGTAGCACTTGAAAATCGATACTC 60.052 44.000 0.00 0.00 0.00 2.59
2185 5532 0.830444 AGGACCACCGTAGCACTTGA 60.830 55.000 0.00 0.00 41.83 3.02
2187 5534 1.671742 CAGGACCACCGTAGCACTT 59.328 57.895 0.00 0.00 41.83 3.16
2249 5596 6.569780 AGCCTTCGTCAATTTTGTAGTTTTT 58.430 32.000 0.00 0.00 0.00 1.94
2250 5597 6.144078 AGCCTTCGTCAATTTTGTAGTTTT 57.856 33.333 0.00 0.00 0.00 2.43
2251 5598 5.767816 AGCCTTCGTCAATTTTGTAGTTT 57.232 34.783 0.00 0.00 0.00 2.66
2252 5599 5.995897 ACTAGCCTTCGTCAATTTTGTAGTT 59.004 36.000 0.00 0.00 0.00 2.24
2253 5600 5.548406 ACTAGCCTTCGTCAATTTTGTAGT 58.452 37.500 0.00 0.00 0.00 2.73
2254 5601 5.869888 AGACTAGCCTTCGTCAATTTTGTAG 59.130 40.000 0.00 0.00 32.68 2.74
2255 5602 5.790593 AGACTAGCCTTCGTCAATTTTGTA 58.209 37.500 0.00 0.00 32.68 2.41
2256 5603 4.642429 AGACTAGCCTTCGTCAATTTTGT 58.358 39.130 0.00 0.00 32.68 2.83
2257 5604 6.535150 TGATAGACTAGCCTTCGTCAATTTTG 59.465 38.462 0.00 0.00 32.68 2.44
2258 5605 6.640518 TGATAGACTAGCCTTCGTCAATTTT 58.359 36.000 0.00 0.00 32.68 1.82
2259 5606 6.222038 TGATAGACTAGCCTTCGTCAATTT 57.778 37.500 0.00 0.00 32.68 1.82
2260 5607 5.854010 TGATAGACTAGCCTTCGTCAATT 57.146 39.130 0.00 0.00 32.68 2.32
2261 5608 5.594725 TCTTGATAGACTAGCCTTCGTCAAT 59.405 40.000 0.00 0.00 32.68 2.57
2262 5609 4.948004 TCTTGATAGACTAGCCTTCGTCAA 59.052 41.667 0.00 0.00 32.68 3.18
2263 5610 4.524053 TCTTGATAGACTAGCCTTCGTCA 58.476 43.478 0.00 0.00 32.68 4.35
2264 5611 5.163642 TGTTCTTGATAGACTAGCCTTCGTC 60.164 44.000 0.00 0.00 0.00 4.20
2265 5612 4.705507 TGTTCTTGATAGACTAGCCTTCGT 59.294 41.667 0.00 0.00 0.00 3.85
2266 5613 5.038033 GTGTTCTTGATAGACTAGCCTTCG 58.962 45.833 0.00 0.00 0.00 3.79
2267 5614 5.967088 TGTGTTCTTGATAGACTAGCCTTC 58.033 41.667 0.00 0.00 0.00 3.46
2268 5615 6.360370 TTGTGTTCTTGATAGACTAGCCTT 57.640 37.500 0.00 0.00 0.00 4.35
2269 5616 6.360370 TTTGTGTTCTTGATAGACTAGCCT 57.640 37.500 0.00 0.00 0.00 4.58
2270 5617 8.768955 CATATTTGTGTTCTTGATAGACTAGCC 58.231 37.037 0.00 0.00 0.00 3.93
2271 5618 8.768955 CCATATTTGTGTTCTTGATAGACTAGC 58.231 37.037 0.00 0.00 0.00 3.42
2274 5621 9.911788 AATCCATATTTGTGTTCTTGATAGACT 57.088 29.630 0.00 0.00 0.00 3.24
2285 5632 9.806203 CACATGACATTAATCCATATTTGTGTT 57.194 29.630 0.00 0.00 0.00 3.32
2286 5633 8.970020 ACACATGACATTAATCCATATTTGTGT 58.030 29.630 0.00 13.39 34.56 3.72
2287 5634 9.240159 CACACATGACATTAATCCATATTTGTG 57.760 33.333 0.00 12.60 33.28 3.33
2288 5635 8.970020 ACACACATGACATTAATCCATATTTGT 58.030 29.630 0.00 0.00 0.00 2.83
2292 5639 8.733458 GCATACACACATGACATTAATCCATAT 58.267 33.333 0.00 0.00 0.00 1.78
2293 5640 7.718753 TGCATACACACATGACATTAATCCATA 59.281 33.333 0.00 0.00 0.00 2.74
2294 5641 6.546772 TGCATACACACATGACATTAATCCAT 59.453 34.615 0.00 0.00 0.00 3.41
2295 5642 5.884792 TGCATACACACATGACATTAATCCA 59.115 36.000 0.00 0.00 0.00 3.41
2296 5643 6.375945 TGCATACACACATGACATTAATCC 57.624 37.500 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.