Multiple sequence alignment - TraesCS2A01G474200

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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 TraesCS2A01G474200 chr2A 100.000 2779 0 0 1 2779 715404705 715407483 0.000000e+00 5132
1 TraesCS2A01G474200 chr2D 94.614 2785 108 24 1 2779 577326532 577329280 0.000000e+00 4274
2 TraesCS2A01G474200 chr2D 88.125 160 17 2 3 162 556926944 556927101 3.650000e-44 189
3 TraesCS2A01G474200 chr2B 93.861 1857 91 15 1 1843 694265491 694267338 0.000000e+00 2776
4 TraesCS2A01G474200 chr2B 90.476 546 38 5 2235 2779 694267961 694268493 0.000000e+00 708
5 TraesCS2A01G474200 chr2B 90.805 261 24 0 1978 2238 694267608 694267868 1.580000e-92 350
6 TraesCS2A01G474200 chr2B 97.794 136 2 1 1844 1979 694267312 694267446 1.660000e-57 233
7 TraesCS2A01G474200 chr7D 88.961 154 15 2 1 154 500775608 500775457 3.650000e-44 189
8 TraesCS2A01G474200 chr5A 88.387 155 16 2 1 155 320214254 320214406 4.730000e-43 185
9 TraesCS2A01G474200 chr6B 86.826 167 17 5 1 164 481857861 481858025 6.110000e-42 182
10 TraesCS2A01G474200 chr5B 86.747 166 18 3 1 166 418818682 418818843 6.110000e-42 182
11 TraesCS2A01G474200 chr1D 87.500 160 17 3 1 159 324412379 324412222 6.110000e-42 182
12 TraesCS2A01G474200 chr7A 85.380 171 23 2 1 171 691723798 691723630 2.840000e-40 176


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 TraesCS2A01G474200 chr2A 715404705 715407483 2778 False 5132.00 5132 100.000 1 2779 1 chr2A.!!$F1 2778
1 TraesCS2A01G474200 chr2D 577326532 577329280 2748 False 4274.00 4274 94.614 1 2779 1 chr2D.!!$F2 2778
2 TraesCS2A01G474200 chr2B 694265491 694268493 3002 False 1016.75 2776 93.234 1 2779 4 chr2B.!!$F1 2778

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
441 444 0.833834 ACCACCAGTACAGCAGCTCT 60.834 55.0 0.0 0.0 0.00 4.09 F
1149 1179 0.545309 TGGGTCACCAAGGAGGAGAG 60.545 60.0 0.0 0.0 45.87 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1506 0.893727 GGGCGGTGTTCATGTCCTTT 60.894 55.000 0.00 0.0 0.0 3.11 R
2639 2930 2.104281 AGTTGCAACCTCCGTAAAGACT 59.896 45.455 25.62 0.0 0.0 3.24 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
68 69 3.438087 ACGGAGCAAAATGAGTGAATCTG 59.562 43.478 0.00 0.00 0.00 2.90
91 92 9.232473 TCTGCACTCGAAAGTATGTCTATATAT 57.768 33.333 0.00 0.00 33.25 0.86
156 157 8.908786 TGCATTTAGAAATAGAGGGAGTATTG 57.091 34.615 0.00 0.00 0.00 1.90
231 232 5.217978 ACACGTGTCCCTTATAAACTGAA 57.782 39.130 17.22 0.00 0.00 3.02
245 246 9.462606 CTTATAAACTGAAAGGGAGGTAATGTT 57.537 33.333 0.00 0.00 39.30 2.71
258 259 5.335661 GGAGGTAATGTTGAACCACACATTC 60.336 44.000 0.90 0.00 38.30 2.67
276 277 8.137437 CACACATTCTTTTTCCTACTCACAAAT 58.863 33.333 0.00 0.00 0.00 2.32
318 319 8.184192 CAGAAAACTTTGTAGATTCACAGTGTT 58.816 33.333 0.00 0.00 31.00 3.32
406 409 4.103311 AGAATATGTAACCCCTTGAGCTCC 59.897 45.833 12.15 0.00 0.00 4.70
441 444 0.833834 ACCACCAGTACAGCAGCTCT 60.834 55.000 0.00 0.00 0.00 4.09
447 450 3.118956 ACCAGTACAGCAGCTCTATCAAC 60.119 47.826 0.00 0.00 0.00 3.18
454 457 2.507058 AGCAGCTCTATCAACCCATTCA 59.493 45.455 0.00 0.00 0.00 2.57
457 460 4.340381 GCAGCTCTATCAACCCATTCAAAT 59.660 41.667 0.00 0.00 0.00 2.32
458 461 5.532406 GCAGCTCTATCAACCCATTCAAATA 59.468 40.000 0.00 0.00 0.00 1.40
459 462 6.039717 GCAGCTCTATCAACCCATTCAAATAA 59.960 38.462 0.00 0.00 0.00 1.40
460 463 7.646314 CAGCTCTATCAACCCATTCAAATAAG 58.354 38.462 0.00 0.00 0.00 1.73
462 465 7.718753 AGCTCTATCAACCCATTCAAATAAGAG 59.281 37.037 0.00 0.00 0.00 2.85
464 467 9.618890 CTCTATCAACCCATTCAAATAAGAGAA 57.381 33.333 0.00 0.00 0.00 2.87
465 468 9.973661 TCTATCAACCCATTCAAATAAGAGAAA 57.026 29.630 0.00 0.00 0.00 2.52
468 471 6.488683 TCAACCCATTCAAATAAGAGAAACGT 59.511 34.615 0.00 0.00 0.00 3.99
487 490 2.868583 CGTGGCACAAATGGAGAGATAG 59.131 50.000 19.09 0.00 44.16 2.08
497 500 9.562408 CACAAATGGAGAGATAGTACTAGTAGA 57.438 37.037 8.85 0.00 0.00 2.59
656 659 2.111878 ACCAGCCGGCTATGCATC 59.888 61.111 32.30 0.00 34.57 3.91
724 749 2.678471 TATGCATGATGGCGATCGAT 57.322 45.000 21.57 3.73 36.28 3.59
725 750 1.817357 ATGCATGATGGCGATCGATT 58.183 45.000 21.57 1.34 36.28 3.34
726 751 0.869730 TGCATGATGGCGATCGATTG 59.130 50.000 21.57 8.40 36.28 2.67
727 752 1.150827 GCATGATGGCGATCGATTGA 58.849 50.000 21.57 0.00 0.00 2.57
728 753 1.736126 GCATGATGGCGATCGATTGAT 59.264 47.619 21.57 3.71 37.60 2.57
729 754 2.222976 GCATGATGGCGATCGATTGATC 60.223 50.000 21.57 12.39 46.24 2.92
791 816 7.782049 AGAGACCATTACAACGATAAGATTCA 58.218 34.615 0.00 0.00 0.00 2.57
798 823 9.817365 CATTACAACGATAAGATTCATCCATTC 57.183 33.333 0.00 0.00 0.00 2.67
799 824 9.784531 ATTACAACGATAAGATTCATCCATTCT 57.215 29.630 0.00 0.00 0.00 2.40
918 944 3.760035 CAGCACGAGCCGTACCCT 61.760 66.667 0.00 0.00 43.56 4.34
944 970 1.478471 CCATCCAGAACACAACACCCA 60.478 52.381 0.00 0.00 0.00 4.51
956 982 2.174854 ACAACACCCACCTAGAAGCTTT 59.825 45.455 0.00 0.00 0.00 3.51
1121 1151 1.333308 CGTGGCATCAACAGACAACAA 59.667 47.619 0.00 0.00 0.00 2.83
1133 1163 2.816087 CAGACAACAAACAGGAGATGGG 59.184 50.000 0.00 0.00 0.00 4.00
1149 1179 0.545309 TGGGTCACCAAGGAGGAGAG 60.545 60.000 0.00 0.00 45.87 3.20
1476 1506 4.858850 AGTCAATTCTAACCATGGATGCA 58.141 39.130 21.47 0.00 0.00 3.96
1520 1550 4.183865 CTGGTATGTTCGAGAAGCAATCA 58.816 43.478 0.00 0.00 0.00 2.57
1549 1579 5.913137 TCTCTTTCTAGCTTCCTTCAGAG 57.087 43.478 0.00 0.00 0.00 3.35
1561 1591 6.213600 AGCTTCCTTCAGAGGTTGTTTAGATA 59.786 38.462 0.00 0.00 43.97 1.98
1605 1635 8.564574 TCTTACAATTGTGTGTTCCTGAAATAC 58.435 33.333 21.42 0.00 38.82 1.89
1632 1662 2.821546 CCAAGTATTTCCTCGATGCGA 58.178 47.619 0.00 0.00 0.00 5.10
1641 1671 1.435105 CTCGATGCGAGCTCAAGGA 59.565 57.895 15.40 0.00 46.75 3.36
1724 1754 5.093849 TGCATGAGTTCAATGATCTGAGA 57.906 39.130 0.00 0.00 0.00 3.27
1805 1835 3.991773 TGTTCATGTACTGTAAGAACGCC 59.008 43.478 16.98 3.31 40.95 5.68
2051 2244 7.481798 GTGAGGAAAACTTTGTATATTGCTTCG 59.518 37.037 0.00 0.00 0.00 3.79
2084 2277 8.353684 TGTATGTGTACCGAAACATTTCAAATT 58.646 29.630 5.28 0.00 38.05 1.82
2095 2288 8.594687 CGAAACATTTCAAATTTCAAGTTGAGT 58.405 29.630 5.56 0.00 42.87 3.41
2193 2386 4.265073 AGCTTCGGTCAGATTTTTATGCT 58.735 39.130 0.00 0.00 0.00 3.79
2274 2563 7.857885 GGTTAGCAATAGCATCAAGTGAAATAC 59.142 37.037 0.00 0.00 45.49 1.89
2278 2567 6.293626 GCAATAGCATCAAGTGAAATACGGAT 60.294 38.462 0.00 0.00 41.58 4.18
2439 2730 0.888285 AGAACTGACAGGCAAGCTGC 60.888 55.000 7.51 0.00 44.08 5.25
2472 2763 5.934625 TCTGACACAAAGGCTAATCTTTCTC 59.065 40.000 0.00 0.00 35.04 2.87
2544 2835 2.676748 AGCAGAAGGGGTATCTCTGAG 58.323 52.381 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 7.890655 ACTCCCTCTATTTCTAAATGCAAGTTT 59.109 33.333 0.00 0.00 0.00 2.66
127 128 7.406104 ACTCCCTCTATTTCTAAATGCAAGTT 58.594 34.615 0.00 0.00 0.00 2.66
144 145 4.944317 GCTACAAAAAGCAATACTCCCTCT 59.056 41.667 0.00 0.00 42.30 3.69
231 232 3.139397 TGTGGTTCAACATTACCTCCCTT 59.861 43.478 0.00 0.00 35.41 3.95
245 246 6.126409 AGTAGGAAAAAGAATGTGTGGTTCA 58.874 36.000 0.00 0.00 0.00 3.18
302 303 3.901222 TGGGAGAACACTGTGAATCTACA 59.099 43.478 22.58 18.39 0.00 2.74
303 304 4.246458 GTGGGAGAACACTGTGAATCTAC 58.754 47.826 15.86 16.48 38.32 2.59
312 313 5.674525 ACATGTATATGTGGGAGAACACTG 58.325 41.667 4.06 0.00 45.54 3.66
339 340 5.865552 GCATGCACATGTTCTAAAAGAATGT 59.134 36.000 14.21 0.00 40.80 2.71
340 341 5.865013 TGCATGCACATGTTCTAAAAGAATG 59.135 36.000 18.46 0.00 40.80 2.67
396 399 0.253044 TTTGGATCCGGAGCTCAAGG 59.747 55.000 20.86 17.84 0.00 3.61
406 409 1.737793 GTGGTAACTGCTTTGGATCCG 59.262 52.381 7.39 0.00 37.61 4.18
441 444 8.673711 CGTTTCTCTTATTTGAATGGGTTGATA 58.326 33.333 0.00 0.00 0.00 2.15
447 450 5.640732 CCACGTTTCTCTTATTTGAATGGG 58.359 41.667 0.00 0.00 0.00 4.00
454 457 5.508200 TTTGTGCCACGTTTCTCTTATTT 57.492 34.783 0.00 0.00 0.00 1.40
457 460 3.252215 CCATTTGTGCCACGTTTCTCTTA 59.748 43.478 0.00 0.00 0.00 2.10
458 461 2.034558 CCATTTGTGCCACGTTTCTCTT 59.965 45.455 0.00 0.00 0.00 2.85
459 462 1.608590 CCATTTGTGCCACGTTTCTCT 59.391 47.619 0.00 0.00 0.00 3.10
460 463 1.606668 TCCATTTGTGCCACGTTTCTC 59.393 47.619 0.00 0.00 0.00 2.87
462 465 1.606668 TCTCCATTTGTGCCACGTTTC 59.393 47.619 0.00 0.00 0.00 2.78
464 467 1.202758 TCTCTCCATTTGTGCCACGTT 60.203 47.619 0.00 0.00 0.00 3.99
465 468 0.396435 TCTCTCCATTTGTGCCACGT 59.604 50.000 0.00 0.00 0.00 4.49
466 469 1.742761 ATCTCTCCATTTGTGCCACG 58.257 50.000 0.00 0.00 0.00 4.94
468 471 4.716784 AGTACTATCTCTCCATTTGTGCCA 59.283 41.667 0.00 0.00 0.00 4.92
487 490 8.414778 AGATTGCAGTATTGGTTCTACTAGTAC 58.585 37.037 0.00 0.00 0.00 2.73
497 500 4.406456 TGTTGGAGATTGCAGTATTGGTT 58.594 39.130 0.00 0.00 0.00 3.67
538 541 5.679734 TTTCTGCTCTTTTCTAACTGCAG 57.320 39.130 13.48 13.48 46.21 4.41
539 542 5.590259 AGTTTTCTGCTCTTTTCTAACTGCA 59.410 36.000 0.00 0.00 0.00 4.41
656 659 1.602888 AGCAGCAGAAGCAGTTGGG 60.603 57.895 0.00 0.00 45.49 4.12
724 749 3.518634 TCGATCATTGTGACCGATCAA 57.481 42.857 0.00 0.00 36.31 2.57
725 750 3.733443 ATCGATCATTGTGACCGATCA 57.267 42.857 3.46 0.00 35.37 2.92
727 752 3.384668 GTGATCGATCATTGTGACCGAT 58.615 45.455 29.53 8.83 41.85 4.18
728 753 2.794631 CGTGATCGATCATTGTGACCGA 60.795 50.000 29.53 0.00 39.30 4.69
729 754 1.518515 CGTGATCGATCATTGTGACCG 59.481 52.381 29.53 21.50 39.30 4.79
730 755 1.860950 CCGTGATCGATCATTGTGACC 59.139 52.381 29.53 14.48 39.30 4.02
731 756 2.809446 TCCGTGATCGATCATTGTGAC 58.191 47.619 29.53 15.16 39.30 3.67
732 757 3.518634 TTCCGTGATCGATCATTGTGA 57.481 42.857 29.53 19.55 39.30 3.58
733 758 4.801147 AATTCCGTGATCGATCATTGTG 57.199 40.909 29.53 18.84 39.30 3.33
734 759 6.931281 AGAATAATTCCGTGATCGATCATTGT 59.069 34.615 29.53 15.26 39.30 2.71
735 760 7.356641 AGAATAATTCCGTGATCGATCATTG 57.643 36.000 29.53 23.30 39.30 2.82
736 761 6.309009 CGAGAATAATTCCGTGATCGATCATT 59.691 38.462 29.53 20.88 39.30 2.57
737 762 5.802451 CGAGAATAATTCCGTGATCGATCAT 59.198 40.000 29.53 15.71 39.30 2.45
747 772 6.210078 GTCTCTTGATCGAGAATAATTCCGT 58.790 40.000 13.77 0.00 41.38 4.69
791 816 6.593770 GCCCGTTTTAAAAATTGAGAATGGAT 59.406 34.615 1.31 0.00 0.00 3.41
798 823 2.410392 GGCGCCCGTTTTAAAAATTGAG 59.590 45.455 18.11 0.00 0.00 3.02
799 824 2.223971 TGGCGCCCGTTTTAAAAATTGA 60.224 40.909 26.77 0.00 0.00 2.57
918 944 2.557924 GTTGTGTTCTGGATGGAATGCA 59.442 45.455 0.00 0.00 44.71 3.96
944 970 4.764172 CAGCAGTGATAAAGCTTCTAGGT 58.236 43.478 0.00 0.00 36.26 3.08
956 982 0.105593 GCAGGCTAGCAGCAGTGATA 59.894 55.000 22.02 0.00 44.75 2.15
1121 1151 1.352352 CTTGGTGACCCATCTCCTGTT 59.648 52.381 0.00 0.00 41.49 3.16
1133 1163 1.599576 GCCTCTCCTCCTTGGTGAC 59.400 63.158 0.00 0.00 34.88 3.67
1149 1179 2.626840 GAGAAATCACTGTCAGAGGCC 58.373 52.381 6.91 0.00 0.00 5.19
1414 1444 4.093472 TGCTGGTTACCTGTACAACAAT 57.907 40.909 9.93 0.00 0.00 2.71
1447 1477 6.825213 TCCATGGTTAGAATTGACTTCATGAG 59.175 38.462 12.58 0.00 36.24 2.90
1476 1506 0.893727 GGGCGGTGTTCATGTCCTTT 60.894 55.000 0.00 0.00 0.00 3.11
1520 1550 7.563188 TGAAGGAAGCTAGAAAGAGATGATAGT 59.437 37.037 0.00 0.00 0.00 2.12
1605 1635 2.019984 GAGGAAATACTTGGCCTGCAG 58.980 52.381 6.78 6.78 0.00 4.41
1632 1662 2.046507 CGCCTGCTTCCTTGAGCT 60.047 61.111 0.00 0.00 43.11 4.09
1634 1664 1.018226 CAGTCGCCTGCTTCCTTGAG 61.018 60.000 0.00 0.00 0.00 3.02
1724 1754 3.574396 GGACTAAGCAAAGCCCTTTCTTT 59.426 43.478 9.22 0.00 36.78 2.52
2002 2195 6.965500 CACTGTCATGCACTTGAATATTTCTC 59.035 38.462 0.00 0.00 0.00 2.87
2084 2277 6.404293 GCACTGAGGTTTTAACTCAACTTGAA 60.404 38.462 0.00 0.00 43.74 2.69
2095 2288 5.000591 TGATGAATCGCACTGAGGTTTTAA 58.999 37.500 0.00 0.00 0.00 1.52
2256 2545 8.939929 CATAATCCGTATTTCACTTGATGCTAT 58.060 33.333 0.00 0.00 0.00 2.97
2439 2730 4.999950 AGCCTTTGTGTCAGAAGAGTATTG 59.000 41.667 0.00 0.00 0.00 1.90
2472 2763 7.012138 TGGTACTTTCTAGTGAGTAGCGATTAG 59.988 40.741 21.18 0.00 45.23 1.73
2638 2929 2.163818 TGCAACCTCCGTAAAGACTG 57.836 50.000 0.00 0.00 0.00 3.51
2639 2930 2.104281 AGTTGCAACCTCCGTAAAGACT 59.896 45.455 25.62 0.00 0.00 3.24
2640 2931 2.490991 AGTTGCAACCTCCGTAAAGAC 58.509 47.619 25.62 0.00 0.00 3.01
2641 2932 2.922740 AGTTGCAACCTCCGTAAAGA 57.077 45.000 25.62 0.00 0.00 2.52
2642 2933 2.415512 GCTAGTTGCAACCTCCGTAAAG 59.584 50.000 25.62 11.09 42.31 1.85
2643 2934 2.419667 GCTAGTTGCAACCTCCGTAAA 58.580 47.619 25.62 1.28 42.31 2.01
2698 2989 4.672251 GCCTCCTTGTGATGGCAT 57.328 55.556 0.00 0.00 44.34 4.40


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

AutoCloner maintained by Alex Coulton.