Multiple sequence alignment - TraesCS5B01G221300

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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 TraesCS5B01G221300 chr5B 100.000 2240 0 0 1 2240 395915563 395917802 0.000000e+00 4137
1 TraesCS5B01G221300 chr5A 96.839 1487 43 2 757 2240 438466311 438467796 0.000000e+00 2483
2 TraesCS5B01G221300 chr5A 84.172 815 61 36 1 758 438465473 438466276 0.000000e+00 728
3 TraesCS5B01G221300 chr5D 94.493 1489 54 13 756 2240 337296236 337297700 0.000000e+00 2270
4 TraesCS5B01G221300 chr5D 87.405 786 51 19 1 758 337295440 337296205 0.000000e+00 859
5 TraesCS5B01G221300 chrUn 81.435 237 24 12 443 667 92822526 92822754 2.290000e-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 TraesCS5B01G221300 chr5B 395915563 395917802 2239 False 4137.0 4137 100.0000 1 2240 1 chr5B.!!$F1 2239
1 TraesCS5B01G221300 chr5A 438465473 438467796 2323 False 1605.5 2483 90.5055 1 2240 2 chr5A.!!$F1 2239
2 TraesCS5B01G221300 chr5D 337295440 337297700 2260 False 1564.5 2270 90.9490 1 2240 2 chr5D.!!$F1 2239

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
305 348 0.034337 GCCTGTGTCTGGTCGGTTTA 59.966 55.0 0.0 0.0 0.0 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 1647 1.05666 TTCCCTCAACCCTCTCACAC 58.943 55.0 0.0 0.0 0.0 3.82 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
93 123 2.445654 CCCTCCCCCTCTCTGCTC 60.446 72.222 0.00 0.00 0.00 4.26
99 129 0.695347 CCCCCTCTCTGCTCTTGTTT 59.305 55.000 0.00 0.00 0.00 2.83
213 252 2.125065 CAGCAGCAGCAGGAGGAG 60.125 66.667 3.17 0.00 45.49 3.69
220 259 1.761667 CAGCAGGAGGAGGAGGAGG 60.762 68.421 0.00 0.00 0.00 4.30
305 348 0.034337 GCCTGTGTCTGGTCGGTTTA 59.966 55.000 0.00 0.00 0.00 2.01
336 393 2.740714 CTAGGGTTCGTTGCTGCGC 61.741 63.158 0.00 0.00 0.00 6.09
342 399 4.927782 TCGTTGCTGCGCCCTGTT 62.928 61.111 4.18 0.00 0.00 3.16
400 467 0.830648 TTCAATTCGAGGAGGGCGAT 59.169 50.000 0.00 0.00 37.64 4.58
449 518 5.906285 CAGGTGTTTGTTTGTTTGTTTGTTG 59.094 36.000 0.00 0.00 0.00 3.33
452 521 6.412362 GGTGTTTGTTTGTTTGTTTGTTGTTC 59.588 34.615 0.00 0.00 0.00 3.18
453 522 6.137771 GTGTTTGTTTGTTTGTTTGTTGTTCG 59.862 34.615 0.00 0.00 0.00 3.95
457 534 1.204941 TGTTTGTTTGTTGTTCGGGGG 59.795 47.619 0.00 0.00 0.00 5.40
485 562 4.147449 TGGGCTGTGCGATCGAGG 62.147 66.667 21.57 6.01 0.00 4.63
510 588 5.183530 TGGTTCAATCTGTCAATGGAGAT 57.816 39.130 0.00 0.00 0.00 2.75
554 632 1.343789 CACAGCTCGGATGATCTGGAT 59.656 52.381 0.73 0.00 41.57 3.41
559 637 2.031516 CGGATGATCTGGATGCGCC 61.032 63.158 4.18 0.00 37.10 6.53
698 780 1.375396 CGGATTCTGTGGGCGTCAA 60.375 57.895 0.00 0.00 0.00 3.18
719 804 7.095229 CGTCAATCCTGAGAAATTTGTGTCTTA 60.095 37.037 0.00 0.00 30.14 2.10
720 805 8.233190 GTCAATCCTGAGAAATTTGTGTCTTAG 58.767 37.037 0.00 0.00 30.14 2.18
721 806 7.939039 TCAATCCTGAGAAATTTGTGTCTTAGT 59.061 33.333 0.00 0.00 0.00 2.24
722 807 9.219603 CAATCCTGAGAAATTTGTGTCTTAGTA 57.780 33.333 0.00 0.00 0.00 1.82
754 839 1.272490 CTTGGTCCTCGTTCTAGCACA 59.728 52.381 0.00 0.00 0.00 4.57
758 843 0.811915 TCCTCGTTCTAGCACAGCTC 59.188 55.000 0.00 0.00 40.44 4.09
759 844 0.179124 CCTCGTTCTAGCACAGCTCC 60.179 60.000 0.00 0.00 40.44 4.70
889 1013 1.470098 CAGCAATCCAGCCACACTTAC 59.530 52.381 0.00 0.00 34.23 2.34
895 1019 1.078159 TCCAGCCACACTTACCTCCTA 59.922 52.381 0.00 0.00 0.00 2.94
899 1023 1.405661 GCCACACTTACCTCCTACAGC 60.406 57.143 0.00 0.00 0.00 4.40
900 1024 1.207329 CCACACTTACCTCCTACAGCC 59.793 57.143 0.00 0.00 0.00 4.85
901 1025 1.207329 CACACTTACCTCCTACAGCCC 59.793 57.143 0.00 0.00 0.00 5.19
902 1026 1.078989 ACACTTACCTCCTACAGCCCT 59.921 52.381 0.00 0.00 0.00 5.19
979 1103 2.183478 TCGAGCAAGCCATCAAGAAA 57.817 45.000 0.00 0.00 0.00 2.52
1006 1130 4.082081 CCAATGTAGAGCCAGCAATGAAAA 60.082 41.667 0.00 0.00 0.00 2.29
1011 1135 2.961062 AGAGCCAGCAATGAAAACAACT 59.039 40.909 0.00 0.00 0.00 3.16
1156 1283 7.060633 GTCGTTTGCATCGAAGATTACAAAATT 59.939 33.333 14.33 0.00 45.12 1.82
1403 1530 4.775664 GCAATTTGCACAAAACATCTTCC 58.224 39.130 16.35 0.00 44.26 3.46
1407 1534 7.307870 GCAATTTGCACAAAACATCTTCCATTA 60.308 33.333 16.35 0.00 44.26 1.90
1462 1589 0.551131 AATGCCACCTTCCTCCCTCT 60.551 55.000 0.00 0.00 0.00 3.69
1467 1594 1.553417 CCACCTTCCTCCCTCTCTTGA 60.553 57.143 0.00 0.00 0.00 3.02
1520 1647 2.495155 TGGTCCAACCATGACATCTG 57.505 50.000 0.00 0.00 44.79 2.90
1551 1678 4.711949 AGGGAACAGCTGCCGCAG 62.712 66.667 15.27 16.47 41.46 5.18
1632 1760 6.039829 TGGTACATTGCTTAAACATGTTGACA 59.960 34.615 12.82 5.48 0.00 3.58
1704 1832 9.288576 TGTTTCAAGTGAATCTAGTTGAATGAT 57.711 29.630 12.77 0.00 44.79 2.45
1705 1833 9.766277 GTTTCAAGTGAATCTAGTTGAATGATC 57.234 33.333 12.77 0.00 44.79 2.92
1742 1870 5.064452 CCTAGTCTGATTGTTTGATGTCTGC 59.936 44.000 0.00 0.00 0.00 4.26
1913 2041 4.131649 TGTTGAAGAAACTCGAAGACCA 57.868 40.909 0.00 0.00 39.70 4.02
1916 2044 2.432874 TGAAGAAACTCGAAGACCACCA 59.567 45.455 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 237 3.388703 CTCCTCCTCCTGCTGCTGC 62.389 68.421 8.89 8.89 40.20 5.25
199 238 2.733669 CCTCCTCCTCCTGCTGCTG 61.734 68.421 0.00 0.00 0.00 4.41
200 239 2.365370 CCTCCTCCTCCTGCTGCT 60.365 66.667 0.00 0.00 0.00 4.24
235 274 3.749064 GGCGACAGCTCGGAGACA 61.749 66.667 9.69 0.00 44.37 3.41
305 348 2.699496 CCTAGACCCCCAGCTCCT 59.301 66.667 0.00 0.00 0.00 3.69
342 399 2.289819 ACCGAAAAACTATCTCCCGCAA 60.290 45.455 0.00 0.00 0.00 4.85
457 534 4.106925 CAGCCCAGCACTCCCTCC 62.107 72.222 0.00 0.00 0.00 4.30
462 539 3.965539 ATCGCACAGCCCAGCACTC 62.966 63.158 0.00 0.00 0.00 3.51
485 562 3.826157 TCCATTGACAGATTGAACCAACC 59.174 43.478 0.00 0.00 0.00 3.77
510 588 1.006825 CTCGCAAACATCGTCCGTCA 61.007 55.000 0.00 0.00 0.00 4.35
554 632 4.812476 CGACTGATTCGGGGCGCA 62.812 66.667 10.83 0.00 44.60 6.09
687 769 1.191489 TCTCAGGATTGACGCCCACA 61.191 55.000 0.00 0.00 0.00 4.17
698 780 7.545965 CGTACTAAGACACAAATTTCTCAGGAT 59.454 37.037 0.00 0.00 0.00 3.24
719 804 3.624410 GGACCAAGTGAAACAAACGTACT 59.376 43.478 0.00 0.00 41.43 2.73
720 805 3.624410 AGGACCAAGTGAAACAAACGTAC 59.376 43.478 0.00 0.00 41.43 3.67
721 806 3.872771 GAGGACCAAGTGAAACAAACGTA 59.127 43.478 0.00 0.00 41.43 3.57
722 807 2.681344 GAGGACCAAGTGAAACAAACGT 59.319 45.455 0.00 0.00 41.43 3.99
754 839 0.116143 AGAGTGGAGACTTGGGAGCT 59.884 55.000 0.00 0.00 30.16 4.09
821 942 8.714179 CAAGTCACCTAACACGATTAATTAACA 58.286 33.333 0.00 0.00 0.00 2.41
889 1013 0.543749 CTTTGGAGGGCTGTAGGAGG 59.456 60.000 0.00 0.00 0.00 4.30
895 1019 2.629617 CACATTTTCTTTGGAGGGCTGT 59.370 45.455 0.00 0.00 0.00 4.40
899 1023 2.892852 TGAGCACATTTTCTTTGGAGGG 59.107 45.455 0.00 0.00 0.00 4.30
900 1024 4.491676 CATGAGCACATTTTCTTTGGAGG 58.508 43.478 0.00 0.00 34.15 4.30
901 1025 3.924686 GCATGAGCACATTTTCTTTGGAG 59.075 43.478 0.00 0.00 41.58 3.86
902 1026 3.916761 GCATGAGCACATTTTCTTTGGA 58.083 40.909 0.00 0.00 41.58 3.53
979 1103 4.712051 TTGCTGGCTCTACATTGGATAT 57.288 40.909 0.00 0.00 0.00 1.63
1006 1130 5.539048 AGCGTAAGAAGTATGACAAGTTGT 58.461 37.500 8.61 8.61 43.02 3.32
1011 1135 6.394809 TGATGAAGCGTAAGAAGTATGACAA 58.605 36.000 0.00 0.00 43.02 3.18
1156 1283 2.083774 GAACCAGGAACATGCATCGAA 58.916 47.619 0.00 0.00 0.00 3.71
1413 1540 7.935755 AGATGCACTGCTCATACACTAATAAAT 59.064 33.333 1.98 0.00 0.00 1.40
1462 1589 9.560860 TTATATAATGGAGGCTCCTAATCAAGA 57.439 33.333 32.28 11.66 37.46 3.02
1467 1594 9.567702 AGAAGTTATATAATGGAGGCTCCTAAT 57.432 33.333 32.28 23.23 37.46 1.73
1514 1641 2.301296 CTCAACCCTCTCACACAGATGT 59.699 50.000 0.00 0.00 40.80 3.06
1520 1647 1.056660 TTCCCTCAACCCTCTCACAC 58.943 55.000 0.00 0.00 0.00 3.82
1551 1678 2.940158 ACCCACTTCCAGTACAAAACC 58.060 47.619 0.00 0.00 0.00 3.27
1632 1760 7.875554 ACACACAAAAACCAAGAAAAATACAGT 59.124 29.630 0.00 0.00 0.00 3.55
1704 1832 4.532126 TCAGACTAGGCCAAATGAAGAAGA 59.468 41.667 5.01 0.00 0.00 2.87
1705 1833 4.836825 TCAGACTAGGCCAAATGAAGAAG 58.163 43.478 5.01 0.00 0.00 2.85
1742 1870 2.093075 AGATCTGCAGAAGGTCCACATG 60.093 50.000 22.50 0.00 36.60 3.21
1916 2044 9.020105 GCATTATGCTTCTCAGATGGAACAAGT 62.020 40.741 10.27 0.00 41.20 3.16


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

AutoCloner maintained by Alex Coulton.