Multiple sequence alignment - TraesCS2B01G343700

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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 TraesCS2B01G343700 chr2B 100.000 2300 0 0 1 2300 489486617 489484318 0 4248
1 TraesCS2B01G343700 chr1B 97.299 1555 42 0 743 2297 683730352 683731906 0 2639
2 TraesCS2B01G343700 chr1B 96.613 1565 50 3 737 2300 338896615 338895053 0 2593
3 TraesCS2B01G343700 chr7B 96.919 1558 48 0 743 2300 698143951 698142394 0 2612
4 TraesCS2B01G343700 chr7B 98.367 735 12 0 1 735 743010135 743009401 0 1291
5 TraesCS2B01G343700 chr5B 96.977 1555 46 1 743 2297 713078430 713079983 0 2610
6 TraesCS2B01G343700 chr2A 96.909 1553 48 0 743 2295 563260431 563258879 0 2603
7 TraesCS2B01G343700 chr2A 98.503 735 11 0 1 735 605918587 605917853 0 1297
8 TraesCS2B01G343700 chr3B 96.791 1558 50 0 743 2300 92265646 92264089 0 2601
9 TraesCS2B01G343700 chr3B 96.722 1556 50 1 743 2297 5083350 5084905 0 2590
10 TraesCS2B01G343700 chrUn 96.727 1558 51 0 743 2300 40089651 40088094 0 2595
11 TraesCS2B01G343700 chrUn 98.639 735 10 0 1 735 221556158 221555424 0 1303
12 TraesCS2B01G343700 chrUn 98.639 735 10 0 1 735 229489766 229489032 0 1303
13 TraesCS2B01G343700 chrUn 98.501 734 11 0 2 735 86482125 86481392 0 1295
14 TraesCS2B01G343700 chrUn 98.367 735 12 0 1 735 186187342 186188076 0 1291
15 TraesCS2B01G343700 chr6B 96.727 1558 51 0 743 2300 128915906 128914349 0 2595
16 TraesCS2B01G343700 chr7D 98.503 735 11 0 1 735 579033806 579033072 0 1297
17 TraesCS2B01G343700 chr7A 98.367 735 12 0 1 735 120884519 120883785 0 1291
18 TraesCS2B01G343700 chr1D 98.367 735 12 0 1 735 212463796 212464530 0 1291


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 TraesCS2B01G343700 chr2B 489484318 489486617 2299 True 4248 4248 100.000 1 2300 1 chr2B.!!$R1 2299
1 TraesCS2B01G343700 chr1B 683730352 683731906 1554 False 2639 2639 97.299 743 2297 1 chr1B.!!$F1 1554
2 TraesCS2B01G343700 chr1B 338895053 338896615 1562 True 2593 2593 96.613 737 2300 1 chr1B.!!$R1 1563
3 TraesCS2B01G343700 chr7B 698142394 698143951 1557 True 2612 2612 96.919 743 2300 1 chr7B.!!$R1 1557
4 TraesCS2B01G343700 chr7B 743009401 743010135 734 True 1291 1291 98.367 1 735 1 chr7B.!!$R2 734
5 TraesCS2B01G343700 chr5B 713078430 713079983 1553 False 2610 2610 96.977 743 2297 1 chr5B.!!$F1 1554
6 TraesCS2B01G343700 chr2A 563258879 563260431 1552 True 2603 2603 96.909 743 2295 1 chr2A.!!$R1 1552
7 TraesCS2B01G343700 chr2A 605917853 605918587 734 True 1297 1297 98.503 1 735 1 chr2A.!!$R2 734
8 TraesCS2B01G343700 chr3B 92264089 92265646 1557 True 2601 2601 96.791 743 2300 1 chr3B.!!$R1 1557
9 TraesCS2B01G343700 chr3B 5083350 5084905 1555 False 2590 2590 96.722 743 2297 1 chr3B.!!$F1 1554
10 TraesCS2B01G343700 chrUn 40088094 40089651 1557 True 2595 2595 96.727 743 2300 1 chrUn.!!$R1 1557
11 TraesCS2B01G343700 chrUn 221555424 221556158 734 True 1303 1303 98.639 1 735 1 chrUn.!!$R3 734
12 TraesCS2B01G343700 chrUn 229489032 229489766 734 True 1303 1303 98.639 1 735 1 chrUn.!!$R4 734
13 TraesCS2B01G343700 chrUn 86481392 86482125 733 True 1295 1295 98.501 2 735 1 chrUn.!!$R2 733
14 TraesCS2B01G343700 chrUn 186187342 186188076 734 False 1291 1291 98.367 1 735 1 chrUn.!!$F1 734
15 TraesCS2B01G343700 chr6B 128914349 128915906 1557 True 2595 2595 96.727 743 2300 1 chr6B.!!$R1 1557
16 TraesCS2B01G343700 chr7D 579033072 579033806 734 True 1297 1297 98.503 1 735 1 chr7D.!!$R1 734
17 TraesCS2B01G343700 chr7A 120883785 120884519 734 True 1291 1291 98.367 1 735 1 chr7A.!!$R1 734
18 TraesCS2B01G343700 chr1D 212463796 212464530 734 False 1291 1291 98.367 1 735 1 chr1D.!!$F1 734

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
427 428 0.471591 ACCTGGGCATGGCTTTTTCA 60.472 50.0 19.78 7.09 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1781 0.751277 CCCCTGCAATAATGGTGCGA 60.751 55.0 0.0 0.0 45.27 5.1 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 3.640967 CCAGCTAAGCTAGGAGTCAGAAT 59.359 47.826 0.00 0.00 36.40 2.40
109 110 5.128008 TGGAATTTTATCACCCCGGATTTTC 59.872 40.000 0.73 0.00 0.00 2.29
174 175 1.295292 TGGGAGAGAAGATAGCCCCTT 59.705 52.381 0.00 0.00 38.02 3.95
355 356 7.014736 ACTCCCTCATAATATATGGATCCCT 57.985 40.000 9.90 1.08 0.00 4.20
427 428 0.471591 ACCTGGGCATGGCTTTTTCA 60.472 50.000 19.78 7.09 0.00 2.69
629 630 9.999009 CGATTCCATTCTTTCCAATATCATATG 57.001 33.333 0.00 0.00 0.00 1.78
659 660 5.601729 AGTGAAATGCATCTATCTCCTCTCA 59.398 40.000 0.00 0.00 0.00 3.27
735 736 0.619543 TAGGGCGGGCTTTTCTACCT 60.620 55.000 0.26 0.00 0.00 3.08
761 762 4.525949 GGTAAGACGCCCCGCTCC 62.526 72.222 0.00 0.00 0.00 4.70
853 854 4.566004 TGAAATCTCCGACGAAAAGTGAT 58.434 39.130 0.00 0.00 0.00 3.06
958 959 5.476945 GCTGGTTTCTTCCCATTCTTTCTTA 59.523 40.000 0.00 0.00 0.00 2.10
990 991 8.160106 ACTAATCTAATGGATTCATTCTCCCAC 58.840 37.037 1.37 0.00 42.96 4.61
1013 1014 7.148641 CACCGAGAAGTTATGATACTAGCAAT 58.851 38.462 0.00 0.00 0.00 3.56
1060 1061 5.074115 CCTACCTTGGGTTATGTTTGACAA 58.926 41.667 0.00 0.00 37.09 3.18
1101 1102 6.900194 TCTATTGGTTTCAAAGGAGGATAGG 58.100 40.000 0.00 0.00 36.36 2.57
1158 1159 0.393820 AAAGGTTAACCCTCGACGCA 59.606 50.000 21.30 0.00 45.47 5.24
1200 1201 6.795399 ACTCCTTTTATGCAATTATGAACGG 58.205 36.000 0.00 0.00 0.00 4.44
1222 1223 4.437930 GGAACTTTCTCGATTCCAATGCAG 60.438 45.833 9.39 0.00 41.40 4.41
1487 1490 8.402798 TGCTAAACCAGAAATTCTTATGTTCA 57.597 30.769 0.00 0.00 0.00 3.18
1641 1644 7.589954 GGGACGGTTTATAAATCATCAAATTCG 59.410 37.037 6.85 0.00 0.00 3.34
1719 1722 2.224305 CGTTCCTTCCCCATATGGAGTC 60.224 54.545 24.00 5.01 35.37 3.36
1738 1741 1.688811 CGGGACCCAAGGGAAATCA 59.311 57.895 13.15 0.00 38.96 2.57
1750 1753 5.945784 CCAAGGGAAATCATTGAGTGAACTA 59.054 40.000 0.00 0.00 40.97 2.24
1829 1832 0.538057 TCCGAACTGTACGTGGGACT 60.538 55.000 0.00 0.00 0.00 3.85
1850 1853 3.710209 AGTTTCTGCCTCATACAGCTT 57.290 42.857 0.00 0.00 35.04 3.74
1906 1909 4.641645 CCCAACTGCTGCCGGTCA 62.642 66.667 1.90 0.00 0.00 4.02
1997 2000 2.736670 ACTGACCCAGCAAGAAAACT 57.263 45.000 0.00 0.00 34.37 2.66
2094 2097 3.635373 CGGGATAGGCGGCTAATAGAATA 59.365 47.826 23.58 0.00 0.00 1.75
2198 2201 3.767673 TGGAATGGCTCTCTTAGTTACGT 59.232 43.478 0.00 0.00 0.00 3.57
2297 2301 3.479203 CTATGCTGACCCGGGCCA 61.479 66.667 24.08 16.92 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 5.946942 AGAAGGATAGCTTCATGAGTTCA 57.053 39.130 0.00 0.00 33.57 3.18
109 110 7.526608 TCAAGTATAAAGTGGAAATGAAAGCG 58.473 34.615 0.00 0.00 0.00 4.68
248 249 2.223923 CCCTTACCTCTCATCAGCTTCG 60.224 54.545 0.00 0.00 0.00 3.79
355 356 6.680148 TGTTGGAGGATCAATATTATCCGA 57.320 37.500 13.66 4.54 46.37 4.55
427 428 5.915196 GCTTCTTGCGAAATCAACTAAGTTT 59.085 36.000 0.00 0.00 0.00 2.66
629 630 1.303309 AGATGCATTTCACTAGGCGC 58.697 50.000 0.00 0.00 0.00 6.53
659 660 8.685257 AAATGGATAAAAAGAAAGAAGGGGAT 57.315 30.769 0.00 0.00 0.00 3.85
761 762 9.526713 CTCTATAATTCGAATGATATGTGGAGG 57.473 37.037 14.43 3.27 0.00 4.30
792 793 9.912634 GAAACTTCAATTGATTAATGAGGTCAA 57.087 29.630 9.40 0.00 36.42 3.18
853 854 8.539544 TCATTGGATCTAGAAGTAATCACAACA 58.460 33.333 0.00 0.00 0.00 3.33
990 991 8.516234 ACTATTGCTAGTATCATAACTTCTCGG 58.484 37.037 0.00 0.00 36.40 4.63
1013 1014 5.890752 TCGAGAGGAGAAGAATAGGACTA 57.109 43.478 0.00 0.00 0.00 2.59
1060 1061 5.338708 CCAATAGAAGTTCACTGACCATCCT 60.339 44.000 5.50 0.00 0.00 3.24
1101 1102 0.178978 GAGCCTTCCCCAATGGATCC 60.179 60.000 4.20 4.20 44.66 3.36
1158 1159 3.754850 GGAGTAAAAATAGTGGTTGCGGT 59.245 43.478 0.00 0.00 0.00 5.68
1164 1165 8.644374 TGCATAAAAGGAGTAAAAATAGTGGT 57.356 30.769 0.00 0.00 0.00 4.16
1200 1201 4.656041 CTGCATTGGAATCGAGAAAGTTC 58.344 43.478 0.00 0.00 0.00 3.01
1222 1223 3.751698 ACGTCAACTCCAAAAGGATAAGC 59.248 43.478 0.00 0.00 0.00 3.09
1380 1381 9.950496 AGTGGCTATAGATACAAATCCATTTAG 57.050 33.333 3.21 0.00 31.98 1.85
1396 1397 2.099921 AGCACGACTGAAGTGGCTATAG 59.900 50.000 0.00 0.00 39.80 1.31
1450 1453 4.280677 TCTGGTTTAGCATGTTCCCAAAAG 59.719 41.667 0.00 0.00 0.00 2.27
1453 1456 3.517296 TCTGGTTTAGCATGTTCCCAA 57.483 42.857 0.00 0.00 0.00 4.12
1641 1644 3.367703 CCCACTTCTCATTCCATTTGTGC 60.368 47.826 0.00 0.00 0.00 4.57
1719 1722 1.076995 GATTTCCCTTGGGTCCCGG 60.077 63.158 2.65 0.00 0.00 5.73
1761 1764 5.128171 TGGTGCGACTTAGGTCAACTAATAT 59.872 40.000 5.77 0.00 40.71 1.28
1778 1781 0.751277 CCCCTGCAATAATGGTGCGA 60.751 55.000 0.00 0.00 45.27 5.10
1817 1820 2.029649 GCAGAAACTAGTCCCACGTACA 60.030 50.000 0.00 0.00 0.00 2.90
1829 1832 4.507710 CAAGCTGTATGAGGCAGAAACTA 58.492 43.478 0.00 0.00 36.12 2.24
1906 1909 1.918800 CCCCTTTCCTGTCCGTCCT 60.919 63.158 0.00 0.00 0.00 3.85
2094 2097 5.238868 AGACGACGACTACTGCACATATTAT 59.761 40.000 0.00 0.00 0.00 1.28
2248 2251 1.627864 GGCCCTAATGTTGTGTTGGT 58.372 50.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.