Multiple sequence alignment - TraesCS2B01G251000

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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 TraesCS2B01G251000 chr2B 100.000 3444 0 0 1 3444 261018128 261021571 0 6360
1 TraesCS2B01G251000 chr2B 96.284 3445 121 7 1 3444 209875996 209872558 0 5646
2 TraesCS2B01G251000 chr2B 96.116 3450 121 13 1 3444 379155446 379158888 0 5616
3 TraesCS2B01G251000 chr2B 95.563 3448 138 14 1 3444 259485622 259482186 0 5505
4 TraesCS2B01G251000 chr2B 95.478 3450 145 10 1 3444 75310981 75307537 0 5496
5 TraesCS2B01G251000 chr3B 97.043 3449 96 6 1 3444 252185471 252188918 0 5799
6 TraesCS2B01G251000 chr3B 96.084 3447 126 9 1 3444 236260869 236257429 0 5609
7 TraesCS2B01G251000 chr1B 96.664 3447 107 8 1 3444 330756298 330759739 0 5722
8 TraesCS2B01G251000 chr7B 96.605 3446 109 6 1 3444 430145635 430149074 0 5709
9 TraesCS2B01G251000 chr6B 95.564 3449 141 11 1 3444 378838155 378841596 0 5511


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 TraesCS2B01G251000 chr2B 261018128 261021571 3443 False 6360 6360 100.000 1 3444 1 chr2B.!!$F1 3443
1 TraesCS2B01G251000 chr2B 209872558 209875996 3438 True 5646 5646 96.284 1 3444 1 chr2B.!!$R2 3443
2 TraesCS2B01G251000 chr2B 379155446 379158888 3442 False 5616 5616 96.116 1 3444 1 chr2B.!!$F2 3443
3 TraesCS2B01G251000 chr2B 259482186 259485622 3436 True 5505 5505 95.563 1 3444 1 chr2B.!!$R3 3443
4 TraesCS2B01G251000 chr2B 75307537 75310981 3444 True 5496 5496 95.478 1 3444 1 chr2B.!!$R1 3443
5 TraesCS2B01G251000 chr3B 252185471 252188918 3447 False 5799 5799 97.043 1 3444 1 chr3B.!!$F1 3443
6 TraesCS2B01G251000 chr3B 236257429 236260869 3440 True 5609 5609 96.084 1 3444 1 chr3B.!!$R1 3443
7 TraesCS2B01G251000 chr1B 330756298 330759739 3441 False 5722 5722 96.664 1 3444 1 chr1B.!!$F1 3443
8 TraesCS2B01G251000 chr7B 430145635 430149074 3439 False 5709 5709 96.605 1 3444 1 chr7B.!!$F1 3443
9 TraesCS2B01G251000 chr6B 378838155 378841596 3441 False 5511 5511 95.564 1 3444 1 chr6B.!!$F1 3443

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
564 576 1.354337 CCATCAACACCGACGCTGAG 61.354 60.0 0.0 0.0 0.00 3.35 F
1191 1204 0.105760 AGGCCGATGAGGTGATCTCT 60.106 55.0 0.0 0.0 42.86 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 2420 0.738762 GGGGCGGTCGTAGAAGTTTC 60.739 60.0 0.0 0.0 39.69 2.78 R
3175 3196 1.319614 GCTCGCCCTCTCTCTTGACT 61.320 60.0 0.0 0.0 0.00 3.41 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
21 22 2.437359 GCCCGCTGAAGCAGTGAT 60.437 61.111 9.38 0.00 43.78 3.06
495 507 4.562082 TCACTGGTATTTGGTACGTTCAG 58.438 43.478 0.00 0.00 33.94 3.02
516 528 5.070446 TCAGTTACACTTCAATCACCAGTCT 59.930 40.000 0.00 0.00 0.00 3.24
564 576 1.354337 CCATCAACACCGACGCTGAG 61.354 60.000 0.00 0.00 0.00 3.35
705 717 2.992543 CAGCTTGACAAGACTAGTCAGC 59.007 50.000 24.44 20.97 45.72 4.26
710 722 5.474578 TTGACAAGACTAGTCAGCTCAAT 57.525 39.130 24.44 0.00 45.72 2.57
976 989 7.093333 ACAAACCAAAAACTTCTCTCTCCAAAT 60.093 33.333 0.00 0.00 0.00 2.32
1041 1054 1.519234 GCGTCATCATGCCGAGACA 60.519 57.895 0.00 0.00 0.00 3.41
1077 1090 5.242434 AGCAACCTCATCAACATTAACGTA 58.758 37.500 0.00 0.00 0.00 3.57
1100 1113 3.969631 CGAGAAGCGCGAGTACAG 58.030 61.111 12.10 0.00 0.00 2.74
1149 1162 0.737715 GCAACGAGACGCTGGAGATT 60.738 55.000 0.00 0.00 0.00 2.40
1179 1192 0.743345 GCGTACCAGAAAAGGCCGAT 60.743 55.000 0.00 0.00 0.00 4.18
1191 1204 0.105760 AGGCCGATGAGGTGATCTCT 60.106 55.000 0.00 0.00 42.86 3.10
1231 1244 1.392710 CGGCAGGGTTCGTAGGATCT 61.393 60.000 0.00 0.00 0.00 2.75
1280 1293 1.203492 AGATGAACCTCCCCAGAAGGT 60.203 52.381 0.00 0.00 37.57 3.50
1372 1386 3.459598 AGCAATCCTACTCATTTGCCCTA 59.540 43.478 3.10 0.00 44.21 3.53
1462 1476 6.769512 AGATGTACTAGTGTGGTTTGTGAAT 58.230 36.000 5.39 0.00 0.00 2.57
1764 1780 7.512992 TGTGTTATCCCATTTCAACCAAAAAT 58.487 30.769 0.00 0.00 0.00 1.82
1936 1953 7.687941 AAAAACTACTTCATGGATTCATCGT 57.312 32.000 0.00 0.00 0.00 3.73
2436 2453 0.537371 CGCCCCTATTGCCCCTTTAG 60.537 60.000 0.00 0.00 0.00 1.85
2482 2499 4.567971 TGCCTTCGTTTTACTTCCGATTA 58.432 39.130 0.00 0.00 0.00 1.75
2845 2862 4.758674 AGTCCGTAAGCGCTACTATGAATA 59.241 41.667 12.05 0.00 33.24 1.75
3055 3075 6.867293 AGTCGAGTACTAGATTCAAACAAACC 59.133 38.462 9.03 0.00 36.36 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.873817 TGTGACTGCATTCAAAAGGATTG 58.126 39.130 8.50 0.00 0.00 2.67
193 198 5.653769 ACTATGCCTTTTGTACTACCGACTA 59.346 40.000 0.00 0.00 0.00 2.59
495 507 5.297547 TCAGACTGGTGATTGAAGTGTAAC 58.702 41.667 1.81 0.00 0.00 2.50
516 528 3.977134 ACTCCTCTACTGTCGTACTCA 57.023 47.619 0.00 0.00 0.00 3.41
564 576 0.727398 GCTTATCCCAGTTGCACGTC 59.273 55.000 0.00 0.00 0.00 4.34
573 585 4.348863 ACTTATCAGCTGCTTATCCCAG 57.651 45.455 9.47 0.72 0.00 4.45
710 722 7.879160 ACCGTCCATGTGAAATAGTTTTTACTA 59.121 33.333 0.00 0.00 33.66 1.82
1041 1054 0.250513 GGTTGCTCCTCTTGTCCGAT 59.749 55.000 0.00 0.00 0.00 4.18
1066 1079 0.246086 TCGCCGGGTACGTTAATGTT 59.754 50.000 5.48 0.00 38.78 2.71
1149 1162 2.342279 GGTACGCTGGTGCAGACA 59.658 61.111 0.00 0.00 39.64 3.41
1179 1192 2.424091 CCAGAGCCTAGAGATCACCTCA 60.424 54.545 0.00 0.00 44.40 3.86
1191 1204 1.487976 CCAAGCTTCATCCAGAGCCTA 59.512 52.381 0.00 0.00 0.00 3.93
1231 1244 2.646117 TAGTGCACACCAACGCCGAA 62.646 55.000 21.04 0.00 0.00 4.30
1581 1596 9.778741 TTGTATCAACTTCAGAAACTTCACTAT 57.221 29.630 0.00 0.00 0.00 2.12
2403 2420 0.738762 GGGGCGGTCGTAGAAGTTTC 60.739 60.000 0.00 0.00 39.69 2.78
2436 2453 4.754114 GGCTCTGATGTTATCTTCATCCAC 59.246 45.833 0.00 0.00 40.38 4.02
2482 2499 5.473066 ACAACAAGATAAAAGGCAAGCAT 57.527 34.783 0.00 0.00 0.00 3.79
2845 2862 6.940867 TGTAGACTGAGTTGTACTGATAGTGT 59.059 38.462 7.35 0.00 0.00 3.55
3175 3196 1.319614 GCTCGCCCTCTCTCTTGACT 61.320 60.000 0.00 0.00 0.00 3.41
3344 3365 0.623723 TTTTCCGGCCCAGATAGCTT 59.376 50.000 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.