Multiple sequence alignment - TraesCS6B01G233200

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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 TraesCS6B01G233200 chr6B 100.000 2648 0 0 1 2648 388346386 388343739 0 4891
1 TraesCS6B01G233200 chr6B 96.648 2655 82 6 1 2648 388156064 388153410 0 4403
2 TraesCS6B01G233200 chrUn 97.477 2656 59 7 1 2648 171044494 171047149 0 4527
3 TraesCS6B01G233200 chr6D 96.949 2655 72 8 1 2648 283206954 283209606 0 4446
4 TraesCS6B01G233200 chr6D 96.500 2657 84 8 1 2648 425972830 425975486 0 4383
5 TraesCS6B01G233200 chr4D 96.121 2655 95 7 1 2648 241073951 241076604 0 4325
6 TraesCS6B01G233200 chr4D 95.593 2655 106 10 1 2648 241283572 241280922 0 4244
7 TraesCS6B01G233200 chr4D 95.394 2323 91 11 1 2317 241367396 241365084 0 3683
8 TraesCS6B01G233200 chr3D 96.121 2655 95 7 1 2648 193371595 193374248 0 4325
9 TraesCS6B01G233200 chr1D 95.970 2655 83 9 1 2647 351013443 351010805 0 4289
10 TraesCS6B01G233200 chr7B 97.358 795 16 4 1859 2648 743088769 743089563 0 1347


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 TraesCS6B01G233200 chr6B 388343739 388346386 2647 True 4891 4891 100.000 1 2648 1 chr6B.!!$R2 2647
1 TraesCS6B01G233200 chr6B 388153410 388156064 2654 True 4403 4403 96.648 1 2648 1 chr6B.!!$R1 2647
2 TraesCS6B01G233200 chrUn 171044494 171047149 2655 False 4527 4527 97.477 1 2648 1 chrUn.!!$F1 2647
3 TraesCS6B01G233200 chr6D 283206954 283209606 2652 False 4446 4446 96.949 1 2648 1 chr6D.!!$F1 2647
4 TraesCS6B01G233200 chr6D 425972830 425975486 2656 False 4383 4383 96.500 1 2648 1 chr6D.!!$F2 2647
5 TraesCS6B01G233200 chr4D 241073951 241076604 2653 False 4325 4325 96.121 1 2648 1 chr4D.!!$F1 2647
6 TraesCS6B01G233200 chr4D 241280922 241283572 2650 True 4244 4244 95.593 1 2648 1 chr4D.!!$R1 2647
7 TraesCS6B01G233200 chr4D 241365084 241367396 2312 True 3683 3683 95.394 1 2317 1 chr4D.!!$R2 2316
8 TraesCS6B01G233200 chr3D 193371595 193374248 2653 False 4325 4325 96.121 1 2648 1 chr3D.!!$F1 2647
9 TraesCS6B01G233200 chr1D 351010805 351013443 2638 True 4289 4289 95.970 1 2647 1 chr1D.!!$R1 2646
10 TraesCS6B01G233200 chr7B 743088769 743089563 794 False 1347 1347 97.358 1859 2648 1 chr7B.!!$F1 789

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
795 797 0.889186 TTGGAAAGCGAACTCCCTGC 60.889 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 2128 0.552615 ACCCCACATAGGCCTTCCTT 60.553 55.0 12.58 0.0 40.66 3.36 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
103 104 4.459337 TCGCTGTGAGAAGAAGATCTACAA 59.541 41.667 0.00 0.00 0.00 2.41
190 191 6.918067 TCTTTCTTCTCAATCTACACCTCA 57.082 37.500 0.00 0.00 0.00 3.86
194 195 7.487822 TTCTTCTCAATCTACACCTCATTCT 57.512 36.000 0.00 0.00 0.00 2.40
463 464 5.531634 AGTTTGTGTTCGCATTTCATCAAT 58.468 33.333 0.00 0.00 0.00 2.57
563 564 4.058124 GTGTCTTGTCTTGCACATACTCA 58.942 43.478 0.00 0.00 33.90 3.41
715 717 6.805713 TCATTTCAGAACGATCAGCATACTA 58.194 36.000 0.00 0.00 0.00 1.82
795 797 0.889186 TTGGAAAGCGAACTCCCTGC 60.889 55.000 0.00 0.00 0.00 4.85
890 892 4.642445 TGACGACTGAATAAATAGCCGA 57.358 40.909 0.00 0.00 0.00 5.54
954 956 6.067217 AGGAAATGCAGTACCTATTCTGTT 57.933 37.500 6.57 0.00 34.57 3.16
1121 1126 8.563123 TTTATTCCTCTCTATATCGTCGTCAT 57.437 34.615 0.00 0.00 0.00 3.06
1285 1291 3.656559 AGTGCTTATTGCTTGCCAAAAG 58.343 40.909 0.00 0.00 43.37 2.27
1415 1421 8.101419 GGATCGGTTAAACATTCTATTAGGGAT 58.899 37.037 0.00 0.00 0.00 3.85
1453 1459 4.494484 TCTGTGTGGTATTCATTCTCGTG 58.506 43.478 0.00 0.00 0.00 4.35
1723 1729 1.065272 GGCCCGGGTATGTAAGTTCAA 60.065 52.381 24.63 0.00 0.00 2.69
1736 1743 9.377383 GTATGTAAGTTCAACATGTACAAACAC 57.623 33.333 15.93 9.45 38.78 3.32
1971 1983 0.527817 CATGTTCCTACGGCTCGGAC 60.528 60.000 0.00 0.00 0.00 4.79
1973 1985 3.136123 TTCCTACGGCTCGGACGG 61.136 66.667 4.20 0.00 39.02 4.79
1992 2004 9.412460 TCGGACGGGTATAGTTATTTATATCAT 57.588 33.333 0.00 0.00 0.00 2.45
2044 2057 7.719193 CCATTAACAAAACATCCCCTTTTCTTT 59.281 33.333 0.00 0.00 0.00 2.52
2221 2235 3.630312 ACTGCGTTTTCAAAAGCTTCCTA 59.370 39.130 0.00 0.00 42.61 2.94
2541 2556 7.829378 ATAAAAACCTAGTTCACTCGCTAAG 57.171 36.000 0.00 0.00 0.00 2.18
2566 2584 1.589716 GGCTGAATGGTGAAAGCGCT 61.590 55.000 2.64 2.64 36.92 5.92
2606 2625 7.125053 AGGAAAATTGGTCAAAAAGTAGGTTCA 59.875 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.137086 AGCGAGCACTTGATTACGGAT 59.863 47.619 0.00 0.00 0.00 4.18
103 104 2.092212 CAGGGAGAAATGGGTACATGCT 60.092 50.000 0.00 0.00 37.40 3.79
190 191 3.153919 GAGGATAGGTCTCTCGCAGAAT 58.846 50.000 0.00 0.00 34.09 2.40
194 195 3.008141 CGAGGATAGGTCTCTCGCA 57.992 57.895 0.00 0.00 42.70 5.10
341 342 8.758715 CAAGACTTTCCATTCATCTTTTTGTTC 58.241 33.333 0.00 0.00 0.00 3.18
419 420 4.202503 ACTTCAGGCATCCAAGAAAGAAGA 60.203 41.667 0.00 0.00 36.15 2.87
463 464 3.737702 GGTACAGCCCACTTTTCCA 57.262 52.632 0.00 0.00 0.00 3.53
484 485 5.297547 ACACGAGCAACTCTTTTCTTCATA 58.702 37.500 0.00 0.00 0.00 2.15
563 564 1.556911 AGATGAACCATTCACCGAGCT 59.443 47.619 0.00 0.00 43.48 4.09
715 717 3.986970 TGTCACGCAGAAGTCACAT 57.013 47.368 0.00 0.00 0.00 3.21
954 956 3.008835 AGCTTTGCATGATTAGCTCCA 57.991 42.857 0.00 0.00 39.67 3.86
1121 1126 7.546250 TTTTCAAAACCTATCATTAAGGGCA 57.454 32.000 0.00 0.00 38.54 5.36
1415 1421 1.257743 CAGAAGAGTCAAGACCGGGA 58.742 55.000 6.32 0.00 0.00 5.14
1453 1459 0.659957 GATGTGATTCCAAGAGCCGC 59.340 55.000 0.00 0.00 0.00 6.53
1489 1495 0.313672 GTGGTTGGATTTTGCGAGCA 59.686 50.000 0.00 0.00 0.00 4.26
1723 1729 9.615295 GTAAAATAAATCCGTGTTTGTACATGT 57.385 29.630 2.69 2.69 39.23 3.21
1874 1885 6.201044 CGAAGACTTAAATGAATAGCCATCGT 59.799 38.462 0.00 0.00 0.00 3.73
1992 2004 5.865085 ACAAGGAACTGTTTATAGCTGTCA 58.135 37.500 0.00 0.00 40.86 3.58
2114 2128 0.552615 ACCCCACATAGGCCTTCCTT 60.553 55.000 12.58 0.00 40.66 3.36
2221 2235 1.760613 TGAAATAGGAGCCGGTTCGAT 59.239 47.619 12.54 5.40 0.00 3.59
2541 2556 1.838112 TTCACCATTCAGCCATGGAC 58.162 50.000 18.40 7.03 46.18 4.02
2566 2584 5.538433 CCAATTTTCCTTTCTAGGTTGGTGA 59.462 40.000 0.00 0.00 42.60 4.02
2588 2607 6.040391 CAGGAATTGAACCTACTTTTTGACCA 59.960 38.462 0.00 0.00 35.84 4.02


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

AutoCloner maintained by Alex Coulton.