Multiple sequence alignment - TraesCS3A01G188100

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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 TraesCS3A01G188100 chr3A 100.000 2528 0 0 1 2528 227631791 227634318 0 4669
1 TraesCS3A01G188100 chr2A 96.451 2536 79 8 1 2528 423420233 423417701 0 4174
2 TraesCS3A01G188100 chr5B 95.491 2528 103 7 1 2521 34121984 34124507 0 4026
3 TraesCS3A01G188100 chr1B 96.098 2358 71 11 1 2348 638719402 638717056 0 3825
4 TraesCS3A01G188100 chr6B 95.711 2355 86 12 1 2348 128411133 128413479 0 3775
5 TraesCS3A01G188100 chr6B 95.458 2356 92 12 1 2348 265001345 265003693 0 3744
6 TraesCS3A01G188100 chr3B 95.512 2362 96 6 1 2355 730354985 730352627 0 3766
7 TraesCS3A01G188100 chr2B 96.037 2296 79 9 62 2348 760923918 760926210 0 3725
8 TraesCS3A01G188100 chr7B 95.946 2294 83 7 64 2348 47165380 47163088 0 3712
9 TraesCS3A01G188100 chr7D 97.577 2022 40 6 1 2014 381881843 381879823 0 3454
10 TraesCS3A01G188100 chr1A 96.124 516 17 3 2014 2528 94581532 94582045 0 839


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 TraesCS3A01G188100 chr3A 227631791 227634318 2527 False 4669 4669 100.000 1 2528 1 chr3A.!!$F1 2527
1 TraesCS3A01G188100 chr2A 423417701 423420233 2532 True 4174 4174 96.451 1 2528 1 chr2A.!!$R1 2527
2 TraesCS3A01G188100 chr5B 34121984 34124507 2523 False 4026 4026 95.491 1 2521 1 chr5B.!!$F1 2520
3 TraesCS3A01G188100 chr1B 638717056 638719402 2346 True 3825 3825 96.098 1 2348 1 chr1B.!!$R1 2347
4 TraesCS3A01G188100 chr6B 128411133 128413479 2346 False 3775 3775 95.711 1 2348 1 chr6B.!!$F1 2347
5 TraesCS3A01G188100 chr6B 265001345 265003693 2348 False 3744 3744 95.458 1 2348 1 chr6B.!!$F2 2347
6 TraesCS3A01G188100 chr3B 730352627 730354985 2358 True 3766 3766 95.512 1 2355 1 chr3B.!!$R1 2354
7 TraesCS3A01G188100 chr2B 760923918 760926210 2292 False 3725 3725 96.037 62 2348 1 chr2B.!!$F1 2286
8 TraesCS3A01G188100 chr7B 47163088 47165380 2292 True 3712 3712 95.946 64 2348 1 chr7B.!!$R1 2284
9 TraesCS3A01G188100 chr7D 381879823 381881843 2020 True 3454 3454 97.577 1 2014 1 chr7D.!!$R1 2013
10 TraesCS3A01G188100 chr1A 94581532 94582045 513 False 839 839 96.124 2014 2528 1 chr1A.!!$F1 514

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
782 791 0.819582 AGCCAATTTCCATCAAGGCG 59.18 50.0 0.0 0.0 46.34 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1729 0.105039 GCTATTGCGGCTACACCTCT 59.895 55.0 0.0 0.0 35.61 3.69 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
39 40 4.935808 CCTATGTAGCCGTTTGTTTTCTCT 59.064 41.667 0.00 0.00 0.00 3.10
158 159 7.440198 GGGTCTACCTACCTTATGACATTTAC 58.560 42.308 0.00 0.00 39.65 2.01
261 262 3.895232 GAGGTATGTCTCCATGTGTGT 57.105 47.619 0.00 0.00 32.29 3.72
373 374 5.946972 TCTCTCTCGTCCAATAAGAGTTTCT 59.053 40.000 0.00 0.00 38.15 2.52
425 427 3.384467 TCCAAAGCTCCACAAGGAAAAAG 59.616 43.478 0.00 0.00 45.19 2.27
552 558 8.707938 AAACTTCTTCATGAAAGGTCAAAAAG 57.292 30.769 9.88 5.96 37.30 2.27
592 598 6.014840 TGGGTTTCTTAATGACTAGTCGTTCT 60.015 38.462 29.17 13.11 39.36 3.01
655 663 4.609691 TTTCCGAATGACCTTATTTCGC 57.390 40.909 0.00 0.00 0.00 4.70
656 664 2.557317 TCCGAATGACCTTATTTCGCC 58.443 47.619 0.00 0.00 0.00 5.54
728 736 4.531854 TCGCCAAAATGGGATGAATCTTA 58.468 39.130 0.00 0.00 38.19 2.10
737 745 5.314718 TGGGATGAATCTTATCATGCAGT 57.685 39.130 10.29 0.00 46.44 4.40
782 791 0.819582 AGCCAATTTCCATCAAGGCG 59.180 50.000 0.00 0.00 46.34 5.52
786 795 2.368439 CAATTTCCATCAAGGCGAGGA 58.632 47.619 0.00 0.00 37.29 3.71
809 819 3.394940 GGTAAATAAGGGGGAAGAGGAGG 59.605 52.174 0.00 0.00 0.00 4.30
937 947 4.260784 CCGAGCAATCTTAGTTATTGGTGC 60.261 45.833 5.34 0.00 43.17 5.01
956 966 0.945265 CGGGTTCGGTTCGTTAGCAA 60.945 55.000 0.00 0.00 0.00 3.91
1195 1206 2.105821 AGGGAATTTGTTCGGTGTCTCA 59.894 45.455 0.00 0.00 0.00 3.27
1444 1456 1.558756 CCAGTCTTCTTCATCTGGCCT 59.441 52.381 3.32 0.00 40.43 5.19
1552 1566 5.014966 AGGATCTTATAGGTCGGGTAGCTTA 59.985 44.000 0.00 0.00 37.13 3.09
1623 1640 6.245408 GGCATCCCAACAATTATATACCTGA 58.755 40.000 0.00 0.00 0.00 3.86
1712 1729 2.734175 CGCAGTATACCTGACAAAGCGA 60.734 50.000 0.00 0.00 44.49 4.93
1944 1963 5.477984 TCTTCTTGTTCTTTGCCATAATGCT 59.522 36.000 0.00 0.00 0.00 3.79
2330 2350 1.202604 GGAAGGTTGTGAAGACCGTCA 60.203 52.381 10.50 0.00 44.32 4.35
2488 2508 1.196012 TGTTGGTTTGGTGGGGAAAC 58.804 50.000 0.00 0.00 33.34 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.472361 GTATCGCCTCATACAAATTAGTTAAGA 57.528 33.333 0.00 0.00 30.61 2.10
158 159 6.525280 CCCCTTAATACAACGTTCATTTTTCG 59.475 38.462 0.00 0.00 0.00 3.46
261 262 6.304882 CGTATAATGATAGACGCTTCTTCGA 58.695 40.000 0.00 0.00 39.54 3.71
425 427 8.451908 AAGCAATATTGTTGTCCTATTACTCC 57.548 34.615 16.61 0.00 0.00 3.85
552 558 5.012893 AGAAACCCATGAAATCCAAGTCTC 58.987 41.667 0.00 0.00 0.00 3.36
592 598 3.243602 GCCGGTTTCTTAAGGCTTCAAAA 60.244 43.478 1.30 0.04 45.67 2.44
638 646 4.035091 TGATTGGCGAAATAAGGTCATTCG 59.965 41.667 3.02 3.02 46.36 3.34
655 663 5.181245 ACAGATTTGTCGGTTAGTTGATTGG 59.819 40.000 0.00 0.00 29.46 3.16
656 664 6.241207 ACAGATTTGTCGGTTAGTTGATTG 57.759 37.500 0.00 0.00 29.46 2.67
782 791 4.304659 TCTTCCCCCTTATTTACCTCCTC 58.695 47.826 0.00 0.00 0.00 3.71
786 795 4.308128 CTCCTCTTCCCCCTTATTTACCT 58.692 47.826 0.00 0.00 0.00 3.08
809 819 9.141400 AGTCATTTCTCTTTTCTATCGTTACAC 57.859 33.333 0.00 0.00 0.00 2.90
877 887 4.406456 TCAAATGCTGGTTAAGTGTGGAT 58.594 39.130 0.00 0.00 0.00 3.41
937 947 0.945265 TTGCTAACGAACCGAACCCG 60.945 55.000 0.00 0.00 0.00 5.28
1623 1640 0.401738 CGGGGTGGGCATCAGATTAT 59.598 55.000 0.00 0.00 0.00 1.28
1712 1729 0.105039 GCTATTGCGGCTACACCTCT 59.895 55.000 0.00 0.00 35.61 3.69
1944 1963 0.901114 TCCAACTCGTCCCGGAATGA 60.901 55.000 0.73 0.00 0.00 2.57
2213 2233 4.864247 GCAATTTAAACATGTTCGCATCCT 59.136 37.500 12.39 0.00 35.23 3.24
2287 2307 2.623416 CCGGAGGCTTTTCTCTGTTTTT 59.377 45.455 0.00 0.00 46.14 1.94
2330 2350 2.966516 GTCCTTTCCTCCGGAGTCATAT 59.033 50.000 29.25 0.00 31.21 1.78
2488 2508 0.692419 AGCCCTCATACCCACTCCTG 60.692 60.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.