Multiple sequence alignment - TraesCS4A01G156100

Loading Multiple Alignment...

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 TraesCS4A01G156100 chr4A 100.000 2469 0 0 1 2469 310788252 310790720 0 4560
1 TraesCS4A01G156100 chr5D 96.244 2476 85 5 1 2469 503226444 503223970 0 4050
2 TraesCS4A01G156100 chr5D 96.003 2477 90 6 1 2469 503270100 503272575 0 4017
3 TraesCS4A01G156100 chr5D 95.724 2479 94 7 1 2469 503236761 503234285 0 3980
4 TraesCS4A01G156100 chr3A 96.042 2476 89 6 1 2469 66009397 66011870 0 4021
5 TraesCS4A01G156100 chrUn 95.756 2474 99 4 1 2469 216510382 216512854 0 3982
6 TraesCS4A01G156100 chr1B 95.434 2475 103 8 1 2469 633745673 633748143 0 3936
7 TraesCS4A01G156100 chr2B 95.432 2474 104 7 1 2469 474916664 474914195 0 3934
8 TraesCS4A01G156100 chr2B 94.460 2437 125 9 1 2430 272614550 272616983 0 3744


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 TraesCS4A01G156100 chr4A 310788252 310790720 2468 False 4560 4560 100.000 1 2469 1 chr4A.!!$F1 2468
1 TraesCS4A01G156100 chr5D 503223970 503226444 2474 True 4050 4050 96.244 1 2469 1 chr5D.!!$R1 2468
2 TraesCS4A01G156100 chr5D 503270100 503272575 2475 False 4017 4017 96.003 1 2469 1 chr5D.!!$F1 2468
3 TraesCS4A01G156100 chr5D 503234285 503236761 2476 True 3980 3980 95.724 1 2469 1 chr5D.!!$R2 2468
4 TraesCS4A01G156100 chr3A 66009397 66011870 2473 False 4021 4021 96.042 1 2469 1 chr3A.!!$F1 2468
5 TraesCS4A01G156100 chrUn 216510382 216512854 2472 False 3982 3982 95.756 1 2469 1 chrUn.!!$F1 2468
6 TraesCS4A01G156100 chr1B 633745673 633748143 2470 False 3936 3936 95.434 1 2469 1 chr1B.!!$F1 2468
7 TraesCS4A01G156100 chr2B 474914195 474916664 2469 True 3934 3934 95.432 1 2469 1 chr2B.!!$R1 2468
8 TraesCS4A01G156100 chr2B 272614550 272616983 2433 False 3744 3744 94.460 1 2430 1 chr2B.!!$F1 2429

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
497 498 1.622312 GTTTCGTAAGGGGACTGGAGT 59.378 52.381 0.0 0.0 42.68 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 1994 2.965831 CTCTCCATCGGAACAATAGGGA 59.034 50.0 0.0 0.0 0.0 4.2 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
58 59 2.266279 ACGAGGAAAAGGATCCCTTCA 58.734 47.619 20.43 0.00 43.92 3.02
102 103 6.931281 CCGTATGAGGTGAAAATCTCATGTAT 59.069 38.462 10.97 0.00 46.50 2.29
129 130 3.320129 TGTAAAGGGACAGTAAGGGTGT 58.680 45.455 0.00 0.00 0.00 4.16
135 136 5.216665 AGGGACAGTAAGGGTGTCTTATA 57.783 43.478 3.44 0.00 43.34 0.98
200 201 5.416947 CCTTACGTAAAGTTGCCAGAGTAT 58.583 41.667 9.68 0.00 32.89 2.12
263 264 9.466497 CTGGTATTGGCCATAATATACAAGAAT 57.534 33.333 19.19 3.85 37.96 2.40
295 296 6.375418 AGTATTAGTAAGAGGAGGAAGGGTC 58.625 44.000 0.00 0.00 0.00 4.46
305 306 4.384465 AGGAGGAAGGGTCAAGGATTTAT 58.616 43.478 0.00 0.00 0.00 1.40
357 358 3.187700 CCCTAGATGTTGTCGCAGTAAC 58.812 50.000 0.00 0.00 0.00 2.50
464 465 6.372659 AGAAACATGTGAAGTGTATGGCTAAG 59.627 38.462 0.00 0.00 0.00 2.18
497 498 1.622312 GTTTCGTAAGGGGACTGGAGT 59.378 52.381 0.00 0.00 42.68 3.85
599 600 8.547481 AAATTCTTTCAGAGGTTTTCCCTTAA 57.453 30.769 0.00 0.00 46.51 1.85
606 607 6.610830 TCAGAGGTTTTCCCTTAATTTGTCT 58.389 36.000 0.00 0.00 46.51 3.41
614 615 7.595819 TTTCCCTTAATTTGTCTGTGTCAAT 57.404 32.000 0.00 0.00 0.00 2.57
641 643 6.828672 ACAATTCGAAATACCTCGACTTTTC 58.171 36.000 0.00 0.00 46.95 2.29
642 644 6.649557 ACAATTCGAAATACCTCGACTTTTCT 59.350 34.615 0.00 0.00 46.95 2.52
654 656 3.257624 TCGACTTTTCTAGAACAGGTCCC 59.742 47.826 20.06 7.67 0.00 4.46
656 658 4.502604 CGACTTTTCTAGAACAGGTCCCAA 60.503 45.833 20.06 3.27 0.00 4.12
673 675 6.384886 AGGTCCCAATCAAATAGCAATGATTT 59.615 34.615 0.00 0.00 42.12 2.17
724 726 3.437213 TGGAAACCTAAGGACTCGATCA 58.563 45.455 0.00 0.00 0.00 2.92
854 856 6.672218 TCCCTATAGAATTCTGTGGAAAGTCA 59.328 38.462 18.47 0.00 34.90 3.41
980 985 8.584063 AGCCCTTATAAAAAGAAAACGGATTA 57.416 30.769 0.00 0.00 0.00 1.75
1019 1024 3.089284 TCATGTCACATCGAGGTACTGT 58.911 45.455 0.77 0.00 41.55 3.55
1098 1103 7.143514 GGTGGTTAACCGTATTATGAAAACA 57.856 36.000 19.65 0.00 39.81 2.83
1100 1105 7.119553 GGTGGTTAACCGTATTATGAAAACAGA 59.880 37.037 19.65 0.00 39.81 3.41
1143 1148 2.846039 TTCTCTATCGAGCCGTGAAC 57.154 50.000 0.00 0.00 37.19 3.18
1168 1173 8.253113 ACAAGATTCAACAAAAGACAGAAACAT 58.747 29.630 0.00 0.00 0.00 2.71
1209 1214 6.627243 ACGTCAAGCAATATGTAGAGTAACA 58.373 36.000 0.00 0.00 0.00 2.41
1227 1234 9.275572 AGAGTAACACCCAATATAGGAGTAAAA 57.724 33.333 0.00 0.00 0.00 1.52
1279 1286 6.292919 GGAAAGTTCCGATTGAAATAGGATCG 60.293 42.308 5.81 0.00 39.46 3.69
1293 1300 6.546428 AATAGGATCGAAACAAGGAAGAGA 57.454 37.500 0.00 0.00 0.00 3.10
1450 1457 0.620030 TGGCAGAGGCAAATAGAGCA 59.380 50.000 0.00 0.00 43.71 4.26
1479 1486 6.531240 GCACATTTTCGTTAATCCATGAACAT 59.469 34.615 0.00 0.00 0.00 2.71
1506 1513 8.891985 ATCTATGTATGTAGACACATGGATCT 57.108 34.615 4.55 1.67 45.00 2.75
1515 1522 5.946942 AGACACATGGATCTGTACATCTT 57.053 39.130 0.00 0.00 0.00 2.40
1562 1569 5.048643 GGAGAATCGGACGATATCTTTCTCA 60.049 44.000 24.36 0.00 38.34 3.27
1668 1675 9.425248 AAAGAAGAATCTTATGGAAATGGCATA 57.575 29.630 0.00 0.00 45.19 3.14
1709 1716 8.491134 CCTATTCATGGGGATTCCGTAAATATA 58.509 37.037 0.00 0.00 38.76 0.86
1710 1717 9.899661 CTATTCATGGGGATTCCGTAAATATAA 57.100 33.333 0.00 0.00 38.76 0.98
1764 1771 4.038042 TCGGAGATTGGATGCAGTTACTAG 59.962 45.833 0.00 0.00 0.00 2.57
1770 1777 7.341805 AGATTGGATGCAGTTACTAGTTCATT 58.658 34.615 0.00 0.00 0.00 2.57
1775 1782 9.143155 TGGATGCAGTTACTAGTTCATTATCTA 57.857 33.333 0.00 0.00 0.00 1.98
1848 1855 3.893720 AGCGTTTCATTTGCTTCTCTTG 58.106 40.909 0.00 0.00 34.80 3.02
1870 1877 6.491714 TGAATGGAAGTTTCATTTTCCCAA 57.508 33.333 10.79 0.00 41.75 4.12
1927 1934 6.491403 TCTGATGATCGATTCAACCTCTGATA 59.509 38.462 0.00 0.00 38.03 2.15
2112 2119 8.692710 TGTTCAACGTTATGTATTCCTCTATCT 58.307 33.333 0.00 0.00 0.00 1.98
2130 2137 8.741101 CTCTATCTGTAGAGTACATTGAATGC 57.259 38.462 4.84 0.00 45.85 3.56
2185 2192 5.933617 TCGTATTAACAGCTACTCTAGGGA 58.066 41.667 0.00 0.00 0.00 4.20
2212 2219 5.933790 TGTTTTTATGTGGTGCTAACGATC 58.066 37.500 0.00 0.00 0.00 3.69
2415 2427 4.574421 TCGAGCTTCAAGAAATTGTGAACA 59.426 37.500 0.00 0.00 30.73 3.18
2461 2473 4.132122 ACTCCCCAGGAATTTCAATTGT 57.868 40.909 5.13 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.174617 GAGAGTCTCCGCCCTTCTTG 59.825 60.000 9.15 0.00 0.00 3.02
58 59 2.437413 GGCTCCTCGGTCAATTCTTTT 58.563 47.619 0.00 0.00 0.00 2.27
129 130 8.909923 TGATAGTGGAAAAGTCGACATATAAGA 58.090 33.333 19.50 0.00 35.08 2.10
135 136 4.935808 GGTTGATAGTGGAAAAGTCGACAT 59.064 41.667 19.50 1.86 35.08 3.06
200 201 7.890127 AGTGATTTCAAATCCAGAGGTTAATCA 59.110 33.333 7.68 0.00 0.00 2.57
295 296 4.672587 TCTCACTCCGGATAAATCCTTG 57.327 45.455 3.57 0.00 44.93 3.61
357 358 1.289109 ACGCCCTTGTTGACGATTCG 61.289 55.000 4.14 4.14 0.00 3.34
497 498 5.163301 GGATCTTTTGTCTCATGGTAGCCTA 60.163 44.000 0.00 0.00 0.00 3.93
599 600 8.349245 TCGAATTGTTTATTGACACAGACAAAT 58.651 29.630 0.00 0.00 31.69 2.32
606 607 8.788806 AGGTATTTCGAATTGTTTATTGACACA 58.211 29.630 0.00 0.00 0.00 3.72
641 643 5.529060 GCTATTTGATTGGGACCTGTTCTAG 59.471 44.000 0.00 0.00 0.00 2.43
642 644 5.045213 TGCTATTTGATTGGGACCTGTTCTA 60.045 40.000 0.00 0.00 0.00 2.10
654 656 8.114290 GTGCTTCAAATCATTGCTATTTGATTG 58.886 33.333 11.94 9.95 46.93 2.67
656 658 7.553334 AGTGCTTCAAATCATTGCTATTTGAT 58.447 30.769 11.94 0.00 46.93 2.57
673 675 6.321181 AGTGTAATGGAAAAAGAAGTGCTTCA 59.679 34.615 13.58 0.00 41.84 3.02
1143 1148 8.638685 ATGTTTCTGTCTTTTGTTGAATCTTG 57.361 30.769 0.00 0.00 0.00 3.02
1279 1286 3.632145 TGGCAAGTTCTCTTCCTTGTTTC 59.368 43.478 0.00 0.00 40.13 2.78
1450 1457 5.446143 TGGATTAACGAAAATGTGCAAGT 57.554 34.783 0.00 0.00 0.00 3.16
1506 1513 7.102993 TGATTCTTTTCCGATCAAGATGTACA 58.897 34.615 0.00 0.00 0.00 2.90
1515 1522 7.564793 TCCTTCTATTGATTCTTTTCCGATCA 58.435 34.615 0.00 0.00 0.00 2.92
1577 1584 9.034544 CATGATTTCCGTTTTCTCTTTCTTTTT 57.965 29.630 0.00 0.00 0.00 1.94
1663 1670 8.870075 AATAGGATCAAACCTTATTCTATGCC 57.130 34.615 0.00 0.00 41.00 4.40
1668 1675 7.946776 CCCATGAATAGGATCAAACCTTATTCT 59.053 37.037 0.00 0.00 41.00 2.40
1734 1741 3.274288 GCATCCAATCTCCGAAAAGTCT 58.726 45.455 0.00 0.00 0.00 3.24
1764 1771 9.481340 TCATTCTGTACATGCTAGATAATGAAC 57.519 33.333 0.00 0.00 0.00 3.18
1770 1777 9.890629 AAGTTTTCATTCTGTACATGCTAGATA 57.109 29.630 0.00 0.00 0.00 1.98
1775 1782 6.882610 TGAAGTTTTCATTCTGTACATGCT 57.117 33.333 0.00 0.00 34.08 3.79
1848 1855 7.800155 TTTTGGGAAAATGAAACTTCCATTC 57.200 32.000 3.44 0.00 42.56 2.67
1987 1994 2.965831 CTCTCCATCGGAACAATAGGGA 59.034 50.000 0.00 0.00 0.00 4.20
2112 2119 9.836864 ATTTCTATGCATTCAATGTACTCTACA 57.163 29.630 3.54 0.00 43.80 2.74
2130 2137 9.553064 AGAAACTCTGTTATAGCCATTTCTATG 57.447 33.333 0.00 0.00 33.54 2.23
2159 2166 7.040617 TCCCTAGAGTAGCTGTTAATACGAATG 60.041 40.741 0.00 0.00 0.00 2.67
2185 2192 6.205853 TCGTTAGCACCACATAAAAACATTCT 59.794 34.615 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.