Multiple sequence alignment - TraesCS6A01G145200

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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 TraesCS6A01G145200 chr6A 100.000 3349 0 0 1 3349 123445179 123448527 0 6185
1 TraesCS6A01G145200 chr6D 97.310 2862 57 14 501 3349 102114482 102117336 0 4841
2 TraesCS6A01G145200 chr6D 95.445 483 21 1 1 483 102113937 102114418 0 769
3 TraesCS6A01G145200 chr6B 95.114 1576 39 15 1791 3349 187832521 187834075 0 2449
4 TraesCS6A01G145200 chr6B 96.453 1297 29 9 501 1788 187830996 187832284 0 2124
5 TraesCS6A01G145200 chr6B 95.859 483 20 0 1 483 187830450 187830932 0 782


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 TraesCS6A01G145200 chr6A 123445179 123448527 3348 False 6185 6185 100.000000 1 3349 1 chr6A.!!$F1 3348
1 TraesCS6A01G145200 chr6D 102113937 102117336 3399 False 2805 4841 96.377500 1 3349 2 chr6D.!!$F1 3348
2 TraesCS6A01G145200 chr6B 187830450 187834075 3625 False 1785 2449 95.808667 1 3349 3 chr6B.!!$F1 3348

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
496 497 0.104855 GTCATGGGCTCACGCAGATA 59.895 55.0 0.00 0.00 42.66 1.98 F
497 498 0.104855 TCATGGGCTCACGCAGATAC 59.895 55.0 0.00 0.00 42.66 2.24 F
1151 1202 0.169009 GAAGTTCTTCGTGGCATGCC 59.831 55.0 30.54 30.54 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2379 0.957395 AAGGTCTTGCATGGACGCAG 60.957 55.000 12.20 0.0 44.14 5.18 R
2272 2575 2.105128 CATCGTCAGAGACCCGGC 59.895 66.667 0.00 0.0 0.00 6.13 R
2415 2719 2.370281 ATTCTGTCAGTAGTGCACCG 57.630 50.000 14.63 0.0 0.00 4.94 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
65 66 3.733337 TGTTTTTGTGTGCTTTGTTGGT 58.267 36.364 0.00 0.00 0.00 3.67
190 191 3.879295 CGGAACCAGCATCTGTGAAATAT 59.121 43.478 0.00 0.00 0.00 1.28
304 305 3.437213 TCAGGCTTACCAGCTAACTGTA 58.563 45.455 0.00 0.00 46.44 2.74
317 318 8.100791 ACCAGCTAACTGTAATGATCTGTTTTA 58.899 33.333 0.00 0.00 42.81 1.52
387 388 5.390145 CCACCGTTGTAACTTATTAGTGCAC 60.390 44.000 9.40 9.40 34.01 4.57
483 484 9.546428 TGTAGAATACTGTAATCAATGTCATGG 57.454 33.333 5.74 0.00 43.54 3.66
484 485 8.993121 GTAGAATACTGTAATCAATGTCATGGG 58.007 37.037 5.74 0.00 38.91 4.00
485 486 6.488006 AGAATACTGTAATCAATGTCATGGGC 59.512 38.462 5.74 0.00 0.00 5.36
487 488 4.202441 ACTGTAATCAATGTCATGGGCTC 58.798 43.478 0.00 0.00 0.00 4.70
488 489 4.201657 CTGTAATCAATGTCATGGGCTCA 58.798 43.478 0.00 0.00 0.00 4.26
489 490 3.947196 TGTAATCAATGTCATGGGCTCAC 59.053 43.478 0.00 0.00 0.00 3.51
490 491 1.671979 ATCAATGTCATGGGCTCACG 58.328 50.000 0.00 0.00 0.00 4.35
493 494 1.028330 AATGTCATGGGCTCACGCAG 61.028 55.000 0.00 0.00 42.66 5.18
494 495 1.902765 ATGTCATGGGCTCACGCAGA 61.903 55.000 0.00 0.00 42.66 4.26
495 496 1.153289 GTCATGGGCTCACGCAGAT 60.153 57.895 0.00 0.00 42.66 2.90
496 497 0.104855 GTCATGGGCTCACGCAGATA 59.895 55.000 0.00 0.00 42.66 1.98
497 498 0.104855 TCATGGGCTCACGCAGATAC 59.895 55.000 0.00 0.00 42.66 2.24
622 672 4.458989 ACGAAATGATTTTGCAGCTCCTTA 59.541 37.500 5.08 0.00 0.00 2.69
778 828 2.948315 CTCCTTCATAAAGCAAGGCTCC 59.052 50.000 0.00 0.00 38.25 4.70
900 951 4.324563 CCACTAAACACCCCATCTCTCATT 60.325 45.833 0.00 0.00 0.00 2.57
973 1024 5.204833 CAACAAAGAACACATAGAACACCG 58.795 41.667 0.00 0.00 0.00 4.94
1087 1138 3.656559 GTTTGGAGTTTTGCAGCATCAT 58.343 40.909 0.00 0.00 0.00 2.45
1151 1202 0.169009 GAAGTTCTTCGTGGCATGCC 59.831 55.000 30.54 30.54 0.00 4.40
1282 1333 1.544691 GTCCGGCGATATGTCTACCAT 59.455 52.381 9.30 0.00 37.58 3.55
1723 1784 5.863935 TGAATTACGATGGCTGATAGAATCG 59.136 40.000 10.71 10.71 45.60 3.34
2008 2311 8.718102 ACATACATATGAAAACTACCTGTCAC 57.282 34.615 10.38 0.00 37.15 3.67
2076 2379 5.241662 AGAAGAAAGACTTGTCAGCATACC 58.758 41.667 3.49 0.00 39.13 2.73
2415 2719 5.053811 GCTCTTTATCTCTTGGACTAAGCC 58.946 45.833 0.00 0.00 36.31 4.35
3193 3506 6.211584 ACACTAGGAAACAGATTCAGAGCTAA 59.788 38.462 0.00 0.00 39.98 3.09
3245 3558 1.595794 GAAACAACAGCGACGAAGGAA 59.404 47.619 0.00 0.00 0.00 3.36
3246 3559 1.658994 AACAACAGCGACGAAGGAAA 58.341 45.000 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 1.746615 CACAGATGCTGGTTCCGGG 60.747 63.158 0.00 0.00 35.51 5.73
242 243 9.921637 TGTTTCTTGTAAAATTTCAGTCACTTT 57.078 25.926 0.00 0.00 0.00 2.66
317 318 9.504708 TGAAAATCTGAAAATACCATGCAAAAT 57.495 25.926 0.00 0.00 0.00 1.82
387 388 7.905604 TTCAGTATCAGGTTGAATTACTGTG 57.094 36.000 14.61 0.00 39.33 3.66
426 427 7.517614 TTACCTGCATGAACATAAGTTTTCA 57.482 32.000 0.00 0.00 38.30 2.69
464 465 5.104569 TGAGCCCATGACATTGATTACAGTA 60.105 40.000 0.00 0.00 0.00 2.74
468 469 3.002656 CGTGAGCCCATGACATTGATTAC 59.997 47.826 0.00 0.00 0.00 1.89
483 484 4.872664 ACTAATAAGTATCTGCGTGAGCC 58.127 43.478 0.00 0.00 46.41 4.70
485 486 7.197017 AGTCAACTAATAAGTATCTGCGTGAG 58.803 38.462 0.00 0.00 33.75 3.51
487 488 7.757097 AAGTCAACTAATAAGTATCTGCGTG 57.243 36.000 0.00 0.00 33.75 5.34
488 489 8.773404 AAAAGTCAACTAATAAGTATCTGCGT 57.227 30.769 0.00 0.00 33.75 5.24
489 490 9.690434 GAAAAAGTCAACTAATAAGTATCTGCG 57.310 33.333 0.00 0.00 33.75 5.18
561 608 5.308825 CACTCTGTGGTAAAGTTGATCCTT 58.691 41.667 0.00 0.00 0.00 3.36
661 711 2.487265 GGTGCCGGGATGTCATATTTCT 60.487 50.000 2.18 0.00 0.00 2.52
778 828 9.254133 CCTTAATATATGGAACTATCATGCGAG 57.746 37.037 0.00 0.00 0.00 5.03
900 951 3.819337 AGAGTACGTGTAGCTTGTGAAGA 59.181 43.478 0.00 0.00 0.00 2.87
973 1024 3.592059 TGTATGTCGGTGTAAAGCCTTC 58.408 45.455 0.00 0.00 0.00 3.46
1020 1071 7.523293 TGAACTTAAATGAGGAAGCATGAAA 57.477 32.000 0.00 0.00 0.00 2.69
1087 1138 0.609957 CTGGCTTCCACATTGCCTGA 60.610 55.000 0.00 0.00 46.23 3.86
1151 1202 2.825836 GGCGTGCTCATGGAAGGG 60.826 66.667 0.00 0.00 0.00 3.95
1282 1333 3.263503 CTCCAGCCGAACGACGTCA 62.264 63.158 17.16 0.00 40.78 4.35
1696 1757 5.773575 TCTATCAGCCATCGTAATTCAGTC 58.226 41.667 0.00 0.00 0.00 3.51
2008 2311 5.065090 TGAAAAGGATGCATATGAGTGAACG 59.935 40.000 6.97 0.00 0.00 3.95
2076 2379 0.957395 AAGGTCTTGCATGGACGCAG 60.957 55.000 12.20 0.00 44.14 5.18
2272 2575 2.105128 CATCGTCAGAGACCCGGC 59.895 66.667 0.00 0.00 0.00 6.13
2415 2719 2.370281 ATTCTGTCAGTAGTGCACCG 57.630 50.000 14.63 0.00 0.00 4.94
2643 2947 4.083110 ACATGATCGCTTGCATAATTAGGC 60.083 41.667 14.99 14.99 0.00 3.93
2655 2959 5.268118 TGAGAGTGATAACATGATCGCTT 57.732 39.130 10.75 3.41 44.74 4.68
2937 3241 3.579586 ACGGTAGATTCCTTGTGTGGTAA 59.420 43.478 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.