Multiple sequence alignment - TraesCS6A01G171900

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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 TraesCS6A01G171900 chr6A 100.000 2624 0 0 1 2624 183187116 183189739 0.000000e+00 4846
1 TraesCS6A01G171900 chr6D 93.485 2640 109 35 1 2620 139915270 139917866 0.000000e+00 3864
2 TraesCS6A01G171900 chr6B 94.669 2101 44 14 540 2624 239728751 239730799 0.000000e+00 3197
3 TraesCS6A01G171900 chr6B 86.680 518 65 4 1 515 239727143 239727659 2.930000e-159 571
4 TraesCS6A01G171900 chr2A 91.525 177 13 2 1071 1246 680357725 680357550 2.610000e-60 243
5 TraesCS6A01G171900 chr2B 90.960 177 14 2 1071 1246 640765313 640765138 1.210000e-58 237
6 TraesCS6A01G171900 chr2D 90.395 177 15 2 1071 1246 538055273 538055098 5.650000e-57 231
7 TraesCS6A01G171900 chr1B 85.185 216 29 3 1035 1249 552474296 552474083 4.400000e-53 219
8 TraesCS6A01G171900 chr1D 88.068 176 19 2 1075 1249 410072045 410071871 9.520000e-50 207
9 TraesCS6A01G171900 chr1A 88.068 176 19 2 1075 1249 505925841 505925667 9.520000e-50 207
10 TraesCS6A01G171900 chr7D 81.301 246 32 13 1070 1311 547681352 547681117 1.240000e-43 187


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 TraesCS6A01G171900 chr6A 183187116 183189739 2623 False 4846 4846 100.0000 1 2624 1 chr6A.!!$F1 2623
1 TraesCS6A01G171900 chr6D 139915270 139917866 2596 False 3864 3864 93.4850 1 2620 1 chr6D.!!$F1 2619
2 TraesCS6A01G171900 chr6B 239727143 239730799 3656 False 1884 3197 90.6745 1 2624 2 chr6B.!!$F1 2623

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
386 391 0.041576 GCCCGAGACGTTGTTCAAAC 60.042 55.0 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 3352 4.517075 AGCAGCCAAAGTAAACTTCTCTTC 59.483 41.667 0.0 0.0 34.61 2.87 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
55 56 4.052159 TGGCAATAACACCACAACAAAG 57.948 40.909 0.00 0.00 0.00 2.77
88 89 4.088056 AGCTATCAGAAAGAGCATGCAT 57.912 40.909 21.98 4.82 38.73 3.96
90 91 5.239351 AGCTATCAGAAAGAGCATGCATAG 58.761 41.667 21.98 15.44 38.73 2.23
98 99 6.704937 CAGAAAGAGCATGCATAGATAACTCA 59.295 38.462 21.98 0.00 0.00 3.41
121 123 1.658994 TTATCCTTGGCGCTAAACCG 58.341 50.000 7.84 0.00 0.00 4.44
145 147 6.523201 CGAAGGTAAATGTTGCATGTAAGAAC 59.477 38.462 0.00 0.00 0.00 3.01
162 164 2.336554 AACACGAAGTTCATGCATGC 57.663 45.000 22.25 11.82 41.61 4.06
174 176 0.954449 ATGCATGCTGATAGCGAGGC 60.954 55.000 20.33 0.00 46.26 4.70
191 193 1.583986 GCGGCATTTAGGTTGCACA 59.416 52.632 0.00 0.00 41.95 4.57
207 209 8.492415 AGGTTGCACATAAGAATATAGTAGGA 57.508 34.615 0.00 0.00 0.00 2.94
208 210 9.105844 AGGTTGCACATAAGAATATAGTAGGAT 57.894 33.333 0.00 0.00 0.00 3.24
219 222 9.669887 AAGAATATAGTAGGATAGTAGGTGACG 57.330 37.037 0.00 0.00 28.45 4.35
232 235 2.774687 AGGTGACGGTTCATGGTAAAC 58.225 47.619 0.00 0.00 33.11 2.01
242 245 4.250464 GTTCATGGTAAACGAGATGGTGA 58.750 43.478 0.00 0.00 0.00 4.02
265 268 1.924731 TCGGAGAGTCCTGATGTGTT 58.075 50.000 0.00 0.00 33.30 3.32
266 269 1.546029 TCGGAGAGTCCTGATGTGTTG 59.454 52.381 0.00 0.00 33.30 3.33
314 318 5.578005 ATGTTTGCAATGATGAGGAAGAG 57.422 39.130 0.00 0.00 0.00 2.85
321 325 4.197750 CAATGATGAGGAAGAGACAAGGG 58.802 47.826 0.00 0.00 0.00 3.95
345 349 3.529252 GGATCATCCTGCCTCATCG 57.471 57.895 0.00 0.00 32.53 3.84
349 353 0.471191 TCATCCTGCCTCATCGCATT 59.529 50.000 0.00 0.00 38.30 3.56
350 354 0.591659 CATCCTGCCTCATCGCATTG 59.408 55.000 0.00 0.00 38.30 2.82
366 371 2.607771 GCATTGCGCCGGATATCAAATT 60.608 45.455 5.05 0.00 32.94 1.82
377 382 2.684001 TATCAAATTGCCCGAGACGT 57.316 45.000 0.00 0.00 0.00 4.34
379 384 0.871722 TCAAATTGCCCGAGACGTTG 59.128 50.000 0.00 0.00 0.00 4.10
386 391 0.041576 GCCCGAGACGTTGTTCAAAC 60.042 55.000 0.00 0.00 0.00 2.93
391 396 1.329599 GAGACGTTGTTCAAACGCCTT 59.670 47.619 10.28 0.00 46.58 4.35
419 424 5.171476 AGACAAATCCTATCACGTCACAAG 58.829 41.667 0.00 0.00 0.00 3.16
463 468 5.721480 ACTTTGGCATTTAGGGAGCTAATTT 59.279 36.000 0.00 0.00 0.00 1.82
476 481 4.331717 GGAGCTAATTTGGACGAATTTCGA 59.668 41.667 24.50 2.72 43.74 3.71
489 494 3.623863 GAATTTCGAGCCAAAAACACGA 58.376 40.909 0.00 0.00 0.00 4.35
490 495 2.748461 TTTCGAGCCAAAAACACGAG 57.252 45.000 0.00 0.00 34.64 4.18
496 501 3.432252 CGAGCCAAAAACACGAGACTATT 59.568 43.478 0.00 0.00 0.00 1.73
498 503 3.432252 AGCCAAAAACACGAGACTATTCG 59.568 43.478 0.00 0.00 45.70 3.34
512 517 7.621991 CGAGACTATTCGTCAAATATTTGCTT 58.378 34.615 21.15 7.94 45.32 3.91
513 518 8.752254 CGAGACTATTCGTCAAATATTTGCTTA 58.248 33.333 21.15 7.51 45.32 3.09
522 527 9.391006 TCGTCAAATATTTGCTTATAGGAAACT 57.609 29.630 21.15 0.00 38.34 2.66
557 1636 6.946340 AGAAACAACCAAGGAAACAAATCTT 58.054 32.000 0.00 0.00 0.00 2.40
558 1637 7.041721 AGAAACAACCAAGGAAACAAATCTTC 58.958 34.615 0.00 0.00 0.00 2.87
559 1638 5.930837 ACAACCAAGGAAACAAATCTTCA 57.069 34.783 0.00 0.00 0.00 3.02
560 1639 6.293004 ACAACCAAGGAAACAAATCTTCAA 57.707 33.333 0.00 0.00 0.00 2.69
561 1640 6.706295 ACAACCAAGGAAACAAATCTTCAAA 58.294 32.000 0.00 0.00 0.00 2.69
653 1732 3.641648 CATTGACACAGCCGTTTGAAAT 58.358 40.909 0.00 0.00 0.00 2.17
659 1738 3.052036 CACAGCCGTTTGAAATGAAAGG 58.948 45.455 0.00 0.00 0.00 3.11
660 1739 2.955660 ACAGCCGTTTGAAATGAAAGGA 59.044 40.909 0.00 0.00 0.00 3.36
702 1781 3.318275 AGGAGAAAAGAAAAGGCGAAACC 59.682 43.478 0.00 0.00 39.61 3.27
849 1941 0.621571 CACCTTCCCATCCTCCTCCA 60.622 60.000 0.00 0.00 0.00 3.86
854 1946 1.768077 CCCATCCTCCTCCACCTCC 60.768 68.421 0.00 0.00 0.00 4.30
855 1947 1.316266 CCATCCTCCTCCACCTCCT 59.684 63.158 0.00 0.00 0.00 3.69
856 1948 0.762461 CCATCCTCCTCCACCTCCTC 60.762 65.000 0.00 0.00 0.00 3.71
897 1995 2.354821 CTCAAAATTCCCGATTCCCGTC 59.645 50.000 0.00 0.00 36.31 4.79
898 1996 2.026636 TCAAAATTCCCGATTCCCGTCT 60.027 45.455 0.00 0.00 36.31 4.18
900 1998 1.200519 AATTCCCGATTCCCGTCTCA 58.799 50.000 0.00 0.00 36.31 3.27
902 2000 0.248289 TTCCCGATTCCCGTCTCAAC 59.752 55.000 0.00 0.00 36.31 3.18
958 2056 1.887707 GCCACGTGATTCCGATCCC 60.888 63.158 19.30 0.00 0.00 3.85
993 2091 4.863925 GCTCGGCTCGGCTCTGTC 62.864 72.222 0.00 0.00 0.00 3.51
1257 2355 2.692741 CCCCTCTCCCTTCCCCAC 60.693 72.222 0.00 0.00 0.00 4.61
1262 2360 3.717294 CTCCCTTCCCCACCACCG 61.717 72.222 0.00 0.00 0.00 4.94
1494 2592 3.606065 CTCGGTGGTGGACGACGAC 62.606 68.421 0.00 0.00 35.04 4.34
1884 2982 5.594317 ACATTTTACTTGCTTCCTCTTGTGT 59.406 36.000 0.00 0.00 0.00 3.72
1959 3058 6.127897 ACTGTTACTCATTTAGGCTCATTTGC 60.128 38.462 0.00 0.00 0.00 3.68
2253 3352 6.729187 TGATGTAGATGTCTGTCATAGAACG 58.271 40.000 0.00 0.00 37.12 3.95
2417 3516 5.256474 AGCATGTATAATTGGGCATACTCC 58.744 41.667 0.00 0.00 0.00 3.85
2498 3597 9.289782 AGATTAGTTCTGACAATTAGCAAAGTT 57.710 29.630 0.00 0.00 31.79 2.66
2620 3719 8.241367 TGCTAACGAGATTATATTCGATTGCTA 58.759 33.333 10.62 0.00 39.55 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.457443 TTTGTGTGCGGTTGAATGCA 59.543 45.000 0.00 0.00 39.13 3.96
17 18 0.453793 CCACTTTGTGTGCGGTTGAA 59.546 50.000 0.00 0.00 44.92 2.69
63 64 5.882000 TGCATGCTCTTTCTGATAGCTAAAA 59.118 36.000 20.33 0.00 37.16 1.52
66 67 4.677673 TGCATGCTCTTTCTGATAGCTA 57.322 40.909 20.33 0.00 37.16 3.32
67 68 3.555527 TGCATGCTCTTTCTGATAGCT 57.444 42.857 20.33 0.00 37.16 3.32
74 75 6.824553 TGAGTTATCTATGCATGCTCTTTCT 58.175 36.000 20.33 7.01 0.00 2.52
88 89 7.764443 GCGCCAAGGATAATTATGAGTTATCTA 59.236 37.037 1.78 0.00 38.19 1.98
90 91 6.595716 AGCGCCAAGGATAATTATGAGTTATC 59.404 38.462 2.29 0.00 37.67 1.75
98 99 4.454504 CGGTTTAGCGCCAAGGATAATTAT 59.545 41.667 2.29 0.00 0.00 1.28
108 110 0.321021 TACCTTCGGTTTAGCGCCAA 59.679 50.000 2.29 0.00 37.09 4.52
121 123 7.326063 GTGTTCTTACATGCAACATTTACCTTC 59.674 37.037 0.00 0.00 36.50 3.46
125 127 6.367421 TCGTGTTCTTACATGCAACATTTAC 58.633 36.000 0.00 0.00 40.41 2.01
130 132 3.874543 ACTTCGTGTTCTTACATGCAACA 59.125 39.130 0.00 0.00 40.41 3.33
145 147 1.465777 TCAGCATGCATGAACTTCGTG 59.534 47.619 30.64 13.57 36.50 4.35
152 154 2.140717 CTCGCTATCAGCATGCATGAA 58.859 47.619 30.64 14.51 42.58 2.57
162 164 0.882042 AAATGCCGCCTCGCTATCAG 60.882 55.000 0.00 0.00 0.00 2.90
174 176 3.376859 TCTTATGTGCAACCTAAATGCCG 59.623 43.478 0.00 0.00 43.16 5.69
207 209 3.371965 ACCATGAACCGTCACCTACTAT 58.628 45.455 0.00 0.00 36.31 2.12
208 210 2.811410 ACCATGAACCGTCACCTACTA 58.189 47.619 0.00 0.00 36.31 1.82
209 211 1.640917 ACCATGAACCGTCACCTACT 58.359 50.000 0.00 0.00 36.31 2.57
210 212 3.598019 TTACCATGAACCGTCACCTAC 57.402 47.619 0.00 0.00 36.31 3.18
217 220 3.259064 CATCTCGTTTACCATGAACCGT 58.741 45.455 0.00 0.00 0.00 4.83
219 222 3.374058 CACCATCTCGTTTACCATGAACC 59.626 47.826 0.00 0.00 0.00 3.62
232 235 1.950216 TCTCCGATCTTCACCATCTCG 59.050 52.381 0.00 0.00 0.00 4.04
242 245 2.692557 CACATCAGGACTCTCCGATCTT 59.307 50.000 0.00 0.00 42.75 2.40
265 268 8.801299 TGTACAAATGATTCATTCTTAAAGCCA 58.199 29.630 12.15 0.48 32.43 4.75
266 269 9.638239 TTGTACAAATGATTCATTCTTAAAGCC 57.362 29.630 12.15 0.00 32.43 4.35
314 318 4.222588 CAGGATGATCCTCTATCCCTTGTC 59.777 50.000 11.91 0.00 45.66 3.18
321 325 3.439154 TGAGGCAGGATGATCCTCTATC 58.561 50.000 11.91 9.86 45.66 2.08
345 349 0.310543 TTTGATATCCGGCGCAATGC 59.689 50.000 10.83 0.00 45.38 3.56
349 353 0.310543 GCAATTTGATATCCGGCGCA 59.689 50.000 10.83 0.00 0.00 6.09
350 354 0.387239 GGCAATTTGATATCCGGCGC 60.387 55.000 0.00 0.00 0.00 6.53
353 357 1.806542 CTCGGGCAATTTGATATCCGG 59.193 52.381 15.49 0.00 38.21 5.14
355 359 2.480419 CGTCTCGGGCAATTTGATATCC 59.520 50.000 0.00 0.00 0.00 2.59
359 364 1.468520 CAACGTCTCGGGCAATTTGAT 59.531 47.619 0.00 0.00 0.00 2.57
366 371 0.462225 TTTGAACAACGTCTCGGGCA 60.462 50.000 0.00 0.00 0.00 5.36
377 382 5.710984 TGTCTTTAAAAGGCGTTTGAACAA 58.289 33.333 8.71 0.00 35.37 2.83
379 384 6.635166 TTTGTCTTTAAAAGGCGTTTGAAC 57.365 33.333 8.71 0.00 35.37 3.18
386 391 6.967199 GTGATAGGATTTGTCTTTAAAAGGCG 59.033 38.462 0.00 0.00 35.37 5.52
391 396 7.658167 TGTGACGTGATAGGATTTGTCTTTAAA 59.342 33.333 0.00 0.00 0.00 1.52
419 424 8.678199 CCAAAGTTAAATTTGACTCTCCTATCC 58.322 37.037 25.53 0.00 41.71 2.59
463 468 1.885560 TTTGGCTCGAAATTCGTCCA 58.114 45.000 20.91 20.91 41.35 4.02
476 481 3.432252 CGAATAGTCTCGTGTTTTTGGCT 59.568 43.478 0.00 0.00 34.08 4.75
496 501 9.391006 AGTTTCCTATAAGCAAATATTTGACGA 57.609 29.630 28.33 13.83 40.55 4.20
535 540 6.706295 TGAAGATTTGTTTCCTTGGTTGTTT 58.294 32.000 0.00 0.00 0.00 2.83
536 541 6.293004 TGAAGATTTGTTTCCTTGGTTGTT 57.707 33.333 0.00 0.00 0.00 2.83
537 542 5.930837 TGAAGATTTGTTTCCTTGGTTGT 57.069 34.783 0.00 0.00 0.00 3.32
538 543 7.495279 TGATTTGAAGATTTGTTTCCTTGGTTG 59.505 33.333 0.00 0.00 0.00 3.77
541 1620 8.436046 TTTGATTTGAAGATTTGTTTCCTTGG 57.564 30.769 0.00 0.00 0.00 3.61
607 1686 3.385384 GGGCTGCTTTTGGGCCTC 61.385 66.667 4.53 0.00 44.70 4.70
653 1732 5.433526 TCTTCTTCCGACTTTTTCCTTTCA 58.566 37.500 0.00 0.00 0.00 2.69
659 1738 5.758784 TCCTCTTTCTTCTTCCGACTTTTTC 59.241 40.000 0.00 0.00 0.00 2.29
660 1739 5.681639 TCCTCTTTCTTCTTCCGACTTTTT 58.318 37.500 0.00 0.00 0.00 1.94
703 1782 3.617143 TTCTCGGTCTCGCGGGAGA 62.617 63.158 26.55 26.55 46.90 3.71
897 1995 2.125350 GCAGGAGGGCTCGTTGAG 60.125 66.667 0.00 0.00 0.00 3.02
898 1996 4.069232 CGCAGGAGGGCTCGTTGA 62.069 66.667 0.00 0.00 0.00 3.18
958 2056 1.960612 CCTCGGGATTCCTCTAGCG 59.039 63.158 2.01 0.00 0.00 4.26
1884 2982 7.607615 AAGTTACTTTAGGTGTCTACTTCCA 57.392 36.000 0.00 0.00 0.00 3.53
1919 3018 5.235516 AGTAACAGTAACACATGTGGCTAC 58.764 41.667 28.64 25.39 34.19 3.58
1959 3058 6.917477 TGTTTTCCATTGTTCTCAATTCGAAG 59.083 34.615 3.35 0.00 41.66 3.79
2253 3352 4.517075 AGCAGCCAAAGTAAACTTCTCTTC 59.483 41.667 0.00 0.00 34.61 2.87
2385 3484 7.450944 TGCCCAATTATACATGCTAATGATTCA 59.549 33.333 0.00 0.00 37.24 2.57
2417 3516 4.274214 TGTTGTCTGTTGATTTCAGCTCAG 59.726 41.667 0.00 0.00 33.48 3.35
2522 3621 9.893305 AAAATCCTTTTACTTTCATGTTACTCG 57.107 29.630 0.00 0.00 0.00 4.18
2566 3665 7.586300 ACATCAAACAGAAACGAAAAATCTACG 59.414 33.333 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.