Multiple sequence alignment - TraesCS7A01G406500

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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 TraesCS7A01G406500 chr7A 100.000 2618 0 0 1 2618 591878871 591881488 0.000000e+00 4835.0
1 TraesCS7A01G406500 chr7D 93.150 2394 107 30 241 2616 517152934 517155288 0.000000e+00 3459.0
2 TraesCS7A01G406500 chr7D 90.129 233 21 2 1 232 517152637 517152868 4.230000e-78 302.0
3 TraesCS7A01G406500 chr7B 93.182 1276 53 21 447 1711 549930084 549931336 0.000000e+00 1844.0
4 TraesCS7A01G406500 chr7B 87.601 742 53 18 1724 2437 549931387 549932117 0.000000e+00 824.0
5 TraesCS7A01G406500 chr7B 86.444 450 49 6 1 447 549926155 549926595 1.410000e-132 483.0
6 TraesCS7A01G406500 chr7B 95.349 43 1 1 2444 2485 549934413 549934455 1.680000e-07 67.6


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 TraesCS7A01G406500 chr7A 591878871 591881488 2617 False 4835.00 4835 100.0000 1 2618 1 chr7A.!!$F1 2617
1 TraesCS7A01G406500 chr7D 517152637 517155288 2651 False 1880.50 3459 91.6395 1 2616 2 chr7D.!!$F1 2615
2 TraesCS7A01G406500 chr7B 549926155 549934455 8300 False 804.65 1844 90.6440 1 2485 4 chr7B.!!$F1 2484

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
985 4544 1.226435 GTCTGTACTCAGCGCGAGG 60.226 63.158 25.38 12.91 46.98 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 5576 0.106918 TCCAACCGCAACCAAGACTT 60.107 50.0 0.0 0.0 0.0 3.01 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
29 30 5.814764 TGTGTTTGTACCGTGTTTAACAT 57.185 34.783 0.00 0.00 0.00 2.71
31 32 7.312657 TGTGTTTGTACCGTGTTTAACATAA 57.687 32.000 0.00 0.00 0.00 1.90
61 62 2.401583 ATTGTGCATTACTCCGCTCA 57.598 45.000 0.00 0.00 0.00 4.26
77 79 7.671302 ACTCCGCTCATTTAAGATACATATGT 58.329 34.615 13.93 13.93 0.00 2.29
79 81 7.441836 TCCGCTCATTTAAGATACATATGTGT 58.558 34.615 18.81 12.06 42.39 3.72
96 98 7.492669 ACATATGTGTGTGTAAGTCTAGCATTC 59.507 37.037 7.78 0.00 37.14 2.67
115 117 5.507985 GCATTCTTGCTGGAAGTTAAGTGTT 60.508 40.000 8.80 0.00 45.77 3.32
126 128 5.506815 GGAAGTTAAGTGTTAAACCTGGTGC 60.507 44.000 0.00 0.00 0.00 5.01
131 133 2.092103 AGTGTTAAACCTGGTGCCAGAA 60.092 45.455 19.04 3.16 46.30 3.02
140 142 2.372264 CTGGTGCCAGAATGCTAATGT 58.628 47.619 12.66 0.00 46.30 2.71
173 176 4.572389 CAGGCGTTATTCTTACTGCATTCT 59.428 41.667 0.00 0.00 0.00 2.40
177 180 6.403200 GGCGTTATTCTTACTGCATTCTGAAA 60.403 38.462 0.00 0.00 0.00 2.69
196 199 9.664332 TTCTGAAATTTTTGTTTCTCAATCCAA 57.336 25.926 0.00 0.00 38.58 3.53
213 216 3.218453 TCCAAAGTTCTCGGATTGCAAA 58.782 40.909 1.71 0.00 0.00 3.68
234 237 8.750298 TGCAAAATAATTAGTTATTTCCGGGAA 58.250 29.630 14.24 5.09 45.27 3.97
244 304 6.718294 AGTTATTTCCGGGAACAAGATAGTT 58.282 36.000 9.46 0.00 0.00 2.24
256 316 6.979238 GGAACAAGATAGTTAGTTAGTGCGAT 59.021 38.462 0.00 0.00 0.00 4.58
286 346 5.393461 GCAAGCCTATTAGAAGTGTGCATTT 60.393 40.000 0.00 0.00 0.00 2.32
288 348 4.641989 AGCCTATTAGAAGTGTGCATTTGG 59.358 41.667 0.00 0.00 0.00 3.28
305 365 5.669357 GCATTTGGCAATTTCATCAAAGTCG 60.669 40.000 0.00 0.00 43.97 4.18
344 404 6.346120 GCACACTCTACATCTATAATTGCACG 60.346 42.308 0.00 0.00 0.00 5.34
363 423 6.851609 TGCACGCATTCTCTTGTTTTAATAT 58.148 32.000 0.00 0.00 0.00 1.28
400 460 5.567138 AATGTGCACCTTAATTGACTAGC 57.433 39.130 15.69 0.00 0.00 3.42
415 475 7.701539 ATTGACTAGCAATACCATTGTTCAA 57.298 32.000 9.70 5.68 45.16 2.69
417 477 6.000840 TGACTAGCAATACCATTGTTCAACA 58.999 36.000 0.00 0.00 0.00 3.33
418 478 6.658816 TGACTAGCAATACCATTGTTCAACAT 59.341 34.615 0.00 0.00 0.00 2.71
420 480 5.981088 AGCAATACCATTGTTCAACATGA 57.019 34.783 0.00 0.00 0.00 3.07
421 481 6.534475 AGCAATACCATTGTTCAACATGAT 57.466 33.333 0.00 0.00 0.00 2.45
425 485 9.964303 GCAATACCATTGTTCAACATGATTATA 57.036 29.630 0.00 0.00 0.00 0.98
540 4091 3.118555 TGTGTAATATCTTCACCCACCCG 60.119 47.826 0.00 0.00 0.00 5.28
606 4157 9.662947 TCCACTCTAGATGATATTGCAATATTG 57.337 33.333 28.16 19.32 31.96 1.90
641 4192 7.504924 TTCTGCGGGGTAATATTAGATTTTG 57.495 36.000 0.00 0.00 0.00 2.44
684 4238 7.187824 ACATCACTTTCTCAGGCTATTTAGA 57.812 36.000 0.00 0.00 0.00 2.10
918 4477 2.300152 TGGTCACTGCAAAACAACCAAA 59.700 40.909 4.22 0.00 34.44 3.28
944 4503 1.826054 CCAACCACCACGAGCCAAA 60.826 57.895 0.00 0.00 0.00 3.28
985 4544 1.226435 GTCTGTACTCAGCGCGAGG 60.226 63.158 25.38 12.91 46.98 4.63
1693 5252 1.298413 CGTACGCATAGCAGCTCGT 60.298 57.895 11.89 11.89 38.75 4.18
1897 5516 4.728608 GCGCTCGTTAAAATTTCCTGTATG 59.271 41.667 0.00 0.00 0.00 2.39
1911 5530 3.820467 TCCTGTATGGCACTTGTTTCTTG 59.180 43.478 0.00 0.00 35.26 3.02
1943 5568 3.267483 GCATTTGCATCTTGCTGGATTT 58.733 40.909 8.34 0.00 45.31 2.17
1944 5569 3.063452 GCATTTGCATCTTGCTGGATTTG 59.937 43.478 8.34 0.00 45.31 2.32
1945 5570 3.322211 TTTGCATCTTGCTGGATTTGG 57.678 42.857 0.75 0.00 45.31 3.28
1946 5571 2.219080 TGCATCTTGCTGGATTTGGA 57.781 45.000 0.75 0.00 45.31 3.53
1947 5572 2.742348 TGCATCTTGCTGGATTTGGAT 58.258 42.857 0.75 0.00 45.31 3.41
1948 5573 3.101437 TGCATCTTGCTGGATTTGGATT 58.899 40.909 0.75 0.00 45.31 3.01
1951 5576 4.382254 GCATCTTGCTGGATTTGGATTCAA 60.382 41.667 0.00 0.00 40.96 2.69
2018 5643 2.507102 CAGCTAGACACCCACGCG 60.507 66.667 3.53 3.53 0.00 6.01
2151 5778 6.882610 TTCATAATTGCCCTGTGATATGAC 57.117 37.500 0.00 0.00 0.00 3.06
2185 5812 6.918569 ACATCGAGTTTGGATCTTAATAGTCG 59.081 38.462 0.00 0.00 0.00 4.18
2223 5853 2.803956 ACACCTCTGTCGTCCTATGAA 58.196 47.619 0.00 0.00 0.00 2.57
2239 5869 9.326413 CGTCCTATGAAGGTGTTTATAAGATTT 57.674 33.333 0.00 0.00 44.09 2.17
2322 5955 0.250901 AGCATTTCGTGGCTGTTCCT 60.251 50.000 0.00 0.00 39.30 3.36
2362 5995 2.620112 GCTGTGCGACATGGCAGTT 61.620 57.895 0.00 0.00 44.93 3.16
2363 5996 1.499056 CTGTGCGACATGGCAGTTC 59.501 57.895 0.00 0.00 44.93 3.01
2397 6030 1.000739 CCATGGGCCCACAATGACT 59.999 57.895 31.51 6.21 0.00 3.41
2418 6051 3.920446 TGTGTCAGCAATAACGCTAGAA 58.080 40.909 0.00 0.00 41.38 2.10
2423 6056 2.677836 CAGCAATAACGCTAGAAAGCCA 59.322 45.455 0.00 0.00 46.68 4.75
2427 6060 2.325583 TAACGCTAGAAAGCCATGGG 57.674 50.000 15.13 0.00 46.68 4.00
2428 6061 0.394352 AACGCTAGAAAGCCATGGGG 60.394 55.000 15.13 0.00 46.68 4.96
2550 8474 9.461734 AATTAAGGTTATACCCACCTATCTCTT 57.538 33.333 0.00 0.00 44.48 2.85
2551 8475 6.749036 AAGGTTATACCCACCTATCTCTTG 57.251 41.667 0.00 0.00 44.48 3.02
2552 8476 6.039415 AGGTTATACCCACCTATCTCTTGA 57.961 41.667 0.00 0.00 43.34 3.02
2562 8486 2.036089 CCTATCTCTTGACGGTTAGGGC 59.964 54.545 0.00 0.00 0.00 5.19
2566 8490 2.304761 TCTCTTGACGGTTAGGGCAAAT 59.695 45.455 0.00 0.00 0.00 2.32
2570 8494 2.706890 TGACGGTTAGGGCAAATTCTC 58.293 47.619 0.00 0.00 0.00 2.87
2584 8508 2.816777 ATTCTCCCTTCCAAGCTTCC 57.183 50.000 0.00 0.00 0.00 3.46
2616 8540 0.324738 TGGATTCGCCTGTCCTCTCT 60.325 55.000 0.00 0.00 37.63 3.10
2617 8541 0.103937 GGATTCGCCTGTCCTCTCTG 59.896 60.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.814764 TGTTAAACACGGTACAAACACAT 57.185 34.783 0.00 0.00 0.00 3.21
31 32 8.184192 CGGAGTAATGCACAATAGATTCTTTTT 58.816 33.333 0.00 0.00 0.00 1.94
96 98 6.039382 AGGTTTAACACTTAACTTCCAGCAAG 59.961 38.462 0.00 0.00 38.21 4.01
115 117 1.075374 AGCATTCTGGCACCAGGTTTA 59.925 47.619 16.52 1.15 43.75 2.01
126 128 6.652062 TGAGCATACATACATTAGCATTCTGG 59.348 38.462 0.00 0.00 0.00 3.86
131 133 4.940046 GCCTGAGCATACATACATTAGCAT 59.060 41.667 0.00 0.00 39.53 3.79
140 142 5.468540 AGAATAACGCCTGAGCATACATA 57.531 39.130 0.00 0.00 39.83 2.29
173 176 9.447157 ACTTTGGATTGAGAAACAAAAATTTCA 57.553 25.926 0.00 0.00 42.03 2.69
177 180 9.317936 GAGAACTTTGGATTGAGAAACAAAAAT 57.682 29.630 0.00 0.00 42.03 1.82
196 199 8.739972 ACTAATTATTTTGCAATCCGAGAACTT 58.260 29.630 0.00 0.00 0.00 2.66
213 216 9.689501 TCTTGTTCCCGGAAATAACTAATTATT 57.310 29.630 0.73 0.00 41.82 1.40
244 304 5.637810 GGCTTGCATAATATCGCACTAACTA 59.362 40.000 0.00 0.00 38.00 2.24
256 316 7.173218 GCACACTTCTAATAGGCTTGCATAATA 59.827 37.037 0.00 0.00 0.00 0.98
286 346 2.352617 GCCGACTTTGATGAAATTGCCA 60.353 45.455 0.00 0.00 0.00 4.92
288 348 2.945278 TGCCGACTTTGATGAAATTGC 58.055 42.857 0.00 0.00 0.00 3.56
290 350 4.021192 ACCATTGCCGACTTTGATGAAATT 60.021 37.500 0.00 0.00 0.00 1.82
363 423 8.523915 AGGTGCACATTATAAGATCAAAATCA 57.476 30.769 20.43 0.00 34.07 2.57
384 444 7.807977 ATGGTATTGCTAGTCAATTAAGGTG 57.192 36.000 14.72 0.00 42.48 4.00
398 458 5.981088 TCATGTTGAACAATGGTATTGCT 57.019 34.783 0.62 0.00 0.00 3.91
462 4012 4.930405 TGTTTGGCACTCATTAAATGCATG 59.070 37.500 0.00 0.00 41.27 4.06
470 4020 3.568007 GTCTTGGTGTTTGGCACTCATTA 59.432 43.478 0.00 0.00 46.86 1.90
540 4091 5.163457 TGTTCTCCTTTTTCATTTGGACACC 60.163 40.000 0.00 0.00 0.00 4.16
574 4125 8.164070 TGCAATATCATCTAGAGTGGAGTAGTA 58.836 37.037 0.00 0.00 0.00 1.82
575 4126 7.007116 TGCAATATCATCTAGAGTGGAGTAGT 58.993 38.462 0.00 0.00 0.00 2.73
576 4127 7.459795 TGCAATATCATCTAGAGTGGAGTAG 57.540 40.000 0.00 0.00 0.00 2.57
619 4170 7.687941 ATCAAAATCTAATATTACCCCGCAG 57.312 36.000 0.00 0.00 0.00 5.18
659 4213 7.268586 TCTAAATAGCCTGAGAAAGTGATGTC 58.731 38.462 0.00 0.00 0.00 3.06
672 4226 7.875971 AGAAGTGTTGTTTTCTAAATAGCCTG 58.124 34.615 0.00 0.00 32.13 4.85
918 4477 0.746563 CGTGGTGGTTGGTCAGTTGT 60.747 55.000 0.00 0.00 0.00 3.32
944 4503 2.056906 GAGTGGTGTGGGTTGGCTCT 62.057 60.000 0.00 0.00 0.00 4.09
985 4544 2.961768 CATTGTTGGGCCCGTGAC 59.038 61.111 19.37 16.26 0.00 3.67
996 4555 2.436646 CCGGAGCGAGGCATTGTT 60.437 61.111 0.00 0.00 0.00 2.83
1429 4988 3.357079 GTTGCTCAGGTGCCACCG 61.357 66.667 8.52 3.74 44.90 4.94
1693 5252 5.485353 CCCAAGATTATAGAGCACCAGGATA 59.515 44.000 0.00 0.00 0.00 2.59
1860 5457 2.021380 GCGCACGCGGTTAATCAG 59.979 61.111 12.47 0.00 40.19 2.90
1897 5516 3.365969 CGTTATCCCAAGAAACAAGTGCC 60.366 47.826 0.00 0.00 0.00 5.01
1911 5530 0.730265 TGCAAATGCGTCGTTATCCC 59.270 50.000 0.35 0.00 45.83 3.85
1943 5568 2.293122 CGCAACCAAGACTTTGAATCCA 59.707 45.455 0.00 0.00 36.36 3.41
1944 5569 2.351738 CCGCAACCAAGACTTTGAATCC 60.352 50.000 0.00 0.00 36.36 3.01
1945 5570 2.293399 ACCGCAACCAAGACTTTGAATC 59.707 45.455 0.00 0.00 36.36 2.52
1946 5571 2.306847 ACCGCAACCAAGACTTTGAAT 58.693 42.857 0.00 0.00 36.36 2.57
1947 5572 1.757682 ACCGCAACCAAGACTTTGAA 58.242 45.000 0.00 0.00 36.36 2.69
1948 5573 1.403679 CAACCGCAACCAAGACTTTGA 59.596 47.619 0.00 0.00 36.36 2.69
1951 5576 0.106918 TCCAACCGCAACCAAGACTT 60.107 50.000 0.00 0.00 0.00 3.01
2116 5741 5.435557 GGCAATTATGAAAACGAGATCGAG 58.564 41.667 9.58 0.00 43.02 4.04
2151 5778 5.068234 TCCAAACTCGATGTACTACCTTG 57.932 43.478 0.00 0.00 0.00 3.61
2254 5884 0.381089 CGAGGTCAGGATCACGTACC 59.619 60.000 0.00 0.00 0.00 3.34
2262 5895 0.544357 TGGGAACACGAGGTCAGGAT 60.544 55.000 0.00 0.00 33.40 3.24
2288 5921 0.957395 ATGCTCTGCCCAAACACTCG 60.957 55.000 0.00 0.00 0.00 4.18
2322 5955 5.813672 AGCTTAAGCCGACAATAAATTCGTA 59.186 36.000 23.71 0.00 43.38 3.43
2379 6012 1.000739 AGTCATTGTGGGCCCATGG 59.999 57.895 31.45 17.75 0.00 3.66
2397 6030 3.586100 TCTAGCGTTATTGCTGACACA 57.414 42.857 0.00 0.00 46.70 3.72
2418 6051 0.466189 CGCATAGTTCCCCATGGCTT 60.466 55.000 6.09 0.00 0.00 4.35
2423 6056 2.643551 CAAAGACGCATAGTTCCCCAT 58.356 47.619 0.00 0.00 0.00 4.00
2427 6060 2.608090 GCTACCAAAGACGCATAGTTCC 59.392 50.000 0.00 0.00 0.00 3.62
2428 6061 3.522553 AGCTACCAAAGACGCATAGTTC 58.477 45.455 0.00 0.00 0.00 3.01
2438 6071 4.383770 GGGCAACTATGTAGCTACCAAAGA 60.384 45.833 21.01 2.19 0.00 2.52
2525 8449 8.881262 CAAGAGATAGGTGGGTATAACCTTAAT 58.119 37.037 8.63 0.00 46.14 1.40
2539 8463 3.068307 CCCTAACCGTCAAGAGATAGGTG 59.932 52.174 0.00 0.00 37.59 4.00
2540 8464 3.297736 CCCTAACCGTCAAGAGATAGGT 58.702 50.000 0.00 0.00 38.66 3.08
2541 8465 2.036089 GCCCTAACCGTCAAGAGATAGG 59.964 54.545 0.00 0.00 0.00 2.57
2542 8466 2.693591 TGCCCTAACCGTCAAGAGATAG 59.306 50.000 0.00 0.00 0.00 2.08
2543 8467 2.742348 TGCCCTAACCGTCAAGAGATA 58.258 47.619 0.00 0.00 0.00 1.98
2544 8468 1.568504 TGCCCTAACCGTCAAGAGAT 58.431 50.000 0.00 0.00 0.00 2.75
2545 8469 1.344065 TTGCCCTAACCGTCAAGAGA 58.656 50.000 0.00 0.00 0.00 3.10
2546 8470 2.178912 TTTGCCCTAACCGTCAAGAG 57.821 50.000 0.00 0.00 0.00 2.85
2547 8471 2.871096 ATTTGCCCTAACCGTCAAGA 57.129 45.000 0.00 0.00 0.00 3.02
2548 8472 3.081804 AGAATTTGCCCTAACCGTCAAG 58.918 45.455 0.00 0.00 0.00 3.02
2549 8473 3.078837 GAGAATTTGCCCTAACCGTCAA 58.921 45.455 0.00 0.00 0.00 3.18
2550 8474 2.617021 GGAGAATTTGCCCTAACCGTCA 60.617 50.000 0.00 0.00 0.00 4.35
2551 8475 2.014857 GGAGAATTTGCCCTAACCGTC 58.985 52.381 0.00 0.00 0.00 4.79
2552 8476 1.340697 GGGAGAATTTGCCCTAACCGT 60.341 52.381 8.83 0.00 41.31 4.83
2562 8486 3.194329 GGAAGCTTGGAAGGGAGAATTTG 59.806 47.826 2.10 0.00 0.00 2.32
2566 8490 0.698818 GGGAAGCTTGGAAGGGAGAA 59.301 55.000 2.10 0.00 0.00 2.87
2570 8494 1.000396 CTGGGGAAGCTTGGAAGGG 60.000 63.158 2.10 0.00 0.00 3.95
2584 8508 1.442526 GAATCCACATGCTCGCTGGG 61.443 60.000 0.00 0.00 0.00 4.45
2590 8514 0.745845 ACAGGCGAATCCACATGCTC 60.746 55.000 0.00 0.00 37.29 4.26
2594 8518 0.179000 GAGGACAGGCGAATCCACAT 59.821 55.000 7.35 0.00 37.47 3.21


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

AutoCloner maintained by Alex Coulton.