Multiple sequence alignment - TraesCS6A01G159800

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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 TraesCS6A01G159800 chr6A 100.000 2662 0 0 597 3258 152062298 152059637 0.000000e+00 4916
1 TraesCS6A01G159800 chr6A 100.000 140 0 0 1 140 152062894 152062755 3.220000e-65 259
2 TraesCS6A01G159800 chr6D 94.349 1929 70 16 597 2523 126870315 126872206 0.000000e+00 2922
3 TraesCS6A01G159800 chr6D 94.220 692 36 3 2568 3258 126872285 126872973 0.000000e+00 1053
4 TraesCS6A01G159800 chr6D 99.286 140 1 0 1 140 126870133 126870272 1.500000e-63 254
5 TraesCS6A01G159800 chr6B 95.396 1086 40 5 1252 2333 225867483 225868562 0.000000e+00 1720
6 TraesCS6A01G159800 chr6B 97.706 654 15 0 597 1250 225866723 225867376 0.000000e+00 1125
7 TraesCS6A01G159800 chr6B 95.745 564 15 2 2702 3258 225869111 225869672 0.000000e+00 900
8 TraesCS6A01G159800 chr6B 100.000 140 0 0 1 140 225866540 225866679 3.220000e-65 259
9 TraesCS6A01G159800 chr1D 85.612 139 20 0 1916 2054 472561544 472561682 2.620000e-31 147
10 TraesCS6A01G159800 chr1D 80.851 141 21 6 1917 2054 452264436 452264299 4.450000e-19 106
11 TraesCS6A01G159800 chr5B 84.892 139 21 0 1916 2054 532877282 532877420 1.220000e-29 141
12 TraesCS6A01G159800 chr5A 84.892 139 21 0 1916 2054 553421511 553421649 1.220000e-29 141
13 TraesCS6A01G159800 chr1B 85.000 140 19 2 1916 2054 657272693 657272831 1.220000e-29 141
14 TraesCS6A01G159800 chr1A 84.892 139 21 0 1916 2054 566564801 566564939 1.220000e-29 141
15 TraesCS6A01G159800 chr5D 83.453 139 23 0 1916 2054 438360600 438360738 2.640000e-26 130


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 TraesCS6A01G159800 chr6A 152059637 152062894 3257 True 2587.500000 4916 100.000000 1 3258 2 chr6A.!!$R1 3257
1 TraesCS6A01G159800 chr6D 126870133 126872973 2840 False 1409.666667 2922 95.951667 1 3258 3 chr6D.!!$F1 3257
2 TraesCS6A01G159800 chr6B 225866540 225869672 3132 False 1001.000000 1720 97.211750 1 3258 4 chr6B.!!$F1 3257

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
748 751 4.626604 ACACAAAAATTGCAACTGTCTGTG 59.373 37.5 20.36 20.36 38.06 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2399 0.110486 AGGGAAAGAAAGGCGCAGAA 59.89 50.0 10.83 0.0 0.0 3.02 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
747 750 4.819769 ACACAAAAATTGCAACTGTCTGT 58.180 34.783 0.00 0.00 0.00 3.41
748 751 4.626604 ACACAAAAATTGCAACTGTCTGTG 59.373 37.500 20.36 20.36 38.06 3.66
1064 1070 2.837291 CGGAGCAGGAGGAGGAGG 60.837 72.222 0.00 0.00 0.00 4.30
1065 1071 2.693017 GGAGCAGGAGGAGGAGGA 59.307 66.667 0.00 0.00 0.00 3.71
1066 1072 1.457455 GGAGCAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
1189 1195 1.513158 CTTCGTCGTCAGGGCATCT 59.487 57.895 0.00 0.00 0.00 2.90
1224 1230 2.820787 CCAAGGTCAGTTCGACTCTAGT 59.179 50.000 0.00 0.00 44.70 2.57
1230 1236 3.127895 GTCAGTTCGACTCTAGTCATGCT 59.872 47.826 10.55 2.09 44.99 3.79
1238 1244 3.529533 ACTCTAGTCATGCTGCATGTTC 58.470 45.455 34.14 27.54 41.98 3.18
1243 1249 3.418995 AGTCATGCTGCATGTTCTCTTT 58.581 40.909 34.14 15.14 41.98 2.52
1269 1380 3.137360 TCTGATGAGAGCTAGCTGGAGTA 59.863 47.826 24.99 4.04 0.00 2.59
1273 1384 3.283751 TGAGAGCTAGCTGGAGTAGTTC 58.716 50.000 24.99 4.14 0.00 3.01
1285 1396 5.870433 GCTGGAGTAGTTCCTAACTTTCTTC 59.130 44.000 0.00 0.00 46.92 2.87
1329 1441 0.684153 ACAACAGGCAGCTGTGGTTT 60.684 50.000 16.64 1.22 38.24 3.27
1402 1517 6.458206 GCAACATATTACACCTGGTGTATGTG 60.458 42.308 32.03 29.51 46.36 3.21
1404 1519 7.426606 ACATATTACACCTGGTGTATGTGTA 57.573 36.000 31.35 23.82 46.36 2.90
1417 1532 2.584835 ATGTGTATTGGCAGTGTGGT 57.415 45.000 0.00 0.00 0.00 4.16
1419 1534 3.052455 TGTGTATTGGCAGTGTGGTAG 57.948 47.619 0.00 0.00 0.00 3.18
2167 2282 0.661552 TGAGCGTGCGAGAGGTATAC 59.338 55.000 0.00 0.00 0.00 1.47
2280 2395 4.478206 TCTCTCATCATCTTCACCAACC 57.522 45.455 0.00 0.00 0.00 3.77
2281 2396 3.840078 TCTCTCATCATCTTCACCAACCA 59.160 43.478 0.00 0.00 0.00 3.67
2282 2397 4.286808 TCTCTCATCATCTTCACCAACCAA 59.713 41.667 0.00 0.00 0.00 3.67
2283 2398 4.326826 TCTCATCATCTTCACCAACCAAC 58.673 43.478 0.00 0.00 0.00 3.77
2284 2399 4.042062 TCTCATCATCTTCACCAACCAACT 59.958 41.667 0.00 0.00 0.00 3.16
2289 2404 2.297701 TCTTCACCAACCAACTTCTGC 58.702 47.619 0.00 0.00 0.00 4.26
2291 2406 1.008538 CACCAACCAACTTCTGCGC 60.009 57.895 0.00 0.00 0.00 6.09
2303 2418 0.110486 TTCTGCGCCTTTCTTTCCCT 59.890 50.000 4.18 0.00 0.00 4.20
2305 2420 1.589716 CTGCGCCTTTCTTTCCCTGG 61.590 60.000 4.18 0.00 0.00 4.45
2306 2421 2.994671 GCGCCTTTCTTTCCCTGGC 61.995 63.158 0.00 0.00 40.14 4.85
2311 2426 0.405585 CTTTCTTTCCCTGGCCCTCA 59.594 55.000 0.00 0.00 0.00 3.86
2316 2431 0.549902 TTTCCCTGGCCCTCATCTGA 60.550 55.000 0.00 0.00 0.00 3.27
2318 2433 0.765903 TCCCTGGCCCTCATCTGATC 60.766 60.000 0.00 0.00 0.00 2.92
2319 2434 1.058428 CCCTGGCCCTCATCTGATCA 61.058 60.000 0.00 0.00 0.00 2.92
2336 2451 5.402270 TCTGATCATATCGTACGTGCAATTG 59.598 40.000 16.05 0.00 0.00 2.32
2353 2542 4.012374 CAATTGGGCGGCTAGATTATGAT 58.988 43.478 9.56 0.00 0.00 2.45
2356 2545 2.028112 TGGGCGGCTAGATTATGATGAC 60.028 50.000 9.56 0.00 0.00 3.06
2359 2548 2.670414 GCGGCTAGATTATGATGACAGC 59.330 50.000 0.00 0.00 0.00 4.40
2364 2553 1.696336 AGATTATGATGACAGCGGCCT 59.304 47.619 0.00 0.00 0.00 5.19
2366 2555 3.324846 AGATTATGATGACAGCGGCCTTA 59.675 43.478 0.00 0.00 0.00 2.69
2367 2556 3.769739 TTATGATGACAGCGGCCTTAT 57.230 42.857 0.00 0.00 0.00 1.73
2368 2557 2.645838 ATGATGACAGCGGCCTTATT 57.354 45.000 0.00 0.00 0.00 1.40
2369 2558 1.667236 TGATGACAGCGGCCTTATTG 58.333 50.000 0.00 0.00 0.00 1.90
2370 2559 0.308993 GATGACAGCGGCCTTATTGC 59.691 55.000 0.00 0.00 0.00 3.56
2490 2679 4.398549 TGCTGTAAGAAAATACACGTGC 57.601 40.909 17.22 0.00 34.07 5.34
2515 2704 3.806949 TGGGAAAAGGCTTATCACAGT 57.193 42.857 0.00 0.00 0.00 3.55
2523 2712 6.780457 AAAGGCTTATCACAGTATGCAAAT 57.220 33.333 0.00 0.00 42.53 2.32
2524 2713 6.382869 AAGGCTTATCACAGTATGCAAATC 57.617 37.500 0.00 0.00 42.53 2.17
2525 2714 5.688807 AGGCTTATCACAGTATGCAAATCT 58.311 37.500 0.00 0.00 42.53 2.40
2526 2715 5.762218 AGGCTTATCACAGTATGCAAATCTC 59.238 40.000 0.00 0.00 42.53 2.75
2528 2717 6.293298 GGCTTATCACAGTATGCAAATCTCTG 60.293 42.308 0.00 0.00 42.53 3.35
2531 2720 4.611310 CACAGTATGCAAATCTCTGTGG 57.389 45.455 21.21 10.63 46.64 4.17
2532 2721 3.012518 ACAGTATGCAAATCTCTGTGGC 58.987 45.455 0.00 0.00 42.53 5.01
2534 2723 3.311871 CAGTATGCAAATCTCTGTGGCTC 59.688 47.826 0.00 0.00 0.00 4.70
2537 2726 2.430465 TGCAAATCTCTGTGGCTCTTC 58.570 47.619 0.00 0.00 0.00 2.87
2538 2727 1.742268 GCAAATCTCTGTGGCTCTTCC 59.258 52.381 0.00 0.00 0.00 3.46
2539 2728 2.363683 CAAATCTCTGTGGCTCTTCCC 58.636 52.381 0.00 0.00 0.00 3.97
2540 2729 0.539051 AATCTCTGTGGCTCTTCCCG 59.461 55.000 0.00 0.00 0.00 5.14
2541 2730 1.965754 ATCTCTGTGGCTCTTCCCGC 61.966 60.000 0.00 0.00 35.93 6.13
2546 2735 1.302511 GTGGCTCTTCCCGCAGAAA 60.303 57.895 0.00 0.00 35.46 2.52
2547 2736 0.889186 GTGGCTCTTCCCGCAGAAAA 60.889 55.000 0.00 0.00 35.46 2.29
2548 2737 0.179004 TGGCTCTTCCCGCAGAAAAA 60.179 50.000 0.00 0.00 32.88 1.94
2583 2806 3.491619 CGTGGCTCTATGCTTACAGTGAT 60.492 47.826 0.00 0.00 42.39 3.06
2597 2820 9.066892 TGCTTACAGTGATGAAGTTCTTAAATT 57.933 29.630 4.17 0.00 0.00 1.82
2667 2890 0.311165 CGGTTAGATCATCCGCGACT 59.689 55.000 8.23 0.00 37.90 4.18
2690 2913 2.770259 GTCGCCGTCTTCTTTCGC 59.230 61.111 0.00 0.00 0.00 4.70
2694 2917 2.101233 GCCGTCTTCTTTCGCCTCC 61.101 63.158 0.00 0.00 0.00 4.30
2839 3194 0.804364 TAGTGTACGCGTTCGGTGAT 59.196 50.000 20.78 0.00 40.69 3.06
3074 3429 1.445095 CATCTCCTCTGCCCTTCGG 59.555 63.158 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
617 618 6.427242 GGGGATCTTTCGGATTACTAAATCAC 59.573 42.308 0.00 0.00 42.88 3.06
694 695 3.006967 AGAGTATGCATTCCGTGGGATAC 59.993 47.826 3.54 0.00 38.24 2.24
747 750 1.895231 CAGCAGCTTGTGGACAGCA 60.895 57.895 0.00 0.00 0.00 4.41
748 751 1.168407 TTCAGCAGCTTGTGGACAGC 61.168 55.000 0.00 0.00 0.00 4.40
829 832 2.742116 GGGTGCGCTGGGATAAGGA 61.742 63.158 9.73 0.00 0.00 3.36
1064 1070 0.108945 GCCATTGTTCCTGCAAGCTC 60.109 55.000 0.00 0.00 0.00 4.09
1065 1071 1.870055 CGCCATTGTTCCTGCAAGCT 61.870 55.000 0.00 0.00 0.00 3.74
1066 1072 1.444895 CGCCATTGTTCCTGCAAGC 60.445 57.895 0.00 0.00 0.00 4.01
1224 1230 3.822167 TCAAAAGAGAACATGCAGCATGA 59.178 39.130 36.91 12.70 43.81 3.07
1230 1236 5.941647 TCATCAGATCAAAAGAGAACATGCA 59.058 36.000 0.00 0.00 0.00 3.96
1238 1244 5.693104 GCTAGCTCTCATCAGATCAAAAGAG 59.307 44.000 7.70 1.21 34.69 2.85
1243 1249 3.321396 CCAGCTAGCTCTCATCAGATCAA 59.679 47.826 16.15 0.00 0.00 2.57
1269 1380 8.710239 AGAAGAAGAAGAAGAAAGTTAGGAACT 58.290 33.333 0.00 0.00 45.46 3.01
1273 1384 9.554395 AAAGAGAAGAAGAAGAAGAAAGTTAGG 57.446 33.333 0.00 0.00 0.00 2.69
1285 1396 7.590689 GTCATTTTGCTGAAAGAGAAGAAGAAG 59.409 37.037 0.00 0.00 34.07 2.85
1329 1441 3.240134 GAGGGACTGCTTGGACGCA 62.240 63.158 0.00 0.00 41.55 5.24
1376 1491 3.352648 ACACCAGGTGTAATATGTTGCC 58.647 45.455 24.77 0.00 45.56 4.52
1402 1517 3.447586 TCTCTCTACCACACTGCCAATAC 59.552 47.826 0.00 0.00 0.00 1.89
1404 1519 2.540383 TCTCTCTACCACACTGCCAAT 58.460 47.619 0.00 0.00 0.00 3.16
1417 1532 5.596361 CACCTCCTAAATCAGCTTCTCTCTA 59.404 44.000 0.00 0.00 0.00 2.43
1419 1534 4.161377 ACACCTCCTAAATCAGCTTCTCTC 59.839 45.833 0.00 0.00 0.00 3.20
1684 1799 2.992476 CCAGTACTGGTAGGTGCCT 58.008 57.895 30.57 0.00 45.53 4.75
1798 1913 0.678048 GGCCCAGGAAGTACTGCTTG 60.678 60.000 5.98 5.98 37.59 4.01
2167 2282 0.322098 TTTACACCCACCCTCGCATG 60.322 55.000 0.00 0.00 0.00 4.06
2280 2395 2.605580 GGAAAGAAAGGCGCAGAAGTTG 60.606 50.000 10.83 0.00 0.00 3.16
2281 2396 1.609072 GGAAAGAAAGGCGCAGAAGTT 59.391 47.619 10.83 0.00 0.00 2.66
2282 2397 1.239347 GGAAAGAAAGGCGCAGAAGT 58.761 50.000 10.83 0.00 0.00 3.01
2283 2398 0.523519 GGGAAAGAAAGGCGCAGAAG 59.476 55.000 10.83 0.00 0.00 2.85
2284 2399 0.110486 AGGGAAAGAAAGGCGCAGAA 59.890 50.000 10.83 0.00 0.00 3.02
2289 2404 2.343426 GGCCAGGGAAAGAAAGGCG 61.343 63.158 0.00 0.00 46.12 5.52
2291 2406 0.323816 GAGGGCCAGGGAAAGAAAGG 60.324 60.000 6.18 0.00 0.00 3.11
2303 2418 2.498885 CGATATGATCAGATGAGGGCCA 59.501 50.000 7.74 0.00 0.00 5.36
2305 2420 3.883830 ACGATATGATCAGATGAGGGC 57.116 47.619 7.74 0.00 0.00 5.19
2306 2421 4.396478 ACGTACGATATGATCAGATGAGGG 59.604 45.833 24.41 0.00 0.00 4.30
2311 2426 4.766404 TGCACGTACGATATGATCAGAT 57.234 40.909 24.41 1.59 0.00 2.90
2316 2431 3.745975 CCCAATTGCACGTACGATATGAT 59.254 43.478 24.41 6.20 0.00 2.45
2318 2433 2.349438 GCCCAATTGCACGTACGATATG 60.349 50.000 24.41 11.30 0.00 1.78
2319 2434 1.871039 GCCCAATTGCACGTACGATAT 59.129 47.619 24.41 6.33 0.00 1.63
2336 2451 2.028112 TGTCATCATAATCTAGCCGCCC 60.028 50.000 0.00 0.00 0.00 6.13
2353 2542 0.394216 ATGCAATAAGGCCGCTGTCA 60.394 50.000 0.00 0.00 0.00 3.58
2356 2545 1.002033 GAAGATGCAATAAGGCCGCTG 60.002 52.381 0.00 0.00 0.00 5.18
2359 2548 5.695851 ATAAAGAAGATGCAATAAGGCCG 57.304 39.130 0.00 0.00 0.00 6.13
2416 2605 9.775854 ATCACATATACTACTCAGTACGTAGTT 57.224 33.333 14.65 7.79 43.61 2.24
2462 2651 8.561212 ACGTGTATTTTCTTACAGCAACAATTA 58.439 29.630 0.00 0.00 32.92 1.40
2477 2666 4.551388 TCCCAAAATGCACGTGTATTTTC 58.449 39.130 37.92 15.98 44.52 2.29
2481 2670 4.555262 CTTTTCCCAAAATGCACGTGTAT 58.445 39.130 18.38 16.07 0.00 2.29
2482 2671 3.243569 CCTTTTCCCAAAATGCACGTGTA 60.244 43.478 18.38 14.09 0.00 2.90
2490 2679 5.792741 TGTGATAAGCCTTTTCCCAAAATG 58.207 37.500 0.00 0.00 0.00 2.32
2505 2694 7.783090 ACAGAGATTTGCATACTGTGATAAG 57.217 36.000 15.37 0.00 39.76 1.73
2515 2704 3.920231 AGAGCCACAGAGATTTGCATA 57.080 42.857 0.00 0.00 0.00 3.14
2523 2712 2.650116 GCGGGAAGAGCCACAGAGA 61.650 63.158 0.00 0.00 38.95 3.10
2524 2713 2.125350 GCGGGAAGAGCCACAGAG 60.125 66.667 0.00 0.00 38.95 3.35
2525 2714 2.922503 TGCGGGAAGAGCCACAGA 60.923 61.111 0.00 0.00 38.95 3.41
2526 2715 2.435586 CTGCGGGAAGAGCCACAG 60.436 66.667 0.00 0.00 38.95 3.66
2528 2717 0.889186 TTTTCTGCGGGAAGAGCCAC 60.889 55.000 0.00 0.00 38.95 5.01
2546 2735 4.583073 AGAGCCACGGAGTTTATTTGTTTT 59.417 37.500 0.00 0.00 41.61 2.43
2547 2736 4.142038 AGAGCCACGGAGTTTATTTGTTT 58.858 39.130 0.00 0.00 41.61 2.83
2548 2737 3.751518 AGAGCCACGGAGTTTATTTGTT 58.248 40.909 0.00 0.00 41.61 2.83
2549 2738 3.418684 AGAGCCACGGAGTTTATTTGT 57.581 42.857 0.00 0.00 41.61 2.83
2550 2739 4.260784 GCATAGAGCCACGGAGTTTATTTG 60.261 45.833 0.00 0.00 41.61 2.32
2553 2742 3.113260 GCATAGAGCCACGGAGTTTAT 57.887 47.619 0.00 0.00 41.61 1.40
2554 2743 2.596904 GCATAGAGCCACGGAGTTTA 57.403 50.000 0.00 0.00 41.61 2.01
2555 2744 3.460648 GCATAGAGCCACGGAGTTT 57.539 52.632 0.00 0.00 41.61 2.66
2565 2754 5.355596 ACTTCATCACTGTAAGCATAGAGC 58.644 41.667 0.00 0.00 46.19 4.09
2566 2755 7.264221 AGAACTTCATCACTGTAAGCATAGAG 58.736 38.462 0.00 0.00 37.60 2.43
2583 2806 2.823154 CCGGCCCAATTTAAGAACTTCA 59.177 45.455 0.00 0.00 0.00 3.02
2690 2913 4.821589 GCAGCCGTCGAAGGGAGG 62.822 72.222 19.34 3.82 0.00 4.30
2765 3120 3.154473 AAGCGCGGATAGGAGGCA 61.154 61.111 8.83 0.00 0.00 4.75
2768 3123 2.106938 TGCAAGCGCGGATAGGAG 59.893 61.111 8.83 0.00 42.97 3.69
3074 3429 6.428159 AGTTCAATTCATATACTGATTCGCCC 59.572 38.462 0.00 0.00 32.72 6.13
3234 3596 1.614903 CCAGAAAGAAATGGTGCTGCA 59.385 47.619 0.00 0.00 0.00 4.41
3235 3597 1.670967 GCCAGAAAGAAATGGTGCTGC 60.671 52.381 0.00 0.00 38.91 5.25


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

AutoCloner maintained by Alex Coulton.