Multiple sequence alignment - TraesCS6A01G063200

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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 TraesCS6A01G063200 chr6A 100.000 2464 0 0 522 2985 33952150 33954613 0.000000e+00 4551
1 TraesCS6A01G063200 chr6A 100.000 64 0 0 1 64 33951629 33951692 5.230000e-23 119
2 TraesCS6A01G063200 chr6B 93.561 2252 87 21 765 2985 61492521 61494745 0.000000e+00 3302
3 TraesCS6A01G063200 chr6B 87.293 181 14 5 594 766 61492295 61492474 6.530000e-47 198
4 TraesCS6A01G063200 chr6D 93.243 2220 101 21 786 2985 28702005 28699815 0.000000e+00 3223
5 TraesCS6A01G063200 chr6D 85.714 217 21 5 525 732 28702323 28702108 1.390000e-53 220
6 TraesCS6A01G063200 chr6D 96.875 64 2 0 1 64 28702464 28702401 1.130000e-19 108
7 TraesCS6A01G063200 chr2D 87.500 936 93 15 1471 2397 248777383 248776463 0.000000e+00 1059
8 TraesCS6A01G063200 chr5D 89.955 667 56 7 2011 2674 539743483 539742825 0.000000e+00 850
9 TraesCS6A01G063200 chr5D 96.842 95 2 1 2891 2985 539742508 539742415 1.110000e-34 158
10 TraesCS6A01G063200 chr3A 90.528 644 48 7 2009 2649 94173874 94173241 0.000000e+00 839
11 TraesCS6A01G063200 chr3A 96.364 110 4 0 2876 2985 94172971 94172862 6.570000e-42 182
12 TraesCS6A01G063200 chr1A 89.118 680 61 7 2002 2678 17885223 17884554 0.000000e+00 833
13 TraesCS6A01G063200 chr1A 94.545 110 5 1 2876 2985 17884537 17884429 5.120000e-38 169
14 TraesCS6A01G063200 chr3B 88.593 675 63 8 2002 2671 735003779 735003114 0.000000e+00 808
15 TraesCS6A01G063200 chr3B 90.085 353 29 6 2002 2351 735004599 735004250 1.260000e-123 453
16 TraesCS6A01G063200 chr3B 93.636 110 7 0 2876 2985 735002827 735002718 6.620000e-37 165


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 TraesCS6A01G063200 chr6A 33951629 33954613 2984 False 2335.000000 4551 100.000000 1 2985 2 chr6A.!!$F1 2984
1 TraesCS6A01G063200 chr6B 61492295 61494745 2450 False 1750.000000 3302 90.427000 594 2985 2 chr6B.!!$F1 2391
2 TraesCS6A01G063200 chr6D 28699815 28702464 2649 True 1183.666667 3223 91.944000 1 2985 3 chr6D.!!$R1 2984
3 TraesCS6A01G063200 chr2D 248776463 248777383 920 True 1059.000000 1059 87.500000 1471 2397 1 chr2D.!!$R1 926
4 TraesCS6A01G063200 chr5D 539742415 539743483 1068 True 504.000000 850 93.398500 2011 2985 2 chr5D.!!$R1 974
5 TraesCS6A01G063200 chr3A 94172862 94173874 1012 True 510.500000 839 93.446000 2009 2985 2 chr3A.!!$R1 976
6 TraesCS6A01G063200 chr1A 17884429 17885223 794 True 501.000000 833 91.831500 2002 2985 2 chr1A.!!$R1 983
7 TraesCS6A01G063200 chr3B 735002718 735004599 1881 True 475.333333 808 90.771333 2002 2985 3 chr3B.!!$R1 983

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
979 1051 0.390472 GAGCTCAAGAACTCCCACCG 60.39 60.0 9.4 0.0 0.00 4.94 F
1916 2001 0.610232 AGGAGTTGTTGAGCATGGGC 60.61 55.0 0.0 0.0 41.61 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2042 0.460459 TTTTGACACTGACGCCGTCA 60.460 50.0 20.04 20.04 40.5 4.35 R
2956 3983 2.616510 CGATTGGAGGCAGAAGAGGTTT 60.617 50.0 0.00 0.00 0.0 3.27 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
25 26 4.084507 GCAATCTCAGTTCACGAATTTCG 58.915 43.478 16.84 16.84 46.93 3.46
540 541 1.609408 ATAGCTACCCCCTCCCACCA 61.609 60.000 0.00 0.00 0.00 4.17
543 544 3.622263 TACCCCCTCCCACCAGCT 61.622 66.667 0.00 0.00 0.00 4.24
549 550 3.324930 CTCCCACCAGCTGGAGCA 61.325 66.667 39.19 18.44 43.95 4.26
550 551 2.611800 TCCCACCAGCTGGAGCAT 60.612 61.111 39.19 14.42 43.95 3.79
566 567 4.050934 ATGCCACGTCGCACGAGA 62.051 61.111 10.83 0.00 46.05 4.04
574 575 4.116328 TCGCACGAGAAGAGGCCG 62.116 66.667 0.00 0.00 0.00 6.13
588 589 4.626081 GCCGGGTAGATGCGCCAT 62.626 66.667 4.18 0.00 0.00 4.40
592 593 1.376466 GGGTAGATGCGCCATCCAT 59.624 57.895 4.18 0.00 41.36 3.41
600 601 2.346766 TGCGCCATCCATAGAACATT 57.653 45.000 4.18 0.00 0.00 2.71
603 604 1.267806 CGCCATCCATAGAACATTGCC 59.732 52.381 0.00 0.00 0.00 4.52
625 626 0.545787 TTTCCTCCCGCTACCTCCAA 60.546 55.000 0.00 0.00 0.00 3.53
634 635 1.585006 CTACCTCCAACTGCGACGT 59.415 57.895 0.00 0.00 0.00 4.34
638 639 4.351938 TCCAACTGCGACGTCCCG 62.352 66.667 10.58 0.24 0.00 5.14
639 640 4.351938 CCAACTGCGACGTCCCGA 62.352 66.667 10.58 0.00 0.00 5.14
641 642 1.736645 CAACTGCGACGTCCCGATT 60.737 57.895 10.58 0.00 0.00 3.34
643 644 2.149803 AACTGCGACGTCCCGATTCA 62.150 55.000 10.58 0.00 0.00 2.57
644 645 2.126228 TGCGACGTCCCGATTCAC 60.126 61.111 10.58 0.00 0.00 3.18
645 646 2.884207 GCGACGTCCCGATTCACC 60.884 66.667 10.58 0.00 0.00 4.02
655 664 1.885388 CGATTCACCGGCGGCAATA 60.885 57.895 28.71 9.66 0.00 1.90
690 699 3.438087 CGACATTGAATGGAAGCAGAACT 59.562 43.478 10.27 0.00 33.60 3.01
696 705 0.392193 ATGGAAGCAGAACTCGGCAG 60.392 55.000 4.67 0.00 39.54 4.85
732 741 0.930726 AGACTCGAAGGAGGGGAGAT 59.069 55.000 0.00 0.00 44.93 2.75
869 939 1.256812 CCTCCAATTCACCACCAACC 58.743 55.000 0.00 0.00 0.00 3.77
870 940 1.256812 CTCCAATTCACCACCAACCC 58.743 55.000 0.00 0.00 0.00 4.11
871 941 0.856982 TCCAATTCACCACCAACCCT 59.143 50.000 0.00 0.00 0.00 4.34
929 1000 1.152567 CATCTCCTCCGCCCTCTCT 60.153 63.158 0.00 0.00 0.00 3.10
931 1002 0.469144 ATCTCCTCCGCCCTCTCTTC 60.469 60.000 0.00 0.00 0.00 2.87
979 1051 0.390472 GAGCTCAAGAACTCCCACCG 60.390 60.000 9.40 0.00 0.00 4.94
1147 1223 2.811317 CGCAGGACGACCTCAAGC 60.811 66.667 2.57 4.00 45.94 4.01
1453 1534 4.022068 ACCGTACCATTTTAGTTCTGACGA 60.022 41.667 0.00 0.00 0.00 4.20
1513 1595 8.613922 ATTTTTCCCAAGAACCATCTATGATT 57.386 30.769 0.00 0.00 33.77 2.57
1514 1596 9.713684 ATTTTTCCCAAGAACCATCTATGATTA 57.286 29.630 0.00 0.00 33.77 1.75
1515 1597 9.540538 TTTTTCCCAAGAACCATCTATGATTAA 57.459 29.630 0.00 0.00 33.77 1.40
1516 1598 9.713684 TTTTCCCAAGAACCATCTATGATTAAT 57.286 29.630 0.00 0.00 33.77 1.40
1603 1688 1.187087 GAGCCCTTCTCCGAGAGAAA 58.813 55.000 14.58 3.24 46.18 2.52
1916 2001 0.610232 AGGAGTTGTTGAGCATGGGC 60.610 55.000 0.00 0.00 41.61 5.36
1957 2042 4.080469 ACTTCAGTGATCATTGCTGGATCT 60.080 41.667 13.08 0.00 41.35 2.75
1987 2072 5.324697 GTCAGTGTCAAAACAAAGTGAGTC 58.675 41.667 0.00 0.00 37.08 3.36
1992 2077 7.382218 CAGTGTCAAAACAAAGTGAGTCTTTTT 59.618 33.333 0.00 0.00 42.95 1.94
2052 2141 8.703604 TTTCAGTGAATAAGCTATCTGTGTAC 57.296 34.615 6.36 0.00 0.00 2.90
2062 2151 4.413520 AGCTATCTGTGTACAATGGGGAAT 59.586 41.667 0.00 0.00 0.00 3.01
2063 2152 4.516698 GCTATCTGTGTACAATGGGGAATG 59.483 45.833 0.00 0.00 0.00 2.67
2115 2210 2.325583 TCGTTGGCTCTCACAGTTTT 57.674 45.000 0.00 0.00 0.00 2.43
2213 3132 8.025445 ACAAGTCAATGACATTAATCTTCTTGC 58.975 33.333 16.38 0.00 34.60 4.01
2230 3149 1.010350 GCGCGCCAATCATCTTCTG 60.010 57.895 23.24 0.00 0.00 3.02
2285 3204 9.096160 CCTGCATGTATATCAGATAATTCAGAC 57.904 37.037 0.00 0.00 0.00 3.51
2298 3217 3.883830 ATTCAGACTACAGCTCACCAG 57.116 47.619 0.00 0.00 0.00 4.00
2300 3219 3.093057 TCAGACTACAGCTCACCAGAT 57.907 47.619 0.00 0.00 0.00 2.90
2316 3235 6.057533 TCACCAGATGCTTATTCATTACCTG 58.942 40.000 0.00 0.00 0.00 4.00
2331 3250 6.515832 TCATTACCTGACATGCTACATACTG 58.484 40.000 0.00 0.00 0.00 2.74
2391 3310 3.922910 AGTCGTACCTGTTAAAAGCTCC 58.077 45.455 0.00 0.00 0.00 4.70
2433 3354 3.384789 AGAAGAAGTGTCGGCTGCATATA 59.615 43.478 0.50 0.00 0.00 0.86
2440 3361 2.102252 TGTCGGCTGCATATACATGTGA 59.898 45.455 9.11 0.00 34.40 3.58
2441 3362 3.130633 GTCGGCTGCATATACATGTGAA 58.869 45.455 9.11 0.00 34.40 3.18
2442 3363 3.748048 GTCGGCTGCATATACATGTGAAT 59.252 43.478 9.11 0.00 34.40 2.57
2443 3364 3.747529 TCGGCTGCATATACATGTGAATG 59.252 43.478 9.11 12.63 34.40 2.67
2444 3365 3.499537 CGGCTGCATATACATGTGAATGT 59.500 43.478 9.11 0.00 38.49 2.71
2445 3366 4.612033 CGGCTGCATATACATGTGAATGTG 60.612 45.833 9.11 4.81 36.08 3.21
2456 3377 8.797350 ATACATGTGAATGTGATCTTTCAAGA 57.203 30.769 9.11 0.00 38.70 3.02
2490 3412 7.764443 GCCTACACTGAAACAGTCTTATCAATA 59.236 37.037 1.22 0.00 43.43 1.90
2537 3459 7.641411 CAGCCGAATTACAACTTTATTCAGATG 59.359 37.037 0.00 0.00 0.00 2.90
2538 3460 6.414987 GCCGAATTACAACTTTATTCAGATGC 59.585 38.462 0.00 0.00 0.00 3.91
2561 3483 5.803967 GCCAGCAAAATCTTCAGATAACTTG 59.196 40.000 0.00 0.00 33.73 3.16
2590 3518 9.431887 GTATTGAAGTACATCCAAGAACTGTTA 57.568 33.333 0.00 0.00 0.00 2.41
2757 3687 9.719355 AATTATTGTGGGTTTATGTTTTCCTTC 57.281 29.630 0.00 0.00 0.00 3.46
2874 3841 1.134159 CAAGATCCCCAGCTCCTGAAG 60.134 57.143 0.00 0.00 32.44 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.463116 ACCTTGGTTCACGGTGTCAC 60.463 55.000 8.17 6.37 34.66 3.67
521 522 1.239235 GGTGGGAGGGGGTAGCTAT 59.761 63.158 0.00 0.00 0.00 2.97
522 523 2.252012 CTGGTGGGAGGGGGTAGCTA 62.252 65.000 0.00 0.00 0.00 3.32
523 524 3.622263 TGGTGGGAGGGGGTAGCT 61.622 66.667 0.00 0.00 0.00 3.32
524 525 3.090532 CTGGTGGGAGGGGGTAGC 61.091 72.222 0.00 0.00 0.00 3.58
525 526 3.090532 GCTGGTGGGAGGGGGTAG 61.091 72.222 0.00 0.00 0.00 3.18
526 527 3.622263 AGCTGGTGGGAGGGGGTA 61.622 66.667 0.00 0.00 0.00 3.69
540 541 3.965539 GACGTGGCATGCTCCAGCT 62.966 63.158 18.92 0.00 42.66 4.24
545 546 4.152625 GTGCGACGTGGCATGCTC 62.153 66.667 27.94 11.65 45.99 4.26
549 550 3.567478 TTCTCGTGCGACGTGGCAT 62.567 57.895 27.94 0.00 45.99 4.40
550 551 4.273257 TTCTCGTGCGACGTGGCA 62.273 61.111 21.95 21.95 43.14 4.92
566 567 2.797278 CGCATCTACCCGGCCTCTT 61.797 63.158 0.00 0.00 0.00 2.85
574 575 0.613260 TATGGATGGCGCATCTACCC 59.387 55.000 10.83 1.38 40.39 3.69
588 589 3.627237 GGAAAGGGGCAATGTTCTATGGA 60.627 47.826 0.00 0.00 0.00 3.41
592 593 2.025321 GGAGGAAAGGGGCAATGTTCTA 60.025 50.000 0.00 0.00 0.00 2.10
600 601 3.935456 TAGCGGGAGGAAAGGGGCA 62.935 63.158 0.00 0.00 0.00 5.36
603 604 1.687297 GAGGTAGCGGGAGGAAAGGG 61.687 65.000 0.00 0.00 0.00 3.95
638 639 0.238289 CATATTGCCGCCGGTGAATC 59.762 55.000 18.79 5.74 0.00 2.52
639 640 0.465460 ACATATTGCCGCCGGTGAAT 60.465 50.000 18.79 11.86 0.00 2.57
641 642 1.078072 AACATATTGCCGCCGGTGA 60.078 52.632 18.79 0.00 0.00 4.02
643 644 1.373590 GACAACATATTGCCGCCGGT 61.374 55.000 4.45 0.00 39.66 5.28
644 645 1.095228 AGACAACATATTGCCGCCGG 61.095 55.000 0.00 0.00 39.66 6.13
645 646 0.304705 GAGACAACATATTGCCGCCG 59.695 55.000 0.00 0.00 39.66 6.46
647 648 0.304705 CGGAGACAACATATTGCCGC 59.695 55.000 0.00 0.00 39.66 6.53
649 650 1.593006 CGACGGAGACAACATATTGCC 59.407 52.381 0.00 0.00 39.66 4.52
650 651 2.281762 GTCGACGGAGACAACATATTGC 59.718 50.000 0.00 0.00 39.66 3.56
690 699 1.471501 CGAGATCCAACATTCTGCCGA 60.472 52.381 0.00 0.00 0.00 5.54
696 705 2.432510 AGTCTCCCGAGATCCAACATTC 59.567 50.000 0.00 0.00 39.97 2.67
732 741 2.832838 AGCCATGGGGATATATCGTCA 58.167 47.619 15.13 7.67 35.59 4.35
869 939 3.057337 AACGACGGGTTGAGGAGG 58.943 61.111 0.00 0.00 37.50 4.30
929 1000 2.610859 GGGGAGCTGGTGGAGGAA 60.611 66.667 0.00 0.00 0.00 3.36
931 1002 2.693864 ATGGGGAGCTGGTGGAGG 60.694 66.667 0.00 0.00 0.00 4.30
1478 1559 4.083565 TCTTGGGAAAAATTAAGGGGACG 58.916 43.478 0.00 0.00 0.00 4.79
1597 1682 0.108138 CGGCCTCGACCATTTTCTCT 60.108 55.000 0.00 0.00 39.00 3.10
1603 1688 4.814294 GACGCGGCCTCGACCATT 62.814 66.667 24.18 0.00 39.00 3.16
1957 2042 0.460459 TTTTGACACTGACGCCGTCA 60.460 50.000 20.04 20.04 40.50 4.35
1987 2072 2.541588 CCGACAACAGCTGACCAAAAAG 60.542 50.000 23.35 3.62 0.00 2.27
1992 2077 1.227527 CACCGACAACAGCTGACCA 60.228 57.895 23.35 0.00 0.00 4.02
2052 2141 6.720112 ATAGAACAACATCATTCCCCATTG 57.280 37.500 0.00 0.00 0.00 2.82
2115 2210 5.068460 TCCGATTCTCTTTTCAAGCCAAAAA 59.932 36.000 0.00 0.00 0.00 1.94
2122 2217 4.337763 CGCAATCCGATTCTCTTTTCAAG 58.662 43.478 0.00 0.00 40.02 3.02
2123 2218 3.126858 CCGCAATCCGATTCTCTTTTCAA 59.873 43.478 0.00 0.00 40.02 2.69
2125 2220 2.936498 TCCGCAATCCGATTCTCTTTTC 59.064 45.455 0.00 0.00 40.02 2.29
2126 2221 2.985896 TCCGCAATCCGATTCTCTTTT 58.014 42.857 0.00 0.00 40.02 2.27
2137 2232 2.468532 CGGTGTTTTATCCGCAATCC 57.531 50.000 0.00 0.00 40.28 3.01
2175 3092 6.262720 TGTCATTGACTTGTCATGATCACAAA 59.737 34.615 17.26 0.00 33.36 2.83
2213 3132 0.580578 CTCAGAAGATGATTGGCGCG 59.419 55.000 0.00 0.00 37.28 6.86
2230 3149 7.435192 CCCAAGTTTATTCAAAGTGTTGTTCTC 59.565 37.037 0.00 0.00 36.07 2.87
2285 3204 2.687700 AAGCATCTGGTGAGCTGTAG 57.312 50.000 0.00 0.00 38.86 2.74
2298 3217 6.206243 AGCATGTCAGGTAATGAATAAGCATC 59.794 38.462 0.00 0.00 40.43 3.91
2300 3219 5.439721 AGCATGTCAGGTAATGAATAAGCA 58.560 37.500 0.00 0.00 40.43 3.91
2433 3354 6.487668 TGTCTTGAAAGATCACATTCACATGT 59.512 34.615 7.78 0.00 39.73 3.21
2440 3361 5.709164 CCCTTCTGTCTTGAAAGATCACATT 59.291 40.000 0.00 0.00 37.39 2.71
2441 3362 5.251764 CCCTTCTGTCTTGAAAGATCACAT 58.748 41.667 0.00 0.00 37.39 3.21
2442 3363 4.645535 CCCTTCTGTCTTGAAAGATCACA 58.354 43.478 0.00 0.00 37.39 3.58
2443 3364 3.438434 GCCCTTCTGTCTTGAAAGATCAC 59.562 47.826 0.00 0.00 37.39 3.06
2444 3365 3.560025 GGCCCTTCTGTCTTGAAAGATCA 60.560 47.826 0.00 0.00 37.39 2.92
2445 3366 3.013219 GGCCCTTCTGTCTTGAAAGATC 58.987 50.000 0.00 0.00 37.39 2.75
2456 3377 1.729586 TTCAGTGTAGGCCCTTCTGT 58.270 50.000 0.00 0.00 0.00 3.41
2490 3412 7.754924 CGGCTGTTCATGTTTTTGTATTTCTAT 59.245 33.333 0.00 0.00 0.00 1.98
2507 3429 6.811253 ATAAAGTTGTAATTCGGCTGTTCA 57.189 33.333 0.00 0.00 0.00 3.18
2537 3459 5.573337 AGTTATCTGAAGATTTTGCTGGC 57.427 39.130 0.00 0.00 36.05 4.85
2538 3460 6.917533 ACAAGTTATCTGAAGATTTTGCTGG 58.082 36.000 0.00 0.00 36.05 4.85
2561 3483 9.088512 CAGTTCTTGGATGTACTTCAATACTAC 57.911 37.037 10.60 2.35 0.00 2.73
2590 3518 8.735692 AAACCATGTTGACATTTTGAGAAAAT 57.264 26.923 0.00 0.00 41.57 1.82
2874 3841 2.805099 CAGTTGCTCCAACAAGAGAGAC 59.195 50.000 10.34 0.00 45.66 3.36
2956 3983 2.616510 CGATTGGAGGCAGAAGAGGTTT 60.617 50.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.