Multiple sequence alignment - TraesCS6A01G165500

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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 TraesCS6A01G165500 chr6A 100.000 2579 0 0 1 2579 166508556 166505978 0.000000e+00 4763
1 TraesCS6A01G165500 chr6D 92.868 2608 122 30 1 2578 129150562 129153135 0.000000e+00 3727
2 TraesCS6A01G165500 chr6B 91.441 1659 85 32 364 1997 227268495 227270121 0.000000e+00 2224
3 TraesCS6A01G165500 chr6B 86.971 591 39 10 1993 2578 227270175 227270732 4.680000e-177 630
4 TraesCS6A01G165500 chr6B 93.931 379 22 1 1 378 227267792 227268170 2.880000e-159 571
5 TraesCS6A01G165500 chr7D 79.065 535 82 20 1052 1580 512281824 512281314 8.840000e-90 340
6 TraesCS6A01G165500 chr7A 78.090 534 89 19 1052 1580 585066490 585065980 1.930000e-81 313
7 TraesCS6A01G165500 chr7B 77.861 533 92 17 1052 1580 544139563 544139053 8.960000e-80 307


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 TraesCS6A01G165500 chr6A 166505978 166508556 2578 True 4763.000000 4763 100.000 1 2579 1 chr6A.!!$R1 2578
1 TraesCS6A01G165500 chr6D 129150562 129153135 2573 False 3727.000000 3727 92.868 1 2578 1 chr6D.!!$F1 2577
2 TraesCS6A01G165500 chr6B 227267792 227270732 2940 False 1141.666667 2224 90.781 1 2578 3 chr6B.!!$F1 2577
3 TraesCS6A01G165500 chr7D 512281314 512281824 510 True 340.000000 340 79.065 1052 1580 1 chr7D.!!$R1 528
4 TraesCS6A01G165500 chr7A 585065980 585066490 510 True 313.000000 313 78.090 1052 1580 1 chr7A.!!$R1 528
5 TraesCS6A01G165500 chr7B 544139053 544139563 510 True 307.000000 307 77.861 1052 1580 1 chr7B.!!$R1 528

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
471 822 0.034059 CGAAGGAGTTCTGTGTGGCT 59.966 55.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2530 0.171903 ATGTTTGCCATTGCTCTCGC 59.828 50.0 0.0 0.0 38.71 5.03 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
53 54 1.002624 CCACTTTAGAAGCCGGCCA 60.003 57.895 26.15 2.56 0.00 5.36
102 104 1.606313 CAAACCCAATCCCAGCCGT 60.606 57.895 0.00 0.00 0.00 5.68
421 772 2.655685 GCTCGATTCGGCGTCTCC 60.656 66.667 6.85 0.00 0.00 3.71
423 774 1.009449 CTCGATTCGGCGTCTCCTC 60.009 63.158 6.85 0.00 0.00 3.71
424 775 1.440938 CTCGATTCGGCGTCTCCTCT 61.441 60.000 6.85 0.00 0.00 3.69
450 801 1.083015 CGCGTGGGTTTTGTTCTCG 60.083 57.895 0.00 0.00 0.00 4.04
452 803 0.041576 GCGTGGGTTTTGTTCTCGAC 60.042 55.000 0.00 0.00 0.00 4.20
462 813 2.701073 TGTTCTCGACGAAGGAGTTC 57.299 50.000 0.00 0.00 33.26 3.01
464 815 2.031069 TGTTCTCGACGAAGGAGTTCTG 60.031 50.000 0.00 0.00 33.26 3.02
465 816 1.893544 TCTCGACGAAGGAGTTCTGT 58.106 50.000 0.00 0.00 33.26 3.41
467 818 1.267261 CTCGACGAAGGAGTTCTGTGT 59.733 52.381 0.00 0.00 0.00 3.72
468 819 1.001706 TCGACGAAGGAGTTCTGTGTG 60.002 52.381 0.00 0.00 0.00 3.82
470 821 0.249911 ACGAAGGAGTTCTGTGTGGC 60.250 55.000 0.00 0.00 0.00 5.01
471 822 0.034059 CGAAGGAGTTCTGTGTGGCT 59.966 55.000 0.00 0.00 0.00 4.75
472 823 1.802069 GAAGGAGTTCTGTGTGGCTC 58.198 55.000 0.00 0.00 0.00 4.70
473 824 1.346068 GAAGGAGTTCTGTGTGGCTCT 59.654 52.381 0.00 0.00 0.00 4.09
548 900 2.109593 GTTCGGTGGTTGGTCCGT 59.890 61.111 3.64 0.00 45.88 4.69
551 903 0.394080 TTCGGTGGTTGGTCCGTTTT 60.394 50.000 3.64 0.00 45.88 2.43
579 931 4.156008 AGAAGTCTTTGCGTGTTGTTTTCT 59.844 37.500 0.00 0.00 0.00 2.52
598 950 4.357918 TCTCCTTTTCTGTTCCTTCTGG 57.642 45.455 0.00 0.00 0.00 3.86
600 952 2.783510 TCCTTTTCTGTTCCTTCTGGGT 59.216 45.455 0.00 0.00 36.25 4.51
651 1009 4.411256 AATTAAAGCCGTCCGGATTAGA 57.589 40.909 7.81 2.26 43.82 2.10
659 1017 3.318017 CCGTCCGGATTAGATGAATCAC 58.682 50.000 7.81 0.00 45.15 3.06
664 1022 2.755650 GGATTAGATGAATCACGCGGT 58.244 47.619 12.47 0.00 45.15 5.68
666 1024 1.286501 TTAGATGAATCACGCGGTGC 58.713 50.000 12.47 0.00 32.98 5.01
985 1358 3.827876 TGCTCTTGGAAGATTGCAATTGA 59.172 39.130 14.33 3.42 37.86 2.57
1037 1410 0.864455 GTCTGTTCTGTGTGCAGCTC 59.136 55.000 0.00 0.00 42.29 4.09
1039 1412 0.585357 CTGTTCTGTGTGCAGCTCAC 59.415 55.000 18.83 18.83 45.82 3.51
1185 1559 2.092753 GGAGATGGTCATGAAGCAGGAA 60.093 50.000 0.00 0.00 39.11 3.36
1266 1640 1.147376 ACCTGTTGTTGCGGCTGTA 59.853 52.632 0.00 0.00 0.00 2.74
1585 1959 3.522553 CTCGACAAGATTTAGGTGTCCC 58.477 50.000 0.00 0.00 38.76 4.46
1693 2074 3.359654 GCATTTCCTAAATTGTACGGCG 58.640 45.455 4.80 4.80 0.00 6.46
1905 2288 2.541588 GGTTCATCATATTGCGTGTGGC 60.542 50.000 0.00 0.00 43.96 5.01
2000 2441 6.981559 TGTTAGTTTGGAAAATTGTACTTGGC 59.018 34.615 0.00 0.00 0.00 4.52
2004 2445 6.549736 AGTTTGGAAAATTGTACTTGGCTAGT 59.450 34.615 6.84 6.84 41.04 2.57
2010 2451 5.499004 AATTGTACTTGGCTAGTTCTCCA 57.501 39.130 6.96 0.00 38.33 3.86
2056 2498 5.382618 AAGAGCAATGAGAAACATGGTTC 57.617 39.130 15.99 15.99 39.45 3.62
2079 2521 8.766151 GTTCTGGTTCTCAAGTTTTAGTTCTAG 58.234 37.037 0.00 0.00 0.00 2.43
2086 2531 8.311650 TCTCAAGTTTTAGTTCTAGAACATGC 57.688 34.615 31.80 18.46 43.47 4.06
2118 2563 4.037446 TGGCAAACATGGTTACAGTTCTTC 59.963 41.667 0.00 0.00 0.00 2.87
2119 2564 4.278419 GGCAAACATGGTTACAGTTCTTCT 59.722 41.667 0.00 0.00 0.00 2.85
2120 2565 5.221244 GGCAAACATGGTTACAGTTCTTCTT 60.221 40.000 0.00 0.00 0.00 2.52
2165 2610 8.502105 TGATGATATGTGGATTATGATGAAGC 57.498 34.615 0.00 0.00 0.00 3.86
2200 2645 1.147817 AGAATGGAGGCCTTGTGGTTT 59.852 47.619 6.77 0.00 35.27 3.27
2275 2721 1.531149 CGTATGATTGGGAATGCGGAC 59.469 52.381 0.00 0.00 0.00 4.79
2304 2751 5.709631 TCTGCCTTGTTGCTGTATTCATTTA 59.290 36.000 0.00 0.00 0.00 1.40
2449 2898 7.557719 CCAGGAGATAGGATTTTCTTTTGCTTA 59.442 37.037 0.00 0.00 0.00 3.09
2474 2923 1.001760 GGTCAGGCCCCTCTAGACA 59.998 63.158 0.00 0.00 0.00 3.41
2475 2924 0.399233 GGTCAGGCCCCTCTAGACAT 60.399 60.000 0.00 0.00 0.00 3.06
2555 3004 4.928981 AGGCACTGATTCCTCCCT 57.071 55.556 0.00 0.00 37.18 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.152226 GGATGGGTCCTCGGGAGAT 60.152 63.158 0.00 0.00 41.60 2.75
89 91 2.438434 GTGGACGGCTGGGATTGG 60.438 66.667 0.00 0.00 0.00 3.16
296 299 4.150454 AGGAGGAGGGCGAGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
297 300 2.520741 GAGGAGGAGGGCGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
298 301 4.144727 GGAGGAGGAGGGCGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
419 770 2.437895 ACGCGGATCGACAGAGGA 60.438 61.111 12.47 0.00 41.67 3.71
421 772 2.278206 CCACGCGGATCGACAGAG 60.278 66.667 12.47 0.00 41.67 3.35
423 774 3.642778 AACCCACGCGGATCGACAG 62.643 63.158 12.47 0.00 41.67 3.51
424 775 2.718747 AAAACCCACGCGGATCGACA 62.719 55.000 12.47 0.00 41.67 4.35
450 801 1.784525 CCACACAGAACTCCTTCGTC 58.215 55.000 0.00 0.00 0.00 4.20
452 803 0.034059 AGCCACACAGAACTCCTTCG 59.966 55.000 0.00 0.00 0.00 3.79
488 840 4.587189 GCCCCCTTCCGTCGATCG 62.587 72.222 9.36 9.36 39.52 3.69
548 900 3.314080 CACGCAAAGACTTCTACCCAAAA 59.686 43.478 0.00 0.00 0.00 2.44
551 903 1.414919 ACACGCAAAGACTTCTACCCA 59.585 47.619 0.00 0.00 0.00 4.51
579 931 2.783510 ACCCAGAAGGAACAGAAAAGGA 59.216 45.455 0.00 0.00 39.89 3.36
669 1027 2.052237 GAACACAACGTGCGCCAG 60.052 61.111 4.18 0.15 36.98 4.85
715 1073 4.851558 CACCGAATTCAAATCTCGAAAACC 59.148 41.667 6.22 0.00 34.52 3.27
883 1248 2.552599 TCCAGGCACAAACAATCGTA 57.447 45.000 0.00 0.00 0.00 3.43
927 1300 1.468520 CCACGCAACAAGAATCCGAAT 59.531 47.619 0.00 0.00 0.00 3.34
930 1303 1.154225 GCCACGCAACAAGAATCCG 60.154 57.895 0.00 0.00 0.00 4.18
985 1358 4.478206 TCAGCATCGAAAGAGGAAGAAT 57.522 40.909 0.00 0.00 46.52 2.40
1037 1410 4.454161 TGTGTTCCATCTTGAATAACCGTG 59.546 41.667 0.00 0.00 0.00 4.94
1039 1412 5.391950 CCTTGTGTTCCATCTTGAATAACCG 60.392 44.000 0.00 0.00 0.00 4.44
1040 1413 5.710099 TCCTTGTGTTCCATCTTGAATAACC 59.290 40.000 0.00 0.00 0.00 2.85
1286 1660 1.013596 CACGTCAACTTGAGCAACCA 58.986 50.000 0.00 0.00 0.00 3.67
1585 1959 1.962807 TGCAACCATTTCTTCCCTGTG 59.037 47.619 0.00 0.00 0.00 3.66
1905 2288 9.132521 GAACATACTCAAACATGGAAAATGAAG 57.867 33.333 0.00 0.00 0.00 3.02
2000 2441 9.906660 GATGTATATTTGAGAGTGGAGAACTAG 57.093 37.037 0.00 0.00 40.07 2.57
2004 2445 7.675161 TGGATGTATATTTGAGAGTGGAGAA 57.325 36.000 0.00 0.00 0.00 2.87
2010 2451 9.265901 CTTCGATTTGGATGTATATTTGAGAGT 57.734 33.333 0.00 0.00 0.00 3.24
2056 2498 8.766151 GTTCTAGAACTAAAACTTGAGAACCAG 58.234 37.037 25.30 0.00 36.93 4.00
2085 2530 0.171903 ATGTTTGCCATTGCTCTCGC 59.828 50.000 0.00 0.00 38.71 5.03
2086 2531 1.468565 CCATGTTTGCCATTGCTCTCG 60.469 52.381 0.00 0.00 38.71 4.04
2165 2610 5.068723 CCTCCATTCTTTTCATCCTGGATTG 59.931 44.000 6.42 3.25 32.66 2.67
2200 2645 9.391006 CTAAGGCATAGTTTTTAACTGGTGATA 57.609 33.333 2.45 0.00 42.84 2.15
2211 2656 7.524717 TCAGCTTTTCTAAGGCATAGTTTTT 57.475 32.000 0.00 0.00 33.08 1.94
2216 2661 6.749923 AACTTCAGCTTTTCTAAGGCATAG 57.250 37.500 0.00 0.00 31.76 2.23
2434 2882 8.825745 TGACCACAAATTAAGCAAAAGAAAATC 58.174 29.630 0.00 0.00 0.00 2.17
2449 2898 4.539235 GGGGCCTGACCACAAATT 57.461 55.556 0.84 0.00 43.87 1.82
2474 2923 6.771267 AGAGTTGATCAATGTGCACATCATAT 59.229 34.615 31.45 23.08 35.10 1.78
2475 2924 6.117488 AGAGTTGATCAATGTGCACATCATA 58.883 36.000 31.45 19.70 35.10 2.15


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

AutoCloner maintained by Alex Coulton.