Multiple sequence alignment - TraesCS6A01G279800

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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 TraesCS6A01G279800 chr6A 100.000 2414 0 0 1 2414 507144312 507146725 0.000000e+00 4458.0
1 TraesCS6A01G279800 chr6B 91.682 1611 64 22 638 2190 552497895 552499493 0.000000e+00 2169.0
2 TraesCS6A01G279800 chr6B 96.460 226 8 0 2189 2414 552499533 552499758 8.150000e-100 374.0
3 TraesCS6A01G279800 chr6D 93.068 1457 53 15 638 2063 366699667 366701106 0.000000e+00 2087.0
4 TraesCS6A01G279800 chr6D 96.108 334 7 4 2087 2414 366701265 366701598 7.590000e-150 540.0
5 TraesCS6A01G279800 chr1A 96.516 574 14 4 1 570 259200958 259201529 0.000000e+00 944.0
6 TraesCS6A01G279800 chr1A 95.556 45 2 0 526 570 223993254 223993210 3.330000e-09 73.1
7 TraesCS6A01G279800 chr4A 95.741 540 17 6 1 537 277893334 277892798 0.000000e+00 865.0
8 TraesCS6A01G279800 chr4A 90.000 260 21 4 1 256 549883389 549883131 4.970000e-87 331.0
9 TraesCS6A01G279800 chr4A 94.231 52 2 1 521 571 277892526 277892475 7.160000e-11 78.7
10 TraesCS6A01G279800 chr3D 90.421 261 18 6 1 256 608308487 608308745 1.070000e-88 337.0
11 TraesCS6A01G279800 chr7A 89.272 261 21 5 1 256 520792909 520792651 1.080000e-83 320.0
12 TraesCS6A01G279800 chr2B 88.235 221 21 4 1 218 794385262 794385044 2.380000e-65 259.0
13 TraesCS6A01G279800 chr5A 95.918 49 2 0 522 570 198149006 198149054 1.990000e-11 80.5
14 TraesCS6A01G279800 chr2A 97.778 45 1 0 526 570 211700580 211700536 7.160000e-11 78.7


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 TraesCS6A01G279800 chr6A 507144312 507146725 2413 False 4458.00 4458 100.000 1 2414 1 chr6A.!!$F1 2413
1 TraesCS6A01G279800 chr6B 552497895 552499758 1863 False 1271.50 2169 94.071 638 2414 2 chr6B.!!$F1 1776
2 TraesCS6A01G279800 chr6D 366699667 366701598 1931 False 1313.50 2087 94.588 638 2414 2 chr6D.!!$F1 1776
3 TraesCS6A01G279800 chr1A 259200958 259201529 571 False 944.00 944 96.516 1 570 1 chr1A.!!$F1 569
4 TraesCS6A01G279800 chr4A 277892475 277893334 859 True 471.85 865 94.986 1 571 2 chr4A.!!$R2 570

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
448 452 0.325577 TGCCATGGAGACCTAGCAGA 60.326 55.0 18.4 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 2143 0.251077 CAAGCAGGAAAGACAGCCCT 60.251 55.0 0.0 0.0 0.0 5.19 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
103 104 5.620206 TGTGAGACCAAAGTTATGTGTGAT 58.380 37.500 0.00 0.00 0.00 3.06
307 310 3.519107 AGCCCCTATTTGGTGAAATTTGG 59.481 43.478 0.00 0.00 33.63 3.28
309 312 3.843619 CCCCTATTTGGTGAAATTTGGGT 59.156 43.478 0.00 0.00 39.78 4.51
356 359 9.053840 TGTGGTTCAATGTACGAGTTATTTTTA 57.946 29.630 0.00 0.00 0.00 1.52
448 452 0.325577 TGCCATGGAGACCTAGCAGA 60.326 55.000 18.40 0.00 0.00 4.26
571 862 2.159627 GCATGTGCACGCTTACTAGTTT 59.840 45.455 13.13 0.00 41.59 2.66
572 863 3.725010 GCATGTGCACGCTTACTAGTTTC 60.725 47.826 13.13 0.00 41.59 2.78
573 864 3.100658 TGTGCACGCTTACTAGTTTCA 57.899 42.857 13.13 0.00 0.00 2.69
574 865 2.798283 TGTGCACGCTTACTAGTTTCAC 59.202 45.455 13.13 0.00 0.00 3.18
575 866 3.057734 GTGCACGCTTACTAGTTTCACT 58.942 45.455 0.00 0.00 0.00 3.41
576 867 4.232221 GTGCACGCTTACTAGTTTCACTA 58.768 43.478 0.00 0.00 0.00 2.74
577 868 4.682860 GTGCACGCTTACTAGTTTCACTAA 59.317 41.667 0.00 0.00 29.00 2.24
578 869 5.176223 GTGCACGCTTACTAGTTTCACTAAA 59.824 40.000 0.00 0.00 29.00 1.85
579 870 5.754406 TGCACGCTTACTAGTTTCACTAAAA 59.246 36.000 0.00 0.00 29.00 1.52
580 871 6.258287 TGCACGCTTACTAGTTTCACTAAAAA 59.742 34.615 0.00 0.00 29.00 1.94
581 872 7.041644 TGCACGCTTACTAGTTTCACTAAAAAT 60.042 33.333 0.00 0.00 29.00 1.82
582 873 8.437742 GCACGCTTACTAGTTTCACTAAAAATA 58.562 33.333 0.00 0.00 29.00 1.40
583 874 9.737025 CACGCTTACTAGTTTCACTAAAAATAC 57.263 33.333 0.00 0.00 29.00 1.89
584 875 9.480053 ACGCTTACTAGTTTCACTAAAAATACA 57.520 29.630 0.00 0.00 29.00 2.29
585 876 9.737025 CGCTTACTAGTTTCACTAAAAATACAC 57.263 33.333 0.00 0.00 29.00 2.90
590 881 9.623000 ACTAGTTTCACTAAAAATACACTTGGT 57.377 29.630 0.00 0.00 29.00 3.67
593 884 9.185680 AGTTTCACTAAAAATACACTTGGTTCT 57.814 29.630 0.00 0.00 0.00 3.01
601 892 8.601845 AAAAATACACTTGGTTCTAATTTGCC 57.398 30.769 0.00 0.00 0.00 4.52
602 893 6.909550 AATACACTTGGTTCTAATTTGCCA 57.090 33.333 0.00 0.00 0.00 4.92
603 894 6.909550 ATACACTTGGTTCTAATTTGCCAA 57.090 33.333 0.00 0.00 38.51 4.52
604 895 5.806654 ACACTTGGTTCTAATTTGCCAAT 57.193 34.783 0.00 0.00 39.84 3.16
605 896 5.783111 ACACTTGGTTCTAATTTGCCAATC 58.217 37.500 0.00 0.00 39.84 2.67
606 897 5.539955 ACACTTGGTTCTAATTTGCCAATCT 59.460 36.000 0.00 0.00 39.84 2.40
607 898 6.041979 ACACTTGGTTCTAATTTGCCAATCTT 59.958 34.615 0.00 0.00 39.84 2.40
608 899 6.930722 CACTTGGTTCTAATTTGCCAATCTTT 59.069 34.615 0.00 0.00 39.84 2.52
609 900 7.442062 CACTTGGTTCTAATTTGCCAATCTTTT 59.558 33.333 0.00 0.00 39.84 2.27
610 901 7.992608 ACTTGGTTCTAATTTGCCAATCTTTTT 59.007 29.630 0.00 0.00 39.84 1.94
611 902 7.961325 TGGTTCTAATTTGCCAATCTTTTTC 57.039 32.000 0.00 0.00 0.00 2.29
612 903 7.734942 TGGTTCTAATTTGCCAATCTTTTTCT 58.265 30.769 0.00 0.00 0.00 2.52
613 904 8.210265 TGGTTCTAATTTGCCAATCTTTTTCTT 58.790 29.630 0.00 0.00 0.00 2.52
614 905 9.056005 GGTTCTAATTTGCCAATCTTTTTCTTT 57.944 29.630 0.00 0.00 0.00 2.52
617 908 9.829507 TCTAATTTGCCAATCTTTTTCTTTTGA 57.170 25.926 0.00 0.00 0.00 2.69
771 1081 3.327404 CCCAGGCCCACTAACGGT 61.327 66.667 0.00 0.00 0.00 4.83
803 1114 4.290622 ACCACCCAGGCCAGCAAG 62.291 66.667 5.01 0.00 43.14 4.01
1008 1322 4.143333 GCAGCAGCCATGGCCAAG 62.143 66.667 33.14 23.18 43.17 3.61
1104 1421 4.052229 ACCGTCGAGTCCGCCTTG 62.052 66.667 0.00 0.00 35.37 3.61
1180 1497 4.608774 ACCCCGACGAGGACACCA 62.609 66.667 0.95 0.00 45.00 4.17
1276 1605 2.364961 CCGAGGAGAAGGACCCCT 59.635 66.667 0.00 0.00 33.87 4.79
1277 1606 1.758906 CCGAGGAGAAGGACCCCTC 60.759 68.421 4.78 4.78 42.24 4.30
1278 1607 1.308326 CGAGGAGAAGGACCCCTCT 59.692 63.158 11.45 3.58 43.21 3.69
1357 1719 2.756283 AGGAGAAGGGAGCGGACG 60.756 66.667 0.00 0.00 0.00 4.79
1419 1781 1.289066 CAAGGCCGAGTGAAGACGA 59.711 57.895 0.00 0.00 0.00 4.20
1480 1842 3.422546 GCTGTGAATCTAATCTACGCGTC 59.577 47.826 18.63 0.00 0.00 5.19
1557 1919 3.553828 TTAGGGCCCGTCTTAAGATTG 57.446 47.619 18.44 4.65 0.00 2.67
1573 1935 0.919710 ATTGAGGCTTACCCTGGGTC 59.080 55.000 24.45 8.22 46.60 4.46
1575 1937 0.474854 TGAGGCTTACCCTGGGTCAA 60.475 55.000 24.45 13.76 46.60 3.18
1580 1942 2.100197 GCTTACCCTGGGTCAATTTCC 58.900 52.381 24.45 1.28 37.09 3.13
1641 2003 7.338800 ACATCTGTATGGATGGTTTCATTTC 57.661 36.000 8.91 0.00 45.11 2.17
1660 2022 0.679640 CCCATGGAAACCGCTTGCTA 60.680 55.000 15.22 0.00 0.00 3.49
1661 2023 1.392589 CCATGGAAACCGCTTGCTAT 58.607 50.000 5.56 0.00 0.00 2.97
1693 2055 6.879458 GGACAGGAAACTTATTGTCACATAGT 59.121 38.462 5.91 0.00 41.22 2.12
1811 2173 4.158394 TCTTTCCTGCTTGGTTTATGCATC 59.842 41.667 0.19 0.00 38.58 3.91
2095 2572 7.338800 ACCTGTTAATCCTATTTTGATGCTG 57.661 36.000 0.00 0.00 0.00 4.41
2367 2908 8.553459 TTCCATTTCTAGATCACTTCTTGAAC 57.447 34.615 0.00 0.00 43.07 3.18
2380 2921 6.204108 TCACTTCTTGAACCTTTCGGTATTTC 59.796 38.462 0.00 0.00 44.73 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 7.195374 AGTTAGGCCTCACATTACAGAATTA 57.805 36.000 19.16 0.00 0.00 1.40
307 310 3.493503 CCGAAAAGTGTGTTCAGACTACC 59.506 47.826 3.16 0.00 0.00 3.18
309 312 4.116961 CACCGAAAAGTGTGTTCAGACTA 58.883 43.478 3.16 0.00 32.89 2.59
356 359 9.868277 TTGAAAAATGTGTTCAGATTGTAAAGT 57.132 25.926 0.00 0.00 36.41 2.66
375 378 7.494298 GGCCTTCATGTAAAAGAACTTGAAAAA 59.506 33.333 0.00 0.00 40.74 1.94
553 844 2.798283 GTGAAACTAGTAAGCGTGCACA 59.202 45.455 18.64 0.00 0.00 4.57
575 866 9.699703 GGCAAATTAGAACCAAGTGTATTTTTA 57.300 29.630 0.00 0.00 0.00 1.52
576 867 8.207545 TGGCAAATTAGAACCAAGTGTATTTTT 58.792 29.630 0.00 0.00 0.00 1.94
577 868 7.731054 TGGCAAATTAGAACCAAGTGTATTTT 58.269 30.769 0.00 0.00 0.00 1.82
578 869 7.296628 TGGCAAATTAGAACCAAGTGTATTT 57.703 32.000 0.00 0.00 0.00 1.40
579 870 6.909550 TGGCAAATTAGAACCAAGTGTATT 57.090 33.333 0.00 0.00 0.00 1.89
580 871 6.909550 TTGGCAAATTAGAACCAAGTGTAT 57.090 33.333 0.00 0.00 37.26 2.29
581 872 6.719370 AGATTGGCAAATTAGAACCAAGTGTA 59.281 34.615 3.01 0.00 44.88 2.90
582 873 5.539955 AGATTGGCAAATTAGAACCAAGTGT 59.460 36.000 3.01 0.00 44.88 3.55
583 874 6.029346 AGATTGGCAAATTAGAACCAAGTG 57.971 37.500 3.01 0.00 44.88 3.16
584 875 6.670695 AAGATTGGCAAATTAGAACCAAGT 57.329 33.333 3.01 0.00 44.88 3.16
585 876 7.967890 AAAAGATTGGCAAATTAGAACCAAG 57.032 32.000 3.01 0.00 44.88 3.61
586 877 8.210265 AGAAAAAGATTGGCAAATTAGAACCAA 58.790 29.630 3.01 0.00 45.68 3.67
587 878 7.734942 AGAAAAAGATTGGCAAATTAGAACCA 58.265 30.769 3.01 0.00 0.00 3.67
588 879 8.607441 AAGAAAAAGATTGGCAAATTAGAACC 57.393 30.769 3.01 0.00 0.00 3.62
591 882 9.829507 TCAAAAGAAAAAGATTGGCAAATTAGA 57.170 25.926 3.01 0.00 0.00 2.10
621 912 8.165239 TCAGAAGAAAATGATTCCTCGAAAAA 57.835 30.769 0.00 0.00 0.00 1.94
622 913 7.744087 TCAGAAGAAAATGATTCCTCGAAAA 57.256 32.000 0.00 0.00 0.00 2.29
623 914 7.744087 TTCAGAAGAAAATGATTCCTCGAAA 57.256 32.000 0.00 0.00 0.00 3.46
624 915 7.744087 TTTCAGAAGAAAATGATTCCTCGAA 57.256 32.000 0.00 0.00 40.61 3.71
625 916 7.148188 CCATTTCAGAAGAAAATGATTCCTCGA 60.148 37.037 9.52 0.00 46.06 4.04
626 917 6.971184 CCATTTCAGAAGAAAATGATTCCTCG 59.029 38.462 9.52 0.00 46.06 4.63
627 918 7.972832 GTCCATTTCAGAAGAAAATGATTCCTC 59.027 37.037 9.52 0.00 46.06 3.71
628 919 7.673082 AGTCCATTTCAGAAGAAAATGATTCCT 59.327 33.333 9.52 0.00 46.06 3.36
629 920 7.834803 AGTCCATTTCAGAAGAAAATGATTCC 58.165 34.615 9.52 0.00 46.06 3.01
630 921 7.972832 GGAGTCCATTTCAGAAGAAAATGATTC 59.027 37.037 3.60 7.33 46.06 2.52
631 922 7.452501 TGGAGTCCATTTCAGAAGAAAATGATT 59.547 33.333 8.12 0.01 46.06 2.57
632 923 6.950041 TGGAGTCCATTTCAGAAGAAAATGAT 59.050 34.615 8.12 0.00 46.06 2.45
633 924 6.207417 GTGGAGTCCATTTCAGAAGAAAATGA 59.793 38.462 16.67 0.15 46.06 2.57
634 925 6.385033 GTGGAGTCCATTTCAGAAGAAAATG 58.615 40.000 16.67 2.38 46.06 2.32
635 926 5.478332 GGTGGAGTCCATTTCAGAAGAAAAT 59.522 40.000 16.67 0.00 46.06 1.82
636 927 4.827284 GGTGGAGTCCATTTCAGAAGAAAA 59.173 41.667 16.67 0.00 46.06 2.29
756 1060 2.125673 CGACCGTTAGTGGGCCTG 60.126 66.667 4.53 0.00 31.06 4.85
996 1310 4.453892 GCTCCCTTGGCCATGGCT 62.454 66.667 34.70 0.00 41.60 4.75
1104 1421 2.184579 CGGTCGAGGAAGGGCTTC 59.815 66.667 0.00 0.00 38.80 3.86
1357 1719 4.097361 GCCCAGTTCGACCTCCCC 62.097 72.222 0.00 0.00 0.00 4.81
1480 1842 3.211865 CATCATCCATCACAACCTCCAG 58.788 50.000 0.00 0.00 0.00 3.86
1557 1919 0.919710 ATTGACCCAGGGTAAGCCTC 59.080 55.000 12.69 0.00 35.25 4.70
1573 1935 5.406175 ACTGAATGCAAAATGTCGGAAATTG 59.594 36.000 0.00 0.00 0.00 2.32
1575 1937 5.138125 ACTGAATGCAAAATGTCGGAAAT 57.862 34.783 0.00 0.00 0.00 2.17
1580 1942 5.688823 TCAAGTACTGAATGCAAAATGTCG 58.311 37.500 0.00 0.00 0.00 4.35
1616 1978 7.502226 GGAAATGAAACCATCCATACAGATGTA 59.498 37.037 0.00 0.00 41.79 2.29
1617 1979 6.322201 GGAAATGAAACCATCCATACAGATGT 59.678 38.462 1.26 0.00 41.79 3.06
1625 1987 3.712733 CCATGGGAAATGAAACCATCCAT 59.287 43.478 2.85 0.00 42.85 3.41
1641 2003 0.679640 TAGCAAGCGGTTTCCATGGG 60.680 55.000 13.02 0.00 0.00 4.00
1652 2014 1.009829 GTCCACAGGAATAGCAAGCG 58.990 55.000 0.00 0.00 31.38 4.68
1781 2143 0.251077 CAAGCAGGAAAGACAGCCCT 60.251 55.000 0.00 0.00 0.00 5.19
1987 2349 9.546428 AAGCAAGAAAAGTAGCACAAAATAATT 57.454 25.926 0.00 0.00 0.00 1.40
2270 2811 9.727627 GAAAACCTGAATATTTCTAGCAAGATG 57.272 33.333 0.00 0.00 31.86 2.90
2380 2921 2.562298 ACTGGGCAAACATGTTACATGG 59.438 45.455 26.30 11.99 0.00 3.66


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

AutoCloner maintained by Alex Coulton.