Multiple sequence alignment - TraesCS6A01G358700

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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 TraesCS6A01G358700 chr6A 100.000 2870 0 0 1 2870 588606121 588603252 0.000000e+00 5301
1 TraesCS6A01G358700 chr6D 95.862 2175 55 11 716 2870 440664631 440662472 0.000000e+00 3485
2 TraesCS6A01G358700 chr6D 79.032 434 81 10 21 449 77867496 77867068 3.620000e-74 289
3 TraesCS6A01G358700 chr6B 96.856 1654 45 4 757 2406 665716865 665715215 0.000000e+00 2760
4 TraesCS6A01G358700 chr6B 91.697 554 45 1 1 553 49945888 49946441 0.000000e+00 767
5 TraesCS6A01G358700 chr6B 83.208 399 29 16 2474 2870 665715218 665714856 5.930000e-87 331
6 TraesCS6A01G358700 chr6B 85.625 160 22 1 554 713 49946473 49946631 1.770000e-37 167
7 TraesCS6A01G358700 chr6B 79.885 174 21 6 1851 2020 665713673 665713510 6.500000e-22 115
8 TraesCS6A01G358700 chr1B 97.974 691 14 0 1 691 161573711 161573021 0.000000e+00 1199
9 TraesCS6A01G358700 chr1B 85.584 548 75 4 9 553 625984575 625985121 3.210000e-159 571
10 TraesCS6A01G358700 chr3B 91.155 554 48 1 1 553 811073212 811072659 0.000000e+00 750
11 TraesCS6A01G358700 chr3B 75.527 474 102 14 8 474 220748007 220748473 1.340000e-53 220
12 TraesCS6A01G358700 chr4A 84.116 554 87 1 1 553 708425203 708425756 4.210000e-148 534
13 TraesCS6A01G358700 chr4A 83.303 557 79 12 9 557 232383120 232383670 4.270000e-138 501
14 TraesCS6A01G358700 chr7A 76.312 705 137 25 1060 1749 397125784 397125095 1.640000e-92 350
15 TraesCS6A01G358700 chr7D 76.840 652 125 22 1057 1695 350094517 350095155 7.610000e-91 344
16 TraesCS6A01G358700 chr7B 76.028 705 139 25 1060 1749 355906453 355905764 3.540000e-89 339
17 TraesCS6A01G358700 chr2A 78.220 427 82 11 29 450 71141873 71142293 2.190000e-66 263


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 TraesCS6A01G358700 chr6A 588603252 588606121 2869 True 5301.000000 5301 100.000000 1 2870 1 chr6A.!!$R1 2869
1 TraesCS6A01G358700 chr6D 440662472 440664631 2159 True 3485.000000 3485 95.862000 716 2870 1 chr6D.!!$R2 2154
2 TraesCS6A01G358700 chr6B 665713510 665716865 3355 True 1068.666667 2760 86.649667 757 2870 3 chr6B.!!$R1 2113
3 TraesCS6A01G358700 chr6B 49945888 49946631 743 False 467.000000 767 88.661000 1 713 2 chr6B.!!$F1 712
4 TraesCS6A01G358700 chr1B 161573021 161573711 690 True 1199.000000 1199 97.974000 1 691 1 chr1B.!!$R1 690
5 TraesCS6A01G358700 chr1B 625984575 625985121 546 False 571.000000 571 85.584000 9 553 1 chr1B.!!$F1 544
6 TraesCS6A01G358700 chr3B 811072659 811073212 553 True 750.000000 750 91.155000 1 553 1 chr3B.!!$R1 552
7 TraesCS6A01G358700 chr4A 708425203 708425756 553 False 534.000000 534 84.116000 1 553 1 chr4A.!!$F2 552
8 TraesCS6A01G358700 chr4A 232383120 232383670 550 False 501.000000 501 83.303000 9 557 1 chr4A.!!$F1 548
9 TraesCS6A01G358700 chr7A 397125095 397125784 689 True 350.000000 350 76.312000 1060 1749 1 chr7A.!!$R1 689
10 TraesCS6A01G358700 chr7D 350094517 350095155 638 False 344.000000 344 76.840000 1057 1695 1 chr7D.!!$F1 638
11 TraesCS6A01G358700 chr7B 355905764 355906453 689 True 339.000000 339 76.028000 1060 1749 1 chr7B.!!$R1 689

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
705 740 0.544357 TCACCAATCGGGACTGACCT 60.544 55.0 0.0 0.0 41.15 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2307 1.004745 ACGGATGGTGGCATTTTCTCT 59.995 47.619 0.0 0.0 0.0 3.1 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
61 62 6.239714 GGTTTCCTATATCCTCTGCTGAATCA 60.240 42.308 0.00 0.00 0.00 2.57
226 227 1.204146 CCTTCCTCTTCCCCGATTCA 58.796 55.000 0.00 0.00 0.00 2.57
532 536 0.546747 CCTAGGGTTCCTGGTGGTGA 60.547 60.000 0.00 0.00 34.61 4.02
638 673 0.966370 ACACCAGAGACTAGGTCGCC 60.966 60.000 0.00 0.00 37.67 5.54
668 703 3.506059 ATCGCCTCCGCAATCTCCG 62.506 63.158 0.00 0.00 34.03 4.63
693 728 2.740826 CCGCGAACCGTCACCAAT 60.741 61.111 8.23 0.00 34.38 3.16
700 735 2.978824 CCGTCACCAATCGGGACT 59.021 61.111 0.00 0.00 42.61 3.85
705 740 0.544357 TCACCAATCGGGACTGACCT 60.544 55.000 0.00 0.00 41.15 3.85
708 743 1.553704 ACCAATCGGGACTGACCTTAC 59.446 52.381 0.00 0.00 41.15 2.34
710 745 2.236395 CCAATCGGGACTGACCTTACTT 59.764 50.000 0.00 0.00 40.01 2.24
711 746 3.449737 CCAATCGGGACTGACCTTACTTA 59.550 47.826 0.00 0.00 40.01 2.24
712 747 4.101119 CCAATCGGGACTGACCTTACTTAT 59.899 45.833 0.00 0.00 40.01 1.73
713 748 5.303589 CCAATCGGGACTGACCTTACTTATA 59.696 44.000 0.00 0.00 40.01 0.98
714 749 6.014499 CCAATCGGGACTGACCTTACTTATAT 60.014 42.308 0.00 0.00 40.01 0.86
720 755 7.466860 CGGGACTGACCTTACTTATATTTTTGC 60.467 40.741 0.00 0.00 38.98 3.68
933 982 0.924090 CCTCCCCCGGGTCTAAAAAT 59.076 55.000 21.85 0.00 36.47 1.82
1167 1216 2.047655 GTCGCCATGGACACCGAA 60.048 61.111 18.40 0.00 36.91 4.30
1275 1324 2.593978 CACCTCATCCAGCTGGGG 59.406 66.667 32.23 25.89 42.96 4.96
1842 1894 1.982073 GCGTGCTGTATGGGCTCAAC 61.982 60.000 0.00 0.00 0.00 3.18
1886 1938 2.945080 TGATGGATGATGCTCCCTTC 57.055 50.000 0.00 0.00 34.12 3.46
2039 2092 7.734538 ATTTGAACGTAGTGTTTTTCAGTTG 57.265 32.000 0.00 0.00 45.00 3.16
2042 2095 6.670233 TGAACGTAGTGTTTTTCAGTTGTTT 58.330 32.000 0.00 0.00 45.00 2.83
2171 2224 6.945435 TCCAGTTCAATATGGCAAAAAGACTA 59.055 34.615 0.00 0.00 36.47 2.59
2273 2326 1.755179 AGAGAAAATGCCACCATCCG 58.245 50.000 0.00 0.00 0.00 4.18
2277 2330 1.272212 GAAAATGCCACCATCCGTGTT 59.728 47.619 0.00 0.00 41.26 3.32
2368 2422 1.918262 TGTCCTTCTGGAGAATGCCAT 59.082 47.619 0.00 0.00 44.16 4.40
2418 2472 9.039870 GTGTTAATCTCCATTTAGATCTCAGTG 57.960 37.037 0.00 0.00 35.10 3.66
2452 2506 6.569226 GCAAAGTATTTTCTGATGCTGTCAGT 60.569 38.462 15.96 3.71 45.46 3.41
2529 2584 7.932491 TGATTGAAAAATGTGTTGTTGATGGAT 59.068 29.630 0.00 0.00 0.00 3.41
2783 2842 2.413837 TCATGATGCGATGCTGATCAG 58.586 47.619 18.84 18.84 29.85 2.90
2801 2860 7.925483 GCTGATCAGAACAAGTATATCTGTCTT 59.075 37.037 27.04 0.00 41.04 3.01
2839 2898 7.880160 ATTGCTGTTGATGCTAATTACCTTA 57.120 32.000 0.00 0.00 0.00 2.69
2840 2899 7.695480 TTGCTGTTGATGCTAATTACCTTAA 57.305 32.000 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 2.242965 TCCTCTTGGCATGATGAATGGT 59.757 45.455 3.31 0.00 36.71 3.55
226 227 4.214119 CAGTTCATGTTCACGTTCTTCCAT 59.786 41.667 0.00 0.00 0.00 3.41
532 536 4.701286 CTAGGGCCTAGGGTCGTT 57.299 61.111 29.55 0.00 31.03 3.85
693 728 7.427989 AAAATATAAGTAAGGTCAGTCCCGA 57.572 36.000 0.00 0.00 36.75 5.14
720 755 4.500477 GCCTTGCAAATAACGCTCATAAAG 59.500 41.667 0.00 0.00 0.00 1.85
738 773 1.242076 CAGAGGTGAAGGTTGCCTTG 58.758 55.000 5.01 0.00 44.82 3.61
933 982 0.271927 ATGGGGGAAGGCTCTGGATA 59.728 55.000 0.00 0.00 0.00 2.59
1167 1216 2.505982 CAGACGATGCCCGGGAAT 59.494 61.111 29.31 23.09 43.93 3.01
1275 1324 4.475135 GGGCCCGAGAAGGTGAGC 62.475 72.222 5.69 0.00 38.74 4.26
1470 1522 1.227205 CGAGGACATGAGCAGCTCC 60.227 63.158 20.16 4.64 0.00 4.70
1503 1555 2.282674 ACCCAGTAGACGGCGTCA 60.283 61.111 37.71 22.62 34.60 4.35
1842 1894 1.073964 CACTGACACCATTCTCTGCG 58.926 55.000 0.00 0.00 0.00 5.18
1886 1938 3.185246 ACCCATTCACAGAGCTATTCG 57.815 47.619 0.00 0.00 0.00 3.34
2039 2092 6.417930 GCAGAAAACACTAGTTCAATGGAAAC 59.582 38.462 0.00 0.00 36.84 2.78
2042 2095 5.376625 AGCAGAAAACACTAGTTCAATGGA 58.623 37.500 0.00 0.00 36.84 3.41
2241 2294 8.893727 GTGGCATTTTCTCTTGTAGTGTTATAT 58.106 33.333 0.00 0.00 0.00 0.86
2252 2305 2.159338 CGGATGGTGGCATTTTCTCTTG 60.159 50.000 0.00 0.00 0.00 3.02
2253 2306 2.094675 CGGATGGTGGCATTTTCTCTT 58.905 47.619 0.00 0.00 0.00 2.85
2254 2307 1.004745 ACGGATGGTGGCATTTTCTCT 59.995 47.619 0.00 0.00 0.00 3.10
2273 2326 8.338259 GGAATATACATGTGAACATCAGAACAC 58.662 37.037 9.11 0.00 33.61 3.32
2277 2330 8.021898 TGAGGAATATACATGTGAACATCAGA 57.978 34.615 9.11 0.00 33.61 3.27
2368 2422 9.791820 CACTTATTCTCATTGCAAATTATGTGA 57.208 29.630 1.71 0.00 0.00 3.58
2535 2590 7.817418 AGATAACAGAACACTTTAGCCAAAA 57.183 32.000 0.00 0.00 0.00 2.44
2536 2591 8.154856 AGTAGATAACAGAACACTTTAGCCAAA 58.845 33.333 0.00 0.00 0.00 3.28
2691 2749 6.931840 TGCATAATCCGTACATGCTACAAATA 59.068 34.615 14.14 0.00 44.27 1.40
2693 2751 5.007234 GTGCATAATCCGTACATGCTACAAA 59.993 40.000 14.14 0.00 44.27 2.83
2699 2757 2.224079 CCTGTGCATAATCCGTACATGC 59.776 50.000 7.89 7.89 44.23 4.06
2702 2760 2.764010 ACTCCTGTGCATAATCCGTACA 59.236 45.455 0.00 0.00 0.00 2.90
2707 2765 5.297029 GGACTTTAACTCCTGTGCATAATCC 59.703 44.000 0.00 0.00 0.00 3.01
2822 2881 8.494433 ACAGGAGATTAAGGTAATTAGCATCAA 58.506 33.333 16.53 7.55 0.00 2.57


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

AutoCloner maintained by Alex Coulton.