Multiple sequence alignment - TraesCS6A01G114600

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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 TraesCS6A01G114600 chr6A 100.000 2816 0 0 1 2816 84442692 84445507 0 5201
1 TraesCS6A01G114600 chr6A 98.654 1857 24 1 1 1856 608874687 608872831 0 3290
2 TraesCS6A01G114600 chr6A 94.549 954 46 2 1863 2816 573092060 573091113 0 1469
3 TraesCS6A01G114600 chr1A 98.924 1858 18 2 1 1856 238117485 238119342 0 3319
4 TraesCS6A01G114600 chr1A 98.707 1856 24 0 1 1856 238121408 238123263 0 3295
5 TraesCS6A01G114600 chr1A 94.346 955 46 2 1863 2816 105009179 105010126 0 1458
6 TraesCS6A01G114600 chr1A 94.340 954 48 2 1863 2816 303257735 303258682 0 1458
7 TraesCS6A01G114600 chrUn 98.922 1856 20 0 1 1856 86449117 86450972 0 3317
8 TraesCS6A01G114600 chrUn 98.869 1857 20 1 1 1856 222680160 222678304 0 3312
9 TraesCS6A01G114600 chrUn 98.761 1857 21 2 1 1856 86455117 86456972 0 3301
10 TraesCS6A01G114600 chr5B 98.869 1857 20 1 1 1856 533066664 533068520 0 3312
11 TraesCS6A01G114600 chr7B 98.708 1858 22 2 1 1856 742925241 742927098 0 3297
12 TraesCS6A01G114600 chr6B 98.707 1856 24 0 1 1856 596628844 596630699 0 3295
13 TraesCS6A01G114600 chr2A 95.073 954 39 3 1863 2816 693126449 693127394 0 1495
14 TraesCS6A01G114600 chr2A 94.654 954 43 3 1863 2816 147030087 147029142 0 1472
15 TraesCS6A01G114600 chr5A 94.864 954 42 3 1863 2816 275989379 275988433 0 1483
16 TraesCS6A01G114600 chr4A 94.654 954 44 5 1863 2816 590758904 590759850 0 1472
17 TraesCS6A01G114600 chr7A 94.549 954 45 3 1863 2816 305547645 305546699 0 1467
18 TraesCS6A01G114600 chr3A 94.340 954 47 5 1863 2816 191900034 191899088 0 1456


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 TraesCS6A01G114600 chr6A 84442692 84445507 2815 False 5201 5201 100.0000 1 2816 1 chr6A.!!$F1 2815
1 TraesCS6A01G114600 chr6A 608872831 608874687 1856 True 3290 3290 98.6540 1 1856 1 chr6A.!!$R2 1855
2 TraesCS6A01G114600 chr6A 573091113 573092060 947 True 1469 1469 94.5490 1863 2816 1 chr6A.!!$R1 953
3 TraesCS6A01G114600 chr1A 238117485 238123263 5778 False 3307 3319 98.8155 1 1856 2 chr1A.!!$F3 1855
4 TraesCS6A01G114600 chr1A 105009179 105010126 947 False 1458 1458 94.3460 1863 2816 1 chr1A.!!$F1 953
5 TraesCS6A01G114600 chr1A 303257735 303258682 947 False 1458 1458 94.3400 1863 2816 1 chr1A.!!$F2 953
6 TraesCS6A01G114600 chrUn 86449117 86450972 1855 False 3317 3317 98.9220 1 1856 1 chrUn.!!$F1 1855
7 TraesCS6A01G114600 chrUn 222678304 222680160 1856 True 3312 3312 98.8690 1 1856 1 chrUn.!!$R1 1855
8 TraesCS6A01G114600 chrUn 86455117 86456972 1855 False 3301 3301 98.7610 1 1856 1 chrUn.!!$F2 1855
9 TraesCS6A01G114600 chr5B 533066664 533068520 1856 False 3312 3312 98.8690 1 1856 1 chr5B.!!$F1 1855
10 TraesCS6A01G114600 chr7B 742925241 742927098 1857 False 3297 3297 98.7080 1 1856 1 chr7B.!!$F1 1855
11 TraesCS6A01G114600 chr6B 596628844 596630699 1855 False 3295 3295 98.7070 1 1856 1 chr6B.!!$F1 1855
12 TraesCS6A01G114600 chr2A 693126449 693127394 945 False 1495 1495 95.0730 1863 2816 1 chr2A.!!$F1 953
13 TraesCS6A01G114600 chr2A 147029142 147030087 945 True 1472 1472 94.6540 1863 2816 1 chr2A.!!$R1 953
14 TraesCS6A01G114600 chr5A 275988433 275989379 946 True 1483 1483 94.8640 1863 2816 1 chr5A.!!$R1 953
15 TraesCS6A01G114600 chr4A 590758904 590759850 946 False 1472 1472 94.6540 1863 2816 1 chr4A.!!$F1 953
16 TraesCS6A01G114600 chr7A 305546699 305547645 946 True 1467 1467 94.5490 1863 2816 1 chr7A.!!$R1 953
17 TraesCS6A01G114600 chr3A 191899088 191900034 946 True 1456 1456 94.3400 1863 2816 1 chr3A.!!$R1 953

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
979 982 0.618981 ATGGTCCCGGAGAAAGGAAC 59.381 55.0 0.73 0.0 40.53 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 6189 0.178953 AATGCCAAGTCTGCCAAGGT 60.179 50.0 0.0 0.0 0.0 3.5 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
181 182 4.218417 GGCAATTCCTGAGAAAAGTGCTAA 59.782 41.667 15.62 0.00 37.95 3.09
282 283 3.771577 ACTTCTTGAACCACCGAATCT 57.228 42.857 0.00 0.00 0.00 2.40
801 804 2.257409 CTGCGTGCTGGGGGATTAGT 62.257 60.000 0.00 0.00 0.00 2.24
979 982 0.618981 ATGGTCCCGGAGAAAGGAAC 59.381 55.000 0.73 0.00 40.53 3.62
1211 1215 5.050904 TGGACTCGTATTTTGTTTGTACACG 60.051 40.000 0.00 0.00 32.98 4.49
1307 1313 8.907222 ATAAGTCATCAAATTTGGTGCTTTTT 57.093 26.923 29.24 20.59 39.14 1.94
1610 1616 2.234300 TCTGTGGAAACCTTCACGAC 57.766 50.000 0.00 0.00 36.74 4.34
1649 1655 2.494073 TGGTTTTTCCGCTTTTCACAGT 59.506 40.909 0.00 0.00 39.52 3.55
1672 1678 1.077716 CTTTCCACACCCCCGGATC 60.078 63.158 0.73 0.00 0.00 3.36
1763 1769 4.659111 TTGTACAAGTTCGTGAAGAGGA 57.341 40.909 3.59 0.00 0.00 3.71
1798 1804 2.186903 GGGAAAGCGGCTCGATCA 59.813 61.111 1.45 0.00 0.00 2.92
1856 1862 9.903682 AACTTCAAAAGTCACTATCAATGAATG 57.096 29.630 0.00 0.00 41.91 2.67
1857 1863 9.288576 ACTTCAAAAGTCACTATCAATGAATGA 57.711 29.630 0.00 0.00 39.01 2.57
1858 1864 9.770503 CTTCAAAAGTCACTATCAATGAATGAG 57.229 33.333 0.00 0.00 42.53 2.90
1859 1865 8.272545 TCAAAAGTCACTATCAATGAATGAGG 57.727 34.615 0.00 0.00 42.53 3.86
1860 1866 8.102676 TCAAAAGTCACTATCAATGAATGAGGA 58.897 33.333 0.00 0.00 42.53 3.71
1866 2117 7.550551 GTCACTATCAATGAATGAGGAACTTCA 59.449 37.037 0.00 0.00 41.55 3.02
1945 2919 2.289547 CCGATTTCCTTGTTCGTTGTGT 59.710 45.455 0.00 0.00 0.00 3.72
2014 2988 0.548197 TTATCCCCGAACACCCCAGT 60.548 55.000 0.00 0.00 0.00 4.00
2069 3043 6.528321 TCGCCATCTCTCAGAATTGATAAAT 58.472 36.000 0.00 0.00 31.68 1.40
2083 3057 4.400529 TGATAAATAGCCGCACAGAAGA 57.599 40.909 0.00 0.00 0.00 2.87
2290 5570 2.144078 TGGCCCGTCCTTCACAAGA 61.144 57.895 0.00 0.00 35.26 3.02
2780 6189 1.280998 GGAGGGTCTTTTGGGATTCGA 59.719 52.381 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 182 3.763897 GACATGACCAAAACAAGGGCTAT 59.236 43.478 0.00 0.00 34.31 2.97
282 283 7.362920 GGAGCTAGTTATCCATTTTCAAAAGCA 60.363 37.037 6.05 0.00 35.54 3.91
650 651 9.371136 GTTCTTCTTTTGGTCTTCAAGAAATTT 57.629 29.630 0.00 0.00 36.37 1.82
671 672 4.554723 CGCTCATTTTGAAGGTTCGTTCTT 60.555 41.667 6.76 0.00 0.00 2.52
801 804 5.502089 TTCCTTTACGACAAAATCCCCTA 57.498 39.130 0.00 0.00 0.00 3.53
979 982 1.216710 GCCGGACTGAAGAGACTGG 59.783 63.158 5.05 0.00 41.80 4.00
1041 1045 6.385649 AGAAAAGTTTCTGGTGCGAAATTA 57.614 33.333 5.50 0.00 45.27 1.40
1649 1655 1.152830 GGGGGTGTGGAAAGAGCAA 59.847 57.895 0.00 0.00 0.00 3.91
1688 1694 4.081309 TCGAATATATAAGGAAAGGGGCGG 60.081 45.833 0.00 0.00 0.00 6.13
1763 1769 2.025226 TCCCTCATTCTACTCGTCCAGT 60.025 50.000 0.00 0.00 39.41 4.00
1856 1862 8.812147 AATTTTAAATTTCGGTGAAGTTCCTC 57.188 30.769 0.00 0.00 0.00 3.71
1945 2919 2.994995 TTCGAGGGAGGCGCTCAA 60.995 61.111 7.64 3.34 42.44 3.02
2014 2988 3.556306 GCCCCCATGCCGCTAGTA 61.556 66.667 0.00 0.00 0.00 1.82
2069 3043 8.896320 TTAAAATATTATCTTCTGTGCGGCTA 57.104 30.769 0.00 0.00 0.00 3.93
2097 3071 6.536224 GCTAAGCAATGCTGTTGGAATTTAAT 59.464 34.615 9.14 0.00 39.62 1.40
2098 3072 5.868801 GCTAAGCAATGCTGTTGGAATTTAA 59.131 36.000 9.14 0.00 39.62 1.52
2099 3073 5.410067 GCTAAGCAATGCTGTTGGAATTTA 58.590 37.500 9.14 0.00 39.62 1.40
2100 3074 4.248058 GCTAAGCAATGCTGTTGGAATTT 58.752 39.130 9.14 0.00 39.62 1.82
2101 3075 3.674138 CGCTAAGCAATGCTGTTGGAATT 60.674 43.478 9.14 0.00 39.62 2.17
2102 3076 2.159338 CGCTAAGCAATGCTGTTGGAAT 60.159 45.455 9.14 0.00 39.62 3.01
2103 3077 1.199789 CGCTAAGCAATGCTGTTGGAA 59.800 47.619 9.14 0.00 39.62 3.53
2290 5570 2.097825 GGCAAGCTGGATGTTGAGAAT 58.902 47.619 0.00 0.00 0.00 2.40
2770 6179 0.322456 CTGCCAAGGTCGAATCCCAA 60.322 55.000 0.00 0.00 0.00 4.12
2780 6189 0.178953 AATGCCAAGTCTGCCAAGGT 60.179 50.000 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.