Multiple sequence alignment - TraesCS7A01G306800

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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 TraesCS7A01G306800 chr7A 100.000 3332 0 0 1 3332 433363638 433366969 0.000000e+00 6154.0
1 TraesCS7A01G306800 chr7D 94.922 3210 96 17 149 3332 385395529 385398697 0.000000e+00 4963.0
2 TraesCS7A01G306800 chr7B 95.069 2535 68 12 809 3332 379730810 379733298 0.000000e+00 3936.0
3 TraesCS7A01G306800 chr7B 91.930 570 32 10 43 605 379728864 379729426 0.000000e+00 785.0
4 TraesCS7A01G306800 chr7B 89.916 119 12 0 614 732 379730548 379730666 1.600000e-33 154.0
5 TraesCS7A01G306800 chr7B 93.750 48 3 0 756 803 379730665 379730712 4.610000e-09 73.1
6 TraesCS7A01G306800 chr5B 92.793 111 6 2 1081 1189 13384673 13384563 3.440000e-35 159.0
7 TraesCS7A01G306800 chr4D 93.396 106 7 0 1080 1185 97381256 97381361 1.240000e-34 158.0


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 TraesCS7A01G306800 chr7A 433363638 433366969 3331 False 6154.000 6154 100.00000 1 3332 1 chr7A.!!$F1 3331
1 TraesCS7A01G306800 chr7D 385395529 385398697 3168 False 4963.000 4963 94.92200 149 3332 1 chr7D.!!$F1 3183
2 TraesCS7A01G306800 chr7B 379728864 379733298 4434 False 1237.025 3936 92.66625 43 3332 4 chr7B.!!$F1 3289

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
350 358 1.068741 GATGGCTCCTGTAGGTTACCG 59.931 57.143 0.0 0.0 36.34 4.02 F
365 373 1.103803 TACCGTGTCTCCATCTCTGC 58.896 55.000 0.0 0.0 0.00 4.26 F
746 1867 1.215244 GAAGATTAACCCGCCTACGC 58.785 55.000 0.0 0.0 38.22 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 2610 3.507009 GACGGAGGAGGACGACGG 61.507 72.222 0.0 0.00 0.00 4.79 R
2186 3413 5.397142 AAGAGGTGCTGAATCAAAATTCC 57.603 39.130 0.0 0.00 40.57 3.01 R
2424 3651 3.555139 GCACTAGACACTTGATCAGATGC 59.445 47.826 0.0 2.73 0.00 3.91 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
26 27 9.204570 ACTTACGCCATATAAATTACTCATCAC 57.795 33.333 0.00 0.00 0.00 3.06
27 28 8.542497 TTACGCCATATAAATTACTCATCACC 57.458 34.615 0.00 0.00 0.00 4.02
28 29 5.938125 ACGCCATATAAATTACTCATCACCC 59.062 40.000 0.00 0.00 0.00 4.61
29 30 6.173339 CGCCATATAAATTACTCATCACCCT 58.827 40.000 0.00 0.00 0.00 4.34
30 31 6.092670 CGCCATATAAATTACTCATCACCCTG 59.907 42.308 0.00 0.00 0.00 4.45
31 32 6.127897 GCCATATAAATTACTCATCACCCTGC 60.128 42.308 0.00 0.00 0.00 4.85
32 33 6.942005 CCATATAAATTACTCATCACCCTGCA 59.058 38.462 0.00 0.00 0.00 4.41
33 34 7.448161 CCATATAAATTACTCATCACCCTGCAA 59.552 37.037 0.00 0.00 0.00 4.08
34 35 8.849168 CATATAAATTACTCATCACCCTGCAAA 58.151 33.333 0.00 0.00 0.00 3.68
35 36 7.716799 ATAAATTACTCATCACCCTGCAAAA 57.283 32.000 0.00 0.00 0.00 2.44
36 37 6.418057 AAATTACTCATCACCCTGCAAAAA 57.582 33.333 0.00 0.00 0.00 1.94
71 72 9.851043 TTGTTATTTTGCAACTTATTTTTACGC 57.149 25.926 0.00 0.00 0.00 4.42
161 167 5.522460 TGCAAAATTCCGTACTAGTAGATGC 59.478 40.000 1.87 5.82 0.00 3.91
216 223 9.586435 AAGAAAGAAAAGGAACAAATGTACAAG 57.414 29.630 0.00 0.00 0.00 3.16
224 232 6.981722 AGGAACAAATGTACAAGGTTTGATC 58.018 36.000 21.47 18.79 36.58 2.92
279 287 9.769093 CCAAGCATTACTTTACTTGTAACATAC 57.231 33.333 0.00 0.00 38.24 2.39
328 336 4.503714 ACCAATAATCCCGTGAGTCATT 57.496 40.909 0.00 0.00 0.00 2.57
350 358 1.068741 GATGGCTCCTGTAGGTTACCG 59.931 57.143 0.00 0.00 36.34 4.02
365 373 1.103803 TACCGTGTCTCCATCTCTGC 58.896 55.000 0.00 0.00 0.00 4.26
497 505 9.270576 CTGTCTTGAAGATTTGAACATTAATCG 57.729 33.333 0.00 0.00 36.21 3.34
572 580 2.357952 GGTAACGGCCATCATCCTTTTC 59.642 50.000 2.24 0.00 0.00 2.29
573 581 2.214376 AACGGCCATCATCCTTTTCA 57.786 45.000 2.24 0.00 0.00 2.69
575 583 2.301346 ACGGCCATCATCCTTTTCATC 58.699 47.619 2.24 0.00 0.00 2.92
605 613 4.460382 AGAAGCAAATCCACGATGAACAAT 59.540 37.500 0.00 0.00 0.00 2.71
606 614 5.647658 AGAAGCAAATCCACGATGAACAATA 59.352 36.000 0.00 0.00 0.00 1.90
607 615 5.490139 AGCAAATCCACGATGAACAATAG 57.510 39.130 0.00 0.00 0.00 1.73
609 617 6.112734 AGCAAATCCACGATGAACAATAGTA 58.887 36.000 0.00 0.00 0.00 1.82
610 618 6.037172 AGCAAATCCACGATGAACAATAGTAC 59.963 38.462 0.00 0.00 0.00 2.73
612 620 7.625395 GCAAATCCACGATGAACAATAGTACAA 60.625 37.037 0.00 0.00 0.00 2.41
616 1737 8.415192 TCCACGATGAACAATAGTACAATAAC 57.585 34.615 0.00 0.00 0.00 1.89
687 1808 5.411361 TCAACTGAATGACCAAAAGATACGG 59.589 40.000 0.00 0.00 0.00 4.02
746 1867 1.215244 GAAGATTAACCCGCCTACGC 58.785 55.000 0.00 0.00 38.22 4.42
754 1875 3.849951 CCGCCTACGCACAGGGAT 61.850 66.667 2.94 0.00 38.22 3.85
926 2149 1.442773 CTCCCCCACATCATCATCCT 58.557 55.000 0.00 0.00 0.00 3.24
980 2203 2.048127 GACTCGCTCCACCACCAC 60.048 66.667 0.00 0.00 0.00 4.16
981 2204 3.591254 GACTCGCTCCACCACCACC 62.591 68.421 0.00 0.00 0.00 4.61
982 2205 3.625897 CTCGCTCCACCACCACCA 61.626 66.667 0.00 0.00 0.00 4.17
983 2206 3.883744 CTCGCTCCACCACCACCAC 62.884 68.421 0.00 0.00 0.00 4.16
985 2208 3.884774 GCTCCACCACCACCACCA 61.885 66.667 0.00 0.00 0.00 4.17
986 2209 2.113139 CTCCACCACCACCACCAC 59.887 66.667 0.00 0.00 0.00 4.16
987 2210 3.491598 CTCCACCACCACCACCACC 62.492 68.421 0.00 0.00 0.00 4.61
988 2211 3.498071 CCACCACCACCACCACCT 61.498 66.667 0.00 0.00 0.00 4.00
1016 2239 2.418060 CCTCCGCCTCTTCTTCTTCTTC 60.418 54.545 0.00 0.00 0.00 2.87
1017 2240 2.495669 CTCCGCCTCTTCTTCTTCTTCT 59.504 50.000 0.00 0.00 0.00 2.85
1018 2241 2.900546 TCCGCCTCTTCTTCTTCTTCTT 59.099 45.455 0.00 0.00 0.00 2.52
1019 2242 3.056465 TCCGCCTCTTCTTCTTCTTCTTC 60.056 47.826 0.00 0.00 0.00 2.87
1020 2243 3.056179 CCGCCTCTTCTTCTTCTTCTTCT 60.056 47.826 0.00 0.00 0.00 2.85
1021 2244 4.562552 CCGCCTCTTCTTCTTCTTCTTCTT 60.563 45.833 0.00 0.00 0.00 2.52
1022 2245 4.625311 CGCCTCTTCTTCTTCTTCTTCTTC 59.375 45.833 0.00 0.00 0.00 2.87
1023 2246 5.566627 CGCCTCTTCTTCTTCTTCTTCTTCT 60.567 44.000 0.00 0.00 0.00 2.85
1024 2247 6.230472 GCCTCTTCTTCTTCTTCTTCTTCTT 58.770 40.000 0.00 0.00 0.00 2.52
2202 3429 8.871862 CAAATTTATCGGAATTTTGATTCAGCA 58.128 29.630 10.35 0.00 37.17 4.41
2299 3526 2.408271 TGTAGCAGAGCTGGAAATGG 57.592 50.000 0.00 0.00 40.10 3.16
2301 3528 2.305635 TGTAGCAGAGCTGGAAATGGAA 59.694 45.455 0.00 0.00 40.10 3.53
2307 3534 1.005924 GAGCTGGAAATGGAAAGGGGA 59.994 52.381 0.00 0.00 0.00 4.81
2424 3651 7.413767 CCAGTCTGAAATGTCACAAGTATGATG 60.414 40.741 0.00 0.00 0.00 3.07
2481 3709 6.461927 GCTCCATTGCAAATGATCCTATTTCA 60.462 38.462 1.71 0.00 0.00 2.69
2547 3775 2.562738 CGTGTATCTGCCTATCATCCCA 59.437 50.000 0.00 0.00 0.00 4.37
2788 4026 3.273434 GCATGAGCATACTGTTCTCCAA 58.727 45.455 0.00 0.00 41.58 3.53
2798 4036 7.941238 AGCATACTGTTCTCCAAATAATATGCT 59.059 33.333 8.67 8.67 44.77 3.79
2837 4075 0.597072 AACTCACGGAGGACTCGTTC 59.403 55.000 5.98 0.00 38.94 3.95
2841 4079 2.683867 CTCACGGAGGACTCGTTCTTAT 59.316 50.000 0.00 0.00 38.94 1.73
2858 4096 6.183360 CGTTCTTATTTGCATCATCCTGAACT 60.183 38.462 0.00 0.00 0.00 3.01
2860 4098 7.707624 TCTTATTTGCATCATCCTGAACTTT 57.292 32.000 0.00 0.00 0.00 2.66
2870 4108 9.890352 GCATCATCCTGAACTTTAGATTAATTC 57.110 33.333 0.00 0.00 0.00 2.17
2984 4222 6.935208 ACCTGTCCTGAATAAACTGTCTAAAC 59.065 38.462 0.00 0.00 0.00 2.01
3005 4243 5.803020 ACGCTTTAAGATGGAAGACAATC 57.197 39.130 0.00 0.00 0.00 2.67
3016 4254 3.523157 TGGAAGACAATCAGGCCATTAGA 59.477 43.478 5.01 0.00 0.00 2.10
3038 4276 3.871485 AGAGCCATGTGATTCTCTCAAC 58.129 45.455 0.00 0.00 35.07 3.18
3040 4278 3.341823 AGCCATGTGATTCTCTCAACAC 58.658 45.455 0.00 0.00 35.07 3.32
3066 4304 5.405873 GCTTGTGTCACTCTAGTCCTTAAAC 59.594 44.000 4.27 0.00 0.00 2.01
3300 4538 5.546434 ACGCAATTGTTTTTCTTTTCGTTG 58.454 33.333 7.40 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.204570 GTGATGAGTAATTTATATGGCGTAAGT 57.795 33.333 0.00 0.00 41.68 2.24
1 2 8.656849 GGTGATGAGTAATTTATATGGCGTAAG 58.343 37.037 0.00 0.00 43.44 2.34
2 3 7.604927 GGGTGATGAGTAATTTATATGGCGTAA 59.395 37.037 0.00 0.00 0.00 3.18
3 4 7.038587 AGGGTGATGAGTAATTTATATGGCGTA 60.039 37.037 0.00 0.00 0.00 4.42
4 5 5.938125 GGGTGATGAGTAATTTATATGGCGT 59.062 40.000 0.00 0.00 0.00 5.68
5 6 6.092670 CAGGGTGATGAGTAATTTATATGGCG 59.907 42.308 0.00 0.00 0.00 5.69
6 7 6.127897 GCAGGGTGATGAGTAATTTATATGGC 60.128 42.308 0.00 0.00 0.00 4.40
7 8 6.942005 TGCAGGGTGATGAGTAATTTATATGG 59.058 38.462 0.00 0.00 0.00 2.74
8 9 7.984422 TGCAGGGTGATGAGTAATTTATATG 57.016 36.000 0.00 0.00 0.00 1.78
9 10 8.995027 TTTGCAGGGTGATGAGTAATTTATAT 57.005 30.769 0.00 0.00 0.00 0.86
10 11 8.815565 TTTTGCAGGGTGATGAGTAATTTATA 57.184 30.769 0.00 0.00 0.00 0.98
11 12 7.716799 TTTTGCAGGGTGATGAGTAATTTAT 57.283 32.000 0.00 0.00 0.00 1.40
12 13 7.531857 TTTTTGCAGGGTGATGAGTAATTTA 57.468 32.000 0.00 0.00 0.00 1.40
13 14 6.418057 TTTTTGCAGGGTGATGAGTAATTT 57.582 33.333 0.00 0.00 0.00 1.82
46 47 8.488764 GGCGTAAAAATAAGTTGCAAAATAACA 58.511 29.630 0.00 0.00 0.00 2.41
55 56 4.739195 TGGATGGCGTAAAAATAAGTTGC 58.261 39.130 0.00 0.00 0.00 4.17
88 89 6.877668 TTCACTGGTTAATGGGTCAGTATA 57.122 37.500 0.00 0.00 38.27 1.47
144 145 8.915057 ATTAGTTAGCATCTACTAGTACGGAA 57.085 34.615 0.00 0.00 0.00 4.30
161 167 8.027189 GGAGTTTGGCCAACTTTAATTAGTTAG 58.973 37.037 20.35 0.00 46.53 2.34
224 232 7.329582 CACGCAACACAAAAGAAATTAAGAAG 58.670 34.615 0.00 0.00 0.00 2.85
240 248 4.614673 CTTGGAAGCACGCAACAC 57.385 55.556 0.00 0.00 0.00 3.32
304 312 4.258543 TGACTCACGGGATTATTGGTTTC 58.741 43.478 0.00 0.00 0.00 2.78
338 346 2.165167 TGGAGACACGGTAACCTACAG 58.835 52.381 0.00 0.00 33.40 2.74
365 373 9.010029 GTGTTAAATATATAGTTGATGTGGGGG 57.990 37.037 5.70 0.00 0.00 5.40
497 505 3.769536 CCATTATTCTGTTTTCGTGGGC 58.230 45.455 0.00 0.00 0.00 5.36
572 580 2.096496 GGATTTGCTTCTCGTGTGGATG 59.904 50.000 0.00 0.00 0.00 3.51
573 581 2.290260 TGGATTTGCTTCTCGTGTGGAT 60.290 45.455 0.00 0.00 0.00 3.41
575 583 1.197721 GTGGATTTGCTTCTCGTGTGG 59.802 52.381 0.00 0.00 0.00 4.17
605 613 7.814107 CAGTTTCTGTAACGGGTTATTGTACTA 59.186 37.037 0.00 0.00 41.78 1.82
606 614 6.647895 CAGTTTCTGTAACGGGTTATTGTACT 59.352 38.462 0.00 0.00 41.78 2.73
607 615 6.619232 GCAGTTTCTGTAACGGGTTATTGTAC 60.619 42.308 0.00 0.00 41.78 2.90
609 617 4.214758 GCAGTTTCTGTAACGGGTTATTGT 59.785 41.667 0.00 0.00 41.78 2.71
610 618 4.214545 TGCAGTTTCTGTAACGGGTTATTG 59.785 41.667 0.00 0.00 41.78 1.90
612 620 4.010667 TGCAGTTTCTGTAACGGGTTAT 57.989 40.909 0.00 0.00 41.78 1.89
616 1737 2.218603 ACTTGCAGTTTCTGTAACGGG 58.781 47.619 0.00 0.00 41.78 5.28
642 1763 8.793592 AGTTGAGTATCTTTTGGTCATTTTACC 58.206 33.333 0.00 0.00 36.54 2.85
687 1808 2.535984 CGCAGTAACTGTCGGATGAATC 59.464 50.000 0.00 0.00 33.43 2.52
741 1862 0.824109 TTCCTCATCCCTGTGCGTAG 59.176 55.000 0.00 0.00 0.00 3.51
746 1867 2.431954 ATTGCTTCCTCATCCCTGTG 57.568 50.000 0.00 0.00 0.00 3.66
754 1875 3.434167 GGCAGATCCTAATTGCTTCCTCA 60.434 47.826 4.15 0.00 37.93 3.86
803 1924 2.277057 CATCTCGTCGTACGCGCA 60.277 61.111 21.61 13.60 42.21 6.09
806 1927 0.660595 CCATCCATCTCGTCGTACGC 60.661 60.000 11.24 4.96 42.21 4.42
980 2203 1.687493 GAGGAGGAGGAGGTGGTGG 60.687 68.421 0.00 0.00 0.00 4.61
981 2204 1.687493 GGAGGAGGAGGAGGTGGTG 60.687 68.421 0.00 0.00 0.00 4.17
982 2205 2.781406 GGAGGAGGAGGAGGTGGT 59.219 66.667 0.00 0.00 0.00 4.16
983 2206 2.443016 CGGAGGAGGAGGAGGTGG 60.443 72.222 0.00 0.00 0.00 4.61
984 2207 3.151022 GCGGAGGAGGAGGAGGTG 61.151 72.222 0.00 0.00 0.00 4.00
985 2208 4.467107 GGCGGAGGAGGAGGAGGT 62.467 72.222 0.00 0.00 0.00 3.85
986 2209 4.150454 AGGCGGAGGAGGAGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
987 2210 2.520741 GAGGCGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
988 2211 2.575455 GAAGAGGCGGAGGAGGAGGA 62.575 65.000 0.00 0.00 0.00 3.71
1016 2239 2.104792 TGTGGGACTGTGGAAGAAGAAG 59.895 50.000 0.00 0.00 0.00 2.85
1017 2240 2.123589 TGTGGGACTGTGGAAGAAGAA 58.876 47.619 0.00 0.00 0.00 2.52
1018 2241 1.416401 GTGTGGGACTGTGGAAGAAGA 59.584 52.381 0.00 0.00 0.00 2.87
1019 2242 1.873903 CGTGTGGGACTGTGGAAGAAG 60.874 57.143 0.00 0.00 0.00 2.85
1020 2243 0.105964 CGTGTGGGACTGTGGAAGAA 59.894 55.000 0.00 0.00 0.00 2.52
1021 2244 1.745890 CGTGTGGGACTGTGGAAGA 59.254 57.895 0.00 0.00 0.00 2.87
1022 2245 1.961277 GCGTGTGGGACTGTGGAAG 60.961 63.158 0.00 0.00 0.00 3.46
1023 2246 1.978455 AAGCGTGTGGGACTGTGGAA 61.978 55.000 0.00 0.00 0.00 3.53
1024 2247 1.978455 AAAGCGTGTGGGACTGTGGA 61.978 55.000 0.00 0.00 0.00 4.02
1383 2610 3.507009 GACGGAGGAGGACGACGG 61.507 72.222 0.00 0.00 0.00 4.79
2186 3413 5.397142 AAGAGGTGCTGAATCAAAATTCC 57.603 39.130 0.00 0.00 40.57 3.01
2424 3651 3.555139 GCACTAGACACTTGATCAGATGC 59.445 47.826 0.00 2.73 0.00 3.91
2788 4026 8.753133 TGTCGGATCTCTATTGAGCATATTATT 58.247 33.333 0.00 0.00 40.03 1.40
2798 4036 6.096846 TGAGTTCAATGTCGGATCTCTATTGA 59.903 38.462 9.52 9.52 36.35 2.57
2884 4122 6.371271 TCATCAGATGAAAACAGCAATAACGA 59.629 34.615 10.93 0.00 36.11 3.85
2984 4222 5.220739 CCTGATTGTCTTCCATCTTAAAGCG 60.221 44.000 0.00 0.00 0.00 4.68
3005 4243 2.228059 CATGGCTCTTCTAATGGCCTG 58.772 52.381 3.32 0.00 44.36 4.85
3016 4254 4.260170 GTTGAGAGAATCACATGGCTCTT 58.740 43.478 0.00 0.00 37.81 2.85
3040 4278 2.560542 AGGACTAGAGTGACACAAGCAG 59.439 50.000 8.59 2.00 0.00 4.24
3066 4304 7.467557 AATTGTAATCAAAGTTGCACACTTG 57.532 32.000 12.87 5.13 45.77 3.16
3300 4538 7.155328 TCTCTCACACAGAAAGAAATAGGAAC 58.845 38.462 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.