Multiple sequence alignment - TraesCS6B01G202500

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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 TraesCS6B01G202500 chr6B 100.000 7286 0 0 1 7286 247392379 247399664 0 13455
1 TraesCS6B01G202500 chr6B 94.814 6576 247 34 1 6510 379095861 379089314 0 10168
2 TraesCS6B01G202500 chr6B 96.268 777 26 3 6510 7286 378844789 378845562 0 1271
3 TraesCS6B01G202500 chr7B 97.103 7317 173 16 1 7286 207971328 207978636 0 12301
4 TraesCS6B01G202500 chr7B 94.779 6569 263 33 1 6510 430145641 430152188 0 10157
5 TraesCS6B01G202500 chr7B 96.280 1855 59 6 5292 7136 206189759 206187905 0 3035
6 TraesCS6B01G202500 chr7B 95.238 777 33 4 6510 7286 430152307 430153079 0 1227
7 TraesCS6B01G202500 chr2B 96.530 7320 191 26 1 7286 179064062 179071352 0 12052
8 TraesCS6B01G202500 chr2B 95.255 6576 226 36 1 6510 261018134 261024689 0 10336
9 TraesCS6B01G202500 chr2B 94.947 6571 247 36 1 6510 209875990 209869444 0 10216
10 TraesCS6B01G202500 chr2B 94.967 6140 215 43 1 6077 701270983 701264875 0 9540
11 TraesCS6B01G202500 chr2B 95.216 5268 201 30 1 5233 379155452 379160703 0 8285
12 TraesCS6B01G202500 chr2B 95.546 3615 121 20 2996 6578 155679235 155675629 0 5747
13 TraesCS6B01G202500 chr2B 96.139 777 27 3 6510 7286 701264359 701263586 0 1266
14 TraesCS6B01G202500 chr2B 96.010 777 29 2 6510 7286 379162819 379163593 0 1262
15 TraesCS6B01G202500 chr2B 95.355 775 31 5 6510 7284 261024809 261025578 0 1227
16 TraesCS6B01G202500 chr3B 94.784 6576 248 41 1 6510 252185477 252192023 0 10155
17 TraesCS6B01G202500 chr3B 94.935 6041 223 35 1 5978 236260863 236254843 0 9383
18 TraesCS6B01G202500 chr3B 96.960 4638 107 13 1900 6510 477784052 477788682 0 7753
19 TraesCS6B01G202500 chr3B 92.168 1264 89 8 5237 6497 572142693 572141437 0 1777
20 TraesCS6B01G202500 chr3B 97.001 767 18 5 6510 7276 477788802 477789563 0 1284
21 TraesCS6B01G202500 chr1B 95.094 5769 198 40 1 5709 330756304 330762047 0 9007
22 TraesCS6B01G202500 chr5B 96.818 1477 38 7 5106 6578 524602113 524603584 0 2459
23 TraesCS6B01G202500 chr6D 87.174 1380 132 26 3846 5195 249264293 249265657 0 1526
24 TraesCS6B01G202500 chr6D 85.799 1352 162 25 3846 5195 179218481 179217158 0 1406


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 TraesCS6B01G202500 chr6B 247392379 247399664 7285 False 13455.0 13455 100.0000 1 7286 1 chr6B.!!$F1 7285
1 TraesCS6B01G202500 chr6B 379089314 379095861 6547 True 10168.0 10168 94.8140 1 6510 1 chr6B.!!$R1 6509
2 TraesCS6B01G202500 chr6B 378844789 378845562 773 False 1271.0 1271 96.2680 6510 7286 1 chr6B.!!$F2 776
3 TraesCS6B01G202500 chr7B 207971328 207978636 7308 False 12301.0 12301 97.1030 1 7286 1 chr7B.!!$F1 7285
4 TraesCS6B01G202500 chr7B 430145641 430153079 7438 False 5692.0 10157 95.0085 1 7286 2 chr7B.!!$F2 7285
5 TraesCS6B01G202500 chr7B 206187905 206189759 1854 True 3035.0 3035 96.2800 5292 7136 1 chr7B.!!$R1 1844
6 TraesCS6B01G202500 chr2B 179064062 179071352 7290 False 12052.0 12052 96.5300 1 7286 1 chr2B.!!$F1 7285
7 TraesCS6B01G202500 chr2B 209869444 209875990 6546 True 10216.0 10216 94.9470 1 6510 1 chr2B.!!$R2 6509
8 TraesCS6B01G202500 chr2B 261018134 261025578 7444 False 5781.5 10336 95.3050 1 7284 2 chr2B.!!$F2 7283
9 TraesCS6B01G202500 chr2B 155675629 155679235 3606 True 5747.0 5747 95.5460 2996 6578 1 chr2B.!!$R1 3582
10 TraesCS6B01G202500 chr2B 701263586 701270983 7397 True 5403.0 9540 95.5530 1 7286 2 chr2B.!!$R3 7285
11 TraesCS6B01G202500 chr2B 379155452 379163593 8141 False 4773.5 8285 95.6130 1 7286 2 chr2B.!!$F3 7285
12 TraesCS6B01G202500 chr3B 252185477 252192023 6546 False 10155.0 10155 94.7840 1 6510 1 chr3B.!!$F1 6509
13 TraesCS6B01G202500 chr3B 236254843 236260863 6020 True 9383.0 9383 94.9350 1 5978 1 chr3B.!!$R1 5977
14 TraesCS6B01G202500 chr3B 477784052 477789563 5511 False 4518.5 7753 96.9805 1900 7276 2 chr3B.!!$F2 5376
15 TraesCS6B01G202500 chr3B 572141437 572142693 1256 True 1777.0 1777 92.1680 5237 6497 1 chr3B.!!$R2 1260
16 TraesCS6B01G202500 chr1B 330756304 330762047 5743 False 9007.0 9007 95.0940 1 5709 1 chr1B.!!$F1 5708
17 TraesCS6B01G202500 chr5B 524602113 524603584 1471 False 2459.0 2459 96.8180 5106 6578 1 chr5B.!!$F1 1472
18 TraesCS6B01G202500 chr6D 249264293 249265657 1364 False 1526.0 1526 87.1740 3846 5195 1 chr6D.!!$F1 1349
19 TraesCS6B01G202500 chr6D 179217158 179218481 1323 True 1406.0 1406 85.7990 3846 5195 1 chr6D.!!$R1 1349

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
794 804 2.136298 TGACACAAGGGACTGCAAAA 57.864 45.000 0.00 0.00 40.86 2.44 F
1083 1094 1.216178 CGACATTAACGTCCCCGGT 59.784 57.895 0.00 0.00 38.78 5.28 F
2317 2341 0.955178 CCTCATCGAGTACGCAGGAT 59.045 55.000 0.00 0.00 39.58 3.24 F
2330 2354 2.417339 GCAGGATTAGATGCGTACGA 57.583 50.000 21.65 4.52 31.87 3.43 F
2557 2581 3.728845 ACCAGTATGATTATGTCGTGCC 58.271 45.455 0.00 0.00 39.69 5.01 F
4035 4088 2.357637 CACCACAACGAACAATCTGGTT 59.642 45.455 0.00 0.00 30.30 3.67 F
5111 5209 2.619165 CCACATCGCAGCAGCAACA 61.619 57.895 0.82 0.00 42.27 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2214 1.020861 CGCTGGCTGCAACATCAGTA 61.021 55.000 16.76 0.00 43.06 2.74 R
2330 2354 1.269883 TGAACCATGACTTGTACGCGT 60.270 47.619 19.17 19.17 0.00 6.01 R
3377 3421 2.166907 TGGTGGGGTGTTTTGTTGAT 57.833 45.000 0.00 0.00 0.00 2.57 R
4035 4088 7.507616 AGGTTGGGTGTTTGAGATTATTTTACA 59.492 33.333 0.00 0.00 0.00 2.41 R
4460 4549 5.121454 CCTTGATTAGTCTTGTCAAGCTGTC 59.879 44.000 7.78 10.74 44.58 3.51 R
5983 6160 1.401761 TTCCACTTGCACTGCATGTT 58.598 45.000 17.58 3.72 42.78 2.71 R
6612 6985 1.133823 ACTGCATGTTGTCCTTGGTCA 60.134 47.619 0.00 0.00 0.00 4.02 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
622 631 2.364324 ACTATACGAATCGGTGCCACAT 59.636 45.455 7.80 0.00 0.00 3.21
630 639 5.298276 ACGAATCGGTGCCACATTAAAATAT 59.702 36.000 7.80 0.00 0.00 1.28
642 651 8.308931 GCCACATTAAAATATCATCATCACCAT 58.691 33.333 0.00 0.00 0.00 3.55
651 660 2.631545 TCATCATCACCATCGCAGAGAT 59.368 45.455 0.00 0.00 43.63 2.75
773 783 4.314440 GTGCCACCCACTGAGCGA 62.314 66.667 0.00 0.00 41.35 4.93
794 804 2.136298 TGACACAAGGGACTGCAAAA 57.864 45.000 0.00 0.00 40.86 2.44
795 805 2.665165 TGACACAAGGGACTGCAAAAT 58.335 42.857 0.00 0.00 40.86 1.82
853 863 3.876589 GAACGAACCGCCTCCTGCA 62.877 63.158 0.00 0.00 41.33 4.41
854 864 3.469863 AACGAACCGCCTCCTGCAA 62.470 57.895 0.00 0.00 41.33 4.08
855 865 2.668212 CGAACCGCCTCCTGCAAA 60.668 61.111 0.00 0.00 41.33 3.68
1005 1016 4.113815 CGGAGGAAGGCCATGGCA 62.114 66.667 36.56 0.00 44.11 4.92
1083 1094 1.216178 CGACATTAACGTCCCCGGT 59.784 57.895 0.00 0.00 38.78 5.28
1334 1345 2.054458 TGGTGTACCACATCGCAGT 58.946 52.632 0.00 0.00 42.01 4.40
1373 1385 3.181483 GCAATCTTACTCATTTGCCCTGG 60.181 47.826 0.00 0.00 38.77 4.45
1662 1678 7.639113 AAAGGTGTTTCTGAACTTGATGTAA 57.361 32.000 0.00 0.00 36.70 2.41
2070 2094 2.933260 GTTGTTCACATTTGCCGGTTTT 59.067 40.909 1.90 0.00 0.00 2.43
2186 2210 2.288030 ACACCGGAAAAGAGTACGACTG 60.288 50.000 9.46 0.00 0.00 3.51
2190 2214 3.057734 CGGAAAAGAGTACGACTGCTTT 58.942 45.455 0.00 0.00 31.63 3.51
2317 2341 0.955178 CCTCATCGAGTACGCAGGAT 59.045 55.000 0.00 0.00 39.58 3.24
2330 2354 2.417339 GCAGGATTAGATGCGTACGA 57.583 50.000 21.65 4.52 31.87 3.43
2371 2395 4.640201 TCATGATCGACTACATCACAGACA 59.360 41.667 0.00 0.00 33.04 3.41
2557 2581 3.728845 ACCAGTATGATTATGTCGTGCC 58.271 45.455 0.00 0.00 39.69 5.01
2867 2895 6.621613 TGCACTATCAGTACAACTTAGTCTG 58.378 40.000 0.00 0.00 0.00 3.51
2994 3024 5.415701 ACACTCACACAAAACTGACAAGAAT 59.584 36.000 0.00 0.00 0.00 2.40
3033 3068 4.523173 CAGTCTACTGGTGGAGTCAAGTAA 59.477 45.833 2.01 0.00 40.20 2.24
4035 4088 2.357637 CACCACAACGAACAATCTGGTT 59.642 45.455 0.00 0.00 30.30 3.67
4198 4281 8.145767 ACACAGTACTAAAACATAAGTGCACTA 58.854 33.333 22.01 9.11 31.54 2.74
4460 4549 5.440610 AGTGGGATTTAGCAGATTGTAAGG 58.559 41.667 0.00 0.00 0.00 2.69
4523 4617 4.931661 TGTCTTGGACGTTAGTTCTTCT 57.068 40.909 0.00 0.00 34.95 2.85
5111 5209 2.619165 CCACATCGCAGCAGCAACA 61.619 57.895 0.82 0.00 42.27 3.33
5739 5907 4.888038 TCTGAACTACATTCATGCATGC 57.112 40.909 22.25 11.82 46.37 4.06
5849 6026 9.219603 CTAATCTTTAGAAAATGTGTGTCTCCA 57.780 33.333 0.00 0.00 0.00 3.86
5983 6160 3.304911 TCAACCCCAACAACTTCATCA 57.695 42.857 0.00 0.00 0.00 3.07
6309 6559 6.500684 AAGTCTGCATTCGTTATGTTGAAT 57.499 33.333 0.00 0.00 36.57 2.57
6389 6640 3.537580 TCGTTTTGTTGAACCAGCTACT 58.462 40.909 0.00 0.00 0.00 2.57
6419 6670 3.157881 TGTGTGTCAGGGTTTGAACAAA 58.842 40.909 0.00 0.00 37.61 2.83
6497 6748 6.670695 AGCTTCCTATTTTGTTGAACCATT 57.329 33.333 0.00 0.00 0.00 3.16
6694 7070 7.394016 TCACTAAGTAATGCATCAGGAAAAGA 58.606 34.615 0.00 0.00 0.00 2.52
6811 7188 1.235724 AAAAGGAACGGGAAGCTTCG 58.764 50.000 19.91 12.87 0.00 3.79
6976 7353 9.599866 AGAAGACCAAAAACTAAATCAAAAAGG 57.400 29.630 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
462 471 3.941483 CCAAATACCAGTGAGACCATGTC 59.059 47.826 0.00 0.00 0.00 3.06
622 631 7.661027 TCTGCGATGGTGATGATGATATTTTAA 59.339 33.333 0.00 0.00 0.00 1.52
630 639 2.034124 TCTCTGCGATGGTGATGATGA 58.966 47.619 0.00 0.00 0.00 2.92
642 651 0.671472 CCACTTGCACATCTCTGCGA 60.671 55.000 0.00 0.00 40.31 5.10
651 660 0.758310 TGCCAAATCCCACTTGCACA 60.758 50.000 0.00 0.00 0.00 4.57
773 783 2.363306 TTGCAGTCCCTTGTGTCAAT 57.637 45.000 0.00 0.00 0.00 2.57
855 865 1.228306 TGCGTGGACGGGGATTTTT 60.228 52.632 0.71 0.00 40.23 1.94
1005 1016 2.920912 TTGGCGGACGGTTCCTCT 60.921 61.111 0.00 0.00 40.23 3.69
1083 1094 0.312729 TTGTGTACTCGCGCTTCTCA 59.687 50.000 5.56 0.00 0.00 3.27
1403 1415 7.725251 AGCAAGTGTGATTAATTTTTCAGGAA 58.275 30.769 0.00 0.00 0.00 3.36
1642 1658 8.345565 ACTTCATTACATCAAGTTCAGAAACAC 58.654 33.333 0.00 0.00 37.88 3.32
2070 2094 4.314961 TCTCTTTGTCGCTTTCAATGCTA 58.685 39.130 0.00 0.00 0.00 3.49
2186 2210 1.541147 TGGCTGCAACATCAGTAAAGC 59.459 47.619 0.50 0.00 36.49 3.51
2190 2214 1.020861 CGCTGGCTGCAACATCAGTA 61.021 55.000 16.76 0.00 43.06 2.74
2330 2354 1.269883 TGAACCATGACTTGTACGCGT 60.270 47.619 19.17 19.17 0.00 6.01
2371 2395 2.866762 GCTCTTTCGCATATTCCGAACT 59.133 45.455 7.31 0.00 43.48 3.01
2557 2581 7.253750 GCAACTAAACTTGTTCAAACATGACAG 60.254 37.037 13.74 3.89 38.95 3.51
2867 2895 2.348666 CAGAACTATGGTACTTGCGTGC 59.651 50.000 0.00 0.00 0.00 5.34
2994 3024 9.706691 CCAGTAGACTGATACTTTTTGTTCTAA 57.293 33.333 11.31 0.00 46.59 2.10
3119 3163 2.367567 TGTGCGGATTACTAGGGATTCC 59.632 50.000 0.00 0.00 0.00 3.01
3334 3378 2.196925 CGGCCCAGATAGCTCGTCT 61.197 63.158 0.00 0.00 0.00 4.18
3377 3421 2.166907 TGGTGGGGTGTTTTGTTGAT 57.833 45.000 0.00 0.00 0.00 2.57
4035 4088 7.507616 AGGTTGGGTGTTTGAGATTATTTTACA 59.492 33.333 0.00 0.00 0.00 2.41
4460 4549 5.121454 CCTTGATTAGTCTTGTCAAGCTGTC 59.879 44.000 7.78 10.74 44.58 3.51
5561 5723 5.340667 CGCTGCTTGATTCAAGTTTAGTTTC 59.659 40.000 23.66 8.38 42.77 2.78
5698 5865 8.890718 GTTCAGAAACTAGTACAAAAAGTCCTT 58.109 33.333 0.00 0.00 32.36 3.36
5983 6160 1.401761 TTCCACTTGCACTGCATGTT 58.598 45.000 17.58 3.72 42.78 2.71
6309 6559 4.344968 ACACACATAGCATATGGTAGCTGA 59.655 41.667 18.72 0.00 41.97 4.26
6389 6640 4.568072 ACCCTGACACACATAGCATAAA 57.432 40.909 0.00 0.00 0.00 1.40
6419 6670 7.600375 CGATGTACTTGATAGACATAGGCAAAT 59.400 37.037 0.00 0.00 33.99 2.32
6497 6748 9.120538 GTCCAAGGCTACTATCAATTTCAAATA 57.879 33.333 0.00 0.00 0.00 1.40
6612 6985 1.133823 ACTGCATGTTGTCCTTGGTCA 60.134 47.619 0.00 0.00 0.00 4.02
6694 7070 7.166167 AGGAAATACGTACTGATGGTTCTTTT 58.834 34.615 0.00 0.00 0.00 2.27
6811 7188 4.751652 TCACTGTTTTAGGGAATGGGAACC 60.752 45.833 0.00 0.00 43.14 3.62
6816 7193 4.023193 GTGTGTCACTGTTTTAGGGAATGG 60.023 45.833 4.27 0.00 41.45 3.16
6985 7362 7.403312 TTCTTGTGATTTTTCTCCTTTGTCA 57.597 32.000 0.00 0.00 0.00 3.58
7198 8479 6.999950 TCATAGTACAAGTTAAAGCACTGGA 58.000 36.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.