Multiple sequence alignment - TraesCS6A01G064900

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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 TraesCS6A01G064900 chr6A 100.000 2699 0 0 1 2699 34391469 34388771 0.000000e+00 4985.0
1 TraesCS6A01G064900 chr6A 92.541 2735 133 28 1 2699 34274075 34271376 0.000000e+00 3855.0
2 TraesCS6A01G064900 chr6A 95.585 2061 62 11 1 2040 34278902 34276850 0.000000e+00 3275.0
3 TraesCS6A01G064900 chrUn 92.296 2544 144 27 1 2501 101988347 101985813 0.000000e+00 3565.0
4 TraesCS6A01G064900 chrUn 90.976 2183 118 37 542 2699 101984429 101982301 0.000000e+00 2867.0
5 TraesCS6A01G064900 chrUn 100.000 424 0 0 482 905 476643204 476642781 0.000000e+00 784.0
6 TraesCS6A01G064900 chr6B 93.964 2187 115 7 523 2699 62618882 62616703 0.000000e+00 3291.0
7 TraesCS6A01G064900 chr6B 91.717 2318 149 27 215 2501 62689453 62687148 0.000000e+00 3177.0
8 TraesCS6A01G064900 chr6B 91.996 2224 108 21 523 2699 62676575 62674375 0.000000e+00 3057.0
9 TraesCS6A01G064900 chr6B 90.799 1576 80 17 523 2057 62630860 62629309 0.000000e+00 2047.0
10 TraesCS6A01G064900 chr6B 93.077 1170 56 2 523 1689 62681122 62679975 0.000000e+00 1688.0
11 TraesCS6A01G064900 chr6B 87.872 1443 109 33 509 1896 62634437 62633006 0.000000e+00 1635.0
12 TraesCS6A01G064900 chr6B 94.094 745 36 5 1962 2699 62683088 62682345 0.000000e+00 1125.0
13 TraesCS6A01G064900 chr6B 89.146 820 54 20 1897 2699 62632952 62632151 0.000000e+00 989.0
14 TraesCS6A01G064900 chr6B 94.928 414 17 3 1962 2372 62679209 62678797 0.000000e+00 645.0
15 TraesCS6A01G064900 chr6B 93.313 329 18 2 2375 2699 62678507 62678179 1.450000e-132 483.0
16 TraesCS6A01G064900 chr6B 93.313 329 18 2 2375 2699 62684581 62684253 1.450000e-132 483.0
17 TraesCS6A01G064900 chr6B 91.266 229 19 1 2 230 62689625 62689398 7.260000e-81 311.0
18 TraesCS6A01G064900 chr3B 84.467 1867 194 50 763 2562 780295755 780293918 0.000000e+00 1753.0
19 TraesCS6A01G064900 chr3B 76.798 862 127 43 1687 2503 780317743 780316910 1.490000e-112 416.0
20 TraesCS6A01G064900 chr3B 76.798 862 127 43 1687 2503 780327722 780326889 1.490000e-112 416.0
21 TraesCS6A01G064900 chr3B 85.625 320 19 9 1583 1894 780306049 780305749 7.260000e-81 311.0
22 TraesCS6A01G064900 chr7B 84.444 90 11 3 384 472 244635265 244635352 4.790000e-13 86.1
23 TraesCS6A01G064900 chr4A 77.953 127 16 6 2574 2699 645762185 645762070 4.820000e-08 69.4


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 TraesCS6A01G064900 chr6A 34388771 34391469 2698 True 4985.000 4985 100.000000 1 2699 1 chr6A.!!$R1 2698
1 TraesCS6A01G064900 chr6A 34271376 34278902 7526 True 3565.000 3855 94.063000 1 2699 2 chr6A.!!$R2 2698
2 TraesCS6A01G064900 chrUn 101982301 101988347 6046 True 3216.000 3565 91.636000 1 2699 2 chrUn.!!$R2 2698
3 TraesCS6A01G064900 chr6B 62616703 62618882 2179 True 3291.000 3291 93.964000 523 2699 1 chr6B.!!$R1 2176
4 TraesCS6A01G064900 chr6B 62629309 62634437 5128 True 1557.000 2047 89.272333 509 2699 3 chr6B.!!$R2 2190
5 TraesCS6A01G064900 chr6B 62674375 62689625 15250 True 1371.125 3177 92.963000 2 2699 8 chr6B.!!$R3 2697
6 TraesCS6A01G064900 chr3B 780293918 780295755 1837 True 1753.000 1753 84.467000 763 2562 1 chr3B.!!$R1 1799
7 TraesCS6A01G064900 chr3B 780316910 780317743 833 True 416.000 416 76.798000 1687 2503 1 chr3B.!!$R3 816
8 TraesCS6A01G064900 chr3B 780326889 780327722 833 True 416.000 416 76.798000 1687 2503 1 chr3B.!!$R4 816

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
933 1005 4.564041 CAGAGCAGTAGACACATCAAACT 58.436 43.478 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 23213 0.688487 TTTTCCACCTGACCTACCCG 59.312 55.0 0.0 0.0 0.0 5.28 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
154 155 9.203421 CATGCTCTACGTATTAACAATAATCCA 57.797 33.333 0.0 0.00 33.75 3.41
933 1005 4.564041 CAGAGCAGTAGACACATCAAACT 58.436 43.478 0.0 0.00 0.00 2.66
1144 17114 1.205893 GCGATGGTCTCAGGAGTCTTT 59.794 52.381 0.0 0.00 0.00 2.52
1246 17216 2.845797 GGAGAGATGGGATGCTCCA 58.154 57.895 0.0 1.15 44.91 3.86
1386 17356 2.543777 AGTCTTTTACTCGCTTGGCA 57.456 45.000 0.0 0.00 30.33 4.92
1571 17541 5.509670 GCAAGGCATTTTACAAGAAGAAGGT 60.510 40.000 0.0 0.00 0.00 3.50
1572 17542 6.515832 CAAGGCATTTTACAAGAAGAAGGTT 58.484 36.000 0.0 0.00 0.00 3.50
1575 17545 6.098266 AGGCATTTTACAAGAAGAAGGTTGTT 59.902 34.615 0.0 0.00 37.96 2.83
1581 17551 4.494484 ACAAGAAGAAGGTTGTTGTTTGC 58.506 39.130 0.0 0.00 32.92 3.68
1614 17587 2.548875 CAGGAGTTAGAGTGCAGCATC 58.451 52.381 0.0 0.00 0.00 3.91
1639 17612 3.779183 AGATCTTCAGAATGGAGCAGGAA 59.221 43.478 0.0 0.00 43.21 3.36
1640 17613 4.226846 AGATCTTCAGAATGGAGCAGGAAA 59.773 41.667 0.0 0.00 43.21 3.13
1695 22470 6.712241 TCTCTTTTAAACATTCTCAGCTCG 57.288 37.500 0.0 0.00 0.00 5.03
1720 22495 7.012515 CGTAAATACTCCACATCACTCTACTCT 59.987 40.741 0.0 0.00 0.00 3.24
1725 22500 2.757314 CCACATCACTCTACTCTCTGCA 59.243 50.000 0.0 0.00 0.00 4.41
2144 23065 5.565592 TGCTTGCACATAAATCAACTAGG 57.434 39.130 0.0 0.00 0.00 3.02
2192 23136 7.227314 TGGCTTCATATGCTCAGTTAGTATTTG 59.773 37.037 0.0 0.00 32.88 2.32
2601 23569 4.253685 GTTAGCAGAACCAGATAGCACAA 58.746 43.478 0.0 0.00 0.00 3.33
2692 23660 5.634896 CAGATGAGTTTGCCACTAACAATC 58.365 41.667 0.0 0.00 35.01 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 155 3.728385 AGTTTAGATCAGGCCTTGCTT 57.272 42.857 0.00 0.00 0.00 3.91
318 322 4.000331 CTGATACTCCGGAATCAGCATT 58.000 45.455 25.80 0.00 41.80 3.56
905 977 1.815613 GTGTCTACTGCTCTGCTCAGA 59.184 52.381 0.00 0.00 35.61 3.27
1144 17114 8.007405 TCTTCAAGACCATCGTAGATATTTGA 57.993 34.615 0.00 0.00 45.12 2.69
1246 17216 4.501915 GCTGCAGAGATCTAAGAGCTCAAT 60.502 45.833 20.43 6.90 46.10 2.57
1386 17356 3.966665 TGAAATGTTTCCTGGCCTTCTTT 59.033 39.130 3.32 0.00 36.36 2.52
1581 17551 0.392193 ACTCCTGCAATTGCTCCTCG 60.392 55.000 29.37 16.38 42.66 4.63
1614 17587 2.102084 TGCTCCATTCTGAAGATCTCCG 59.898 50.000 0.00 0.00 0.00 4.63
1639 17612 7.020827 TCTGGACTAATTTCCTGAACAGATT 57.979 36.000 3.19 0.00 39.84 2.40
1640 17613 6.627087 TCTGGACTAATTTCCTGAACAGAT 57.373 37.500 3.19 0.00 39.84 2.90
1689 22464 4.504461 GTGATGTGGAGTATTTACGAGCTG 59.496 45.833 0.00 0.00 0.00 4.24
1695 22470 8.228035 AGAGTAGAGTGATGTGGAGTATTTAC 57.772 38.462 0.00 0.00 0.00 2.01
2144 23065 2.855963 CCATTTGCAACGATGAATCTGC 59.144 45.455 11.85 0.00 0.00 4.26
2263 23213 0.688487 TTTTCCACCTGACCTACCCG 59.312 55.000 0.00 0.00 0.00 5.28
2274 23224 9.710900 AGAACATTTAGATTTCATTTTTCCACC 57.289 29.630 0.00 0.00 0.00 4.61
2381 23341 8.904834 GCTCGATCCAATATTTATCTCCTAGTA 58.095 37.037 0.00 0.00 0.00 1.82
2382 23342 7.397476 TGCTCGATCCAATATTTATCTCCTAGT 59.603 37.037 0.00 0.00 0.00 2.57
2403 23363 6.035866 GCCATCTCAGAAATCTATAATGCTCG 59.964 42.308 0.00 0.00 0.00 5.03
2601 23569 2.592102 ATCAGCATGTTGTTCCAGGT 57.408 45.000 9.54 0.00 37.40 4.00


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

AutoCloner maintained by Alex Coulton.