Multiple sequence alignment - TraesCS6A01G161100

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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 TraesCS6A01G161100 chr6A 100.000 2243 0 0 1 2243 155857299 155859541 0 4143
1 TraesCS6A01G161100 chr6A 96.300 2243 82 1 1 2243 375860759 375858518 0 3681
2 TraesCS6A01G161100 chr3B 97.189 2241 61 2 1 2240 483333212 483335451 0 3788
3 TraesCS6A01G161100 chr3B 96.214 2245 82 3 1 2243 575839742 575837499 0 3672
4 TraesCS6A01G161100 chr4B 96.833 2242 67 4 1 2240 209242557 209244796 0 3744
5 TraesCS6A01G161100 chr2A 96.613 2244 75 1 1 2243 750453591 750451348 0 3722
6 TraesCS6A01G161100 chr4A 96.389 2243 81 0 1 2243 350172240 350174482 0 3694
7 TraesCS6A01G161100 chr3A 96.038 2019 68 8 235 2243 230228527 230226511 0 3275
8 TraesCS6A01G161100 chr7B 97.863 1310 28 0 1 1310 742948738 742947429 0 2265
9 TraesCS6A01G161100 chr7A 97.858 1307 28 0 1 1307 60084936 60086242 0 2259
10 TraesCS6A01G161100 chr5B 97.893 1044 21 1 1201 2243 439641088 439642131 0 1805
11 TraesCS6A01G161100 chrUn 97.889 1042 20 2 1201 2240 171017238 171018279 0 1801
12 TraesCS6A01G161100 chr6B 92.435 727 52 3 1054 1779 401858415 401859139 0 1035


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 TraesCS6A01G161100 chr6A 155857299 155859541 2242 False 4143 4143 100.000 1 2243 1 chr6A.!!$F1 2242
1 TraesCS6A01G161100 chr6A 375858518 375860759 2241 True 3681 3681 96.300 1 2243 1 chr6A.!!$R1 2242
2 TraesCS6A01G161100 chr3B 483333212 483335451 2239 False 3788 3788 97.189 1 2240 1 chr3B.!!$F1 2239
3 TraesCS6A01G161100 chr3B 575837499 575839742 2243 True 3672 3672 96.214 1 2243 1 chr3B.!!$R1 2242
4 TraesCS6A01G161100 chr4B 209242557 209244796 2239 False 3744 3744 96.833 1 2240 1 chr4B.!!$F1 2239
5 TraesCS6A01G161100 chr2A 750451348 750453591 2243 True 3722 3722 96.613 1 2243 1 chr2A.!!$R1 2242
6 TraesCS6A01G161100 chr4A 350172240 350174482 2242 False 3694 3694 96.389 1 2243 1 chr4A.!!$F1 2242
7 TraesCS6A01G161100 chr3A 230226511 230228527 2016 True 3275 3275 96.038 235 2243 1 chr3A.!!$R1 2008
8 TraesCS6A01G161100 chr7B 742947429 742948738 1309 True 2265 2265 97.863 1 1310 1 chr7B.!!$R1 1309
9 TraesCS6A01G161100 chr7A 60084936 60086242 1306 False 2259 2259 97.858 1 1307 1 chr7A.!!$F1 1306
10 TraesCS6A01G161100 chr5B 439641088 439642131 1043 False 1805 1805 97.893 1201 2243 1 chr5B.!!$F1 1042
11 TraesCS6A01G161100 chrUn 171017238 171018279 1041 False 1801 1801 97.889 1201 2240 1 chrUn.!!$F1 1039
12 TraesCS6A01G161100 chr6B 401858415 401859139 724 False 1035 1035 92.435 1054 1779 1 chr6B.!!$F1 725

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
758 762 0.112218 CCACAAGGGTTGATGGACCA 59.888 55.0 0.0 0.0 41.65 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1671 2.091555 AGGGGCCAAAGTAGTGAAAACA 60.092 45.455 4.39 0.0 0.0 2.83 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
104 106 4.745620 GCTCTTTTATCGCGGAATTAGACT 59.254 41.667 6.13 0.00 0.00 3.24
146 148 4.039357 CAGTCGCGTCGGGTCTGT 62.039 66.667 22.19 0.37 0.00 3.41
177 179 6.543831 AGTTGAAAGCTATGAAACAAGTCTGT 59.456 34.615 0.00 0.00 37.39 3.41
471 473 9.816354 CAAAAATCTTTCTTAGAAAAAGGTGGA 57.184 29.630 8.82 2.18 36.22 4.02
506 508 4.015084 AGAAAGATGGAACCAGATGCTTG 58.985 43.478 0.00 0.00 0.00 4.01
708 712 2.860971 AGCCACAAGGGGGAGCTT 60.861 61.111 0.00 0.00 37.04 3.74
736 740 2.354328 AGTTCAGAATACCCCACCCAA 58.646 47.619 0.00 0.00 0.00 4.12
758 762 0.112218 CCACAAGGGTTGATGGACCA 59.888 55.000 0.00 0.00 41.65 4.02
959 963 7.169158 ACAAGAAATCCAAGAAAGAACAACA 57.831 32.000 0.00 0.00 0.00 3.33
1107 1111 4.773674 AGTTCTTTGATTCATTCCATGGCA 59.226 37.500 6.96 0.00 0.00 4.92
1110 1114 1.391577 TGATTCATTCCATGGCACGG 58.608 50.000 6.96 0.00 0.00 4.94
1276 1282 9.561069 AAAGAAATGTGAGAATGTAGTTACAGT 57.439 29.630 0.00 0.00 39.92 3.55
1318 1325 4.278310 TCGTTCTCTTGGTCCATAGATGA 58.722 43.478 5.51 4.87 0.00 2.92
1322 1329 2.702478 CTCTTGGTCCATAGATGAGGCA 59.298 50.000 0.00 0.00 0.00 4.75
1358 1365 1.686052 GAATGAGGAGCCTCTGTCGAT 59.314 52.381 16.87 0.00 43.12 3.59
1424 1432 2.151202 GTCGGTGATTCAAGCCAAGAA 58.849 47.619 0.00 0.00 0.00 2.52
1660 1669 6.323739 ACAGAAAGTTTTGGAAAATGGAGCTA 59.676 34.615 0.00 0.00 0.00 3.32
1662 1671 6.551227 AGAAAGTTTTGGAAAATGGAGCTACT 59.449 34.615 0.00 0.00 0.00 2.57
1679 1688 4.515567 AGCTACTGTTTTCACTACTTTGGC 59.484 41.667 0.00 0.00 0.00 4.52
1814 1823 8.643324 TGGCTTAGAATAAGAAACCTATCTCTC 58.357 37.037 0.76 0.00 0.00 3.20
1875 1884 3.364441 TTGCTGCATCGCCACCAC 61.364 61.111 1.84 0.00 0.00 4.16
1885 1894 1.302431 CGCCACCACATTCCTGACA 60.302 57.895 0.00 0.00 0.00 3.58
1924 1933 1.768684 TTTTCTCGGGGCTGCAGTCT 61.769 55.000 19.48 0.00 0.00 3.24
2174 2191 5.711036 AGGGAAGGTGCTATAGTATCTAACG 59.289 44.000 3.84 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 106 5.221303 ACGGATAAGCCAACGTTAATAGCTA 60.221 40.000 12.78 0.00 35.90 3.32
146 148 3.592898 TCATAGCTTTCAACTGAGCGA 57.407 42.857 0.00 0.00 43.53 4.93
177 179 4.038642 GCCAATTCCAGTTTTGAACTACCA 59.961 41.667 0.00 0.00 40.46 3.25
471 473 8.727910 GGTTCCATCTTTCTTTCGTTAGTTAAT 58.272 33.333 0.00 0.00 0.00 1.40
506 508 6.662414 AAGGCAAAGTGCTTTCTTTTAAAC 57.338 33.333 0.00 0.00 38.32 2.01
708 712 4.264668 TGGGGTATTCTGAACTACTGGAGA 60.265 45.833 0.00 0.00 0.00 3.71
723 727 1.468405 TGGGGTTGGGTGGGGTATT 60.468 57.895 0.00 0.00 0.00 1.89
758 762 7.842260 TCATCAGGTATAGGTATAGGTAGGT 57.158 40.000 0.00 0.00 0.00 3.08
959 963 7.877612 ACACTTTTCTTGTCATGTTTTTCCTTT 59.122 29.630 0.00 0.00 0.00 3.11
1107 1111 3.576078 TTAGCCAATGATGGATTCCGT 57.424 42.857 0.00 0.00 44.90 4.69
1110 1114 6.808829 TGATTGTTTAGCCAATGATGGATTC 58.191 36.000 0.00 0.00 44.90 2.52
1318 1325 2.260639 ATCCATCGGATAGGATGCCT 57.739 50.000 16.26 0.00 41.16 4.75
1322 1329 4.408270 CCTCATTCATCCATCGGATAGGAT 59.592 45.833 13.06 13.06 40.98 3.24
1358 1365 9.466497 AAAAGCAGAATCCTATCATTTCACTAA 57.534 29.630 0.00 0.00 0.00 2.24
1409 1417 1.473677 CCGCATTCTTGGCTTGAATCA 59.526 47.619 3.31 0.00 32.47 2.57
1424 1432 1.452108 GCTCTTAAGGTGCCCGCAT 60.452 57.895 1.85 0.00 0.00 4.73
1660 1669 2.956333 GGGCCAAAGTAGTGAAAACAGT 59.044 45.455 4.39 0.00 0.00 3.55
1662 1671 2.091555 AGGGGCCAAAGTAGTGAAAACA 60.092 45.455 4.39 0.00 0.00 2.83
1679 1688 2.550830 AGCAACAATATCGCTAGGGG 57.449 50.000 6.99 0.00 33.25 4.79
1875 1884 5.048224 AGTTCAGAAAAGCATGTCAGGAATG 60.048 40.000 0.00 0.00 0.00 2.67
1885 1894 4.660789 AACAAGCAGTTCAGAAAAGCAT 57.339 36.364 9.94 0.00 34.74 3.79
1924 1933 4.714632 AGAAGCAAACCACTAAGCAACTA 58.285 39.130 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.