Multiple sequence alignment - TraesCS6B01G357200

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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 TraesCS6B01G357200 chr6B 100.000 2228 0 0 1 2228 625617122 625614895 0 4115
1 TraesCS6B01G357200 chrUn 97.629 1223 24 2 1 1218 406475681 406474459 0 2093
2 TraesCS6B01G357200 chr1B 97.625 1221 26 2 1 1218 619189740 619188520 0 2091
3 TraesCS6B01G357200 chr3A 97.543 1221 27 2 1 1218 495099168 495097948 0 2085
4 TraesCS6B01G357200 chr3A 97.297 1221 29 4 1 1218 66010167 66011386 0 2069
5 TraesCS6B01G357200 chr3A 97.631 1013 24 0 1216 2228 66011413 66012425 0 1738
6 TraesCS6B01G357200 chr6A 97.465 1223 26 2 1 1218 84403956 84402734 0 2082
7 TraesCS6B01G357200 chr5D 97.461 1221 28 3 1 1218 503225674 503224454 0 2080
8 TraesCS6B01G357200 chr5D 97.297 1221 30 3 1 1218 503270871 503272091 0 2069
9 TraesCS6B01G357200 chr5D 98.026 1013 20 0 1216 2228 503224427 503223415 0 1760
10 TraesCS6B01G357200 chr2B 97.297 1221 30 2 1 1218 449213742 449212522 0 2069
11 TraesCS6B01G357200 chr2B 97.828 1013 22 0 1216 2228 449212495 449211483 0 1749
12 TraesCS6B01G357200 chr3D 97.293 1219 31 2 1 1218 589268463 589269680 0 2067
13 TraesCS6B01G357200 chr3D 98.026 1013 20 0 1216 2228 589270748 589271760 0 1760
14 TraesCS6B01G357200 chr3B 98.124 1013 19 0 1216 2228 101917388 101916376 0 1766
15 TraesCS6B01G357200 chr1A 97.927 1013 21 0 1216 2228 278530773 278531785 0 1755
16 TraesCS6B01G357200 chr1A 97.631 1013 24 0 1216 2228 278528031 278529043 0 1738
17 TraesCS6B01G357200 chr1D 97.835 1016 19 1 1216 2228 254388877 254389892 0 1751
18 TraesCS6B01G357200 chr6D 97.532 1013 24 1 1216 2228 458921523 458920512 0 1731


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 TraesCS6B01G357200 chr6B 625614895 625617122 2227 True 4115.0 4115 100.0000 1 2228 1 chr6B.!!$R1 2227
1 TraesCS6B01G357200 chrUn 406474459 406475681 1222 True 2093.0 2093 97.6290 1 1218 1 chrUn.!!$R1 1217
2 TraesCS6B01G357200 chr1B 619188520 619189740 1220 True 2091.0 2091 97.6250 1 1218 1 chr1B.!!$R1 1217
3 TraesCS6B01G357200 chr3A 495097948 495099168 1220 True 2085.0 2085 97.5430 1 1218 1 chr3A.!!$R1 1217
4 TraesCS6B01G357200 chr3A 66010167 66012425 2258 False 1903.5 2069 97.4640 1 2228 2 chr3A.!!$F1 2227
5 TraesCS6B01G357200 chr6A 84402734 84403956 1222 True 2082.0 2082 97.4650 1 1218 1 chr6A.!!$R1 1217
6 TraesCS6B01G357200 chr5D 503270871 503272091 1220 False 2069.0 2069 97.2970 1 1218 1 chr5D.!!$F1 1217
7 TraesCS6B01G357200 chr5D 503223415 503225674 2259 True 1920.0 2080 97.7435 1 2228 2 chr5D.!!$R1 2227
8 TraesCS6B01G357200 chr2B 449211483 449213742 2259 True 1909.0 2069 97.5625 1 2228 2 chr2B.!!$R1 2227
9 TraesCS6B01G357200 chr3D 589268463 589271760 3297 False 1913.5 2067 97.6595 1 2228 2 chr3D.!!$F1 2227
10 TraesCS6B01G357200 chr3B 101916376 101917388 1012 True 1766.0 1766 98.1240 1216 2228 1 chr3B.!!$R1 1012
11 TraesCS6B01G357200 chr1A 278528031 278531785 3754 False 1746.5 1755 97.7790 1216 2228 2 chr1A.!!$F1 1012
12 TraesCS6B01G357200 chr1D 254388877 254389892 1015 False 1751.0 1751 97.8350 1216 2228 1 chr1D.!!$F1 1012
13 TraesCS6B01G357200 chr6D 458920512 458921523 1011 True 1731.0 1731 97.5320 1216 2228 1 chr6D.!!$R1 1012

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
633 639 1.779061 GCCAAAGGGAGTGGAGGTGA 61.779 60.0 0.0 0.0 38.54 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 3620 2.043526 AGATTCATTGTTCCTGGCCCTT 59.956 45.455 0.0 0.0 0.0 3.95 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
109 110 7.322938 CGTATTCGATGAAAGTCGTATGTATGT 59.677 37.037 0.00 0.00 42.07 2.29
206 211 9.758651 GATTTTAGCCCTTAGAAAAAGAAAACA 57.241 29.630 0.00 0.00 0.00 2.83
388 394 4.749598 GCCGTGAAAAAGATTCAACCAAAT 59.250 37.500 0.00 0.00 0.00 2.32
628 634 1.792757 ATGCTGCCAAAGGGAGTGGA 61.793 55.000 6.44 0.00 43.30 4.02
633 639 1.779061 GCCAAAGGGAGTGGAGGTGA 61.779 60.000 0.00 0.00 38.54 4.02
666 672 3.034635 AGGAAGCGACTCATAGAATGGT 58.965 45.455 0.00 0.00 0.00 3.55
855 1370 3.300388 TGATCAACTAAGCCCTCTCGAT 58.700 45.455 0.00 0.00 0.00 3.59
974 1489 7.857734 AAAATCAAAACAATCGGGACTTTTT 57.142 28.000 0.00 0.00 0.00 1.94
1017 1532 7.229308 ACTAATTCATGATCTGGCATGTACAT 58.771 34.615 1.41 1.41 44.59 2.29
1272 2971 6.416750 ACGAACAATTTCAACGAAATCTTTCC 59.583 34.615 2.62 0.00 40.77 3.13
1396 3095 3.070302 CAGCTACTCTAGGGGGAATGTTC 59.930 52.174 0.00 0.00 0.00 3.18
1399 3098 4.443598 GCTACTCTAGGGGGAATGTTCTTG 60.444 50.000 0.00 0.00 0.00 3.02
1411 3110 4.218417 GGAATGTTCTTGTGTGGTGCTAAT 59.782 41.667 0.00 0.00 0.00 1.73
1495 3194 6.780901 TGGATATACCAAGAGAGATCTACGT 58.219 40.000 0.00 0.00 46.75 3.57
1619 3321 4.574421 TCGAGCTTCAAGAAATTGTGAACA 59.426 37.500 0.00 0.00 30.73 3.18
1680 3382 6.822667 TTCAATTGCGCTTATATCCATCAT 57.177 33.333 9.73 0.00 0.00 2.45
1722 3424 1.754234 CCCCAGCCCCTTTTCATCG 60.754 63.158 0.00 0.00 0.00 3.84
1807 3509 2.362077 CTCTGAGGTGTTTGGGTTTTGG 59.638 50.000 0.00 0.00 0.00 3.28
1923 3625 6.775594 ATAACAATTAAGGTGAAGAAGGGC 57.224 37.500 0.00 0.00 0.00 5.19
2044 3746 5.409520 TGCTTGAATTATCGATGTAGATGCC 59.590 40.000 8.54 0.00 32.39 4.40
2066 3768 4.848357 CACATAGTGGGTTCTCATCCTTT 58.152 43.478 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 3.013417 AGAGGAAAGATCTCCCTCCAAGA 59.987 47.826 27.53 0.00 45.77 3.02
628 634 3.134574 TCCTTTTTGCGTATGTCACCT 57.865 42.857 0.00 0.00 0.00 4.00
633 639 2.611974 CGCTTCCTTTTTGCGTATGT 57.388 45.000 0.00 0.00 44.00 2.29
666 672 3.452264 TGCAAGAGCTCTATTTGCCTCTA 59.548 43.478 27.79 12.64 44.91 2.43
855 1370 7.665559 TCTTCTTTCTTATTCTTAAGCAAGCCA 59.334 33.333 0.00 0.00 38.09 4.75
891 1406 7.449704 AGGATCAAACCTTATTCCATGCTATTC 59.550 37.037 0.00 0.00 36.86 1.75
974 1489 5.692115 TTAGTAACTGCATCCAATCTCCA 57.308 39.130 0.00 0.00 0.00 3.86
1151 1666 8.552296 ACCAAGGTCTATCATTTTTATCAGAGT 58.448 33.333 0.00 0.00 0.00 3.24
1164 1679 8.324191 AGATGAAATAGAACCAAGGTCTATCA 57.676 34.615 2.75 0.00 0.00 2.15
1396 3095 9.289303 GTTATTAAATCATTAGCACCACACAAG 57.711 33.333 0.00 0.00 0.00 3.16
1680 3382 4.717279 AGCTTAAACCCAAGTCCTACAA 57.283 40.909 0.00 0.00 0.00 2.41
1722 3424 3.215151 TCATAGACGTCAGGAGTCCATC 58.785 50.000 19.50 0.74 39.31 3.51
1918 3620 2.043526 AGATTCATTGTTCCTGGCCCTT 59.956 45.455 0.00 0.00 0.00 3.95
1923 3625 7.870509 TCATAAAGAGATTCATTGTTCCTGG 57.129 36.000 0.00 0.00 0.00 4.45
2017 3719 8.659491 GCATCTACATCGATAATTCAAGCATTA 58.341 33.333 0.00 0.00 0.00 1.90
2044 3746 4.494091 AAGGATGAGAACCCACTATGTG 57.506 45.455 0.00 0.00 0.00 3.21
2066 3768 6.183360 TGCTCCTATTACACTCGTAGTCTCTA 60.183 42.308 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.