Multiple sequence alignment - TraesCS3B01G029700

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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 TraesCS3B01G029700 chr3B 100.000 2303 0 0 1 2303 13510460 13512762 0 4253
1 TraesCS3B01G029700 chr3B 96.947 1900 46 5 1 1890 13529469 13531366 0 3177
2 TraesCS3B01G029700 chr3B 95.808 1455 47 6 1 1444 726424646 726426097 0 2337
3 TraesCS3B01G029700 chr3B 96.081 842 22 6 1445 2281 761348906 761349741 0 1362
4 TraesCS3B01G029700 chr1B 97.443 1447 32 4 1 1444 539849648 539848204 0 2462
5 TraesCS3B01G029700 chr7D 92.897 1450 78 10 1 1444 525734033 525735463 0 2084
6 TraesCS3B01G029700 chr2B 92.376 1456 75 11 1 1444 80552365 80550934 0 2041
7 TraesCS3B01G029700 chr2B 95.491 865 30 6 1445 2302 565774464 565773602 0 1373
8 TraesCS3B01G029700 chr1A 92.367 1415 78 12 44 1444 572001078 571999680 0 1988
9 TraesCS3B01G029700 chr2A 92.302 1390 81 6 63 1444 38506995 38505624 0 1951
10 TraesCS3B01G029700 chr3A 91.871 1390 85 9 63 1444 22778730 22777361 0 1916
11 TraesCS3B01G029700 chr6A 91.307 1415 95 13 44 1444 116690356 116691756 0 1906
12 TraesCS3B01G029700 chr5B 95.607 865 27 5 1445 2303 11564594 11563735 0 1376
13 TraesCS3B01G029700 chr4B 95.491 865 29 4 1446 2303 466601557 466602418 0 1373
14 TraesCS3B01G029700 chr4B 95.386 867 31 4 1445 2303 564448519 564449384 0 1371
15 TraesCS3B01G029700 chr4B 95.293 871 29 5 1443 2303 605926438 605925570 0 1371
16 TraesCS3B01G029700 chr7B 95.029 865 35 5 1445 2303 585249859 585250721 0 1352
17 TraesCS3B01G029700 chrUn 94.913 865 36 4 1445 2303 31557812 31558674 0 1347


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 TraesCS3B01G029700 chr3B 13510460 13512762 2302 False 4253 4253 100.000 1 2303 1 chr3B.!!$F1 2302
1 TraesCS3B01G029700 chr3B 13529469 13531366 1897 False 3177 3177 96.947 1 1890 1 chr3B.!!$F2 1889
2 TraesCS3B01G029700 chr3B 726424646 726426097 1451 False 2337 2337 95.808 1 1444 1 chr3B.!!$F3 1443
3 TraesCS3B01G029700 chr3B 761348906 761349741 835 False 1362 1362 96.081 1445 2281 1 chr3B.!!$F4 836
4 TraesCS3B01G029700 chr1B 539848204 539849648 1444 True 2462 2462 97.443 1 1444 1 chr1B.!!$R1 1443
5 TraesCS3B01G029700 chr7D 525734033 525735463 1430 False 2084 2084 92.897 1 1444 1 chr7D.!!$F1 1443
6 TraesCS3B01G029700 chr2B 80550934 80552365 1431 True 2041 2041 92.376 1 1444 1 chr2B.!!$R1 1443
7 TraesCS3B01G029700 chr2B 565773602 565774464 862 True 1373 1373 95.491 1445 2302 1 chr2B.!!$R2 857
8 TraesCS3B01G029700 chr1A 571999680 572001078 1398 True 1988 1988 92.367 44 1444 1 chr1A.!!$R1 1400
9 TraesCS3B01G029700 chr2A 38505624 38506995 1371 True 1951 1951 92.302 63 1444 1 chr2A.!!$R1 1381
10 TraesCS3B01G029700 chr3A 22777361 22778730 1369 True 1916 1916 91.871 63 1444 1 chr3A.!!$R1 1381
11 TraesCS3B01G029700 chr6A 116690356 116691756 1400 False 1906 1906 91.307 44 1444 1 chr6A.!!$F1 1400
12 TraesCS3B01G029700 chr5B 11563735 11564594 859 True 1376 1376 95.607 1445 2303 1 chr5B.!!$R1 858
13 TraesCS3B01G029700 chr4B 466601557 466602418 861 False 1373 1373 95.491 1446 2303 1 chr4B.!!$F1 857
14 TraesCS3B01G029700 chr4B 564448519 564449384 865 False 1371 1371 95.386 1445 2303 1 chr4B.!!$F2 858
15 TraesCS3B01G029700 chr4B 605925570 605926438 868 True 1371 1371 95.293 1443 2303 1 chr4B.!!$R1 860
16 TraesCS3B01G029700 chr7B 585249859 585250721 862 False 1352 1352 95.029 1445 2303 1 chr7B.!!$F1 858
17 TraesCS3B01G029700 chrUn 31557812 31558674 862 False 1347 1347 94.913 1445 2303 1 chrUn.!!$F1 858

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
82 85 3.814283 CACTGCTTCTTTTCTTCTGCTCT 59.186 43.478 0.00 0.0 0.00 4.09 F
843 868 4.573900 CCAAGCTCTGGGATATGTATCAC 58.426 47.826 6.96 0.0 42.17 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1050 1075 1.059098 TCTTTGCCTGCTCCTCAAGA 58.941 50.000 0.00 0.0 0.00 3.02 R
1666 1693 1.603455 CCGGTTCATGCCACCAACT 60.603 57.895 12.84 0.0 33.36 3.16 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
78 81 4.384056 TCTCCACTGCTTCTTTTCTTCTG 58.616 43.478 0.00 0.0 0.00 3.02
82 85 3.814283 CACTGCTTCTTTTCTTCTGCTCT 59.186 43.478 0.00 0.0 0.00 4.09
290 307 6.844388 AGTTCATATATGGGAGGTGTAGTTGA 59.156 38.462 12.78 0.0 0.00 3.18
291 308 7.514127 AGTTCATATATGGGAGGTGTAGTTGAT 59.486 37.037 12.78 0.0 0.00 2.57
739 763 9.474313 TGAAGAATAAAGCCCACTGTAAATTAT 57.526 29.630 0.00 0.0 0.00 1.28
843 868 4.573900 CCAAGCTCTGGGATATGTATCAC 58.426 47.826 6.96 0.0 42.17 3.06
903 928 7.201866 GCTCATGAGATAGAGGTTGAGAAACTA 60.202 40.741 27.04 0.0 34.00 2.24
915 940 6.270231 AGGTTGAGAAACTAAAGAAGGAGCTA 59.730 38.462 0.00 0.0 0.00 3.32
1050 1075 6.715280 TGAACTTAAGGAGAAGAAGCATCAT 58.285 36.000 7.53 0.0 0.00 2.45
1073 1098 1.101331 GAGGAGCAGGCAAAGATTGG 58.899 55.000 0.00 0.0 0.00 3.16
1088 1113 4.614967 AGATTGGGGTTCAAATGGAGAT 57.385 40.909 0.00 0.0 39.05 2.75
1246 1273 4.162888 TCATTGCTGATCTCTTGAAGGCTA 59.837 41.667 0.00 0.0 0.00 3.93
1588 1615 1.377229 GGTCATTGGTCCCGGTTCA 59.623 57.895 0.00 0.0 0.00 3.18
1666 1693 1.154921 CCCACAACCATTGGTCCCA 59.845 57.895 9.22 0.0 33.12 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 81 4.838486 CGTCGCCGGAGTGAGAGC 62.838 72.222 5.05 0.00 31.79 4.09
290 307 9.823647 GCTACAGCAGGAAACACATATATATAT 57.176 33.333 0.00 0.00 41.59 0.86
313 330 3.093814 TCACAGTATCCGGAGTTTGCTA 58.906 45.455 11.34 0.00 0.00 3.49
430 447 4.225942 TCCTATGAATCTTCTGCCTGTGTT 59.774 41.667 0.00 0.00 0.00 3.32
739 763 8.474025 ACAGTTCACACAATCCTGAAAATTTAA 58.526 29.630 0.00 0.00 0.00 1.52
843 868 2.424246 GACTCTACCAAGGTTCTCCTCG 59.576 54.545 0.00 0.00 44.35 4.63
1050 1075 1.059098 TCTTTGCCTGCTCCTCAAGA 58.941 50.000 0.00 0.00 0.00 3.02
1073 1098 4.440663 GCTTAAGCATCTCCATTTGAACCC 60.441 45.833 22.59 0.00 41.59 4.11
1088 1113 5.368145 TCTGTTCTTTCTTGAGCTTAAGCA 58.632 37.500 28.39 6.82 45.16 3.91
1246 1273 2.787994 CTTCTCTTTGCACCCATGACT 58.212 47.619 0.00 0.00 0.00 3.41
1506 1533 2.443324 CCCCATTGGTCCCGGTTT 59.557 61.111 0.00 0.00 0.00 3.27
1666 1693 1.603455 CCGGTTCATGCCACCAACT 60.603 57.895 12.84 0.00 33.36 3.16


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

AutoCloner maintained by Alex Coulton.