Multiple sequence alignment - TraesCS3B01G301200

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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 TraesCS3B01G301200 chr3B 100.000 2342 0 0 1 2342 483333112 483335453 0 4325
1 TraesCS3B01G301200 chr3B 96.800 2344 72 3 1 2342 575839842 575837500 0 3910
2 TraesCS3B01G301200 chr4B 97.183 2343 64 2 1 2342 209242457 209244798 0 3960
3 TraesCS3B01G301200 chr6A 97.181 2341 64 2 1 2340 155857199 155859538 0 3956
4 TraesCS3B01G301200 chr6A 96.497 2341 79 3 1 2340 375860859 375858521 0 3866
5 TraesCS3B01G301200 chr2A 97.010 2341 69 1 1 2340 750453691 750451351 0 3934
6 TraesCS3B01G301200 chr4A 96.241 2341 86 2 1 2340 350172140 350174479 0 3834
7 TraesCS3B01G301200 chr3A 96.133 2017 65 6 334 2340 230228527 230226514 0 3280
8 TraesCS3B01G301200 chr7B 97.730 1410 31 1 1 1409 742948838 742947429 0 2425
9 TraesCS3B01G301200 chr7B 97.726 1407 31 1 1 1406 716784507 716785913 0 2420
10 TraesCS3B01G301200 chrUn 99.138 1044 8 1 1300 2342 171017238 171018281 0 1877
11 TraesCS3B01G301200 chr5B 99.135 1041 9 0 1300 2340 439641088 439642128 0 1873
12 TraesCS3B01G301200 chr6B 93.260 727 46 3 1153 1878 401858415 401859139 0 1068


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 TraesCS3B01G301200 chr3B 483333112 483335453 2341 False 4325 4325 100.000 1 2342 1 chr3B.!!$F1 2341
1 TraesCS3B01G301200 chr3B 575837500 575839842 2342 True 3910 3910 96.800 1 2342 1 chr3B.!!$R1 2341
2 TraesCS3B01G301200 chr4B 209242457 209244798 2341 False 3960 3960 97.183 1 2342 1 chr4B.!!$F1 2341
3 TraesCS3B01G301200 chr6A 155857199 155859538 2339 False 3956 3956 97.181 1 2340 1 chr6A.!!$F1 2339
4 TraesCS3B01G301200 chr6A 375858521 375860859 2338 True 3866 3866 96.497 1 2340 1 chr6A.!!$R1 2339
5 TraesCS3B01G301200 chr2A 750451351 750453691 2340 True 3934 3934 97.010 1 2340 1 chr2A.!!$R1 2339
6 TraesCS3B01G301200 chr4A 350172140 350174479 2339 False 3834 3834 96.241 1 2340 1 chr4A.!!$F1 2339
7 TraesCS3B01G301200 chr3A 230226514 230228527 2013 True 3280 3280 96.133 334 2340 1 chr3A.!!$R1 2006
8 TraesCS3B01G301200 chr7B 742947429 742948838 1409 True 2425 2425 97.730 1 1409 1 chr7B.!!$R1 1408
9 TraesCS3B01G301200 chr7B 716784507 716785913 1406 False 2420 2420 97.726 1 1406 1 chr7B.!!$F1 1405
10 TraesCS3B01G301200 chrUn 171017238 171018281 1043 False 1877 1877 99.138 1300 2342 1 chrUn.!!$F1 1042
11 TraesCS3B01G301200 chr5B 439641088 439642128 1040 False 1873 1873 99.135 1300 2340 1 chr5B.!!$F1 1040
12 TraesCS3B01G301200 chr6B 401858415 401859139 724 False 1068 1068 93.260 1153 1878 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
355 357 0.798776 GTCAGACCTTGATGTTGCGG 59.201 55.0 0.0 0.0 38.29 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 1950 1.290203 CAGCAACGATACGCATTCCT 58.71 50.0 0.0 0.0 0.0 3.36 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
98 99 0.997196 GACTGCGTTACCCGTGATTC 59.003 55.000 0.00 0.00 39.32 2.52
232 234 1.820519 ACGTTGGCTTATCCGTCAGTA 59.179 47.619 0.00 0.00 37.80 2.74
289 291 4.134563 ACAAGTCTGCGGTAGTTCAAAAT 58.865 39.130 0.00 0.00 0.00 1.82
350 352 3.814504 ATTTGGGTCAGACCTTGATGT 57.185 42.857 19.57 0.00 38.64 3.06
355 357 0.798776 GTCAGACCTTGATGTTGCGG 59.201 55.000 0.00 0.00 38.29 5.69
508 510 8.704668 TGCCACTAGACAGAATTTCTCAATATA 58.295 33.333 0.00 0.00 0.00 0.86
605 607 5.441718 AGAAAGATGGAACCAGATGCTTA 57.558 39.130 0.00 0.00 0.00 3.09
704 706 2.725203 TTCTCGCCAACTGAACCCCG 62.725 60.000 0.00 0.00 0.00 5.73
705 707 4.323477 TCGCCAACTGAACCCCGG 62.323 66.667 0.00 0.00 0.00 5.73
774 778 1.091537 GCCATGCGTAAACCAAGCTA 58.908 50.000 0.00 0.00 32.19 3.32
791 795 2.312140 AGCTACTGAGAGTCTACCCCAA 59.688 50.000 0.00 0.00 0.00 4.12
798 802 2.572104 GAGAGTCTACCCCAACCACAAT 59.428 50.000 0.00 0.00 0.00 2.71
939 943 7.884257 TCATTTTCTTGAATATGTGACAAGCA 58.116 30.769 11.49 0.00 40.20 3.91
1144 1148 0.322456 TGCCGGAGCTGCTACAATTT 60.322 50.000 13.19 0.00 40.80 1.82
1151 1155 4.870426 CGGAGCTGCTACAATTTCTTTAGA 59.130 41.667 13.19 0.00 0.00 2.10
1175 1179 3.539604 GAGCTGCTGTCAGTATTGGAAT 58.460 45.455 7.01 0.00 42.29 3.01
1243 1247 8.819974 CATTGGCTAAACAATCATTTGGTTATC 58.180 33.333 0.00 0.00 42.57 1.75
1309 1313 3.293337 CCAATGATGGCCTTTCTGATCA 58.707 45.455 3.32 3.65 40.58 2.92
1315 1319 3.438216 TGGCCTTTCTGATCACATTCA 57.562 42.857 3.32 0.00 0.00 2.57
1450 1456 2.224475 CGATGGATGAATGAGGAGCCTT 60.224 50.000 0.00 0.00 0.00 4.35
1943 1950 1.616159 GCTTTTCACTACCCCTTGCA 58.384 50.000 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 1.299541 ACGTCTCCAGCTTGTGTTTG 58.700 50.000 0.00 0.0 0.00 2.93
289 291 2.223456 CGCGATATTGTGCCAATTCCAA 60.223 45.455 0.00 0.0 0.00 3.53
350 352 0.744414 GAGTAATGCCTGAGCCGCAA 60.744 55.000 0.00 0.0 40.22 4.85
355 357 4.202305 ACCTCTATTGAGTAATGCCTGAGC 60.202 45.833 3.47 0.0 38.61 4.26
605 607 7.441157 GGTAAGGCAAAGTGCTTTCTTTTAAAT 59.559 33.333 0.45 0.0 38.32 1.40
704 706 5.168569 GCAAAAAGTCCAAAATAGCCTACC 58.831 41.667 0.00 0.0 0.00 3.18
705 707 5.633601 GTGCAAAAAGTCCAAAATAGCCTAC 59.366 40.000 0.00 0.0 0.00 3.18
774 778 1.149288 TGGTTGGGGTAGACTCTCAGT 59.851 52.381 0.00 0.0 0.00 3.41
791 795 2.036256 GCAGCTCCCCATTGTGGT 59.964 61.111 0.00 0.0 35.17 4.16
906 910 7.062605 CACATATTCAAGAAAATGAGTTGTGGC 59.937 37.037 0.00 0.0 31.95 5.01
1144 1148 1.202582 GACAGCAGCTCCGTCTAAAGA 59.797 52.381 5.77 0.0 0.00 2.52
1151 1155 0.898320 AATACTGACAGCAGCTCCGT 59.102 50.000 1.25 0.0 46.26 4.69
1175 1179 4.600692 TGAATCAAAGAACTGAGGACGA 57.399 40.909 0.00 0.0 0.00 4.20
1309 1313 5.749596 TTATGCGATCGGAAAATGAATGT 57.250 34.783 14.89 0.0 0.00 2.71
1315 1319 6.189677 TGACTTTTTATGCGATCGGAAAAT 57.810 33.333 14.89 0.0 0.00 1.82
1450 1456 6.769134 TCCTATCATTTCACTACTCGACAA 57.231 37.500 0.00 0.0 0.00 3.18
1900 1907 5.456763 CCATTAGGGGGAAGAGATAGGTTTG 60.457 48.000 0.00 0.0 0.00 2.93
1943 1950 1.290203 CAGCAACGATACGCATTCCT 58.710 50.000 0.00 0.0 0.00 3.36


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

AutoCloner maintained by Alex Coulton.