Multiple sequence alignment - TraesCS1B01G068800

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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 TraesCS1B01G068800 chr1B 100.000 2319 0 0 1 2319 53331466 53333784 0 4283
1 TraesCS1B01G068800 chr5A 98.103 2320 43 1 1 2319 300072979 300075298 0 4039
2 TraesCS1B01G068800 chr5A 97.628 2319 52 2 1 2319 16602919 16600604 0 3975
3 TraesCS1B01G068800 chr2A 98.017 2320 45 1 1 2319 618279956 618277637 0 4028
4 TraesCS1B01G068800 chrUn 97.888 2320 48 1 1 2319 189392539 189394858 0 4012
5 TraesCS1B01G068800 chr7B 97.845 2320 49 1 1 2319 743086199 743088518 0 4006
6 TraesCS1B01G068800 chr7D 97.802 2320 50 1 1 2319 626698490 626696171 0 4000
7 TraesCS1B01G068800 chr6A 97.758 2319 51 1 1 2319 289128632 289130949 0 3993
8 TraesCS1B01G068800 chr7A 97.504 2324 53 1 1 2319 4959838 4962161 0 3965


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 TraesCS1B01G068800 chr1B 53331466 53333784 2318 False 4283 4283 100.000 1 2319 1 chr1B.!!$F1 2318
1 TraesCS1B01G068800 chr5A 300072979 300075298 2319 False 4039 4039 98.103 1 2319 1 chr5A.!!$F1 2318
2 TraesCS1B01G068800 chr5A 16600604 16602919 2315 True 3975 3975 97.628 1 2319 1 chr5A.!!$R1 2318
3 TraesCS1B01G068800 chr2A 618277637 618279956 2319 True 4028 4028 98.017 1 2319 1 chr2A.!!$R1 2318
4 TraesCS1B01G068800 chrUn 189392539 189394858 2319 False 4012 4012 97.888 1 2319 1 chrUn.!!$F1 2318
5 TraesCS1B01G068800 chr7B 743086199 743088518 2319 False 4006 4006 97.845 1 2319 1 chr7B.!!$F1 2318
6 TraesCS1B01G068800 chr7D 626696171 626698490 2319 True 4000 4000 97.802 1 2319 1 chr7D.!!$R1 2318
7 TraesCS1B01G068800 chr6A 289128632 289130949 2317 False 3993 3993 97.758 1 2319 1 chr6A.!!$F1 2318
8 TraesCS1B01G068800 chr7A 4959838 4962161 2323 False 3965 3965 97.504 1 2319 1 chr7A.!!$F1 2318

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
167 168 1.498576 TCTAGAGCCCAGCATCTCTCT 59.501 52.381 0.0 0.0 40.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1789 1.512735 AGCCCTAACTCCCCATTCTC 58.487 55.0 0.0 0.0 0.0 2.87 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
32 33 2.296190 GCTTCGACAAGGGGTTTGATTT 59.704 45.455 0.00 0.00 39.21 2.17
167 168 1.498576 TCTAGAGCCCAGCATCTCTCT 59.501 52.381 0.00 0.00 40.00 3.10
258 259 2.489971 GGTCAGGAAACGACAATGACA 58.510 47.619 6.04 0.00 41.58 3.58
269 270 5.409643 ACGACAATGACACTTCTTCTTTG 57.590 39.130 0.00 0.00 35.35 2.77
405 406 8.522830 CAACTTAAGGAATCTTTAGATTTGGCA 58.477 33.333 7.53 0.00 44.14 4.92
429 430 4.202305 GCTATAGACTCAAAGGGCACAGAT 60.202 45.833 3.21 0.00 0.00 2.90
475 477 6.231951 AGCTAACTAAAGTCCAACTTCCTTC 58.768 40.000 0.00 0.00 37.47 3.46
476 478 5.995897 GCTAACTAAAGTCCAACTTCCTTCA 59.004 40.000 0.00 0.00 37.47 3.02
905 908 3.380479 TCGGACTCGACTCACATTTTT 57.620 42.857 0.00 0.00 40.88 1.94
914 917 7.837863 ACTCGACTCACATTTTTATCTCCTAA 58.162 34.615 0.00 0.00 0.00 2.69
1017 1020 9.342308 AGATTCAATATGTTGATTGTACCGAAT 57.658 29.630 5.66 0.00 43.49 3.34
1093 1096 6.381994 ACACGTCCTGTTCCCTATAAATAAGA 59.618 38.462 0.00 0.00 0.00 2.10
1320 1325 6.899393 TCAAAGAAGCATTGTGGAATAGTT 57.101 33.333 0.00 0.00 0.00 2.24
1327 1332 5.797051 AGCATTGTGGAATAGTTGCATTTT 58.203 33.333 0.00 0.00 32.24 1.82
1427 1432 1.888215 CATAGCGGCATCATCCAAGT 58.112 50.000 1.45 0.00 0.00 3.16
1458 1463 2.903135 CTCCTCAGTCAAGGGTCTTCTT 59.097 50.000 0.00 0.00 37.02 2.52
1586 1596 4.053295 CCGATTCATCCAATCCAATTTGC 58.947 43.478 0.00 0.00 38.17 3.68
1657 1667 7.885399 ACAAAACCATTCTCAGCTAATAGAAGT 59.115 33.333 10.15 3.04 35.32 3.01
1658 1668 8.734386 CAAAACCATTCTCAGCTAATAGAAGTT 58.266 33.333 10.15 7.52 35.32 2.66
1739 1749 5.913137 AATCCATTGCGATTAGAAACCAA 57.087 34.783 0.00 0.00 30.59 3.67
1769 1779 1.895707 CCAGGGCTTGATGGCGATC 60.896 63.158 1.08 1.08 42.84 3.69
1779 1789 5.101628 GCTTGATGGCGATCTAAGATAGAG 58.898 45.833 18.18 4.47 38.38 2.43
1848 1858 2.608268 CAAATCATTTGCCGACATGCA 58.392 42.857 0.00 0.00 40.07 3.96
2297 2307 1.726352 AGTTAGGGGTAAGAGGGGACA 59.274 52.381 0.00 0.00 0.00 4.02
2299 2309 1.702699 TAGGGGTAAGAGGGGACAGA 58.297 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.346751 ACCTTATCTTTTTGCTCAAAGAACA 57.653 32.000 12.95 4.28 44.18 3.18
167 168 1.138069 TCTGCAGAAGGTGTCGTTCAA 59.862 47.619 15.67 0.00 31.65 2.69
258 259 1.202818 AGCTTCCCGCAAAGAAGAAGT 60.203 47.619 10.63 0.00 42.80 3.01
269 270 2.902343 GTGCCCATAGCTTCCCGC 60.902 66.667 0.00 0.00 44.23 6.13
371 372 5.633830 AGATTCCTTAAGTTGTCGTACGA 57.366 39.130 15.28 15.28 0.00 3.43
405 406 3.107601 TGTGCCCTTTGAGTCTATAGCT 58.892 45.455 0.00 0.00 0.00 3.32
475 477 4.041740 TCCGTTACATCCTCTTTCGATG 57.958 45.455 0.00 0.00 42.37 3.84
476 478 4.341235 TGATCCGTTACATCCTCTTTCGAT 59.659 41.667 0.00 0.00 0.00 3.59
905 908 5.046304 ACTGTGAAAGCAAGCTTAGGAGATA 60.046 40.000 7.85 0.00 34.84 1.98
914 917 0.538287 GGGGACTGTGAAAGCAAGCT 60.538 55.000 0.00 0.00 0.00 3.74
974 977 3.396911 CTACGCTTGCTCGGCTCGA 62.397 63.158 10.50 0.00 0.00 4.04
1054 1057 2.546778 GACGTGTGACTTCCTCAAACA 58.453 47.619 0.00 0.00 36.97 2.83
1216 1221 4.644685 TGACACGAGAATAGATCACATCCA 59.355 41.667 0.00 0.00 0.00 3.41
1320 1325 7.976135 ACATTTTAGCCATTAACAAAATGCA 57.024 28.000 15.04 0.00 45.61 3.96
1327 1332 9.290988 TCACTAAGAACATTTTAGCCATTAACA 57.709 29.630 0.00 0.00 32.58 2.41
1427 1432 2.028876 TGACTGAGGAGACGTGTTTGA 58.971 47.619 0.00 0.00 0.00 2.69
1458 1463 7.596621 TGTTATGTTTTTGATCTTATTTGCGCA 59.403 29.630 5.66 5.66 0.00 6.09
1604 1614 5.766174 AGGAAAGGTTTCGCTATACAACAAA 59.234 36.000 0.00 0.00 38.06 2.83
1657 1667 5.022122 CCCTGATCTGGATAGATAGCTCAA 58.978 45.833 19.59 0.00 43.63 3.02
1658 1668 4.045207 ACCCTGATCTGGATAGATAGCTCA 59.955 45.833 19.59 0.00 43.63 4.26
1739 1749 2.216148 GCCCTGGCTGTAGAGTCAT 58.784 57.895 0.00 0.00 31.88 3.06
1759 1769 5.810095 TCTCTCTATCTTAGATCGCCATCA 58.190 41.667 0.00 0.00 33.66 3.07
1769 1779 7.396055 CCTAACTCCCCATTCTCTCTATCTTAG 59.604 44.444 0.00 0.00 0.00 2.18
1779 1789 1.512735 AGCCCTAACTCCCCATTCTC 58.487 55.000 0.00 0.00 0.00 2.87
1848 1858 6.441924 TCATCCCATAAAAGAGAAGTGAGTCT 59.558 38.462 0.00 0.00 0.00 3.24
1901 1911 5.385198 ACTTGTTGTACTTGATTCACCCAT 58.615 37.500 0.00 0.00 0.00 4.00
2179 2189 2.133520 ACCCTATCCACTCTCGTCCTA 58.866 52.381 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.