Multiple sequence alignment - TraesCS1B01G208200

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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 TraesCS1B01G208200 chr1B 100.000 2255 0 0 1 2255 377802237 377804491 0 4165
1 TraesCS1B01G208200 chr1B 96.585 2255 77 0 1 2255 672477345 672479599 0 3738
2 TraesCS1B01G208200 chr1B 96.277 2256 82 2 1 2255 638702482 638700228 0 3699
3 TraesCS1B01G208200 chr1D 96.851 2255 70 1 1 2255 141314951 141312698 0 3770
4 TraesCS1B01G208200 chr7B 96.676 2256 74 1 1 2255 644465627 644467882 0 3749
5 TraesCS1B01G208200 chr7A 96.674 2255 75 0 1 2255 60150103 60147849 0 3749
6 TraesCS1B01G208200 chr7A 95.917 2253 91 1 3 2255 46399060 46396809 0 3650
7 TraesCS1B01G208200 chr3A 96.674 2255 75 0 1 2255 633109438 633111692 0 3749
8 TraesCS1B01G208200 chr6B 96.319 2255 83 0 1 2255 306997806 306995552 0 3705


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 TraesCS1B01G208200 chr1B 377802237 377804491 2254 False 4165 4165 100.000 1 2255 1 chr1B.!!$F1 2254
1 TraesCS1B01G208200 chr1B 672477345 672479599 2254 False 3738 3738 96.585 1 2255 1 chr1B.!!$F2 2254
2 TraesCS1B01G208200 chr1B 638700228 638702482 2254 True 3699 3699 96.277 1 2255 1 chr1B.!!$R1 2254
3 TraesCS1B01G208200 chr1D 141312698 141314951 2253 True 3770 3770 96.851 1 2255 1 chr1D.!!$R1 2254
4 TraesCS1B01G208200 chr7B 644465627 644467882 2255 False 3749 3749 96.676 1 2255 1 chr7B.!!$F1 2254
5 TraesCS1B01G208200 chr7A 60147849 60150103 2254 True 3749 3749 96.674 1 2255 1 chr7A.!!$R2 2254
6 TraesCS1B01G208200 chr7A 46396809 46399060 2251 True 3650 3650 95.917 3 2255 1 chr7A.!!$R1 2252
7 TraesCS1B01G208200 chr3A 633109438 633111692 2254 False 3749 3749 96.674 1 2255 1 chr3A.!!$F1 2254
8 TraesCS1B01G208200 chr6B 306995552 306997806 2254 True 3705 3705 96.319 1 2255 1 chr6B.!!$R1 2254

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
405 406 0.24746 CGGTGAGCCAGACATCAAGA 59.753 55.0 0.0 0.0 34.09 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 1511 0.332972 GGAGAAAGCTGGTTGGGGAT 59.667 55.0 0.0 0.0 0.0 3.85 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
33 34 3.945921 CTGTCTCAACTCGTGGACCTATA 59.054 47.826 0.00 0.00 30.52 1.31
76 77 1.906574 AGGGGTTTGCTATTCTCACGA 59.093 47.619 0.00 0.00 0.00 4.35
228 229 9.168451 TGTCAATTGTAAAAAGTAGTTGAGTCA 57.832 29.630 5.13 0.00 0.00 3.41
236 237 5.455056 AAAGTAGTTGAGTCATGTCTCGT 57.545 39.130 14.03 5.33 37.28 4.18
237 238 4.427096 AGTAGTTGAGTCATGTCTCGTG 57.573 45.455 14.03 0.00 37.28 4.35
405 406 0.247460 CGGTGAGCCAGACATCAAGA 59.753 55.000 0.00 0.00 34.09 3.02
436 437 7.861629 TGGACATACAATCAAAGAGTAAGGAT 58.138 34.615 0.00 0.00 0.00 3.24
453 454 8.579850 AGTAAGGATCAGTTATTTGCAATGAA 57.420 30.769 0.00 0.00 0.00 2.57
471 472 1.909302 GAAGGGTGGATTGGTCAGAGA 59.091 52.381 0.00 0.00 0.00 3.10
477 478 3.285484 GTGGATTGGTCAGAGATGCAAT 58.715 45.455 0.00 0.00 0.00 3.56
521 522 5.648572 GATAAAGAGCTTGCTTCAATGCTT 58.351 37.500 0.00 0.00 31.72 3.91
662 663 3.142174 GTCCTATCATTAGTTGGCCAGC 58.858 50.000 12.39 12.39 0.00 4.85
691 692 7.436933 AGCAATTTAAGTAGAAAGCTTGCTTT 58.563 30.769 13.52 18.93 39.72 3.51
708 709 4.800023 TGCTTTGGGATCAGATCATTCAT 58.200 39.130 12.66 0.00 0.00 2.57
818 819 5.343307 AAACAGATTTGCAAGGAGTTTGT 57.657 34.783 15.71 7.53 39.08 2.83
825 826 2.733956 TGCAAGGAGTTTGTCAAAGGT 58.266 42.857 0.00 0.00 39.08 3.50
912 914 3.856638 GCCGCTTGTGTGAATTTCATTGA 60.857 43.478 1.78 0.00 0.00 2.57
982 984 2.448926 TCAATTTCTTGACTCCGCGA 57.551 45.000 8.23 0.00 36.46 5.87
1060 1062 6.593978 GTCGGCATTTACTTATTATGCTCTG 58.406 40.000 0.00 0.00 43.17 3.35
1188 1190 7.433680 AGATAAGGATTTCGCAAAACTTTTGT 58.566 30.769 14.36 0.00 0.00 2.83
1310 1312 3.784178 TCCTCATCTGGTGATAGATCCC 58.216 50.000 0.00 0.00 35.28 3.85
1320 1322 4.977739 TGGTGATAGATCCCCATCTTCTTT 59.022 41.667 0.00 0.00 40.18 2.52
1413 1415 4.581409 TGATCGACCTCGTTTATGTCCATA 59.419 41.667 0.00 0.00 40.80 2.74
1425 1427 8.953313 TCGTTTATGTCCATAGTATCATCGTAT 58.047 33.333 0.00 0.00 0.00 3.06
1453 1455 6.897966 ACCTTCTACTATCAACCAGATGAGAA 59.102 38.462 0.00 0.00 37.57 2.87
1475 1477 2.175715 AGGGCTTTGAAAGGTCAGAGTT 59.824 45.455 7.09 0.00 38.09 3.01
1509 1511 7.496591 TCTTTTTCTTTTAGGTCGTTTAGCAGA 59.503 33.333 0.00 0.00 0.00 4.26
1547 1549 0.391793 CCCGAGAAAGCCTTCCTGAC 60.392 60.000 0.00 0.00 31.28 3.51
1549 1551 1.674221 CCGAGAAAGCCTTCCTGACAG 60.674 57.143 0.00 0.00 31.28 3.51
1558 1560 2.810852 GCCTTCCTGACAGTCAAAGAAG 59.189 50.000 24.26 24.26 36.95 2.85
1773 1775 5.289595 ACTGATATAAGAATTTCGCGAGCA 58.710 37.500 9.59 0.00 0.00 4.26
1830 1832 4.923871 GCTTGGAAAAGCCTTAAGTTTAGC 59.076 41.667 0.97 0.00 39.81 3.09
1858 1860 4.963318 TCCTTCACTGAACTGATTCACT 57.037 40.909 0.00 0.00 40.01 3.41
1955 1957 1.763770 CTCCTCTTGGTTGGTGCCT 59.236 57.895 0.00 0.00 34.23 4.75
2007 2010 2.357760 CCTTTCGTTCGGGCCGAA 60.358 61.111 35.71 35.71 43.75 4.30
2159 2163 4.392921 AAGAGGTGATCAGAATGGTACG 57.607 45.455 0.00 0.00 36.16 3.67
2160 2164 3.366396 AGAGGTGATCAGAATGGTACGT 58.634 45.455 0.00 0.00 36.16 3.57
2189 2193 1.108776 TACGATCCCGAGTTTCCAGG 58.891 55.000 0.00 0.00 39.50 4.45
2208 2212 1.737735 CACATCGCACTTCCGCTCA 60.738 57.895 0.00 0.00 0.00 4.26
2212 2216 1.320344 ATCGCACTTCCGCTCAGGTA 61.320 55.000 0.00 0.00 41.99 3.08
2213 2217 1.080093 CGCACTTCCGCTCAGGTAA 60.080 57.895 0.00 0.00 41.99 2.85
2237 2241 2.997315 CCACTCGGCCCTCAGACA 60.997 66.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 229 2.154462 CTTTTTGCTCCCACGAGACAT 58.846 47.619 0.00 0.00 38.52 3.06
236 237 4.214310 TCATTTCACTCTTTTTGCTCCCA 58.786 39.130 0.00 0.00 0.00 4.37
237 238 4.321527 CCTCATTTCACTCTTTTTGCTCCC 60.322 45.833 0.00 0.00 0.00 4.30
436 437 4.220382 CCACCCTTCATTGCAAATAACTGA 59.780 41.667 1.71 0.00 0.00 3.41
453 454 1.842562 CATCTCTGACCAATCCACCCT 59.157 52.381 0.00 0.00 0.00 4.34
471 472 4.375272 CATAACCGAGTCTCTCATTGCAT 58.625 43.478 0.00 0.00 0.00 3.96
477 478 0.738975 CGCCATAACCGAGTCTCTCA 59.261 55.000 0.00 0.00 0.00 3.27
521 522 5.483937 TGCTCTTACTTTCTACCTGAATCCA 59.516 40.000 0.00 0.00 34.24 3.41
662 663 7.433425 GCAAGCTTTCTACTTAAATTGCTATGG 59.567 37.037 0.00 0.00 38.90 2.74
691 692 6.044054 AGCTTTAGATGAATGATCTGATCCCA 59.956 38.462 14.71 10.25 41.86 4.37
708 709 1.596934 CCGGCCTGACAGCTTTAGA 59.403 57.895 0.00 0.00 0.00 2.10
818 819 6.458232 TTTTCCGAATGAGAAAACCTTTGA 57.542 33.333 0.00 0.00 38.08 2.69
912 914 2.429930 CACACACGGGACCCACAT 59.570 61.111 12.15 0.00 0.00 3.21
964 966 2.789092 GCATCGCGGAGTCAAGAAATTG 60.789 50.000 6.13 0.00 0.00 2.32
982 984 3.815401 GCCATAAACTCGATAACCAGCAT 59.185 43.478 0.00 0.00 0.00 3.79
1060 1062 4.838904 ACCAAGGGACCACTATTAGAAC 57.161 45.455 0.00 0.00 0.00 3.01
1154 1156 5.084385 CGAAATCCTTATCTTTCGGCTTC 57.916 43.478 9.00 0.00 46.04 3.86
1310 1312 4.382362 GGGATTTGAGCCAAAAGAAGATGG 60.382 45.833 4.76 0.00 36.90 3.51
1320 1322 6.127083 GGATATGAAAAAGGGATTTGAGCCAA 60.127 38.462 0.00 0.00 0.00 4.52
1392 1394 4.583489 ACTATGGACATAAACGAGGTCGAT 59.417 41.667 6.35 0.00 39.86 3.59
1425 1427 7.123383 TCATCTGGTTGATAGTAGAAGGTACA 58.877 38.462 0.00 0.00 33.36 2.90
1453 1455 2.175715 ACTCTGACCTTTCAAAGCCCTT 59.824 45.455 0.00 0.00 0.00 3.95
1475 1477 7.015001 ACGACCTAAAAGAAAAAGAGGAGACTA 59.985 37.037 0.00 0.00 44.43 2.59
1509 1511 0.332972 GGAGAAAGCTGGTTGGGGAT 59.667 55.000 0.00 0.00 0.00 3.85
1547 1549 5.358160 ACCTTCAAACCTTCTTCTTTGACTG 59.642 40.000 0.00 0.00 36.38 3.51
1549 1551 5.836821 ACCTTCAAACCTTCTTCTTTGAC 57.163 39.130 0.00 0.00 36.38 3.18
1558 1560 4.457257 CCAGAGATCAACCTTCAAACCTTC 59.543 45.833 0.00 0.00 0.00 3.46
1685 1687 2.556287 CGGCTCGCTTCGCTTTTT 59.444 55.556 0.00 0.00 0.00 1.94
1709 1711 4.678044 CGCTCATAAAGGAAGAGTAGCACA 60.678 45.833 0.00 0.00 0.00 4.57
1711 1713 3.699538 TCGCTCATAAAGGAAGAGTAGCA 59.300 43.478 0.00 0.00 0.00 3.49
1756 1758 4.391830 TCAGTTTGCTCGCGAAATTCTTAT 59.608 37.500 11.33 0.00 0.00 1.73
1763 1765 1.569493 GCTCAGTTTGCTCGCGAAA 59.431 52.632 11.33 0.00 0.00 3.46
1765 1767 3.105782 CGCTCAGTTTGCTCGCGA 61.106 61.111 9.26 9.26 41.37 5.87
1773 1775 0.392193 CCTCATGGCTCGCTCAGTTT 60.392 55.000 0.00 0.00 0.00 2.66
1830 1832 1.981495 AGTTCAGTGAAGGAAGGGAGG 59.019 52.381 5.62 0.00 0.00 4.30
1907 1909 6.056884 GCTCTCTCCAATCATTCTGAAGATT 58.943 40.000 0.00 3.29 34.96 2.40
1908 1910 5.455040 GGCTCTCTCCAATCATTCTGAAGAT 60.455 44.000 0.00 0.00 0.00 2.40
1955 1957 3.083349 CCCATCACTCTCGGGCCA 61.083 66.667 4.39 0.00 31.89 5.36
2007 2010 0.575333 ATAGATCAGGGCCCCTCCTT 59.425 55.000 21.43 4.30 34.31 3.36
2159 2163 3.724374 TCGGGATCGTAAATGGATTCAC 58.276 45.455 0.00 0.00 37.69 3.18
2160 2164 3.386726 ACTCGGGATCGTAAATGGATTCA 59.613 43.478 0.00 0.00 37.69 2.57
2189 2193 3.088500 GAGCGGAAGTGCGATGTGC 62.089 63.158 0.00 0.00 46.70 4.57
2208 2212 1.296715 CGAGTGGCAGCCTTTACCT 59.703 57.895 14.15 0.28 0.00 3.08


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

AutoCloner maintained by Alex Coulton.