Multiple sequence alignment - TraesCS2A01G290400

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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 TraesCS2A01G290400 chr2A 100.000 2395 0 0 1 2395 500531818 500529424 0 4423
1 TraesCS2A01G290400 chr2B 95.828 1630 50 8 776 2395 439224519 439222898 0 2617
2 TraesCS2A01G290400 chr2B 88.710 806 49 13 1 783 439225331 439224545 0 946
3 TraesCS2A01G290400 chr2D 94.911 1631 66 7 776 2395 369480572 369478948 0 2536
4 TraesCS2A01G290400 chr2D 90.652 813 33 13 1 783 369481397 369480598 0 1040


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 TraesCS2A01G290400 chr2A 500529424 500531818 2394 True 4423.0 4423 100.0000 1 2395 1 chr2A.!!$R1 2394
1 TraesCS2A01G290400 chr2B 439222898 439225331 2433 True 1781.5 2617 92.2690 1 2395 2 chr2B.!!$R1 2394
2 TraesCS2A01G290400 chr2D 369478948 369481397 2449 True 1788.0 2536 92.7815 1 2395 2 chr2D.!!$R1 2394

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
393 395 0.331616 AAATGGAAACCGGGAGAGGG 59.668 55.0 6.32 0.0 35.02 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1575 2.938956 AGCAGGCAACACTCTTTACT 57.061 45.0 0.0 0.0 41.41 2.24 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
143 145 9.046296 GGTTCTGGTGTGATAGTCAATAATAAG 57.954 37.037 0.00 0.00 0.00 1.73
203 205 7.302524 GGTGCGAACAGATATCTTTTGTTAAA 58.697 34.615 8.84 0.00 35.35 1.52
282 284 1.299541 CCGCTCTTATTCGGCATTGT 58.700 50.000 0.00 0.00 39.14 2.71
393 395 0.331616 AAATGGAAACCGGGAGAGGG 59.668 55.000 6.32 0.00 35.02 4.30
445 454 3.458872 CTGCTGAGTTTGCGGGATA 57.541 52.632 0.00 0.00 33.50 2.59
452 461 2.752354 TGAGTTTGCGGGATACATTTGG 59.248 45.455 0.00 0.00 39.74 3.28
483 500 3.008594 CACAAGGTGTTATGTGGTAGGGA 59.991 47.826 0.00 0.00 42.46 4.20
622 645 3.357079 GCACCGTTGTCCCTGCTG 61.357 66.667 0.00 0.00 0.00 4.41
643 666 3.271706 CTGCCAATGCACACCACGG 62.272 63.158 0.00 0.00 44.23 4.94
649 672 2.355197 CAATGCACACCACGGATTCTA 58.645 47.619 0.00 0.00 0.00 2.10
692 730 2.995939 TGACACATCAATTCTGACGAGC 59.004 45.455 0.00 0.00 33.30 5.03
694 732 1.667724 CACATCAATTCTGACGAGCCC 59.332 52.381 0.00 0.00 33.30 5.19
701 739 1.410004 TTCTGACGAGCCCCGATTAT 58.590 50.000 2.99 0.00 41.76 1.28
702 740 1.410004 TCTGACGAGCCCCGATTATT 58.590 50.000 2.99 0.00 41.76 1.40
703 741 1.068588 TCTGACGAGCCCCGATTATTG 59.931 52.381 2.99 0.00 41.76 1.90
727 769 6.319658 TGCTTTCACAAGAAGAGACAAGAATT 59.680 34.615 0.00 0.00 34.71 2.17
999 1082 0.884704 TTCCTCTGCGTTTGTGCTCC 60.885 55.000 0.00 0.00 35.36 4.70
1048 1131 2.285707 TGGAGGTAGGAGTAGTCCAGT 58.714 52.381 19.00 1.41 46.80 4.00
1060 1143 2.649531 AGTCCAGTATCGGAGAGAGG 57.350 55.000 0.00 0.00 43.63 3.69
1186 1270 3.709633 AGTCCAGGCGCATGCAGA 61.710 61.111 18.18 6.73 45.35 4.26
1467 1556 7.039293 TCGTATTTCAGCTATGTATGTATGGGT 60.039 37.037 0.00 0.00 0.00 4.51
1479 1568 6.509656 TGTATGTATGGGTCGTTACAAGATC 58.490 40.000 0.00 0.00 32.46 2.75
1486 1575 3.196254 GGGTCGTTACAAGATCAACCCTA 59.804 47.826 0.00 0.00 41.37 3.53
1489 1578 5.126061 GGTCGTTACAAGATCAACCCTAGTA 59.874 44.000 0.00 0.00 0.00 1.82
1901 1990 0.882474 GCGGTATCTCGTAGCCATCT 59.118 55.000 0.00 0.00 0.00 2.90
1957 2046 8.960591 CCTCAATACAACACCTGAAAGATAAAT 58.039 33.333 0.00 0.00 34.07 1.40
2011 2100 8.986847 CATATGAACAAGATAAAGTAGCAGAGG 58.013 37.037 0.00 0.00 0.00 3.69
2220 2309 9.438228 AGACAATAAAAGGAAGAGTAAGCTAAC 57.562 33.333 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
203 205 1.072331 AGTCTCGGTGCACCTTTTGAT 59.928 47.619 32.28 11.99 0.00 2.57
393 395 3.933332 CCGGACTGGTCTTTTTCATAGAC 59.067 47.826 0.00 0.00 41.00 2.59
410 412 2.281276 GGACCCAACACACCGGAC 60.281 66.667 9.46 0.00 0.00 4.79
411 413 2.446994 AGGACCCAACACACCGGA 60.447 61.111 9.46 0.00 0.00 5.14
412 414 2.281484 CAGGACCCAACACACCGG 60.281 66.667 0.00 0.00 0.00 5.28
413 415 2.978010 GCAGGACCCAACACACCG 60.978 66.667 0.00 0.00 0.00 4.94
414 416 1.898574 CAGCAGGACCCAACACACC 60.899 63.158 0.00 0.00 0.00 4.16
452 461 1.589803 AACACCTTGTGGTCGCTAAC 58.410 50.000 0.00 0.00 46.60 2.34
483 500 0.776080 ACCAGGATTCACCACCCCTT 60.776 55.000 0.00 0.00 42.04 3.95
605 628 3.357079 CAGCAGGGACAACGGTGC 61.357 66.667 0.00 0.00 36.10 5.01
692 730 3.694072 TCTTGTGAAAGCAATAATCGGGG 59.306 43.478 0.00 0.00 0.00 5.73
694 732 6.092670 TCTCTTCTTGTGAAAGCAATAATCGG 59.907 38.462 0.00 0.00 0.00 4.18
701 739 5.185454 TCTTGTCTCTTCTTGTGAAAGCAA 58.815 37.500 0.00 0.00 0.00 3.91
702 740 4.769688 TCTTGTCTCTTCTTGTGAAAGCA 58.230 39.130 0.00 0.00 0.00 3.91
703 741 5.741388 TTCTTGTCTCTTCTTGTGAAAGC 57.259 39.130 0.00 0.00 0.00 3.51
727 769 3.690628 TCTCGTGTATTGTGACGATACCA 59.309 43.478 17.87 5.94 43.26 3.25
999 1082 1.100510 CATGGCTGGATCACCAACAG 58.899 55.000 5.56 0.00 46.32 3.16
1048 1131 2.028839 CGCTCTCTACCTCTCTCCGATA 60.029 54.545 0.00 0.00 0.00 2.92
1060 1143 3.949031 GTCCATGGACGCTCTCTAC 57.051 57.895 28.52 3.79 35.30 2.59
1171 1255 4.783621 GGTCTGCATGCGCCTGGA 62.784 66.667 14.09 10.81 37.32 3.86
1246 1330 4.309950 GGTGAGACGCCGGTTGGT 62.310 66.667 1.90 0.00 37.67 3.67
1264 1348 4.112341 GACCCGACGGTGGACGAG 62.112 72.222 13.94 0.00 44.88 4.18
1467 1556 6.839124 TTACTAGGGTTGATCTTGTAACGA 57.161 37.500 0.00 0.00 31.31 3.85
1486 1575 2.938956 AGCAGGCAACACTCTTTACT 57.061 45.000 0.00 0.00 41.41 2.24
1489 1578 3.423539 TCATAGCAGGCAACACTCTTT 57.576 42.857 0.00 0.00 41.41 2.52
1656 1745 3.020274 GTGCCAGAGTGTAGAGATCTCA 58.980 50.000 24.39 8.03 0.00 3.27
1688 1777 3.686241 TCACAATCGAGCAAATCAAGGAG 59.314 43.478 0.00 0.00 0.00 3.69
1901 1990 9.008965 GGGTTTATTTACGGTAAAAGGAAAGTA 57.991 33.333 16.49 1.36 0.00 2.24
2011 2100 5.368989 CAAATACCCATCCTCAGGTTAGAC 58.631 45.833 0.00 0.00 37.59 2.59
2220 2309 6.683974 AAGTTATATTGTGTTGCCTAGCAG 57.316 37.500 0.00 0.00 40.61 4.24
2310 2408 4.462834 GCTTGCTATCCTGGTTAAACCTTT 59.537 41.667 0.00 0.00 39.58 3.11


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

AutoCloner maintained by Alex Coulton.