Multiple sequence alignment - TraesCS4B01G158800

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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 TraesCS4B01G158800 chr4B 100.000 2160 0 0 1 2160 308676547 308678706 0.000000e+00 3989
1 TraesCS4B01G158800 chr2D 96.764 2163 63 7 1 2160 638427724 638425566 0.000000e+00 3600
2 TraesCS4B01G158800 chr2D 96.623 1155 35 4 1 1151 628293606 628294760 0.000000e+00 1914
3 TraesCS4B01G158800 chr1D 96.212 2165 74 8 1 2160 254438255 254436094 0.000000e+00 3537
4 TraesCS4B01G158800 chr1D 95.520 2165 89 8 1 2160 51868723 51870884 0.000000e+00 3454
5 TraesCS4B01G158800 chr5D 96.076 2166 76 9 1 2160 503295094 503292932 0.000000e+00 3520
6 TraesCS4B01G158800 chr5D 95.425 2164 74 10 1 2160 6173713 6175855 0.000000e+00 3424
7 TraesCS4B01G158800 chr4A 93.848 2162 110 6 1 2160 309486601 309488741 0.000000e+00 3234
8 TraesCS4B01G158800 chrUn 96.755 1664 49 5 105 1765 381152045 381153706 0.000000e+00 2769
9 TraesCS4B01G158800 chr4D 93.829 1669 89 9 500 2160 207065510 207067172 0.000000e+00 2499
10 TraesCS4B01G158800 chr1B 96.781 1491 44 4 672 2160 633710241 633708753 0.000000e+00 2484
11 TraesCS4B01G158800 chr5B 96.166 626 20 3 1 624 410386240 410385617 0.000000e+00 1020
12 TraesCS4B01G158800 chr7B 95.556 360 14 2 1047 1405 590980814 590981172 1.860000e-160 575


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 TraesCS4B01G158800 chr4B 308676547 308678706 2159 False 3989 3989 100.000 1 2160 1 chr4B.!!$F1 2159
1 TraesCS4B01G158800 chr2D 638425566 638427724 2158 True 3600 3600 96.764 1 2160 1 chr2D.!!$R1 2159
2 TraesCS4B01G158800 chr2D 628293606 628294760 1154 False 1914 1914 96.623 1 1151 1 chr2D.!!$F1 1150
3 TraesCS4B01G158800 chr1D 254436094 254438255 2161 True 3537 3537 96.212 1 2160 1 chr1D.!!$R1 2159
4 TraesCS4B01G158800 chr1D 51868723 51870884 2161 False 3454 3454 95.520 1 2160 1 chr1D.!!$F1 2159
5 TraesCS4B01G158800 chr5D 503292932 503295094 2162 True 3520 3520 96.076 1 2160 1 chr5D.!!$R1 2159
6 TraesCS4B01G158800 chr5D 6173713 6175855 2142 False 3424 3424 95.425 1 2160 1 chr5D.!!$F1 2159
7 TraesCS4B01G158800 chr4A 309486601 309488741 2140 False 3234 3234 93.848 1 2160 1 chr4A.!!$F1 2159
8 TraesCS4B01G158800 chrUn 381152045 381153706 1661 False 2769 2769 96.755 105 1765 1 chrUn.!!$F1 1660
9 TraesCS4B01G158800 chr4D 207065510 207067172 1662 False 2499 2499 93.829 500 2160 1 chr4D.!!$F1 1660
10 TraesCS4B01G158800 chr1B 633708753 633710241 1488 True 2484 2484 96.781 672 2160 1 chr1B.!!$R1 1488
11 TraesCS4B01G158800 chr5B 410385617 410386240 623 True 1020 1020 96.166 1 624 1 chr5B.!!$R1 623

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
159 161 0.669077 AGTAAAGGCGAGCGATCGAT 59.331 50.0 29.29 14.21 34.64 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1686 0.105862 AGATACGGGTCCGATTCCCA 60.106 55.0 16.9 0.0 44.81 4.37 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
159 161 0.669077 AGTAAAGGCGAGCGATCGAT 59.331 50.000 29.29 14.21 34.64 3.59
162 165 2.440539 AAAGGCGAGCGATCGATTAT 57.559 45.000 29.29 6.65 34.64 1.28
178 181 3.667261 CGATTATAAGTACCAACGGCTCG 59.333 47.826 0.00 0.00 0.00 5.03
480 484 5.116180 TGGCGATTTGTATCCAAAGACTAG 58.884 41.667 0.00 0.00 43.45 2.57
741 755 4.965532 TGGAAACCCAATTCTTTTCCTCAA 59.034 37.500 17.13 2.10 45.84 3.02
776 790 7.611213 ATGAAATTAGGGAACGAAGTAAGTG 57.389 36.000 0.00 0.00 45.00 3.16
785 799 5.984323 GGGAACGAAGTAAGTGGATTAGATC 59.016 44.000 0.00 0.00 45.00 2.75
973 987 7.416022 ACGTTAAAAATAATCAACCAACGTCA 58.584 30.769 3.59 0.00 45.12 4.35
1001 1015 1.143889 GCCCTAGCCTTCCAAGCTAAT 59.856 52.381 0.00 0.00 42.07 1.73
1004 1018 3.471680 CCTAGCCTTCCAAGCTAATGAC 58.528 50.000 0.00 0.00 42.07 3.06
1161 1191 1.479709 AGCTCACGAGGCTCATAACT 58.520 50.000 15.95 1.79 34.70 2.24
1248 1278 6.417503 TTCTCTATATATGGTAGAGGGGCA 57.582 41.667 19.03 5.29 43.38 5.36
1261 1291 3.946242 GGGGCATATCCAACCCTTT 57.054 52.632 0.00 0.00 43.68 3.11
1308 1338 5.743636 AGAGGGCAAAATTGAGCAATTTA 57.256 34.783 18.37 0.00 46.76 1.40
1389 1419 8.950208 AAATAAAAATGAAACGAAAGGGACAA 57.050 26.923 0.00 0.00 0.00 3.18
1527 1560 0.251742 TGGGATGCAAAGGAAGGGTG 60.252 55.000 0.00 0.00 0.00 4.61
1652 1686 3.675619 AATTAAGCGGGCGAGCGGT 62.676 57.895 0.00 0.00 43.00 5.68
1733 1767 8.066595 CGCTCGCTACGGTATATATTTTATAGT 58.933 37.037 0.00 0.00 0.00 2.12
1876 1912 9.994432 ATTTCATAATACTGAAAGAGAAAAGCG 57.006 29.630 5.60 0.00 45.50 4.68
2056 2093 6.910191 AGTCCAATCCATAATGATGTACCAA 58.090 36.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 161 2.760092 ACCGAGCCGTTGGTACTTATAA 59.240 45.455 0.00 0.00 38.91 0.98
162 165 0.244450 CACCGAGCCGTTGGTACTTA 59.756 55.000 0.00 0.00 38.59 2.24
178 181 2.859165 TGGAGAAGGTTCATGACACC 57.141 50.000 15.33 15.33 34.06 4.16
501 506 6.199342 GCGACTCTGTACTCTTAATCCAATTC 59.801 42.308 0.00 0.00 0.00 2.17
512 517 0.448593 GCTTCGCGACTCTGTACTCT 59.551 55.000 9.15 0.00 0.00 3.24
571 577 8.553085 TCTTCATCCATAGATCCTTTACTCAA 57.447 34.615 0.00 0.00 0.00 3.02
687 701 9.216117 GCTAAAACAATATACGGATGGTTCTAT 57.784 33.333 0.00 0.00 0.00 1.98
700 714 6.316890 GGTTTCCACCGAGCTAAAACAATATA 59.683 38.462 0.00 0.00 31.60 0.86
741 755 7.497249 CGTTCCCTAATTTCATTCAAGAGATCT 59.503 37.037 0.00 0.00 0.00 2.75
836 850 2.426522 TGAATGGAACCAAAGCTCTCG 58.573 47.619 0.00 0.00 0.00 4.04
907 921 9.225201 CGAACATGATATTTTGATTTCATTCGT 57.775 29.630 0.00 0.00 31.22 3.85
924 938 7.413000 CGTCTCTAATTCAAAACCGAACATGAT 60.413 37.037 0.00 0.00 0.00 2.45
981 995 0.546598 TTAGCTTGGAAGGCTAGGGC 59.453 55.000 0.00 0.00 42.22 5.19
1001 1015 2.125832 GGAATCGAACCCGCGTCA 60.126 61.111 4.92 0.00 35.37 4.35
1161 1191 0.682852 ATCGAACCCGTGACCTCAAA 59.317 50.000 0.00 0.00 37.05 2.69
1232 1262 5.497285 TGGATATGCCCCTCTACCATATA 57.503 43.478 0.00 0.00 33.57 0.86
1261 1291 3.634910 GGCCGGGAGCTAATGAATAAAAA 59.365 43.478 2.18 0.00 43.05 1.94
1332 1362 2.360475 AGAAGCCTTGCGCCTTCC 60.360 61.111 17.15 0.00 38.78 3.46
1389 1419 3.805360 AAAGGGAAGGGAGAGGTAGAT 57.195 47.619 0.00 0.00 0.00 1.98
1468 1499 2.168521 CCGGAGGCAGAAATAGAACTCA 59.831 50.000 0.00 0.00 46.14 3.41
1507 1540 0.712380 ACCCTTCCTTTGCATCCCAT 59.288 50.000 0.00 0.00 0.00 4.00
1527 1560 4.080687 AGTGCCGTATCCCTTACTATCTC 58.919 47.826 0.00 0.00 0.00 2.75
1652 1686 0.105862 AGATACGGGTCCGATTCCCA 60.106 55.000 16.90 0.00 44.81 4.37
1661 1695 1.202545 GCCAAGGAGAAGATACGGGTC 60.203 57.143 0.00 0.00 0.00 4.46
1733 1767 0.178984 TCGACCCAGGCGGATATACA 60.179 55.000 0.00 0.00 34.64 2.29
1872 1908 1.787847 CGTTCCGAATTGCTCGCTT 59.212 52.632 0.00 0.00 46.71 4.68
1876 1912 2.262572 ATTTGCGTTCCGAATTGCTC 57.737 45.000 9.04 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.