Multiple sequence alignment - TraesCS3B01G067200

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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 TraesCS3B01G067200 chr3B 100.000 2235 0 0 1 2235 39877101 39874867 0 4128
1 TraesCS3B01G067200 chr3B 94.152 2240 103 10 1 2235 173945259 173943043 0 3386
2 TraesCS3B01G067200 chr3B 94.292 1892 94 5 344 2235 368845918 368847795 0 2883
3 TraesCS3B01G067200 chr6B 97.231 2239 56 4 1 2235 596601833 596604069 0 3786
4 TraesCS3B01G067200 chrUn 96.963 2239 62 4 1 2235 171008311 171006075 0 3753
5 TraesCS3B01G067200 chr7A 96.828 2238 64 4 1 2233 638507639 638509874 0 3733
6 TraesCS3B01G067200 chr7A 96.741 2240 65 6 1 2235 708245650 708243414 0 3725
7 TraesCS3B01G067200 chr1B 96.738 2238 67 6 1 2235 672541247 672539013 0 3723
8 TraesCS3B01G067200 chr5B 96.562 2240 71 3 1 2235 567280021 567277783 0 3705
9 TraesCS3B01G067200 chr2B 96.475 2241 72 3 1 2235 391225216 391227455 0 3694
10 TraesCS3B01G067200 chr7D 96.515 2238 69 3 1 2235 382089824 382087593 0 3692


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 TraesCS3B01G067200 chr3B 39874867 39877101 2234 True 4128 4128 100.000 1 2235 1 chr3B.!!$R1 2234
1 TraesCS3B01G067200 chr3B 173943043 173945259 2216 True 3386 3386 94.152 1 2235 1 chr3B.!!$R2 2234
2 TraesCS3B01G067200 chr3B 368845918 368847795 1877 False 2883 2883 94.292 344 2235 1 chr3B.!!$F1 1891
3 TraesCS3B01G067200 chr6B 596601833 596604069 2236 False 3786 3786 97.231 1 2235 1 chr6B.!!$F1 2234
4 TraesCS3B01G067200 chrUn 171006075 171008311 2236 True 3753 3753 96.963 1 2235 1 chrUn.!!$R1 2234
5 TraesCS3B01G067200 chr7A 638507639 638509874 2235 False 3733 3733 96.828 1 2233 1 chr7A.!!$F1 2232
6 TraesCS3B01G067200 chr7A 708243414 708245650 2236 True 3725 3725 96.741 1 2235 1 chr7A.!!$R1 2234
7 TraesCS3B01G067200 chr1B 672539013 672541247 2234 True 3723 3723 96.738 1 2235 1 chr1B.!!$R1 2234
8 TraesCS3B01G067200 chr5B 567277783 567280021 2238 True 3705 3705 96.562 1 2235 1 chr5B.!!$R1 2234
9 TraesCS3B01G067200 chr2B 391225216 391227455 2239 False 3694 3694 96.475 1 2235 1 chr2B.!!$F1 2234
10 TraesCS3B01G067200 chr7D 382087593 382089824 2231 True 3692 3692 96.515 1 2235 1 chr7D.!!$R1 2234

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
308 309 0.106318 AGGAGGAAGCCATGCATTCC 60.106 55.0 15.79 15.79 44.49 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 1890 1.072505 GACGAGGAACAAAGGGCCA 59.927 57.895 6.18 0.0 0.0 5.36 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
118 119 8.324659 AGCCGACGCTCTTCTTATAAAAGAAAT 61.325 37.037 2.53 2.22 44.17 2.17
159 160 3.082548 TGAATCTCGTCTTTCTCTCGGT 58.917 45.455 0.00 0.00 0.00 4.69
201 202 1.321074 GGGTCGATCAGAGGTTCGGT 61.321 60.000 0.00 0.00 36.97 4.69
267 268 3.633525 TGCCATAGCAGCAGGATTTTAAG 59.366 43.478 0.00 0.00 46.52 1.85
308 309 0.106318 AGGAGGAAGCCATGCATTCC 60.106 55.000 15.79 15.79 44.49 3.01
530 537 0.114954 TCAATTGGCTGGCTTCCCTT 59.885 50.000 5.42 0.00 0.00 3.95
600 607 1.134220 GCCCGATGGGTCTACATTCAA 60.134 52.381 3.40 0.00 46.51 2.69
616 623 1.234821 TCAACCCTGAATGTTGTCGC 58.765 50.000 0.00 0.00 42.82 5.19
758 767 1.700186 GACCCAGGAGTTCACTTTCCT 59.300 52.381 0.00 0.00 44.59 3.36
771 780 5.164620 TCACTTTCCTGTATGAGCATTCA 57.835 39.130 0.00 0.00 37.81 2.57
876 885 2.953821 CCGCGGTTCATTGCTGTT 59.046 55.556 19.50 0.00 0.00 3.16
965 974 2.478514 GGGTTTATTGCACAAAAAGGCG 59.521 45.455 0.00 0.00 0.00 5.52
1081 1091 1.003580 GAGCAGACCCCATTGAAGACA 59.996 52.381 0.00 0.00 0.00 3.41
1202 1212 3.449018 TCCTCTAGAAGTCATGGAAGTGC 59.551 47.826 0.00 0.00 0.00 4.40
1216 1226 2.933906 GGAAGTGCGGATAAATCGACAA 59.066 45.455 0.00 0.00 0.00 3.18
1272 1282 3.572642 TCCTAAATATGGACGGAGAGCA 58.427 45.455 0.00 0.00 0.00 4.26
1296 1306 0.034337 CGAGTTTTTCGGGGTCCTCA 59.966 55.000 0.00 0.00 45.54 3.86
1314 1324 4.081142 TCCTCAAGATCGCATTTTAGGTCA 60.081 41.667 0.00 0.00 0.00 4.02
1349 1359 1.276622 GAGTCTGTGGGCTTCCCTTA 58.723 55.000 3.27 0.00 45.70 2.69
1378 1388 4.054671 CAAGATGGCCTCTATCGTCTTTC 58.945 47.826 3.32 0.00 37.19 2.62
1399 1409 4.344865 GAGCCTCCCGTTTGCCCA 62.345 66.667 0.00 0.00 0.00 5.36
1591 1601 9.465199 CTACTCCTACTTTAAACTTAGAGTCCT 57.535 37.037 8.65 0.00 31.48 3.85
1774 1784 0.674581 CGTTTCCGGTAAAGGGGGAC 60.675 60.000 0.00 0.00 30.87 4.46
1812 1822 2.391724 GACCTTCGAAGTGCCCCACA 62.392 60.000 23.03 0.00 36.74 4.17
1880 1890 5.151454 AGAGGTAATTTCGATGATCTCCCT 58.849 41.667 0.00 0.00 0.00 4.20
2106 2117 6.588373 GCCAATCGCTTATAAAAAGAAACCAA 59.412 34.615 0.00 0.00 0.00 3.67
2149 2160 5.242838 TGGCCAATTCACTTCGAAAAACTAT 59.757 36.000 0.61 0.00 37.12 2.12
2152 2163 7.302524 GCCAATTCACTTCGAAAAACTATGTA 58.697 34.615 0.00 0.00 37.12 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 8.807118 AGATTCAGTAAGTAATTCAGTGAGTGA 58.193 33.333 0.00 0.00 0.00 3.41
159 160 1.944024 ACACGTCAAAAATTCTCGGCA 59.056 42.857 0.00 0.00 0.00 5.69
201 202 1.778383 AGGGTGGGGGAGAAGCAAA 60.778 57.895 0.00 0.00 0.00 3.68
308 309 3.092301 GGGGGTTTGGAGATTCTTTCAG 58.908 50.000 0.00 0.00 0.00 3.02
362 369 3.046374 ACCGGGCCTAGATTAGATGTTT 58.954 45.455 6.32 0.00 0.00 2.83
530 537 1.595993 GGCGACACCAGTCTGAGCTA 61.596 60.000 0.00 0.00 42.73 3.32
600 607 0.319083 TACGCGACAACATTCAGGGT 59.681 50.000 15.93 0.00 0.00 4.34
611 618 1.068748 GGAAGTGAAGAGTACGCGACA 60.069 52.381 15.93 0.00 0.00 4.35
616 623 0.458025 GCGGGGAAGTGAAGAGTACG 60.458 60.000 0.00 0.00 0.00 3.67
771 780 9.869667 ACTCTTCCACTGACTTATATATGTACT 57.130 33.333 1.48 0.00 0.00 2.73
846 855 2.106332 CGCGGCGAACCCTCTAAT 59.894 61.111 19.16 0.00 0.00 1.73
876 885 3.752359 AGGGTAGCCTAGTGTGTAAGA 57.248 47.619 12.99 0.00 0.00 2.10
995 1004 2.476854 GGCTTTGCATCTGACATTCGTC 60.477 50.000 0.00 0.00 42.93 4.20
1059 1068 1.988107 TCTTCAATGGGGTCTGCTCTT 59.012 47.619 0.00 0.00 0.00 2.85
1081 1091 1.348036 GCCTTGTTGTACCTCACTCCT 59.652 52.381 0.00 0.00 0.00 3.69
1202 1212 8.905103 ATAAAAACCTTTTGTCGATTTATCCG 57.095 30.769 0.00 0.00 0.00 4.18
1240 1250 4.917040 TCCATATTTAGGATGGTTAGGGCA 59.083 41.667 1.78 0.00 43.79 5.36
1296 1306 6.640518 TCTACTTGACCTAAAATGCGATCTT 58.359 36.000 0.00 0.00 0.00 2.40
1314 1324 2.506644 AGACTCCCTAGCGTCTCTACTT 59.493 50.000 2.78 0.00 35.72 2.24
1349 1359 2.822707 AGAGGCCATCTTGAAATGCT 57.177 45.000 5.01 0.00 32.99 3.79
1378 1388 2.125512 CAAACGGGAGGCTCTCGG 60.126 66.667 37.08 20.92 46.41 4.63
1399 1409 2.292389 TGGATGTCAAATGCCCCTTGAT 60.292 45.455 0.00 0.00 35.36 2.57
1481 1491 1.194772 CTCCTTTTGAGACCGCGAAAC 59.805 52.381 8.23 0.00 44.42 2.78
1537 1547 1.478916 AGAGGCTCGCTTAGAAGGAAC 59.521 52.381 9.22 0.00 0.00 3.62
1591 1601 8.704849 TTGTCTTTGGAAGAATTGGAAGAATA 57.295 30.769 0.00 0.00 39.67 1.75
1812 1822 2.124693 CACAACGCCAACCCTGGTT 61.125 57.895 0.00 0.00 45.53 3.67
1852 1862 5.777732 AGATCATCGAAATTACCTCTAGCCT 59.222 40.000 0.00 0.00 0.00 4.58
1880 1890 1.072505 GACGAGGAACAAAGGGCCA 59.927 57.895 6.18 0.00 0.00 5.36
1958 1969 5.191124 AGAATTCCATTCGGTACCTTTAGGT 59.809 40.000 10.90 6.67 46.46 3.08
1961 1972 7.427989 AGTAGAATTCCATTCGGTACCTTTA 57.572 36.000 10.90 0.00 43.92 1.85
2068 2079 2.917971 GCGATTGGCGTCACTATAGATC 59.082 50.000 6.78 0.00 43.41 2.75
2149 2160 7.284489 ACCAATTTTTCTGCTCAAGTTAGTACA 59.716 33.333 0.00 0.00 0.00 2.90
2152 2163 6.461509 CCACCAATTTTTCTGCTCAAGTTAGT 60.462 38.462 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.