Multiple sequence alignment - TraesCS5B01G031100

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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 TraesCS5B01G031100 chr5B 100.000 2255 0 0 1 2255 34148218 34145964 0 4165
1 TraesCS5B01G031100 chr1D 97.115 2253 64 1 3 2255 141314949 141312698 0 3799
2 TraesCS5B01G031100 chr7B 97.028 2254 66 1 3 2255 644465629 644467882 0 3790
3 TraesCS5B01G031100 chr3A 96.937 2253 69 0 3 2255 633109440 633111692 0 3779
4 TraesCS5B01G031100 chr7A 96.804 2253 72 0 3 2255 60150101 60147849 0 3762
5 TraesCS5B01G031100 chr7A 96.186 2255 85 1 1 2255 46399062 46396809 0 3687
6 TraesCS5B01G031100 chr1B 96.673 2254 73 2 3 2255 638702480 638700228 0 3746
7 TraesCS5B01G031100 chr1B 96.671 2253 75 0 3 2255 672477347 672479599 0 3746
8 TraesCS5B01G031100 chr4B 96.627 2253 75 1 3 2255 209079331 209077080 0 3738
9 TraesCS5B01G031100 chr6B 96.582 2253 77 0 3 2255 306997804 306995552 0 3735


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 TraesCS5B01G031100 chr5B 34145964 34148218 2254 True 4165 4165 100.000 1 2255 1 chr5B.!!$R1 2254
1 TraesCS5B01G031100 chr1D 141312698 141314949 2251 True 3799 3799 97.115 3 2255 1 chr1D.!!$R1 2252
2 TraesCS5B01G031100 chr7B 644465629 644467882 2253 False 3790 3790 97.028 3 2255 1 chr7B.!!$F1 2252
3 TraesCS5B01G031100 chr3A 633109440 633111692 2252 False 3779 3779 96.937 3 2255 1 chr3A.!!$F1 2252
4 TraesCS5B01G031100 chr7A 60147849 60150101 2252 True 3762 3762 96.804 3 2255 1 chr7A.!!$R2 2252
5 TraesCS5B01G031100 chr7A 46396809 46399062 2253 True 3687 3687 96.186 1 2255 1 chr7A.!!$R1 2254
6 TraesCS5B01G031100 chr1B 638700228 638702480 2252 True 3746 3746 96.673 3 2255 1 chr1B.!!$R1 2252
7 TraesCS5B01G031100 chr1B 672477347 672479599 2252 False 3746 3746 96.671 3 2255 1 chr1B.!!$F1 2252
8 TraesCS5B01G031100 chr4B 209077080 209079331 2251 True 3738 3738 96.627 3 2255 1 chr4B.!!$R1 2252
9 TraesCS5B01G031100 chr6B 306995552 306997804 2252 True 3735 3735 96.582 3 2255 1 chr6B.!!$R1 2252

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
923 925 0.187117 TTTCATTGCTGTGGGTCCCA 59.813 50.0 6.47 6.47 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2228 1.198094 TTTGATCCGTCTGAGGGCCA 61.198 55.0 6.18 8.93 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
23 24 2.362397 AGAACTTCTCTGTCGCAACTCA 59.638 45.455 0.00 0.00 31.12 3.41
135 136 1.537202 CTTGTTTCAGCCCTTCCTTCG 59.463 52.381 0.00 0.00 0.00 3.79
157 158 4.922103 CGTCTGAACCTTCCAAGTACTAAC 59.078 45.833 0.00 0.00 0.00 2.34
234 235 7.037438 TGTAAAAAGTAGTTGAGTCGTGTCTT 58.963 34.615 0.00 0.00 0.00 3.01
385 386 6.351286 GGAATGGCTTTTTCATGTACCAGATT 60.351 38.462 0.00 0.00 0.00 2.40
454 455 4.338879 AGGAGCAGTTATTTGCAATGACT 58.661 39.130 0.00 1.84 46.47 3.41
456 457 4.082571 GGAGCAGTTATTTGCAATGACTGT 60.083 41.667 25.32 17.46 46.47 3.55
471 472 2.972021 TGACTGTTGGATTGGTCAGAGA 59.028 45.455 0.00 0.00 34.38 3.10
691 692 7.436933 AGCAATTTAAGTAGAAAGCTTGCTTT 58.563 30.769 13.52 18.93 39.72 3.51
701 702 1.831580 AGCTTGCTTTGGGATCAGAC 58.168 50.000 0.00 0.00 0.00 3.51
717 718 6.349300 GGATCAGACCATTCAACTAAAGCTA 58.651 40.000 0.00 0.00 0.00 3.32
923 925 0.187117 TTTCATTGCTGTGGGTCCCA 59.813 50.000 6.47 6.47 0.00 4.37
924 926 0.251297 TTCATTGCTGTGGGTCCCAG 60.251 55.000 12.21 0.98 32.34 4.45
994 996 1.977854 ACTCTGTGGTGCTGGTTATCA 59.022 47.619 0.00 0.00 0.00 2.15
1005 1007 4.157656 GTGCTGGTTATCAAGTTTATGGCA 59.842 41.667 0.00 0.00 0.00 4.92
1006 1008 4.955450 TGCTGGTTATCAAGTTTATGGCAT 59.045 37.500 4.88 4.88 0.00 4.40
1009 1011 5.189928 TGGTTATCAAGTTTATGGCATCGT 58.810 37.500 1.65 0.00 0.00 3.73
1010 1012 5.650266 TGGTTATCAAGTTTATGGCATCGTT 59.350 36.000 1.65 0.00 0.00 3.85
1075 1077 4.902443 TGCTCTCTTCTAATAGTGGTCG 57.098 45.455 0.00 0.00 0.00 4.79
1176 1178 6.834168 AAAAGCCGAAAGATAAGGATTTCA 57.166 33.333 0.00 0.00 42.02 2.69
1230 1232 4.658435 AGAAAACCTTACCATTTTTGGGCT 59.342 37.500 0.00 0.00 0.00 5.19
1566 1568 9.942850 TTCTTGAGATTCAAAGAAAAAGGTTTT 57.057 25.926 10.46 0.00 35.73 2.43
1597 1599 4.871822 TCTCTGGGATCAGTGATAGTTCA 58.128 43.478 5.38 1.81 41.59 3.18
1635 1637 4.907879 GCTGAAAAGCCATAGTGCTAAT 57.092 40.909 0.00 0.00 41.80 1.73
1669 1671 8.276252 TGTAGTTTTGAAGCTAAAAAGACAGT 57.724 30.769 7.33 0.00 31.92 3.55
1673 1675 6.935741 TTTGAAGCTAAAAAGACAGTAGCA 57.064 33.333 4.86 0.00 42.22 3.49
1872 1874 0.767446 TTCACCCGGGTCCAAACCTA 60.767 55.000 27.51 0.00 45.66 3.08
1875 1877 0.116940 ACCCGGGTCCAAACCTACTA 59.883 55.000 24.16 0.00 45.66 1.82
1953 1955 1.456287 GCCTCCTCTTGGTTGGTGT 59.544 57.895 0.00 0.00 33.23 4.16
2061 2064 1.463553 AAAACAGGCTTTGCTCCCCG 61.464 55.000 0.00 0.00 0.00 5.73
2225 2228 4.021925 GGGTCGAGGCTGCCACTT 62.022 66.667 22.65 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.736951 AGATAGATAGGTCCATGAGTTGC 57.263 43.478 0.00 0.00 0.00 4.17
51 52 5.010719 CGTGAGAATAGCAAACCCCTATCTA 59.989 44.000 0.00 0.00 0.00 1.98
135 136 5.011840 AGGTTAGTACTTGGAAGGTTCAGAC 59.988 44.000 0.00 0.00 0.00 3.51
345 346 3.578688 CCATTCCTTTTCGCTTTCCTTG 58.421 45.455 0.00 0.00 0.00 3.61
385 386 0.247460 CTTGATGTCTGGCTCACCGA 59.753 55.000 0.00 0.00 39.70 4.69
454 455 2.040145 TGCATCTCTGACCAATCCAACA 59.960 45.455 0.00 0.00 0.00 3.33
456 457 3.349927 CTTGCATCTCTGACCAATCCAA 58.650 45.455 0.00 0.00 0.00 3.53
471 472 1.270907 AACCGAGTCTCTCCTTGCAT 58.729 50.000 0.00 0.00 0.00 3.96
614 615 8.162878 ACCTATCTTGATGCTTTGAATATGTG 57.837 34.615 0.00 0.00 0.00 3.21
618 619 8.150945 GGACTACCTATCTTGATGCTTTGAATA 58.849 37.037 0.00 0.00 0.00 1.75
691 692 5.500234 CTTTAGTTGAATGGTCTGATCCCA 58.500 41.667 0.00 0.00 36.16 4.37
701 702 5.008415 CAGCCTGATAGCTTTAGTTGAATGG 59.992 44.000 0.00 0.00 42.61 3.16
717 718 0.257039 CAAAGCCTACCCAGCCTGAT 59.743 55.000 0.00 0.00 0.00 2.90
923 925 4.207891 ACAATCTTATTCGAGCACACCT 57.792 40.909 0.00 0.00 0.00 4.00
924 926 4.946784 AACAATCTTATTCGAGCACACC 57.053 40.909 0.00 0.00 0.00 4.16
978 980 2.949177 ACTTGATAACCAGCACCACA 57.051 45.000 0.00 0.00 0.00 4.17
980 982 4.704540 CCATAAACTTGATAACCAGCACCA 59.295 41.667 0.00 0.00 0.00 4.17
994 996 3.417101 TGGTCAACGATGCCATAAACTT 58.583 40.909 5.05 0.00 30.85 2.66
1005 1007 4.141287 TGACTTTTTGGATGGTCAACGAT 58.859 39.130 0.00 0.00 36.04 3.73
1006 1008 3.546724 TGACTTTTTGGATGGTCAACGA 58.453 40.909 0.00 0.00 36.04 3.85
1009 1011 6.462768 CCATCTTTGACTTTTTGGATGGTCAA 60.463 38.462 10.53 0.00 43.81 3.18
1010 1012 5.010922 CCATCTTTGACTTTTTGGATGGTCA 59.989 40.000 10.53 0.00 42.80 4.02
1075 1077 6.152831 AGGATTTTACAACCTGAATACCAAGC 59.847 38.462 0.00 0.00 32.39 4.01
1176 1178 5.699001 AGAAAAAGGAACGCAAAAGTTTTGT 59.301 32.000 25.20 9.50 34.00 2.83
1277 1279 6.977282 TCACCAGATGAGGAAATGGAAACAAT 60.977 38.462 0.00 0.00 36.94 2.71
1392 1394 5.684704 ACCATGGACATAAACAAGATCGAT 58.315 37.500 21.47 0.00 0.00 3.59
1397 1399 6.705825 CGATGATACCATGGACATAAACAAGA 59.294 38.462 21.47 0.00 32.09 3.02
1400 1402 5.924356 ACGATGATACCATGGACATAAACA 58.076 37.500 21.47 8.65 33.43 2.83
1597 1599 1.075659 GCCTCCCTTTGCTGGTTCT 59.924 57.895 0.00 0.00 0.00 3.01
1635 1637 2.284754 TCAAAACTACAGGGCATGCA 57.715 45.000 21.36 0.00 0.00 3.96
1639 1641 2.656947 AGCTTCAAAACTACAGGGCA 57.343 45.000 0.00 0.00 0.00 5.36
1704 1706 2.721425 AGGAAGAGTAGCTCGCTAGT 57.279 50.000 5.99 5.99 35.36 2.57
1711 1713 3.954904 TCGCTCATAAAGGAAGAGTAGCT 59.045 43.478 0.00 0.00 0.00 3.32
1767 1769 2.024319 GCTTGCTCAGTTCGCTCGT 61.024 57.895 0.00 0.00 0.00 4.18
1872 1874 8.880750 CGTAAAGGAAAAATTAGCTAGCTTAGT 58.119 33.333 24.88 10.75 0.00 2.24
1875 1877 7.822822 TCTCGTAAAGGAAAAATTAGCTAGCTT 59.177 33.333 24.88 2.63 0.00 3.74
1915 1917 1.813092 CGGGGCTCTCTCCAATCATTG 60.813 57.143 0.00 0.00 0.00 2.82
1953 1955 3.147595 CATCACTCTCGGGCCCGA 61.148 66.667 42.62 42.62 46.87 5.14
2014 2016 5.471424 TCCCTCAATTGATAGATCAGGACT 58.529 41.667 8.96 0.00 38.19 3.85
2016 2018 4.285517 GCTCCCTCAATTGATAGATCAGGA 59.714 45.833 8.96 6.14 38.19 3.86
2225 2228 1.198094 TTTGATCCGTCTGAGGGCCA 61.198 55.000 6.18 8.93 0.00 5.36


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

AutoCloner maintained by Alex Coulton.