Multiple sequence alignment - TraesCS5D01G215000

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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 TraesCS5D01G215000 chr5D 100.000 2303 0 0 1 2303 324421371 324423673 0 4253
1 TraesCS5D01G215000 chrUn 97.577 2311 45 8 1 2303 86508844 86506537 0 3947
2 TraesCS5D01G215000 chr6B 97.362 2312 49 8 1 2303 596621491 596623799 0 3921
3 TraesCS5D01G215000 chr6A 97.401 2309 47 9 1 2303 608882068 608879767 0 3919
4 TraesCS5D01G215000 chr6A 97.145 2312 54 9 1 2303 84435312 84437620 0 3893
5 TraesCS5D01G215000 chr2B 97.186 2310 52 9 1 2303 30669445 30667142 0 3893
6 TraesCS5D01G215000 chr3B 97.143 2310 55 9 1 2303 92319005 92321310 0 3890
7 TraesCS5D01G215000 chr4D 97.143 2310 51 8 1 2303 123424882 123427183 0 3886
8 TraesCS5D01G215000 chr4A 96.975 2314 56 9 1 2303 67575517 67573207 0 3873


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 TraesCS5D01G215000 chr5D 324421371 324423673 2302 False 4253 4253 100.000 1 2303 1 chr5D.!!$F1 2302
1 TraesCS5D01G215000 chrUn 86506537 86508844 2307 True 3947 3947 97.577 1 2303 1 chrUn.!!$R1 2302
2 TraesCS5D01G215000 chr6B 596621491 596623799 2308 False 3921 3921 97.362 1 2303 1 chr6B.!!$F1 2302
3 TraesCS5D01G215000 chr6A 608879767 608882068 2301 True 3919 3919 97.401 1 2303 1 chr6A.!!$R1 2302
4 TraesCS5D01G215000 chr6A 84435312 84437620 2308 False 3893 3893 97.145 1 2303 1 chr6A.!!$F1 2302
5 TraesCS5D01G215000 chr2B 30667142 30669445 2303 True 3893 3893 97.186 1 2303 1 chr2B.!!$R1 2302
6 TraesCS5D01G215000 chr3B 92319005 92321310 2305 False 3890 3890 97.143 1 2303 1 chr3B.!!$F1 2302
7 TraesCS5D01G215000 chr4D 123424882 123427183 2301 False 3886 3886 97.143 1 2303 1 chr4D.!!$F1 2302
8 TraesCS5D01G215000 chr4A 67573207 67575517 2310 True 3873 3873 96.975 1 2303 1 chr4A.!!$R1 2302

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
543 551 0.320421 TACAGTCAAAGTCAGCGGCC 60.32 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1580 1606 0.833287 CACCTCAGGGATTCGTGGAT 59.167 55.0 0.0 0.0 36.25 3.41 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
108 109 7.724305 TCGCTAGGTGTTTATGGAATAATTC 57.276 36.000 0.00 0.00 38.83 2.17
278 282 4.934797 TCTTTCATTCATCAAGGGGTCT 57.065 40.909 0.00 0.00 0.00 3.85
290 294 1.518367 AGGGGTCTGTCACTTTTCCA 58.482 50.000 0.00 0.00 0.00 3.53
387 391 4.193826 TGTCAAGCTGGTCTCACTATTC 57.806 45.455 0.00 0.00 0.00 1.75
462 470 1.288335 AGGACCTGACGGTTCTCCTAT 59.712 52.381 0.00 0.00 46.82 2.57
543 551 0.320421 TACAGTCAAAGTCAGCGGCC 60.320 55.000 0.00 0.00 0.00 6.13
619 627 3.322541 GGCTTAGGGATAAGAGAGTGTCC 59.677 52.174 0.00 0.00 0.00 4.02
620 628 3.961408 GCTTAGGGATAAGAGAGTGTCCA 59.039 47.826 0.00 0.00 32.31 4.02
621 629 4.202172 GCTTAGGGATAAGAGAGTGTCCAC 60.202 50.000 0.00 0.00 32.31 4.02
624 632 1.476891 GGATAAGAGAGTGTCCACGCA 59.523 52.381 4.04 0.00 36.20 5.24
672 680 3.181479 ACACAAAGTCACTTAGCTCGACA 60.181 43.478 0.00 0.00 31.92 4.35
716 725 6.635021 AGGAATACCCTACATAGAGAACCAT 58.365 40.000 0.00 0.00 45.48 3.55
763 772 4.733725 TCCCCGGGGCTAAGCTGT 62.734 66.667 36.68 0.00 34.68 4.40
842 851 2.146342 AGCCTTTGTCATTGTCAGTCG 58.854 47.619 0.00 0.00 0.00 4.18
890 900 5.461526 CGAATCCGTAAATCAGAGAGCATA 58.538 41.667 0.00 0.00 0.00 3.14
1416 1440 1.567649 ACCCAGCCAGATGATGATGTT 59.432 47.619 0.00 0.00 0.00 2.71
1580 1606 4.201724 CCAACGCAATTCAAAAACGGAAAA 60.202 37.500 0.00 0.00 0.00 2.29
1607 1633 3.134804 CGAATCCCTGAGGTGGATAAGTT 59.865 47.826 0.00 0.00 41.80 2.66
1706 1732 1.056660 AGGTTCGAAGAAGGAAGGCA 58.943 50.000 0.00 0.00 45.90 4.75
1742 1768 0.106149 CACCCATAGCCGGTCTAACC 59.894 60.000 1.90 0.00 34.05 2.85
1743 1769 0.325860 ACCCATAGCCGGTCTAACCA 60.326 55.000 1.90 0.00 38.47 3.67
1744 1770 0.834612 CCCATAGCCGGTCTAACCAA 59.165 55.000 1.90 0.00 38.47 3.67
1909 1935 3.627577 GCTCTGTCAAGGAAGTGAAACAA 59.372 43.478 0.00 0.00 41.43 2.83
2083 2109 2.203938 TTGCCTCCTCCTTCCCGT 60.204 61.111 0.00 0.00 0.00 5.28
2208 2234 7.255977 CCTTGATGAGTAAGCTTAGCTATACCA 60.256 40.741 7.32 11.82 38.25 3.25
2244 2270 1.283029 AGCAAGCTCCCTTCTAATGCA 59.717 47.619 4.25 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 4.201930 CGTCTTACTAGACCAACCTGCTAG 60.202 50.000 0.00 0.00 46.63 3.42
150 152 6.049955 CCAATTGGTCCGTATATCATAGGT 57.950 41.667 16.90 0.00 0.00 3.08
278 282 1.228124 CCGGCCTGGAAAAGTGACA 60.228 57.895 7.77 0.00 42.00 3.58
290 294 2.042843 ACTTCTCGATCCCGGCCT 60.043 61.111 0.00 0.00 36.24 5.19
457 465 8.054572 TCATGTTCTTTCATCCATCAAATAGGA 58.945 33.333 0.00 0.00 38.50 2.94
462 470 7.764141 TTCTCATGTTCTTTCATCCATCAAA 57.236 32.000 0.00 0.00 0.00 2.69
543 551 4.094684 CGAGGCTAGGCAAACTCG 57.905 61.111 19.70 14.60 45.34 4.18
574 582 1.063649 CGCTAACTCGCTCGCCTAA 59.936 57.895 0.00 0.00 0.00 2.69
633 641 8.458212 ACTTTGTGTAGCGTAGTAGAATTAAC 57.542 34.615 0.00 0.00 0.00 2.01
636 644 6.585322 GTGACTTTGTGTAGCGTAGTAGAATT 59.415 38.462 0.00 0.00 0.00 2.17
763 772 7.820386 TCTTAATTAACTATCAGTGGTGCGAAA 59.180 33.333 0.00 0.00 0.00 3.46
817 826 1.266718 GACAATGACAAAGGCTTGCGA 59.733 47.619 0.00 0.00 35.84 5.10
974 988 2.632028 CTCATCCCGATCACAAGGAGAT 59.368 50.000 0.00 0.00 31.94 2.75
1022 1046 1.413077 AGGAAACTCCGATTCGATCCC 59.587 52.381 7.83 0.33 42.75 3.85
1061 1085 6.775594 AGCACAAAAGTTTAAGGAGAACTT 57.224 33.333 0.00 0.00 46.27 2.66
1078 1102 2.159114 GCTTCTTTTCCACCAAGCACAA 60.159 45.455 0.00 0.00 40.86 3.33
1271 1295 1.668793 TCACGCCTAGACGACGACA 60.669 57.895 5.13 0.00 36.70 4.35
1416 1440 1.347707 CCTCTCACTACCAACCAGCAA 59.652 52.381 0.00 0.00 0.00 3.91
1580 1606 0.833287 CACCTCAGGGATTCGTGGAT 59.167 55.000 0.00 0.00 36.25 3.41
1607 1633 2.261586 ACTGCTGCTGAGTCGTCGA 61.262 57.895 13.69 0.00 0.00 4.20
1706 1732 4.113085 TGGGTGGGTTGGTTATATACTGT 58.887 43.478 0.00 0.00 0.00 3.55
1909 1935 3.200165 GGTAACCTCAACCTAGGAATGCT 59.800 47.826 17.98 0.00 39.15 3.79
2083 2109 4.398319 GAGGAAAAGAATGAAGGTGTGGA 58.602 43.478 0.00 0.00 0.00 4.02
2208 2234 1.691196 TGCTGCTTTGCAACCTAAGT 58.309 45.000 0.00 0.00 40.29 2.24
2244 2270 3.209410 CGAGAAGGCTCCAAGCAATAAT 58.791 45.455 0.86 0.00 44.75 1.28


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

AutoCloner maintained by Alex Coulton.