Multiple sequence alignment - TraesCS5D01G214900

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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 TraesCS5D01G214900 chr5D 100.000 2487 0 0 1 2487 324420203 324422689 0 4593
1 TraesCS5D01G214900 chr6B 97.157 2497 57 8 1 2487 596620321 596622813 0 4205
2 TraesCS5D01G214900 chrUn 97.115 2496 60 7 1 2487 282364699 282362207 0 4200
3 TraesCS5D01G214900 chrUn 97.075 2496 61 7 1 2487 86510015 86507523 0 4194
4 TraesCS5D01G214900 chr6A 96.876 2497 67 7 1 2487 84434141 84436636 0 4169
5 TraesCS5D01G214900 chr3B 96.874 2495 65 9 1 2487 92317835 92320324 0 4163
6 TraesCS5D01G214900 chr2B 96.874 2495 63 9 1 2487 30670614 30668127 0 4161
7 TraesCS5D01G214900 chr4A 96.759 2499 65 9 1 2487 67576687 67574193 0 4152
8 TraesCS5D01G214900 chr3A 96.232 2495 82 9 1 2487 694375573 694373083 0 4076
9 TraesCS5D01G214900 chr7A 95.915 2497 83 10 1 2487 46402290 46404777 0 4028


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 TraesCS5D01G214900 chr5D 324420203 324422689 2486 False 4593 4593 100.000 1 2487 1 chr5D.!!$F1 2486
1 TraesCS5D01G214900 chr6B 596620321 596622813 2492 False 4205 4205 97.157 1 2487 1 chr6B.!!$F1 2486
2 TraesCS5D01G214900 chrUn 282362207 282364699 2492 True 4200 4200 97.115 1 2487 1 chrUn.!!$R2 2486
3 TraesCS5D01G214900 chrUn 86507523 86510015 2492 True 4194 4194 97.075 1 2487 1 chrUn.!!$R1 2486
4 TraesCS5D01G214900 chr6A 84434141 84436636 2495 False 4169 4169 96.876 1 2487 1 chr6A.!!$F1 2486
5 TraesCS5D01G214900 chr3B 92317835 92320324 2489 False 4163 4163 96.874 1 2487 1 chr3B.!!$F1 2486
6 TraesCS5D01G214900 chr2B 30668127 30670614 2487 True 4161 4161 96.874 1 2487 1 chr2B.!!$R1 2486
7 TraesCS5D01G214900 chr4A 67574193 67576687 2494 True 4152 4152 96.759 1 2487 1 chr4A.!!$R1 2486
8 TraesCS5D01G214900 chr3A 694373083 694375573 2490 True 4076 4076 96.232 1 2487 1 chr3A.!!$R1 2486
9 TraesCS5D01G214900 chr7A 46402290 46404777 2487 False 4028 4028 95.915 1 2487 1 chr7A.!!$F1 2486

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
67 68 0.036858 GGACAGAACAGGCCTCAGTC 60.037 60.0 0.0 4.73 0.00 3.51 F
68 69 0.681733 GACAGAACAGGCCTCAGTCA 59.318 55.0 0.0 0.00 31.58 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1013 1018 0.531200 ATCAGGACCCTTTCGACGTC 59.469 55.000 5.18 5.18 0.0 4.34 R
1742 1755 1.063649 CGCTAACTCGCTCGCCTAA 59.936 57.895 0.00 0.00 0.0 2.69 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
22 23 5.296151 TGCTTTCGGAATCTTCCTATGAT 57.704 39.130 7.35 0.00 45.33 2.45
67 68 0.036858 GGACAGAACAGGCCTCAGTC 60.037 60.000 0.00 4.73 0.00 3.51
68 69 0.681733 GACAGAACAGGCCTCAGTCA 59.318 55.000 0.00 0.00 31.58 3.41
272 273 5.355910 TCAAAAGCCGATTACCAAATCTACC 59.644 40.000 0.00 0.00 39.56 3.18
367 368 8.188139 ACAACTTTCTATTTTGTCGAACAACAT 58.812 29.630 0.00 0.00 37.90 2.71
485 490 5.455872 TCTAGAGTTCCGGGATTACTTCAT 58.544 41.667 0.00 0.00 0.00 2.57
666 671 6.423001 TCGCAATATTTCTGATCATGACTCAG 59.577 38.462 20.37 20.37 41.23 3.35
905 910 6.650807 GCCCGATCATGAGTGAATAGAAAATA 59.349 38.462 0.09 0.00 38.01 1.40
966 971 8.255905 TGTTTAATTCTACCACTTCTACTAGGC 58.744 37.037 0.00 0.00 0.00 3.93
1013 1018 3.602062 CGTAAAGTAATGGCTTTTGTGCG 59.398 43.478 0.00 0.00 39.22 5.34
1044 1049 2.398588 GGTCCTGATGTAGTGGGATCA 58.601 52.381 0.00 0.00 0.00 2.92
1276 1281 7.724305 TCGCTAGGTGTTTATGGAATAATTC 57.276 36.000 0.00 0.00 38.83 2.17
1446 1454 4.934797 TCTTTCATTCATCAAGGGGTCT 57.065 40.909 0.00 0.00 0.00 3.85
1458 1466 1.518367 AGGGGTCTGTCACTTTTCCA 58.482 50.000 0.00 0.00 0.00 3.53
1555 1563 4.193826 TGTCAAGCTGGTCTCACTATTC 57.806 45.455 0.00 0.00 0.00 1.75
1630 1643 1.288335 AGGACCTGACGGTTCTCCTAT 59.712 52.381 0.00 0.00 46.82 2.57
1711 1724 0.320421 TACAGTCAAAGTCAGCGGCC 60.320 55.000 0.00 0.00 0.00 6.13
1787 1800 3.322541 GGCTTAGGGATAAGAGAGTGTCC 59.677 52.174 0.00 0.00 0.00 4.02
1788 1801 3.961408 GCTTAGGGATAAGAGAGTGTCCA 59.039 47.826 0.00 0.00 32.31 4.02
1789 1802 4.202172 GCTTAGGGATAAGAGAGTGTCCAC 60.202 50.000 0.00 0.00 32.31 4.02
1792 1805 1.476891 GGATAAGAGAGTGTCCACGCA 59.523 52.381 4.04 0.00 36.20 5.24
1840 1853 3.181479 ACACAAAGTCACTTAGCTCGACA 60.181 43.478 0.00 0.00 31.92 4.35
1884 1898 6.635021 AGGAATACCCTACATAGAGAACCAT 58.365 40.000 0.00 0.00 45.48 3.55
1931 1945 4.733725 TCCCCGGGGCTAAGCTGT 62.734 66.667 36.68 0.00 34.68 4.40
2010 2024 2.146342 AGCCTTTGTCATTGTCAGTCG 58.854 47.619 0.00 0.00 0.00 4.18
2058 2073 5.461526 CGAATCCGTAAATCAGAGAGCATA 58.538 41.667 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 2.035783 GGTTGAGTTGAGGGGGCC 59.964 66.667 0.00 0.00 0.00 5.80
272 273 4.382754 GTGCGGTTTCAAGATGCTAAAAAG 59.617 41.667 0.00 0.00 0.00 2.27
367 368 3.254657 GGAATTGTTCATTGGGTTCGACA 59.745 43.478 0.00 0.00 0.00 4.35
412 413 9.647797 TTGTTAAATATCGCGAATATAGTGGAT 57.352 29.630 15.24 0.00 30.04 3.41
485 490 5.050363 GTGCTTAGGCGAAAATCGATATCAA 60.050 40.000 0.00 0.00 43.74 2.57
549 554 3.646611 TGACTCGTTTTCGGTGTATCA 57.353 42.857 0.00 0.00 44.25 2.15
666 671 2.024306 GCAATCCCCTTTCCTAGTGGC 61.024 57.143 0.00 0.00 0.00 5.01
966 971 3.307242 CAGCTAGCACTAAAAAGGCTACG 59.693 47.826 18.83 0.00 39.01 3.51
1013 1018 0.531200 ATCAGGACCCTTTCGACGTC 59.469 55.000 5.18 5.18 0.00 4.34
1044 1049 5.116882 GCTAGAGGTTGTAACAATCCGAAT 58.883 41.667 0.00 0.00 0.00 3.34
1276 1281 4.201930 CGTCTTACTAGACCAACCTGCTAG 60.202 50.000 0.00 0.00 46.63 3.42
1318 1324 6.049955 CCAATTGGTCCGTATATCATAGGT 57.950 41.667 16.90 0.00 0.00 3.08
1446 1454 1.228124 CCGGCCTGGAAAAGTGACA 60.228 57.895 7.77 0.00 42.00 3.58
1458 1466 2.042843 ACTTCTCGATCCCGGCCT 60.043 61.111 0.00 0.00 36.24 5.19
1625 1638 8.054572 TCATGTTCTTTCATCCATCAAATAGGA 58.945 33.333 0.00 0.00 38.50 2.94
1630 1643 7.764141 TTCTCATGTTCTTTCATCCATCAAA 57.236 32.000 0.00 0.00 0.00 2.69
1711 1724 4.094684 CGAGGCTAGGCAAACTCG 57.905 61.111 19.70 14.60 45.34 4.18
1742 1755 1.063649 CGCTAACTCGCTCGCCTAA 59.936 57.895 0.00 0.00 0.00 2.69
1801 1814 8.458212 ACTTTGTGTAGCGTAGTAGAATTAAC 57.542 34.615 0.00 0.00 0.00 2.01
1804 1817 6.585322 GTGACTTTGTGTAGCGTAGTAGAATT 59.415 38.462 0.00 0.00 0.00 2.17
1931 1945 7.820386 TCTTAATTAACTATCAGTGGTGCGAAA 59.180 33.333 0.00 0.00 0.00 3.46
1985 1999 1.266718 GACAATGACAAAGGCTTGCGA 59.733 47.619 0.00 0.00 35.84 5.10
2142 2160 2.632028 CTCATCCCGATCACAAGGAGAT 59.368 50.000 0.00 0.00 31.94 2.75
2190 2211 1.413077 AGGAAACTCCGATTCGATCCC 59.587 52.381 7.83 0.33 42.75 3.85
2229 2250 6.775594 AGCACAAAAGTTTAAGGAGAACTT 57.224 33.333 0.00 0.00 46.27 2.66
2246 2267 2.159114 GCTTCTTTTCCACCAAGCACAA 60.159 45.455 0.00 0.00 40.86 3.33
2439 2460 1.668793 TCACGCCTAGACGACGACA 60.669 57.895 5.13 0.00 36.70 4.35


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

AutoCloner maintained by Alex Coulton.