Multiple sequence alignment - TraesCS1D01G153000

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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 TraesCS1D01G153000 chr1D 100.000 2577 0 0 1 2577 212468996 212466420 0 4759
1 TraesCS1D01G153000 chr7D 98.689 2593 16 6 1 2577 579028591 579031181 0 4584
2 TraesCS1D01G153000 chr4D 98.650 2592 20 6 1 2577 123655989 123653398 0 4578
3 TraesCS1D01G153000 chr4D 98.611 2592 21 6 1 2577 123509290 123506699 0 4573
4 TraesCS1D01G153000 chr4D 98.497 2595 19 9 1 2577 123738787 123736195 0 4558
5 TraesCS1D01G153000 chr6D 97.879 2593 38 7 1 2577 108466575 108469166 0 4468
6 TraesCS1D01G153000 chrUn 95.625 2606 66 25 1 2577 221549555 221546969 0 4137
7 TraesCS1D01G153000 chrUn 95.463 2601 80 22 1 2577 186192553 186189967 0 4115
8 TraesCS1D01G153000 chr7B 95.238 2604 81 25 1 2577 743004925 743007512 0 4082
9 TraesCS1D01G153000 chr7B 96.664 1439 35 4 1 1427 139543318 139541881 0 2379
10 TraesCS1D01G153000 chr4B 97.377 1563 20 7 1035 2577 209271422 209269861 0 2639
11 TraesCS1D01G153000 chr5A 96.949 1442 29 3 1 1427 534932661 534934102 0 2405
12 TraesCS1D01G153000 chr7A 96.736 1440 33 4 1 1427 211291172 211292610 0 2386
13 TraesCS1D01G153000 chr2B 97.220 1403 28 6 1 1392 357246177 357244775 0 2364


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 TraesCS1D01G153000 chr1D 212466420 212468996 2576 True 4759 4759 100.000 1 2577 1 chr1D.!!$R1 2576
1 TraesCS1D01G153000 chr7D 579028591 579031181 2590 False 4584 4584 98.689 1 2577 1 chr7D.!!$F1 2576
2 TraesCS1D01G153000 chr4D 123653398 123655989 2591 True 4578 4578 98.650 1 2577 1 chr4D.!!$R2 2576
3 TraesCS1D01G153000 chr4D 123506699 123509290 2591 True 4573 4573 98.611 1 2577 1 chr4D.!!$R1 2576
4 TraesCS1D01G153000 chr4D 123736195 123738787 2592 True 4558 4558 98.497 1 2577 1 chr4D.!!$R3 2576
5 TraesCS1D01G153000 chr6D 108466575 108469166 2591 False 4468 4468 97.879 1 2577 1 chr6D.!!$F1 2576
6 TraesCS1D01G153000 chrUn 221546969 221549555 2586 True 4137 4137 95.625 1 2577 1 chrUn.!!$R2 2576
7 TraesCS1D01G153000 chrUn 186189967 186192553 2586 True 4115 4115 95.463 1 2577 1 chrUn.!!$R1 2576
8 TraesCS1D01G153000 chr7B 743004925 743007512 2587 False 4082 4082 95.238 1 2577 1 chr7B.!!$F1 2576
9 TraesCS1D01G153000 chr7B 139541881 139543318 1437 True 2379 2379 96.664 1 1427 1 chr7B.!!$R1 1426
10 TraesCS1D01G153000 chr4B 209269861 209271422 1561 True 2639 2639 97.377 1035 2577 1 chr4B.!!$R1 1542
11 TraesCS1D01G153000 chr5A 534932661 534934102 1441 False 2405 2405 96.949 1 1427 1 chr5A.!!$F1 1426
12 TraesCS1D01G153000 chr7A 211291172 211292610 1438 False 2386 2386 96.736 1 1427 1 chr7A.!!$F1 1426
13 TraesCS1D01G153000 chr2B 357244775 357246177 1402 True 2364 2364 97.220 1 1392 1 chr2B.!!$R1 1391


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
979 987 1.573026 GCGGCTTAAGCTCTTCCTAC 58.427 55.0 25.88 6.71 41.7 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2395 2432 2.048503 GCGGTGAAGTAGGCACGT 60.049 61.111 0.0 0.0 37.13 4.49 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
979 987 1.573026 GCGGCTTAAGCTCTTCCTAC 58.427 55.000 25.88 6.71 41.70 3.18
1087 1095 1.482593 AGCCCTACTTGGTCGATGAAG 59.517 52.381 5.16 5.16 0.00 3.02
1088 1096 1.941325 CCCTACTTGGTCGATGAAGC 58.059 55.000 6.35 0.00 0.00 3.86
1729 1764 0.108615 CCGGCGATGATAGGTGGATC 60.109 60.000 9.30 0.00 0.00 3.36
1886 1921 2.166907 CTGGGTGGACAGTCTATCCT 57.833 55.000 16.77 0.00 37.13 3.24
2348 2385 9.613428 TGATAAGTATAGGTGTTCTTGGATTTG 57.387 33.333 0.00 0.00 0.00 2.32
2395 2432 2.563620 TGTGGGCTTAGACGTTGATACA 59.436 45.455 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1087 1095 0.102481 TCCAGATAGGAACGAAGCGC 59.898 55.000 0.00 0.0 45.65 5.92
1729 1764 5.183140 AGAATCGGAACAAACCAATTACCAG 59.817 40.000 0.00 0.0 0.00 4.00
1886 1921 3.457012 GGCTGGTAATACCACTTAAGGGA 59.543 47.826 8.27 0.0 44.79 4.20
2055 2091 2.826128 AGGAATGCTGTCACTAGAACGA 59.174 45.455 0.00 0.0 0.00 3.85
2348 2385 6.699575 AAACATATGATGAGCCCAAACTAC 57.300 37.500 10.38 0.0 0.00 2.73
2395 2432 2.048503 GCGGTGAAGTAGGCACGT 60.049 61.111 0.00 0.0 37.13 4.49
2442 2479 7.253422 AGCGATCCAACTAAAGATTTTGATTG 58.747 34.615 0.00 0.0 0.00 2.67



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

AutoCloner maintained by Alex Coulton.