Multiple sequence alignment - TraesCS2B01G039000

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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 TraesCS2B01G039000 chr2B 100.000 2390 0 0 1 2390 17993890 17996279 0.000000e+00 4414
1 TraesCS2B01G039000 chr2B 98.911 1745 18 1 647 2390 65089699 65087955 0.000000e+00 3116
2 TraesCS2B01G039000 chr2B 83.218 435 54 11 3 434 17924517 17924935 4.820000e-102 381
3 TraesCS2B01G039000 chr6A 99.026 1745 16 1 647 2390 593775859 593774115 0.000000e+00 3127
4 TraesCS2B01G039000 chr7A 98.968 1745 18 0 646 2390 40032043 40033787 0.000000e+00 3123
5 TraesCS2B01G039000 chr4B 98.969 1746 16 1 647 2390 437234399 437236144 0.000000e+00 3123
6 TraesCS2B01G039000 chr7B 98.968 1745 17 1 647 2390 697603941 697602197 0.000000e+00 3121
7 TraesCS2B01G039000 chr4A 98.968 1745 17 1 647 2390 724630114 724631858 0.000000e+00 3121
8 TraesCS2B01G039000 chr1B 98.911 1744 19 0 647 2390 637367014 637365271 0.000000e+00 3116
9 TraesCS2B01G039000 chr3A 98.911 1744 15 2 647 2390 658743970 658742231 0.000000e+00 3112
10 TraesCS2B01G039000 chr5B 98.853 1744 20 0 647 2390 705811763 705813506 0.000000e+00 3110
11 TraesCS2B01G039000 chr2D 94.427 646 32 4 1 646 11548469 11549110 0.000000e+00 990
12 TraesCS2B01G039000 chr2A 84.962 665 77 13 3 646 12158059 12158721 0.000000e+00 652
13 TraesCS2B01G039000 chr2A 85.950 121 17 0 12 132 12177753 12177873 1.930000e-26 130
14 TraesCS2B01G039000 chrUn 83.360 631 80 16 12 624 2009721 2010344 5.770000e-156 560


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 TraesCS2B01G039000 chr2B 17993890 17996279 2389 False 4414 4414 100.000 1 2390 1 chr2B.!!$F2 2389
1 TraesCS2B01G039000 chr2B 65087955 65089699 1744 True 3116 3116 98.911 647 2390 1 chr2B.!!$R1 1743
2 TraesCS2B01G039000 chr6A 593774115 593775859 1744 True 3127 3127 99.026 647 2390 1 chr6A.!!$R1 1743
3 TraesCS2B01G039000 chr7A 40032043 40033787 1744 False 3123 3123 98.968 646 2390 1 chr7A.!!$F1 1744
4 TraesCS2B01G039000 chr4B 437234399 437236144 1745 False 3123 3123 98.969 647 2390 1 chr4B.!!$F1 1743
5 TraesCS2B01G039000 chr7B 697602197 697603941 1744 True 3121 3121 98.968 647 2390 1 chr7B.!!$R1 1743
6 TraesCS2B01G039000 chr4A 724630114 724631858 1744 False 3121 3121 98.968 647 2390 1 chr4A.!!$F1 1743
7 TraesCS2B01G039000 chr1B 637365271 637367014 1743 True 3116 3116 98.911 647 2390 1 chr1B.!!$R1 1743
8 TraesCS2B01G039000 chr3A 658742231 658743970 1739 True 3112 3112 98.911 647 2390 1 chr3A.!!$R1 1743
9 TraesCS2B01G039000 chr5B 705811763 705813506 1743 False 3110 3110 98.853 647 2390 1 chr5B.!!$F1 1743
10 TraesCS2B01G039000 chr2D 11548469 11549110 641 False 990 990 94.427 1 646 1 chr2D.!!$F1 645
11 TraesCS2B01G039000 chr2A 12158059 12158721 662 False 652 652 84.962 3 646 1 chr2A.!!$F1 643
12 TraesCS2B01G039000 chrUn 2009721 2010344 623 False 560 560 83.360 12 624 1 chrUn.!!$F1 612

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
951 979 1.776969 CCTGCCCCTTTCCTTTCCT 59.223 57.895 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1881 1.475751 CCAACATCTATTCGGCAGCCT 60.476 52.381 10.54 0.0 0.0 4.58 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
27 28 8.779354 AAGGTCATGTAGAAATACTTTCACTC 57.221 34.615 2.76 0.00 42.10 3.51
35 36 8.999431 TGTAGAAATACTTTCACTCCACAATTC 58.001 33.333 2.76 0.00 42.10 2.17
47 48 5.296283 CACTCCACAATTCAAATTTGCCAAA 59.704 36.000 13.54 3.36 0.00 3.28
48 49 5.884792 ACTCCACAATTCAAATTTGCCAAAA 59.115 32.000 13.54 3.00 0.00 2.44
49 50 6.376581 ACTCCACAATTCAAATTTGCCAAAAA 59.623 30.769 13.54 2.62 0.00 1.94
211 212 7.174946 TCTCCCACATTAATGAAAACAGAGAAC 59.825 37.037 22.16 0.00 0.00 3.01
305 309 7.397192 AGAAACACTCCAATAAATAGCATGGTT 59.603 33.333 1.12 0.00 34.50 3.67
399 418 5.242795 ACTGTGCTAGGGAAATTACAGTT 57.757 39.130 0.00 0.00 44.32 3.16
410 429 5.758784 GGGAAATTACAGTTAGAGAATCGGG 59.241 44.000 0.00 0.00 42.67 5.14
951 979 1.776969 CCTGCCCCTTTCCTTTCCT 59.223 57.895 0.00 0.00 0.00 3.36
1339 1367 2.307496 ATGTGGGCATTTTGAGTGGA 57.693 45.000 0.00 0.00 29.54 4.02
1875 1905 0.465460 GCCGAATAGATGTTGGGCCA 60.465 55.000 0.00 0.00 44.35 5.36
1926 1956 1.064389 GCCCAAAATAGAGACCAGCCT 60.064 52.381 0.00 0.00 0.00 4.58
2232 2265 2.708216 TGAAGATGGTGTGTGTGTGT 57.292 45.000 0.00 0.00 0.00 3.72
2379 2412 2.666272 TTGCAACCCATAGTTCCACA 57.334 45.000 0.00 0.00 36.18 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 9.528489 TGTAAGTTCTTCCTTGGCTATTAAATT 57.472 29.630 0.00 0.00 0.00 1.82
50 51 8.957466 GTGTAAGTTCTTCCTTGGCTATTAAAT 58.043 33.333 0.00 0.00 0.00 1.40
51 52 8.161425 AGTGTAAGTTCTTCCTTGGCTATTAAA 58.839 33.333 0.00 0.00 0.00 1.52
346 364 3.788797 GCAAGTTAACTCTGTGTGTGTGC 60.789 47.826 8.95 7.92 0.00 4.57
347 365 3.373748 TGCAAGTTAACTCTGTGTGTGTG 59.626 43.478 8.95 1.20 0.00 3.82
399 418 0.261991 AGTGCTCCCCCGATTCTCTA 59.738 55.000 0.00 0.00 0.00 2.43
466 485 0.319211 TACCACTGCAACTTCGACCG 60.319 55.000 0.00 0.00 0.00 4.79
951 979 4.525024 CGGAGTAGAGGAAGAAGAAGGTA 58.475 47.826 0.00 0.00 0.00 3.08
1095 1123 2.869801 CCTCACACAAGTCAAACGCTTA 59.130 45.455 0.00 0.00 0.00 3.09
1339 1367 7.864108 TCAACCTTTCAACATATTCATCGAT 57.136 32.000 0.00 0.00 0.00 3.59
1409 1437 3.749981 CTTGTTCCACGGCAAGCT 58.250 55.556 0.00 0.00 36.17 3.74
1851 1881 1.475751 CCAACATCTATTCGGCAGCCT 60.476 52.381 10.54 0.00 0.00 4.58
1875 1905 4.934797 TTCTCAGGGTCCATTTTCTCAT 57.065 40.909 0.00 0.00 0.00 2.90
2232 2265 3.559171 GGGTTGCTACACCTCAATCTCAA 60.559 47.826 0.00 0.00 36.97 3.02


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

AutoCloner maintained by Alex Coulton.