Multiple sequence alignment - TraesCS2B01G264500

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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 TraesCS2B01G264500 chr2B 100.000 2411 0 0 1 2411 357246197 357243787 0 4453
1 TraesCS2B01G264500 chr2B 98.085 992 19 0 1420 2411 391171867 391172858 0 1727
2 TraesCS2B01G264500 chr4D 97.893 1424 29 1 1 1423 123656009 123654586 0 2462
3 TraesCS2B01G264500 chr4D 97.758 1427 28 2 1 1423 123738807 123737381 0 2455
4 TraesCS2B01G264500 chr4D 97.753 1424 31 1 1 1423 123509310 123507887 0 2451
5 TraesCS2B01G264500 chr7D 97.616 1426 29 2 1 1423 579028571 579029994 0 2440
6 TraesCS2B01G264500 chr7B 97.257 1422 37 2 1 1421 139543338 139541918 0 2409
7 TraesCS2B01G264500 chr7B 98.085 992 18 1 1420 2411 716909849 716910839 0 1725
8 TraesCS2B01G264500 chr7B 97.984 992 18 2 1420 2411 716778033 716779022 0 1720
9 TraesCS2B01G264500 chr1D 97.189 1423 29 6 1 1423 212469016 212467605 0 2396
10 TraesCS2B01G264500 chr6D 96.912 1425 42 1 1 1423 108466555 108467979 0 2386
11 TraesCS2B01G264500 chr6B 96.772 1425 44 1 1 1423 625642336 625640912 0 2375
12 TraesCS2B01G264500 chr5A 96.356 1427 48 2 1 1423 534932641 534934067 0 2344
13 TraesCS2B01G264500 chr5A 98.085 992 18 1 1420 2411 16538006 16538996 0 1725
14 TraesCS2B01G264500 chr7A 98.387 992 16 0 1420 2411 60348483 60349474 0 1744
15 TraesCS2B01G264500 chr7A 98.185 992 16 2 1420 2411 60157487 60158476 0 1731
16 TraesCS2B01G264500 chr7A 97.986 993 19 1 1420 2411 60175100 60174108 0 1722
17 TraesCS2B01G264500 chrUn 97.782 992 21 1 1420 2411 222878608 222879598 0 1709
18 TraesCS2B01G264500 chr1B 97.681 992 21 1 1420 2411 583568123 583567134 0 1703


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 TraesCS2B01G264500 chr2B 357243787 357246197 2410 True 4453 4453 100.000 1 2411 1 chr2B.!!$R1 2410
1 TraesCS2B01G264500 chr2B 391171867 391172858 991 False 1727 1727 98.085 1420 2411 1 chr2B.!!$F1 991
2 TraesCS2B01G264500 chr4D 123654586 123656009 1423 True 2462 2462 97.893 1 1423 1 chr4D.!!$R2 1422
3 TraesCS2B01G264500 chr4D 123737381 123738807 1426 True 2455 2455 97.758 1 1423 1 chr4D.!!$R3 1422
4 TraesCS2B01G264500 chr4D 123507887 123509310 1423 True 2451 2451 97.753 1 1423 1 chr4D.!!$R1 1422
5 TraesCS2B01G264500 chr7D 579028571 579029994 1423 False 2440 2440 97.616 1 1423 1 chr7D.!!$F1 1422
6 TraesCS2B01G264500 chr7B 139541918 139543338 1420 True 2409 2409 97.257 1 1421 1 chr7B.!!$R1 1420
7 TraesCS2B01G264500 chr7B 716909849 716910839 990 False 1725 1725 98.085 1420 2411 1 chr7B.!!$F2 991
8 TraesCS2B01G264500 chr7B 716778033 716779022 989 False 1720 1720 97.984 1420 2411 1 chr7B.!!$F1 991
9 TraesCS2B01G264500 chr1D 212467605 212469016 1411 True 2396 2396 97.189 1 1423 1 chr1D.!!$R1 1422
10 TraesCS2B01G264500 chr6D 108466555 108467979 1424 False 2386 2386 96.912 1 1423 1 chr6D.!!$F1 1422
11 TraesCS2B01G264500 chr6B 625640912 625642336 1424 True 2375 2375 96.772 1 1423 1 chr6B.!!$R1 1422
12 TraesCS2B01G264500 chr5A 534932641 534934067 1426 False 2344 2344 96.356 1 1423 1 chr5A.!!$F2 1422
13 TraesCS2B01G264500 chr5A 16538006 16538996 990 False 1725 1725 98.085 1420 2411 1 chr5A.!!$F1 991
14 TraesCS2B01G264500 chr7A 60348483 60349474 991 False 1744 1744 98.387 1420 2411 1 chr7A.!!$F2 991
15 TraesCS2B01G264500 chr7A 60157487 60158476 989 False 1731 1731 98.185 1420 2411 1 chr7A.!!$F1 991
16 TraesCS2B01G264500 chr7A 60174108 60175100 992 True 1722 1722 97.986 1420 2411 1 chr7A.!!$R1 991
17 TraesCS2B01G264500 chrUn 222878608 222879598 990 False 1709 1709 97.782 1420 2411 1 chrUn.!!$F1 991
18 TraesCS2B01G264500 chr1B 583567134 583568123 989 True 1703 1703 97.681 1420 2411 1 chr1B.!!$R1 991

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
588 589 0.988063 GTTCTTCTCTTCCAGCCCCT 59.012 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1883 0.183492 AACTCAACCTCAGCCTTGCA 59.817 50.0 0.0 0.0 0.0 4.08 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
49 50 4.892934 TGTTGAGCAAATGAGTTTAAGGGT 59.107 37.500 0.00 0.0 0.00 4.34
217 218 6.611613 TTTGAGTTATGATGAGGAGTGAGT 57.388 37.500 0.00 0.0 0.00 3.41
316 317 3.135530 AGTCTCAGGCATGATAGTTTCCC 59.864 47.826 0.00 0.0 34.12 3.97
380 381 9.595823 TTAGTAATAGCATGAAGTAAGTTGTCC 57.404 33.333 0.00 0.0 0.00 4.02
441 442 9.803507 AAAGCATCCAGAAATATCATAGAATGA 57.196 29.630 0.00 0.0 44.55 2.57
588 589 0.988063 GTTCTTCTCTTCCAGCCCCT 59.012 55.000 0.00 0.0 0.00 4.79
622 623 9.173021 TCTCTGATAAGTCAAGTTTTCAAAACA 57.827 29.630 15.41 0.0 33.05 2.83
1203 1208 1.482177 CGGGAGAATGAGGGAGGATCT 60.482 57.143 0.00 0.0 33.73 2.75
1336 1341 2.079925 GCAAGGCAAGTCTCGAAAGAT 58.920 47.619 0.00 0.0 40.84 2.40
1443 1454 2.065993 TTCGCTGGAGAAAGAGAACG 57.934 50.000 0.00 0.0 32.00 3.95
1483 1495 7.606858 TTTTGATTCAACAAATGCAAGTTCA 57.393 28.000 0.00 0.0 39.09 3.18
1833 1845 2.306219 GGGGCTGTAGAGGAGAGTTTTT 59.694 50.000 0.00 0.0 0.00 1.94
1874 1886 0.539986 GGTAACGGGGAGAATCTGCA 59.460 55.000 3.77 0.0 33.73 4.41
1890 1902 0.183492 TGCAAGGCTGAGGTTGAGTT 59.817 50.000 0.00 0.0 0.00 3.01
2103 2115 3.019564 GGCAGGCATTACTGTGATCTTT 58.980 45.455 0.00 0.0 40.59 2.52
2322 2334 3.591527 TCCTGGATTATCCCTGTGTTTGT 59.408 43.478 8.98 0.0 35.03 2.83
2337 2349 4.338118 TGTGTTTGTTGTTTCCAGATCCTC 59.662 41.667 0.00 0.0 0.00 3.71
2376 2388 3.637229 GCTCAAGTCTATGGCCAGTACTA 59.363 47.826 13.05 0.0 0.00 1.82
2379 2391 3.961408 CAAGTCTATGGCCAGTACTACCT 59.039 47.826 13.05 0.0 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 218 6.086222 GCTTTCTTCAACAATGCGAATCTAA 58.914 36.000 0.00 0.00 0.00 2.10
380 381 3.502211 CCTTTTACCTAATGCCGGCTATG 59.498 47.826 29.70 12.05 0.00 2.23
588 589 3.181329 TGACTTATCAGAGAAGGGCCAA 58.819 45.455 6.18 0.00 0.00 4.52
622 623 7.655328 TCGAACCATATTTGTCATTTGCTTTTT 59.345 29.630 0.00 0.00 0.00 1.94
970 973 1.670811 CTTAAGCCGCCCAAGTATGTG 59.329 52.381 0.00 0.00 0.00 3.21
1275 1280 1.469940 CGGATCCTCTGTTCCACTTCG 60.470 57.143 10.75 0.00 31.66 3.79
1483 1495 4.637534 CCCATTGACAAATCAGACGAAGAT 59.362 41.667 0.00 0.00 35.83 2.40
1762 1774 8.099364 TCCTTTAACTGATTCAAGTGATTCAC 57.901 34.615 8.82 8.82 32.84 3.18
1871 1883 0.183492 AACTCAACCTCAGCCTTGCA 59.817 50.000 0.00 0.00 0.00 4.08
1874 1886 0.475906 AGCAACTCAACCTCAGCCTT 59.524 50.000 0.00 0.00 0.00 4.35
1890 1902 7.423844 TTCTATATTCTCAAGGAAGTGAGCA 57.576 36.000 0.00 0.00 44.01 4.26
2046 2058 4.693566 GGGTACGAATGTCATGTTCAAAGA 59.306 41.667 0.00 0.00 0.00 2.52
2322 2334 3.260205 AGAAGGGAGGATCTGGAAACAA 58.740 45.455 0.00 0.00 42.06 2.83
2337 2349 0.890996 AGCGCAAAGGACAAGAAGGG 60.891 55.000 11.47 0.00 0.00 3.95
2376 2388 1.852965 ACTGCTAATATTGCCCCAGGT 59.147 47.619 0.00 0.00 0.00 4.00
2379 2391 4.402155 CAGAAAACTGCTAATATTGCCCCA 59.598 41.667 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.