Multiple sequence alignment - TraesCS6A01G160900

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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 TraesCS6A01G160900 chr6A 100.000 1319 0 0 1 1319 155846782 155845464 0 2436
1 TraesCS6A01G160900 chr6A 100.000 1074 0 0 1484 2557 155845299 155844226 0 1984
2 TraesCS6A01G160900 chr2D 98.484 1319 20 0 1 1319 644703264 644701946 0 2326
3 TraesCS6A01G160900 chr2D 98.413 1071 12 1 1492 2557 635069142 635070212 0 1879
4 TraesCS6A01G160900 chrUn 98.408 1319 21 0 1 1319 45100792 45099474 0 2320
5 TraesCS6A01G160900 chrUn 98.256 1319 23 0 1 1319 261513064 261514382 0 2309
6 TraesCS6A01G160900 chrUn 98.146 1079 14 2 1484 2557 45099459 45098382 0 1877
7 TraesCS6A01G160900 chrUn 98.056 1080 14 3 1484 2557 186162449 186161371 0 1871
8 TraesCS6A01G160900 chrUn 98.054 1079 15 2 1484 2557 261514399 261515476 0 1871
9 TraesCS6A01G160900 chr5B 98.408 1319 21 0 1 1319 130614901 130613583 0 2320
10 TraesCS6A01G160900 chr5B 98.105 1319 25 0 1 1319 130609877 130608559 0 2298
11 TraesCS6A01G160900 chr5B 98.029 1319 26 0 1 1319 130568755 130570073 0 2292
12 TraesCS6A01G160900 chr5B 98.241 1080 12 3 1484 2557 130608544 130607466 0 1882
13 TraesCS6A01G160900 chr5B 98.146 1079 15 1 1484 2557 130613568 130612490 0 1877
14 TraesCS6A01G160900 chr7D 98.180 1319 24 0 1 1319 626650265 626648947 0 2303
15 TraesCS6A01G160900 chr3A 98.105 1319 25 0 1 1319 66030313 66031631 0 2298
16 TraesCS6A01G160900 chr3A 98.054 1079 15 2 1484 2557 66031647 66032724 0 1871
17 TraesCS6A01G160900 chr7B 98.029 1319 26 0 1 1319 743033700 743035018 0 2292
18 TraesCS6A01G160900 chr7B 97.965 1081 15 2 1484 2557 743035034 743036114 0 1868
19 TraesCS6A01G160900 chr1D 98.516 1078 12 2 1484 2557 493803119 493802042 0 1899


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 TraesCS6A01G160900 chr6A 155844226 155846782 2556 True 2210.00 2436 100.0000 1 2557 2 chr6A.!!$R1 2556
1 TraesCS6A01G160900 chr2D 644701946 644703264 1318 True 2326.00 2326 98.4840 1 1319 1 chr2D.!!$R1 1318
2 TraesCS6A01G160900 chr2D 635069142 635070212 1070 False 1879.00 1879 98.4130 1492 2557 1 chr2D.!!$F1 1065
3 TraesCS6A01G160900 chrUn 45098382 45100792 2410 True 2098.50 2320 98.2770 1 2557 2 chrUn.!!$R2 2556
4 TraesCS6A01G160900 chrUn 261513064 261515476 2412 False 2090.00 2309 98.1550 1 2557 2 chrUn.!!$F1 2556
5 TraesCS6A01G160900 chrUn 186161371 186162449 1078 True 1871.00 1871 98.0560 1484 2557 1 chrUn.!!$R1 1073
6 TraesCS6A01G160900 chr5B 130568755 130570073 1318 False 2292.00 2292 98.0290 1 1319 1 chr5B.!!$F1 1318
7 TraesCS6A01G160900 chr5B 130607466 130614901 7435 True 2094.25 2320 98.2250 1 2557 4 chr5B.!!$R1 2556
8 TraesCS6A01G160900 chr7D 626648947 626650265 1318 True 2303.00 2303 98.1800 1 1319 1 chr7D.!!$R1 1318
9 TraesCS6A01G160900 chr3A 66030313 66032724 2411 False 2084.50 2298 98.0795 1 2557 2 chr3A.!!$F1 2556
10 TraesCS6A01G160900 chr7B 743033700 743036114 2414 False 2080.00 2292 97.9970 1 2557 2 chr7B.!!$F1 2556
11 TraesCS6A01G160900 chr1D 493802042 493803119 1077 True 1899.00 1899 98.5160 1484 2557 1 chr1D.!!$R1 1073

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
936 937 0.392863 CCTTGCATGTGGATCGTCCA 60.393 55.0 3.02 3.02 45.98 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 7485 0.512952 GCGTGGTTGATGTGTCACTC 59.487 55.0 4.27 0.43 33.11 3.51 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
75 76 1.295792 GCTCCGATAACGCAATTCCA 58.704 50.000 0.00 0.00 38.29 3.53
332 333 1.233369 CCATAGGACCCCGTCTCCT 59.767 63.158 0.00 0.00 41.36 3.69
432 433 4.031636 ACAACTACGTAGAGGGTCTCTT 57.968 45.455 28.74 7.26 41.50 2.85
486 487 2.482796 TAGTAGTCCGGTCGCACCCA 62.483 60.000 0.00 0.00 33.75 4.51
527 528 5.361857 AGGGAAATGCACCTAAGATCAAATG 59.638 40.000 0.00 0.00 34.71 2.32
572 573 9.317936 GGAAAATTCAGACTTTCTTTTTGATGT 57.682 29.630 4.78 0.00 33.06 3.06
581 582 6.449698 ACTTTCTTTTTGATGTTGCGATCAT 58.550 32.000 0.00 0.00 32.35 2.45
639 640 5.864418 ACATGGCAATTAAATCATGAGCT 57.136 34.783 0.09 0.00 39.27 4.09
709 710 5.072055 TGAATTCAGAAGCATCAAACCTCA 58.928 37.500 3.38 0.00 0.00 3.86
919 920 0.393808 ACCACACGTGCAAGTTTCCT 60.394 50.000 17.22 0.00 0.00 3.36
936 937 0.392863 CCTTGCATGTGGATCGTCCA 60.393 55.000 3.02 3.02 45.98 4.02
963 964 3.074412 ACTTCTTCGGATTTGCGTGAAT 58.926 40.909 0.00 0.00 0.00 2.57
967 968 4.250464 TCTTCGGATTTGCGTGAATTAGT 58.750 39.130 0.00 0.00 0.00 2.24
1230 1231 4.973396 TCGTCGTATGTATGTTCGACTTT 58.027 39.130 13.09 0.00 46.55 2.66
1257 1258 0.249031 GGTGCAATAGAATTGGCGGC 60.249 55.000 0.00 0.00 0.00 6.53
1528 1529 0.179073 CTGGTGATCCCTAGGTTGCG 60.179 60.000 8.29 0.00 0.00 4.85
1715 1716 0.179092 GTACGATTAGCCGGCCTTGT 60.179 55.000 26.15 19.83 0.00 3.16
1759 1760 1.518367 CCCCATGCTAAGGTTCCCTA 58.482 55.000 0.00 0.00 31.13 3.53
1812 1813 2.164422 CGATAATAGCTCCTCCGCATCA 59.836 50.000 0.00 0.00 0.00 3.07
2123 2124 6.036926 TCTAATTCCCTTCTCAGATCCTCT 57.963 41.667 0.00 0.00 0.00 3.69
2453 7484 1.614226 CCCCTTCCTACGGGTTCCA 60.614 63.158 0.00 0.00 40.24 3.53
2454 7485 1.623542 CCCCTTCCTACGGGTTCCAG 61.624 65.000 0.00 0.00 40.24 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 0.324460 CCCAACTACCGACTCCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
332 333 3.074504 ACGCGCGAAAGATAAGATACA 57.925 42.857 39.36 0.00 0.00 2.29
527 528 2.561373 CGGAAGCCGGCTCAAAAC 59.439 61.111 32.93 17.89 44.15 2.43
808 809 8.409358 ACTATTGCCCATTTATTCTGGAATAC 57.591 34.615 2.90 0.00 35.70 1.89
929 930 4.341235 TCCGAAGAAGTTATCATGGACGAT 59.659 41.667 0.00 0.00 0.00 3.73
936 937 4.876107 ACGCAAATCCGAAGAAGTTATCAT 59.124 37.500 0.00 0.00 0.00 2.45
967 968 1.933021 ACCACTTAGTGATCGGTCCA 58.067 50.000 14.66 0.00 35.23 4.02
1061 1062 4.349342 AGGGGACATGATCAATAGAACCTC 59.651 45.833 0.00 3.27 0.00 3.85
1257 1258 6.815641 GTGACTGATCCTGCCATAATATACTG 59.184 42.308 0.00 0.00 0.00 2.74
1528 1529 2.049248 TTAACGACCGGACGTGCC 60.049 61.111 31.17 0.00 45.83 5.01
1715 1716 0.329931 TCCTAATCCTTTTGCCGCCA 59.670 50.000 0.00 0.00 0.00 5.69
1999 2000 9.408069 GAAAGTAGAAGAAGTTATCGAAACTCA 57.592 33.333 11.62 0.00 0.00 3.41
2123 2124 5.670818 TGAGTAGGATAAGGAGGAGTAGTCA 59.329 44.000 0.00 0.00 0.00 3.41
2453 7484 1.873903 GCGTGGTTGATGTGTCACTCT 60.874 52.381 4.27 0.00 33.11 3.24
2454 7485 0.512952 GCGTGGTTGATGTGTCACTC 59.487 55.000 4.27 0.43 33.11 3.51


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

AutoCloner maintained by Alex Coulton.