Multiple sequence alignment - TraesCS6A01G374900

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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 TraesCS6A01G374900 chr6A 100.000 2537 0 0 1 2537 597467864 597465328 0.000000e+00 4686
1 TraesCS6A01G374900 chr6A 97.617 2224 51 2 316 2537 602797503 602795280 0.000000e+00 3812
2 TraesCS6A01G374900 chr6A 96.942 2224 63 5 316 2537 555104436 555102216 0.000000e+00 3725
3 TraesCS6A01G374900 chr6A 97.492 319 7 1 1 319 602798192 602797875 6.170000e-151 544
4 TraesCS6A01G374900 chr7A 96.899 2225 64 5 316 2537 15521532 15519310 0.000000e+00 3722
5 TraesCS6A01G374900 chr7A 96.363 2227 67 13 316 2537 41970709 41972926 0.000000e+00 3651
6 TraesCS6A01G374900 chr7A 95.461 2225 73 17 318 2537 204191657 204193858 0.000000e+00 3524
7 TraesCS6A01G374900 chr3A 95.777 2226 86 8 316 2537 17913651 17911430 0.000000e+00 3583
8 TraesCS6A01G374900 chr3A 94.753 1296 48 9 1262 2537 38170700 38171995 0.000000e+00 1999
9 TraesCS6A01G374900 chr5A 95.687 2226 76 12 316 2537 565286674 565284465 0.000000e+00 3561
10 TraesCS6A01G374900 chr5A 95.831 1895 70 9 648 2537 693843422 693845312 0.000000e+00 3053
11 TraesCS6A01G374900 chr5A 94.481 1667 65 13 894 2537 153574966 153573304 0.000000e+00 2543
12 TraesCS6A01G374900 chr6B 94.254 2158 95 10 316 2469 319457651 319459783 0.000000e+00 3271
13 TraesCS6A01G374900 chr6B 94.062 320 17 2 1 319 319456960 319457278 3.790000e-133 484
14 TraesCS6A01G374900 chr6B 93.210 324 16 5 1 319 353552625 353552303 2.950000e-129 472
15 TraesCS6A01G374900 chr4B 95.000 320 15 1 1 319 603291652 603291333 3.770000e-138 501
16 TraesCS6A01G374900 chr2B 94.375 320 17 1 1 319 512426637 512426318 8.160000e-135 490
17 TraesCS6A01G374900 chr2B 93.438 320 17 2 1 319 19851609 19851925 2.950000e-129 472
18 TraesCS6A01G374900 chrUn 93.750 320 19 1 1 319 76238885 76239204 1.770000e-131 479
19 TraesCS6A01G374900 chr4A 93.146 321 20 2 1 319 713792864 713792544 1.060000e-128 470
20 TraesCS6A01G374900 chr3D 87.900 281 25 6 39 317 305618201 305617928 3.150000e-84 322


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 TraesCS6A01G374900 chr6A 597465328 597467864 2536 True 4686.0 4686 100.0000 1 2537 1 chr6A.!!$R2 2536
1 TraesCS6A01G374900 chr6A 555102216 555104436 2220 True 3725.0 3725 96.9420 316 2537 1 chr6A.!!$R1 2221
2 TraesCS6A01G374900 chr6A 602795280 602798192 2912 True 2178.0 3812 97.5545 1 2537 2 chr6A.!!$R3 2536
3 TraesCS6A01G374900 chr7A 15519310 15521532 2222 True 3722.0 3722 96.8990 316 2537 1 chr7A.!!$R1 2221
4 TraesCS6A01G374900 chr7A 41970709 41972926 2217 False 3651.0 3651 96.3630 316 2537 1 chr7A.!!$F1 2221
5 TraesCS6A01G374900 chr7A 204191657 204193858 2201 False 3524.0 3524 95.4610 318 2537 1 chr7A.!!$F2 2219
6 TraesCS6A01G374900 chr3A 17911430 17913651 2221 True 3583.0 3583 95.7770 316 2537 1 chr3A.!!$R1 2221
7 TraesCS6A01G374900 chr3A 38170700 38171995 1295 False 1999.0 1999 94.7530 1262 2537 1 chr3A.!!$F1 1275
8 TraesCS6A01G374900 chr5A 565284465 565286674 2209 True 3561.0 3561 95.6870 316 2537 1 chr5A.!!$R2 2221
9 TraesCS6A01G374900 chr5A 693843422 693845312 1890 False 3053.0 3053 95.8310 648 2537 1 chr5A.!!$F1 1889
10 TraesCS6A01G374900 chr5A 153573304 153574966 1662 True 2543.0 2543 94.4810 894 2537 1 chr5A.!!$R1 1643
11 TraesCS6A01G374900 chr6B 319456960 319459783 2823 False 1877.5 3271 94.1580 1 2469 2 chr6B.!!$F1 2468

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
917 1300 0.036388 GTGTGCTACTGGCTTGCCTA 60.036 55.0 13.18 0.0 42.39 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2554 3.074412 ACCATAGGCAAGTTCAGTTTCG 58.926 45.455 0.0 0.0 0.0 3.46 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
23 24 6.332735 TCTGATGTGTCCCGATTCTATTAG 57.667 41.667 0.00 0.00 0.00 1.73
129 130 6.183360 ACAACTTTGAAAACTTATGCCATGGA 60.183 34.615 18.40 0.31 0.00 3.41
357 735 9.297037 ACATAGGTACTGAAAGCAAAAATAGTT 57.703 29.630 0.00 0.00 41.52 2.24
485 864 5.934625 CACTTCAAAGTAGCACTTCTATGGT 59.065 40.000 0.00 0.00 37.47 3.55
508 887 4.609301 AGTATGCTTGCTTCCCCAAAATA 58.391 39.130 0.00 0.00 0.00 1.40
691 1073 6.942532 TGACTTGCCTGATTATATGGTTTC 57.057 37.500 0.00 0.00 0.00 2.78
917 1300 0.036388 GTGTGCTACTGGCTTGCCTA 60.036 55.000 13.18 0.00 42.39 3.93
925 1308 5.163248 TGCTACTGGCTTGCCTATATTTACA 60.163 40.000 13.18 0.00 42.39 2.41
1406 1791 2.441410 TGCATATTCCTTGCAAACGGA 58.559 42.857 0.00 1.29 46.48 4.69
1451 1838 3.326588 TCAAGGAAGGATCTCAAAACCGA 59.673 43.478 0.00 0.00 0.00 4.69
1541 1929 6.715718 CAGAAAAGATTCCCATGCTAGATGAT 59.284 38.462 0.00 0.00 36.12 2.45
1619 2007 8.814038 ATGATGATAGTAAAGGCAAAAAGAGT 57.186 30.769 0.00 0.00 0.00 3.24
1933 2324 3.255642 TGTTTCTTAGCCCATCAACAAGC 59.744 43.478 0.00 0.00 0.00 4.01
1988 2380 5.669477 TGCTTCAAACAAATGCCTTAGTTT 58.331 33.333 0.00 0.00 34.78 2.66
2366 2784 3.493002 CCCAAGCTTTGCATTTGAGTTGA 60.493 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.827177 TGTTATAAGCAACTAATAGAATCGGG 57.173 34.615 0.00 0.00 0.00 5.14
14 15 9.613428 TGCACTGTTATAAGCAACTAATAGAAT 57.387 29.630 0.00 0.00 33.48 2.40
23 24 8.020819 TGTCTATTTTGCACTGTTATAAGCAAC 58.979 33.333 8.82 0.47 45.53 4.17
295 297 8.049117 AGAAAGAGTTGCCTTGACATCATTATA 58.951 33.333 0.00 0.00 0.00 0.98
357 735 7.436118 GGGCATGATTGCTCTTTTATATTCAA 58.564 34.615 0.00 0.00 46.44 2.69
485 864 3.730215 TTTGGGGAAGCAAGCATACTA 57.270 42.857 0.00 0.00 0.00 1.82
508 887 6.595772 TTTCTTAAACGCATGCAACATTTT 57.404 29.167 19.57 10.38 0.00 1.82
651 1033 6.992715 GGCAAGTCAAACTATATATGTCAGGT 59.007 38.462 0.00 0.00 0.00 4.00
691 1073 0.391661 AGTGCACTATCAGGCAACCG 60.392 55.000 20.16 0.00 42.45 4.44
1147 1532 1.701847 ACTTGACTGCCCATCTGTCTT 59.298 47.619 0.00 0.00 42.19 3.01
1269 1654 1.243902 AACCATTACCAACAGTGCCG 58.756 50.000 0.00 0.00 0.00 5.69
1403 1788 8.970691 ACTATTCATTTTGATTGAAAACTCCG 57.029 30.769 0.00 0.00 36.35 4.63
1451 1838 7.404671 ACAAACTGTTGTTTTATCAACTCCT 57.595 32.000 10.18 0.00 46.01 3.69
1541 1929 6.330004 TCATCTTTTGCTTGCTCAACAATA 57.670 33.333 0.00 0.00 37.72 1.90
1716 2104 1.448985 GGATGGTTGTGCTCGCTAAA 58.551 50.000 0.00 0.00 0.00 1.85
1944 2335 5.300034 AGCAAATCAGTGACATGTTTCAAGA 59.700 36.000 0.00 0.00 0.00 3.02
1988 2380 5.500234 AGCAATTTAGTGGCACTATCAAGA 58.500 37.500 26.71 9.92 29.64 3.02
2142 2554 3.074412 ACCATAGGCAAGTTCAGTTTCG 58.926 45.455 0.00 0.00 0.00 3.46
2146 2558 4.532521 AGACTAACCATAGGCAAGTTCAGT 59.467 41.667 0.00 0.00 39.88 3.41
2366 2784 6.691508 AGTTTCTTTTCTGTTTTCAGCAAGT 58.308 32.000 0.00 0.00 46.59 3.16
2475 2893 5.359194 TGAGTTCTGTCCCATAGAAATCC 57.641 43.478 11.21 0.00 44.33 3.01
2500 2918 8.050325 TGTAATGTGTTTAGTGCCATAAGGTAT 58.950 33.333 0.00 0.00 37.19 2.73


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

AutoCloner maintained by Alex Coulton.