Multiple sequence alignment - TraesCS1D01G027900

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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 TraesCS1D01G027900 chr1D 100.000 2707 0 0 1 2707 11122709 11125415 0.000000e+00 4944
1 TraesCS1D01G027900 chr1D 97.772 808 3 1 340 1132 11040358 11041165 0.000000e+00 1378
2 TraesCS1D01G027900 chr1D 99.566 692 3 0 441 1132 11089185 11089876 0.000000e+00 1262
3 TraesCS1D01G027900 chr1D 90.881 658 24 7 2053 2707 11041514 11042138 0.000000e+00 850
4 TraesCS1D01G027900 chr1D 90.592 659 25 8 2053 2707 11090228 11090853 0.000000e+00 839
5 TraesCS1D01G027900 chr1D 100.000 324 0 0 1 324 11039991 11040314 1.390000e-167 599
6 TraesCS1D01G027900 chr1D 100.000 324 0 0 1 324 11088679 11089002 1.390000e-167 599
7 TraesCS1D01G027900 chr1D 99.054 317 1 2 1 316 11039477 11039792 3.910000e-158 568
8 TraesCS1D01G027900 chr1D 99.288 281 2 0 1 281 11008617 11008897 2.400000e-140 508
9 TraesCS1D01G027900 chr1D 99.454 183 1 0 340 522 11009165 11009347 1.550000e-87 333
10 TraesCS1D01G027900 chr1A 97.227 2308 40 10 416 2707 22634733 22632434 0.000000e+00 3886
11 TraesCS1D01G027900 chr1A 94.002 1067 55 3 914 1979 12698839 12697781 0.000000e+00 1607
12 TraesCS1D01G027900 chr1A 93.333 330 20 2 2062 2390 12688957 12688629 1.130000e-133 486
13 TraesCS1D01G027900 chr1A 93.103 145 2 3 2380 2524 12686710 12686574 3.530000e-49 206
14 TraesCS1D01G027900 chr1A 90.323 155 9 2 1 150 22646039 22645886 5.910000e-47 198
15 TraesCS1D01G027900 chr1B 90.998 2344 160 33 392 2704 16477731 16480054 0.000000e+00 3112
16 TraesCS1D01G027900 chr1B 93.212 1429 80 6 1224 2648 16645423 16646838 0.000000e+00 2085
17 TraesCS1D01G027900 chr1B 91.008 1568 103 19 456 2000 16692509 16694061 0.000000e+00 2080
18 TraesCS1D01G027900 chr7B 93.103 145 2 3 2380 2524 192786231 192786095 3.530000e-49 206
19 TraesCS1D01G027900 chr2B 93.103 145 2 3 2380 2524 47184053 47184189 3.530000e-49 206


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 TraesCS1D01G027900 chr1D 11122709 11125415 2706 False 4944.00 4944 100.000000 1 2707 1 chr1D.!!$F1 2706
1 TraesCS1D01G027900 chr1D 11088679 11090853 2174 False 900.00 1262 96.719333 1 2707 3 chr1D.!!$F4 2706
2 TraesCS1D01G027900 chr1D 11039477 11042138 2661 False 848.75 1378 96.926750 1 2707 4 chr1D.!!$F3 2706
3 TraesCS1D01G027900 chr1D 11008617 11009347 730 False 420.50 508 99.371000 1 522 2 chr1D.!!$F2 521
4 TraesCS1D01G027900 chr1A 22632434 22634733 2299 True 3886.00 3886 97.227000 416 2707 1 chr1A.!!$R2 2291
5 TraesCS1D01G027900 chr1A 12697781 12698839 1058 True 1607.00 1607 94.002000 914 1979 1 chr1A.!!$R1 1065
6 TraesCS1D01G027900 chr1A 12686574 12688957 2383 True 346.00 486 93.218000 2062 2524 2 chr1A.!!$R4 462
7 TraesCS1D01G027900 chr1B 16477731 16480054 2323 False 3112.00 3112 90.998000 392 2704 1 chr1B.!!$F1 2312
8 TraesCS1D01G027900 chr1B 16645423 16646838 1415 False 2085.00 2085 93.212000 1224 2648 1 chr1B.!!$F2 1424
9 TraesCS1D01G027900 chr1B 16692509 16694061 1552 False 2080.00 2080 91.008000 456 2000 1 chr1B.!!$F3 1544

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
1113 1862 6.237901 TGCTTTCTGCCAATAAGTTTCTCTA 58.762 36.0 0.0 0.0 42.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 3153 0.240411 AACCAGACGTCGAGTGCTAC 59.76 55.0 10.46 0.0 0.0 3.58 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
1113 1862 6.237901 TGCTTTCTGCCAATAAGTTTCTCTA 58.762 36.000 0.00 0.00 42.00 2.43
1221 1971 6.887545 TGTAGTCTGAACCAAAAAGGAAAGAA 59.112 34.615 0.00 0.00 41.22 2.52
1274 2024 8.774586 GTTATTGTGATTTGTAGTCTGAACTGT 58.225 33.333 0.00 0.00 36.92 3.55
1628 2378 7.509141 AATCATGGATGAATAAATACACGCA 57.491 32.000 0.00 0.00 40.69 5.24
1932 2683 1.412453 TTAGTGTGACCCCGTGCCTT 61.412 55.000 0.00 0.00 0.00 4.35
1933 2684 1.412453 TAGTGTGACCCCGTGCCTTT 61.412 55.000 0.00 0.00 0.00 3.11
2327 3097 2.286732 AGCTTGGGAGGGATGCCT 60.287 61.111 4.97 4.97 0.00 4.75
2359 3148 2.657237 CCACCAGGTGAGGACGTC 59.343 66.667 22.37 7.13 35.23 4.34
2360 3149 2.258591 CACCAGGTGAGGACGTCG 59.741 66.667 15.35 0.00 35.23 5.12
2361 3150 3.681835 ACCAGGTGAGGACGTCGC 61.682 66.667 9.92 4.73 34.63 5.19
2366 3155 3.434319 GTGAGGACGTCGCCGGTA 61.434 66.667 9.92 0.00 38.78 4.02
2367 3156 3.129502 TGAGGACGTCGCCGGTAG 61.130 66.667 9.92 0.00 38.78 3.18
2368 3157 4.549516 GAGGACGTCGCCGGTAGC 62.550 72.222 9.92 0.00 38.78 3.58
2371 3160 4.112341 GACGTCGCCGGTAGCACT 62.112 66.667 1.90 0.00 44.04 4.40
2372 3161 4.112341 ACGTCGCCGGTAGCACTC 62.112 66.667 1.90 0.00 44.04 3.51
2699 5424 5.709631 AGTTTGGCACATACACATACATGAA 59.290 36.000 0.00 0.00 42.66 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1176 1925 8.565896 ACTACAGATCAAAACAATGCTAATGA 57.434 30.769 0.00 0.00 0.00 2.57
1221 1971 5.271598 TGGCCCAAATAGTTCATCAAATCT 58.728 37.500 0.00 0.00 0.00 2.40
1274 2024 8.306038 AGCTGCAAACAATTGATCAAAATAGTA 58.694 29.630 13.09 0.09 38.94 1.82
1628 2378 0.246360 TCGACACACGCCATTGATCT 59.754 50.000 0.00 0.00 42.26 2.75
2357 3146 3.807538 TCGAGTGCTACCGGCGAC 61.808 66.667 9.30 0.00 45.43 5.19
2358 3147 3.807538 GTCGAGTGCTACCGGCGA 61.808 66.667 9.30 0.00 45.43 5.54
2360 3149 4.112341 ACGTCGAGTGCTACCGGC 62.112 66.667 0.00 0.00 42.22 6.13
2361 3150 2.099831 GACGTCGAGTGCTACCGG 59.900 66.667 0.00 0.00 0.00 5.28
2362 3151 1.226046 CAGACGTCGAGTGCTACCG 60.226 63.158 10.46 0.00 0.00 4.02
2363 3152 1.136984 CCAGACGTCGAGTGCTACC 59.863 63.158 10.46 0.00 0.00 3.18
2364 3153 0.240411 AACCAGACGTCGAGTGCTAC 59.760 55.000 10.46 0.00 0.00 3.58
2365 3154 0.520404 GAACCAGACGTCGAGTGCTA 59.480 55.000 10.46 0.00 0.00 3.49
2366 3155 1.286260 GAACCAGACGTCGAGTGCT 59.714 57.895 10.46 0.00 0.00 4.40
2367 3156 2.081212 CGAACCAGACGTCGAGTGC 61.081 63.158 10.46 9.31 0.00 4.40
2368 3157 1.442184 CCGAACCAGACGTCGAGTG 60.442 63.158 10.46 2.88 0.00 3.51
2369 3158 2.952245 CCGAACCAGACGTCGAGT 59.048 61.111 10.46 8.84 0.00 4.18
2370 3159 2.504244 GCCGAACCAGACGTCGAG 60.504 66.667 10.46 8.14 0.00 4.04
2371 3160 3.263503 CTGCCGAACCAGACGTCGA 62.264 63.158 10.46 0.00 34.77 4.20
2372 3161 2.805353 CTGCCGAACCAGACGTCG 60.805 66.667 10.46 5.16 34.77 5.12
2641 5364 4.101114 TCCAGGGTAGATTAAGACAAGCA 58.899 43.478 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.