Multiple sequence alignment - TraesCS5A01G068200

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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 TraesCS5A01G068200 chr5A 100.000 2777 0 0 1 2777 76493214 76495990 0.000000e+00 5129
1 TraesCS5A01G068200 chr5A 98.311 2783 31 5 1 2777 76519645 76522417 0.000000e+00 4865
2 TraesCS5A01G068200 chr5A 98.239 2783 33 5 1 2777 76546407 76549179 0.000000e+00 4854
3 TraesCS5A01G068200 chr5A 96.339 601 21 1 2178 2777 76698635 76699235 0.000000e+00 987
4 TraesCS5A01G068200 chr5A 95.360 431 17 1 1 431 75340578 75341005 0.000000e+00 682
5 TraesCS5A01G068200 chr5A 92.079 202 16 0 5 206 75349774 75349975 4.530000e-73 285
6 TraesCS5A01G068200 chr5A 88.034 234 28 0 1931 2164 51452970 51452737 7.580000e-71 278
7 TraesCS5A01G068200 chr5A 95.652 115 5 0 451 565 75349233 75349347 4.720000e-43 185
8 TraesCS5A01G068200 chr5D 93.987 1081 49 9 430 1497 80303367 80304444 0.000000e+00 1622
9 TraesCS5A01G068200 chr5D 94.931 434 13 2 1 428 80301717 80302147 0.000000e+00 671
10 TraesCS5A01G068200 chr5D 92.225 373 25 4 1557 1928 298473098 298472729 2.450000e-145 525
11 TraesCS5A01G068200 chr5D 91.045 134 12 0 2042 2175 61348901 61348768 6.110000e-42 182
12 TraesCS5A01G068200 chr5B 92.247 1148 63 12 434 1560 88863785 88864927 0.000000e+00 1604
13 TraesCS5A01G068200 chr5B 96.471 340 12 0 1 340 88861148 88861487 1.870000e-156 562
14 TraesCS5A01G068200 chr5B 96.281 242 9 0 1931 2172 88976167 88976408 5.570000e-107 398
15 TraesCS5A01G068200 chr5B 87.190 242 31 0 1931 2172 69305428 69305669 2.720000e-70 276
16 TraesCS5A01G068200 chr5B 97.000 100 3 0 332 431 88862645 88862744 4.760000e-38 169
17 TraesCS5A01G068200 chr7D 96.026 604 22 2 2176 2777 478683063 478682460 0.000000e+00 981
18 TraesCS5A01G068200 chr7D 92.225 373 27 2 1557 1928 360436957 360437328 6.810000e-146 527
19 TraesCS5A01G068200 chr4D 95.847 602 24 1 2177 2777 327400583 327401184 0.000000e+00 972
20 TraesCS5A01G068200 chr4D 92.149 242 18 1 1931 2172 48465060 48465300 9.530000e-90 340
21 TraesCS5A01G068200 chr2D 95.410 610 26 2 2170 2777 163059508 163060117 0.000000e+00 970
22 TraesCS5A01G068200 chr2D 92.225 373 27 2 1557 1928 148909239 148908868 6.810000e-146 527
23 TraesCS5A01G068200 chr2D 78.994 795 138 15 436 1221 328459579 328458805 1.470000e-142 516
24 TraesCS5A01G068200 chr3D 95.826 599 24 1 2180 2777 556259997 556259399 0.000000e+00 966
25 TraesCS5A01G068200 chr3D 95.380 606 26 2 2174 2777 230707393 230707998 0.000000e+00 963
26 TraesCS5A01G068200 chr6D 95.515 602 25 2 2178 2777 459851500 459850899 0.000000e+00 961
27 TraesCS5A01G068200 chr6D 92.473 372 25 3 1557 1927 161340607 161340238 1.890000e-146 529
28 TraesCS5A01G068200 chr6D 79.514 288 43 10 961 1234 455841706 455841991 1.020000e-44 191
29 TraesCS5A01G068200 chrUn 97.561 410 5 1 1208 1612 477681166 477681575 0.000000e+00 697
30 TraesCS5A01G068200 chr1D 91.689 373 29 2 1557 1928 113515299 113514928 1.470000e-142 516
31 TraesCS5A01G068200 chr1D 91.689 373 29 2 1557 1928 218456357 218456728 1.470000e-142 516
32 TraesCS5A01G068200 chr1D 91.711 374 28 3 1557 1928 308121897 308122269 1.470000e-142 516
33 TraesCS5A01G068200 chr2A 78.491 795 144 13 436 1221 434957825 434957049 1.920000e-136 496
34 TraesCS5A01G068200 chr3B 78.256 814 141 26 431 1223 207050511 207051309 8.940000e-135 490
35 TraesCS5A01G068200 chr3B 78.378 666 107 22 573 1223 194323780 194323137 5.570000e-107 398
36 TraesCS5A01G068200 chr4A 88.571 245 27 1 1931 2175 549394788 549394545 2.090000e-76 296
37 TraesCS5A01G068200 chr6B 81.250 240 38 3 1002 1234 693079857 693080096 1.310000e-43 187


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 TraesCS5A01G068200 chr5A 76493214 76495990 2776 False 5129.000000 5129 100.000000 1 2777 1 chr5A.!!$F2 2776
1 TraesCS5A01G068200 chr5A 76519645 76522417 2772 False 4865.000000 4865 98.311000 1 2777 1 chr5A.!!$F3 2776
2 TraesCS5A01G068200 chr5A 76546407 76549179 2772 False 4854.000000 4854 98.239000 1 2777 1 chr5A.!!$F4 2776
3 TraesCS5A01G068200 chr5A 76698635 76699235 600 False 987.000000 987 96.339000 2178 2777 1 chr5A.!!$F5 599
4 TraesCS5A01G068200 chr5A 75349233 75349975 742 False 235.000000 285 93.865500 5 565 2 chr5A.!!$F6 560
5 TraesCS5A01G068200 chr5D 80301717 80304444 2727 False 1146.500000 1622 94.459000 1 1497 2 chr5D.!!$F1 1496
6 TraesCS5A01G068200 chr5B 88861148 88864927 3779 False 778.333333 1604 95.239333 1 1560 3 chr5B.!!$F3 1559
7 TraesCS5A01G068200 chr7D 478682460 478683063 603 True 981.000000 981 96.026000 2176 2777 1 chr7D.!!$R1 601
8 TraesCS5A01G068200 chr4D 327400583 327401184 601 False 972.000000 972 95.847000 2177 2777 1 chr4D.!!$F2 600
9 TraesCS5A01G068200 chr2D 163059508 163060117 609 False 970.000000 970 95.410000 2170 2777 1 chr2D.!!$F1 607
10 TraesCS5A01G068200 chr2D 328458805 328459579 774 True 516.000000 516 78.994000 436 1221 1 chr2D.!!$R2 785
11 TraesCS5A01G068200 chr3D 556259399 556259997 598 True 966.000000 966 95.826000 2180 2777 1 chr3D.!!$R1 597
12 TraesCS5A01G068200 chr3D 230707393 230707998 605 False 963.000000 963 95.380000 2174 2777 1 chr3D.!!$F1 603
13 TraesCS5A01G068200 chr6D 459850899 459851500 601 True 961.000000 961 95.515000 2178 2777 1 chr6D.!!$R2 599
14 TraesCS5A01G068200 chr2A 434957049 434957825 776 True 496.000000 496 78.491000 436 1221 1 chr2A.!!$R1 785
15 TraesCS5A01G068200 chr3B 207050511 207051309 798 False 490.000000 490 78.256000 431 1223 1 chr3B.!!$F1 792
16 TraesCS5A01G068200 chr3B 194323137 194323780 643 True 398.000000 398 78.378000 573 1223 1 chr3B.!!$R1 650

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
392 2102 4.168101 TCCCTCTGCCCTACAATATAAGG 58.832 47.826 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 5306 6.869913 CCTTCATGTGCAATGTTTTACATTCT 59.13 34.615 2.22 0.0 44.91 2.4 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
392 2102 4.168101 TCCCTCTGCCCTACAATATAAGG 58.832 47.826 0.0 0.0 0.00 2.69
1341 4314 9.908152 AAATTCTTTAGAAAATGTTAAGGGTCG 57.092 29.630 0.0 0.0 37.61 4.79
1586 4559 0.539986 GTGAAACCTATGGCCCTCGA 59.460 55.000 0.0 0.0 0.00 4.04
1587 4560 0.539986 TGAAACCTATGGCCCTCGAC 59.460 55.000 0.0 0.0 0.00 4.20
2123 5097 3.417101 CTTGGGTAGGTGCATTTGTACA 58.583 45.455 0.0 0.0 32.02 2.90
2196 5170 4.710324 TGGTGTAGGATCGAAAGTTTGTT 58.290 39.130 0.0 0.0 0.00 2.83
2329 5306 4.402474 TGCAAGTCTAAGAGTATAGCAGCA 59.598 41.667 0.0 0.0 0.00 4.41
2651 5628 4.447290 TCAACTTCACAATCTTGACGGAA 58.553 39.130 0.0 0.0 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
392 2102 5.048083 TGAAGTCATCAACAATTAACCAGGC 60.048 40.000 0.00 0.00 34.30 4.85
2196 5170 7.123847 GTCAAGTAGTTAATCACCCTCCTCTAA 59.876 40.741 0.00 0.00 0.00 2.10
2238 5214 7.560368 TGCCAAGACTTAAAATTGGAAAAAGA 58.440 30.769 14.22 0.00 45.19 2.52
2244 5220 6.916360 AATCTGCCAAGACTTAAAATTGGA 57.084 33.333 14.22 2.89 45.19 3.53
2329 5306 6.869913 CCTTCATGTGCAATGTTTTACATTCT 59.130 34.615 2.22 0.00 44.91 2.40
2515 5492 3.746045 AGACAAGGTTGCTTCTTCGTA 57.254 42.857 0.00 0.00 0.00 3.43
2651 5628 1.348036 GTTAGGTGTCACTTGGGAGCT 59.652 52.381 2.35 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.