Multiple sequence alignment - TraesCS6A01G072700

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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 TraesCS6A01G072700 chr6A 100.000 3146 0 0 1 3146 39629734 39626589 0.000000e+00 5810.0
1 TraesCS6A01G072700 chr6A 97.047 3149 88 5 1 3146 39581945 39578799 0.000000e+00 5295.0
2 TraesCS6A01G072700 chr6A 97.968 2412 45 2 736 3146 39670788 39668380 0.000000e+00 4180.0
3 TraesCS6A01G072700 chr6A 96.966 725 21 1 1 724 39539786 39539062 0.000000e+00 1216.0
4 TraesCS6A01G072700 chr6A 78.358 1437 221 59 751 2124 39878012 39876603 0.000000e+00 848.0
5 TraesCS6A01G072700 chr6A 86.838 623 76 5 2525 3146 39588752 39588135 0.000000e+00 691.0
6 TraesCS6A01G072700 chr6A 86.517 623 79 4 2525 3146 39546635 39546017 0.000000e+00 680.0
7 TraesCS6A01G072700 chr6A 86.035 623 81 4 2525 3146 39636544 39635927 0.000000e+00 664.0
8 TraesCS6A01G072700 chr6A 81.864 794 107 19 1476 2255 39548202 39547432 4.430000e-178 634.0
9 TraesCS6A01G072700 chr6A 81.288 823 117 19 1476 2284 39590315 39589516 1.590000e-177 632.0
10 TraesCS6A01G072700 chr6D 94.054 2035 83 8 1142 3146 36084580 36082554 0.000000e+00 3053.0
11 TraesCS6A01G072700 chr6D 84.472 1391 185 23 792 2174 35717988 35716621 0.000000e+00 1343.0
12 TraesCS6A01G072700 chr6D 79.111 1417 226 44 762 2139 35667511 35666126 0.000000e+00 913.0
13 TraesCS6A01G072700 chr6D 77.521 1517 264 41 766 2255 35642070 35640604 0.000000e+00 841.0
14 TraesCS6A01G072700 chr6D 86.356 623 80 4 2525 3146 35639835 35639217 0.000000e+00 675.0
15 TraesCS6A01G072700 chr6D 92.701 411 28 1 737 1147 36090482 36090074 2.700000e-165 592.0
16 TraesCS6A01G072700 chr6D 80.707 622 102 13 765 1374 36106099 36105484 4.750000e-128 468.0
17 TraesCS6A01G072700 chr6D 87.097 93 10 2 2591 2682 27847193 27847284 1.540000e-18 104.0
18 TraesCS6A01G072700 chr6D 88.462 52 4 1 2322 2373 27537715 27537666 9.420000e-06 62.1
19 TraesCS6A01G072700 chr6B 93.933 1533 87 5 747 2279 75526326 75524800 0.000000e+00 2311.0
20 TraesCS6A01G072700 chr6B 84.221 1540 206 24 762 2289 75423484 75421970 0.000000e+00 1463.0
21 TraesCS6A01G072700 chr6B 95.667 877 28 5 2271 3146 75524620 75523753 0.000000e+00 1400.0
22 TraesCS6A01G072700 chr6B 78.324 1527 261 48 789 2287 75510341 75508857 0.000000e+00 922.0
23 TraesCS6A01G072700 chr6B 85.947 861 96 17 2304 3146 75044692 75043839 0.000000e+00 896.0
24 TraesCS6A01G072700 chr6B 76.349 1260 244 32 759 2000 75046725 75045502 7.410000e-176 627.0
25 TraesCS6A01G072700 chr7A 96.970 726 20 2 1 724 3193155 3193880 0.000000e+00 1218.0
26 TraesCS6A01G072700 chr7A 95.868 726 28 2 1 724 722330048 722329323 0.000000e+00 1173.0
27 TraesCS6A01G072700 chr2A 96.832 726 21 2 1 724 97248612 97249337 0.000000e+00 1212.0
28 TraesCS6A01G072700 chr1A 96.276 725 26 1 1 724 583107276 583106552 0.000000e+00 1188.0
29 TraesCS6A01G072700 chr3A 96.006 726 27 2 1 724 735501200 735501925 0.000000e+00 1179.0
30 TraesCS6A01G072700 chr5A 95.172 725 32 3 1 724 15178071 15178793 0.000000e+00 1142.0
31 TraesCS6A01G072700 chr5A 94.897 725 34 3 1 724 15213245 15213967 0.000000e+00 1131.0
32 TraesCS6A01G072700 chr1D 82.143 952 139 19 759 1705 37880013 37880938 0.000000e+00 787.0
33 TraesCS6A01G072700 chr1D 83.006 712 86 20 2314 3004 37883110 37883807 2.070000e-171 612.0
34 TraesCS6A01G072700 chr1B 81.780 955 144 20 759 1704 57615177 57616110 0.000000e+00 773.0
35 TraesCS6A01G072700 chr1B 84.129 712 85 22 2314 3004 57617313 57618017 0.000000e+00 664.0
36 TraesCS6A01G072700 chr1B 78.938 565 84 20 1743 2289 57616188 57616735 4.990000e-93 351.0


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 TraesCS6A01G072700 chr6A 39626589 39629734 3145 True 5810.0 5810 100.000000 1 3146 1 chr6A.!!$R3 3145
1 TraesCS6A01G072700 chr6A 39578799 39581945 3146 True 5295.0 5295 97.047000 1 3146 1 chr6A.!!$R2 3145
2 TraesCS6A01G072700 chr6A 39668380 39670788 2408 True 4180.0 4180 97.968000 736 3146 1 chr6A.!!$R5 2410
3 TraesCS6A01G072700 chr6A 39539062 39539786 724 True 1216.0 1216 96.966000 1 724 1 chr6A.!!$R1 723
4 TraesCS6A01G072700 chr6A 39876603 39878012 1409 True 848.0 848 78.358000 751 2124 1 chr6A.!!$R6 1373
5 TraesCS6A01G072700 chr6A 39635927 39636544 617 True 664.0 664 86.035000 2525 3146 1 chr6A.!!$R4 621
6 TraesCS6A01G072700 chr6A 39588135 39590315 2180 True 661.5 691 84.063000 1476 3146 2 chr6A.!!$R8 1670
7 TraesCS6A01G072700 chr6A 39546017 39548202 2185 True 657.0 680 84.190500 1476 3146 2 chr6A.!!$R7 1670
8 TraesCS6A01G072700 chr6D 36082554 36084580 2026 True 3053.0 3053 94.054000 1142 3146 1 chr6D.!!$R4 2004
9 TraesCS6A01G072700 chr6D 35716621 35717988 1367 True 1343.0 1343 84.472000 792 2174 1 chr6D.!!$R3 1382
10 TraesCS6A01G072700 chr6D 35666126 35667511 1385 True 913.0 913 79.111000 762 2139 1 chr6D.!!$R2 1377
11 TraesCS6A01G072700 chr6D 35639217 35642070 2853 True 758.0 841 81.938500 766 3146 2 chr6D.!!$R7 2380
12 TraesCS6A01G072700 chr6D 36105484 36106099 615 True 468.0 468 80.707000 765 1374 1 chr6D.!!$R6 609
13 TraesCS6A01G072700 chr6B 75523753 75526326 2573 True 1855.5 2311 94.800000 747 3146 2 chr6B.!!$R4 2399
14 TraesCS6A01G072700 chr6B 75421970 75423484 1514 True 1463.0 1463 84.221000 762 2289 1 chr6B.!!$R1 1527
15 TraesCS6A01G072700 chr6B 75508857 75510341 1484 True 922.0 922 78.324000 789 2287 1 chr6B.!!$R2 1498
16 TraesCS6A01G072700 chr6B 75043839 75046725 2886 True 761.5 896 81.148000 759 3146 2 chr6B.!!$R3 2387
17 TraesCS6A01G072700 chr7A 3193155 3193880 725 False 1218.0 1218 96.970000 1 724 1 chr7A.!!$F1 723
18 TraesCS6A01G072700 chr7A 722329323 722330048 725 True 1173.0 1173 95.868000 1 724 1 chr7A.!!$R1 723
19 TraesCS6A01G072700 chr2A 97248612 97249337 725 False 1212.0 1212 96.832000 1 724 1 chr2A.!!$F1 723
20 TraesCS6A01G072700 chr1A 583106552 583107276 724 True 1188.0 1188 96.276000 1 724 1 chr1A.!!$R1 723
21 TraesCS6A01G072700 chr3A 735501200 735501925 725 False 1179.0 1179 96.006000 1 724 1 chr3A.!!$F1 723
22 TraesCS6A01G072700 chr5A 15178071 15178793 722 False 1142.0 1142 95.172000 1 724 1 chr5A.!!$F1 723
23 TraesCS6A01G072700 chr5A 15213245 15213967 722 False 1131.0 1131 94.897000 1 724 1 chr5A.!!$F2 723
24 TraesCS6A01G072700 chr1D 37880013 37883807 3794 False 699.5 787 82.574500 759 3004 2 chr1D.!!$F1 2245
25 TraesCS6A01G072700 chr1B 57615177 57618017 2840 False 596.0 773 81.615667 759 3004 3 chr1B.!!$F1 2245

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
921 927 1.153289 CATCTCTGACCCCGGCTTG 60.153 63.158 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2898 4817 5.537295 AGGCCCGAGTTAATAAACAAAGTTT 59.463 36.0 0.0 0.51 38.12 2.66 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
37 38 3.558674 GCTGTGTCAGGCTATGGTT 57.441 52.632 0.00 0.00 31.21 3.67
70 71 2.564062 CCCACGAAGACCTTTAGTACCA 59.436 50.000 0.00 0.00 0.00 3.25
111 112 6.867293 CGGTACTAGAGTTTCTTTGTAAGCTT 59.133 38.462 3.48 3.48 0.00 3.74
164 165 4.816385 GCAGTATGAGCAGTTTATAAGCCA 59.184 41.667 0.00 0.00 39.69 4.75
482 484 4.669206 TTCTGAATGGCTTGAAGCAAAA 57.331 36.364 19.89 4.17 44.75 2.44
583 587 2.787723 AAGCGACGTCATCAATTTCG 57.212 45.000 17.16 0.00 0.00 3.46
921 927 1.153289 CATCTCTGACCCCGGCTTG 60.153 63.158 0.00 0.00 0.00 4.01
1088 1110 3.513909 CATCTTCATGCCCTTGGGATA 57.486 47.619 10.36 0.00 30.15 2.59
1131 1153 0.036199 ACCAATTAGCGCGGTACCAA 60.036 50.000 18.99 5.92 0.00 3.67
1296 1329 0.319383 AGACAGACGAGCAGCAACAG 60.319 55.000 0.00 0.00 0.00 3.16
1510 1567 4.394300 AGTTTGATTTGGAGAAGCAGATCG 59.606 41.667 0.00 0.00 0.00 3.69
1891 1997 6.428465 TCATCCGTTTGAAAGTGTTTATGCTA 59.572 34.615 0.00 0.00 0.00 3.49
2063 2194 5.378292 TGATCTCCTCAACATATAGCGAC 57.622 43.478 0.00 0.00 0.00 5.19
2521 4439 8.217111 TCAATGCCCAATAATCTGATACAACTA 58.783 33.333 0.00 0.00 0.00 2.24
2638 4556 5.183904 GGACATGATGGAGCTAAACTTTTGT 59.816 40.000 0.00 0.00 0.00 2.83
2898 4817 0.326595 TACCTCGGCATTTGGCTTCA 59.673 50.000 2.49 0.00 44.01 3.02
2947 4869 9.836864 CTATATAGGTTGCATTTCATATGGCTA 57.163 33.333 2.13 0.00 0.00 3.93
3129 5054 2.163010 TCTCGAGTTATGGACCGTCAAC 59.837 50.000 13.13 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 2.572556 TGGCGAGGTGGGACTAAAAATA 59.427 45.455 0.00 0.00 0.00 1.40
164 165 2.071540 CGTCATTGTCTGTGCACTCAT 58.928 47.619 19.41 0.00 0.00 2.90
372 374 1.225855 TGACGTCGCTTTGAATGCTT 58.774 45.000 11.62 0.00 0.00 3.91
464 466 5.221601 TGGTTATTTTGCTTCAAGCCATTCA 60.222 36.000 7.01 0.00 41.51 2.57
482 484 2.814805 AGAGGTGCAATGCTGGTTAT 57.185 45.000 6.82 0.00 0.00 1.89
531 535 5.008613 GCATACTGAACACAAAAGAAGTCCA 59.991 40.000 0.00 0.00 0.00 4.02
583 587 6.919662 ACAACAAATGATGTCAGAACATGTTC 59.080 34.615 27.69 27.69 46.20 3.18
741 747 2.829003 CTACTCCTCTCGCCCGCA 60.829 66.667 0.00 0.00 0.00 5.69
743 749 3.597728 GGCTACTCCTCTCGCCCG 61.598 72.222 0.00 0.00 36.56 6.13
921 927 4.083862 AGAAGGAAGCGGCGGGAC 62.084 66.667 9.78 0.00 0.00 4.46
1088 1110 3.480133 GTAGGAGGCCATGGCGGT 61.480 66.667 29.90 20.03 43.06 5.68
1131 1153 0.178861 AGGGATCCCACACCAAGAGT 60.179 55.000 32.69 4.64 38.92 3.24
1510 1567 3.244112 ACTGGTACTGGTTTCACAGCTAC 60.244 47.826 0.00 0.00 42.21 3.58
1891 1997 6.837312 TGTAAAGGCATATGCTATTACCTGT 58.163 36.000 30.85 18.57 39.22 4.00
2063 2194 6.632834 CACAAACATACAAAAAGAAGACTCCG 59.367 38.462 0.00 0.00 0.00 4.63
2472 4372 8.593492 TGATGAGATATTTGGATAAACTCACG 57.407 34.615 0.00 0.00 37.69 4.35
2898 4817 5.537295 AGGCCCGAGTTAATAAACAAAGTTT 59.463 36.000 0.00 0.51 38.12 2.66
2947 4869 8.608185 AGGTATTACAACAATCCCAAATGAAT 57.392 30.769 0.00 0.00 0.00 2.57
3033 4956 8.524870 AGAATGACAAACAAAAATATGCTGAC 57.475 30.769 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.