Multiple sequence alignment - TraesCS6A01G193000

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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 TraesCS6A01G193000 chr6A 100.000 2366 0 0 1 2366 266026583 266028948 0.000000e+00 4370
1 TraesCS6A01G193000 chr6A 96.913 2365 70 2 1 2364 266018705 266021067 0.000000e+00 3960
2 TraesCS6A01G193000 chr6A 87.047 1351 140 28 1 1328 259362613 259361275 0.000000e+00 1493
3 TraesCS6A01G193000 chr6A 84.743 1265 152 32 1 1233 430709014 430707759 0.000000e+00 1229
4 TraesCS6A01G193000 chr6A 93.659 757 44 4 1294 2048 259361195 259360441 0.000000e+00 1129
5 TraesCS6A01G193000 chr6A 89.484 523 50 5 1845 2366 312689354 312689872 0.000000e+00 656
6 TraesCS6A01G193000 chr5A 96.332 2372 78 5 1 2366 176943795 176941427 0.000000e+00 3890
7 TraesCS6A01G193000 chr5A 88.473 694 66 12 1 686 131342932 131342245 0.000000e+00 826
8 TraesCS6A01G193000 chr3A 95.407 2373 98 7 1 2366 347832940 347830572 0.000000e+00 3768
9 TraesCS6A01G193000 chr3A 89.565 690 66 5 1 685 293307462 293308150 0.000000e+00 870
10 TraesCS6A01G193000 chr4A 93.976 2374 133 9 1 2366 197215294 197212923 0.000000e+00 3583
11 TraesCS6A01G193000 chr4A 86.074 1350 153 28 1 1328 205932272 205933608 0.000000e+00 1419
12 TraesCS6A01G193000 chr4A 86.010 1351 146 32 1 1328 205924346 205925676 0.000000e+00 1408
13 TraesCS6A01G193000 chr4A 93.404 758 36 5 1298 2054 205925761 205926505 0.000000e+00 1110
14 TraesCS6A01G193000 chr4A 92.857 728 39 4 1323 2049 205933716 205934431 0.000000e+00 1044
15 TraesCS6A01G193000 chr7A 95.455 1738 73 5 630 2366 420702004 420703736 0.000000e+00 2767
16 TraesCS6A01G193000 chr7A 95.312 640 27 2 1 637 420701344 420701983 0.000000e+00 1013
17 TraesCS6A01G193000 chr7A 90.051 392 29 8 1498 1886 324976859 324977243 1.260000e-137 499
18 TraesCS6A01G193000 chr7A 90.975 277 19 6 1295 1570 324967844 324968115 3.720000e-98 368
19 TraesCS6A01G193000 chr7A 92.683 82 5 1 1248 1328 324967678 324967759 1.490000e-22 117
20 TraesCS6A01G193000 chr2A 88.584 692 69 10 1 686 305105792 305106479 0.000000e+00 832
21 TraesCS6A01G193000 chr2A 88.551 690 71 8 1 686 305113645 305114330 0.000000e+00 830
22 TraesCS6A01G193000 chr2A 84.321 759 89 23 1 740 663732717 663731970 0.000000e+00 715
23 TraesCS6A01G193000 chr1A 91.762 522 40 2 1845 2366 326543230 326542712 0.000000e+00 723
24 TraesCS6A01G193000 chr1A 91.571 522 41 2 1845 2366 385002421 385002939 0.000000e+00 717
25 TraesCS6A01G193000 chr1A 90.979 521 44 2 1846 2366 326535656 326535139 0.000000e+00 699


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 TraesCS6A01G193000 chr6A 266026583 266028948 2365 False 4370.0 4370 100.0000 1 2366 1 chr6A.!!$F2 2365
1 TraesCS6A01G193000 chr6A 266018705 266021067 2362 False 3960.0 3960 96.9130 1 2364 1 chr6A.!!$F1 2363
2 TraesCS6A01G193000 chr6A 259360441 259362613 2172 True 1311.0 1493 90.3530 1 2048 2 chr6A.!!$R2 2047
3 TraesCS6A01G193000 chr6A 430707759 430709014 1255 True 1229.0 1229 84.7430 1 1233 1 chr6A.!!$R1 1232
4 TraesCS6A01G193000 chr6A 312689354 312689872 518 False 656.0 656 89.4840 1845 2366 1 chr6A.!!$F3 521
5 TraesCS6A01G193000 chr5A 176941427 176943795 2368 True 3890.0 3890 96.3320 1 2366 1 chr5A.!!$R2 2365
6 TraesCS6A01G193000 chr5A 131342245 131342932 687 True 826.0 826 88.4730 1 686 1 chr5A.!!$R1 685
7 TraesCS6A01G193000 chr3A 347830572 347832940 2368 True 3768.0 3768 95.4070 1 2366 1 chr3A.!!$R1 2365
8 TraesCS6A01G193000 chr3A 293307462 293308150 688 False 870.0 870 89.5650 1 685 1 chr3A.!!$F1 684
9 TraesCS6A01G193000 chr4A 197212923 197215294 2371 True 3583.0 3583 93.9760 1 2366 1 chr4A.!!$R1 2365
10 TraesCS6A01G193000 chr4A 205924346 205926505 2159 False 1259.0 1408 89.7070 1 2054 2 chr4A.!!$F1 2053
11 TraesCS6A01G193000 chr4A 205932272 205934431 2159 False 1231.5 1419 89.4655 1 2049 2 chr4A.!!$F2 2048
12 TraesCS6A01G193000 chr7A 420701344 420703736 2392 False 1890.0 2767 95.3835 1 2366 2 chr7A.!!$F3 2365
13 TraesCS6A01G193000 chr2A 305105792 305106479 687 False 832.0 832 88.5840 1 686 1 chr2A.!!$F1 685
14 TraesCS6A01G193000 chr2A 305113645 305114330 685 False 830.0 830 88.5510 1 686 1 chr2A.!!$F2 685
15 TraesCS6A01G193000 chr2A 663731970 663732717 747 True 715.0 715 84.3210 1 740 1 chr2A.!!$R1 739
16 TraesCS6A01G193000 chr1A 326542712 326543230 518 True 723.0 723 91.7620 1845 2366 1 chr1A.!!$R2 521
17 TraesCS6A01G193000 chr1A 385002421 385002939 518 False 717.0 717 91.5710 1845 2366 1 chr1A.!!$F1 521
18 TraesCS6A01G193000 chr1A 326535139 326535656 517 True 699.0 699 90.9790 1846 2366 1 chr1A.!!$R1 520

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
259 269 1.106944 AGGCCGGAACAACAAACCAG 61.107 55.0 5.05 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1910 0.033991 TCTCTCAACTCCCTCTCCGG 60.034 60.0 0.0 0.0 0.0 5.14 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
165 172 5.425630 AGTTCGATCTTGTTTATGTACCCC 58.574 41.667 0.00 0.0 0.00 4.95
259 269 1.106944 AGGCCGGAACAACAAACCAG 61.107 55.000 5.05 0.0 0.00 4.00
831 908 2.354401 CCTTGCAGGAGGAGCTCGA 61.354 63.158 7.83 0.0 37.67 4.04
894 971 3.900855 GGGACGAGCGAGTCACTA 58.099 61.111 14.73 0.0 41.15 2.74
986 1063 1.217057 ACAGGGAAGCATGGACCCAT 61.217 55.000 0.00 0.0 45.43 4.00
1044 1121 4.069232 CAGCTCGGCGTCCTCCAA 62.069 66.667 6.85 0.0 0.00 3.53
1198 1275 1.721664 CGGATCGAACGTAGCAGGGA 61.722 60.000 4.89 0.0 0.00 4.20
1236 1313 1.675641 GCTCGATTTGGCCAGTGGT 60.676 57.895 11.74 0.0 0.00 4.16
1537 1953 1.900486 GAGGAGAAGGAAACGGGAAGA 59.100 52.381 0.00 0.0 0.00 2.87
1693 2109 2.292521 TGGTGCAGACTAGGGAGAGATT 60.293 50.000 0.00 0.0 0.00 2.40
1722 2138 2.360726 GGCTACGGTTTGGGTGGG 60.361 66.667 0.00 0.0 0.00 4.61
1815 2231 3.577313 GCGGCGGCTTCAGGATTC 61.577 66.667 9.78 0.0 35.83 2.52
2049 2469 0.953471 CTGGGACAATTTCGGACGCA 60.953 55.000 0.00 0.0 38.70 5.24
2187 2612 1.850345 GAGGGGGAGAAGAGAGAGAGA 59.150 57.143 0.00 0.0 0.00 3.10
2188 2613 1.852965 AGGGGGAGAAGAGAGAGAGAG 59.147 57.143 0.00 0.0 0.00 3.20
2189 2614 1.850345 GGGGGAGAAGAGAGAGAGAGA 59.150 57.143 0.00 0.0 0.00 3.10
2190 2615 2.158608 GGGGGAGAAGAGAGAGAGAGAG 60.159 59.091 0.00 0.0 0.00 3.20
2210 2635 2.267642 CCCGGCATCTGTTTCCGA 59.732 61.111 0.00 0.0 45.53 4.55
2244 2669 1.808945 CCGACGTTAGACCGGCTATAT 59.191 52.381 0.00 0.0 36.62 0.86
2285 2710 1.626321 TGGGCTATCAAACGAACTCCA 59.374 47.619 0.00 0.0 0.00 3.86
2294 2719 3.997681 TCAAACGAACTCCAAATGCGATA 59.002 39.130 0.00 0.0 0.00 2.92
2311 2736 2.159707 CGATAAAACTTGACAGGCGGTG 60.160 50.000 0.00 0.0 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
259 269 4.750598 GCATATAAGGAGTTTCCGGACTTC 59.249 45.833 1.83 0.00 42.75 3.01
687 746 1.422531 TTTTTCATGTTGGGCCAGCT 58.577 45.000 21.45 4.29 0.00 4.24
740 814 1.298157 CTCCGCAAACATGCCGAAGA 61.298 55.000 0.00 0.00 0.00 2.87
894 971 5.467063 CCTTTCTTCTTTAGAAACGAGCAGT 59.533 40.000 0.00 0.00 45.60 4.40
921 998 1.226030 GCCGCTGTTTTACCTGTCGT 61.226 55.000 0.00 0.00 0.00 4.34
986 1063 1.133482 TCTGCATCACCTAGATCCGGA 60.133 52.381 6.61 6.61 33.72 5.14
1198 1275 2.204151 CCCCAGGGTCCCTCTGTT 60.204 66.667 7.76 0.00 0.00 3.16
1494 1910 0.033991 TCTCTCAACTCCCTCTCCGG 60.034 60.000 0.00 0.00 0.00 5.14
1537 1953 1.284313 CTCTTCTGCTCCCCTTCCTT 58.716 55.000 0.00 0.00 0.00 3.36
1693 2109 1.379977 CGTAGCCCTCCACCTCTCA 60.380 63.158 0.00 0.00 0.00 3.27
1809 2225 0.266152 ATCCACTCCTCCCGAATCCT 59.734 55.000 0.00 0.00 0.00 3.24
1815 2231 2.041922 TCCCATCCACTCCTCCCG 60.042 66.667 0.00 0.00 0.00 5.14
1978 2397 2.224606 CGGATCATCCCCAAACATCTG 58.775 52.381 0.00 0.00 31.13 2.90
2031 2450 1.071642 TGCGTCCGAAATTGTCCCA 59.928 52.632 0.00 0.00 0.00 4.37
2049 2469 1.292223 CATCGAACCCCTGACGTGT 59.708 57.895 0.00 0.00 0.00 4.49
2055 2475 1.003355 ACAGTGCATCGAACCCCTG 60.003 57.895 0.00 0.00 0.00 4.45
2188 2613 3.645268 AAACAGATGCCGGGCCCTC 62.645 63.158 22.43 10.85 0.00 4.30
2189 2614 3.645268 GAAACAGATGCCGGGCCCT 62.645 63.158 22.43 10.92 0.00 5.19
2190 2615 3.140814 GAAACAGATGCCGGGCCC 61.141 66.667 17.97 13.57 0.00 5.80
2244 2669 3.249986 ACCGTTAAACTATAGCGGCAA 57.750 42.857 13.63 0.00 45.53 4.52
2285 2710 4.485163 GCCTGTCAAGTTTTATCGCATTT 58.515 39.130 0.00 0.00 0.00 2.32
2294 2719 2.335316 TACACCGCCTGTCAAGTTTT 57.665 45.000 0.00 0.00 33.91 2.43


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

AutoCloner maintained by Alex Coulton.