Multiple sequence alignment - TraesCS6A01G186400

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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 TraesCS6A01G186400 chr6A 100.000 2729 0 0 1 2729 221553154 221555882 0.000000e+00 5040.0
1 TraesCS6A01G186400 chr6A 89.357 855 81 3 889 1733 601134356 601133502 0.000000e+00 1066.0
2 TraesCS6A01G186400 chr6A 90.507 769 67 3 983 1745 601006054 601005286 0.000000e+00 1011.0
3 TraesCS6A01G186400 chr6A 99.038 208 0 1 2044 2249 221560199 221560406 3.320000e-99 372.0
4 TraesCS6A01G186400 chr6A 89.189 74 5 3 890 961 601006180 601006108 3.740000e-14 89.8
5 TraesCS6A01G186400 chr6B 96.429 1456 44 5 593 2044 300242899 300241448 0.000000e+00 2394.0
6 TraesCS6A01G186400 chr6B 89.825 855 73 5 889 1729 691749641 691748787 0.000000e+00 1085.0
7 TraesCS6A01G186400 chr6B 89.950 597 48 8 1 591 300243536 300242946 0.000000e+00 760.0
8 TraesCS6A01G186400 chr6D 96.110 1388 38 9 593 1971 162125469 162126849 0.000000e+00 2250.0
9 TraesCS6A01G186400 chr6D 90.971 875 72 3 889 1756 454800726 454799852 0.000000e+00 1171.0
10 TraesCS6A01G186400 chr6D 89.202 852 78 10 886 1729 454686208 454687053 0.000000e+00 1051.0
11 TraesCS6A01G186400 chr6D 86.492 459 52 7 131 584 162124962 162125415 1.890000e-136 496.0
12 TraesCS6A01G186400 chr6D 90.667 150 9 4 3 149 162124709 162124856 7.710000e-46 195.0
13 TraesCS6A01G186400 chr3B 98.171 656 10 1 2076 2729 8463790 8464445 0.000000e+00 1144.0
14 TraesCS6A01G186400 chr3B 98.551 207 1 1 2044 2248 8468753 8468959 5.550000e-97 364.0
15 TraesCS6A01G186400 chr5B 95.052 485 21 2 2044 2526 274843722 274843239 0.000000e+00 760.0
16 TraesCS6A01G186400 chr5B 77.049 671 122 26 1034 1685 494026885 494026228 9.290000e-95 357.0
17 TraesCS6A01G186400 chr5B 94.419 215 12 0 2515 2729 274843210 274842996 5.630000e-87 331.0
18 TraesCS6A01G186400 chr5B 97.849 186 2 1 2044 2227 274839087 274838902 1.220000e-83 320.0
19 TraesCS6A01G186400 chr5D 83.173 416 55 10 991 1394 411785584 411785172 1.540000e-97 366.0
20 TraesCS6A01G186400 chr5D 92.857 98 6 1 1 97 6204949 6204852 1.020000e-29 141.0
21 TraesCS6A01G186400 chr5D 92.857 98 6 1 1 97 240134030 240134127 1.020000e-29 141.0
22 TraesCS6A01G186400 chr5D 92.857 98 6 1 1 97 449152827 449152730 1.020000e-29 141.0
23 TraesCS6A01G186400 chr3D 76.065 493 76 30 2265 2729 441040110 441040588 4.580000e-53 219.0
24 TraesCS6A01G186400 chr3D 75.410 488 89 22 2265 2729 441035047 441035526 9.900000e-50 207.0
25 TraesCS6A01G186400 chr3D 82.353 136 17 4 2230 2359 615236421 615236555 7.990000e-21 111.0
26 TraesCS6A01G186400 chrUn 92.857 98 6 1 1 97 441828183 441828086 1.020000e-29 141.0
27 TraesCS6A01G186400 chr4D 92.857 98 6 1 1 97 417109135 417109038 1.020000e-29 141.0
28 TraesCS6A01G186400 chr1D 92.857 98 6 1 1 97 254492538 254492635 1.020000e-29 141.0
29 TraesCS6A01G186400 chr1D 92.857 98 6 1 1 97 254493182 254493085 1.020000e-29 141.0
30 TraesCS6A01G186400 chr1A 81.098 164 21 9 2206 2362 588957850 588958010 3.690000e-24 122.0


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 TraesCS6A01G186400 chr6A 221553154 221555882 2728 False 5040.000000 5040 100.000000 1 2729 1 chr6A.!!$F1 2728
1 TraesCS6A01G186400 chr6A 601133502 601134356 854 True 1066.000000 1066 89.357000 889 1733 1 chr6A.!!$R1 844
2 TraesCS6A01G186400 chr6A 601005286 601006180 894 True 550.400000 1011 89.848000 890 1745 2 chr6A.!!$R2 855
3 TraesCS6A01G186400 chr6B 300241448 300243536 2088 True 1577.000000 2394 93.189500 1 2044 2 chr6B.!!$R2 2043
4 TraesCS6A01G186400 chr6B 691748787 691749641 854 True 1085.000000 1085 89.825000 889 1729 1 chr6B.!!$R1 840
5 TraesCS6A01G186400 chr6D 454799852 454800726 874 True 1171.000000 1171 90.971000 889 1756 1 chr6D.!!$R1 867
6 TraesCS6A01G186400 chr6D 454686208 454687053 845 False 1051.000000 1051 89.202000 886 1729 1 chr6D.!!$F1 843
7 TraesCS6A01G186400 chr6D 162124709 162126849 2140 False 980.333333 2250 91.089667 3 1971 3 chr6D.!!$F2 1968
8 TraesCS6A01G186400 chr3B 8463790 8464445 655 False 1144.000000 1144 98.171000 2076 2729 1 chr3B.!!$F1 653
9 TraesCS6A01G186400 chr5B 274838902 274843722 4820 True 470.333333 760 95.773333 2044 2729 3 chr5B.!!$R2 685
10 TraesCS6A01G186400 chr5B 494026228 494026885 657 True 357.000000 357 77.049000 1034 1685 1 chr5B.!!$R1 651

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
755 934 0.107945 CCTCTTGAGGAAAGCTCCCG 60.108 60.0 11.02 0.0 43.64 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2304 1.27249 TCAGTTAGCCAGAGGACAACG 59.728 52.381 0.0 0.0 0.0 4.1 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
115 120 5.471797 TGAGAATGCGAACTCAATGGTAAAA 59.528 36.000 0.00 0.00 39.68 1.52
116 121 6.016693 TGAGAATGCGAACTCAATGGTAAAAA 60.017 34.615 0.00 0.00 39.68 1.94
117 122 6.381801 AGAATGCGAACTCAATGGTAAAAAG 58.618 36.000 0.00 0.00 0.00 2.27
118 123 5.957842 ATGCGAACTCAATGGTAAAAAGA 57.042 34.783 0.00 0.00 0.00 2.52
119 124 5.759506 TGCGAACTCAATGGTAAAAAGAA 57.240 34.783 0.00 0.00 0.00 2.52
164 292 5.227152 ACATTTTTCGTCTGGCAAATTACC 58.773 37.500 0.00 0.00 0.00 2.85
206 334 5.892119 ACTAGTGATTGGACGATTAGGAAGA 59.108 40.000 0.00 0.00 0.00 2.87
212 340 3.427573 TGGACGATTAGGAAGACAGTGA 58.572 45.455 0.00 0.00 0.00 3.41
218 346 6.071984 ACGATTAGGAAGACAGTGATATCCT 58.928 40.000 15.91 15.91 42.89 3.24
226 354 2.435805 GACAGTGATATCCTCAGCCCAA 59.564 50.000 0.00 0.00 33.51 4.12
241 369 2.043526 AGCCCAACAGGGATCAAATCTT 59.956 45.455 4.37 0.00 46.20 2.40
269 397 8.673711 GGTTTACATTTTGTGTCTCATATAGCA 58.326 33.333 0.00 0.00 42.29 3.49
271 399 9.665719 TTTACATTTTGTGTCTCATATAGCAGA 57.334 29.630 0.00 0.00 42.29 4.26
319 449 4.701651 TTCGTCTATAGAGAGGTGCCTA 57.298 45.455 1.64 0.00 38.48 3.93
422 556 7.009540 CCATAGCGCAAAGAAAGGAAAAATAAG 59.990 37.037 11.47 0.00 0.00 1.73
423 557 5.842907 AGCGCAAAGAAAGGAAAAATAAGT 58.157 33.333 11.47 0.00 0.00 2.24
435 569 7.588497 AGGAAAAATAAGTGAAAGACAAGCT 57.412 32.000 0.00 0.00 0.00 3.74
454 588 5.531122 AGCTAGGCGTCTATGTGATTTTA 57.469 39.130 0.00 0.00 0.00 1.52
476 610 0.181350 AATCTCAAGATCCACCGGCC 59.819 55.000 0.00 0.00 32.75 6.13
507 641 3.229293 GAGGACGCTTATAGGGGTACTT 58.771 50.000 16.60 2.79 42.26 2.24
525 659 5.934625 GGTACTTGCATACTCATAAGGGATG 59.065 44.000 0.00 0.00 36.82 3.51
533 667 8.043113 TGCATACTCATAAGGGATGAATGTATC 58.957 37.037 0.00 0.00 44.14 2.24
537 671 8.727100 ACTCATAAGGGATGAATGTATCTACA 57.273 34.615 0.00 0.00 44.14 2.74
562 696 7.946655 TGTTTGTGAGAGTCTGTATTTGTAG 57.053 36.000 0.00 0.00 0.00 2.74
699 878 0.670162 CAGTTGACCCAACCAAGCAG 59.330 55.000 6.24 0.00 44.49 4.24
755 934 0.107945 CCTCTTGAGGAAAGCTCCCG 60.108 60.000 11.02 0.00 43.64 5.14
791 970 1.173444 AGAGAGTGACACGTCGCCTT 61.173 55.000 7.11 0.00 40.77 4.35
831 1010 0.525029 GAAGCCAGTACGTACTCCGC 60.525 60.000 25.10 25.78 41.42 5.54
833 1012 2.803479 CCAGTACGTACTCCGCCC 59.197 66.667 25.10 0.00 41.42 6.13
896 1084 6.711645 GGGTTCCAACGCATACCTATAAATAA 59.288 38.462 1.82 0.00 41.07 1.40
954 1150 0.108472 CTCTCACTCCAGCGCAATCA 60.108 55.000 11.47 0.00 0.00 2.57
1041 1268 0.264359 CTCCCTCCTCCTCATCCACT 59.736 60.000 0.00 0.00 0.00 4.00
1557 1796 1.593196 CACTGGACATGGACGTGTTT 58.407 50.000 0.00 0.00 31.16 2.83
1914 2159 2.423892 TGGCAAAAAGACGTACAAGCAA 59.576 40.909 0.00 0.00 0.00 3.91
2053 2298 6.127451 CCCTTTGGTATATCCTGTTGGAAAAC 60.127 42.308 0.00 0.00 46.80 2.43
2059 2304 1.104577 TCCTGTTGGAAAACGCCCAC 61.105 55.000 0.00 0.00 39.87 4.61
2705 2991 1.178276 CGAGTCTGGCAACTACTCCT 58.822 55.000 14.93 0.00 43.28 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.977762 AATTAATCGTTATCGTTTCAAGGTTAC 57.022 29.630 0.00 0.00 38.33 2.50
164 292 5.182001 CACTAGTTGGTTCTCTTTTCCCATG 59.818 44.000 0.00 0.00 0.00 3.66
206 334 2.171448 GTTGGGCTGAGGATATCACTGT 59.829 50.000 4.83 0.00 33.22 3.55
226 354 7.027874 TGTAAACCTAAGATTTGATCCCTGT 57.972 36.000 0.00 0.00 0.00 4.00
269 397 7.939039 TGTTGACTTCCACTCAAAGAATATTCT 59.061 33.333 12.37 12.37 39.74 2.40
271 399 8.641498 ATGTTGACTTCCACTCAAAGAATATT 57.359 30.769 0.00 0.00 29.44 1.28
281 409 4.511826 AGACGAAAATGTTGACTTCCACTC 59.488 41.667 0.00 0.00 0.00 3.51
295 423 4.896482 AGGCACCTCTCTATAGACGAAAAT 59.104 41.667 0.00 0.00 0.00 1.82
332 462 9.002600 CCTTATCCATTTTCATTGATCGTATGA 57.997 33.333 6.30 6.30 0.00 2.15
422 556 1.727335 GACGCCTAGCTTGTCTTTCAC 59.273 52.381 0.00 0.00 0.00 3.18
423 557 1.618837 AGACGCCTAGCTTGTCTTTCA 59.381 47.619 0.00 0.00 39.87 2.69
435 569 8.367911 AGATTGATAAAATCACATAGACGCCTA 58.632 33.333 1.30 0.00 39.39 3.93
454 588 2.486191 GCCGGTGGATCTTGAGATTGAT 60.486 50.000 1.90 0.00 34.37 2.57
476 610 1.884235 AAGCGTCCTCAAAAGACTGG 58.116 50.000 0.00 0.00 31.83 4.00
507 641 6.191657 ACATTCATCCCTTATGAGTATGCA 57.808 37.500 0.00 0.00 45.32 3.96
525 659 8.709386 ACTCTCACAAACATGTAGATACATTC 57.291 34.615 0.00 0.00 43.99 2.67
533 667 8.438513 CAAATACAGACTCTCACAAACATGTAG 58.561 37.037 0.00 0.00 0.00 2.74
537 671 8.150945 ACTACAAATACAGACTCTCACAAACAT 58.849 33.333 0.00 0.00 0.00 2.71
584 718 3.548415 GCCGAACGTGGTTAATTTTCACA 60.548 43.478 0.00 0.00 0.00 3.58
673 852 0.668535 GTTGGGTCAACTGCTTCCAC 59.331 55.000 3.78 0.00 40.73 4.02
699 878 9.982291 TCTGCTTAAACAATTAACGATAATGAC 57.018 29.630 0.00 0.00 32.06 3.06
820 999 2.824041 GGACGGGCGGAGTACGTA 60.824 66.667 0.00 0.00 46.52 3.57
1338 1565 1.971357 ACGTCAGAGAGGTTGGTGAAT 59.029 47.619 0.00 0.00 0.00 2.57
1510 1749 1.805254 CCTCAAAAGCGGCATCAGG 59.195 57.895 1.45 0.00 0.00 3.86
1557 1796 1.581934 CAAACAAGCAGTCGAGGTCA 58.418 50.000 0.00 0.00 0.00 4.02
1823 2068 6.415206 AACATCATCCATTCCATCCAATTC 57.585 37.500 0.00 0.00 0.00 2.17
2053 2298 2.738521 CAGAGGACAACGTGGGCG 60.739 66.667 0.00 0.00 44.93 6.13
2059 2304 1.272490 TCAGTTAGCCAGAGGACAACG 59.728 52.381 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.