Multiple sequence alignment - TraesCS6B01G155800

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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 TraesCS6B01G155800 chr6B 100.000 2936 0 0 1 2936 158195087 158192152 0.000000e+00 5422.0
1 TraesCS6B01G155800 chr6B 79.766 1883 358 18 1063 2936 157109323 157107455 0.000000e+00 1345.0
2 TraesCS6B01G155800 chr6B 81.032 601 107 4 1067 1665 125052187 125051592 3.430000e-129 472.0
3 TraesCS6B01G155800 chr6B 84.416 231 36 0 2598 2828 159375253 159375483 8.190000e-56 228.0
4 TraesCS6B01G155800 chr6B 90.741 54 5 0 485 538 156533147 156533094 4.060000e-09 73.1
5 TraesCS6B01G155800 chr6A 97.007 1938 55 2 999 2936 100368183 100366249 0.000000e+00 3254.0
6 TraesCS6B01G155800 chr6A 79.193 1884 367 18 1063 2936 98888042 98886174 0.000000e+00 1284.0
7 TraesCS6B01G155800 chr6A 90.171 997 41 14 9 971 100369145 100368172 0.000000e+00 1245.0
8 TraesCS6B01G155800 chr6A 78.783 1890 364 29 1063 2936 99016116 99014248 0.000000e+00 1234.0
9 TraesCS6B01G155800 chr6A 78.367 1886 382 22 1063 2936 98982310 98980439 0.000000e+00 1199.0
10 TraesCS6B01G155800 chr6A 73.700 1962 461 46 1003 2936 98323856 98321922 0.000000e+00 713.0
11 TraesCS6B01G155800 chr6A 73.792 1904 424 60 1063 2936 100087860 100086002 0.000000e+00 682.0
12 TraesCS6B01G155800 chr6A 87.145 599 65 8 2338 2935 100736478 100737065 0.000000e+00 669.0
13 TraesCS6B01G155800 chr6D 93.042 1624 71 15 42 1638 83213951 83212343 0.000000e+00 2335.0
14 TraesCS6B01G155800 chr6D 96.080 1301 30 3 1634 2934 83210510 83209231 0.000000e+00 2100.0
15 TraesCS6B01G155800 chr6D 87.874 1270 130 9 1669 2936 46902105 46903352 0.000000e+00 1471.0
16 TraesCS6B01G155800 chr6D 80.551 1887 336 25 1063 2936 82203919 82202051 0.000000e+00 1423.0
17 TraesCS6B01G155800 chr6D 79.618 1884 360 20 1063 2936 82220430 82218561 0.000000e+00 1330.0
18 TraesCS6B01G155800 chr6D 79.191 1879 372 15 1063 2934 83108477 83106611 0.000000e+00 1286.0
19 TraesCS6B01G155800 chr5D 74.305 1942 465 25 1005 2934 372064106 372062187 0.000000e+00 791.0
20 TraesCS6B01G155800 chr5D 73.181 1883 446 49 1079 2936 372060267 372058419 2.480000e-175 625.0


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 TraesCS6B01G155800 chr6B 158192152 158195087 2935 True 5422.0 5422 100.000 1 2936 1 chr6B.!!$R4 2935
1 TraesCS6B01G155800 chr6B 157107455 157109323 1868 True 1345.0 1345 79.766 1063 2936 1 chr6B.!!$R3 1873
2 TraesCS6B01G155800 chr6B 125051592 125052187 595 True 472.0 472 81.032 1067 1665 1 chr6B.!!$R1 598
3 TraesCS6B01G155800 chr6A 100366249 100369145 2896 True 2249.5 3254 93.589 9 2936 2 chr6A.!!$R6 2927
4 TraesCS6B01G155800 chr6A 98886174 98888042 1868 True 1284.0 1284 79.193 1063 2936 1 chr6A.!!$R2 1873
5 TraesCS6B01G155800 chr6A 99014248 99016116 1868 True 1234.0 1234 78.783 1063 2936 1 chr6A.!!$R4 1873
6 TraesCS6B01G155800 chr6A 98980439 98982310 1871 True 1199.0 1199 78.367 1063 2936 1 chr6A.!!$R3 1873
7 TraesCS6B01G155800 chr6A 98321922 98323856 1934 True 713.0 713 73.700 1003 2936 1 chr6A.!!$R1 1933
8 TraesCS6B01G155800 chr6A 100086002 100087860 1858 True 682.0 682 73.792 1063 2936 1 chr6A.!!$R5 1873
9 TraesCS6B01G155800 chr6A 100736478 100737065 587 False 669.0 669 87.145 2338 2935 1 chr6A.!!$F1 597
10 TraesCS6B01G155800 chr6D 83209231 83213951 4720 True 2217.5 2335 94.561 42 2934 2 chr6D.!!$R4 2892
11 TraesCS6B01G155800 chr6D 46902105 46903352 1247 False 1471.0 1471 87.874 1669 2936 1 chr6D.!!$F1 1267
12 TraesCS6B01G155800 chr6D 82202051 82203919 1868 True 1423.0 1423 80.551 1063 2936 1 chr6D.!!$R1 1873
13 TraesCS6B01G155800 chr6D 82218561 82220430 1869 True 1330.0 1330 79.618 1063 2936 1 chr6D.!!$R2 1873
14 TraesCS6B01G155800 chr6D 83106611 83108477 1866 True 1286.0 1286 79.191 1063 2934 1 chr6D.!!$R3 1871
15 TraesCS6B01G155800 chr5D 372058419 372064106 5687 True 708.0 791 73.743 1005 2936 2 chr5D.!!$R1 1931

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
562 568 0.395311 TCTCGCAGGTCGGTTCCTAT 60.395 55.0 0.00 0.00 39.05 2.57 F
990 1023 0.820891 CTGGTGCCCATATGCCAGTC 60.821 60.0 15.37 4.42 42.47 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1584 1.915614 GCATTGAGTGCGACCAGGTG 61.916 60.0 0.00 0.00 45.23 4.00 R
2819 8458 0.975040 AGTCTAGGACCTGCAGGCTG 60.975 60.0 33.06 17.22 39.32 4.85 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
35 36 4.380781 TTCCGGAATGACGCGCCA 62.381 61.111 14.35 0.00 0.00 5.69
72 74 2.038387 ACGGAAAACAACAGCAGACT 57.962 45.000 0.00 0.00 0.00 3.24
75 77 4.134563 ACGGAAAACAACAGCAGACTTAT 58.865 39.130 0.00 0.00 0.00 1.73
104 106 0.673437 AACACCGGCATGACAAAAGG 59.327 50.000 0.00 0.00 0.00 3.11
149 151 3.788227 TCCATGAGGCTACAAACTTGT 57.212 42.857 0.00 0.07 38.91 3.16
152 154 3.560025 CCATGAGGCTACAAACTTGTCCT 60.560 47.826 0.00 0.53 42.35 3.85
182 184 6.672266 TGTTACCAGAGTCTCAATTCTTCT 57.328 37.500 1.94 0.00 0.00 2.85
255 261 7.177744 GGTATCCCTTATTTTTCCACAACAAGA 59.822 37.037 0.00 0.00 0.00 3.02
325 331 1.056660 AAAGAACTCCAGAAGGGCGA 58.943 50.000 0.00 0.00 36.21 5.54
374 380 4.853007 AGCAACCATCTGAAGAATAAGCT 58.147 39.130 0.00 0.00 0.00 3.74
411 417 9.702253 TTTATAAGAAAAGTGGCATAATACCCA 57.298 29.630 0.00 0.00 0.00 4.51
412 418 7.823745 ATAAGAAAAGTGGCATAATACCCAG 57.176 36.000 0.00 0.00 0.00 4.45
413 419 3.954258 AGAAAAGTGGCATAATACCCAGC 59.046 43.478 0.00 0.00 0.00 4.85
415 421 0.478507 AGTGGCATAATACCCAGCCC 59.521 55.000 0.00 0.00 46.45 5.19
416 422 0.478507 GTGGCATAATACCCAGCCCT 59.521 55.000 0.00 0.00 46.45 5.19
417 423 0.771127 TGGCATAATACCCAGCCCTC 59.229 55.000 0.00 0.00 46.45 4.30
418 424 0.771127 GGCATAATACCCAGCCCTCA 59.229 55.000 0.00 0.00 41.25 3.86
436 442 4.518249 CCTCATTTTACAGACCTTCCCTC 58.482 47.826 0.00 0.00 0.00 4.30
552 558 0.610687 CCTCTTCCTTTCTCGCAGGT 59.389 55.000 0.00 0.00 32.59 4.00
562 568 0.395311 TCTCGCAGGTCGGTTCCTAT 60.395 55.000 0.00 0.00 39.05 2.57
625 656 7.316640 AGTAGACTCATTAGTACAACTTGCAG 58.683 38.462 0.00 0.00 35.56 4.41
646 677 8.437360 TGCAGAATCTTACGAAATCATGTAAT 57.563 30.769 0.00 0.00 30.76 1.89
657 688 5.755375 CGAAATCATGTAATAGAGCACCAGT 59.245 40.000 0.00 0.00 0.00 4.00
723 756 2.289631 TGACCAGACCACTAATGCTGTG 60.290 50.000 0.00 0.00 35.39 3.66
947 980 6.072618 GGAGCACGCTCTATAATACTGTAGAA 60.073 42.308 17.99 0.00 42.38 2.10
986 1019 2.649831 CATCTGGTGCCCATATGCC 58.350 57.895 0.00 0.00 32.78 4.40
990 1023 0.820891 CTGGTGCCCATATGCCAGTC 60.821 60.000 15.37 4.42 42.47 3.51
997 1030 3.244665 TGCCCATATGCCAGTCTCATAAG 60.245 47.826 0.00 0.00 31.08 1.73
998 1031 3.008375 GCCCATATGCCAGTCTCATAAGA 59.992 47.826 0.00 0.00 31.08 2.10
999 1032 4.505566 GCCCATATGCCAGTCTCATAAGAA 60.506 45.833 0.00 0.00 31.93 2.52
1000 1033 5.624159 CCCATATGCCAGTCTCATAAGAAA 58.376 41.667 0.00 0.00 31.93 2.52
1001 1034 6.243900 CCCATATGCCAGTCTCATAAGAAAT 58.756 40.000 0.00 0.00 31.93 2.17
1076 1109 3.016736 CGATAAGTTCCCTTGGCATTGT 58.983 45.455 0.00 0.00 31.89 2.71
1081 1114 2.893489 AGTTCCCTTGGCATTGTTCTTC 59.107 45.455 0.00 0.00 0.00 2.87
1269 1304 2.924290 GACGGTTACTGATGTCTTGCTC 59.076 50.000 0.00 0.00 0.00 4.26
1753 3628 1.407258 GGACTCTCCCAGATGAACTCG 59.593 57.143 0.00 0.00 0.00 4.18
2151 4026 4.497006 GCAGAAATCTAATTGCACTGCGAT 60.497 41.667 0.00 0.00 36.17 4.58
2819 8458 2.821969 AGAATCAACATGCAACCTCACC 59.178 45.455 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.841556 TTCCCCGGCTTCACTCACT 60.842 57.895 0.00 0.00 0.00 3.41
88 90 1.606313 CCCCTTTTGTCATGCCGGT 60.606 57.895 1.90 0.00 0.00 5.28
104 106 0.467290 TGACCTGGTGTTCTTTGCCC 60.467 55.000 2.82 0.00 0.00 5.36
169 171 7.382898 AGGTCTAGTCAAAGAAGAATTGAGAC 58.617 38.462 0.00 0.00 37.46 3.36
176 178 5.983720 CGTCAAAGGTCTAGTCAAAGAAGAA 59.016 40.000 0.00 0.00 0.00 2.52
182 184 3.462483 TGCGTCAAAGGTCTAGTCAAA 57.538 42.857 0.00 0.00 0.00 2.69
255 261 1.624336 ATGGTGTGACATGCAGCTTT 58.376 45.000 0.00 0.00 35.60 3.51
389 395 5.592688 GCTGGGTATTATGCCACTTTTCTTA 59.407 40.000 1.13 0.00 0.00 2.10
397 403 0.478507 AGGGCTGGGTATTATGCCAC 59.521 55.000 1.13 0.00 46.53 5.01
399 405 0.771127 TGAGGGCTGGGTATTATGCC 59.229 55.000 0.00 0.00 44.22 4.40
400 406 2.887151 ATGAGGGCTGGGTATTATGC 57.113 50.000 0.00 0.00 0.00 3.14
401 407 6.068010 TGTAAAATGAGGGCTGGGTATTATG 58.932 40.000 0.00 0.00 0.00 1.90
402 408 6.102615 TCTGTAAAATGAGGGCTGGGTATTAT 59.897 38.462 0.00 0.00 0.00 1.28
403 409 5.430417 TCTGTAAAATGAGGGCTGGGTATTA 59.570 40.000 0.00 0.00 0.00 0.98
404 410 4.229582 TCTGTAAAATGAGGGCTGGGTATT 59.770 41.667 0.00 0.00 0.00 1.89
405 411 3.785887 TCTGTAAAATGAGGGCTGGGTAT 59.214 43.478 0.00 0.00 0.00 2.73
406 412 3.054655 GTCTGTAAAATGAGGGCTGGGTA 60.055 47.826 0.00 0.00 0.00 3.69
407 413 1.992557 TCTGTAAAATGAGGGCTGGGT 59.007 47.619 0.00 0.00 0.00 4.51
409 415 2.025887 AGGTCTGTAAAATGAGGGCTGG 60.026 50.000 0.00 0.00 0.00 4.85
411 417 3.308473 GGAAGGTCTGTAAAATGAGGGCT 60.308 47.826 0.00 0.00 0.00 5.19
412 418 3.017442 GGAAGGTCTGTAAAATGAGGGC 58.983 50.000 0.00 0.00 0.00 5.19
413 419 3.267031 AGGGAAGGTCTGTAAAATGAGGG 59.733 47.826 0.00 0.00 0.00 4.30
414 420 4.226168 AGAGGGAAGGTCTGTAAAATGAGG 59.774 45.833 0.00 0.00 0.00 3.86
415 421 5.428184 AGAGGGAAGGTCTGTAAAATGAG 57.572 43.478 0.00 0.00 0.00 2.90
416 422 5.843019 AAGAGGGAAGGTCTGTAAAATGA 57.157 39.130 0.00 0.00 0.00 2.57
417 423 6.241645 AGAAAGAGGGAAGGTCTGTAAAATG 58.758 40.000 0.00 0.00 0.00 2.32
418 424 6.455690 AGAAAGAGGGAAGGTCTGTAAAAT 57.544 37.500 0.00 0.00 0.00 1.82
436 442 4.695455 TGTTATGCCTCTTTTCGGAGAAAG 59.305 41.667 0.00 6.42 45.90 2.62
552 558 2.100916 GCAGCTTGTCTATAGGAACCGA 59.899 50.000 0.00 0.00 0.00 4.69
562 568 2.890945 TGTACACAGAGCAGCTTGTCTA 59.109 45.455 1.30 0.00 0.00 2.59
646 677 2.289694 GCTCAAGGAAACTGGTGCTCTA 60.290 50.000 0.00 0.00 45.42 2.43
657 688 4.865905 TGGCCATTTATAGCTCAAGGAAA 58.134 39.130 0.00 0.00 0.00 3.13
977 1010 4.897509 TCTTATGAGACTGGCATATGGG 57.102 45.455 4.56 0.00 0.00 4.00
986 1019 7.487189 GCATGGTTTTCATTTCTTATGAGACTG 59.513 37.037 0.00 0.00 32.92 3.51
990 1023 6.255020 GCTGCATGGTTTTCATTTCTTATGAG 59.745 38.462 0.00 0.00 32.92 2.90
997 1030 2.738314 GTGGCTGCATGGTTTTCATTTC 59.262 45.455 0.50 0.00 32.92 2.17
998 1031 2.369532 AGTGGCTGCATGGTTTTCATTT 59.630 40.909 0.50 0.00 32.92 2.32
999 1032 1.972795 AGTGGCTGCATGGTTTTCATT 59.027 42.857 0.50 0.00 32.92 2.57
1000 1033 1.547372 GAGTGGCTGCATGGTTTTCAT 59.453 47.619 0.50 0.00 36.31 2.57
1001 1034 0.961019 GAGTGGCTGCATGGTTTTCA 59.039 50.000 0.50 0.00 0.00 2.69
1213 1246 0.541863 GTGATCCCTTCCCACGTGAT 59.458 55.000 19.30 0.00 0.00 3.06
1214 1247 1.550130 GGTGATCCCTTCCCACGTGA 61.550 60.000 19.30 0.00 0.00 4.35
1269 1304 0.674895 CCTGAAGACCCTTGGAAGCG 60.675 60.000 0.00 0.00 0.00 4.68
1302 1337 3.123620 GCGAGGCTGCCAAGAGTG 61.124 66.667 22.65 4.54 0.00 3.51
1546 1584 1.915614 GCATTGAGTGCGACCAGGTG 61.916 60.000 0.00 0.00 45.23 4.00
1753 3628 3.858247 ACTCCAACGAGGTAGCATTAAC 58.142 45.455 0.00 0.00 40.77 2.01
1932 3807 8.040002 TCCCCATACATGATATTACTGTTCAA 57.960 34.615 0.00 0.00 0.00 2.69
1933 3808 7.625498 TCCCCATACATGATATTACTGTTCA 57.375 36.000 0.00 0.00 0.00 3.18
2151 4026 4.879545 GCCGTGGAACTTATTGGAAGATAA 59.120 41.667 0.00 0.00 31.75 1.75
2819 8458 0.975040 AGTCTAGGACCTGCAGGCTG 60.975 60.000 33.06 17.22 39.32 4.85


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

AutoCloner maintained by Alex Coulton.