Multiple sequence alignment - TraesCS6A01G237900

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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 TraesCS6A01G237900 chr6A 100.000 3248 0 0 1 3248 447180191 447176944 0.000000e+00 5999
1 TraesCS6A01G237900 chr6D 96.321 3262 83 13 1 3248 310889354 310886116 0.000000e+00 5325
2 TraesCS6A01G237900 chr6B 91.189 2372 147 29 912 3246 515577543 515579889 0.000000e+00 3166
3 TraesCS6A01G237900 chr6B 90.826 436 24 12 491 918 515577092 515577519 1.310000e-158 569
4 TraesCS6A01G237900 chr4A 86.066 244 32 2 1295 1537 739587219 739587461 8.940000e-66 261
5 TraesCS6A01G237900 chr4A 81.008 258 34 12 1280 1526 691247036 691247289 1.190000e-44 191
6 TraesCS6A01G237900 chr7D 85.656 244 33 2 1295 1537 4026495 4026253 4.160000e-64 255
7 TraesCS6A01G237900 chr7A 84.836 244 35 2 1295 1537 3859880 3859638 9.000000e-61 244
8 TraesCS6A01G237900 chr4D 82.988 241 37 4 1296 1534 481912293 481912055 7.060000e-52 215
9 TraesCS6A01G237900 chr2B 82.511 223 39 0 1301 1523 470472233 470472011 2.560000e-46 196
10 TraesCS6A01G237900 chr2A 82.589 224 37 2 1301 1523 535241934 535241712 2.560000e-46 196
11 TraesCS6A01G237900 chr2D 81.166 223 42 0 1301 1523 398087123 398086901 2.570000e-41 180


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 TraesCS6A01G237900 chr6A 447176944 447180191 3247 True 5999.0 5999 100.0000 1 3248 1 chr6A.!!$R1 3247
1 TraesCS6A01G237900 chr6D 310886116 310889354 3238 True 5325.0 5325 96.3210 1 3248 1 chr6D.!!$R1 3247
2 TraesCS6A01G237900 chr6B 515577092 515579889 2797 False 1867.5 3166 91.0075 491 3246 2 chr6B.!!$F1 2755

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
219 225 0.679960 ACCCTTTTCCTACATGCCGC 60.68 55.000 0.00 0.0 0.00 6.53 F
324 335 1.080498 TCCTGGGAAGGAGGCTTAAGA 59.92 52.381 6.67 0.0 33.38 2.10 F
1971 2041 1.079819 CCTGTCGTCGACCAGCAAT 60.08 57.895 22.05 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1474 0.106918 TTCCGACAAGGCAGTGGTTT 60.107 50.000 0.0 0.0 40.77 3.27 R
2221 2300 0.031857 CACAGATGAGCCGAGCCTAG 59.968 60.000 0.0 0.0 0.00 3.02 R
3116 3207 1.278127 TCCTCCCCTCTTTTAAGTGCG 59.722 52.381 0.0 0.0 0.00 5.34 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
22 23 1.003718 GTGGACCTGTGGTAGTGCC 60.004 63.158 0.00 0.00 35.25 5.01
23 24 2.221299 TGGACCTGTGGTAGTGCCC 61.221 63.158 0.00 0.00 35.25 5.36
44 46 3.056107 CCCATACGAAGTCTTCACTCCAA 60.056 47.826 12.99 0.00 43.93 3.53
45 47 4.383118 CCCATACGAAGTCTTCACTCCAAT 60.383 45.833 12.99 0.00 43.93 3.16
46 48 5.163447 CCCATACGAAGTCTTCACTCCAATA 60.163 44.000 12.99 0.00 43.93 1.90
47 49 5.980116 CCATACGAAGTCTTCACTCCAATAG 59.020 44.000 12.99 0.00 43.93 1.73
48 50 6.183360 CCATACGAAGTCTTCACTCCAATAGA 60.183 42.308 12.99 0.00 43.93 1.98
49 51 5.923733 ACGAAGTCTTCACTCCAATAGAT 57.076 39.130 12.99 0.00 29.74 1.98
50 52 5.897050 ACGAAGTCTTCACTCCAATAGATC 58.103 41.667 12.99 0.00 29.74 2.75
51 53 5.419155 ACGAAGTCTTCACTCCAATAGATCA 59.581 40.000 12.99 0.00 29.74 2.92
52 54 6.071334 ACGAAGTCTTCACTCCAATAGATCAA 60.071 38.462 12.99 0.00 29.74 2.57
96 98 0.826715 TCCACATGGACTCAGCTAGC 59.173 55.000 6.62 6.62 39.78 3.42
141 147 5.670485 TGCAGTTAACTGTATATCCACCTG 58.330 41.667 30.90 7.70 45.45 4.00
142 148 5.188948 TGCAGTTAACTGTATATCCACCTGT 59.811 40.000 30.90 0.00 45.45 4.00
143 149 6.381707 TGCAGTTAACTGTATATCCACCTGTA 59.618 38.462 30.90 3.78 45.45 2.74
144 150 6.924060 GCAGTTAACTGTATATCCACCTGTAG 59.076 42.308 30.90 5.54 45.45 2.74
145 151 7.201884 GCAGTTAACTGTATATCCACCTGTAGA 60.202 40.741 30.90 0.00 45.45 2.59
159 165 7.514721 TCCACCTGTAGAGTACAATTTTTCTT 58.485 34.615 0.00 0.00 38.38 2.52
216 222 2.092323 GGTCACCCTTTTCCTACATGC 58.908 52.381 0.00 0.00 0.00 4.06
219 225 0.679960 ACCCTTTTCCTACATGCCGC 60.680 55.000 0.00 0.00 0.00 6.53
257 263 2.293122 TGGTTTCATTGTCCGCTGAAAG 59.707 45.455 0.00 0.00 40.86 2.62
274 280 8.531530 CCGCTGAAAGTATTTGTTATTTTATGC 58.468 33.333 0.00 0.00 39.27 3.14
324 335 1.080498 TCCTGGGAAGGAGGCTTAAGA 59.920 52.381 6.67 0.00 33.38 2.10
344 355 9.403110 CTTAAGAGCATGCATAAATTTGGATAC 57.597 33.333 21.98 0.00 0.00 2.24
361 372 5.537188 TGGATACATTTTCAGTGCCAAAAC 58.463 37.500 0.00 0.00 46.17 2.43
367 378 5.047377 ACATTTTCAGTGCCAAAACGGATAT 60.047 36.000 0.00 0.00 36.56 1.63
369 380 4.695217 TTCAGTGCCAAAACGGATATTC 57.305 40.909 0.00 0.00 36.56 1.75
404 415 5.450818 AGCCTTTTATCTGTGTTCCCATA 57.549 39.130 0.00 0.00 0.00 2.74
431 442 5.725551 TCCCATGTCATACTACCCAAATT 57.274 39.130 0.00 0.00 0.00 1.82
443 454 5.983540 ACTACCCAAATTTTGTTTGAAGCA 58.016 33.333 8.26 0.00 0.00 3.91
454 465 5.820926 TTGTTTGAAGCATCGTATTTTGC 57.179 34.783 0.00 0.00 39.17 3.68
504 515 1.821216 TTTCGGCTGAAAGGTCCATC 58.179 50.000 16.83 0.00 39.13 3.51
558 573 3.626930 ACACAAAAGTAACCTGGCAAGA 58.373 40.909 0.00 0.00 0.00 3.02
573 588 5.745294 CCTGGCAAGAACATTGAATTAATCG 59.255 40.000 0.00 0.00 0.00 3.34
594 609 6.190954 TCGGGTTATCGTATATGTGATGAG 57.809 41.667 2.69 0.00 0.00 2.90
598 613 7.251994 GGGTTATCGTATATGTGATGAGAGTC 58.748 42.308 2.69 0.00 0.00 3.36
638 653 5.204409 TGTCATGATTGCTTGCTTTTTCT 57.796 34.783 0.00 0.00 0.00 2.52
746 761 4.320608 AACTTGGGTACAAAGCAACATG 57.679 40.909 7.30 0.00 35.89 3.21
1238 1290 5.336150 ACACTGAACTCATTGATCGATCT 57.664 39.130 25.02 4.07 31.86 2.75
1432 1486 3.149196 CATCTACACAAACCACTGCCTT 58.851 45.455 0.00 0.00 0.00 4.35
1450 1504 2.622436 CTTGTCGGAATGAGGAAGACC 58.378 52.381 0.00 0.00 0.00 3.85
1493 1547 1.663739 CCCAACGGTCAGAAGTCGA 59.336 57.895 0.00 0.00 0.00 4.20
1562 1616 3.362831 CACGCCCGTATGTATTATTCGTC 59.637 47.826 0.00 0.00 0.00 4.20
1725 1786 4.451150 GACGACCATGGCGCTGGA 62.451 66.667 21.44 0.00 39.73 3.86
1797 1858 2.520458 CACCCCCAGAACTTGGCA 59.480 61.111 0.00 0.00 46.32 4.92
1971 2041 1.079819 CCTGTCGTCGACCAGCAAT 60.080 57.895 22.05 0.00 0.00 3.56
2061 2131 2.818274 GGTGAATCGTCGGCCACC 60.818 66.667 2.24 13.07 41.72 4.61
2202 2272 2.053244 CATGAAGAGGCCCTGGACTAT 58.947 52.381 0.00 0.00 30.74 2.12
2221 2300 2.892425 CTTCGACATCTGCCGGCC 60.892 66.667 26.77 5.93 0.00 6.13
2222 2301 3.376935 CTTCGACATCTGCCGGCCT 62.377 63.158 26.77 5.57 0.00 5.19
2279 2358 2.559668 CAAGCACAACTCCATTGGACAT 59.440 45.455 0.00 0.00 43.20 3.06
2656 2741 8.680903 ACCATGTATCTCTCAATTCATTGAAAC 58.319 33.333 2.68 0.00 45.26 2.78
2738 2823 7.800092 AGGATACACTAGAGAATGAAGCAATT 58.200 34.615 0.00 0.00 41.41 2.32
3116 3207 1.305930 CCAGAAGTTTAGGTGGCGGC 61.306 60.000 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.496070 TGGAGTGAAGACTTCGTATGGG 59.504 50.000 10.56 0.00 28.70 4.00
23 24 3.868757 TGGAGTGAAGACTTCGTATGG 57.131 47.619 10.56 0.00 28.70 2.74
48 50 7.056635 ACTCATTAGGATCAACCGAATTTGAT 58.943 34.615 6.59 6.59 46.73 2.57
49 51 6.414732 ACTCATTAGGATCAACCGAATTTGA 58.585 36.000 0.00 0.00 40.96 2.69
50 52 6.238484 GGACTCATTAGGATCAACCGAATTTG 60.238 42.308 0.00 0.00 40.96 2.32
51 53 5.823045 GGACTCATTAGGATCAACCGAATTT 59.177 40.000 0.00 0.00 40.96 1.82
52 54 5.368989 GGACTCATTAGGATCAACCGAATT 58.631 41.667 0.00 0.00 40.96 2.17
87 89 2.203401 GAGTGCATTCTGCTAGCTGAG 58.797 52.381 21.56 13.77 45.31 3.35
179 185 1.831106 GACCCCAAACCCAATTCATCC 59.169 52.381 0.00 0.00 0.00 3.51
209 215 2.015736 AGAACAAGAGCGGCATGTAG 57.984 50.000 1.45 0.00 0.00 2.74
216 222 2.932614 CACCTTCATAGAACAAGAGCGG 59.067 50.000 0.00 0.00 0.00 5.52
219 225 5.997746 TGAAACCACCTTCATAGAACAAGAG 59.002 40.000 0.00 0.00 30.31 2.85
277 283 7.023171 TCCTTTTATGAAACTAAGGCAGGTA 57.977 36.000 0.00 0.00 37.62 3.08
284 290 7.121315 CCCAGGACTTCCTTTTATGAAACTAAG 59.879 40.741 0.00 0.00 46.09 2.18
289 295 5.592587 TCCCAGGACTTCCTTTTATGAAA 57.407 39.130 0.00 0.00 46.09 2.69
324 335 8.967664 AAAATGTATCCAAATTTATGCATGCT 57.032 26.923 20.33 7.07 30.21 3.79
344 355 3.090952 TCCGTTTTGGCACTGAAAATG 57.909 42.857 0.00 0.00 37.80 2.32
349 360 3.950397 AGAATATCCGTTTTGGCACTGA 58.050 40.909 0.00 0.00 37.80 3.41
350 361 7.604164 AGATATAGAATATCCGTTTTGGCACTG 59.396 37.037 3.80 0.00 37.80 3.66
361 372 9.877178 AAGGCTAAACAAGATATAGAATATCCG 57.123 33.333 3.80 0.00 0.00 4.18
404 415 7.401060 TTGGGTAGTATGACATGGGATTAAT 57.599 36.000 0.00 0.00 0.00 1.40
410 421 6.154363 ACAAAATTTGGGTAGTATGACATGGG 59.846 38.462 10.71 0.00 34.12 4.00
431 442 6.209129 GCAAAATACGATGCTTCAAACAAA 57.791 33.333 0.08 0.00 39.46 2.83
454 465 3.120025 ACATGATCGAGCTAGCGTATGAG 60.120 47.826 9.55 0.00 0.00 2.90
488 499 1.207089 TGTAGATGGACCTTTCAGCCG 59.793 52.381 0.00 0.00 0.00 5.52
504 515 5.499139 AAGGTTTGTGAACACACATGTAG 57.501 39.130 7.16 0.00 42.81 2.74
523 538 4.580580 ACTTTTGTGTCAAGGAAGCTAAGG 59.419 41.667 0.00 0.00 0.00 2.69
558 573 7.562454 ACGATAACCCGATTAATTCAATGTT 57.438 32.000 0.00 0.00 0.00 2.71
573 588 7.121463 AGACTCTCATCACATATACGATAACCC 59.879 40.741 0.00 0.00 0.00 4.11
594 609 8.082852 TGACAGTAGATAAAAAGTGTCAGACTC 58.917 37.037 8.51 0.00 46.15 3.36
800 815 5.492895 TCAGTTGTAGTTCCTCACAAAACA 58.507 37.500 0.00 0.00 36.47 2.83
801 816 6.431198 TTCAGTTGTAGTTCCTCACAAAAC 57.569 37.500 0.00 0.00 36.47 2.43
802 817 6.431543 TGTTTCAGTTGTAGTTCCTCACAAAA 59.568 34.615 0.00 0.00 36.47 2.44
803 818 5.941058 TGTTTCAGTTGTAGTTCCTCACAAA 59.059 36.000 0.00 0.00 36.47 2.83
804 819 5.353123 GTGTTTCAGTTGTAGTTCCTCACAA 59.647 40.000 0.00 0.00 32.40 3.33
852 867 9.770097 CTCAATTAGGGCACATGGTATATATAG 57.230 37.037 0.00 0.00 0.00 1.31
1208 1259 6.698008 TCAATGAGTTCAGTGTTTGTGATT 57.302 33.333 9.11 0.00 42.03 2.57
1238 1290 1.821759 CATTAATCGGGGCACGGCA 60.822 57.895 10.28 0.00 44.45 5.69
1420 1474 0.106918 TTCCGACAAGGCAGTGGTTT 60.107 50.000 0.00 0.00 40.77 3.27
1432 1486 0.902531 GGGTCTTCCTCATTCCGACA 59.097 55.000 0.00 0.00 0.00 4.35
1493 1547 2.418746 GGTACTCGTGCATGATCCAGTT 60.419 50.000 9.53 0.00 0.00 3.16
1562 1616 4.196193 TGCATAAAGGTAAGGATGGAACG 58.804 43.478 0.00 0.00 0.00 3.95
1725 1786 2.933287 TCCGGCATGAACCCACCT 60.933 61.111 0.00 0.00 0.00 4.00
1797 1858 3.238497 TGCTGGCTGTGGTACGGT 61.238 61.111 0.00 0.00 0.00 4.83
1956 2026 1.352156 GGTGATTGCTGGTCGACGAC 61.352 60.000 19.70 19.70 0.00 4.34
2061 2131 0.675837 TGTCGAGGTACCTCCAGTCG 60.676 60.000 31.78 22.27 39.77 4.18
2221 2300 0.031857 CACAGATGAGCCGAGCCTAG 59.968 60.000 0.00 0.00 0.00 3.02
2222 2301 1.395045 CCACAGATGAGCCGAGCCTA 61.395 60.000 0.00 0.00 0.00 3.93
2279 2358 7.990886 GGTCTGGATTGTATAAATTGTGTAGGA 59.009 37.037 0.00 0.00 0.00 2.94
2429 2513 6.550108 GTCCAGAGACCTGATACCAAATAGTA 59.450 42.308 0.00 0.00 43.02 1.82
2430 2514 5.364157 GTCCAGAGACCTGATACCAAATAGT 59.636 44.000 0.00 0.00 43.02 2.12
2431 2515 5.848406 GTCCAGAGACCTGATACCAAATAG 58.152 45.833 0.00 0.00 43.02 1.73
2685 2770 3.259374 TCTGACCAGAGGAGTAAAAGCAG 59.741 47.826 0.00 0.00 32.82 4.24
3116 3207 1.278127 TCCTCCCCTCTTTTAAGTGCG 59.722 52.381 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.