Multiple sequence alignment - TraesCS6D01G257300

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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 TraesCS6D01G257300 chr6D 100.000 3473 0 0 1 3473 363260422 363256950 0.000000e+00 6414.0
1 TraesCS6D01G257300 chr6D 85.714 84 10 2 3391 3473 363244300 363244218 1.720000e-13 87.9
2 TraesCS6D01G257300 chr6B 94.421 2886 87 24 1 2864 545271790 545268957 0.000000e+00 4370.0
3 TraesCS6D01G257300 chr6B 95.586 589 18 7 2892 3473 545268963 545268376 0.000000e+00 937.0
4 TraesCS6D01G257300 chr6A 96.152 2391 72 13 1091 3473 503820857 503818479 0.000000e+00 3888.0
5 TraesCS6D01G257300 chr6A 92.177 1061 42 9 1 1034 503822241 503821195 0.000000e+00 1461.0
6 TraesCS6D01G257300 chr6A 86.076 79 9 2 3396 3473 503814107 503814030 2.220000e-12 84.2
7 TraesCS6D01G257300 chr6A 89.474 57 5 1 599 655 163207988 163208043 1.730000e-08 71.3
8 TraesCS6D01G257300 chr1D 80.628 191 22 8 559 746 354724192 354724014 2.170000e-27 134.0
9 TraesCS6D01G257300 chr1B 80.105 191 23 8 559 746 39905240 39905418 1.010000e-25 128.0
10 TraesCS6D01G257300 chr4B 79.167 192 24 9 559 746 51669182 51669003 6.090000e-23 119.0
11 TraesCS6D01G257300 chr2A 79.167 192 24 10 559 746 710789428 710789607 6.090000e-23 119.0


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 TraesCS6D01G257300 chr6D 363256950 363260422 3472 True 6414.0 6414 100.0000 1 3473 1 chr6D.!!$R2 3472
1 TraesCS6D01G257300 chr6B 545268376 545271790 3414 True 2653.5 4370 95.0035 1 3473 2 chr6B.!!$R1 3472
2 TraesCS6D01G257300 chr6A 503818479 503822241 3762 True 2674.5 3888 94.1645 1 3473 2 chr6A.!!$R2 3472

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
555 565 0.977395 GCACTGGAGGAAGGTACAGT 59.023 55.000 0.00 0.0 44.36 3.55 F
1158 1471 2.132996 CCTCTGCGAGATCCTGGCT 61.133 63.158 7.07 0.0 36.21 4.75 F
1866 2179 0.602905 CACCGGGCGAGAAGTTTCTT 60.603 55.000 6.32 0.0 37.73 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 2086 1.981256 TGGAAGAGCCACTTGAAACC 58.019 50.000 0.0 0.0 43.33 3.27 R
2256 2569 2.066393 TGGAGGCAGGCTATTCGCT 61.066 57.895 0.0 0.0 39.13 4.93 R
2940 3254 3.195825 AGAAACGTAGCAGGAATACAGCT 59.804 43.478 0.0 0.0 42.14 4.24 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
71 72 3.118408 TGACTGTATAACCAGGCATGTCC 60.118 47.826 0.00 0.00 45.50 4.02
232 234 8.500837 TTTTTCAAATACGCAGATGTAAACTG 57.499 30.769 0.00 0.00 40.09 3.16
247 249 1.636148 AACTGCCCAACTGAATGCAT 58.364 45.000 0.00 0.00 32.53 3.96
255 257 3.934579 CCCAACTGAATGCATTTTAAGGC 59.065 43.478 14.33 0.00 36.03 4.35
289 291 5.630061 TGAATCAATATTGTGCGAACTGTG 58.370 37.500 14.97 0.00 0.00 3.66
304 306 2.708051 ACTGTGAAGATGATGTGCAGG 58.292 47.619 0.00 0.00 0.00 4.85
305 307 2.014857 CTGTGAAGATGATGTGCAGGG 58.985 52.381 0.00 0.00 0.00 4.45
330 332 3.417069 AACCCAATCGAATGTGTCTCA 57.583 42.857 0.00 0.00 0.00 3.27
431 437 1.202806 GCCAAGCTGCTCATACCCATA 60.203 52.381 1.00 0.00 0.00 2.74
552 562 1.348036 ACAAGCACTGGAGGAAGGTAC 59.652 52.381 0.00 0.00 0.00 3.34
553 563 1.347707 CAAGCACTGGAGGAAGGTACA 59.652 52.381 0.00 0.00 0.00 2.90
554 564 1.270907 AGCACTGGAGGAAGGTACAG 58.729 55.000 0.00 0.00 37.01 2.74
555 565 0.977395 GCACTGGAGGAAGGTACAGT 59.023 55.000 0.00 0.00 44.36 3.55
556 566 2.176889 GCACTGGAGGAAGGTACAGTA 58.823 52.381 0.00 0.00 41.85 2.74
913 932 4.142556 ACGGTTCAAGAACACACGAAAAAT 60.143 37.500 14.25 0.00 42.85 1.82
948 967 4.340489 TCCGACCCATCCACCCCA 62.340 66.667 0.00 0.00 0.00 4.96
1158 1471 2.132996 CCTCTGCGAGATCCTGGCT 61.133 63.158 7.07 0.00 36.21 4.75
1500 1813 3.841222 GCGTTTGTGGAAATGCCG 58.159 55.556 0.00 0.00 44.99 5.69
1701 2014 4.307908 GTTGCGCGCGAGGTGTTT 62.308 61.111 37.18 0.00 0.00 2.83
1719 2032 2.202171 GACGAAATGGTGCACGCG 60.202 61.111 11.45 3.53 0.00 6.01
1773 2086 4.369182 ACGACTCTTTCCTTACAACACTG 58.631 43.478 0.00 0.00 0.00 3.66
1866 2179 0.602905 CACCGGGCGAGAAGTTTCTT 60.603 55.000 6.32 0.00 37.73 2.52
1881 2194 3.730761 CTTCGTGCTGCACTGGCC 61.731 66.667 28.04 0.00 40.13 5.36
2256 2569 0.542467 AGGTGTGGAAATGCATGGCA 60.542 50.000 0.00 0.00 44.86 4.92
2308 2621 4.142687 GCGGTAACATGCTTGTATCAAAGT 60.143 41.667 5.56 0.00 34.06 2.66
2488 2801 5.277825 CGCACTAGGTTCTTCTCTCTTATG 58.722 45.833 0.00 0.00 0.00 1.90
2609 2922 9.811995 ATAAGAAGTTGTTAGTCGTGCATATAA 57.188 29.630 0.00 0.00 0.00 0.98
2859 3172 9.163899 CTGGTAAGTAAGGGTAGAAAAGAAATC 57.836 37.037 0.00 0.00 0.00 2.17
2919 3232 1.477553 TGAAGCCAATGGGAATGAGC 58.522 50.000 0.00 0.00 35.59 4.26
2940 3254 6.939730 TGAGCATCAAATACTTGGTACTTTCA 59.060 34.615 0.00 0.00 45.97 2.69
3310 3631 2.092699 TGGGGATGACGTCAATATTGCA 60.093 45.455 24.13 3.41 0.00 4.08
3405 3729 1.066929 GGTTCGGATGCTTGGCAAAAT 60.067 47.619 0.00 0.00 43.62 1.82
3459 3783 5.671493 AGCCGTTATCAAGCTTTACAGTAT 58.329 37.500 0.00 0.00 31.27 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.173356 TGATGGGCTGTAAGATTGGGAG 59.827 50.000 0.00 0.00 34.07 4.30
71 72 2.408271 TATGCAAGTGAAGGCCTGAG 57.592 50.000 5.69 0.00 0.00 3.35
232 234 3.934579 CCTTAAAATGCATTCAGTTGGGC 59.065 43.478 13.38 0.00 30.13 5.36
255 257 7.307160 GCACAATATTGATTCATGGCAGAATTG 60.307 37.037 22.16 5.02 38.30 2.32
263 265 5.684184 CAGTTCGCACAATATTGATTCATGG 59.316 40.000 22.16 4.33 0.00 3.66
274 276 4.565022 TCATCTTCACAGTTCGCACAATA 58.435 39.130 0.00 0.00 0.00 1.90
289 291 3.498774 ATACCCCTGCACATCATCTTC 57.501 47.619 0.00 0.00 0.00 2.87
305 307 5.365619 AGACACATTCGATTGGGTTATACC 58.634 41.667 15.79 3.83 32.06 2.73
323 325 9.695884 CGTTTAGCGAATGGTGTATTGAGACAC 62.696 44.444 0.43 0.43 45.08 3.67
324 326 3.610040 AGCGAATGGTGTATTGAGACA 57.390 42.857 0.00 0.00 0.00 3.41
325 327 5.500290 CGTTTAGCGAATGGTGTATTGAGAC 60.500 44.000 0.00 0.00 44.77 3.36
461 467 1.741706 CAAGGCTGGACTGCAATGTAG 59.258 52.381 0.00 0.00 34.04 2.74
523 533 2.945008 CTCCAGTGCTTGTCTTTGTTGA 59.055 45.455 0.00 0.00 0.00 3.18
552 562 2.415512 GCCGCTCAGGTAAAAACTACTG 59.584 50.000 0.00 0.00 43.70 2.74
553 563 2.696506 GCCGCTCAGGTAAAAACTACT 58.303 47.619 0.00 0.00 43.70 2.57
554 564 1.392510 CGCCGCTCAGGTAAAAACTAC 59.607 52.381 0.00 0.00 43.70 2.73
555 565 1.273048 TCGCCGCTCAGGTAAAAACTA 59.727 47.619 0.00 0.00 43.70 2.24
556 566 0.034337 TCGCCGCTCAGGTAAAAACT 59.966 50.000 0.00 0.00 43.70 2.66
586 596 4.329545 GGCTCCGGCAAGACCACA 62.330 66.667 0.00 0.00 40.87 4.17
858 877 3.964031 CCTGAGCCTATACAAACTCCTCT 59.036 47.826 0.00 0.00 0.00 3.69
859 878 3.961408 TCCTGAGCCTATACAAACTCCTC 59.039 47.826 0.00 0.00 0.00 3.71
860 879 3.995636 TCCTGAGCCTATACAAACTCCT 58.004 45.455 0.00 0.00 0.00 3.69
873 892 1.070289 CCGTTAACCCTATCCTGAGCC 59.930 57.143 0.00 0.00 0.00 4.70
913 932 3.948719 GACGTGGCCAAGGTGGGA 61.949 66.667 23.09 0.00 38.19 4.37
948 967 4.716977 GGACTCTCGGGGGTGGGT 62.717 72.222 0.00 0.00 0.00 4.51
988 1020 2.473760 CCGACATCTCGCCTCGACT 61.474 63.158 0.00 0.00 38.70 4.18
1500 1813 2.106332 CGGTCCATGCCGTACCTC 59.894 66.667 3.80 0.00 46.11 3.85
1701 2014 2.942879 GCGTGCACCATTTCGTCA 59.057 55.556 12.15 0.00 0.00 4.35
1773 2086 1.981256 TGGAAGAGCCACTTGAAACC 58.019 50.000 0.00 0.00 43.33 3.27
1881 2194 3.716006 CGTGCCTCAAGGTGTGCG 61.716 66.667 0.00 0.00 37.57 5.34
2256 2569 2.066393 TGGAGGCAGGCTATTCGCT 61.066 57.895 0.00 0.00 39.13 4.93
2308 2621 3.009363 TCAGGCAACATCTCATCCTTCAA 59.991 43.478 0.00 0.00 41.41 2.69
2488 2801 7.875327 AACCCAAAACCATACAGTATATGAC 57.125 36.000 0.00 0.00 0.00 3.06
2503 2816 5.265989 TCCCAATCCTACATAACCCAAAAC 58.734 41.667 0.00 0.00 0.00 2.43
2504 2817 5.538082 TCCCAATCCTACATAACCCAAAA 57.462 39.130 0.00 0.00 0.00 2.44
2919 3232 7.094634 ACAGCTGAAAGTACCAAGTATTTGATG 60.095 37.037 23.35 0.00 34.14 3.07
2940 3254 3.195825 AGAAACGTAGCAGGAATACAGCT 59.804 43.478 0.00 0.00 42.14 4.24
3310 3631 3.535561 CCCTCAGAATTACATTGCTCGT 58.464 45.455 0.00 0.00 0.00 4.18
3405 3729 4.004982 GCCTAGTTCCGGAATAAACACAA 58.995 43.478 22.04 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.