Multiple sequence alignment - TraesCS6D01G314800

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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 TraesCS6D01G314800 chr6D 100.000 2372 0 0 1 2372 423390058 423387687 0.000000e+00 4381.0
1 TraesCS6D01G314800 chr6B 93.913 2382 128 13 1 2372 638250904 638248530 0.000000e+00 3579.0
2 TraesCS6D01G314800 chr6A 94.411 1002 47 3 751 1747 566891577 566890580 0.000000e+00 1531.0
3 TraesCS6D01G314800 chr6A 94.654 636 34 0 1737 2372 566890277 566889642 0.000000e+00 987.0
4 TraesCS6D01G314800 chr6A 92.217 591 39 3 1 585 566892165 566891576 0.000000e+00 830.0
5 TraesCS6D01G314800 chr2B 77.128 188 31 9 186 371 699102677 699102500 5.400000e-17 99.0
6 TraesCS6D01G314800 chr7D 91.228 57 3 2 316 371 12436008 12436063 2.530000e-10 76.8
7 TraesCS6D01G314800 chr4B 97.561 41 1 0 331 371 596645061 596645021 1.180000e-08 71.3
8 TraesCS6D01G314800 chr1B 80.000 90 16 2 273 361 633321694 633321782 5.470000e-07 65.8
9 TraesCS6D01G314800 chr2A 92.500 40 2 1 333 371 718110286 718110247 3.290000e-04 56.5


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 TraesCS6D01G314800 chr6D 423387687 423390058 2371 True 4381 4381 100.000000 1 2372 1 chr6D.!!$R1 2371
1 TraesCS6D01G314800 chr6B 638248530 638250904 2374 True 3579 3579 93.913000 1 2372 1 chr6B.!!$R1 2371
2 TraesCS6D01G314800 chr6A 566889642 566892165 2523 True 1116 1531 93.760667 1 2372 3 chr6A.!!$R1 2371

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
497 506 0.397254 TTGGTTTTTCCCTGCCCGAA 60.397 50.0 0.0 0.0 34.77 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1616 0.321564 TTTCGGGACATGGCACTCTG 60.322 55.0 0.0 0.0 0.0 3.35 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
40 41 1.136500 GAATAGGTTCGCTCGACCCTT 59.864 52.381 13.39 0.00 38.10 3.95
55 56 1.063492 ACCCTTCCCGTTGGTTTTTCT 60.063 47.619 0.00 0.00 0.00 2.52
59 60 1.975660 TCCCGTTGGTTTTTCTCCTG 58.024 50.000 0.00 0.00 0.00 3.86
79 81 3.412386 TGCCTTAGTTTTTCTCTCCAGC 58.588 45.455 0.00 0.00 0.00 4.85
80 82 2.750166 GCCTTAGTTTTTCTCTCCAGCC 59.250 50.000 0.00 0.00 0.00 4.85
103 105 5.914898 CCCCCTGGTTTACAAAAATCTAG 57.085 43.478 0.00 0.00 0.00 2.43
137 141 7.861372 GGTGTTTTTCTTTCTTTTCCTACTAGC 59.139 37.037 0.00 0.00 0.00 3.42
169 173 4.629200 CCTGCACTAACTCACTGAAATCTC 59.371 45.833 0.00 0.00 0.00 2.75
410 419 1.449601 GGTACATGCACCTCACCGG 60.450 63.158 7.95 0.00 35.55 5.28
490 499 1.132849 CCCTCCCTTTGGTTTTTCCCT 60.133 52.381 0.00 0.00 34.77 4.20
497 506 0.397254 TTGGTTTTTCCCTGCCCGAA 60.397 50.000 0.00 0.00 34.77 4.30
657 666 9.499479 ACTTATATCAACTTCATTGCTATCCAG 57.501 33.333 0.00 0.00 38.29 3.86
674 683 6.761714 GCTATCCAGGTAATTATATCCAACCG 59.238 42.308 0.00 0.00 35.32 4.44
700 709 9.793252 GAATATCAACATGCAATTAGTGTCTTT 57.207 29.630 0.00 0.00 0.00 2.52
706 715 7.944729 ACATGCAATTAGTGTCTTTCCTAAT 57.055 32.000 0.00 0.00 35.84 1.73
716 725 9.807649 TTAGTGTCTTTCCTAATATTAACGTCC 57.192 33.333 0.00 0.00 0.00 4.79
717 726 6.976925 AGTGTCTTTCCTAATATTAACGTCCG 59.023 38.462 0.00 0.00 0.00 4.79
718 727 6.974622 GTGTCTTTCCTAATATTAACGTCCGA 59.025 38.462 0.00 0.00 0.00 4.55
730 739 5.804692 TTAACGTCCGATGCAATTAACAT 57.195 34.783 0.00 0.00 0.00 2.71
827 836 6.016718 CGTGCAATGCAATTAATTTCTTTGG 58.983 36.000 10.44 7.30 41.47 3.28
844 853 4.881273 TCTTTGGTGATATAGCGTGCATTT 59.119 37.500 0.00 0.00 0.00 2.32
901 913 3.740832 GCAATTCCTAAAACACCAAGCAC 59.259 43.478 0.00 0.00 0.00 4.40
907 919 2.559998 AAAACACCAAGCACGACAAG 57.440 45.000 0.00 0.00 0.00 3.16
920 932 5.539048 AGCACGACAAGACTATAAAAGTGT 58.461 37.500 0.00 0.00 39.07 3.55
949 961 2.079158 CTTGAGGAACATGTCGTGCAT 58.921 47.619 0.00 0.00 38.60 3.96
1037 1049 3.334054 ACTCCTCCTGGCCTTGGC 61.334 66.667 3.32 2.49 0.00 4.52
1142 1154 0.972134 TCTCCATCCATCTCCGCATC 59.028 55.000 0.00 0.00 0.00 3.91
1199 1211 1.750206 TGTGTCAATTGTGCAAGCAGT 59.250 42.857 5.13 0.00 0.00 4.40
1394 1409 1.463674 ATTTAACTGAGCTTGGCCGG 58.536 50.000 0.00 0.00 0.00 6.13
1426 1441 3.704061 TGGAGACGTGTTGATGGATGATA 59.296 43.478 0.00 0.00 0.00 2.15
1596 1611 2.044135 GCAGTGTGCGCTTACTTTTTC 58.956 47.619 9.73 0.00 31.71 2.29
1600 1615 4.024387 CAGTGTGCGCTTACTTTTTCCTTA 60.024 41.667 9.73 0.00 0.00 2.69
1601 1616 4.024302 AGTGTGCGCTTACTTTTTCCTTAC 60.024 41.667 9.73 0.00 0.00 2.34
1602 1617 3.878103 TGTGCGCTTACTTTTTCCTTACA 59.122 39.130 9.73 0.00 0.00 2.41
1619 1635 1.296392 CAGAGTGCCATGTCCCGAA 59.704 57.895 0.00 0.00 0.00 4.30
1652 1668 7.278724 TCCTTCCATAAATAGAAAGACCCAA 57.721 36.000 0.00 0.00 0.00 4.12
1682 1698 1.834188 TCTCACTGGATCGTGTAGCA 58.166 50.000 1.38 0.00 36.33 3.49
1683 1699 2.379005 TCTCACTGGATCGTGTAGCAT 58.621 47.619 1.38 0.00 36.33 3.79
1684 1700 3.551846 TCTCACTGGATCGTGTAGCATA 58.448 45.455 1.38 0.00 36.33 3.14
1766 2099 2.644992 CTTTTGCGCACACCCTCC 59.355 61.111 11.12 0.00 0.00 4.30
1833 2166 4.215109 AGTTAAGCAGCCCTTCAAAAAGA 58.785 39.130 0.00 0.00 34.14 2.52
2046 2379 7.560262 GGGTATACATGCCAGTATATGTCTCTA 59.440 40.741 5.01 0.00 38.71 2.43
2088 2421 8.090788 AGAGTTAAAATTACATCCAGAGCCTA 57.909 34.615 0.00 0.00 0.00 3.93
2128 2461 6.942576 CCTCTTTAAAAGAAGAAGGTGATCCA 59.057 38.462 0.00 0.00 37.02 3.41
2135 2468 3.133721 AGAAGAAGGTGATCCATTCTCCG 59.866 47.826 10.25 0.00 41.90 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.975660 CAGGAGAAAAACCAACGGGA 58.024 50.000 0.00 0.00 38.05 5.14
55 56 3.650942 TGGAGAGAAAAACTAAGGCAGGA 59.349 43.478 0.00 0.00 0.00 3.86
59 60 2.750166 GGCTGGAGAGAAAAACTAAGGC 59.250 50.000 0.00 0.00 0.00 4.35
137 141 2.357009 GAGTTAGTGCAGGGCATGATTG 59.643 50.000 1.99 0.00 41.91 2.67
147 151 5.233225 TGAGATTTCAGTGAGTTAGTGCAG 58.767 41.667 0.00 0.00 0.00 4.41
169 173 2.987413 TGCAGTTTATGGTTTCGCTG 57.013 45.000 0.00 0.00 0.00 5.18
173 177 8.986477 ATTGAGTTAATGCAGTTTATGGTTTC 57.014 30.769 0.00 0.00 0.00 2.78
181 185 9.545105 TTTGATTTGATTGAGTTAATGCAGTTT 57.455 25.926 0.00 0.00 0.00 2.66
308 312 6.591750 TGAATACGGGAAGGCAATTAAAAA 57.408 33.333 0.00 0.00 0.00 1.94
313 317 5.048846 AGTATGAATACGGGAAGGCAATT 57.951 39.130 0.00 0.00 38.28 2.32
410 419 3.530260 CATGGATGGGGCGGTTGC 61.530 66.667 0.00 0.00 41.71 4.17
469 478 1.413953 GGGAAAAACCAAAGGGAGGGT 60.414 52.381 0.00 0.00 41.20 4.34
490 499 4.524714 TGAGAAATAAACCAAATTCGGGCA 59.475 37.500 0.00 0.00 0.00 5.36
497 506 7.420097 GGGGGCAATATGAGAAATAAACCAAAT 60.420 37.037 0.00 0.00 0.00 2.32
653 662 6.750660 TTCGGTTGGATATAATTACCTGGA 57.249 37.500 0.00 0.00 0.00 3.86
674 683 9.793252 AAAGACACTAATTGCATGTTGATATTC 57.207 29.630 0.00 0.00 0.00 1.75
700 709 5.456548 TGCATCGGACGTTAATATTAGGA 57.543 39.130 0.00 0.00 0.00 2.94
706 715 6.905544 TGTTAATTGCATCGGACGTTAATA 57.094 33.333 0.00 0.00 0.00 0.98
709 718 5.804692 AATGTTAATTGCATCGGACGTTA 57.195 34.783 0.00 0.00 0.00 3.18
826 835 4.133856 GTGAAATGCACGCTATATCACC 57.866 45.455 0.00 0.00 37.83 4.02
844 853 5.048782 ACCAAACTAGTAATCGTGTACGTGA 60.049 40.000 0.00 0.00 40.80 4.35
901 913 7.402811 TTGTGACACTTTTATAGTCTTGTCG 57.597 36.000 7.20 0.00 33.85 4.35
920 932 5.408299 CGACATGTTCCTCAAGTAATTGTGA 59.592 40.000 0.00 0.88 0.00 3.58
932 944 2.860735 GTCTATGCACGACATGTTCCTC 59.139 50.000 11.87 0.00 40.06 3.71
949 961 6.321435 GGATGGGATATGTGATGATACGTCTA 59.679 42.308 0.00 0.00 0.00 2.59
1037 1049 0.321564 TGGTGATGAGGCAAGAACGG 60.322 55.000 0.00 0.00 0.00 4.44
1267 1279 1.074405 ACAGTCCATCATGCACTTGGT 59.926 47.619 10.30 0.00 0.00 3.67
1369 1381 4.700213 GGCCAAGCTCAGTTAAATAGTTCA 59.300 41.667 0.00 0.00 0.00 3.18
1394 1409 4.072088 CGTCTCCAAACGGCGTGC 62.072 66.667 15.70 0.00 38.96 5.34
1533 1548 8.700439 ATAACCTACAATACGCCCATTTATTT 57.300 30.769 0.00 0.00 0.00 1.40
1596 1611 1.407437 GGGACATGGCACTCTGTAAGG 60.407 57.143 0.00 0.00 0.00 2.69
1600 1615 1.480212 TTCGGGACATGGCACTCTGT 61.480 55.000 0.00 0.00 0.00 3.41
1601 1616 0.321564 TTTCGGGACATGGCACTCTG 60.322 55.000 0.00 0.00 0.00 3.35
1602 1617 0.400213 TTTTCGGGACATGGCACTCT 59.600 50.000 0.00 0.00 0.00 3.24
1619 1635 4.692523 ATTTATGGAAGGAGGTGGGTTT 57.307 40.909 0.00 0.00 0.00 3.27
1766 2099 6.093495 TGGAAATGATACGAAAAGTAAGCAGG 59.907 38.462 0.00 0.00 39.04 4.85
1863 2196 1.905894 TGTGCCTATGTCCTTGCTACA 59.094 47.619 0.00 0.00 0.00 2.74
1935 2268 7.970061 CACATTTCTTCATTCACGGTATCAATT 59.030 33.333 0.00 0.00 0.00 2.32
2107 2440 8.940397 AGAATGGATCACCTTCTTCTTTTAAA 57.060 30.769 0.00 0.00 33.33 1.52
2176 2509 6.650120 TCCTAGGAGTGTTATTTAGCAAAGG 58.350 40.000 7.62 0.00 0.00 3.11
2319 2652 6.403049 CAATGTATATTCCGCACCTATGGTA 58.597 40.000 0.00 0.00 32.11 3.25


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

AutoCloner maintained by Alex Coulton.