Multiple sequence alignment - TraesCS6B01G063600

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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 TraesCS6B01G063600 chr6B 100.000 3240 0 0 1 3240 42224876 42221637 0 5984
1 TraesCS6B01G063600 chr6B 93.477 3250 189 19 1 3240 667172040 667168804 0 4806
2 TraesCS6B01G063600 chr3B 94.952 3249 150 12 1 3240 183843999 183847242 0 5079
3 TraesCS6B01G063600 chr3B 93.938 3250 179 13 1 3240 797552437 797555678 0 4894
4 TraesCS6B01G063600 chr3B 93.873 3248 176 11 1 3240 752575993 752572761 0 4874
5 TraesCS6B01G063600 chr2B 94.119 3248 177 12 1 3240 425245268 425248509 0 4927
6 TraesCS6B01G063600 chr2B 93.504 3248 192 17 1 3240 172200272 172197036 0 4811
7 TraesCS6B01G063600 chr5B 93.690 3249 186 12 1 3240 657624185 657627423 0 4846
8 TraesCS6B01G063600 chr5B 93.534 3248 194 13 1 3240 552224472 552227711 0 4820
9 TraesCS6B01G063600 chr5B 93.473 3248 200 8 1 3240 591385080 591388323 0 4813


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 TraesCS6B01G063600 chr6B 42221637 42224876 3239 True 5984 5984 100.000 1 3240 1 chr6B.!!$R1 3239
1 TraesCS6B01G063600 chr6B 667168804 667172040 3236 True 4806 4806 93.477 1 3240 1 chr6B.!!$R2 3239
2 TraesCS6B01G063600 chr3B 183843999 183847242 3243 False 5079 5079 94.952 1 3240 1 chr3B.!!$F1 3239
3 TraesCS6B01G063600 chr3B 797552437 797555678 3241 False 4894 4894 93.938 1 3240 1 chr3B.!!$F2 3239
4 TraesCS6B01G063600 chr3B 752572761 752575993 3232 True 4874 4874 93.873 1 3240 1 chr3B.!!$R1 3239
5 TraesCS6B01G063600 chr2B 425245268 425248509 3241 False 4927 4927 94.119 1 3240 1 chr2B.!!$F1 3239
6 TraesCS6B01G063600 chr2B 172197036 172200272 3236 True 4811 4811 93.504 1 3240 1 chr2B.!!$R1 3239
7 TraesCS6B01G063600 chr5B 657624185 657627423 3238 False 4846 4846 93.690 1 3240 1 chr5B.!!$F3 3239
8 TraesCS6B01G063600 chr5B 552224472 552227711 3239 False 4820 4820 93.534 1 3240 1 chr5B.!!$F1 3239
9 TraesCS6B01G063600 chr5B 591385080 591388323 3243 False 4813 4813 93.473 1 3240 1 chr5B.!!$F2 3239

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
786 795 0.627451 TAAGGCGACCTCCCAGACTA 59.373 55.0 0.00 0.0 30.89 2.59 F
1335 1346 0.177604 CCAAGAAGCAGCTCGAGGAT 59.822 55.0 15.58 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 1843 0.883370 AACACCTTTTCCGTCGAGCC 60.883 55.0 0.00 0.0 0.0 4.70 R
3180 3204 0.530744 AGAACAGGCTGCGTCGAATA 59.469 50.0 15.89 0.0 0.0 1.75 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
175 178 1.684049 CTCCTCTGCCCGAAGACCT 60.684 63.158 0.00 0.00 0.00 3.85
330 333 4.089757 AAGCCCCCTCCGCCTCTA 62.090 66.667 0.00 0.00 0.00 2.43
405 413 3.898123 GGAAGGAAAGAAAAGGAAGGCTT 59.102 43.478 0.00 0.00 0.00 4.35
463 472 1.338136 ACCCTTCTGCCGGACTATGG 61.338 60.000 5.05 0.13 0.00 2.74
557 566 1.153369 CCCGAATGACTCATGGCGT 60.153 57.895 11.45 0.00 0.00 5.68
666 675 7.500141 TCTCTGAATTCATCGGATGTGAATAA 58.500 34.615 17.01 4.87 43.49 1.40
767 776 4.270153 TGGTCCTGGAGGTGCCCT 62.270 66.667 0.00 0.00 36.03 5.19
781 790 2.365105 CCCTAAGGCGACCTCCCA 60.365 66.667 0.00 0.00 30.89 4.37
786 795 0.627451 TAAGGCGACCTCCCAGACTA 59.373 55.000 0.00 0.00 30.89 2.59
992 1002 0.896479 TCCATCGACGAGGAACACCA 60.896 55.000 11.71 0.00 0.00 4.17
1031 1041 3.813166 GTGATTCAAAAGGTTCAGTCCGA 59.187 43.478 0.00 0.00 0.00 4.55
1200 1211 9.745880 CTAAAAAGATATACGCAGGAGTCTAAA 57.254 33.333 0.00 0.00 0.00 1.85
1231 1242 2.028112 GTCGATATGGGAATGCAGGCTA 60.028 50.000 0.00 0.00 0.00 3.93
1335 1346 0.177604 CCAAGAAGCAGCTCGAGGAT 59.822 55.000 15.58 0.00 0.00 3.24
1401 1412 5.304101 ACTTGGTTGCAAATAATGACAGGAA 59.696 36.000 0.00 0.00 0.00 3.36
1616 1627 1.376553 AAGCTCGCCTTGGCTCTTC 60.377 57.895 10.12 0.00 37.87 2.87
1643 1654 1.969589 AAAACCGCGAAGGCCGAAT 60.970 52.632 8.23 0.00 46.52 3.34
1805 1816 2.365617 CCCCGTAGTGTATCTGATGCTT 59.634 50.000 7.26 0.00 0.00 3.91
2129 2141 2.574955 AAGCTGGACGCGGAGAAGT 61.575 57.895 12.47 0.00 45.59 3.01
2353 2366 2.610374 GTGCGGCCGTTTATCAAATCTA 59.390 45.455 28.70 0.00 0.00 1.98
2439 2452 1.541588 GCGCTCTTGTTCCCATTCTTT 59.458 47.619 0.00 0.00 0.00 2.52
2643 2657 4.680975 GCGGCATAAGTCTTTAAGGACTCT 60.681 45.833 19.38 12.39 44.67 3.24
2656 2670 1.067071 AGGACTCTAAAAACCTCGCGG 60.067 52.381 6.13 0.00 0.00 6.46
2764 2778 2.432510 GCAGTAGTTCTCCCAGTGCTAT 59.567 50.000 0.00 0.00 36.04 2.97
2770 2784 4.873010 AGTTCTCCCAGTGCTATCTTAGA 58.127 43.478 0.00 0.00 0.00 2.10
3180 3204 4.180377 TCGTTATAGAGACCACCTGGAT 57.820 45.455 0.00 0.00 38.94 3.41
3193 3217 0.946221 CCTGGATATTCGACGCAGCC 60.946 60.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
330 333 2.606751 TCTTCCTCCTCCTCGTCTTT 57.393 50.000 0.00 0.00 0.00 2.52
463 472 2.956964 CGTCTTCGGCATCGGAGC 60.957 66.667 0.00 0.00 41.62 4.70
557 566 7.175797 TCAGAAGCTATCGAATAATAGAGGGA 58.824 38.462 0.00 0.00 31.98 4.20
666 675 2.049433 CCGTCGGAAGTGAAGCGT 60.049 61.111 4.91 0.00 0.00 5.07
713 722 1.074951 CCTTTTGGGACTCCGCCTT 59.925 57.895 0.00 0.00 37.23 4.35
767 776 0.627451 TAGTCTGGGAGGTCGCCTTA 59.373 55.000 0.00 0.00 31.76 2.69
781 790 2.387952 CCCTTTGGGCCTGTAGTCT 58.612 57.895 4.53 0.00 35.35 3.24
992 1002 1.343142 TCACCGCACTCATAACAGTGT 59.657 47.619 0.00 0.00 44.98 3.55
1031 1041 1.898574 CCTGTCAGCCCGCTTTTGT 60.899 57.895 0.00 0.00 0.00 2.83
1200 1211 9.241919 TGCATTCCCATATCGACATATTTTTAT 57.758 29.630 0.00 0.00 0.00 1.40
1231 1242 4.385405 GGCAGAGGTCAGCAGCGT 62.385 66.667 0.00 0.00 0.00 5.07
1552 1563 3.312697 GCTCCAAACTCTCGTGTTTTTCT 59.687 43.478 0.00 0.00 37.98 2.52
1616 1627 1.781025 TTCGCGGTTTTGGCACTCTG 61.781 55.000 6.13 0.00 0.00 3.35
1643 1654 1.925455 CTTGGAGGGCCTTCTGGGA 60.925 63.158 14.33 0.00 37.23 4.37
1805 1816 3.818787 GGCTCGGTAGAACGCGGA 61.819 66.667 12.47 0.00 0.00 5.54
1832 1843 0.883370 AACACCTTTTCCGTCGAGCC 60.883 55.000 0.00 0.00 0.00 4.70
2439 2452 1.457643 CGCCTCCCTAGATGGACCA 60.458 63.158 0.00 0.00 38.35 4.02
2656 2670 2.486042 GAGAGACCGGTCGCTGTC 59.514 66.667 40.38 26.31 39.82 3.51
2764 2778 2.734606 CGTTCCGCAATGTTGTCTAAGA 59.265 45.455 0.00 0.00 0.00 2.10
2770 2784 1.533731 CCTTACGTTCCGCAATGTTGT 59.466 47.619 0.00 0.00 33.54 3.32
2859 2873 1.202770 GGCACCCCGAACTTATAGCAT 60.203 52.381 0.00 0.00 0.00 3.79
3087 3110 5.835280 GGGACATGTCAAATAATCCCATCTT 59.165 40.000 26.47 0.00 44.53 2.40
3158 3182 3.972133 TCCAGGTGGTCTCTATAACGAA 58.028 45.455 0.00 0.00 36.34 3.85
3180 3204 0.530744 AGAACAGGCTGCGTCGAATA 59.469 50.000 15.89 0.00 0.00 1.75
3215 3239 2.354305 ACTCGCCGAACACACGAC 60.354 61.111 0.00 0.00 35.09 4.34


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

AutoCloner maintained by Alex Coulton.