Multiple sequence alignment - TraesCS6D01G253300

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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 TraesCS6D01G253300 chr6D 100.000 3005 0 0 1 3005 357566546 357569550 0 5550
1 TraesCS6D01G253300 chr6A 94.758 3052 105 17 1 3005 499644277 499647320 0 4698
2 TraesCS6D01G253300 chr6B 94.799 2038 59 9 1 1995 539057004 539059037 0 3133
3 TraesCS6D01G253300 chr6B 91.866 1045 34 9 1987 3005 539059057 539060076 0 1411


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 TraesCS6D01G253300 chr6D 357566546 357569550 3004 False 5550 5550 100.0000 1 3005 1 chr6D.!!$F1 3004
1 TraesCS6D01G253300 chr6A 499644277 499647320 3043 False 4698 4698 94.7580 1 3005 1 chr6A.!!$F1 3004
2 TraesCS6D01G253300 chr6B 539057004 539060076 3072 False 2272 3133 93.3325 1 3005 2 chr6B.!!$F1 3004

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
352 362 0.606401 GACCACTAGCTTTGCCTGCA 60.606 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 2377 0.61326 TCCCAAGAGGAACACCATCG 59.387 55.0 0.0 0.0 43.78 3.84 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
177 187 8.259049 TGTATGTAGTTTGTACAGCCAATTAC 57.741 34.615 0.00 0.44 0.00 1.89
241 251 4.919168 TCCGTAAGTTTGTAACATCGACAG 59.081 41.667 0.00 0.00 0.00 3.51
352 362 0.606401 GACCACTAGCTTTGCCTGCA 60.606 55.000 0.00 0.00 0.00 4.41
523 533 5.666969 TCTTCCAATACAAAACGACACAG 57.333 39.130 0.00 0.00 0.00 3.66
547 557 7.590322 CAGATGTTGATGTGAGTTTGAGAAAAG 59.410 37.037 0.00 0.00 0.00 2.27
664 674 4.872124 GGGATGAAATGAAATGACAAAGGC 59.128 41.667 0.00 0.00 0.00 4.35
692 702 3.614092 TCCCAGCAAATCTGAGTGATTC 58.386 45.455 0.00 0.00 45.72 2.52
742 752 4.586884 ACTAGATTAGTGTGGTGAGTCGA 58.413 43.478 0.00 0.00 37.69 4.20
809 819 4.393834 TGCCTACTGCTAACACAAATCAA 58.606 39.130 0.00 0.00 42.00 2.57
842 854 3.895704 ACTGGGTATTGTTGGTTTCCT 57.104 42.857 0.00 0.00 0.00 3.36
1158 1171 3.005554 GCACTATGAAGAGCTGCTGAAA 58.994 45.455 7.01 0.00 36.50 2.69
1191 1204 2.280457 GAGTATGCAGGAGGCCGC 60.280 66.667 0.00 0.00 43.89 6.53
1297 1310 2.952978 AGAAGCCCGTACTCTCATACAG 59.047 50.000 0.00 0.00 0.00 2.74
1298 1311 1.693627 AGCCCGTACTCTCATACAGG 58.306 55.000 0.00 0.00 0.00 4.00
1373 1386 3.955471 AGTCATGGGTGTATGTTCAAGG 58.045 45.455 0.00 0.00 0.00 3.61
1472 1485 6.737254 TTATCTTTTTCCCTCTAGTTTGCG 57.263 37.500 0.00 0.00 0.00 4.85
1616 1629 6.024552 TGGATTTTGCTGGAATTGACTTAC 57.975 37.500 0.00 0.00 0.00 2.34
1622 1635 3.267483 GCTGGAATTGACTTACGCCTTA 58.733 45.455 0.00 0.00 0.00 2.69
1749 1791 1.856629 CTGCCCTGTTCCATTTCCAT 58.143 50.000 0.00 0.00 0.00 3.41
1870 1912 2.163412 TGTTTTGTGCACTCTGTTGACC 59.837 45.455 19.41 0.00 0.00 4.02
1911 1953 5.365619 GACAAGTCAACTCCCTTTTGTCTA 58.634 41.667 7.66 0.00 40.53 2.59
1936 1978 7.462109 TCAACAATGTGCAAATTCAACTAAC 57.538 32.000 0.00 0.00 0.00 2.34
1996 2068 2.069165 AACTCCAGGCAACCTCACCC 62.069 60.000 0.00 0.00 37.17 4.61
2056 2128 3.439857 ACTATGGCCACAATGACACTT 57.560 42.857 8.16 0.00 0.00 3.16
2100 2172 6.148811 CGAATTAAATTGTGAGTACAGTGGGT 59.851 38.462 0.00 0.00 38.23 4.51
2203 2275 8.695456 ACGGGAATGAAAATTCTTTAGCATTAT 58.305 29.630 0.00 0.00 31.88 1.28
2302 2377 0.464554 GGCAGGATAAGGACACCAGC 60.465 60.000 0.00 0.00 35.88 4.85
2622 2726 1.796796 GGCGCTCTTACCAGCAAAG 59.203 57.895 7.64 0.00 39.62 2.77
2721 2829 4.633126 TGTGTGTCGTCATAGGTAGTAGAC 59.367 45.833 0.00 0.00 0.00 2.59
2724 2832 5.942236 TGTGTCGTCATAGGTAGTAGACTTT 59.058 40.000 0.00 0.00 0.00 2.66
2743 2851 4.767409 ACTTTCTACCAAAAGAAGATGGGC 59.233 41.667 3.56 0.00 41.17 5.36
2789 2904 4.307432 TGAAAAACTTCTAGCTGAGGTCG 58.693 43.478 0.00 0.00 33.64 4.79
2790 2905 3.320673 AAAACTTCTAGCTGAGGTCGG 57.679 47.619 0.00 0.00 33.64 4.79
2791 2906 1.187087 AACTTCTAGCTGAGGTCGGG 58.813 55.000 0.00 0.00 33.64 5.14
2792 2907 0.331954 ACTTCTAGCTGAGGTCGGGA 59.668 55.000 0.00 0.00 28.01 5.14
2803 2918 4.436998 GTCGGGAGGGAGCGTGTG 62.437 72.222 0.00 0.00 0.00 3.82
2912 3027 2.977772 CCAAGTTTGGTGCAAAAGGA 57.022 45.000 2.66 0.00 43.43 3.36
2991 3108 4.670735 GCTTTAAGCAGATTTTCGCCGTTA 60.671 41.667 12.54 0.00 41.89 3.18
2994 3111 1.593006 AGCAGATTTTCGCCGTTATCG 59.407 47.619 0.00 0.00 0.00 2.92
3000 3117 0.390078 TTTCGCCGTTATCGCCTTCA 60.390 50.000 0.00 0.00 35.54 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 187 2.361757 TGTCCACCAATTTGCAGTCAAG 59.638 45.455 0.00 0.00 33.12 3.02
241 251 2.555757 GGATAGAAGCATGCAACATCCC 59.444 50.000 21.98 10.23 0.00 3.85
314 324 0.392336 CAGGAGGCCTAGAGTGCATC 59.608 60.000 4.42 0.00 38.72 3.91
352 362 2.638363 GGTCACAAGAAGAGGGGTAAGT 59.362 50.000 0.00 0.00 0.00 2.24
523 533 7.642669 TCTTTTCTCAAACTCACATCAACATC 58.357 34.615 0.00 0.00 0.00 3.06
567 577 0.034089 AACCATGCTCTAAGGGTGCC 60.034 55.000 0.00 0.00 33.00 5.01
664 674 2.768527 TCAGATTTGCTGGGAGACTAGG 59.231 50.000 0.00 0.00 44.98 3.02
742 752 2.025887 AGGGAGCCACGAGAAATTTCAT 60.026 45.455 19.99 5.50 0.00 2.57
842 854 8.622157 GCGTAGATGTGCTATTTATATAGAGGA 58.378 37.037 4.55 0.00 36.62 3.71
1158 1171 4.449131 CATACTCAATGTGATGCAGGTCT 58.551 43.478 0.00 0.00 0.00 3.85
1191 1204 1.067582 GTTGTAGAGGGATCCGCGG 59.932 63.158 22.12 22.12 0.00 6.46
1297 1310 3.825014 AGGATGCACAATGAGATTATGCC 59.175 43.478 0.00 0.00 41.79 4.40
1298 1311 4.760715 AGAGGATGCACAATGAGATTATGC 59.239 41.667 0.00 0.00 42.75 3.14
1390 1403 6.756074 CCAAAAGCTACAAAATCAAGTGACAA 59.244 34.615 0.00 0.00 0.00 3.18
1472 1485 5.105351 AGGAACAAACTATAAAAGGCATGCC 60.105 40.000 30.12 30.12 0.00 4.40
1749 1791 8.623903 GGATCACATGCTTAATTTATCACAAGA 58.376 33.333 0.00 0.00 0.00 3.02
1870 1912 1.734465 GTCTTGCCAAATGGAGTCTCG 59.266 52.381 2.98 0.00 37.39 4.04
1911 1953 7.096106 CGTTAGTTGAATTTGCACATTGTTGAT 60.096 33.333 2.08 0.00 0.00 2.57
1936 1978 7.276658 ACTTCTGTTTATTCTGCTGTATCTTCG 59.723 37.037 0.00 0.00 0.00 3.79
1996 2068 2.074576 GGCAGATCATCATCATGGACG 58.925 52.381 0.00 0.00 0.00 4.79
2056 2128 5.462530 TTCGACACTAAACTGGATCAGAA 57.537 39.130 1.59 0.00 35.18 3.02
2100 2172 8.872134 TGATTACGGGTGTTTATCCATATCTTA 58.128 33.333 0.00 0.00 0.00 2.10
2149 2221 4.643387 ACCTGCTTCACCGCCCAC 62.643 66.667 0.00 0.00 0.00 4.61
2203 2275 1.336148 GCAGCAGCAGCACAAACATAA 60.336 47.619 4.63 0.00 45.49 1.90
2302 2377 0.613260 TCCCAAGAGGAACACCATCG 59.387 55.000 0.00 0.00 43.78 3.84
2622 2726 1.925185 GAGACTCGGTTATGTTTCGGC 59.075 52.381 0.00 0.00 0.00 5.54
2721 2829 4.766891 TGCCCATCTTCTTTTGGTAGAAAG 59.233 41.667 0.00 0.00 37.85 2.62
2724 2832 3.330701 AGTGCCCATCTTCTTTTGGTAGA 59.669 43.478 0.00 0.00 0.00 2.59
2743 2851 5.597806 TCAAACCACTACACAAGTCTAGTG 58.402 41.667 8.20 8.20 42.56 2.74
2824 2939 7.451255 TCAAGAATTTTAACAGTGTGGATCCAT 59.549 33.333 19.62 2.69 0.00 3.41
2825 2940 6.775142 TCAAGAATTTTAACAGTGTGGATCCA 59.225 34.615 11.44 11.44 0.00 3.41
2910 3025 5.964758 TGCCAAATCAGACATGTAAATTCC 58.035 37.500 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.