Multiple sequence alignment - TraesCS5D01G272900

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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 TraesCS5D01G272900 chr5D 100.000 2686 0 0 1 2686 375749381 375746696 0.000000e+00 4961.0
1 TraesCS5D01G272900 chr5B 93.116 2208 106 16 1 2195 448602167 448599993 0.000000e+00 3193.0
2 TraesCS5D01G272900 chr5B 87.970 798 51 21 1918 2686 448599909 448599128 0.000000e+00 900.0
3 TraesCS5D01G272900 chr5A 91.474 2158 122 29 1 2133 476852808 476850688 0.000000e+00 2909.0
4 TraesCS5D01G272900 chr5A 88.292 521 30 13 2193 2686 476850670 476850154 1.780000e-166 595.0
5 TraesCS5D01G272900 chr7A 84.884 86 5 2 539 616 202520842 202520927 2.220000e-11 80.5
6 TraesCS5D01G272900 chr7D 100.000 29 0 0 588 616 192929231 192929259 1.000000e-03 54.7


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 TraesCS5D01G272900 chr5D 375746696 375749381 2685 True 4961.0 4961 100.000 1 2686 1 chr5D.!!$R1 2685
1 TraesCS5D01G272900 chr5B 448599128 448602167 3039 True 2046.5 3193 90.543 1 2686 2 chr5B.!!$R1 2685
2 TraesCS5D01G272900 chr5A 476850154 476852808 2654 True 1752.0 2909 89.883 1 2686 2 chr5A.!!$R1 2685

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 1.226603 GGACGACGATGAGGAACGG 60.227 63.158 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2575 1.008815 TCCCACCATCCATGAGTCTCT 59.991 52.381 0.65 0.0 0.0 3.1 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
136 137 3.714798 ACTCAACCTTTTCACTCTGGGTA 59.285 43.478 0.00 0.00 0.00 3.69
296 297 9.787532 GTATTGCTGATTCAACAAGCTATAAAA 57.212 29.630 8.34 0.00 0.00 1.52
300 301 9.787532 TGCTGATTCAACAAGCTATAAAATAAC 57.212 29.630 0.00 0.00 0.00 1.89
361 364 2.190578 GGAGGTGGAGCCCAATCG 59.809 66.667 0.00 0.00 38.26 3.34
425 434 3.062639 CAGCAGAAACTTATACAGGCACG 59.937 47.826 0.00 0.00 0.00 5.34
441 450 1.264288 GCACGTTTGATAGCATAGGGC 59.736 52.381 0.00 0.00 45.30 5.19
470 479 7.491372 TCACTGTGTATCCAAATAAGATCGAAC 59.509 37.037 7.79 0.00 0.00 3.95
475 484 7.657761 GTGTATCCAAATAAGATCGAACTGGAT 59.342 37.037 14.87 14.87 43.08 3.41
498 507 7.202011 GGATGAGATAAGTAGAAGCAAACCCTA 60.202 40.741 0.00 0.00 0.00 3.53
786 795 1.226603 GGACGACGATGAGGAACGG 60.227 63.158 0.00 0.00 0.00 4.44
792 801 1.246056 ACGATGAGGAACGGACGGAA 61.246 55.000 0.00 0.00 0.00 4.30
961 970 3.049912 GTGGTTTTCGAAATGCCAAGTC 58.950 45.455 26.12 15.79 0.00 3.01
1001 1012 2.224066 CGAATCTTTGTAGATCCGGCCT 60.224 50.000 0.00 0.00 40.26 5.19
1018 1029 2.027653 GGCCTATAAGATCAGTCCCTGC 60.028 54.545 0.00 0.00 0.00 4.85
1022 1040 5.303971 CCTATAAGATCAGTCCCTGCAAAG 58.696 45.833 0.00 0.00 0.00 2.77
1049 1067 4.709397 CCAATCAAAATGTAACAGGGCCTA 59.291 41.667 5.28 0.00 0.00 3.93
1083 1101 0.988832 TGGGCCTTATTTGACGTCCT 59.011 50.000 14.12 0.03 0.00 3.85
1336 1360 4.813526 CACCTCGTCCTCGTCGCG 62.814 72.222 0.00 0.00 38.33 5.87
1623 1647 3.824443 GGGCTCTACTTCTGATCTAGGTC 59.176 52.174 0.00 0.00 0.00 3.85
1626 1650 4.277423 GCTCTACTTCTGATCTAGGTCCAC 59.723 50.000 0.00 0.00 0.00 4.02
1660 1684 4.195416 GGATCTCTTCCTGGTGATGTTTC 58.805 47.826 0.00 0.00 41.78 2.78
1735 1761 9.418045 GCTTTTATGGTTTGCTTTCAATTAGTA 57.582 29.630 0.00 0.00 31.33 1.82
1958 1993 2.846827 AGTAATCTTGGAACCTCAGGGG 59.153 50.000 0.00 0.00 41.89 4.79
1997 2032 9.737427 TGTAACATCATTTTGATTACACGTTTT 57.263 25.926 0.00 0.00 34.28 2.43
2311 2709 9.625747 TGATCTGTTTAAGGTATTTGCATATGA 57.374 29.630 6.97 0.00 0.00 2.15
2340 2766 6.815089 TGATTTTTGTAAGGTGTCTGCAAAT 58.185 32.000 0.00 0.00 32.69 2.32
2630 3056 2.434359 GGCACTCGTCTTTCCCCG 60.434 66.667 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 2.175878 AGTGCGACAGCTTCATTTCT 57.824 45.000 0.00 0.00 45.42 2.52
319 320 6.855914 CACTAGAACGTTGCACATTTGTATTT 59.144 34.615 5.00 0.00 0.00 1.40
382 391 9.864034 CTGCTGTTTAAACGAGTTATTATATGG 57.136 33.333 13.45 0.00 0.00 2.74
425 434 2.143925 GACCGCCCTATGCTATCAAAC 58.856 52.381 0.00 0.00 38.05 2.93
470 479 6.481644 GGTTTGCTTCTACTTATCTCATCCAG 59.518 42.308 0.00 0.00 0.00 3.86
475 484 7.490657 TTAGGGTTTGCTTCTACTTATCTCA 57.509 36.000 0.00 0.00 0.00 3.27
498 507 2.487934 CTCCAGCGATCGATCCATTTT 58.512 47.619 21.57 0.00 0.00 1.82
762 771 0.810426 CCTCATCGTCGTCCTCTCGA 60.810 60.000 0.00 0.00 37.96 4.04
765 774 1.096416 GTTCCTCATCGTCGTCCTCT 58.904 55.000 0.00 0.00 0.00 3.69
777 786 1.007038 CGTTTCCGTCCGTTCCTCA 60.007 57.895 0.00 0.00 0.00 3.86
1018 1029 3.421919 ACATTTTGATTGGGCCCTTTG 57.578 42.857 25.70 10.82 0.00 2.77
1022 1040 3.369366 CCTGTTACATTTTGATTGGGCCC 60.369 47.826 17.59 17.59 0.00 5.80
1049 1067 1.350019 GGCCCAACTGGTGTTAGTACT 59.650 52.381 0.00 0.00 34.60 2.73
1083 1101 4.689549 TCGGCCTGGGAGACGGAA 62.690 66.667 0.00 0.00 0.00 4.30
1128 1146 4.124351 CCATGGCTGCTTGCGGTG 62.124 66.667 0.00 0.00 44.05 4.94
1381 1405 1.648467 GGATGAACTTGCGCTCCACC 61.648 60.000 9.73 0.15 0.00 4.61
1626 1650 2.008242 AGAGATCCATCCGAGAAGGG 57.992 55.000 0.00 0.00 41.52 3.95
1660 1684 2.169352 ACAGATACAGGCAACAGCTAGG 59.831 50.000 0.00 0.00 41.41 3.02
2035 2073 8.883731 CCAGTGTCCAAACATAGTTAGAAATAG 58.116 37.037 0.00 0.00 37.81 1.73
2175 2571 3.033909 CACCATCCATGAGTCTCTGGTA 58.966 50.000 9.70 3.12 35.31 3.25
2178 2574 1.140452 CCCACCATCCATGAGTCTCTG 59.860 57.143 0.65 0.00 0.00 3.35
2179 2575 1.008815 TCCCACCATCCATGAGTCTCT 59.991 52.381 0.65 0.00 0.00 3.10
2180 2576 1.500474 TCCCACCATCCATGAGTCTC 58.500 55.000 0.00 0.00 0.00 3.36
2182 2578 4.437682 TTAATCCCACCATCCATGAGTC 57.562 45.455 0.00 0.00 0.00 3.36
2224 2622 7.817962 ACAATTACAGTTCCACATGTAGAGTAC 59.182 37.037 0.00 0.00 33.66 2.73
2225 2623 7.903145 ACAATTACAGTTCCACATGTAGAGTA 58.097 34.615 0.00 0.00 33.66 2.59
2226 2624 6.769512 ACAATTACAGTTCCACATGTAGAGT 58.230 36.000 0.00 0.00 33.66 3.24
2227 2625 6.313905 GGACAATTACAGTTCCACATGTAGAG 59.686 42.308 0.00 0.00 33.66 2.43
2228 2626 6.170506 GGACAATTACAGTTCCACATGTAGA 58.829 40.000 0.00 0.00 33.66 2.59
2229 2627 5.063438 CGGACAATTACAGTTCCACATGTAG 59.937 44.000 0.00 0.00 33.66 2.74
2311 2709 8.584157 TGCAGACACCTTACAAAAATCATTTAT 58.416 29.630 0.00 0.00 0.00 1.40
2312 2710 7.946207 TGCAGACACCTTACAAAAATCATTTA 58.054 30.769 0.00 0.00 0.00 1.40
2313 2711 6.815089 TGCAGACACCTTACAAAAATCATTT 58.185 32.000 0.00 0.00 0.00 2.32
2315 2713 6.403866 TTGCAGACACCTTACAAAAATCAT 57.596 33.333 0.00 0.00 0.00 2.45
2317 2715 7.713764 AATTTGCAGACACCTTACAAAAATC 57.286 32.000 0.00 0.00 32.72 2.17
2318 2716 8.397148 CAAAATTTGCAGACACCTTACAAAAAT 58.603 29.630 0.00 0.00 32.72 1.82
2320 2718 7.301068 CAAAATTTGCAGACACCTTACAAAA 57.699 32.000 0.00 0.00 32.72 2.44
2340 2766 8.504812 TGCAGACATACAATTCTATAGCAAAA 57.495 30.769 0.00 0.00 0.00 2.44
2388 2814 7.389053 AGTTTCCTCTAAGTACATGCAGAAAAG 59.611 37.037 0.00 0.00 0.00 2.27
2549 2975 8.902806 ACAATTTTGTCACTAGAAGTTGAATCA 58.097 29.630 0.00 0.00 36.50 2.57


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

AutoCloner maintained by Alex Coulton.