Multiple sequence alignment - TraesCS6D01G134200

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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 TraesCS6D01G134200 chr6D 100.000 3356 0 0 1 3356 102113982 102117337 0 6198
1 TraesCS6D01G134200 chr6A 97.311 2863 57 14 501 3356 123445679 123448528 0 4843
2 TraesCS6D01G134200 chr6A 94.977 438 21 1 1 437 123445224 123445661 0 686
3 TraesCS6D01G134200 chr6B 96.552 1798 49 6 1 1793 187830495 187832284 0 2964
4 TraesCS6D01G134200 chr6B 95.232 1573 46 13 1796 3356 187832521 187834076 0 2462


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 TraesCS6D01G134200 chr6D 102113982 102117337 3355 False 6198.0 6198 100.000 1 3356 1 chr6D.!!$F1 3355
1 TraesCS6D01G134200 chr6A 123445224 123448528 3304 False 2764.5 4843 96.144 1 3356 2 chr6A.!!$F1 3355
2 TraesCS6D01G134200 chr6B 187830495 187834076 3581 False 2713.0 2964 95.892 1 3356 2 chr6B.!!$F1 3355

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
941 947 0.984230 TCTTCGTCAAAGCTCCCCAT 59.016 50.000 0.0 0.0 34.76 4.00 F
1729 1735 7.216494 TGAATTACGATGGCTGATAGAATCAA 58.784 34.615 0.0 0.0 39.11 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 2111 2.093235 AGTGCTTCTACCAGCTGATTCC 60.093 50.0 17.39 0.0 40.79 3.01 R
3140 3398 0.610687 GCTACTGCTCAGAACAGGGT 59.389 55.0 5.80 0.0 39.55 4.34 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
127 128 2.745884 TTTGCATGCCGTCCGGAG 60.746 61.111 16.68 0.00 37.50 4.63
251 252 2.648059 GCATCAATCAGGCTTACCAGT 58.352 47.619 0.00 0.00 39.06 4.00
340 341 4.931002 GCCACCGTTGTAACTTATTAGTGA 59.069 41.667 0.00 0.00 34.01 3.41
345 346 8.316046 CACCGTTGTAACTTATTAGTGAATACG 58.684 37.037 0.00 0.00 34.01 3.06
367 368 5.873164 ACGGTAATTCAACCTGATACTGAAC 59.127 40.000 0.00 0.00 37.39 3.18
468 470 6.476378 ACATTCTACTGGAACTGCATTACTT 58.524 36.000 0.00 0.00 36.70 2.24
472 474 7.661536 TCTACTGGAACTGCATTACTTATCT 57.338 36.000 0.00 0.00 0.00 1.98
474 476 6.299805 ACTGGAACTGCATTACTTATCTGA 57.700 37.500 0.00 0.00 0.00 3.27
622 627 3.855950 CGAAATGATTTTGCAGCTCCTTC 59.144 43.478 0.00 0.00 0.00 3.46
678 683 4.334203 CCGTTTTGAAATATGACATCCCGA 59.666 41.667 0.00 0.00 0.00 5.14
680 685 5.263185 GTTTTGAAATATGACATCCCGACG 58.737 41.667 0.00 0.00 0.00 5.12
941 947 0.984230 TCTTCGTCAAAGCTCCCCAT 59.016 50.000 0.00 0.00 34.76 4.00
1646 1652 8.674263 ATTTAGTTCTGATGGCTGAGAAATAG 57.326 34.615 0.00 0.00 32.19 1.73
1729 1735 7.216494 TGAATTACGATGGCTGATAGAATCAA 58.784 34.615 0.00 0.00 39.11 2.57
1871 2111 4.133078 GCTACCTGAAGAATCTGATTGGG 58.867 47.826 7.78 4.86 0.00 4.12
1900 2140 6.605995 TCAGCTGGTAGAAGCACTATAAAGTA 59.394 38.462 15.13 0.00 46.08 2.24
2028 2275 6.868622 ACTACCTGTCAAGTTCACTCATATC 58.131 40.000 0.00 0.00 0.00 1.63
2157 2404 2.286872 GCTGATGATGAGACAACCCAG 58.713 52.381 0.00 0.00 0.00 4.45
2247 2494 1.892209 ATTTTGTCCGGAAGAAGCGT 58.108 45.000 5.23 0.00 0.00 5.07
2696 2944 6.366061 TGTTATCACTCTCAATTCTTGACACG 59.634 38.462 0.00 0.00 35.46 4.49
2997 3249 1.761784 TCATGGGCAGTTGCAGTTTTT 59.238 42.857 6.43 0.00 44.36 1.94
3097 3353 6.662414 TGACCAACATAAGATCAACGAATC 57.338 37.500 0.00 0.00 0.00 2.52
3155 3413 3.685139 TCTAAACCCTGTTCTGAGCAG 57.315 47.619 13.83 13.83 0.00 4.24
3170 3428 7.770433 TGTTCTGAGCAGTAGCAATTATTACAT 59.230 33.333 0.00 0.00 45.49 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 3.806521 AGATGTATTTCACAGATGCTCGC 59.193 43.478 0.00 0.0 41.51 5.03
196 197 8.807581 GTTTCTTGTAAAATTTCAGTCACTTGG 58.192 33.333 0.00 0.0 0.00 3.61
251 252 9.299963 CAAAACAAAACAGATCATCACAGTTAA 57.700 29.630 0.00 0.0 0.00 2.01
340 341 7.788026 TCAGTATCAGGTTGAATTACCGTATT 58.212 34.615 0.00 0.0 43.21 1.89
345 346 8.038944 TGTAGTTCAGTATCAGGTTGAATTACC 58.961 37.037 13.10 0.0 40.42 2.85
452 454 5.757320 CCTCAGATAAGTAATGCAGTTCCAG 59.243 44.000 0.00 0.0 0.00 3.86
468 470 3.081710 TGTCAGGTTCGTCCTCAGATA 57.918 47.619 0.00 0.0 46.24 1.98
472 474 2.169769 AGTTTTGTCAGGTTCGTCCTCA 59.830 45.455 0.00 0.0 46.24 3.86
560 562 5.308237 ACTCTGATTGGTAAAGTTGTCCTCT 59.692 40.000 0.00 0.0 0.00 3.69
599 604 1.922545 GGAGCTGCAAAATCATTTCGC 59.077 47.619 0.00 0.0 0.00 4.70
657 662 5.263185 CGTCGGGATGTCATATTTCAAAAC 58.737 41.667 0.00 0.0 0.00 2.43
941 947 4.594970 TGTGTTCTTTGTTGGAAGAGGAA 58.405 39.130 0.00 0.0 37.01 3.36
1165 1171 3.131396 GTTCTTCTCGTTCTTCTTGGCA 58.869 45.455 0.00 0.0 0.00 4.92
1255 1261 1.595382 ATATCGCCGAACCTGCAGC 60.595 57.895 8.66 0.0 0.00 5.25
1264 1270 0.589708 CGTGGTAGACATATCGCCGA 59.410 55.000 0.00 0.0 0.00 5.54
1364 1370 6.646653 TCAGACAACAATTATCAGACTCACAC 59.353 38.462 0.00 0.0 0.00 3.82
1626 1632 5.181748 ACACTATTTCTCAGCCATCAGAAC 58.818 41.667 0.00 0.0 0.00 3.01
1697 1703 4.391830 TCAGCCATCGTAATTCAGTTGAAC 59.608 41.667 0.00 0.0 36.80 3.18
1871 2111 2.093235 AGTGCTTCTACCAGCTGATTCC 60.093 50.000 17.39 0.0 40.79 3.01
2028 2275 4.651778 TGTACTCAACCTGAAAAGGATGG 58.348 43.478 0.00 0.0 33.24 3.51
2247 2494 3.056821 GTGCACAGATATATGGTCCGCTA 60.057 47.826 13.17 0.0 0.00 4.26
2756 3008 4.700213 TCTGCTTAGCCAAAAATACACTCC 59.300 41.667 0.29 0.0 0.00 3.85
3081 3337 8.864069 ACTGTAGAAGATTCGTTGATCTTATG 57.136 34.615 12.73 0.0 44.27 1.90
3097 3353 7.281999 TGACATGAGAGTATGAGACTGTAGAAG 59.718 40.741 0.00 0.0 39.06 2.85
3140 3398 0.610687 GCTACTGCTCAGAACAGGGT 59.389 55.000 5.80 0.0 39.55 4.34
3170 3428 9.273016 CTCTGAATCTGTTTCCTAGTGTTTTTA 57.727 33.333 0.00 0.0 33.04 1.52
3242 3501 8.624367 TTTTCCTATTATTTTGTCCTTCGTCA 57.376 30.769 0.00 0.0 0.00 4.35
3274 3534 8.625467 AAACCAGGGTAGTAGAAGATAATCTT 57.375 34.615 0.00 0.0 39.87 2.40
3296 3556 9.646427 ATGAGTAGAGTACTTCATTTCTGAAAC 57.354 33.333 4.73 0.0 40.78 2.78


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

AutoCloner maintained by Alex Coulton.