Multiple sequence alignment - TraesCS6A01G273200

Loading Multiple Alignment...

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 TraesCS6A01G273200 chr6A 100.000 2273 0 0 1 2273 499644276 499646548 0.000000e+00 4198
1 TraesCS6A01G273200 chr6D 96.879 2275 63 6 1 2273 357566545 357568813 0.000000e+00 3801
2 TraesCS6A01G273200 chr6B 95.922 1643 53 5 1 1631 539057003 539058643 0.000000e+00 2651
3 TraesCS6A01G273200 chr6B 97.686 389 8 1 1609 1997 539058650 539059037 0.000000e+00 667
4 TraesCS6A01G273200 chr6B 97.193 285 4 2 1989 2273 539059057 539059337 1.580000e-131 479


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 TraesCS6A01G273200 chr6A 499644276 499646548 2272 False 4198.000000 4198 100.000000 1 2273 1 chr6A.!!$F1 2272
1 TraesCS6A01G273200 chr6D 357566545 357568813 2268 False 3801.000000 3801 96.879000 1 2273 1 chr6D.!!$F1 2272
2 TraesCS6A01G273200 chr6B 539057003 539059337 2334 False 1265.666667 2651 96.933667 1 2273 3 chr6B.!!$F1 2272

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
847 861 1.513087 ATTGCTGGCTTCCCCCTCTT 61.513 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1703 3.746492 GCTAGTCAAATTCCACACTTCGT 59.254 43.478 0.0 0.0 0.0 3.85 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
63 64 4.025480 GGTCGTCGACACAAATTGTTAGTT 60.025 41.667 25.64 0.0 39.17 2.24
124 134 5.012561 AGGGCAAATATCCTCTGCTACTAAG 59.987 44.000 0.00 0.0 36.32 2.18
222 232 4.162131 AGCACCTTTGTTCAAAACATTCCT 59.838 37.500 0.00 0.0 41.79 3.36
517 528 5.359576 AGTGTGCTTCTTCCAATACAAAACA 59.640 36.000 0.00 0.0 0.00 2.83
526 537 8.226819 TCTTCCAATACAAAACAACACACATA 57.773 30.769 0.00 0.0 0.00 2.29
691 703 3.349927 TCCCAGCAAATCTGAGTGATTG 58.650 45.455 0.00 0.0 45.72 2.67
847 861 1.513087 ATTGCTGGCTTCCCCCTCTT 61.513 55.000 0.00 0.0 0.00 2.85
970 984 2.962421 CCTGCTGGGGAAACAGTAAAAA 59.038 45.455 0.71 0.0 40.59 1.94
1047 1061 2.839486 ACAAGATCTTTGAGACGGCA 57.161 45.000 4.86 0.0 0.00 5.69
1071 1085 0.445043 CGACGTATGACGAGGACACA 59.555 55.000 5.94 0.0 46.05 3.72
1323 1337 6.832384 ACATAATCTCATTGTGCATCCTCTTT 59.168 34.615 0.00 0.0 35.11 2.52
1326 1340 6.879276 ATCTCATTGTGCATCCTCTTTATG 57.121 37.500 0.00 0.0 0.00 1.90
1362 1376 5.188948 TGTTATGCACTACTAGTCATGGGTT 59.811 40.000 0.00 0.0 0.00 4.11
1455 1469 3.637229 ACGTCCCACACCTAGATTATCTG 59.363 47.826 4.78 0.0 0.00 2.90
1512 1526 7.780271 AGTTTGTTCCTCCTATTCTGTTCTTTT 59.220 33.333 0.00 0.0 0.00 2.27
1754 1797 1.273327 CCTGTTCCATTTCCACCTTGC 59.727 52.381 0.00 0.0 0.00 4.01
2256 2327 5.585390 ACTCAGTGTGCTTTGAAAATTCAG 58.415 37.500 0.00 0.0 38.61 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.423921 ACCTCCCCACTGTAACAAAGG 59.576 52.381 0.00 0.00 0.00 3.11
63 64 6.110411 AGCAAGTACAAGGAAAAGCTAGTA 57.890 37.500 0.00 0.00 0.00 1.82
182 192 0.668401 GCTGTCCACCAATTTGCAGC 60.668 55.000 9.26 9.26 41.65 5.25
554 565 2.706890 AGGGTGCATTTGGTACTTACG 58.293 47.619 0.00 0.00 32.05 3.18
733 745 4.216257 CCACGAGAAATTTCACCAACTCAT 59.784 41.667 19.99 0.00 0.00 2.90
739 751 2.151202 GAGCCACGAGAAATTTCACCA 58.849 47.619 19.99 0.00 0.00 4.17
832 844 4.519906 TTTATAAAGAGGGGGAAGCCAG 57.480 45.455 0.00 0.00 0.00 4.85
847 861 7.658261 AGTGAGCGTAGATGTGCTATTTATAA 58.342 34.615 0.00 0.00 42.60 0.98
911 925 2.285707 AGGTCAGGGGACTAGTAGTGA 58.714 52.381 7.76 0.00 43.77 3.41
914 928 3.983821 AGAAAGGTCAGGGGACTAGTAG 58.016 50.000 0.00 0.00 43.77 2.57
970 984 6.505700 TCTCTATTTTTCCTTTTCTCCTCCCT 59.494 38.462 0.00 0.00 0.00 4.20
1047 1061 0.935898 CCTCGTCATACGTCGCTAGT 59.064 55.000 0.00 0.00 43.14 2.57
1234 1248 2.856000 ACTGCCCCAGGAGTTGCT 60.856 61.111 0.00 0.00 35.51 3.91
1323 1337 3.689161 GCATAACAACAGGTGAGCACATA 59.311 43.478 0.00 0.00 0.00 2.29
1326 1340 1.879380 TGCATAACAACAGGTGAGCAC 59.121 47.619 0.00 0.00 0.00 4.40
1362 1376 6.304356 CAGAAACACTGCTCTTGAACATAA 57.696 37.500 0.00 0.00 39.86 1.90
1455 1469 2.504367 TGCTGCAAACTAGAGGGAAAC 58.496 47.619 0.00 0.00 0.00 2.78
1512 1526 2.948979 CCAGACACTTAAACACAAGCCA 59.051 45.455 0.00 0.00 0.00 4.75
1660 1703 3.746492 GCTAGTCAAATTCCACACTTCGT 59.254 43.478 0.00 0.00 0.00 3.85
1754 1797 7.642669 ACAAGGATCACATGCTTAATTTATCG 58.357 34.615 0.00 0.00 39.01 2.92
2230 2301 4.552166 TTTTCAAAGCACACTGAGTAGC 57.448 40.909 1.44 1.44 0.00 3.58
2231 2302 6.728200 TGAATTTTCAAAGCACACTGAGTAG 58.272 36.000 0.00 0.00 33.55 2.57
2232 2303 6.691754 TGAATTTTCAAAGCACACTGAGTA 57.308 33.333 0.00 0.00 33.55 2.59


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

AutoCloner maintained by Alex Coulton.