Multiple sequence alignment - TraesCS6B01G260000

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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 TraesCS6B01G260000 chr6B 100.000 3389 0 0 1 3389 470131015 470134403 0 6259
1 TraesCS6B01G260000 chr6D 96.036 3406 100 18 1 3389 304286877 304290264 0 5509
2 TraesCS6B01G260000 chr6A 95.796 3330 106 15 84 3389 410895922 410892603 0 5343
3 TraesCS6B01G260000 chr6A 95.561 2005 46 10 1130 3127 441435761 441437729 0 3169
4 TraesCS6B01G260000 chr6A 97.655 1066 19 4 1 1061 441434371 441435435 0 1825


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 TraesCS6B01G260000 chr6B 470131015 470134403 3388 False 6259 6259 100.000 1 3389 1 chr6B.!!$F1 3388
1 TraesCS6B01G260000 chr6D 304286877 304290264 3387 False 5509 5509 96.036 1 3389 1 chr6D.!!$F1 3388
2 TraesCS6B01G260000 chr6A 410892603 410895922 3319 True 5343 5343 95.796 84 3389 1 chr6A.!!$R1 3305
3 TraesCS6B01G260000 chr6A 441434371 441437729 3358 False 2497 3169 96.608 1 3127 2 chr6A.!!$F1 3126

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
713 722 0.545548 GGACTGGGGAGTCTGAGGTT 60.546 60.000 0.0 0.0 38.74 3.50 F
715 724 1.298014 CTGGGGAGTCTGAGGTTGC 59.702 63.158 0.0 0.0 0.00 4.17 F
936 951 1.617850 ACAGACTCCTCTTGTGCTCTG 59.382 52.381 0.0 0.0 0.00 3.35 F
938 953 2.822561 CAGACTCCTCTTGTGCTCTGTA 59.177 50.000 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 2084 0.471617 CTCCATCGGCCTCCATTTCT 59.528 55.000 0.00 0.00 0.00 2.52 R
1904 2188 1.628846 ACCCTTTGTCACCTAGCGAAT 59.371 47.619 0.00 0.00 0.00 3.34 R
2088 2372 2.604686 TCCTTCGCCTCAGCCACT 60.605 61.111 0.00 0.00 34.57 4.00 R
3023 3316 1.160137 GTTCCATGGAGAGTGTGCAC 58.840 55.000 15.53 10.75 0.00 4.57 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
142 148 7.093684 GCATAAATGTACAAAAACTAAGGGGGA 60.094 37.037 0.00 0.00 0.00 4.81
143 149 6.911250 AAATGTACAAAAACTAAGGGGGAG 57.089 37.500 0.00 0.00 0.00 4.30
144 150 4.376225 TGTACAAAAACTAAGGGGGAGG 57.624 45.455 0.00 0.00 0.00 4.30
145 151 2.304221 ACAAAAACTAAGGGGGAGGC 57.696 50.000 0.00 0.00 0.00 4.70
683 692 1.592669 CTAGCCGCATCTGTTCCGG 60.593 63.158 0.00 0.00 44.58 5.14
713 722 0.545548 GGACTGGGGAGTCTGAGGTT 60.546 60.000 0.00 0.00 38.74 3.50
715 724 1.298014 CTGGGGAGTCTGAGGTTGC 59.702 63.158 0.00 0.00 0.00 4.17
806 815 3.998672 GGCCGGTGAGAACGTGGA 61.999 66.667 1.90 0.00 0.00 4.02
807 816 2.029964 GCCGGTGAGAACGTGGAA 59.970 61.111 1.90 0.00 0.00 3.53
934 949 2.829741 AACAGACTCCTCTTGTGCTC 57.170 50.000 0.00 0.00 0.00 4.26
936 951 1.617850 ACAGACTCCTCTTGTGCTCTG 59.382 52.381 0.00 0.00 0.00 3.35
937 952 1.617850 CAGACTCCTCTTGTGCTCTGT 59.382 52.381 0.00 0.00 0.00 3.41
938 953 2.822561 CAGACTCCTCTTGTGCTCTGTA 59.177 50.000 0.00 0.00 0.00 2.74
1846 2130 3.535561 CCAGACACCATCACCTACAATC 58.464 50.000 0.00 0.00 0.00 2.67
1904 2188 3.266686 ATGCCAAGGCGCTGTACCA 62.267 57.895 7.64 0.00 45.51 3.25
2058 2342 5.335976 GCCAGACTTTAAGACAATGAAAGGG 60.336 44.000 0.00 0.00 35.02 3.95
2088 2372 0.323725 GATTGGCAAAGGGAGGCAGA 60.324 55.000 3.01 0.00 42.75 4.26
3023 3316 5.123820 TCAAAGAGCCCAAGAAATATTGTCG 59.876 40.000 0.00 0.00 0.00 4.35
3030 3323 4.158384 CCAAGAAATATTGTCGTGCACAC 58.842 43.478 18.64 14.25 33.41 3.82
3039 3332 1.016130 GTCGTGCACACTCTCCATGG 61.016 60.000 18.64 4.97 0.00 3.66
3075 3368 5.221204 TGCGATGGCATTGCATAATTAGAAA 60.221 36.000 33.19 11.06 46.21 2.52
3370 3668 5.408356 ACAGTGTTAGCTCTATGTTAACCG 58.592 41.667 2.48 0.00 40.26 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 148 0.392998 ATCTGTGCCGAATTTCGCCT 60.393 50.000 13.26 0.00 38.82 5.52
143 149 0.451783 AATCTGTGCCGAATTTCGCC 59.548 50.000 13.26 2.81 38.82 5.54
144 150 3.398954 TTAATCTGTGCCGAATTTCGC 57.601 42.857 13.26 9.32 38.82 4.70
145 151 6.525121 TCTATTAATCTGTGCCGAATTTCG 57.475 37.500 11.81 11.81 40.07 3.46
683 692 2.436646 CCAGTCCCCATCGTGTGC 60.437 66.667 0.00 0.00 0.00 4.57
713 722 0.537188 CTTAAGCTTCCTCTCCCGCA 59.463 55.000 0.00 0.00 0.00 5.69
715 724 0.528684 CGCTTAAGCTTCCTCTCCCG 60.529 60.000 24.33 1.76 39.32 5.14
806 815 5.395324 CGACAGTCCAACTCCTATACCATTT 60.395 44.000 0.00 0.00 0.00 2.32
807 816 4.099573 CGACAGTCCAACTCCTATACCATT 59.900 45.833 0.00 0.00 0.00 3.16
909 924 3.812053 CACAAGAGGAGTCTGTTTTGGAG 59.188 47.826 0.00 0.00 31.37 3.86
934 949 3.520290 TTTGGGCGACAGAGTATACAG 57.480 47.619 5.50 0.00 0.00 2.74
936 951 2.934553 GGTTTTGGGCGACAGAGTATAC 59.065 50.000 0.00 0.00 0.00 1.47
937 952 2.835764 AGGTTTTGGGCGACAGAGTATA 59.164 45.455 0.00 0.00 0.00 1.47
938 953 1.628846 AGGTTTTGGGCGACAGAGTAT 59.371 47.619 0.00 0.00 0.00 2.12
1350 1634 2.660064 GGCTTCGAGGGCCTTCTCA 61.660 63.158 19.80 0.00 45.57 3.27
1800 2084 0.471617 CTCCATCGGCCTCCATTTCT 59.528 55.000 0.00 0.00 0.00 2.52
1846 2130 2.492012 GCAATAGGCAGTCATGAGGAG 58.508 52.381 0.00 0.00 43.97 3.69
1904 2188 1.628846 ACCCTTTGTCACCTAGCGAAT 59.371 47.619 0.00 0.00 0.00 3.34
1969 2253 2.925578 TCAAAATCGCCATGAGCAAG 57.074 45.000 0.00 0.00 44.04 4.01
2058 2342 3.809279 CCTTTGCCAATCCTTCAACAAAC 59.191 43.478 0.00 0.00 0.00 2.93
2088 2372 2.604686 TCCTTCGCCTCAGCCACT 60.605 61.111 0.00 0.00 34.57 4.00
3023 3316 1.160137 GTTCCATGGAGAGTGTGCAC 58.840 55.000 15.53 10.75 0.00 4.57
3030 3323 4.252073 CAAGACAAGAGTTCCATGGAGAG 58.748 47.826 15.53 5.22 0.00 3.20
3075 3368 6.782494 ACCAAGTTATTCCCATTTCACTCTTT 59.218 34.615 0.00 0.00 0.00 2.52
3283 3576 5.407049 AGGCATACCATCTCCTACATTACT 58.593 41.667 0.00 0.00 39.06 2.24


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

AutoCloner maintained by Alex Coulton.