Multiple sequence alignment - TraesCS6D01G167000

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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 TraesCS6D01G167000 chr6D 100.000 3373 0 0 1 3373 149473302 149469930 0.000000e+00 6229.0
1 TraesCS6D01G167000 chr6A 96.730 3394 74 14 1 3373 196784984 196788361 0.000000e+00 5618.0
2 TraesCS6D01G167000 chr6B 96.860 3376 66 13 1 3373 262474448 262471110 0.000000e+00 5611.0
3 TraesCS6D01G167000 chr2D 83.784 111 9 4 2030 2131 49178413 49178523 2.770000e-16 97.1


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 TraesCS6D01G167000 chr6D 149469930 149473302 3372 True 6229 6229 100.00 1 3373 1 chr6D.!!$R1 3372
1 TraesCS6D01G167000 chr6A 196784984 196788361 3377 False 5618 5618 96.73 1 3373 1 chr6A.!!$F1 3372
2 TraesCS6D01G167000 chr6B 262471110 262474448 3338 True 5611 5611 96.86 1 3373 1 chr6B.!!$R1 3372

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
267 270 1.229359 CTAGAGTCTGGGGCGGGTA 59.771 63.158 1.86 0.0 0.0 3.69 F
1133 1146 2.225963 GCTATGATCCATGTCTGCTTGC 59.774 50.000 0.00 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1140 1153 0.897621 GAACCCTTTCAATGGCCAGG 59.102 55.000 13.05 7.59 0.0 4.45 R
2685 2703 1.134371 GTAGCAGACTGGGGTGATTCC 60.134 57.143 4.26 0.00 0.0 3.01 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
84 87 5.890752 TCTCCTTCGTCTAATCTCCTCTA 57.109 43.478 0.00 0.00 0.00 2.43
143 146 1.679032 CGGAGCCTTTCCTCGGATTTT 60.679 52.381 0.00 0.00 44.41 1.82
144 147 2.017782 GGAGCCTTTCCTCGGATTTTC 58.982 52.381 0.00 0.00 43.16 2.29
145 148 2.356227 GGAGCCTTTCCTCGGATTTTCT 60.356 50.000 0.00 0.00 43.16 2.52
146 149 2.939756 GAGCCTTTCCTCGGATTTTCTC 59.060 50.000 0.00 0.00 0.00 2.87
267 270 1.229359 CTAGAGTCTGGGGCGGGTA 59.771 63.158 1.86 0.00 0.00 3.69
593 596 2.977914 TGATTACTTGCTGCAGAGGAC 58.022 47.619 20.43 0.00 0.00 3.85
678 686 3.610242 CAGTCAGTTCGTCTATCTGTTGC 59.390 47.826 0.00 0.00 0.00 4.17
706 714 2.715749 TTGGTGATTCGATGCATCCT 57.284 45.000 20.87 5.96 0.00 3.24
712 720 3.750130 GTGATTCGATGCATCCTATTGCT 59.250 43.478 20.87 0.00 43.18 3.91
809 817 6.825213 TGCAGCATAATACACTTCAGAAATCT 59.175 34.615 0.00 0.00 0.00 2.40
1066 1079 2.626780 GCACCTTTCGGTTCCTGGC 61.627 63.158 0.00 0.00 42.13 4.85
1133 1146 2.225963 GCTATGATCCATGTCTGCTTGC 59.774 50.000 0.00 0.00 0.00 4.01
1140 1153 1.450312 ATGTCTGCTTGCCGGTAGC 60.450 57.895 19.84 19.84 44.14 3.58
1244 1257 4.307432 GACATCCTTGAAGTCTTCGACAA 58.693 43.478 8.06 0.00 34.60 3.18
1453 1466 8.524870 ACTTATTATTTTTGCACAAGCTTCTG 57.475 30.769 0.00 0.00 42.74 3.02
1483 1496 8.585471 ATGCCTGTTATGGAAATTATGGATAG 57.415 34.615 0.00 0.00 0.00 2.08
1487 1500 8.517878 CCTGTTATGGAAATTATGGATAGCTTG 58.482 37.037 0.00 0.00 0.00 4.01
1646 1661 1.227943 TGCTGGTTCACACAGGAGC 60.228 57.895 0.00 0.00 36.48 4.70
1924 1939 7.771361 TGAAAAATGCATGCATGATTCCTTAAT 59.229 29.630 33.59 19.50 36.68 1.40
2073 2088 0.113776 TCCCTACGGTAGCCCCTATG 59.886 60.000 9.70 0.00 0.00 2.23
2685 2703 6.808829 ACAAAGCCATTGATATGTGGTAATG 58.191 36.000 6.83 0.00 41.85 1.90
2812 2831 6.822442 TCAGTATGTTACTTGAACTGTCCAA 58.178 36.000 0.00 0.00 38.88 3.53
2888 2907 4.323792 CCTGACAGTTGACCAACATCCTAT 60.324 45.833 14.42 0.00 43.47 2.57
2901 2920 7.001674 ACCAACATCCTATCTTGTTAAACACA 58.998 34.615 0.00 0.00 34.42 3.72
3359 3381 6.262496 AGGAAAACAAAGGAGTAGTTAAGTGC 59.738 38.462 0.00 0.00 0.00 4.40
3360 3382 6.038936 GGAAAACAAAGGAGTAGTTAAGTGCA 59.961 38.462 1.05 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 87 3.854669 CTGATTCTCCGCCCCGCT 61.855 66.667 0.00 0.00 0.00 5.52
143 146 2.088423 GAAGAAGCACGGAGAGAGAGA 58.912 52.381 0.00 0.00 0.00 3.10
144 147 1.134175 GGAAGAAGCACGGAGAGAGAG 59.866 57.143 0.00 0.00 0.00 3.20
145 148 1.178276 GGAAGAAGCACGGAGAGAGA 58.822 55.000 0.00 0.00 0.00 3.10
146 149 0.174617 GGGAAGAAGCACGGAGAGAG 59.825 60.000 0.00 0.00 0.00 3.20
181 184 4.214383 CTTGCGATGCCGACTGCG 62.214 66.667 0.00 0.00 45.60 5.18
182 185 3.869272 CCTTGCGATGCCGACTGC 61.869 66.667 0.00 0.00 38.22 4.40
183 186 1.577328 AAACCTTGCGATGCCGACTG 61.577 55.000 0.00 0.00 38.22 3.51
267 270 2.093553 CCATCCCCGCATCAAAAACAAT 60.094 45.455 0.00 0.00 0.00 2.71
460 463 7.037945 GGCCAGAAATACTCCTAGAGGAATTAT 60.038 40.741 0.00 0.00 44.91 1.28
536 539 0.319040 CGTATCGCCCACCAGATCAG 60.319 60.000 0.00 0.00 0.00 2.90
569 572 3.755378 CCTCTGCAGCAAGTAATCAAGTT 59.245 43.478 9.47 0.00 0.00 2.66
570 573 3.008375 TCCTCTGCAGCAAGTAATCAAGT 59.992 43.478 9.47 0.00 0.00 3.16
678 686 3.769739 TCGAATCACCAATCCATAGGG 57.230 47.619 0.00 0.00 0.00 3.53
706 714 2.931969 CACGTGCAGATTCAGAGCAATA 59.068 45.455 0.82 0.00 40.35 1.90
922 935 9.995003 AATTGAGCCAATGTGTTCTTAAATTAA 57.005 25.926 1.80 0.00 34.04 1.40
924 937 9.423061 GTAATTGAGCCAATGTGTTCTTAAATT 57.577 29.630 1.80 0.00 34.04 1.82
925 938 8.806146 AGTAATTGAGCCAATGTGTTCTTAAAT 58.194 29.630 1.80 0.00 34.04 1.40
926 939 8.177119 AGTAATTGAGCCAATGTGTTCTTAAA 57.823 30.769 1.80 0.00 34.04 1.52
1133 1146 2.516930 CAATGGCCAGGCTACCGG 60.517 66.667 13.05 0.00 0.00 5.28
1140 1153 0.897621 GAACCCTTTCAATGGCCAGG 59.102 55.000 13.05 7.59 0.00 4.45
1244 1257 4.927267 TCCACAACCTTCCATGAATAGT 57.073 40.909 0.00 0.00 0.00 2.12
1453 1466 7.867403 CCATAATTTCCATAACAGGCATAACAC 59.133 37.037 0.00 0.00 0.00 3.32
1483 1496 1.135141 TGTCAACTGTTTGCCACAAGC 60.135 47.619 0.00 0.00 44.14 4.01
1487 1500 1.798813 GCTGTGTCAACTGTTTGCCAC 60.799 52.381 0.00 0.00 41.14 5.01
1572 1587 5.247507 TGGCGTTAGCGAGTTATTACTAA 57.752 39.130 2.07 0.00 46.35 2.24
1646 1661 2.625790 TGAATTTCCACCTTTTGTCCGG 59.374 45.455 0.00 0.00 0.00 5.14
2073 2088 2.289945 ACTCTTGAGGATGTGCTTGTCC 60.290 50.000 2.55 0.00 34.64 4.02
2503 2521 6.062095 CCCCTTTCTACATGGTTAATACAGG 58.938 44.000 0.00 0.00 0.00 4.00
2659 2677 4.603131 ACCACATATCAATGGCTTTGTCT 58.397 39.130 12.22 5.02 39.84 3.41
2685 2703 1.134371 GTAGCAGACTGGGGTGATTCC 60.134 57.143 4.26 0.00 0.00 3.01
2691 2709 2.283529 CCACGTAGCAGACTGGGGT 61.284 63.158 4.26 0.00 0.00 4.95
2812 2831 9.369904 GTTGAAAATACACCAGCATATTCAAAT 57.630 29.630 0.00 0.00 37.31 2.32
2888 2907 7.083858 GCTATGAGCAAATGTGTTTAACAAGA 58.916 34.615 0.00 0.00 41.13 3.02
3172 3194 3.012518 CCTGTCCAGTATCCTTGCAAAG 58.987 50.000 0.00 0.00 45.69 2.77


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

AutoCloner maintained by Alex Coulton.