Multiple sequence alignment - TraesCS2D01G565900

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 TraesCS2D01G565900 chr2D 100.000 3404 0 0 1 3404 635313693 635310290 0 6287
1 TraesCS2D01G565900 chr2D 97.917 3408 63 6 1 3404 635287672 635284269 0 5893
2 TraesCS2D01G565900 chr2D 96.560 2645 88 3 1 2643 635440690 635438047 0 4377
3 TraesCS2D01G565900 chr2D 95.276 762 31 4 2643 3404 635414013 635413257 0 1203
4 TraesCS2D01G565900 chr2B 96.396 3413 109 10 1 3404 779393340 779389933 0 5609
5 TraesCS2D01G565900 chr2B 96.396 3413 110 9 1 3404 779425494 779422086 0 5609
6 TraesCS2D01G565900 chr2B 96.367 3413 109 11 1 3404 779431949 779428543 0 5602
7 TraesCS2D01G565900 chr2B 96.338 3413 110 11 1 3404 779412591 779409185 0 5596
8 TraesCS2D01G565900 chr2B 96.338 3413 110 11 1 3404 779419040 779415634 0 5596
9 TraesCS2D01G565900 chr2B 96.191 3413 114 13 1 3404 779451238 779447833 0 5568
10 TraesCS2D01G565900 chrUn 96.308 3413 111 11 1 3404 280844429 280847835 0 5590


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 TraesCS2D01G565900 chr2D 635310290 635313693 3403 True 6287.00 6287 100.00000 1 3404 1 chr2D.!!$R2 3403
1 TraesCS2D01G565900 chr2D 635284269 635287672 3403 True 5893.00 5893 97.91700 1 3404 1 chr2D.!!$R1 3403
2 TraesCS2D01G565900 chr2D 635438047 635440690 2643 True 4377.00 4377 96.56000 1 2643 1 chr2D.!!$R4 2642
3 TraesCS2D01G565900 chr2D 635413257 635414013 756 True 1203.00 1203 95.27600 2643 3404 1 chr2D.!!$R3 761
4 TraesCS2D01G565900 chr2B 779389933 779393340 3407 True 5609.00 5609 96.39600 1 3404 1 chr2B.!!$R1 3403
5 TraesCS2D01G565900 chr2B 779409185 779431949 22764 True 5600.75 5609 96.35975 1 3404 4 chr2B.!!$R3 3403
6 TraesCS2D01G565900 chr2B 779447833 779451238 3405 True 5568.00 5568 96.19100 1 3404 1 chr2B.!!$R2 3403
7 TraesCS2D01G565900 chrUn 280844429 280847835 3406 False 5590.00 5590 96.30800 1 3404 1 chrUn.!!$F1 3403

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
203 6660 0.840617 AACCGGGGGCAAAACAAAAT 59.159 45.000 6.32 0.0 0.00 1.82 F
964 13875 1.802880 GCACGTATGATCGCCTCAAGT 60.803 52.381 0.00 0.0 37.44 3.16 F
994 13905 2.945668 GCAAAGGAGTTCTGTGAGTTGT 59.054 45.455 0.00 0.0 32.32 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 14776 0.947244 CAATTACTGCAGATCGGCCC 59.053 55.000 23.35 0.0 0.00 5.80 R
1999 14913 2.039879 TGCTCCCTTGAACCTTTAGGAC 59.960 50.000 2.06 0.0 38.94 3.85 R
2610 15524 3.541632 ACACAGTTGTAGGTTCAACCAG 58.458 45.455 9.90 0.0 45.90 4.00 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
203 6660 0.840617 AACCGGGGGCAAAACAAAAT 59.159 45.000 6.32 0.00 0.00 1.82
409 13318 7.482169 TCCTATATCGCATACAAAGAGGAAT 57.518 36.000 0.00 0.00 0.00 3.01
412 13321 9.307121 CCTATATCGCATACAAAGAGGAATAAG 57.693 37.037 0.00 0.00 0.00 1.73
634 13543 9.725206 AAATACTCCTACAAACTAGGATTAGGA 57.275 33.333 9.88 9.88 42.34 2.94
718 13628 9.507381 GATACCAGTATATATATGCCCCCATAT 57.493 37.037 5.44 2.25 44.64 1.78
964 13875 1.802880 GCACGTATGATCGCCTCAAGT 60.803 52.381 0.00 0.00 37.44 3.16
994 13905 2.945668 GCAAAGGAGTTCTGTGAGTTGT 59.054 45.455 0.00 0.00 32.32 3.32
1054 13965 4.000325 ACCAAAAACCTTGTTTGTGAAGC 59.000 39.130 10.67 0.00 34.75 3.86
1698 14612 5.981088 TTTGTGGTTGCAGATTCATGTAT 57.019 34.783 0.00 0.00 0.00 2.29
1862 14776 4.379813 CCAATGACCCTCAAATCAGAAACG 60.380 45.833 0.00 0.00 0.00 3.60
1999 14913 9.897744 ATGCCGAGTTATCAATGTATTTTTATG 57.102 29.630 0.00 0.00 0.00 1.90
2127 15041 1.021202 GCACGGCAAATATGTGGCTA 58.979 50.000 16.76 0.00 41.74 3.93
2380 15294 9.499479 AGAATATCGCTAATGACATCAAATCTT 57.501 29.630 0.00 0.00 0.00 2.40
2560 15474 4.701171 CCCCGGAGAGAGATGTACTATTAC 59.299 50.000 0.73 0.00 0.00 1.89
2599 15513 5.565592 TTGTACTCTTATTACGCGGAGAA 57.434 39.130 12.47 1.23 0.00 2.87
2603 15517 7.706159 TGTACTCTTATTACGCGGAGAAATTA 58.294 34.615 12.47 0.00 0.00 1.40
2682 15596 1.717194 CAAAAGGCATGCGCTCAATT 58.283 45.000 12.44 4.25 38.60 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
203 6660 3.243636 GGTTCAGTTGTAAGACGGTCAGA 60.244 47.826 11.27 0.00 0.00 3.27
244 6701 3.451540 ACCAACCATGTTAACCGGTTTTT 59.548 39.130 27.64 3.20 41.07 1.94
661 13571 5.070847 GGGCCAATCTGTTTTATGGATTGAT 59.929 40.000 4.39 0.00 45.09 2.57
718 13628 3.610040 ACTTTGGATGACATGCTCGTA 57.390 42.857 8.51 0.00 0.00 3.43
946 13857 2.540515 CAACTTGAGGCGATCATACGT 58.459 47.619 0.00 0.00 37.89 3.57
994 13905 4.349365 TCTACAGGGTATGACATGTGTGA 58.651 43.478 1.15 0.00 0.00 3.58
1054 13965 3.308053 CGCTCAACATAGTCATCCAAGTG 59.692 47.826 0.00 0.00 0.00 3.16
1132 14043 5.764192 CCACAATGGACCAACATTTTTCATT 59.236 36.000 0.00 0.00 40.96 2.57
1698 14612 6.926272 CCCAAACGAATTAATTCCTTTGTCAA 59.074 34.615 29.99 0.00 39.23 3.18
1862 14776 0.947244 CAATTACTGCAGATCGGCCC 59.053 55.000 23.35 0.00 0.00 5.80
1999 14913 2.039879 TGCTCCCTTGAACCTTTAGGAC 59.960 50.000 2.06 0.00 38.94 3.85
2127 15041 9.073475 TGTTCAAACACAAGCTATATTACCTTT 57.927 29.630 0.00 0.00 33.17 3.11
2560 15474 7.275920 AGAGTACAAAGCCCTTGATTATAGTG 58.724 38.462 3.27 0.00 38.50 2.74
2599 15513 9.802039 TTGTAGGTTCAACCAGAATTAGTAATT 57.198 29.630 9.90 7.87 41.95 1.40
2603 15517 6.710744 CAGTTGTAGGTTCAACCAGAATTAGT 59.289 38.462 9.90 0.00 45.90 2.24
2610 15524 3.541632 ACACAGTTGTAGGTTCAACCAG 58.458 45.455 9.90 0.00 45.90 4.00
2774 15688 4.501571 GGCGATGGATGTAGTGAACTATGT 60.502 45.833 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.