Multiple sequence alignment - TraesCS3B01G516800

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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 TraesCS3B01G516800 chr3B 100.000 3086 0 0 1 3086 759910397 759913482 0 5699
1 TraesCS3B01G516800 chr6B 98.413 3087 44 2 1 3086 596596250 596593168 0 5424
2 TraesCS3B01G516800 chr5B 97.668 3087 65 4 1 3086 567285579 567288659 0 5295
3 TraesCS3B01G516800 chr5B 97.182 3087 77 5 1 3086 680052983 680049906 0 5210


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 TraesCS3B01G516800 chr3B 759910397 759913482 3085 False 5699 5699 100.000 1 3086 1 chr3B.!!$F1 3085
1 TraesCS3B01G516800 chr6B 596593168 596596250 3082 True 5424 5424 98.413 1 3086 1 chr6B.!!$R1 3085
2 TraesCS3B01G516800 chr5B 567285579 567288659 3080 False 5295 5295 97.668 1 3086 1 chr5B.!!$F1 3085
3 TraesCS3B01G516800 chr5B 680049906 680052983 3077 True 5210 5210 97.182 1 3086 1 chr5B.!!$R1 3085

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
209 210 0.335019 GGGCTTATGTGGACCCCTTT 59.665 55.000 0.0 0.0 36.24 3.11 F
1243 1245 1.134551 GGGAGATGCACAGAGGAAGAC 60.135 57.143 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1883 1.697982 GGGTATCCGGAGCAATAGGTT 59.302 52.381 11.34 0.0 0.00 3.5 R
2848 2850 1.408822 CCCCTGGTTTGTATCAGAGCC 60.409 57.143 0.00 0.0 33.11 4.7 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
31 32 9.730705 CTTATGGAAAGAGAAGGCATATAATCA 57.269 33.333 0.00 0.00 0.00 2.57
209 210 0.335019 GGGCTTATGTGGACCCCTTT 59.665 55.000 0.00 0.00 36.24 3.11
210 211 1.567175 GGGCTTATGTGGACCCCTTTA 59.433 52.381 0.00 0.00 36.24 1.85
404 405 7.239271 CGAGCAATATAAGCAATTCTGGTATG 58.761 38.462 3.28 0.00 31.48 2.39
412 413 6.446781 AAGCAATTCTGGTATGAACAGATG 57.553 37.500 0.00 0.00 43.82 2.90
417 418 6.630444 ATTCTGGTATGAACAGATGCATTC 57.370 37.500 0.00 0.00 43.82 2.67
577 578 1.274447 GCCTTTTGCCTTTGAGCTCAT 59.726 47.619 19.04 0.00 0.00 2.90
583 584 2.715046 TGCCTTTGAGCTCATTCGATT 58.285 42.857 19.04 0.00 0.00 3.34
614 615 3.308473 GGGAATATAACCTGCCCCTCATC 60.308 52.174 0.00 0.00 32.50 2.92
756 757 6.822667 TCTTTCACCACTACTATCGTAACA 57.177 37.500 0.00 0.00 0.00 2.41
819 820 3.557898 CCACTTTACCTGAGCACTGTGAT 60.558 47.826 12.86 4.69 0.00 3.06
1243 1245 1.134551 GGGAGATGCACAGAGGAAGAC 60.135 57.143 0.00 0.00 0.00 3.01
1524 1526 8.864087 GGAAAAATCATAGGCAAATTCCTATCT 58.136 33.333 3.27 0.00 45.23 1.98
1563 1565 4.657814 AAGAAGAGGCAAATTCCTACCA 57.342 40.909 0.00 0.00 36.38 3.25
1898 1900 4.974645 ATTCAACCTATTGCTCCGGATA 57.025 40.909 3.57 0.00 35.63 2.59
1902 1904 1.348064 CCTATTGCTCCGGATACCCA 58.652 55.000 3.57 0.00 0.00 4.51
2054 2056 5.163099 TGAAAGATCCAAACCTTCCTCTTCA 60.163 40.000 0.00 0.00 0.00 3.02
2208 2210 8.574251 TCTCTGTGGATAGAGATAAAGATAGC 57.426 38.462 1.57 0.00 46.12 2.97
2361 2363 2.191400 CCCAGGAAAGAGGTCAGATCA 58.809 52.381 0.00 0.00 0.00 2.92
2401 2403 7.239438 ACTATAAGTATAAGACTGCTGGCCTA 58.761 38.462 3.32 0.00 38.87 3.93
2458 2460 8.146412 CCCAATTTCTCTTCTTTCTTTTCACAT 58.854 33.333 0.00 0.00 0.00 3.21
2578 2580 8.021396 GCGTAATATAGTGATGTCATGTGTCTA 58.979 37.037 0.00 0.00 0.00 2.59
2682 2684 1.669779 GTCCGCTGTAGTACGAGTGAT 59.330 52.381 12.18 0.00 0.00 3.06
2683 2685 2.868583 GTCCGCTGTAGTACGAGTGATA 59.131 50.000 12.18 1.96 0.00 2.15
2684 2686 3.059733 GTCCGCTGTAGTACGAGTGATAG 60.060 52.174 12.18 0.00 0.00 2.08
2685 2687 3.129109 CCGCTGTAGTACGAGTGATAGA 58.871 50.000 12.18 0.00 0.00 1.98
2848 2850 5.527214 TCATTTTGCCTATTATCAGTGGTCG 59.473 40.000 0.00 0.00 0.00 4.79
3078 3080 1.079956 GCAATGGCATGTTTCGGCA 60.080 52.632 0.00 0.00 43.74 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.220602 AGAAGCAAAGCCGGTCAAATAATT 59.779 37.500 1.90 0.0 0.00 1.40
35 36 1.620822 AGAAGCAAAGCCGGTCAAAT 58.379 45.000 1.90 0.0 0.00 2.32
77 78 3.367395 GCCATGCCCTAAAGAAAGTGAAC 60.367 47.826 0.00 0.0 0.00 3.18
404 405 4.789012 TTCCCAAAGAATGCATCTGTTC 57.211 40.909 0.00 0.0 38.79 3.18
417 418 7.848223 ATTGTTTTCACTTTCTTTCCCAAAG 57.152 32.000 0.00 0.0 39.88 2.77
452 453 5.043432 TGAGAAATCTATCCCCAAAACCCAT 60.043 40.000 0.00 0.0 0.00 4.00
467 468 2.982488 ACCTCAGGGTTGTGAGAAATCT 59.018 45.455 0.00 0.0 46.02 2.40
577 578 9.774413 GGTTATATTCCCTTTCTTCTAATCGAA 57.226 33.333 0.00 0.0 0.00 3.71
583 584 6.183361 GGGCAGGTTATATTCCCTTTCTTCTA 60.183 42.308 0.00 0.0 34.19 2.10
614 615 1.452110 TGCACCATGATTGAAGGACG 58.548 50.000 0.00 0.0 0.00 4.79
756 757 3.126343 GGAAACGTCAGTGTTTTCTGTGT 59.874 43.478 11.68 0.0 41.89 3.72
819 820 2.299013 ACTCAATACTTGACCGACTGCA 59.701 45.455 0.00 0.0 35.46 4.41
1524 1526 6.009589 TCTTCTTTTTCCAACTGATATGGCA 58.990 36.000 0.00 0.0 37.88 4.92
1881 1883 1.697982 GGGTATCCGGAGCAATAGGTT 59.302 52.381 11.34 0.0 0.00 3.50
1898 1900 9.225682 TGATTCTTATCTTCCTAGTAAATGGGT 57.774 33.333 0.00 0.0 0.00 4.51
2054 2056 2.049433 CACGTCCGTTTCCGCTCT 60.049 61.111 0.00 0.0 0.00 4.09
2458 2460 4.103153 TGTTTTATTCCCAATTGTTGCCCA 59.897 37.500 4.43 0.0 0.00 5.36
2578 2580 3.412386 CGACCCACCTTTTCAGAGAAAT 58.588 45.455 0.00 0.0 0.00 2.17
2848 2850 1.408822 CCCCTGGTTTGTATCAGAGCC 60.409 57.143 0.00 0.0 33.11 4.70


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

AutoCloner maintained by Alex Coulton.