Multiple sequence alignment - TraesCS6B01G207500

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 TraesCS6B01G207500 chr6B 100.000 2357 0 0 1 2357 264841176 264838820 0 4353
1 TraesCS6B01G207500 chr6B 97.288 2360 57 6 1 2357 596657306 596654951 0 3997
2 TraesCS6B01G207500 chr1A 97.797 2360 49 3 1 2357 238109745 238107386 0 4067
3 TraesCS6B01G207500 chr1A 97.627 2360 53 3 1 2357 238155130 238152771 0 4045
4 TraesCS6B01G207500 chr5A 97.712 2360 51 3 1 2357 16577920 16575561 0 4056
5 TraesCS6B01G207500 chr7D 97.627 2360 50 5 1 2357 579015578 579017934 0 4043
6 TraesCS6B01G207500 chr7A 97.458 2360 57 3 1 2357 60329010 60326651 0 4023
7 TraesCS6B01G207500 chrUn 97.373 2360 53 6 1 2357 237257830 237255477 0 4006


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 TraesCS6B01G207500 chr6B 264838820 264841176 2356 True 4353 4353 100.000 1 2357 1 chr6B.!!$R1 2356
1 TraesCS6B01G207500 chr6B 596654951 596657306 2355 True 3997 3997 97.288 1 2357 1 chr6B.!!$R2 2356
2 TraesCS6B01G207500 chr1A 238107386 238109745 2359 True 4067 4067 97.797 1 2357 1 chr1A.!!$R1 2356
3 TraesCS6B01G207500 chr1A 238152771 238155130 2359 True 4045 4045 97.627 1 2357 1 chr1A.!!$R2 2356
4 TraesCS6B01G207500 chr5A 16575561 16577920 2359 True 4056 4056 97.712 1 2357 1 chr5A.!!$R1 2356
5 TraesCS6B01G207500 chr7D 579015578 579017934 2356 False 4043 4043 97.627 1 2357 1 chr7D.!!$F1 2356
6 TraesCS6B01G207500 chr7A 60326651 60329010 2359 True 4023 4023 97.458 1 2357 1 chr7A.!!$R1 2356
7 TraesCS6B01G207500 chrUn 237255477 237257830 2353 True 4006 4006 97.373 1 2357 1 chrUn.!!$R1 2356

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
694 695 0.036952 TTCTTGAGCAAGCTCCTCCG 60.037 55.0 18.54 5.37 42.09 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2159 0.523335 GCCATAAAGCGCGAACCAAG 60.523 55.0 12.1 0.0 0.0 3.61 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
32 33 4.115401 TCATGACGAGAATGGACTTCTG 57.885 45.455 0.00 0.00 44.42 3.02
69 70 2.872732 AGAAGAGTCACGGTCCTGTTA 58.127 47.619 0.00 0.00 0.00 2.41
90 91 2.570284 CGCCGGGCTTTTTCCCTTT 61.570 57.895 18.34 0.00 44.30 3.11
162 163 1.079750 GTCGGCTTGACCCTGTCTC 60.080 63.158 0.00 0.00 42.04 3.36
331 332 6.761099 TTCTCGCTCAGTAAAGAAGAGTAT 57.239 37.500 0.00 0.00 0.00 2.12
487 488 2.620627 GGGTTCGAATCCCATTTCCTGT 60.621 50.000 17.16 0.00 44.05 4.00
589 590 2.017782 CTGCTTAGTGACTAGGAGCGA 58.982 52.381 5.87 0.00 36.17 4.93
590 591 2.621055 CTGCTTAGTGACTAGGAGCGAT 59.379 50.000 5.87 0.00 36.17 4.58
694 695 0.036952 TTCTTGAGCAAGCTCCTCCG 60.037 55.000 18.54 5.37 42.09 4.63
777 778 3.565482 CAGCTGGTTAGAGCAAAACAAGA 59.435 43.478 5.57 0.00 41.83 3.02
1010 1012 1.133025 GGCTTTGGTGATGTCGGAATG 59.867 52.381 0.00 0.00 0.00 2.67
1077 1079 2.249844 TTCCACTCGGTGTTCCTTTC 57.750 50.000 3.82 0.00 0.00 2.62
1162 1164 0.036010 CTCCGGTGATGCCAGAAGTT 60.036 55.000 0.00 0.00 36.97 2.66
1372 1374 4.212716 GGAGTAACCACTTTTGAAAGGGT 58.787 43.478 8.23 8.93 37.74 4.34
1502 1506 1.673168 CAGAAGCAAGGAGTATGCCC 58.327 55.000 0.00 0.00 44.91 5.36
1523 1527 1.474017 CGTGTTTCGACGAGAACACT 58.526 50.000 30.46 0.00 42.10 3.55
1620 1624 2.503765 TCCAGGCGAAGGTCATAATTCA 59.496 45.455 0.00 0.00 0.00 2.57
1721 1725 4.878397 AGTCAAGGATTTGCTAGGAATTCG 59.122 41.667 11.29 1.12 34.21 3.34
1789 1793 3.619419 TCGAAATGAATGGAAGATGCCA 58.381 40.909 0.00 0.00 43.23 4.92
1905 1909 5.496133 AATTTCATTGAGAGGAATCAGCG 57.504 39.130 0.00 0.00 0.00 5.18
1931 1935 4.576330 AAAGAAATCTTCTCCGGGTGAT 57.424 40.909 0.00 0.00 39.61 3.06
2024 2028 6.947464 TGATCTTTTAGTAGGCTAAGTTGCT 58.053 36.000 0.00 0.00 38.31 3.91
2048 2052 6.182627 TGAATTCTGAAATCACTACAGGCAT 58.817 36.000 7.05 0.00 33.19 4.40
2094 2098 2.726821 ACAATGTGTCCCCATGATCAC 58.273 47.619 0.00 0.00 0.00 3.06
2096 2100 3.245371 ACAATGTGTCCCCATGATCACTT 60.245 43.478 0.00 0.00 0.00 3.16
2104 2108 5.104941 TGTCCCCATGATCACTTACTTACAG 60.105 44.000 0.00 0.00 0.00 2.74
2105 2109 5.128827 GTCCCCATGATCACTTACTTACAGA 59.871 44.000 0.00 0.00 0.00 3.41
2107 2111 6.386927 TCCCCATGATCACTTACTTACAGAAT 59.613 38.462 0.00 0.00 0.00 2.40
2155 2159 4.932268 TTTGGTTTTCGTATCACGGATC 57.068 40.909 0.00 0.00 42.81 3.36
2208 2212 4.929211 GCAAACTAATCCAATCCCACAAAC 59.071 41.667 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.581085 ACTCTTCTAAACCATTACATGACGC 59.419 40.000 0.00 0.00 0.00 5.19
90 91 6.053650 TGAATATCTCCTTCGTCTAGTCGAA 58.946 40.000 20.73 20.73 45.46 3.71
162 163 2.711922 CCGACCCGACCAAGAGAGG 61.712 68.421 0.00 0.00 0.00 3.69
248 249 1.340991 CGAGACCCCATCCAAACCAAT 60.341 52.381 0.00 0.00 0.00 3.16
487 488 1.290955 CCGTTCTACTTCCGTGCCA 59.709 57.895 0.00 0.00 0.00 4.92
558 559 4.709397 AGTCACTAAGCAGCTATTCTGTCT 59.291 41.667 0.00 0.00 44.66 3.41
589 590 0.251341 AGAACAAGAAAGGGGCGCAT 60.251 50.000 10.83 0.00 0.00 4.73
590 591 0.467290 AAGAACAAGAAAGGGGCGCA 60.467 50.000 10.83 0.00 0.00 6.09
694 695 0.108207 ATGAGCATCCTACCTGCAGC 59.892 55.000 8.66 0.00 42.15 5.25
777 778 1.732259 CGCTAGTTGCTCAATCCGTTT 59.268 47.619 0.00 0.00 40.11 3.60
954 956 3.708220 CTCCTCGCGGCACTCCTTC 62.708 68.421 6.13 0.00 0.00 3.46
1010 1012 9.542462 TCACTAAATAGATACAAATAGGTGCAC 57.458 33.333 8.80 8.80 0.00 4.57
1077 1079 3.694072 TCGAACTATTGGAAGCAAATGGG 59.306 43.478 0.00 0.00 0.00 4.00
1502 1506 1.125266 GTTCTCGTCGAAACACGCG 59.875 57.895 3.53 3.53 39.74 6.01
1620 1624 8.824756 TGACTAAGACTATAGAATGTTCCTGT 57.175 34.615 6.78 0.00 0.00 4.00
1721 1725 3.898741 AGATCTTCCCTTTCTACGATCCC 59.101 47.826 0.00 0.00 0.00 3.85
1789 1793 5.755409 AAAAAGAACCCAAAAGTTCCAGT 57.245 34.783 0.98 0.00 46.00 4.00
1815 1819 2.869636 GCTAGCTGCTTCCATATCGCTT 60.870 50.000 7.79 0.00 38.95 4.68
1816 1820 1.337635 GCTAGCTGCTTCCATATCGCT 60.338 52.381 7.79 0.00 38.95 4.93
1905 1909 5.004448 ACCCGGAGAAGATTTCTTTTCTTC 58.996 41.667 0.73 5.50 46.15 2.87
2024 2028 5.559770 TGCCTGTAGTGATTTCAGAATTCA 58.440 37.500 8.44 3.97 0.00 2.57
2048 2052 2.375174 AGGACCACAATTTCCTGCACTA 59.625 45.455 0.00 0.00 40.98 2.74
2155 2159 0.523335 GCCATAAAGCGCGAACCAAG 60.523 55.000 12.10 0.00 0.00 3.61
2208 2212 8.556517 TTCGATAGTAGTTACATGAACAATCG 57.443 34.615 0.00 12.09 38.57 3.34


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

AutoCloner maintained by Alex Coulton.