Multiple sequence alignment - TraesCS1B01G457900

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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 TraesCS1B01G457900 chr1B 100.000 2888 0 0 1 2888 672473630 672476517 0 5334
1 TraesCS1B01G457900 chr1B 98.479 2892 40 2 1 2888 668810695 668807804 0 5094
2 TraesCS1B01G457900 chr7B 98.719 2889 36 1 1 2888 644461911 644464799 0 5129
3 TraesCS1B01G457900 chr7D 98.650 2888 38 1 1 2888 382063146 382066032 0 5116
4 TraesCS1B01G457900 chr7D 98.615 2889 38 2 1 2888 381960693 381957806 0 5112
5 TraesCS1B01G457900 chr7D 98.408 2889 43 3 1 2888 626684768 626681882 0 5077
6 TraesCS1B01G457900 chrUn 98.615 2889 39 1 1 2888 189405551 189408439 0 5112
7 TraesCS1B01G457900 chr6D 98.476 2888 41 2 1 2888 124530590 124533474 0 5086
8 TraesCS1B01G457900 chr3A 98.442 2888 44 1 1 2888 633105724 633108610 0 5083


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 TraesCS1B01G457900 chr1B 672473630 672476517 2887 False 5334 5334 100.000 1 2888 1 chr1B.!!$F1 2887
1 TraesCS1B01G457900 chr1B 668807804 668810695 2891 True 5094 5094 98.479 1 2888 1 chr1B.!!$R1 2887
2 TraesCS1B01G457900 chr7B 644461911 644464799 2888 False 5129 5129 98.719 1 2888 1 chr7B.!!$F1 2887
3 TraesCS1B01G457900 chr7D 382063146 382066032 2886 False 5116 5116 98.650 1 2888 1 chr7D.!!$F1 2887
4 TraesCS1B01G457900 chr7D 381957806 381960693 2887 True 5112 5112 98.615 1 2888 1 chr7D.!!$R1 2887
5 TraesCS1B01G457900 chr7D 626681882 626684768 2886 True 5077 5077 98.408 1 2888 1 chr7D.!!$R2 2887
6 TraesCS1B01G457900 chrUn 189405551 189408439 2888 False 5112 5112 98.615 1 2888 1 chrUn.!!$F1 2887
7 TraesCS1B01G457900 chr6D 124530590 124533474 2884 False 5086 5086 98.476 1 2888 1 chr6D.!!$F1 2887
8 TraesCS1B01G457900 chr3A 633105724 633108610 2886 False 5083 5083 98.442 1 2888 1 chr3A.!!$F1 2887

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
60 61 0.532573 CTTCCTTGCCGCTGAGACTA 59.467 55.000 0.0 0.0 0.00 2.59 F
718 725 1.457604 AGCTTTGCTCTTCTGGGCA 59.542 52.632 0.0 0.0 30.62 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1363 2.737376 GAGACCACCGTGTTCGCC 60.737 66.667 0.00 0.00 35.54 5.54 R
2359 2367 0.625849 ACATCCAGGGATCCCACAAC 59.374 55.000 32.69 5.08 38.92 3.32 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
60 61 0.532573 CTTCCTTGCCGCTGAGACTA 59.467 55.000 0.00 0.00 0.00 2.59
718 725 1.457604 AGCTTTGCTCTTCTGGGCA 59.542 52.632 0.00 0.00 30.62 5.36
869 876 7.079451 TGTTTTTCTCTCCTTTCCTATCAGT 57.921 36.000 0.00 0.00 0.00 3.41
886 893 3.926616 TCAGTGAGTTCCGATCCTTTTC 58.073 45.455 0.00 0.00 0.00 2.29
972 979 7.782168 CCTATATCAGCTATACATCCTCCTTGA 59.218 40.741 0.00 0.00 0.00 3.02
1119 1126 2.816958 CGCTCTGCTGGATGCGTT 60.817 61.111 14.38 0.00 46.63 4.84
1196 1203 1.647545 GCGCCTGCTCTATTGTTGCA 61.648 55.000 0.00 0.00 38.39 4.08
1356 1363 3.361977 CTTTGTTGGACCGCCGGG 61.362 66.667 8.57 0.00 36.79 5.73
1663 1670 1.075226 TCCGGATTGCTAGCTCCCT 60.075 57.895 17.23 0.00 0.00 4.20
1691 1698 1.741528 TCCGCTACAGACGATACACA 58.258 50.000 0.00 0.00 0.00 3.72
1938 1945 3.880846 CTGGCTGCCGGATTTCGC 61.881 66.667 23.22 0.00 37.59 4.70
2113 2121 5.003804 ACGCCTCACAATCTTCAGTTTTAT 58.996 37.500 0.00 0.00 0.00 1.40
2199 2207 3.008375 TGCAAGATGAGCTTACAGGACTT 59.992 43.478 0.00 0.00 34.31 3.01
2219 2227 1.033746 CCAATCAAGCGAGCCACCAT 61.034 55.000 0.00 0.00 0.00 3.55
2317 2325 0.039074 CATCGATCTAGTGGCCGGTC 60.039 60.000 0.00 0.00 0.00 4.79
2323 2331 1.496060 TCTAGTGGCCGGTCAATCAT 58.504 50.000 14.50 0.09 0.00 2.45
2359 2367 2.159198 GCAGCCACCAGGTTTAATGATG 60.159 50.000 0.00 0.00 37.19 3.07
2415 2423 4.022849 CCGCTTCTTCTTCCACAAAGATTT 60.023 41.667 0.00 0.00 43.50 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 2.738314 CGAAAAGACCCGGAAATAACGT 59.262 45.455 0.73 0.00 0.00 3.99
585 592 1.749634 CTCCGAACGAAGGGAGTGTAT 59.250 52.381 10.77 0.00 43.91 2.29
869 876 4.968259 TCAAAGAAAAGGATCGGAACTCA 58.032 39.130 0.00 0.00 0.00 3.41
886 893 6.890360 GGTACGAACGAAGAAATTTCAAAG 57.110 37.500 19.99 11.99 0.00 2.77
972 979 1.873591 GCGACATCTCCGGCATAAATT 59.126 47.619 0.00 0.00 0.00 1.82
1119 1126 3.055819 GCGAGCTTCTTATATGGGATCCA 60.056 47.826 15.23 0.00 38.19 3.41
1356 1363 2.737376 GAGACCACCGTGTTCGCC 60.737 66.667 0.00 0.00 35.54 5.54
1663 1670 3.441222 TCGTCTGTAGCGGAACTATGAAA 59.559 43.478 0.00 0.00 32.15 2.69
1691 1698 5.016831 AGAACCGCCATAAAAATCTTCCTT 58.983 37.500 0.00 0.00 0.00 3.36
1938 1945 4.867599 GAAGCGCTACGGACGGGG 62.868 72.222 12.05 0.00 0.00 5.73
2019 2027 7.550597 ACTCCAATAGATGCTCATCATAAGA 57.449 36.000 11.90 2.31 40.22 2.10
2199 2207 1.377202 GGTGGCTCGCTTGATTGGA 60.377 57.895 0.00 0.00 0.00 3.53
2219 2227 4.290985 TGGATCCCACCTTATTCTCAAACA 59.709 41.667 9.90 0.00 0.00 2.83
2317 2325 4.201881 TGCTCGCTCTTTGATCAATGATTG 60.202 41.667 20.67 16.31 0.00 2.67
2323 2331 1.081892 GCTGCTCGCTCTTTGATCAA 58.918 50.000 3.38 3.38 35.14 2.57
2359 2367 0.625849 ACATCCAGGGATCCCACAAC 59.374 55.000 32.69 5.08 38.92 3.32
2415 2423 3.695830 ATCCAAGCTCGGTTTTGTCTA 57.304 42.857 0.00 0.00 0.00 2.59
2628 2640 5.294306 TCTTGTTTGATCTGCCGCTATTAAG 59.706 40.000 0.00 0.00 0.00 1.85
2629 2641 5.182487 TCTTGTTTGATCTGCCGCTATTAA 58.818 37.500 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.