Multiple sequence alignment - TraesCS1B01G406700

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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 TraesCS1B01G406700 chr1B 100.000 3811 0 0 1 3811 633746330 633750140 0.000000e+00 7038
1 TraesCS1B01G406700 chr5D 98.715 3814 45 4 1 3811 503225786 503221974 0.000000e+00 6769
2 TraesCS1B01G406700 chr5D 97.771 3814 79 5 1 3811 6196504 6192694 0.000000e+00 6567
3 TraesCS1B01G406700 chr3A 98.479 3814 54 4 1 3811 66010055 66013867 0.000000e+00 6719
4 TraesCS1B01G406700 chr3A 97.693 3815 83 5 1 3811 672902445 672906258 0.000000e+00 6553
5 TraesCS1B01G406700 chrUn 98.243 3813 62 4 1 3811 216511040 216514849 0.000000e+00 6665
6 TraesCS1B01G406700 chrUn 98.243 3813 62 4 1 3811 286272343 286268534 0.000000e+00 6665
7 TraesCS1B01G406700 chr2B 98.165 3814 58 5 1 3811 449213854 449210050 0.000000e+00 6645
8 TraesCS1B01G406700 chr2B 98.084 3811 68 5 3 3811 474916006 474912199 0.000000e+00 6628
9 TraesCS1B01G406700 chr3B 98.008 3816 71 3 1 3811 201534597 201530782 0.000000e+00 6621
10 TraesCS1B01G406700 chr2A 100.000 68 0 0 3744 3811 724270104 724270171 4.000000e-25 126


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 TraesCS1B01G406700 chr1B 633746330 633750140 3810 False 7038 7038 100.000 1 3811 1 chr1B.!!$F1 3810
1 TraesCS1B01G406700 chr5D 503221974 503225786 3812 True 6769 6769 98.715 1 3811 1 chr5D.!!$R2 3810
2 TraesCS1B01G406700 chr5D 6192694 6196504 3810 True 6567 6567 97.771 1 3811 1 chr5D.!!$R1 3810
3 TraesCS1B01G406700 chr3A 66010055 66013867 3812 False 6719 6719 98.479 1 3811 1 chr3A.!!$F1 3810
4 TraesCS1B01G406700 chr3A 672902445 672906258 3813 False 6553 6553 97.693 1 3811 1 chr3A.!!$F2 3810
5 TraesCS1B01G406700 chrUn 216511040 216514849 3809 False 6665 6665 98.243 1 3811 1 chrUn.!!$F1 3810
6 TraesCS1B01G406700 chrUn 286268534 286272343 3809 True 6665 6665 98.243 1 3811 1 chrUn.!!$R1 3810
7 TraesCS1B01G406700 chr2B 449210050 449213854 3804 True 6645 6645 98.165 1 3811 1 chr2B.!!$R1 3810
8 TraesCS1B01G406700 chr2B 474912199 474916006 3807 True 6628 6628 98.084 3 3811 1 chr2B.!!$R2 3808
9 TraesCS1B01G406700 chr3B 201530782 201534597 3815 True 6621 6621 98.008 1 3811 1 chr3B.!!$R1 3810

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
354 357 0.031449 TTCACGCTCATGTCACGTCA 59.969 50.0 7.30 0.0 38.09 4.35 F
608 611 0.037605 AGGATCGACGCGGAAAGTTT 60.038 50.0 12.47 0.0 0.00 2.66 F
1904 1911 0.314302 AGGAGTGTGGTTCGTTCGAG 59.686 55.0 0.00 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1832 3.227614 GGAAAGCTTAAACCCAAGTCCA 58.772 45.455 0.00 0.0 0.0 4.02 R
2453 2460 4.215827 CCTTCCTCGCGTATGTATAAGACT 59.784 45.833 5.77 0.0 0.0 3.24 R
2847 2855 6.183810 TGCATATCCATCATTTGAGTCTCT 57.816 37.500 0.65 0.0 0.0 3.10 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
102 103 6.749036 AAATACAGGATTTCCGATCCTAGT 57.251 37.500 7.22 10.06 46.22 2.57
354 357 0.031449 TTCACGCTCATGTCACGTCA 59.969 50.000 7.30 0.00 38.09 4.35
581 584 7.388712 CAATATAGGAGTAAAAACACGACGTG 58.611 38.462 25.72 25.72 39.75 4.49
608 611 0.037605 AGGATCGACGCGGAAAGTTT 60.038 50.000 12.47 0.00 0.00 2.66
749 753 2.399607 AAAGGGAGTGGGGTGCCAA 61.400 57.895 0.00 0.00 0.00 4.52
778 782 3.104843 AGGAAGCGACTCATAGAATGC 57.895 47.619 0.00 0.00 0.00 3.56
895 899 6.325028 AGAATCAATAGAAGGAGAATCGGACA 59.675 38.462 0.00 0.00 34.37 4.02
939 943 8.239681 ACAAAAAGGAAAAGAAAGAGAAAACG 57.760 30.769 0.00 0.00 0.00 3.60
1100 1104 3.610911 GGACTTTTCGGAGATTGGATGT 58.389 45.455 0.00 0.00 35.04 3.06
1193 1197 4.574599 AGCGTTTCATTTGCTTCTCTTT 57.425 36.364 0.00 0.00 34.80 2.52
1228 1232 9.540538 TTTCATTTTCCCAGAATGTATCCTAAA 57.459 29.630 0.00 0.00 36.23 1.85
1256 1260 6.060136 TGGCCTAATTCTTCTTCTGATGATG 58.940 40.000 3.32 0.00 0.00 3.07
1267 1271 6.813293 TCTTCTGATGATGGATTCAACCTA 57.187 37.500 0.00 0.00 38.03 3.08
1554 1558 6.451393 GGAATGTTTTTATGTGGTGCTAACA 58.549 36.000 0.00 0.00 0.00 2.41
1825 1832 4.071961 TGCGCTTATATCCATCACTGTT 57.928 40.909 9.73 0.00 0.00 3.16
1904 1911 0.314302 AGGAGTGTGGTTCGTTCGAG 59.686 55.000 0.00 0.00 0.00 4.04
1966 1973 6.215845 GTTTTGCAAAACTCCATAGACATGT 58.784 36.000 36.34 0.00 43.68 3.21
2141 2148 5.494390 ACGGGTAGTTCCTACAAAGAATT 57.506 39.130 4.01 0.00 38.58 2.17
2142 2149 6.610075 ACGGGTAGTTCCTACAAAGAATTA 57.390 37.500 4.01 0.00 38.58 1.40
2416 2423 7.263496 TCCTCGAAAAGTTAAGGATTAGTAGC 58.737 38.462 0.00 0.00 33.00 3.58
2453 2460 9.709495 AATCGATTTTGAAAAAGAATGGATTCA 57.291 25.926 4.39 0.00 34.99 2.57
2552 2559 2.871022 GCGAGATGAAAGTCTCATGCAT 59.129 45.455 0.00 0.00 45.23 3.96
2639 2646 6.092944 TCGTTGCTTTTCTTTCTGTTACTTCA 59.907 34.615 0.00 0.00 0.00 3.02
2809 2817 3.120889 CGTATGCTTGCATATTCGTCCAG 60.121 47.826 16.86 1.21 0.00 3.86
2958 2966 2.779755 TGGTCTACGTACCGGAACTA 57.220 50.000 9.46 0.00 42.91 2.24
3384 3393 8.251721 TGCTAGGTCTATTTCTTAGTTCAAGAC 58.748 37.037 0.00 0.00 43.09 3.01
3598 3607 8.375493 ACTCTGTTTACATAGAAATCCCTACA 57.625 34.615 2.71 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 0.111639 CCGTTTCCCTCCTTTTCCCA 59.888 55.000 0.00 0.00 0.00 4.37
608 611 8.482943 TCCTTGTTTAGATCCTATTTCAATCGA 58.517 33.333 0.00 0.00 0.00 3.59
778 782 3.204526 CAAGAGCTCTATTTGCCTCTGG 58.795 50.000 18.59 0.00 0.00 3.86
939 943 5.136105 AGGGCTTAGTTGATCATGATTTCC 58.864 41.667 10.14 0.00 0.00 3.13
1100 1104 8.432013 ACATGCCAGATCATGAATTAGTAACTA 58.568 33.333 0.00 0.00 44.94 2.24
1193 1197 7.847711 TTCTGGGAAAATGAAACTTCCATTA 57.152 32.000 3.44 0.00 42.56 1.90
1228 1232 7.616935 TCATCAGAAGAAGAATTAGGCCAAAAT 59.383 33.333 5.01 0.62 0.00 1.82
1267 1271 8.112183 AGAACCAAGGTCTATCTTTTTGATCAT 58.888 33.333 0.00 0.00 36.65 2.45
1516 1520 4.554553 AACATTCCCCCTAGAGTAGCTA 57.445 45.455 0.00 0.00 0.00 3.32
1825 1832 3.227614 GGAAAGCTTAAACCCAAGTCCA 58.772 45.455 0.00 0.00 0.00 4.02
1966 1973 5.219739 AGTGGGGATAGCATTTCTCTTCTA 58.780 41.667 0.00 0.00 0.00 2.10
2141 2148 8.797266 CAAGCATTGTATACGTCATTAGTCTA 57.203 34.615 0.00 0.00 42.34 2.59
2142 2149 7.700322 CAAGCATTGTATACGTCATTAGTCT 57.300 36.000 0.00 0.00 42.34 3.24
2453 2460 4.215827 CCTTCCTCGCGTATGTATAAGACT 59.784 45.833 5.77 0.00 0.00 3.24
2552 2559 4.261741 GCTTCTTTCTCTCATGCAAAACCA 60.262 41.667 0.00 0.00 0.00 3.67
2809 2817 7.865706 ATAATTACATATCCGATTTGCCCTC 57.134 36.000 0.00 0.00 0.00 4.30
2842 2850 9.205719 CATATCCATCATTTGAGTCTCTAACAG 57.794 37.037 0.65 0.00 0.00 3.16
2847 2855 6.183810 TGCATATCCATCATTTGAGTCTCT 57.816 37.500 0.65 0.00 0.00 3.10
2958 2966 8.627208 AATCCTGCATAATCTCGAATGTTATT 57.373 30.769 0.00 0.00 0.00 1.40
3384 3393 7.858498 TCTTTTATTCCAGTTAGTAAGAGGGG 58.142 38.462 1.75 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.