Multiple sequence alignment - TraesCS1D01G177900

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 TraesCS1D01G177900 chr1D 100.000 2432 0 0 1 2432 252924605 252922174 0.000000e+00 4492.0
1 TraesCS1D01G177900 chr1B 96.271 2387 73 9 53 2432 359894135 359896512 0.000000e+00 3901.0
2 TraesCS1D01G177900 chr1B 100.000 45 0 0 1 45 359894101 359894145 1.550000e-12 84.2
3 TraesCS1D01G177900 chr1A 95.736 2392 71 16 51 2432 324501882 324499512 0.000000e+00 3823.0


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 TraesCS1D01G177900 chr1D 252922174 252924605 2431 True 4492.0 4492 100.0000 1 2432 1 chr1D.!!$R1 2431
1 TraesCS1D01G177900 chr1B 359894101 359896512 2411 False 1992.6 3901 98.1355 1 2432 2 chr1B.!!$F1 2431
2 TraesCS1D01G177900 chr1A 324499512 324501882 2370 True 3823.0 3823 95.7360 51 2432 1 chr1A.!!$R1 2381

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
767 777 0.10741 TGGCAGTTTCGTGAGGTTGT 60.107 50.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 2318 2.398554 GCATTCTGCGGCCGAAGAA 61.399 57.895 42.95 42.95 43.29 2.52 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
40 41 1.954362 CTGTTCCCTGGCGGAGAGAG 61.954 65.000 0.00 0.00 43.39 3.20
41 42 1.682684 GTTCCCTGGCGGAGAGAGA 60.683 63.158 0.00 0.00 43.39 3.10
42 43 1.380515 TTCCCTGGCGGAGAGAGAG 60.381 63.158 0.00 0.00 43.39 3.20
43 44 1.864263 TTCCCTGGCGGAGAGAGAGA 61.864 60.000 0.00 0.00 43.39 3.10
44 45 1.827789 CCCTGGCGGAGAGAGAGAG 60.828 68.421 0.00 0.00 0.00 3.20
45 46 1.225983 CCTGGCGGAGAGAGAGAGA 59.774 63.158 0.00 0.00 0.00 3.10
46 47 0.819259 CCTGGCGGAGAGAGAGAGAG 60.819 65.000 0.00 0.00 0.00 3.20
47 48 0.180171 CTGGCGGAGAGAGAGAGAGA 59.820 60.000 0.00 0.00 0.00 3.10
48 49 0.180171 TGGCGGAGAGAGAGAGAGAG 59.820 60.000 0.00 0.00 0.00 3.20
49 50 0.468226 GGCGGAGAGAGAGAGAGAGA 59.532 60.000 0.00 0.00 0.00 3.10
50 51 1.541233 GGCGGAGAGAGAGAGAGAGAG 60.541 61.905 0.00 0.00 0.00 3.20
51 52 1.412710 GCGGAGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
52 53 2.546795 GCGGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
53 54 2.959030 CGGAGAGAGAGAGAGAGAGAGA 59.041 54.545 0.00 0.00 0.00 3.10
54 55 3.005261 CGGAGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
55 56 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
56 57 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
57 58 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
61 62 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
178 180 3.767673 TCTGCCCTCTATTACGTTGTTCT 59.232 43.478 0.00 0.00 0.00 3.01
186 188 1.787012 TTACGTTGTTCTTCCGAGGC 58.213 50.000 0.00 0.00 0.00 4.70
191 193 2.218603 GTTGTTCTTCCGAGGCTTTCA 58.781 47.619 0.00 0.00 0.00 2.69
247 249 3.607370 GAGACCGTGGGAGGTTGCC 62.607 68.421 0.00 0.00 46.09 4.52
271 273 2.594214 GAGGCGTTTGAATGCGATTTTC 59.406 45.455 2.17 0.00 41.81 2.29
294 296 2.437413 GATCCGAATCCCTAATTGGCC 58.563 52.381 0.00 0.00 0.00 5.36
295 297 0.476771 TCCGAATCCCTAATTGGCCC 59.523 55.000 0.00 0.00 0.00 5.80
336 338 1.202817 GGTTGTTCGTGGTTTTGGTGT 59.797 47.619 0.00 0.00 0.00 4.16
399 403 7.119262 ACCGTTTAGATCTGGTAAAATTGTGAG 59.881 37.037 5.18 0.00 31.60 3.51
450 454 1.114627 CCAGCAGGATTAAAAGGGGC 58.885 55.000 0.00 0.00 36.89 5.80
634 644 3.004315 CCAAAGCGCCAACGGATTTATAT 59.996 43.478 2.29 0.00 40.57 0.86
644 654 6.863126 GCCAACGGATTTATATTGAATCTTGG 59.137 38.462 17.46 17.46 39.45 3.61
728 738 8.408601 GGTCAAAGTATTGCAAATCTGTGATAT 58.591 33.333 21.62 0.00 36.45 1.63
729 739 9.229784 GTCAAAGTATTGCAAATCTGTGATATG 57.770 33.333 21.62 9.94 36.45 1.78
753 763 2.962125 TGCATGCAAATTTAGTGGCAG 58.038 42.857 20.30 1.90 39.95 4.85
767 777 0.107410 TGGCAGTTTCGTGAGGTTGT 60.107 50.000 0.00 0.00 0.00 3.32
951 961 2.427506 GGTTGCAGAAACTCCGATCTT 58.572 47.619 0.00 0.00 38.92 2.40
1164 1174 1.872952 TGCAAACTGACTGGAATGACG 59.127 47.619 0.00 0.00 0.00 4.35
1267 1277 1.539560 GCTCTCACCACTGGAGCTGA 61.540 60.000 0.71 0.00 46.04 4.26
1268 1278 0.246086 CTCTCACCACTGGAGCTGAC 59.754 60.000 0.71 0.00 32.38 3.51
1776 1789 5.078411 TCTTATGCTCTCTTGAGGTTCAC 57.922 43.478 0.00 0.00 40.53 3.18
1851 1867 3.627577 GGTGATGTAAATCCGTTGCAGAT 59.372 43.478 0.00 0.00 35.11 2.90
1852 1868 4.096382 GGTGATGTAAATCCGTTGCAGATT 59.904 41.667 0.00 0.00 35.11 2.40
1853 1869 5.295787 GGTGATGTAAATCCGTTGCAGATTA 59.704 40.000 0.55 0.00 35.11 1.75
1874 1890 7.458170 AGATTACATTATCCTATTTCTCGGGGT 59.542 37.037 0.00 0.00 0.00 4.95
1895 1911 7.148523 CGGGGTGTGAACTTACTAACTAAATTC 60.149 40.741 0.00 0.00 0.00 2.17
2297 2318 5.594317 GTGGAATAGCAAGGTACCATCAAAT 59.406 40.000 15.94 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
41 42 3.312890 CCCTCTCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
42 43 2.370189 CCCCTCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
43 44 2.412591 CCCCTCTCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
44 45 1.202818 GCCCCTCTCTCTCTCTCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
45 46 0.846693 GCCCCTCTCTCTCTCTCTCT 59.153 60.000 0.00 0.00 0.00 3.10
46 47 0.550914 TGCCCCTCTCTCTCTCTCTC 59.449 60.000 0.00 0.00 0.00 3.20
47 48 0.552848 CTGCCCCTCTCTCTCTCTCT 59.447 60.000 0.00 0.00 0.00 3.10
48 49 0.468029 CCTGCCCCTCTCTCTCTCTC 60.468 65.000 0.00 0.00 0.00 3.20
49 50 1.620259 CCTGCCCCTCTCTCTCTCT 59.380 63.158 0.00 0.00 0.00 3.10
50 51 1.457455 CCCTGCCCCTCTCTCTCTC 60.457 68.421 0.00 0.00 0.00 3.20
51 52 1.938596 TCCCTGCCCCTCTCTCTCT 60.939 63.158 0.00 0.00 0.00 3.10
52 53 1.457455 CTCCCTGCCCCTCTCTCTC 60.457 68.421 0.00 0.00 0.00 3.20
53 54 2.695597 CTCCCTGCCCCTCTCTCT 59.304 66.667 0.00 0.00 0.00 3.10
54 55 2.445654 CCTCCCTGCCCCTCTCTC 60.446 72.222 0.00 0.00 0.00 3.20
55 56 4.101077 CCCTCCCTGCCCCTCTCT 62.101 72.222 0.00 0.00 0.00 3.10
56 57 4.095400 TCCCTCCCTGCCCCTCTC 62.095 72.222 0.00 0.00 0.00 3.20
57 58 4.101077 CTCCCTCCCTGCCCCTCT 62.101 72.222 0.00 0.00 0.00 3.69
61 62 3.642741 TTCCTCTCCCTCCCTGCCC 62.643 68.421 0.00 0.00 0.00 5.36
186 188 5.304357 ACACCCCTAAAATTTGAGGTGAAAG 59.696 40.000 24.62 12.26 46.15 2.62
191 193 4.279922 CGAAACACCCCTAAAATTTGAGGT 59.720 41.667 18.81 8.08 0.00 3.85
197 199 3.742385 TCGTCGAAACACCCCTAAAATT 58.258 40.909 0.00 0.00 0.00 1.82
247 249 1.135315 CGCATTCAAACGCCTCCTG 59.865 57.895 0.00 0.00 0.00 3.86
271 273 3.589988 CCAATTAGGGATTCGGATCGAG 58.410 50.000 0.00 0.00 37.14 4.04
275 277 1.075536 GGGCCAATTAGGGATTCGGAT 59.924 52.381 4.39 0.00 38.09 4.18
295 297 0.387622 CACCACAGCGCCAAAATCTG 60.388 55.000 2.29 0.00 0.00 2.90
336 338 2.088423 GCACCACCCACGATAAATTCA 58.912 47.619 0.00 0.00 0.00 2.57
450 454 3.438087 CCTAATTCACAAGTCAGCACCTG 59.562 47.826 0.00 0.00 0.00 4.00
574 584 0.469144 ATCCCACAACACCACAACCC 60.469 55.000 0.00 0.00 0.00 4.11
634 644 7.994425 TTCTAACATTACTGCCAAGATTCAA 57.006 32.000 0.00 0.00 0.00 2.69
728 738 4.558178 CCACTAAATTTGCATGCAAGACA 58.442 39.130 30.25 18.46 37.24 3.41
729 739 3.368843 GCCACTAAATTTGCATGCAAGAC 59.631 43.478 30.25 8.52 37.24 3.01
753 763 0.028902 GTGGCACAACCTCACGAAAC 59.971 55.000 13.86 0.00 44.16 2.78
951 961 3.725267 AGACCCCCTTTTCTTGGTTTCTA 59.275 43.478 0.00 0.00 0.00 2.10
1164 1174 6.454981 GGTTACAGTTTTTGTCACAAATGTGC 60.455 38.462 15.36 9.46 45.25 4.57
1267 1277 2.610859 AATCCCCCTCACTGCCGT 60.611 61.111 0.00 0.00 0.00 5.68
1268 1278 2.190578 GAATCCCCCTCACTGCCG 59.809 66.667 0.00 0.00 0.00 5.69
1302 1312 1.503542 GCACCCTTCATTGCTGTCG 59.496 57.895 0.00 0.00 35.74 4.35
1350 1363 3.010200 CTCTCAAAAGGGGAAGGATGG 57.990 52.381 0.00 0.00 0.00 3.51
1851 1867 6.328148 ACACCCCGAGAAATAGGATAATGTAA 59.672 38.462 0.00 0.00 0.00 2.41
1852 1868 5.842328 ACACCCCGAGAAATAGGATAATGTA 59.158 40.000 0.00 0.00 0.00 2.29
1853 1869 4.658901 ACACCCCGAGAAATAGGATAATGT 59.341 41.667 0.00 0.00 0.00 2.71
1869 1885 3.672767 AGTTAGTAAGTTCACACCCCG 57.327 47.619 0.00 0.00 0.00 5.73
1874 1890 9.498176 GAAGGGAATTTAGTTAGTAAGTTCACA 57.502 33.333 16.11 0.00 41.21 3.58
1895 1911 5.581126 TGCAAAGCACTAATTATGAAGGG 57.419 39.130 0.00 0.00 31.71 3.95
2126 2143 7.708998 TCAACTTAACAAAGGGAACATTACAC 58.291 34.615 0.00 0.00 0.00 2.90
2297 2318 2.398554 GCATTCTGCGGCCGAAGAA 61.399 57.895 42.95 42.95 43.29 2.52
2380 2401 9.331282 CTGGAAAAGACTAATTGTAAGGATAGG 57.669 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.