Multiple sequence alignment - TraesCS1D01G345900

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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 TraesCS1D01G345900 chr1D 100.000 2892 0 0 1 2892 433809927 433807036 0 5341
1 TraesCS1D01G345900 chr1D 95.406 2917 81 10 1 2891 71367506 71364617 0 4595
2 TraesCS1D01G345900 chr1D 93.934 2110 116 11 1 2109 146652877 146650779 0 3177
3 TraesCS1D01G345900 chr7D 96.645 2891 88 8 3 2892 535921602 535918720 0 4793
4 TraesCS1D01G345900 chr4D 96.058 2917 65 7 1 2892 504422676 504425567 0 4704
5 TraesCS1D01G345900 chr6D 95.783 2917 70 10 1 2892 53645894 53648782 0 4656
6 TraesCS1D01G345900 chr6D 95.509 2895 118 8 1 2892 347429012 347426127 0 4615
7 TraesCS1D01G345900 chr6D 95.514 2898 96 9 1 2892 175233114 175230245 0 4601
8 TraesCS1D01G345900 chr6D 94.995 2917 92 11 1 2892 340957024 340959911 0 4529
9 TraesCS1D01G345900 chr6D 94.928 2918 92 12 1 2892 383565233 383568120 0 4518
10 TraesCS1D01G345900 chr3D 95.682 2895 97 11 1 2892 262981030 262978161 0 4628
11 TraesCS1D01G345900 chr3D 94.861 2919 73 15 1 2892 468640610 468643478 0 4488
12 TraesCS1D01G345900 chr5D 95.233 2895 108 6 1 2892 163835937 163833070 0 4554
13 TraesCS1D01G345900 chr5D 96.117 2112 78 3 1 2109 45858802 45856692 0 3443
14 TraesCS1D01G345900 chr6B 88.491 2902 300 28 1 2888 21571103 21568222 0 3478


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 TraesCS1D01G345900 chr1D 433807036 433809927 2891 True 5341 5341 100.000 1 2892 1 chr1D.!!$R3 2891
1 TraesCS1D01G345900 chr1D 71364617 71367506 2889 True 4595 4595 95.406 1 2891 1 chr1D.!!$R1 2890
2 TraesCS1D01G345900 chr1D 146650779 146652877 2098 True 3177 3177 93.934 1 2109 1 chr1D.!!$R2 2108
3 TraesCS1D01G345900 chr7D 535918720 535921602 2882 True 4793 4793 96.645 3 2892 1 chr7D.!!$R1 2889
4 TraesCS1D01G345900 chr4D 504422676 504425567 2891 False 4704 4704 96.058 1 2892 1 chr4D.!!$F1 2891
5 TraesCS1D01G345900 chr6D 53645894 53648782 2888 False 4656 4656 95.783 1 2892 1 chr6D.!!$F1 2891
6 TraesCS1D01G345900 chr6D 347426127 347429012 2885 True 4615 4615 95.509 1 2892 1 chr6D.!!$R2 2891
7 TraesCS1D01G345900 chr6D 175230245 175233114 2869 True 4601 4601 95.514 1 2892 1 chr6D.!!$R1 2891
8 TraesCS1D01G345900 chr6D 340957024 340959911 2887 False 4529 4529 94.995 1 2892 1 chr6D.!!$F2 2891
9 TraesCS1D01G345900 chr6D 383565233 383568120 2887 False 4518 4518 94.928 1 2892 1 chr6D.!!$F3 2891
10 TraesCS1D01G345900 chr3D 262978161 262981030 2869 True 4628 4628 95.682 1 2892 1 chr3D.!!$R1 2891
11 TraesCS1D01G345900 chr3D 468640610 468643478 2868 False 4488 4488 94.861 1 2892 1 chr3D.!!$F1 2891
12 TraesCS1D01G345900 chr5D 163833070 163835937 2867 True 4554 4554 95.233 1 2892 1 chr5D.!!$R2 2891
13 TraesCS1D01G345900 chr5D 45856692 45858802 2110 True 3443 3443 96.117 1 2109 1 chr5D.!!$R1 2108
14 TraesCS1D01G345900 chr6B 21568222 21571103 2881 True 3478 3478 88.491 1 2888 1 chr6B.!!$R1 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
96 97 1.002087 ACTAGGACCGTTCTTTGCTGG 59.998 52.381 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2108 0.034863 TGCATGGCAGATTCAGCAGA 60.035 50.0 3.34 0.0 33.32 4.26 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
23 24 1.539280 GCATAGAGGAGGTCTTTCCGC 60.539 57.143 0.00 0.00 42.29 5.54
96 97 1.002087 ACTAGGACCGTTCTTTGCTGG 59.998 52.381 0.00 0.00 0.00 4.85
176 177 3.560025 GGAGTTTGAAAGGAGCTGGATGA 60.560 47.826 0.00 0.00 0.00 2.92
245 246 1.066430 TGTGGGAGAAGCGAATGTACC 60.066 52.381 0.00 0.00 0.00 3.34
262 263 3.463585 CGGGTGCCGGCCTACTTA 61.464 66.667 26.77 0.00 44.15 2.24
296 297 4.284490 TCTTCCTGTTTCTGCAGACTACAT 59.716 41.667 23.78 0.00 38.70 2.29
483 486 1.918262 ACCAATGGAGAGGCAGATGAA 59.082 47.619 6.16 0.00 0.00 2.57
747 822 3.007074 TGCAGTTGCCATGTTTGATGAAT 59.993 39.130 1.06 0.00 41.18 2.57
949 1048 6.252967 TGCCATGTTTAATGAACTGTAGTG 57.747 37.500 0.00 0.00 39.08 2.74
950 1049 5.095490 GCCATGTTTAATGAACTGTAGTGC 58.905 41.667 0.00 0.00 39.08 4.40
973 1072 5.288472 GCCCATGTTTGAACGAATTGTAATC 59.712 40.000 0.00 0.00 0.00 1.75
979 1078 8.112016 TGTTTGAACGAATTGTAATCCCATTA 57.888 30.769 0.00 0.00 0.00 1.90
1217 1317 2.220479 AAGCGAAGGCGAATACTACC 57.780 50.000 0.00 0.00 46.35 3.18
1296 1396 1.512926 GACTTGAATGCGGTGACACT 58.487 50.000 5.39 0.00 0.00 3.55
1370 1470 1.659954 GCGCCGCAAACATCAAACA 60.660 52.632 3.15 0.00 0.00 2.83
1436 1536 1.298339 GTGAGGCACGTTGTGTTGC 60.298 57.895 0.00 0.00 35.75 4.17
1614 1714 1.002134 CTTCGTCCACAGGGCCATT 60.002 57.895 6.18 0.00 0.00 3.16
1723 1823 8.552034 CGTCCAAAAGAGATAAGATACAAATCC 58.448 37.037 0.00 0.00 31.98 3.01
1929 2034 1.308069 AATAGCTGCAGTTGCCACGG 61.308 55.000 16.64 0.00 41.18 4.94
1956 2084 3.911868 GCACTGAATTTGCCATGTTACA 58.088 40.909 0.00 0.00 33.58 2.41
1970 2098 5.575957 CCATGTTACATGAACTGAATCTGC 58.424 41.667 25.02 0.00 38.98 4.26
1971 2099 5.449588 CCATGTTACATGAACTGAATCTGCC 60.450 44.000 25.02 0.00 38.98 4.85
1972 2100 4.650734 TGTTACATGAACTGAATCTGCCA 58.349 39.130 0.00 0.00 38.98 4.92
1973 2101 5.255687 TGTTACATGAACTGAATCTGCCAT 58.744 37.500 0.00 0.00 38.98 4.40
1974 2102 5.124297 TGTTACATGAACTGAATCTGCCATG 59.876 40.000 15.78 15.78 38.98 3.66
1975 2103 2.426024 ACATGAACTGAATCTGCCATGC 59.574 45.455 16.67 0.00 35.96 4.06
1976 2104 2.203470 TGAACTGAATCTGCCATGCA 57.797 45.000 0.00 0.00 36.92 3.96
1977 2105 2.516906 TGAACTGAATCTGCCATGCAA 58.483 42.857 0.00 0.00 38.41 4.08
1978 2106 3.093814 TGAACTGAATCTGCCATGCAAT 58.906 40.909 0.00 0.00 38.41 3.56
1979 2107 3.512329 TGAACTGAATCTGCCATGCAATT 59.488 39.130 0.00 0.00 38.41 2.32
1980 2108 4.020928 TGAACTGAATCTGCCATGCAATTT 60.021 37.500 0.00 0.00 38.41 1.82
1981 2109 4.119442 ACTGAATCTGCCATGCAATTTC 57.881 40.909 0.00 0.00 38.41 2.17
1982 2110 3.767673 ACTGAATCTGCCATGCAATTTCT 59.232 39.130 0.00 0.00 38.41 2.52
1983 2111 4.112634 CTGAATCTGCCATGCAATTTCTG 58.887 43.478 0.00 7.29 38.41 3.02
2074 2251 9.995003 TTCTACTGAATTTGCCATGTTATTTTT 57.005 25.926 0.00 0.00 0.00 1.94
2181 2404 4.109766 CGCGTAGATTTCCATGTTCAGTA 58.890 43.478 0.00 0.00 0.00 2.74
2242 2468 0.383949 TGGGAAACAAGCTGAAACGC 59.616 50.000 0.00 0.00 0.00 4.84
2408 2643 3.804036 TGTTTTCAGACATCAAGGACGT 58.196 40.909 0.00 0.00 0.00 4.34
2480 2715 7.724305 ACTGAAAACACATAAACGTATCTGT 57.276 32.000 0.00 0.00 0.00 3.41
2732 2969 3.834813 ACAGCTTCCTCTATGAACTCACA 59.165 43.478 0.00 0.00 0.00 3.58
2757 2994 1.231958 TGGACCGCGTGTTGAAATCC 61.232 55.000 4.92 0.00 0.00 3.01
2780 3017 3.444742 TCATTCATCAACCAGTTCCATGC 59.555 43.478 0.00 0.00 0.00 4.06
2815 3053 0.738975 CTCGACGACCATTCCAGCTA 59.261 55.000 0.00 0.00 0.00 3.32
2858 3096 3.578282 CCTTCCCACTTTGCAAGGTATTT 59.422 43.478 14.45 0.00 32.17 1.40
2859 3097 4.040339 CCTTCCCACTTTGCAAGGTATTTT 59.960 41.667 14.45 0.00 32.17 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 177 9.685276 TTGGACTTGATATGTTTCAATCATAGT 57.315 29.630 0.00 0.00 35.20 2.12
262 263 2.283145 ACAGGAAGAAGCACTGCATT 57.717 45.000 3.30 0.00 35.70 3.56
296 297 1.476845 TTGAACCCCTCACTGCGCTA 61.477 55.000 9.73 0.00 32.21 4.26
747 822 4.597404 TCATTAAACATGGCAACTGCAA 57.403 36.364 3.76 0.00 44.36 4.08
949 1048 3.025287 ACAATTCGTTCAAACATGGGC 57.975 42.857 0.00 0.00 0.00 5.36
950 1049 5.804979 GGATTACAATTCGTTCAAACATGGG 59.195 40.000 0.00 0.00 0.00 4.00
973 1072 3.742433 TTGTTTGTTGTGGCTAATGGG 57.258 42.857 0.00 0.00 0.00 4.00
979 1078 2.934801 GCACCTTTTGTTTGTTGTGGCT 60.935 45.455 0.00 0.00 0.00 4.75
1296 1396 2.666272 TATGAAATGGCGGGGCATTA 57.334 45.000 19.04 6.85 0.00 1.90
1370 1470 1.106351 TCATGCACGGCCAAAACTGT 61.106 50.000 2.24 0.00 0.00 3.55
1436 1536 8.044060 TCAATTAGTTCAGCATAGTTCTTTGG 57.956 34.615 0.00 0.00 0.00 3.28
1614 1714 4.863548 TCCTACCTCCGAGTTTTCAGATA 58.136 43.478 0.00 0.00 0.00 1.98
1723 1823 4.168760 GTTTTGCTTGAATCTCCAATCCG 58.831 43.478 0.00 0.00 0.00 4.18
1874 1979 7.750229 TTTTTACTTCAGATTCTGATGCACT 57.250 32.000 22.74 11.08 40.39 4.40
1956 2084 2.730382 TGCATGGCAGATTCAGTTCAT 58.270 42.857 0.00 0.00 33.32 2.57
1975 2103 3.861276 TGGCAGATTCAGCAGAAATTG 57.139 42.857 3.34 0.00 37.29 2.32
1976 2104 3.430374 GCATGGCAGATTCAGCAGAAATT 60.430 43.478 3.34 0.00 37.29 1.82
1977 2105 2.100916 GCATGGCAGATTCAGCAGAAAT 59.899 45.455 3.34 0.00 37.29 2.17
1978 2106 1.475280 GCATGGCAGATTCAGCAGAAA 59.525 47.619 3.34 0.00 37.29 2.52
1979 2107 1.100510 GCATGGCAGATTCAGCAGAA 58.899 50.000 3.34 0.00 38.31 3.02
1980 2108 0.034863 TGCATGGCAGATTCAGCAGA 60.035 50.000 3.34 0.00 33.32 4.26
1981 2109 0.815095 TTGCATGGCAGATTCAGCAG 59.185 50.000 3.34 0.00 40.61 4.24
1982 2110 1.480789 ATTGCATGGCAGATTCAGCA 58.519 45.000 3.34 0.00 40.61 4.41
1983 2111 2.596904 AATTGCATGGCAGATTCAGC 57.403 45.000 0.00 0.00 40.61 4.26
1984 2112 4.112634 CAGAAATTGCATGGCAGATTCAG 58.887 43.478 15.56 7.82 40.61 3.02
1985 2113 4.118093 CAGAAATTGCATGGCAGATTCA 57.882 40.909 15.56 0.00 40.61 2.57
2095 2272 7.759489 ACTAACATGGCAGATTCACTAAAAA 57.241 32.000 0.00 0.00 0.00 1.94
2096 2273 7.230510 ACAACTAACATGGCAGATTCACTAAAA 59.769 33.333 0.00 0.00 0.00 1.52
2097 2274 6.714810 ACAACTAACATGGCAGATTCACTAAA 59.285 34.615 0.00 0.00 0.00 1.85
2098 2275 6.237901 ACAACTAACATGGCAGATTCACTAA 58.762 36.000 0.00 0.00 0.00 2.24
2101 2278 5.643777 AGTACAACTAACATGGCAGATTCAC 59.356 40.000 0.00 0.00 0.00 3.18
2181 2404 5.818136 ATATGTGTGACTAAAATGCGCTT 57.182 34.783 9.73 0.00 0.00 4.68
2242 2468 3.782244 GCGGTTGCTGCACGAGAG 61.782 66.667 15.59 1.80 38.39 3.20
2327 2561 8.166422 AGTTATCGTTCTTTCTTGTTTGGATT 57.834 30.769 0.00 0.00 0.00 3.01
2757 2994 4.439700 GCATGGAACTGGTTGATGAATGAG 60.440 45.833 0.00 0.00 0.00 2.90
2780 3017 1.392168 TCGAGCTCCGCAAAATTTACG 59.608 47.619 8.47 6.56 38.37 3.18
2815 3053 0.175760 CGACGGGTTCCTGTCATCAT 59.824 55.000 24.66 0.00 34.78 2.45


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

AutoCloner maintained by Alex Coulton.