Multiple sequence alignment - TraesCS1D01G009700

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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 TraesCS1D01G009700 chr1D 100.000 3282 0 0 1 3282 5289664 5292945 0.000000e+00 6061.0
1 TraesCS1D01G009700 chr1D 81.643 621 92 18 2600 3211 486255509 486254902 2.270000e-136 496.0
2 TraesCS1D01G009700 chr1D 79.250 400 66 10 2816 3211 488616386 488616772 2.510000e-66 263.0
3 TraesCS1D01G009700 chr1B 95.497 955 34 4 875 1823 8116585 8117536 0.000000e+00 1517.0
4 TraesCS1D01G009700 chr1B 93.133 830 46 4 1900 2718 8117682 8118511 0.000000e+00 1206.0
5 TraesCS1D01G009700 chr4D 94.044 873 45 4 1 867 232695552 232694681 0.000000e+00 1317.0
6 TraesCS1D01G009700 chr4D 92.792 874 54 5 1 868 461474142 461475012 0.000000e+00 1256.0
7 TraesCS1D01G009700 chr2D 93.578 872 50 2 1 866 306476663 306477534 0.000000e+00 1295.0
8 TraesCS1D01G009700 chr2D 92.395 881 54 7 1 872 346102602 346101726 0.000000e+00 1243.0
9 TraesCS1D01G009700 chr2D 79.268 246 46 5 2578 2821 525519741 525519499 2.030000e-37 167.0
10 TraesCS1D01G009700 chr2D 84.375 96 8 4 1811 1906 636593201 636593113 1.620000e-13 87.9
11 TraesCS1D01G009700 chr7D 93.044 877 53 3 1 870 621971645 621970770 0.000000e+00 1275.0
12 TraesCS1D01G009700 chr2B 93.044 877 51 7 1 869 638015739 638014865 0.000000e+00 1273.0
13 TraesCS1D01G009700 chr2B 84.536 388 51 9 2816 3199 621956990 621957372 3.090000e-100 375.0
14 TraesCS1D01G009700 chr6D 92.922 876 55 2 1 869 191801703 191800828 0.000000e+00 1267.0
15 TraesCS1D01G009700 chr7B 92.808 876 55 3 1 869 267255384 267256258 0.000000e+00 1262.0
16 TraesCS1D01G009700 chr7B 92.580 876 57 4 1 870 168964836 168965709 0.000000e+00 1251.0
17 TraesCS1D01G009700 chr3A 85.075 402 50 8 2816 3211 720412508 720412111 5.100000e-108 401.0
18 TraesCS1D01G009700 chr3A 84.795 171 21 4 3045 3211 468730711 468730880 2.030000e-37 167.0
19 TraesCS1D01G009700 chr4A 84.788 401 52 9 2816 3211 441781522 441781126 8.540000e-106 394.0
20 TraesCS1D01G009700 chr7A 81.572 407 47 13 2808 3211 83300758 83300377 8.840000e-81 311.0
21 TraesCS1D01G009700 chr7A 83.696 92 8 4 1812 1903 678752614 678752698 2.710000e-11 80.5
22 TraesCS1D01G009700 chr1A 81.378 392 57 13 2816 3199 587871958 587872341 4.110000e-79 305.0
23 TraesCS1D01G009700 chr4B 81.963 377 38 16 2816 3188 191211676 191212026 3.200000e-75 292.0
24 TraesCS1D01G009700 chr3D 84.409 186 24 5 3029 3211 350872924 350873107 9.360000e-41 178.0
25 TraesCS1D01G009700 chr3B 85.714 98 10 2 1809 1906 795334321 795334414 2.080000e-17 100.0
26 TraesCS1D01G009700 chr3B 80.208 96 12 3 1811 1906 76514111 76514023 7.600000e-07 65.8
27 TraesCS1D01G009700 chr5A 83.505 97 9 3 1811 1907 32836426 32836515 2.100000e-12 84.2
28 TraesCS1D01G009700 chr5D 83.000 100 8 6 1811 1906 562348446 562348352 7.550000e-12 82.4
29 TraesCS1D01G009700 chr5D 81.818 99 11 3 1812 1910 173749755 173749846 3.510000e-10 76.8
30 TraesCS1D01G009700 chr5B 79.825 114 14 5 1798 1910 324299761 324299866 1.260000e-09 75.0
31 TraesCS1D01G009700 chr6A 95.122 41 2 0 1866 1906 62810623 62810583 7.600000e-07 65.8


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 TraesCS1D01G009700 chr1D 5289664 5292945 3281 False 6061.0 6061 100.000 1 3282 1 chr1D.!!$F1 3281
1 TraesCS1D01G009700 chr1D 486254902 486255509 607 True 496.0 496 81.643 2600 3211 1 chr1D.!!$R1 611
2 TraesCS1D01G009700 chr1B 8116585 8118511 1926 False 1361.5 1517 94.315 875 2718 2 chr1B.!!$F1 1843
3 TraesCS1D01G009700 chr4D 232694681 232695552 871 True 1317.0 1317 94.044 1 867 1 chr4D.!!$R1 866
4 TraesCS1D01G009700 chr4D 461474142 461475012 870 False 1256.0 1256 92.792 1 868 1 chr4D.!!$F1 867
5 TraesCS1D01G009700 chr2D 306476663 306477534 871 False 1295.0 1295 93.578 1 866 1 chr2D.!!$F1 865
6 TraesCS1D01G009700 chr2D 346101726 346102602 876 True 1243.0 1243 92.395 1 872 1 chr2D.!!$R1 871
7 TraesCS1D01G009700 chr7D 621970770 621971645 875 True 1275.0 1275 93.044 1 870 1 chr7D.!!$R1 869
8 TraesCS1D01G009700 chr2B 638014865 638015739 874 True 1273.0 1273 93.044 1 869 1 chr2B.!!$R1 868
9 TraesCS1D01G009700 chr6D 191800828 191801703 875 True 1267.0 1267 92.922 1 869 1 chr6D.!!$R1 868
10 TraesCS1D01G009700 chr7B 267255384 267256258 874 False 1262.0 1262 92.808 1 869 1 chr7B.!!$F2 868
11 TraesCS1D01G009700 chr7B 168964836 168965709 873 False 1251.0 1251 92.580 1 870 1 chr7B.!!$F1 869


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
552 558 0.109643 CGTTGATCCGTACGTGGTCA 60.110 55.0 15.21 14.2 33.33 4.02 F
1330 1347 0.108329 TCGGATTTCACGCCTCCTTC 60.108 55.0 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1744 0.307760 GGAGACAAACTGCACGTTGG 59.692 55.0 8.95 5.9 35.61 3.77 R
3242 3342 0.104304 ACGATCTCGCGGCCTTATTT 59.896 50.0 6.13 0.0 44.43 1.40 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)



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AutoCloner maintained by Alex Coulton.