Multiple sequence alignment - TraesCS4A01G153300

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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 TraesCS4A01G153300 chr4A 100.000 2366 0 0 1 2366 309510057 309512422 0.000000e+00 4370
1 TraesCS4A01G153300 chr5D 96.633 2376 60 10 1 2360 483806512 483808883 0.000000e+00 3927
2 TraesCS4A01G153300 chr5D 96.346 2381 67 10 1 2366 503284372 503281997 0.000000e+00 3897
3 TraesCS4A01G153300 chr5D 96.301 2379 70 10 1 2366 6183870 6186243 0.000000e+00 3890
4 TraesCS4A01G153300 chr5D 93.493 584 24 5 2 575 167069012 167068433 0.000000e+00 856
5 TraesCS4A01G153300 chr6D 96.299 2378 71 10 1 2366 45514498 45516870 0.000000e+00 3888
6 TraesCS4A01G153300 chr1D 96.175 2379 65 13 1 2366 254403176 254400811 0.000000e+00 3866
7 TraesCS4A01G153300 chr1D 95.244 2376 91 13 1 2366 51880998 51883361 0.000000e+00 3742
8 TraesCS4A01G153300 chr2A 95.965 2379 77 12 1 2366 335833575 335835947 0.000000e+00 3843
9 TraesCS4A01G153300 chr3D 96.378 2319 56 11 1 2304 598875876 598873571 0.000000e+00 3792
10 TraesCS4A01G153300 chr4B 94.613 2376 96 17 3 2366 308691426 308693781 0.000000e+00 3650
11 TraesCS4A01G153300 chrUn 95.805 2241 75 12 1 2230 261572040 261574272 0.000000e+00 3600
12 TraesCS4A01G153300 chrUn 98.571 70 1 0 1 70 442414360 442414429 8.880000e-25 124


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 TraesCS4A01G153300 chr4A 309510057 309512422 2365 False 4370 4370 100.000 1 2366 1 chr4A.!!$F1 2365
1 TraesCS4A01G153300 chr5D 483806512 483808883 2371 False 3927 3927 96.633 1 2360 1 chr5D.!!$F2 2359
2 TraesCS4A01G153300 chr5D 503281997 503284372 2375 True 3897 3897 96.346 1 2366 1 chr5D.!!$R2 2365
3 TraesCS4A01G153300 chr5D 6183870 6186243 2373 False 3890 3890 96.301 1 2366 1 chr5D.!!$F1 2365
4 TraesCS4A01G153300 chr5D 167068433 167069012 579 True 856 856 93.493 2 575 1 chr5D.!!$R1 573
5 TraesCS4A01G153300 chr6D 45514498 45516870 2372 False 3888 3888 96.299 1 2366 1 chr6D.!!$F1 2365
6 TraesCS4A01G153300 chr1D 254400811 254403176 2365 True 3866 3866 96.175 1 2366 1 chr1D.!!$R1 2365
7 TraesCS4A01G153300 chr1D 51880998 51883361 2363 False 3742 3742 95.244 1 2366 1 chr1D.!!$F1 2365
8 TraesCS4A01G153300 chr2A 335833575 335835947 2372 False 3843 3843 95.965 1 2366 1 chr2A.!!$F1 2365
9 TraesCS4A01G153300 chr3D 598873571 598875876 2305 True 3792 3792 96.378 1 2304 1 chr3D.!!$R1 2303
10 TraesCS4A01G153300 chr4B 308691426 308693781 2355 False 3650 3650 94.613 3 2366 1 chr4B.!!$F1 2363
11 TraesCS4A01G153300 chrUn 261572040 261574272 2232 False 3600 3600 95.805 1 2230 1 chrUn.!!$F1 2229


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
750 765 2.223971 GGAAATCCCATTCTCGCTACGA 60.224 50.0 0.0 0.0 34.14 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1903 1.462283 CGCTCAGTGTGTGATCCAAAG 59.538 52.381 0.0 0.0 33.51 2.77 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
55 56 3.655777 AGGTTGGGTTTTCCTATGAGTGA 59.344 43.478 0.00 0.00 40.46 3.41
200 211 3.062504 GCGATTGGCCTGCAAAAATAAAG 59.937 43.478 3.32 0.00 34.80 1.85
283 297 9.206870 GAGCAGAAAAAGATCTATGGATTAGAG 57.793 37.037 0.00 0.00 40.27 2.43
308 322 4.220602 CCCTTTCTTTCCAGGGTTTGTATG 59.779 45.833 0.00 0.00 44.58 2.39
325 339 6.656632 TTGTATGAAAAATGCAACACCCTA 57.343 33.333 0.00 0.00 0.00 3.53
366 380 9.423061 CACTATGTATCATCATTCGATAAACCA 57.577 33.333 0.00 0.00 0.00 3.67
383 397 5.459536 AAACCAAGAAATGCTTCTTCTCC 57.540 39.130 0.00 0.00 46.88 3.71
386 400 4.289672 ACCAAGAAATGCTTCTTCTCCCTA 59.710 41.667 0.00 0.00 46.88 3.53
477 491 5.216614 ACTTTGTCTACCCACTTCTCTTC 57.783 43.478 0.00 0.00 0.00 2.87
750 765 2.223971 GGAAATCCCATTCTCGCTACGA 60.224 50.000 0.00 0.00 34.14 3.43
801 816 9.673454 GAAATACCAAAGTTTCAGAATTTACGT 57.327 29.630 0.00 0.00 35.09 3.57
1124 1151 8.635765 AAACAATCTTCTTGCTTACCATTAGA 57.364 30.769 0.00 0.00 0.00 2.10
1149 1176 2.846193 TCTGGAACTTTTCTGGAACGG 58.154 47.619 0.00 0.00 0.00 4.44
1262 1289 7.800155 TGCATTATGTTCGATATCAAGGAAA 57.200 32.000 3.12 0.00 0.00 3.13
1363 1393 1.134220 TCTGTTTTTGGACTCAGCCGT 60.134 47.619 0.00 0.00 0.00 5.68
1467 1497 7.118723 TGTTAGTAAGGAATCAAATGCTGGAT 58.881 34.615 0.00 0.00 0.00 3.41
1521 1552 0.896940 TCGATACCATAGTCCCCGCC 60.897 60.000 0.00 0.00 0.00 6.13
1583 1614 4.242811 ACTGGATCAGGGCATCCTATTAA 58.757 43.478 4.22 0.00 42.67 1.40
1600 1637 9.897040 ATCCTATTAATAAACCCATTTGGACAT 57.103 29.630 0.00 0.00 37.39 3.06
1833 1872 5.505173 TGGAAGAAGAGCAAGTTTTTCTG 57.495 39.130 0.00 0.00 30.77 3.02
1838 1877 6.705863 AGAAGAGCAAGTTTTTCTGTGATT 57.294 33.333 0.00 0.00 0.00 2.57
1860 1899 9.712305 TGATTTTCACCAAAACAACTCTTTTTA 57.288 25.926 0.00 0.00 34.24 1.52
1899 1940 3.945285 ACTGAGCGTATTTGGTATTTGGG 59.055 43.478 0.00 0.00 0.00 4.12
2108 2149 8.139989 CCTCTTTGGAATAGAAATTGGCTATTG 58.860 37.037 14.96 4.82 38.35 1.90
2124 2165 5.104109 TGGCTATTGCTACATAGGGAAAGTT 60.104 40.000 0.00 0.00 39.59 2.66
2224 2265 1.543358 GACTAGTTCCGGGTTCGAGTT 59.457 52.381 0.00 0.00 39.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 100 7.928307 ACATCCCTTATTCAATCCATAATCG 57.072 36.000 0.00 0.00 0.00 3.34
308 322 5.863935 GTCAGAATAGGGTGTTGCATTTTTC 59.136 40.000 0.00 0.00 0.00 2.29
325 339 8.377799 TGATACATAGTGCAATATGGTCAGAAT 58.622 33.333 31.07 17.05 37.45 2.40
451 465 8.431910 AAGAGAAGTGGGTAGACAAAGTATTA 57.568 34.615 0.00 0.00 0.00 0.98
477 491 7.043565 GGGCAAATGCATAAATATATTCCTGG 58.956 38.462 0.00 0.00 44.36 4.45
523 537 4.398319 ACAACTATTTCCACAGGTTCAGG 58.602 43.478 0.00 0.00 0.00 3.86
1096 1122 7.759489 ATGGTAAGCAAGAAGATTGTTTACA 57.241 32.000 21.04 12.22 43.35 2.41
1103 1129 9.692325 AAGATTCTAATGGTAAGCAAGAAGATT 57.308 29.630 0.00 0.00 30.30 2.40
1124 1151 5.239525 CGTTCCAGAAAAGTTCCAGAAGATT 59.760 40.000 0.00 0.00 0.00 2.40
1149 1176 6.240549 TCCATCTTCCTAGAAAAGTGGATC 57.759 41.667 16.21 0.00 33.21 3.36
1363 1393 9.639563 TGCTAATTGGTTTATATGGATTCTTCA 57.360 29.630 0.00 0.00 0.00 3.02
1607 1644 9.440773 CAAATCGATCAAGAATATCCCAATCTA 57.559 33.333 0.00 0.00 0.00 1.98
1767 1805 4.680440 GCCGAACCCAATCTTTGCATAAAT 60.680 41.667 0.00 0.00 0.00 1.40
1777 1815 4.340617 TCTAAAAATGCCGAACCCAATCT 58.659 39.130 0.00 0.00 0.00 2.40
1833 1872 7.595311 AAAGAGTTGTTTTGGTGAAAATCAC 57.405 32.000 1.88 1.88 46.23 3.06
1860 1899 4.217118 GCTCAGTGTGTGATCCAAAGAAAT 59.783 41.667 0.00 0.00 33.51 2.17
1862 1901 3.141398 GCTCAGTGTGTGATCCAAAGAA 58.859 45.455 0.00 0.00 33.51 2.52
1864 1903 1.462283 CGCTCAGTGTGTGATCCAAAG 59.538 52.381 0.00 0.00 33.51 2.77
1899 1940 8.301720 TGACCAGGTCATTGATACGTATAATAC 58.698 37.037 19.21 3.15 37.67 1.89
2108 2149 3.127030 GCACACAACTTTCCCTATGTAGC 59.873 47.826 0.00 0.00 0.00 3.58



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

AutoCloner maintained by Alex Coulton.