Multiple sequence alignment - TraesCS4A01G152900

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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 TraesCS4A01G152900 chr4A 100.000 2223 0 0 1 2223 309477660 309479882 0.000000e+00 4106
1 TraesCS4A01G152900 chr3B 97.670 1631 37 1 2 1631 101907486 101909116 0.000000e+00 2800
2 TraesCS4A01G152900 chr3B 95.638 596 24 2 1630 2223 101909432 101910027 0.000000e+00 955
3 TraesCS4A01G152900 chr3B 97.500 200 5 0 1432 1631 795013969 795014168 2.110000e-90 342
4 TraesCS4A01G152900 chr5D 97.180 1631 43 3 2 1631 503304529 503302901 0.000000e+00 2754
5 TraesCS4A01G152900 chr5D 97.118 1631 45 2 2 1631 6164255 6165884 0.000000e+00 2750
6 TraesCS4A01G152900 chr5D 96.750 1631 51 2 2 1631 329151192 329152821 0.000000e+00 2717
7 TraesCS4A01G152900 chr5D 97.351 1397 36 1 236 1631 6263515 6264911 0.000000e+00 2374
8 TraesCS4A01G152900 chr5D 96.746 922 30 0 2 923 6262246 6263167 0.000000e+00 1537
9 TraesCS4A01G152900 chr5D 95.805 596 23 2 1630 2223 6166198 6166793 0.000000e+00 961
10 TraesCS4A01G152900 chr5D 95.805 596 23 2 1630 2223 6265227 6265822 0.000000e+00 961
11 TraesCS4A01G152900 chr5D 94.966 596 27 3 1630 2223 503302585 503301991 0.000000e+00 931
12 TraesCS4A01G152900 chr1D 97.118 1631 44 3 2 1631 254447696 254446068 0.000000e+00 2748
13 TraesCS4A01G152900 chr1D 96.750 1631 52 1 2 1631 51859374 51861004 0.000000e+00 2717
14 TraesCS4A01G152900 chr1D 95.638 596 22 3 1630 2223 254445752 254445159 0.000000e+00 953
15 TraesCS4A01G152900 chr1D 94.295 596 28 4 1630 2223 246423228 246422637 0.000000e+00 907
16 TraesCS4A01G152900 chr1D 94.128 596 32 3 1630 2223 51861320 51861914 0.000000e+00 904
17 TraesCS4A01G152900 chr4D 95.888 1605 61 3 28 1631 19881121 19879521 0.000000e+00 2593
18 TraesCS4A01G152900 chr4D 95.122 820 36 4 567 1385 206989030 206989846 0.000000e+00 1290
19 TraesCS4A01G152900 chr4D 94.622 595 28 2 1630 2223 19879205 19878614 0.000000e+00 918
20 TraesCS4A01G152900 chr4D 93.624 596 34 4 1630 2223 207036164 207036757 0.000000e+00 887


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 TraesCS4A01G152900 chr4A 309477660 309479882 2222 False 4106.0 4106 100.0000 1 2223 1 chr4A.!!$F1 2222
1 TraesCS4A01G152900 chr3B 101907486 101910027 2541 False 1877.5 2800 96.6540 2 2223 2 chr3B.!!$F2 2221
2 TraesCS4A01G152900 chr5D 329151192 329152821 1629 False 2717.0 2717 96.7500 2 1631 1 chr5D.!!$F1 1629
3 TraesCS4A01G152900 chr5D 6164255 6166793 2538 False 1855.5 2750 96.4615 2 2223 2 chr5D.!!$F2 2221
4 TraesCS4A01G152900 chr5D 503301991 503304529 2538 True 1842.5 2754 96.0730 2 2223 2 chr5D.!!$R1 2221
5 TraesCS4A01G152900 chr5D 6262246 6265822 3576 False 1624.0 2374 96.6340 2 2223 3 chr5D.!!$F3 2221
6 TraesCS4A01G152900 chr1D 254445159 254447696 2537 True 1850.5 2748 96.3780 2 2223 2 chr1D.!!$R2 2221
7 TraesCS4A01G152900 chr1D 51859374 51861914 2540 False 1810.5 2717 95.4390 2 2223 2 chr1D.!!$F1 2221
8 TraesCS4A01G152900 chr1D 246422637 246423228 591 True 907.0 907 94.2950 1630 2223 1 chr1D.!!$R1 593
9 TraesCS4A01G152900 chr4D 19878614 19881121 2507 True 1755.5 2593 95.2550 28 2223 2 chr4D.!!$R1 2195
10 TraesCS4A01G152900 chr4D 206989030 206989846 816 False 1290.0 1290 95.1220 567 1385 1 chr4D.!!$F1 818
11 TraesCS4A01G152900 chr4D 207036164 207036757 593 False 887.0 887 93.6240 1630 2223 1 chr4D.!!$F2 593

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
997 2037 2.103601 CCGGGTACTCGGGTTCAAATAT 59.896 50.0 27.18 0.0 45.78 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 3873 1.120437 CGCAAGTTTTCAAAGCCGAC 58.88 50.0 0.0 0.0 0.0 4.79 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
201 203 6.680148 TCCCATTTGATATCTTCGTATCCA 57.320 37.500 3.98 0.00 31.47 3.41
233 235 2.296073 TTCTACCCCGCATTTTTGGT 57.704 45.000 0.00 0.00 34.85 3.67
332 1369 7.381139 GTCCAAAGATTCTTTCGCAAAACAATA 59.619 33.333 8.71 0.00 0.00 1.90
387 1424 2.339769 AGTAGAGGGCCTTGTGACTTT 58.660 47.619 7.89 0.00 0.00 2.66
426 1463 2.786777 AGGTAGGTTTTTGTTAGCCCG 58.213 47.619 0.00 0.00 0.00 6.13
469 1506 5.406477 GGAAATGAGTCCAATTTGAAGTTGC 59.594 40.000 0.00 0.00 37.65 4.17
670 1710 6.770785 TCATGATTAGGTATTCTTTTTCCCCG 59.229 38.462 0.00 0.00 0.00 5.73
719 1759 5.119898 GCGAGCTATAAGATGGTCAGATTTG 59.880 44.000 0.00 0.00 0.00 2.32
831 1871 2.931320 GCTCTTCCTCTAACCGGTTGTG 60.931 54.545 30.08 20.92 0.00 3.33
850 1890 3.962063 TGTGGTGTAACAAGTGAGTAGGA 59.038 43.478 0.00 0.00 39.98 2.94
851 1891 4.406326 TGTGGTGTAACAAGTGAGTAGGAA 59.594 41.667 0.00 0.00 39.98 3.36
882 1922 5.909621 ACACCCATGAATTTTCTCATCAG 57.090 39.130 0.00 0.00 33.66 2.90
997 2037 2.103601 CCGGGTACTCGGGTTCAAATAT 59.896 50.000 27.18 0.00 45.78 1.28
1101 2141 8.150945 TCTCATCAAAGGGTGCTATTCTATAAC 58.849 37.037 0.00 0.00 0.00 1.89
1205 2246 3.992943 TGAAGACCATATCAACGGGTT 57.007 42.857 0.00 0.00 34.39 4.11
1314 2355 5.009210 CCCCAACTTTGATTTCACGTTTCTA 59.991 40.000 0.00 0.00 0.00 2.10
1380 2421 3.526534 TCCATTTCACATCGATAACGCA 58.473 40.909 0.00 0.00 39.58 5.24
1468 2509 2.224548 GGCCCGTAATAATCCAGCTTCT 60.225 50.000 0.00 0.00 0.00 2.85
1470 2511 3.744530 GCCCGTAATAATCCAGCTTCTGT 60.745 47.826 0.00 0.00 0.00 3.41
1541 2582 6.636454 AAATATCACCAGTTTCTACCCAGA 57.364 37.500 0.00 0.00 0.00 3.86
1714 3389 1.795768 TCTAGAGCTGTTTGGCGTTG 58.204 50.000 0.00 0.00 37.29 4.10
1759 3434 0.895530 TCGGACCGAGAAAGCAGAAT 59.104 50.000 13.88 0.00 0.00 2.40
1795 3470 7.290061 TGCATATTAGAACTCATTAAAGCCCT 58.710 34.615 0.00 0.00 0.00 5.19
1839 3514 1.589414 AGGAATGAGAGAACCCCCAG 58.411 55.000 0.00 0.00 0.00 4.45
1852 3527 7.347252 AGAGAACCCCCAGTAGAAAAATATTC 58.653 38.462 0.00 0.00 0.00 1.75
1907 3582 4.889409 TCCCATGCAATAGTCAAGAATTCC 59.111 41.667 0.65 0.00 0.00 3.01
1909 3584 6.064060 CCCATGCAATAGTCAAGAATTCCTA 58.936 40.000 0.65 0.00 0.00 2.94
1953 3628 5.940470 ACATGTTCTTCCTGAATACCTTGAC 59.060 40.000 0.00 0.00 36.99 3.18
1956 3631 4.720649 TCTTCCTGAATACCTTGACTCG 57.279 45.455 0.00 0.00 0.00 4.18
2070 3747 8.492673 TTCTCAGCAGATATTTCATAAAACGT 57.507 30.769 0.00 0.00 0.00 3.99
2114 3791 6.446781 AGTGATCAATTCTCGCATGAATTT 57.553 33.333 0.00 0.06 42.63 1.82
2138 3815 4.993705 AAGGATCCAGTAAGTCCAACAA 57.006 40.909 15.82 0.00 34.42 2.83
2196 3873 5.414360 CCCATAGTGACTCGGATGAATATG 58.586 45.833 2.73 0.00 0.00 1.78
2203 3880 2.365617 ACTCGGATGAATATGTCGGCTT 59.634 45.455 0.00 0.00 0.00 4.35
2204 3881 3.181465 ACTCGGATGAATATGTCGGCTTT 60.181 43.478 0.00 0.00 0.00 3.51
2220 3897 1.858458 GCTTTGAAAACTTGCGGTTCC 59.142 47.619 0.00 0.00 37.12 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 203 4.270008 CGGGGTAGAATTTGTGGATTCTT 58.730 43.478 5.55 0.00 42.24 2.52
249 251 0.037326 AGCGAGCGGAGATGAAAACA 60.037 50.000 0.00 0.00 0.00 2.83
286 288 4.222810 GGACCCATAAAAAGCAGGATTTGT 59.777 41.667 0.00 0.00 0.00 2.83
332 1369 6.894339 AACCGATAAACCAGAAAAAGATGT 57.106 33.333 0.00 0.00 0.00 3.06
387 1424 2.354704 CCTAATGGAGAAGTCGTTGGCA 60.355 50.000 0.00 0.00 34.57 4.92
426 1463 3.697166 TCCCCTCAACAAATAAAGGCTC 58.303 45.455 0.00 0.00 0.00 4.70
584 1624 6.120905 ACTACGATCTTTGGCTCTAGAACTA 58.879 40.000 0.00 0.00 0.00 2.24
670 1710 7.571428 GCCAAGAAATACTTAATGCTACGATCC 60.571 40.741 0.00 0.00 37.03 3.36
748 1788 5.602978 TGGGCTTTAAAAGGATTTGGTGTTA 59.397 36.000 0.00 0.00 39.02 2.41
763 1803 5.011635 GGAGAAATGGAAGTTTGGGCTTTAA 59.988 40.000 0.00 0.00 0.00 1.52
831 1871 4.202284 TGGTTCCTACTCACTTGTTACACC 60.202 45.833 0.00 0.00 0.00 4.16
850 1890 4.657814 ATTCATGGGTGTTCTACTGGTT 57.342 40.909 0.00 0.00 0.00 3.67
851 1891 4.657814 AATTCATGGGTGTTCTACTGGT 57.342 40.909 0.00 0.00 0.00 4.00
1101 2141 1.933853 CGGGGATCTGCTAAAGAAACG 59.066 52.381 0.00 0.00 38.79 3.60
1205 2246 3.439154 TGCCCTATTTGCAAGATGGAAA 58.561 40.909 13.10 0.00 41.75 3.13
1468 2509 4.859245 GCGAGCGAATCATCTTATATCACA 59.141 41.667 0.00 0.00 0.00 3.58
1470 2511 5.316327 AGCGAGCGAATCATCTTATATCA 57.684 39.130 0.00 0.00 0.00 2.15
1541 2582 4.675063 ATGGAGTTGTTAGGTTGGGATT 57.325 40.909 0.00 0.00 0.00 3.01
1714 3389 2.288948 TGCATTGTTGGAACTGGATTGC 60.289 45.455 0.00 0.00 0.00 3.56
1953 3628 3.999663 AGCAGGAAATTCTTTGTCTCGAG 59.000 43.478 5.93 5.93 0.00 4.04
1956 3631 3.505293 AGCAGCAGGAAATTCTTTGTCTC 59.495 43.478 0.00 0.00 0.00 3.36
2070 3747 5.780282 CACTTGTGGGGATCCATATAGAGTA 59.220 44.000 15.23 0.00 46.09 2.59
2076 3753 3.982730 TGATCACTTGTGGGGATCCATAT 59.017 43.478 15.23 0.00 46.09 1.78
2114 3791 5.338632 TGTTGGACTTACTGGATCCTTAGA 58.661 41.667 14.23 0.00 33.34 2.10
2138 3815 3.961480 TGACACGTCTGAAGGAATCAT 57.039 42.857 0.00 0.00 37.44 2.45
2196 3873 1.120437 CGCAAGTTTTCAAAGCCGAC 58.880 50.000 0.00 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.