Multiple sequence alignment - TraesCS6A01G184900

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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 TraesCS6A01G184900 chr6A 100.000 2198 0 0 1 2198 215597779 215599976 0.000000e+00 4060
1 TraesCS6A01G184900 chr3B 98.169 1420 13 1 1 1407 101916062 101914643 0.000000e+00 2466
2 TraesCS6A01G184900 chr3B 97.535 1420 22 1 1 1407 201531910 201530491 0.000000e+00 2416
3 TraesCS6A01G184900 chr3B 97.968 1132 15 6 1 1126 6002607 6001478 0.000000e+00 1956
4 TraesCS6A01G184900 chr5A 98.028 1420 15 1 1 1407 510135610 510137029 0.000000e+00 2455
5 TraesCS6A01G184900 chr3A 97.958 1420 16 1 1 1407 66012739 66014158 0.000000e+00 2449
6 TraesCS6A01G184900 chr3A 97.887 1420 17 1 1 1407 164859179 164860598 0.000000e+00 2444
7 TraesCS6A01G184900 chr6D 97.887 1420 17 1 1 1407 168262552 168261133 0.000000e+00 2444
8 TraesCS6A01G184900 chr6D 95.833 792 32 1 1407 2198 111505931 111505141 0.000000e+00 1279
9 TraesCS6A01G184900 chr5D 97.746 1420 19 1 1 1407 503223102 503221683 0.000000e+00 2433
10 TraesCS6A01G184900 chr5D 98.879 1070 11 1 1 1069 503233416 503232347 0.000000e+00 1908
11 TraesCS6A01G184900 chr5D 95.960 792 31 1 1407 2198 220994465 220993675 0.000000e+00 1284
12 TraesCS6A01G184900 chr1D 97.465 1420 23 1 1 1407 254393230 254394649 0.000000e+00 2410
13 TraesCS6A01G184900 chr1D 95.833 792 32 1 1407 2198 49779054 49779844 0.000000e+00 1279
14 TraesCS6A01G184900 chr4A 96.312 1410 49 2 1 1407 310743454 310742045 0.000000e+00 2313
15 TraesCS6A01G184900 chr1A 97.937 1309 14 1 112 1407 554517023 554515715 0.000000e+00 2255
16 TraesCS6A01G184900 chr7D 96.212 792 29 1 1407 2198 345595357 345594567 0.000000e+00 1295
17 TraesCS6A01G184900 chr7D 95.960 792 30 2 1407 2198 509936737 509937526 0.000000e+00 1284
18 TraesCS6A01G184900 chr7D 98.276 348 6 0 1060 1407 231576017 231575670 5.190000e-171 610
19 TraesCS6A01G184900 chr2D 96.212 792 29 1 1407 2198 572350762 572351552 0.000000e+00 1295
20 TraesCS6A01G184900 chr2D 95.839 793 31 2 1407 2198 473024343 473025134 0.000000e+00 1280
21 TraesCS6A01G184900 chr3D 96.081 791 30 1 1407 2197 449781284 449782073 0.000000e+00 1288
22 TraesCS6A01G184900 chr4D 95.833 792 32 1 1407 2198 48880952 48881742 0.000000e+00 1279
23 TraesCS6A01G184900 chrUn 98.276 348 6 0 1060 1407 441244639 441244292 5.190000e-171 610


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 TraesCS6A01G184900 chr6A 215597779 215599976 2197 False 4060 4060 100.000 1 2198 1 chr6A.!!$F1 2197
1 TraesCS6A01G184900 chr3B 101914643 101916062 1419 True 2466 2466 98.169 1 1407 1 chr3B.!!$R2 1406
2 TraesCS6A01G184900 chr3B 201530491 201531910 1419 True 2416 2416 97.535 1 1407 1 chr3B.!!$R3 1406
3 TraesCS6A01G184900 chr3B 6001478 6002607 1129 True 1956 1956 97.968 1 1126 1 chr3B.!!$R1 1125
4 TraesCS6A01G184900 chr5A 510135610 510137029 1419 False 2455 2455 98.028 1 1407 1 chr5A.!!$F1 1406
5 TraesCS6A01G184900 chr3A 66012739 66014158 1419 False 2449 2449 97.958 1 1407 1 chr3A.!!$F1 1406
6 TraesCS6A01G184900 chr3A 164859179 164860598 1419 False 2444 2444 97.887 1 1407 1 chr3A.!!$F2 1406
7 TraesCS6A01G184900 chr6D 168261133 168262552 1419 True 2444 2444 97.887 1 1407 1 chr6D.!!$R2 1406
8 TraesCS6A01G184900 chr6D 111505141 111505931 790 True 1279 1279 95.833 1407 2198 1 chr6D.!!$R1 791
9 TraesCS6A01G184900 chr5D 503221683 503223102 1419 True 2433 2433 97.746 1 1407 1 chr5D.!!$R2 1406
10 TraesCS6A01G184900 chr5D 503232347 503233416 1069 True 1908 1908 98.879 1 1069 1 chr5D.!!$R3 1068
11 TraesCS6A01G184900 chr5D 220993675 220994465 790 True 1284 1284 95.960 1407 2198 1 chr5D.!!$R1 791
12 TraesCS6A01G184900 chr1D 254393230 254394649 1419 False 2410 2410 97.465 1 1407 1 chr1D.!!$F2 1406
13 TraesCS6A01G184900 chr1D 49779054 49779844 790 False 1279 1279 95.833 1407 2198 1 chr1D.!!$F1 791
14 TraesCS6A01G184900 chr4A 310742045 310743454 1409 True 2313 2313 96.312 1 1407 1 chr4A.!!$R1 1406
15 TraesCS6A01G184900 chr1A 554515715 554517023 1308 True 2255 2255 97.937 112 1407 1 chr1A.!!$R1 1295
16 TraesCS6A01G184900 chr7D 345594567 345595357 790 True 1295 1295 96.212 1407 2198 1 chr7D.!!$R2 791
17 TraesCS6A01G184900 chr7D 509936737 509937526 789 False 1284 1284 95.960 1407 2198 1 chr7D.!!$F1 791
18 TraesCS6A01G184900 chr2D 572350762 572351552 790 False 1295 1295 96.212 1407 2198 1 chr2D.!!$F2 791
19 TraesCS6A01G184900 chr2D 473024343 473025134 791 False 1280 1280 95.839 1407 2198 1 chr2D.!!$F1 791
20 TraesCS6A01G184900 chr3D 449781284 449782073 789 False 1288 1288 96.081 1407 2197 1 chr3D.!!$F1 790
21 TraesCS6A01G184900 chr4D 48880952 48881742 790 False 1279 1279 95.833 1407 2198 1 chr4D.!!$F1 791

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
386 387 2.979678 TCCTCCACTAGCAGGTTTCTTT 59.02 45.455 2.09 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2114 0.534203 GTTCCGCTTCCAGTGACCAA 60.534 55.0 0.0 0.0 0.0 3.67 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
105 106 7.829725 TGCTATTACTCAAACAAGCATGAAAT 58.170 30.769 0.00 0.0 35.54 2.17
386 387 2.979678 TCCTCCACTAGCAGGTTTCTTT 59.020 45.455 2.09 0.0 0.00 2.52
699 700 7.070571 AGCTGCTAGGTCTATTTCTTAGTTCAT 59.929 37.037 0.00 0.0 0.00 2.57
1140 1156 3.092301 CTCAGGCCTATATGACCGATCA 58.908 50.000 3.98 0.0 39.83 2.92
1143 1159 5.269189 TCAGGCCTATATGACCGATCAATA 58.731 41.667 3.98 0.0 38.69 1.90
1252 1268 0.896923 TGCCTTGATGGTGAAATGGC 59.103 50.000 0.00 0.0 38.35 4.40
1479 1495 2.549563 CCTTGATGCACCGCTAGATGAT 60.550 50.000 0.00 0.0 0.00 2.45
1481 1497 1.688197 TGATGCACCGCTAGATGATGA 59.312 47.619 0.00 0.0 0.00 2.92
1708 1726 4.202461 ACAAGGACTTTGCCTACAAGATGA 60.202 41.667 0.00 0.0 40.59 2.92
1842 1860 4.822026 AGTCACTATCACCAAGTTACTGC 58.178 43.478 0.00 0.0 31.79 4.40
1859 1877 2.545526 ACTGCAACTTCGTGATGAACTG 59.454 45.455 0.00 0.0 31.87 3.16
2023 2041 6.717084 AGGGAACTTAAAGAAGAATGACAAGG 59.283 38.462 0.00 0.0 37.44 3.61
2065 2083 0.328258 GCCCAAAGCTAGACCCAAGA 59.672 55.000 0.00 0.0 38.99 3.02
2087 2105 5.770663 AGACTGAAACTGAGTGCTTCTACTA 59.229 40.000 0.00 0.0 0.00 1.82
2096 2114 4.705507 TGAGTGCTTCTACTACGAAGGAAT 59.294 41.667 0.00 0.0 41.90 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 3.802866 TGGACGAATATGCAAGCATACA 58.197 40.909 16.24 6.77 41.09 2.29
214 215 9.050601 CAAAAGTTCCTAGATTCATGGAGATAC 57.949 37.037 0.00 0.00 0.00 2.24
386 387 7.331026 CACACCAGAATAGATAGAGTTTTCCA 58.669 38.462 0.00 0.00 0.00 3.53
699 700 8.618240 TTTATTCCAGTTAGTAAGAGGGATCA 57.382 34.615 0.00 0.00 0.00 2.92
1140 1156 6.674419 AGGTGGAGTCTTGGAGTATTTCTATT 59.326 38.462 0.00 0.00 0.00 1.73
1143 1159 4.430441 AGGTGGAGTCTTGGAGTATTTCT 58.570 43.478 0.00 0.00 0.00 2.52
1252 1268 1.487482 TTTTGAGTCTCGCGTGTCTG 58.513 50.000 12.39 0.00 0.00 3.51
1363 1379 2.273449 CGCCAGGCCCAGATTTCT 59.727 61.111 5.63 0.00 0.00 2.52
1608 1626 6.072783 GCTCTTGGAACATCTTATATGCTTCC 60.073 42.308 0.00 0.00 39.30 3.46
1610 1628 6.485984 CAGCTCTTGGAACATCTTATATGCTT 59.514 38.462 0.00 0.00 39.30 3.91
1684 1702 4.164843 TCTTGTAGGCAAAGTCCTTGTT 57.835 40.909 0.00 0.00 37.36 2.83
1690 1708 4.579869 TCCTTCATCTTGTAGGCAAAGTC 58.420 43.478 0.00 0.00 35.22 3.01
1708 1726 3.840666 TCACTGGTTGAGCTATTCTCCTT 59.159 43.478 0.00 0.00 41.18 3.36
1842 1860 6.901887 GCATATTACAGTTCATCACGAAGTTG 59.098 38.462 0.00 0.00 41.61 3.16
1859 1877 6.371809 TTTTCGTCATCCCTTGCATATTAC 57.628 37.500 0.00 0.00 0.00 1.89
2007 2025 5.221322 GGCAACTTCCTTGTCATTCTTCTTT 60.221 40.000 0.00 0.00 34.29 2.52
2023 2041 1.815003 CTTCATGGGAGTGGCAACTTC 59.185 52.381 0.00 0.00 36.52 3.01
2065 2083 4.946478 AGTAGAAGCACTCAGTTTCAGT 57.054 40.909 0.00 0.00 39.64 3.41
2087 2105 1.697432 TCCAGTGACCAATTCCTTCGT 59.303 47.619 0.00 0.00 0.00 3.85
2096 2114 0.534203 GTTCCGCTTCCAGTGACCAA 60.534 55.000 0.00 0.00 0.00 3.67
2132 2150 4.018506 TCACTTTGCCATCCTTCTTATCCA 60.019 41.667 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.