Multiple sequence alignment - TraesCS6D01G090600

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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 TraesCS6D01G090600 chr6D 100.000 2288 0 0 1 2288 56319558 56321845 0.000000e+00 4226
1 TraesCS6D01G090600 chr6D 98.045 972 18 1 1318 2288 56327791 56328762 0.000000e+00 1688
2 TraesCS6D01G090600 chr6D 93.855 895 50 3 1 891 11696579 11695686 0.000000e+00 1343
3 TraesCS6D01G090600 chr6D 98.288 584 9 1 1706 2288 118368418 118369001 0.000000e+00 1022
4 TraesCS6D01G090600 chr6D 98.113 583 11 0 1706 2288 402328390 402328972 0.000000e+00 1016
5 TraesCS6D01G090600 chr6D 94.159 428 17 8 1287 1709 90384993 90385417 0.000000e+00 645
6 TraesCS6D01G090600 chr6D 89.021 419 31 14 1318 1730 68743042 68743451 2.620000e-139 505
7 TraesCS6D01G090600 chr6D 88.836 421 32 14 1316 1730 68736135 68736546 9.430000e-139 503
8 TraesCS6D01G090600 chr7D 94.033 1324 72 4 1 1318 501629515 501630837 0.000000e+00 2001
9 TraesCS6D01G090600 chr7A 93.976 1328 71 4 1 1320 25850548 25851874 0.000000e+00 2001
10 TraesCS6D01G090600 chr5D 93.707 1319 53 11 5 1318 353957353 353958646 0.000000e+00 1949
11 TraesCS6D01G090600 chr5D 98.288 584 9 1 1706 2288 493324016 493323433 0.000000e+00 1022
12 TraesCS6D01G090600 chr4D 93.500 1323 66 8 1 1317 460670001 460668693 0.000000e+00 1949
13 TraesCS6D01G090600 chr4D 93.750 400 17 7 1316 1710 353381514 353381118 5.440000e-166 593
14 TraesCS6D01G090600 chr3D 93.575 1323 56 10 1 1318 124068665 124067367 0.000000e+00 1945
15 TraesCS6D01G090600 chr3D 93.122 1323 66 10 1 1318 55163855 55165157 0.000000e+00 1916
16 TraesCS6D01G090600 chr3D 98.459 584 8 1 1706 2288 64681265 64681848 0.000000e+00 1027
17 TraesCS6D01G090600 chr3D 97.468 395 6 3 1319 1711 276248577 276248185 0.000000e+00 671
18 TraesCS6D01G090600 chr3D 97.222 396 7 3 1318 1711 276241579 276241186 0.000000e+00 667
19 TraesCS6D01G090600 chr3A 92.981 1325 85 3 1 1318 598875368 598874045 0.000000e+00 1925
20 TraesCS6D01G090600 chr3A 93.273 1219 74 5 101 1313 145634067 145635283 0.000000e+00 1790
21 TraesCS6D01G090600 chr3A 91.735 980 65 14 1319 2288 711637167 711638140 0.000000e+00 1347
22 TraesCS6D01G090600 chr3A 90.457 985 78 8 1318 2288 95593548 95594530 0.000000e+00 1284
23 TraesCS6D01G090600 chr5A 92.846 1328 85 6 1 1320 312260210 312258885 0.000000e+00 1917
24 TraesCS6D01G090600 chr1D 94.681 1222 57 6 101 1318 467504894 467506111 0.000000e+00 1890
25 TraesCS6D01G090600 chr1D 91.278 986 64 17 1319 2288 319090531 319089552 0.000000e+00 1325
26 TraesCS6D01G090600 chr1D 97.229 397 6 4 1318 1711 325633987 325633593 0.000000e+00 667
27 TraesCS6D01G090600 chr4B 86.456 982 93 34 1319 2270 662115699 662114728 0.000000e+00 1040
28 TraesCS6D01G090600 chr7B 91.337 404 28 6 1319 1717 636546960 636546559 1.550000e-151 545


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 TraesCS6D01G090600 chr6D 56319558 56321845 2287 False 4226 4226 100.000 1 2288 1 chr6D.!!$F1 2287
1 TraesCS6D01G090600 chr6D 56327791 56328762 971 False 1688 1688 98.045 1318 2288 1 chr6D.!!$F2 970
2 TraesCS6D01G090600 chr6D 11695686 11696579 893 True 1343 1343 93.855 1 891 1 chr6D.!!$R1 890
3 TraesCS6D01G090600 chr6D 118368418 118369001 583 False 1022 1022 98.288 1706 2288 1 chr6D.!!$F6 582
4 TraesCS6D01G090600 chr6D 402328390 402328972 582 False 1016 1016 98.113 1706 2288 1 chr6D.!!$F7 582
5 TraesCS6D01G090600 chr7D 501629515 501630837 1322 False 2001 2001 94.033 1 1318 1 chr7D.!!$F1 1317
6 TraesCS6D01G090600 chr7A 25850548 25851874 1326 False 2001 2001 93.976 1 1320 1 chr7A.!!$F1 1319
7 TraesCS6D01G090600 chr5D 353957353 353958646 1293 False 1949 1949 93.707 5 1318 1 chr5D.!!$F1 1313
8 TraesCS6D01G090600 chr5D 493323433 493324016 583 True 1022 1022 98.288 1706 2288 1 chr5D.!!$R1 582
9 TraesCS6D01G090600 chr4D 460668693 460670001 1308 True 1949 1949 93.500 1 1317 1 chr4D.!!$R2 1316
10 TraesCS6D01G090600 chr3D 124067367 124068665 1298 True 1945 1945 93.575 1 1318 1 chr3D.!!$R1 1317
11 TraesCS6D01G090600 chr3D 55163855 55165157 1302 False 1916 1916 93.122 1 1318 1 chr3D.!!$F1 1317
12 TraesCS6D01G090600 chr3D 64681265 64681848 583 False 1027 1027 98.459 1706 2288 1 chr3D.!!$F2 582
13 TraesCS6D01G090600 chr3A 598874045 598875368 1323 True 1925 1925 92.981 1 1318 1 chr3A.!!$R1 1317
14 TraesCS6D01G090600 chr3A 145634067 145635283 1216 False 1790 1790 93.273 101 1313 1 chr3A.!!$F2 1212
15 TraesCS6D01G090600 chr3A 711637167 711638140 973 False 1347 1347 91.735 1319 2288 1 chr3A.!!$F3 969
16 TraesCS6D01G090600 chr3A 95593548 95594530 982 False 1284 1284 90.457 1318 2288 1 chr3A.!!$F1 970
17 TraesCS6D01G090600 chr5A 312258885 312260210 1325 True 1917 1917 92.846 1 1320 1 chr5A.!!$R1 1319
18 TraesCS6D01G090600 chr1D 467504894 467506111 1217 False 1890 1890 94.681 101 1318 1 chr1D.!!$F1 1217
19 TraesCS6D01G090600 chr1D 319089552 319090531 979 True 1325 1325 91.278 1319 2288 1 chr1D.!!$R1 969
20 TraesCS6D01G090600 chr4B 662114728 662115699 971 True 1040 1040 86.456 1319 2270 1 chr4B.!!$R1 951

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
991 1019 0.098376 CCTTGCATCGAAGCTTGAGC 59.902 55.0 14.4 2.67 42.49 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2088 4.130286 TGCGGAAATCCAAAAGTTGTTT 57.87 36.364 0.0 0.0 35.14 2.83 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
53 54 3.114616 TCGTCGTCGTCGTCCTCC 61.115 66.667 11.41 0.00 38.33 4.30
73 74 1.022735 GCGGAGTCGAGGTTGATCTA 58.977 55.000 0.00 0.00 39.00 1.98
128 129 1.648467 GCATGTCCACCGCTTCTTCC 61.648 60.000 0.00 0.00 0.00 3.46
305 306 1.736126 CAGCGAATGATGTCAACTGCT 59.264 47.619 0.00 1.87 0.00 4.24
318 319 1.961180 AACTGCTATCGCGCCCTTCT 61.961 55.000 0.00 0.00 39.65 2.85
349 350 2.007360 ATCAGCGTCTTCAGCTCTTG 57.993 50.000 0.00 0.00 44.06 3.02
388 389 5.011090 AGCACTGCATTAGATTCGTTCTA 57.989 39.130 3.30 0.00 35.79 2.10
430 431 2.803155 TTCGAGCACACCTCCATGGC 62.803 60.000 6.96 0.00 40.22 4.40
431 432 2.352422 GAGCACACCTCCATGGCA 59.648 61.111 6.96 0.00 40.22 4.92
582 584 1.084866 TGAGAGAAGAGAGGGGGTGA 58.915 55.000 0.00 0.00 0.00 4.02
648 663 3.306641 GGAGAAGAGTGACAGTCATGCTT 60.307 47.826 16.49 16.49 0.00 3.91
652 667 4.825546 AGAGTGACAGTCATGCTTTTTG 57.174 40.909 6.51 0.00 0.00 2.44
715 741 1.949525 GCCATGAACTCTGTGTTGTGT 59.050 47.619 0.00 0.00 39.30 3.72
863 889 1.677637 GCCGAGGAAGACCCGAAGAT 61.678 60.000 0.00 0.00 40.87 2.40
925 952 1.890041 AACAAGCGCCGCAACTACA 60.890 52.632 13.36 0.00 0.00 2.74
991 1019 0.098376 CCTTGCATCGAAGCTTGAGC 59.902 55.000 14.40 2.67 42.49 4.26
1175 1203 2.700371 TCAAGATCGGCTACATGGTGAT 59.300 45.455 0.00 0.00 0.00 3.06
1219 1247 3.205784 CCCTCAAGGTCATCATCTTCC 57.794 52.381 0.00 0.00 0.00 3.46
1433 1471 2.034305 ACATACCCTTGTAGATCGCGAC 59.966 50.000 12.93 5.67 0.00 5.19
1613 1653 1.216444 GAGATCCAGCAGCACGACA 59.784 57.895 0.00 0.00 0.00 4.35
1616 1656 3.244281 ATCCAGCAGCACGACAGCA 62.244 57.895 0.00 0.00 36.85 4.41
1987 2063 1.137086 CATTCCGGAACTCCTCGTGAT 59.863 52.381 21.56 0.00 0.00 3.06
2012 2088 0.470080 GGATCTCATCCGGGACTCCA 60.470 60.000 0.00 0.00 40.13 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.586564 GATCAACCTCGACTCCGCG 60.587 63.158 0.00 0.00 35.37 6.46
67 68 1.671979 CCGTCGTACCTGGTAGATCA 58.328 55.000 6.84 0.00 0.00 2.92
115 116 1.219393 GAGGAGGAAGAAGCGGTGG 59.781 63.158 0.00 0.00 0.00 4.61
305 306 2.498941 CCCAGAGAAGGGCGCGATA 61.499 63.158 12.10 0.00 43.10 2.92
318 319 0.904865 ACGCTGATTCCTGACCCAGA 60.905 55.000 0.00 0.00 32.44 3.86
349 350 2.162408 GTGCTCATGAAGGCCACTAAAC 59.838 50.000 5.01 0.00 0.00 2.01
430 431 0.443869 CCGCACCAAGTTCGAGAATG 59.556 55.000 0.00 0.00 0.00 2.67
431 432 0.034896 ACCGCACCAAGTTCGAGAAT 59.965 50.000 0.00 0.00 0.00 2.40
538 539 0.121197 AACCTTCCTCCTCCCCATCA 59.879 55.000 0.00 0.00 0.00 3.07
582 584 1.229820 TCACCCTGCCCACCACTAT 60.230 57.895 0.00 0.00 0.00 2.12
648 663 8.023128 GCTAATTGAAGAGCATGTAGTTCAAAA 58.977 33.333 16.99 10.63 41.08 2.44
652 667 5.586243 TGGCTAATTGAAGAGCATGTAGTTC 59.414 40.000 4.54 0.00 40.64 3.01
715 741 3.635836 TGCACACAATTCATGGAGTCAAA 59.364 39.130 0.00 0.00 0.00 2.69
925 952 0.339859 TCCTCCTGATGGTAGTGGCT 59.660 55.000 0.00 0.00 34.23 4.75
951 978 3.055819 GGATGACCTTGCAGAAGTGAGTA 60.056 47.826 0.00 0.00 0.00 2.59
1050 1078 1.966451 GCCGGTGTTGTTCCTGAGG 60.966 63.158 1.90 0.00 0.00 3.86
1175 1203 0.687354 GGGAGTGAGGAGCTTGAACA 59.313 55.000 0.00 0.00 0.00 3.18
1219 1247 0.740868 ACCTCAATGCCATCGTCGTG 60.741 55.000 0.00 0.00 0.00 4.35
1433 1471 0.234884 GTTCACTTGAACGCTTCCGG 59.765 55.000 6.36 0.00 43.97 5.14
1613 1653 1.915078 GCTACCTCCACCACCATGCT 61.915 60.000 0.00 0.00 0.00 3.79
1616 1656 2.367202 CCGCTACCTCCACCACCAT 61.367 63.158 0.00 0.00 0.00 3.55
2012 2088 4.130286 TGCGGAAATCCAAAAGTTGTTT 57.870 36.364 0.00 0.00 35.14 2.83


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

AutoCloner maintained by Alex Coulton.