Multiple sequence alignment - TraesCS5B01G094500

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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 TraesCS5B01G094500 chr5B 100.000 2321 0 0 1 2321 124137448 124139768 0.000000e+00 4287.0
1 TraesCS5B01G094500 chr5B 97.948 2290 47 0 28 2317 124177879 124180168 0.000000e+00 3969.0
2 TraesCS5B01G094500 chr5B 95.911 2299 86 4 3 2301 124192470 124194760 0.000000e+00 3718.0
3 TraesCS5B01G094500 chr5B 92.128 1372 104 3 951 2320 600573412 600574781 0.000000e+00 1932.0
4 TraesCS5B01G094500 chr5B 87.352 253 29 2 481 733 316654314 316654065 1.050000e-73 287.0
5 TraesCS5B01G094500 chr5B 87.302 252 29 2 482 733 316663451 316663203 3.770000e-73 285.0
6 TraesCS5B01G094500 chr7B 92.841 1369 98 0 951 2319 654096798 654098166 0.000000e+00 1986.0
7 TraesCS5B01G094500 chr7B 92.841 1369 97 1 951 2319 654081388 654082755 0.000000e+00 1984.0
8 TraesCS5B01G094500 chr7B 87.059 85 9 2 147 230 126016237 126016320 6.830000e-16 95.3
9 TraesCS5B01G094500 chr1B 90.855 1345 122 1 977 2321 514380122 514381465 0.000000e+00 1801.0
10 TraesCS5B01G094500 chr1B 90.335 1345 129 1 977 2321 514436347 514437690 0.000000e+00 1762.0
11 TraesCS5B01G094500 chr1B 89.855 69 6 1 162 229 329454950 329455018 1.140000e-13 87.9
12 TraesCS5B01G094500 chrUn 90.037 1355 122 9 977 2321 55581437 55580086 0.000000e+00 1753.0
13 TraesCS5B01G094500 chrUn 92.798 1083 73 4 1243 2321 55591870 55590789 0.000000e+00 1563.0
14 TraesCS5B01G094500 chr3D 87.535 353 44 0 950 1302 183085530 183085178 2.150000e-110 409.0
15 TraesCS5B01G094500 chr3D 85.000 260 18 11 475 733 5366005 5365766 6.410000e-61 244.0
16 TraesCS5B01G094500 chr5D 90.119 253 25 0 481 733 473074387 473074639 1.720000e-86 329.0
17 TraesCS5B01G094500 chr5D 82.787 244 27 6 729 958 473074680 473074922 1.090000e-48 204.0
18 TraesCS5B01G094500 chr5D 90.141 142 12 2 11 151 473073421 473073561 1.420000e-42 183.0
19 TraesCS5B01G094500 chr6B 88.716 257 23 2 477 733 310799925 310800175 2.240000e-80 309.0
20 TraesCS5B01G094500 chr6B 89.744 156 16 0 729 884 310763966 310764121 1.410000e-47 200.0
21 TraesCS5B01G094500 chr6B 87.013 154 20 0 729 882 310800214 310800367 8.520000e-40 174.0
22 TraesCS5B01G094500 chr6B 80.081 246 34 6 729 960 310892045 310892289 3.970000e-38 169.0
23 TraesCS5B01G094500 chr6B 95.161 62 3 0 672 733 310763866 310763927 5.280000e-17 99.0
24 TraesCS5B01G094500 chr6B 85.714 84 10 2 147 229 372527034 372526952 1.140000e-13 87.9
25 TraesCS5B01G094500 chr6D 84.646 254 20 5 480 733 190433486 190433720 3.860000e-58 235.0
26 TraesCS5B01G094500 chr6D 89.103 156 16 1 3 158 381111359 381111513 2.350000e-45 193.0
27 TraesCS5B01G094500 chr7A 82.845 239 25 2 729 953 719996300 719996064 1.410000e-47 200.0
28 TraesCS5B01G094500 chr7A 92.941 85 5 1 649 733 719996422 719996339 3.130000e-24 122.0
29 TraesCS5B01G094500 chr3B 90.604 149 13 1 3 151 650836382 650836235 1.820000e-46 196.0
30 TraesCS5B01G094500 chr3B 83.453 139 22 1 3 141 776974174 776974037 6.730000e-26 128.0
31 TraesCS5B01G094500 chr2D 90.323 93 6 3 138 229 335706099 335706189 4.050000e-23 119.0
32 TraesCS5B01G094500 chr3A 94.643 56 3 0 678 733 56789283 56789338 1.140000e-13 87.9
33 TraesCS5B01G094500 chr3A 94.643 56 3 0 678 733 56803435 56803490 1.140000e-13 87.9


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 TraesCS5B01G094500 chr5B 124137448 124139768 2320 False 4287.000000 4287 100.000000 1 2321 1 chr5B.!!$F1 2320
1 TraesCS5B01G094500 chr5B 124177879 124180168 2289 False 3969.000000 3969 97.948000 28 2317 1 chr5B.!!$F2 2289
2 TraesCS5B01G094500 chr5B 124192470 124194760 2290 False 3718.000000 3718 95.911000 3 2301 1 chr5B.!!$F3 2298
3 TraesCS5B01G094500 chr5B 600573412 600574781 1369 False 1932.000000 1932 92.128000 951 2320 1 chr5B.!!$F4 1369
4 TraesCS5B01G094500 chr7B 654096798 654098166 1368 False 1986.000000 1986 92.841000 951 2319 1 chr7B.!!$F3 1368
5 TraesCS5B01G094500 chr7B 654081388 654082755 1367 False 1984.000000 1984 92.841000 951 2319 1 chr7B.!!$F2 1368
6 TraesCS5B01G094500 chr1B 514380122 514381465 1343 False 1801.000000 1801 90.855000 977 2321 1 chr1B.!!$F2 1344
7 TraesCS5B01G094500 chr1B 514436347 514437690 1343 False 1762.000000 1762 90.335000 977 2321 1 chr1B.!!$F3 1344
8 TraesCS5B01G094500 chrUn 55580086 55581437 1351 True 1753.000000 1753 90.037000 977 2321 1 chrUn.!!$R1 1344
9 TraesCS5B01G094500 chrUn 55590789 55591870 1081 True 1563.000000 1563 92.798000 1243 2321 1 chrUn.!!$R2 1078
10 TraesCS5B01G094500 chr5D 473073421 473074922 1501 False 238.666667 329 87.682333 11 958 3 chr5D.!!$F1 947

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
324 507 0.042131 AGAAGACCGGGGTATGTGGA 59.958 55.0 6.32 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 2145 0.251916 CCTCCAATGGCACCGACTTA 59.748 55.0 0.0 0.0 0.0 2.24 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
247 348 2.365635 GGCCAGCCAGGAGAGGTA 60.366 66.667 3.12 0.0 41.22 3.08
321 504 1.192428 GTGAGAAGACCGGGGTATGT 58.808 55.000 6.32 0.0 0.00 2.29
324 507 0.042131 AGAAGACCGGGGTATGTGGA 59.958 55.000 6.32 0.0 0.00 4.02
355 839 0.893270 CACCCCGTCCAAGCATGAAA 60.893 55.000 0.00 0.0 0.00 2.69
433 917 6.836242 TGGATGCCCTTGTTTATTTTTCTTT 58.164 32.000 0.00 0.0 0.00 2.52
506 1020 1.578215 ACAGGAGGAGAAGAGGGCTAT 59.422 52.381 0.00 0.0 0.00 2.97
576 1090 1.214367 CGGCAAACACAACTAGACGT 58.786 50.000 0.00 0.0 0.00 4.34
874 1433 3.458163 CCAAGGAGGAGCGCGGTA 61.458 66.667 12.41 0.0 41.22 4.02
1190 1763 0.882042 GAGCATGTAGGGATGGTGCG 60.882 60.000 0.00 0.0 40.54 5.34
1256 1833 3.529533 CCGTCATCTTCTTCATCAAGCT 58.470 45.455 0.00 0.0 0.00 3.74
1449 2026 2.124193 CGCCCATTGAGGATGCCA 60.124 61.111 0.00 0.0 41.22 4.92
1568 2145 1.066143 ACGCCCGTCATCTTCTTCATT 60.066 47.619 0.00 0.0 0.00 2.57
1593 2170 1.560505 GGTGCCATTGGAGGACAAAT 58.439 50.000 6.95 0.0 43.46 2.32
1643 2220 2.361610 CCACTTTGGATGGCGGCT 60.362 61.111 11.43 0.0 40.96 5.52
1768 2346 3.842923 CGGAGGCATGGAGCTCGT 61.843 66.667 7.83 0.0 44.79 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 1.187567 GGGTTGCCTGCTTGGATTGT 61.188 55.000 0.49 0.00 38.35 2.71
433 917 7.528036 GCCCCTGGTAAATTAAGAATGGAAAAA 60.528 37.037 0.00 0.00 0.00 1.94
440 924 4.231890 TCTGGCCCCTGGTAAATTAAGAAT 59.768 41.667 0.00 0.00 0.00 2.40
506 1020 1.310933 GCGTCTCCTTCTCCCGTACA 61.311 60.000 0.00 0.00 0.00 2.90
576 1090 1.457009 GGTAAAAACGCCACCTGCCA 61.457 55.000 0.00 0.00 36.24 4.92
874 1433 3.593794 GTATCCGTCGAGGGCGCT 61.594 66.667 19.36 1.38 41.52 5.92
1168 1741 0.691078 ACCATCCCTACATGCTCCGT 60.691 55.000 0.00 0.00 0.00 4.69
1256 1833 0.384309 CTTCGTACTCCATAGCGCCA 59.616 55.000 2.29 0.00 0.00 5.69
1449 2026 4.516698 CAGCTTGACAAAGTAGATGTTGGT 59.483 41.667 0.00 0.00 35.69 3.67
1568 2145 0.251916 CCTCCAATGGCACCGACTTA 59.748 55.000 0.00 0.00 0.00 2.24
1593 2170 1.663388 CGTTGTGAGCCTACACGCA 60.663 57.895 0.00 0.00 42.86 5.24
1643 2220 4.116328 CGTCTTGGCGAGCTCCGA 62.116 66.667 8.47 0.00 41.76 4.55
1768 2346 0.400213 GACTTGGTGGTGATGTCCCA 59.600 55.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.