Multiple sequence alignment - TraesCS7A01G076100

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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 TraesCS7A01G076100 chr7A 100.000 2914 0 0 1 2914 41715620 41718533 0 5382
1 TraesCS7A01G076100 chr7A 98.456 2915 43 2 1 2914 41746056 41748969 0 5132
2 TraesCS7A01G076100 chr7A 98.148 2916 52 1 1 2914 41774560 41777475 0 5084
3 TraesCS7A01G076100 chr7D 95.087 2300 100 10 623 2914 42427393 42429687 0 3609
4 TraesCS7A01G076100 chr7D 93.313 2318 140 10 605 2914 42084222 42081912 0 3408
5 TraesCS7A01G076100 chr7D 93.063 2321 146 12 604 2914 42212801 42215116 0 3380
6 TraesCS7A01G076100 chr7D 92.682 2323 145 18 604 2914 41916834 41914525 0 3325
7 TraesCS7A01G076100 chr4A 94.378 2330 114 14 599 2914 649184241 649186567 0 3561
8 TraesCS7A01G076100 chrUn 94.327 2327 117 12 599 2914 250935573 250933251 0 3552
9 TraesCS7A01G076100 chr2B 92.500 2320 160 12 604 2914 783889047 783886733 0 3308
10 TraesCS7A01G076100 chr2B 94.196 603 32 3 1 601 64769986 64769385 0 917
11 TraesCS7A01G076100 chr5B 94.286 560 30 2 1 559 436803110 436802552 0 856
12 TraesCS7A01G076100 chr5B 89.517 601 47 5 1 600 611948487 611949072 0 747


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 TraesCS7A01G076100 chr7A 41715620 41718533 2913 False 5382 5382 100.000 1 2914 1 chr7A.!!$F1 2913
1 TraesCS7A01G076100 chr7A 41746056 41748969 2913 False 5132 5132 98.456 1 2914 1 chr7A.!!$F2 2913
2 TraesCS7A01G076100 chr7A 41774560 41777475 2915 False 5084 5084 98.148 1 2914 1 chr7A.!!$F3 2913
3 TraesCS7A01G076100 chr7D 42427393 42429687 2294 False 3609 3609 95.087 623 2914 1 chr7D.!!$F2 2291
4 TraesCS7A01G076100 chr7D 42081912 42084222 2310 True 3408 3408 93.313 605 2914 1 chr7D.!!$R2 2309
5 TraesCS7A01G076100 chr7D 42212801 42215116 2315 False 3380 3380 93.063 604 2914 1 chr7D.!!$F1 2310
6 TraesCS7A01G076100 chr7D 41914525 41916834 2309 True 3325 3325 92.682 604 2914 1 chr7D.!!$R1 2310
7 TraesCS7A01G076100 chr4A 649184241 649186567 2326 False 3561 3561 94.378 599 2914 1 chr4A.!!$F1 2315
8 TraesCS7A01G076100 chrUn 250933251 250935573 2322 True 3552 3552 94.327 599 2914 1 chrUn.!!$R1 2315
9 TraesCS7A01G076100 chr2B 783886733 783889047 2314 True 3308 3308 92.500 604 2914 1 chr2B.!!$R2 2310
10 TraesCS7A01G076100 chr2B 64769385 64769986 601 True 917 917 94.196 1 601 1 chr2B.!!$R1 600
11 TraesCS7A01G076100 chr5B 436802552 436803110 558 True 856 856 94.286 1 559 1 chr5B.!!$R1 558
12 TraesCS7A01G076100 chr5B 611948487 611949072 585 False 747 747 89.517 1 600 1 chr5B.!!$F1 599

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
573 575 0.179153 GCCTTGAGAGAAAATGGCGC 60.179 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2239 1.800681 GGATCGGCCGGTTTTTGAG 59.199 57.895 27.83 0.0 0.0 3.02 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
84 86 2.069776 CTGGGGAGCAGGACTGAAA 58.930 57.895 3.0 0.00 0.00 2.69
376 378 3.238441 GCGCCAAAAATTATTGTCACGA 58.762 40.909 0.0 0.00 0.00 4.35
403 405 0.869068 TGCACGGTTTCCATAACACG 59.131 50.000 0.0 0.00 0.00 4.49
461 463 1.145803 CACGGGGAAGAACGAAGAAC 58.854 55.000 0.0 0.00 0.00 3.01
573 575 0.179153 GCCTTGAGAGAAAATGGCGC 60.179 55.000 0.0 0.00 0.00 6.53
1156 1168 0.101399 CTACGATCGCCTCAAGCTGT 59.899 55.000 16.6 0.00 40.39 4.40
1173 1185 4.401925 AGCTGTATCTTGCAAAGGAGTTT 58.598 39.130 0.0 0.00 46.24 2.66
1279 1291 8.677300 ACTATGTTGAGCGTTTCAATATTCAAT 58.323 29.630 15.2 0.65 46.85 2.57
1412 1549 0.102844 CTTGTTGTGGCAAGTGGTGG 59.897 55.000 0.0 0.00 40.52 4.61
1618 1755 3.243501 TGTTATACGAAGCCCGGTATGTC 60.244 47.826 0.0 0.00 43.93 3.06
1744 1886 1.597742 CCACCATTAGAAGGATGCGG 58.402 55.000 0.0 0.00 0.00 5.69
1745 1887 0.947244 CACCATTAGAAGGATGCGGC 59.053 55.000 0.0 0.00 0.00 6.53
1944 2087 4.158209 TGTGGTTGCAGATTCATGTAATGG 59.842 41.667 0.0 0.00 46.73 3.16
2096 2239 2.107950 TGGGTCCAATGATCGTCAAC 57.892 50.000 0.0 0.00 0.00 3.18
2490 2641 3.355378 TGGTGAGAGCATGTTAAATGGG 58.645 45.455 0.0 0.00 0.00 4.00
2701 2852 2.356278 GCCTTCCATCACTGGGCA 59.644 61.111 0.0 0.00 43.34 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 3.159213 TGGACCATCAGCAAGAACAAT 57.841 42.857 0.00 0.00 0.00 2.71
211 213 5.529060 CACCTAAAATTATGAGGCCTCAGAC 59.471 44.000 37.03 12.07 43.61 3.51
298 300 0.179468 ACTGTGTAGTTTGTGGCGGT 59.821 50.000 0.00 0.00 31.66 5.68
376 378 0.031994 GGAAACCGTGCATGCTTTGT 59.968 50.000 20.33 9.87 0.00 2.83
583 585 2.624316 TCGTACTAGAGGCAAACACG 57.376 50.000 0.00 0.00 0.00 4.49
585 587 4.325028 TGTTTCGTACTAGAGGCAAACA 57.675 40.909 0.00 3.93 32.68 2.83
1133 1145 2.337749 CTTGAGGCGATCGTAGGCGT 62.338 60.000 17.81 0.70 39.49 5.68
1412 1549 7.663081 TCATTGGAATATTCTCTGCACTATTCC 59.337 37.037 14.95 11.49 45.11 3.01
1618 1755 8.999431 AGGTCAAAAATAATATATAGTGCGTGG 58.001 33.333 0.00 0.00 0.00 4.94
1944 2087 3.430236 CCCAACCGGATTAATTCCTTTGC 60.430 47.826 9.46 0.00 42.99 3.68
2096 2239 1.800681 GGATCGGCCGGTTTTTGAG 59.199 57.895 27.83 0.00 0.00 3.02
2682 2833 2.048603 GCCCAGTGATGGAAGGCAC 61.049 63.158 0.00 0.00 43.32 5.01
2701 2852 4.533707 TCTCATCCTTGATCTTGTTGAGGT 59.466 41.667 13.17 0.00 32.10 3.85


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

AutoCloner maintained by Alex Coulton.