Multiple sequence alignment - TraesCS4B01G081300

Loading Multiple Alignment...

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 TraesCS4B01G081300 chr4B 100.000 2450 0 0 1 2450 78829610 78827161 0 4525
1 TraesCS4B01G081300 chr1B 94.237 2464 107 23 1 2450 106887645 106890087 0 3731
2 TraesCS4B01G081300 chr6B 92.110 2446 176 12 1 2440 459691961 459694395 0 3432
3 TraesCS4B01G081300 chr5B 90.269 2456 211 20 1 2450 547746192 547748625 0 3186
4 TraesCS4B01G081300 chr5B 90.269 2456 211 19 1 2450 547767243 547769676 0 3186
5 TraesCS4B01G081300 chr5B 90.228 2456 212 19 1 2450 547751734 547754167 0 3181
6 TraesCS4B01G081300 chr5B 90.187 2456 212 18 1 2450 547756796 547759228 0 3173


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 TraesCS4B01G081300 chr4B 78827161 78829610 2449 True 4525 4525 100.000 1 2450 1 chr4B.!!$R1 2449
1 TraesCS4B01G081300 chr1B 106887645 106890087 2442 False 3731 3731 94.237 1 2450 1 chr1B.!!$F1 2449
2 TraesCS4B01G081300 chr6B 459691961 459694395 2434 False 3432 3432 92.110 1 2440 1 chr6B.!!$F1 2439
3 TraesCS4B01G081300 chr5B 547767243 547769676 2433 False 3186 3186 90.269 1 2450 1 chr5B.!!$F1 2449
4 TraesCS4B01G081300 chr5B 547746192 547759228 13036 False 3180 3186 90.228 1 2450 3 chr5B.!!$F2 2449

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
691 692 1.33961 GCGAGGTAGTGATCTCAGCAT 59.66 52.381 0.0 0.0 34.49 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 7241 2.225019 CGCATATTCTCATCAAGCACCC 59.775 50.0 0.0 0.0 0.0 4.61 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
37 38 3.896888 TCAAAACCAGCATGTTCCATTCT 59.103 39.130 0.00 0.00 0.00 2.40
61 62 4.072131 GGGACAACAACATTTCAGAGCTA 58.928 43.478 0.00 0.00 0.00 3.32
156 157 6.304624 AGATGATGCAACCATTGTAGATCAT 58.695 36.000 6.44 0.00 36.85 2.45
168 169 6.073058 CCATTGTAGATCATATGGAAACCACG 60.073 42.308 2.13 0.00 35.80 4.94
419 420 1.375523 CACCGGTGGTTGCCTCTAC 60.376 63.158 27.57 0.00 31.02 2.59
691 692 1.339610 GCGAGGTAGTGATCTCAGCAT 59.660 52.381 0.00 0.00 34.49 3.79
710 711 4.660303 AGCATCCCTACCAGATCATGTTAA 59.340 41.667 0.00 0.00 0.00 2.01
965 966 8.264347 TCATTTACCTATTGTCATACAAGAGCA 58.736 33.333 8.54 0.00 43.83 4.26
1426 6969 2.408565 GTGACATCCCTTGGGATCCTA 58.591 52.381 17.71 1.47 0.00 2.94
1471 7014 1.607467 GAAGCAAGGGGGCACACAT 60.607 57.895 0.00 0.00 35.83 3.21
1489 7032 2.902486 ACATGAGGAAGAGTGAAGCTGA 59.098 45.455 0.00 0.00 0.00 4.26
1693 7241 6.980397 GCCCCACTGAATTTTATTTGACATAG 59.020 38.462 0.00 0.00 0.00 2.23
1717 7265 4.214971 GGTGCTTGATGAGAATATGCGAAT 59.785 41.667 0.00 0.00 0.00 3.34
1992 7541 5.425630 CAGACATGGAGAAGTGATGATTCA 58.574 41.667 0.00 0.00 0.00 2.57
2000 7549 8.634335 TGGAGAAGTGATGATTCATGTTTTTA 57.366 30.769 3.32 0.00 33.56 1.52
2278 7829 2.484947 GGGATCGGTGGTATGTTCCTTC 60.485 54.545 0.00 0.00 0.00 3.46
2297 7848 9.374838 GTTCCTTCGGTGAGACTAATAAAATAA 57.625 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.221771 CTCTGAAATGTTGTTGTCCCCA 58.778 45.455 0.00 0.00 0.00 4.96
156 157 2.181125 TCTGCTACCGTGGTTTCCATA 58.819 47.619 0.00 0.00 35.28 2.74
168 169 4.564406 CCATGAGGTATTGGATCTGCTACC 60.564 50.000 0.00 8.99 34.99 3.18
419 420 7.773224 TCTCTGAGATACTCTCTTTAACTGAGG 59.227 40.741 2.58 0.65 43.73 3.86
562 563 3.138304 CAACACGTGGGATCTTCTCAAA 58.862 45.455 21.57 0.00 0.00 2.69
563 564 2.766313 CAACACGTGGGATCTTCTCAA 58.234 47.619 21.57 0.00 0.00 3.02
691 692 4.411869 TGCATTAACATGATCTGGTAGGGA 59.588 41.667 0.00 0.00 31.07 4.20
710 711 3.138839 TGTCCCCATCTGTGAATATGCAT 59.861 43.478 3.79 3.79 0.00 3.96
945 946 6.239217 TCATGCTCTTGTATGACAATAGGT 57.761 37.500 6.80 0.00 39.71 3.08
965 966 8.212259 AGGATTAGATAAACCTGCTACATCAT 57.788 34.615 0.97 0.00 37.13 2.45
1426 6969 1.601171 GCCATGCTCTGACTCCACT 59.399 57.895 0.00 0.00 0.00 4.00
1471 7014 2.289320 GCTTCAGCTTCACTCTTCCTCA 60.289 50.000 0.00 0.00 38.21 3.86
1489 7032 2.687297 TCTCTATCCTCATGCCTGCTT 58.313 47.619 0.00 0.00 0.00 3.91
1693 7241 2.225019 CGCATATTCTCATCAAGCACCC 59.775 50.000 0.00 0.00 0.00 4.61
1717 7265 6.757237 AGTTTACATGGCATTCAACAATCAA 58.243 32.000 0.00 0.00 0.00 2.57
1794 7342 5.269991 AGTGTACTAGGGATTTGAGCACTA 58.730 41.667 0.00 0.00 33.60 2.74
1992 7541 9.638239 ATGAACAACGCATAAGAATAAAAACAT 57.362 25.926 0.00 0.00 0.00 2.71
2039 7588 9.780186 GTAGGTAGCCAGACTTATTTATTCATT 57.220 33.333 0.00 0.00 0.00 2.57
2040 7589 8.934697 TGTAGGTAGCCAGACTTATTTATTCAT 58.065 33.333 0.00 0.00 0.00 2.57
2041 7590 8.313944 TGTAGGTAGCCAGACTTATTTATTCA 57.686 34.615 0.00 0.00 0.00 2.57
2136 7685 9.233649 ACACCTGGTTCGACAATTATATTTTTA 57.766 29.630 0.00 0.00 0.00 1.52
2143 7692 6.126997 TGGTATACACCTGGTTCGACAATTAT 60.127 38.462 5.01 0.00 45.98 1.28
2232 7783 2.477245 ACATGGTATACACCTGGCTCA 58.523 47.619 5.01 0.00 45.98 4.26
2302 7853 9.311916 CCACTTATTGAATTTGAAAGAAACACA 57.688 29.630 0.00 0.00 0.00 3.72
2303 7854 9.313118 ACCACTTATTGAATTTGAAAGAAACAC 57.687 29.630 0.00 0.00 0.00 3.32
2310 7861 8.260818 TGGTTGAACCACTTATTGAATTTGAAA 58.739 29.630 14.05 0.00 44.79 2.69
2372 12984 5.860611 TGATCCCGAGAACAAAAAGAACTA 58.139 37.500 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.