Multiple sequence alignment - TraesCS3A01G453400

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 TraesCS3A01G453400 chr3A 100.000 2515 0 0 1 2515 691692432 691694946 0 4645
1 TraesCS3A01G453400 chr3A 96.576 2541 55 12 1 2515 712370665 712373199 0 4181
2 TraesCS3A01G453400 chr5A 96.772 2540 54 11 1 2515 77893461 77890925 0 4211
3 TraesCS3A01G453400 chr4A 96.654 2540 60 8 1 2515 615419746 615422285 0 4196
4 TraesCS3A01G453400 chr4A 96.496 2540 64 8 1 2515 615396631 615399170 0 4174
5 TraesCS3A01G453400 chr6A 96.538 2542 61 10 1 2515 418607494 418604953 0 4181
6 TraesCS3A01G453400 chr6A 96.497 2541 62 10 1 2515 418581435 418583974 0 4174
7 TraesCS3A01G453400 chr6A 96.422 2543 63 11 1 2515 209775020 209772478 0 4167
8 TraesCS3A01G453400 chr6A 96.379 2541 65 11 1 2515 410857725 410860264 0 4157
9 TraesCS3A01G453400 chr1A 96.417 2540 65 9 1 2515 474209480 474212018 0 4163


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 TraesCS3A01G453400 chr3A 691692432 691694946 2514 False 4645 4645 100.000 1 2515 1 chr3A.!!$F1 2514
1 TraesCS3A01G453400 chr3A 712370665 712373199 2534 False 4181 4181 96.576 1 2515 1 chr3A.!!$F2 2514
2 TraesCS3A01G453400 chr5A 77890925 77893461 2536 True 4211 4211 96.772 1 2515 1 chr5A.!!$R1 2514
3 TraesCS3A01G453400 chr4A 615419746 615422285 2539 False 4196 4196 96.654 1 2515 1 chr4A.!!$F2 2514
4 TraesCS3A01G453400 chr4A 615396631 615399170 2539 False 4174 4174 96.496 1 2515 1 chr4A.!!$F1 2514
5 TraesCS3A01G453400 chr6A 418604953 418607494 2541 True 4181 4181 96.538 1 2515 1 chr6A.!!$R2 2514
6 TraesCS3A01G453400 chr6A 418581435 418583974 2539 False 4174 4174 96.497 1 2515 1 chr6A.!!$F2 2514
7 TraesCS3A01G453400 chr6A 209772478 209775020 2542 True 4167 4167 96.422 1 2515 1 chr6A.!!$R1 2514
8 TraesCS3A01G453400 chr6A 410857725 410860264 2539 False 4157 4157 96.379 1 2515 1 chr6A.!!$F1 2514
9 TraesCS3A01G453400 chr1A 474209480 474212018 2538 False 4163 4163 96.417 1 2515 1 chr1A.!!$F1 2514

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
137 138 0.184451 ACCTCCCGCGGAAGACTATA 59.816 55.000 30.73 0.0 0.0 1.31 F
1187 1196 1.271543 CCTCAAAGAGACATGGCACCA 60.272 52.381 0.00 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1247 1.635663 CCCTTGCTTTGTAGTCGCCG 61.636 60.000 0.0 0.0 0.00 6.46 R
2120 2131 3.519107 TGGTATTCCTGATGACTCTGCAA 59.481 43.478 0.0 0.0 34.23 4.08 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
136 137 1.076192 ACCTCCCGCGGAAGACTAT 60.076 57.895 30.73 0.0 0.00 2.12
137 138 0.184451 ACCTCCCGCGGAAGACTATA 59.816 55.000 30.73 0.0 0.00 1.31
273 274 5.187576 CCACACCCCATAACATCTCATTTTT 59.812 40.000 0.00 0.0 0.00 1.94
281 282 7.820872 CCCATAACATCTCATTTTTCTTTGCTT 59.179 33.333 0.00 0.0 0.00 3.91
412 415 7.112122 TCATACAGCTTATGTTTGGACAGAAT 58.888 34.615 12.59 0.0 39.96 2.40
872 881 5.982516 GCATACTTTTGTTCAAACATGGACA 59.017 36.000 0.00 0.0 38.95 4.02
1187 1196 1.271543 CCTCAAAGAGACATGGCACCA 60.272 52.381 0.00 0.0 0.00 4.17
1238 1247 2.866762 GTCATTTCCCGACTGAGTATGC 59.133 50.000 0.00 0.0 0.00 3.14
1397 1407 3.067180 TCACGTTACTCTTTTCCTCGTGT 59.933 43.478 12.92 0.0 44.42 4.49
1497 1507 0.790814 GGTCGTTGAGCTTCGGAAAG 59.209 55.000 0.00 0.0 35.47 2.62
1544 1554 3.210227 TGAAGATTTCAACAAGCGGTCA 58.790 40.909 0.00 0.0 36.59 4.02
1859 1870 2.028130 ACCGGTTTGATGCTTTGAACA 58.972 42.857 0.00 0.0 0.00 3.18
1866 1877 5.334879 GGTTTGATGCTTTGAACACGTCTAT 60.335 40.000 0.00 0.0 0.00 1.98
2145 2156 4.202295 GCAGAGTCATCAGGAATACCATGA 60.202 45.833 0.00 0.0 38.94 3.07
2297 2308 6.537355 ACAACTAGCATGGCATATTCAGTAT 58.463 36.000 0.00 0.0 0.00 2.12
2322 2357 7.403312 AAAACAGCATGGCATGTTTAGTATA 57.597 32.000 26.94 0.0 46.16 1.47
2391 2426 7.170277 TGCATACATCATGGCAGATTAAGTAT 58.830 34.615 0.00 0.0 34.97 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 216 1.884579 CAGCTCCTTCATGTGCTTGTT 59.115 47.619 0.00 0.00 33.03 2.83
216 217 1.072806 TCAGCTCCTTCATGTGCTTGT 59.927 47.619 0.00 0.00 33.03 3.16
350 353 5.464069 TGGAAGGATCATGCCTACTAAGTA 58.536 41.667 5.85 0.00 37.26 2.24
397 400 8.408043 AATGACTTTGATTCTGTCCAAACATA 57.592 30.769 0.00 0.00 34.13 2.29
412 415 2.162208 GCTCCGCATTGAATGACTTTGA 59.838 45.455 9.76 0.00 0.00 2.69
549 552 6.016024 ACACTGTAATGCATGATTGTCTTGTT 60.016 34.615 0.00 0.00 0.00 2.83
776 785 4.314961 TCAAATAAGTCAGTGTGCACGAT 58.685 39.130 13.13 0.00 36.20 3.73
777 786 3.723260 TCAAATAAGTCAGTGTGCACGA 58.277 40.909 13.13 0.00 36.20 4.35
863 872 6.403866 TGAAATAAAGTTGCTGTCCATGTT 57.596 33.333 0.00 0.00 0.00 2.71
872 881 4.770531 GGGGGTAGTTGAAATAAAGTTGCT 59.229 41.667 0.00 0.00 0.00 3.91
1187 1196 5.013079 TGGACCTTTGAGTGTTCATAGTGAT 59.987 40.000 0.00 0.00 32.44 3.06
1238 1247 1.635663 CCCTTGCTTTGTAGTCGCCG 61.636 60.000 0.00 0.00 0.00 6.46
1397 1407 2.429610 GTGAAAGCCATAGTCCGTCCTA 59.570 50.000 0.00 0.00 0.00 2.94
1408 1418 3.434319 CCAGCGCGTGAAAGCCAT 61.434 61.111 8.43 0.00 0.00 4.40
1514 1524 6.583806 GCTTGTTGAAATCTTCATTCGTCAAT 59.416 34.615 0.00 0.00 39.84 2.57
1544 1554 1.956170 CACAAACTCGCGTGCTCCT 60.956 57.895 5.77 0.00 0.00 3.69
1859 1870 7.960738 CCATCGTTTTTAAAACATCATAGACGT 59.039 33.333 18.81 0.00 0.00 4.34
1866 1877 7.225538 ACATTTGCCATCGTTTTTAAAACATCA 59.774 29.630 18.81 7.09 0.00 3.07
2120 2131 3.519107 TGGTATTCCTGATGACTCTGCAA 59.481 43.478 0.00 0.00 34.23 4.08
2297 2308 5.720371 ACTAAACATGCCATGCTGTTTTA 57.280 34.783 18.34 1.72 41.51 1.52


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

AutoCloner maintained by Alex Coulton.