Multiple sequence alignment - TraesCS4B01G146000

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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 TraesCS4B01G146000 chr4B 100.000 3203 0 0 1 3203 209083927 209080725 0 5915
1 TraesCS4B01G146000 chr7B 98.409 3205 49 2 1 3203 644461029 644464233 0 5635
2 TraesCS4B01G146000 chr7D 98.315 3205 50 4 1 3203 381961575 381958373 0 5616
3 TraesCS4B01G146000 chr7D 98.253 3205 52 4 1 3203 382062264 382065466 0 5605
4 TraesCS4B01G146000 chr6D 98.315 3205 50 4 1 3203 124529708 124532910 0 5616
5 TraesCS4B01G146000 chrUn 98.191 3207 53 4 1 3203 189404668 189407873 0 5596
6 TraesCS4B01G146000 chr1B 98.161 3208 54 4 1 3203 668811577 668808370 0 5592
7 TraesCS4B01G146000 chr3A 98.128 3205 55 5 1 3203 633104843 633108044 0 5581


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 TraesCS4B01G146000 chr4B 209080725 209083927 3202 True 5915 5915 100.000 1 3203 1 chr4B.!!$R1 3202
1 TraesCS4B01G146000 chr7B 644461029 644464233 3204 False 5635 5635 98.409 1 3203 1 chr7B.!!$F1 3202
2 TraesCS4B01G146000 chr7D 381958373 381961575 3202 True 5616 5616 98.315 1 3203 1 chr7D.!!$R1 3202
3 TraesCS4B01G146000 chr7D 382062264 382065466 3202 False 5605 5605 98.253 1 3203 1 chr7D.!!$F1 3202
4 TraesCS4B01G146000 chr6D 124529708 124532910 3202 False 5616 5616 98.315 1 3203 1 chr6D.!!$F1 3202
5 TraesCS4B01G146000 chrUn 189404668 189407873 3205 False 5596 5596 98.191 1 3203 1 chrUn.!!$F1 3202
6 TraesCS4B01G146000 chr1B 668808370 668811577 3207 True 5592 5592 98.161 1 3203 1 chr1B.!!$R1 3202
7 TraesCS4B01G146000 chr3A 633104843 633108044 3201 False 5581 5581 98.128 1 3203 1 chr3A.!!$F1 3202

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
321 322 0.688749 GGATTGGGGGCAGCATTCTT 60.689 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 2263 0.321996 GTTCCTGGTCCTGGTCAGAC 59.678 60.0 14.11 6.25 33.11 3.51 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
43 44 3.071747 GTCTTTCAAGTTCTCACCCTCCT 59.928 47.826 0.00 0.00 0.00 3.69
90 91 6.576662 ACTAGCTAGCTTTTATATCTCGCA 57.423 37.500 24.88 0.00 0.00 5.10
110 111 3.628032 GCAAATAGGGAGTTAAGGAGTGC 59.372 47.826 0.00 0.00 0.00 4.40
257 258 6.695713 GTGGTTTTTCATTTCTACAACAGGTC 59.304 38.462 0.00 0.00 0.00 3.85
321 322 0.688749 GGATTGGGGGCAGCATTCTT 60.689 55.000 0.00 0.00 0.00 2.52
556 558 5.537300 AGCTCTCGCTCTTATCCAATTTA 57.463 39.130 0.00 0.00 45.15 1.40
678 681 8.100791 TGACAATCTTAACCTACTTGCTTACAT 58.899 33.333 0.00 0.00 0.00 2.29
694 697 7.849804 TGCTTACATGATCCTTAAGAAACTC 57.150 36.000 3.36 0.00 0.00 3.01
1229 1234 8.560576 TCTAATTACAACGTATTAACCGCTAC 57.439 34.615 0.00 0.00 0.00 3.58
1230 1235 8.187480 TCTAATTACAACGTATTAACCGCTACA 58.813 33.333 0.00 0.00 0.00 2.74
1236 1241 2.480759 CGTATTAACCGCTACAGCACCT 60.481 50.000 1.61 0.00 42.21 4.00
1481 1491 1.429463 CAGTTGTACACTCCCTTCGC 58.571 55.000 0.00 0.00 30.92 4.70
1685 1695 6.274157 AGATGAAAAAGAGAGAGCTTCGTA 57.726 37.500 0.00 0.00 0.00 3.43
1690 1700 7.772166 TGAAAAAGAGAGAGCTTCGTATATCA 58.228 34.615 0.00 0.00 0.00 2.15
1772 1782 3.064207 CGAGTTCCGATCCTTTTGTTCA 58.936 45.455 0.00 0.00 41.76 3.18
1890 1900 2.182842 CGCCAGTGCTATGGGCTTC 61.183 63.158 9.43 0.00 45.53 3.86
1979 1989 0.793104 GCGGAAAAGAATGGAACGCG 60.793 55.000 3.53 3.53 36.14 6.01
2161 2171 1.141019 GGAGCGCTAATGGACACGA 59.859 57.895 11.50 0.00 0.00 4.35
2200 2210 2.727798 CGTGTCGTTCGTAATGGAAAGT 59.272 45.455 0.00 0.00 0.00 2.66
2238 2248 2.593436 CTTTGTTGGACCGCCGGT 60.593 61.111 9.43 9.43 39.44 5.28
2285 2295 4.703093 GGACCAGGAACCAATTCGAATTTA 59.297 41.667 20.56 0.00 35.48 1.40
2298 2308 7.377928 CCAATTCGAATTTAGATCTTGACATGC 59.622 37.037 20.56 0.00 0.00 4.06
2378 2388 2.520968 GGGTGGCTGGTGGTTTCT 59.479 61.111 0.00 0.00 0.00 2.52
2426 2436 1.410004 CCTCGGGTATTAGCCACAGA 58.590 55.000 12.21 1.05 34.89 3.41
2560 2571 2.296471 CTCCCGTTCATAGTTCCGCTAT 59.704 50.000 0.00 0.00 40.86 2.97
2610 2621 5.123936 GGCGGTTCTTCCTTCTAATTACAT 58.876 41.667 0.00 0.00 0.00 2.29
2823 2834 2.267642 CTGCCGGATTTCGTCCCA 59.732 61.111 5.05 0.00 44.77 4.37
2998 3009 5.389935 CCTCACAATCTTCAGTTTTACGCTC 60.390 44.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 5.014228 AGTTGCACTCCTTAACTCCCTATTT 59.986 40.000 0.00 0.00 29.12 1.40
140 141 7.432869 CATTGATTTACCTCCTCTAGAGAGTG 58.567 42.308 21.76 10.56 46.50 3.51
321 322 5.127845 AGCTAGCAGCAAGTCAAGTAATCTA 59.872 40.000 18.83 0.00 45.56 1.98
367 369 7.936847 TCTCAGACTTAAAGGTAAATGAAAGCA 59.063 33.333 0.00 0.00 0.00 3.91
493 495 4.251103 TGCTAGTGGAGGATTCAGACTA 57.749 45.455 0.00 0.00 0.00 2.59
678 681 6.688073 AAGTCCAGAGTTTCTTAAGGATCA 57.312 37.500 1.85 0.00 0.00 2.92
694 697 2.689983 ACAGAAAGGTGCAAAAGTCCAG 59.310 45.455 0.00 0.00 0.00 3.86
1414 1424 6.843333 TGGAGAGATAGAATGGAGTTCTTCAT 59.157 38.462 0.00 0.00 44.80 2.57
1481 1491 2.770164 ATCAACAAGGGTTCTCCGAG 57.230 50.000 0.00 0.00 41.52 4.63
1685 1695 5.237996 CCGTCAATCTGCTGTTCATTGATAT 59.762 40.000 8.69 0.00 38.48 1.63
1690 1700 3.005554 CTCCGTCAATCTGCTGTTCATT 58.994 45.455 0.00 0.00 0.00 2.57
1797 1807 4.381292 GGAACTGGATTTGATTCTGCAAGG 60.381 45.833 0.00 0.00 0.00 3.61
1890 1900 8.153479 TCATCATTTTTGATCTACATAACCCG 57.847 34.615 0.00 0.00 0.00 5.28
1962 1972 0.456142 GCCGCGTTCCATTCTTTTCC 60.456 55.000 4.92 0.00 0.00 3.13
1990 2000 2.498941 GGGATCCGACGCATCCAGA 61.499 63.158 19.26 0.00 41.68 3.86
2161 2171 3.080121 CTTCGCCTGCTCCCTCCT 61.080 66.667 0.00 0.00 0.00 3.69
2200 2210 2.490903 GAGGCGAAGTAGTGGTGTCTTA 59.509 50.000 0.00 0.00 0.00 2.10
2253 2263 0.321996 GTTCCTGGTCCTGGTCAGAC 59.678 60.000 14.11 6.25 33.11 3.51
2285 2295 1.003580 ACAACCGGCATGTCAAGATCT 59.996 47.619 0.00 0.00 0.00 2.75
2378 2388 1.208535 ACGCATTTTCTACGGGATCCA 59.791 47.619 15.23 0.00 0.00 3.41
2426 2436 8.095169 GGGGTAGAATTACTGAATGAATACGAT 58.905 37.037 0.00 0.00 0.00 3.73
2560 2571 6.446781 AAAATCTTCCTCGTGTATCGTCTA 57.553 37.500 0.00 0.00 40.80 2.59
2610 2621 8.250143 TGGTAAAAGAGAGTCATAGATATGCA 57.750 34.615 0.00 0.00 33.76 3.96
2627 2638 3.944015 CCTCCTGCTTCATCTGGTAAAAG 59.056 47.826 0.00 0.00 0.00 2.27
2679 2690 0.584876 GTACTTCGCACCACAACCAC 59.415 55.000 0.00 0.00 0.00 4.16
2689 2700 1.497991 GTGCACAAGAGTACTTCGCA 58.502 50.000 13.17 0.00 38.45 5.10
2775 2786 1.210478 GCTCTGAATAACCAGCCCAGA 59.790 52.381 0.00 0.00 34.28 3.86
2998 3009 4.455877 AGAACATTTCTTCCCTTAAGCGTG 59.544 41.667 0.00 0.00 36.36 5.34


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

AutoCloner maintained by Alex Coulton.