Multiple sequence alignment - TraesCS6A01G091900

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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 TraesCS6A01G091900 chr6A 100.000 2789 0 0 1 2789 60400228 60397440 0.000000e+00 5151
1 TraesCS6A01G091900 chr2A 98.459 2791 41 2 1 2789 36897455 36894665 0.000000e+00 4915
2 TraesCS6A01G091900 chr2A 97.677 2798 50 8 1 2789 705949689 705946898 0.000000e+00 4793
3 TraesCS6A01G091900 chr7A 98.244 2791 44 3 1 2789 419040178 419042965 0.000000e+00 4878
4 TraesCS6A01G091900 chr6B 85.784 2054 269 22 1 2040 664390530 664392574 0.000000e+00 2154
5 TraesCS6A01G091900 chr3A 86.054 1513 181 25 535 2031 99585233 99583735 0.000000e+00 1598
6 TraesCS6A01G091900 chr2B 80.576 278 41 8 2315 2589 859419 859686 4.710000e-48 202


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 TraesCS6A01G091900 chr6A 60397440 60400228 2788 True 5151 5151 100.000 1 2789 1 chr6A.!!$R1 2788
1 TraesCS6A01G091900 chr2A 36894665 36897455 2790 True 4915 4915 98.459 1 2789 1 chr2A.!!$R1 2788
2 TraesCS6A01G091900 chr2A 705946898 705949689 2791 True 4793 4793 97.677 1 2789 1 chr2A.!!$R2 2788
3 TraesCS6A01G091900 chr7A 419040178 419042965 2787 False 4878 4878 98.244 1 2789 1 chr7A.!!$F1 2788
4 TraesCS6A01G091900 chr6B 664390530 664392574 2044 False 2154 2154 85.784 1 2040 1 chr6B.!!$F1 2039
5 TraesCS6A01G091900 chr3A 99583735 99585233 1498 True 1598 1598 86.054 535 2031 1 chr3A.!!$R1 1496

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
238 241 0.521867 CGTGTTCGCCATGCAGATTG 60.522 55.0 0.0 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2053 1.879575 ACTGCTAATCACCCCTGCTA 58.12 50.0 0.0 0.0 0.0 3.49 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
27 28 9.865321 ATCATCCTTTGTGACTGAAAAATAATG 57.135 29.630 0.00 0.00 0.00 1.90
28 29 9.076781 TCATCCTTTGTGACTGAAAAATAATGA 57.923 29.630 0.00 0.00 0.00 2.57
31 32 9.912634 TCCTTTGTGACTGAAAAATAATGAATC 57.087 29.630 0.00 0.00 0.00 2.52
238 241 0.521867 CGTGTTCGCCATGCAGATTG 60.522 55.000 0.00 0.00 0.00 2.67
276 279 1.110442 CACTCCAGCACCAAACCAAA 58.890 50.000 0.00 0.00 0.00 3.28
480 483 3.810623 AGGTCTCCCTTTGTAATGGGTA 58.189 45.455 13.45 3.43 42.47 3.69
685 690 2.557056 GCAGCATGTGGATTATCAGCAT 59.443 45.455 0.00 0.00 39.31 3.79
816 821 0.744414 GGATGCGGTCTTTGCTGCTA 60.744 55.000 0.00 0.00 41.12 3.49
837 842 2.090775 ACAAAAGGGGAAGGATGTTGGT 60.091 45.455 0.00 0.00 0.00 3.67
1400 1406 2.760092 GGCAACAGGGATATGCAGAAAA 59.240 45.455 0.00 0.00 41.80 2.29
1505 1514 2.370519 TGATTTTCAGGGAAGACACGGA 59.629 45.455 0.00 0.00 0.00 4.69
1989 2001 8.519492 TTATTAAATTTGCAAGCTGTTCTCAC 57.481 30.769 0.00 0.00 0.00 3.51
2041 2053 7.927629 GTGGCATCATTCAAAATACCACATAAT 59.072 33.333 0.00 0.00 44.50 1.28
2378 2390 0.468226 ACTTGCAAGTCTCCGACCAA 59.532 50.000 26.36 0.00 32.86 3.67
2436 2448 3.701542 GTCATGAGATCACTGACCCTACA 59.298 47.826 0.00 0.00 34.55 2.74
2536 2548 7.904205 AGCAGTGTACTAGGTATTTTTACAGT 58.096 34.615 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.463930 AAATAATGAATTAGCTTCCCGATTCA 57.536 30.769 0.00 1.68 41.24 2.57
27 28 9.827411 GTAAATAATGAATTAGCTTCCCGATTC 57.173 33.333 0.00 0.00 32.49 2.52
28 29 9.574516 AGTAAATAATGAATTAGCTTCCCGATT 57.425 29.630 0.00 0.00 32.49 3.34
91 94 2.031012 CTGCAGAACCAGGCGTGA 59.969 61.111 8.42 0.00 0.00 4.35
238 241 2.573941 GGCAACAATCTGCATTCCTC 57.426 50.000 0.00 0.00 44.52 3.71
276 279 4.460382 CCTTGAAGATGTACCTGCAAACAT 59.540 41.667 8.33 8.33 39.00 2.71
480 483 3.437344 GGAGCTCTAGTAGGAGGGTCATT 60.437 52.174 14.64 0.00 34.21 2.57
685 690 5.328565 TGATGTCCATGTATTTTGGGTTGA 58.671 37.500 0.00 0.00 34.85 3.18
816 821 2.090775 ACCAACATCCTTCCCCTTTTGT 60.091 45.455 0.00 0.00 0.00 2.83
1147 1153 7.439381 AGACCATTTGAAGTCGAACTTAACTA 58.561 34.615 0.00 0.00 38.80 2.24
1505 1514 7.071196 TCCTTCCAAAGTGAGTAGCATATATGT 59.929 37.037 14.14 4.18 0.00 2.29
1989 2001 4.093703 TGGTCCGTATGCGAAACAATTAAG 59.906 41.667 4.21 0.00 41.33 1.85
2041 2053 1.879575 ACTGCTAATCACCCCTGCTA 58.120 50.000 0.00 0.00 0.00 3.49
2277 2289 8.947115 GTCACTATTGCCAAAATACTAGAAAGT 58.053 33.333 0.00 0.00 39.91 2.66
2378 2390 5.105310 ACACCGACTAGTCAGCTTGATAAAT 60.105 40.000 22.37 0.00 0.00 1.40
2436 2448 9.790344 TTGTTGGTGGATTTGATGAATTTTTAT 57.210 25.926 0.00 0.00 0.00 1.40
2536 2548 3.057596 GCTGCTGCAACACCTACAATTTA 60.058 43.478 11.11 0.00 39.41 1.40
2602 2617 6.908870 TCAGATCGTGAACTTATTCCATTG 57.091 37.500 0.00 0.00 33.49 2.82


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

AutoCloner maintained by Alex Coulton.