Multiple sequence alignment - TraesCS7A01G052700

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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 TraesCS7A01G052700 chr7A 100.000 3662 0 0 1 3662 25688173 25691834 0.000000e+00 6763.0
1 TraesCS7A01G052700 chr7A 92.855 2743 138 20 909 3609 25746244 25748970 0.000000e+00 3927.0
2 TraesCS7A01G052700 chr7A 88.470 3235 268 47 1 3191 37727569 37724396 0.000000e+00 3810.0
3 TraesCS7A01G052700 chr7A 89.924 397 30 6 3273 3662 37724329 37723936 1.520000e-138 503.0
4 TraesCS7A01G052700 chr7A 94.118 51 3 0 3193 3243 37724374 37724324 1.090000e-10 78.7
5 TraesCS7A01G052700 chr7D 92.238 2319 135 16 1380 3662 24942102 24944411 0.000000e+00 3243.0
6 TraesCS7A01G052700 chr7D 91.756 1031 76 6 325 1349 24940982 24942009 0.000000e+00 1424.0
7 TraesCS7A01G052700 chr4A 91.681 2332 151 22 1363 3662 708618148 708615828 0.000000e+00 3192.0
8 TraesCS7A01G052700 chr4A 97.143 35 1 0 836 870 611267196 611267162 3.950000e-05 60.2
9 TraesCS7A01G052700 chr3A 85.915 71 9 1 694 763 696235936 696236006 1.410000e-09 75.0


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 TraesCS7A01G052700 chr7A 25688173 25691834 3661 False 6763.0 6763 100.000000 1 3662 1 chr7A.!!$F1 3661
1 TraesCS7A01G052700 chr7A 25746244 25748970 2726 False 3927.0 3927 92.855000 909 3609 1 chr7A.!!$F2 2700
2 TraesCS7A01G052700 chr7A 37723936 37727569 3633 True 1463.9 3810 90.837333 1 3662 3 chr7A.!!$R1 3661
3 TraesCS7A01G052700 chr7D 24940982 24944411 3429 False 2333.5 3243 91.997000 325 3662 2 chr7D.!!$F1 3337
4 TraesCS7A01G052700 chr4A 708615828 708618148 2320 True 3192.0 3192 91.681000 1363 3662 1 chr4A.!!$R2 2299


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
259 266 0.249489 ATATGCAACGCCGAGGAGAC 60.249 55.000 0.0 0.0 0.00 3.36 F
1651 1754 1.078918 TCCTGCAACATCCTGCTCG 60.079 57.895 0.0 0.0 43.07 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1928 0.108377 ATCGTAACATCTGGCACGCA 60.108 50.0 0.00 0.0 34.50 5.24 R
3483 3634 0.395686 AAGAGCTGAGCTGCTGACAA 59.604 50.0 13.71 0.0 44.17 3.18 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)



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

AutoCloner maintained by Alex Coulton.