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
TraesCS7B01G273200
chr7B
100.000
2589
0
0
1
2589
501321325
501318737
0.000000e+00
4782
1
TraesCS7B01G273200
chr7D
93.983
1878
63
21
1
1858
476759940
476758093
0.000000e+00
2796
2
TraesCS7B01G273200
chr7D
93.438
381
16
7
1
376
476777036
476776660
8.090000e-155
556
3
TraesCS7B01G273200
chr4B
99.045
733
7
0
1857
2589
661635436
661636168
0.000000e+00
1315
4
TraesCS7B01G273200
chr7A
99.042
731
7
0
1859
2589
317174179
317173449
0.000000e+00
1312
5
TraesCS7B01G273200
chr7A
82.824
1473
108
57
450
1847
519091633
519093035
0.000000e+00
1184
6
TraesCS7B01G273200
chr7A
89.738
458
30
11
6
453
519091144
519091594
1.040000e-158
569
7
TraesCS7B01G273200
chr5B
99.042
731
7
0
1859
2589
224614631
224613901
0.000000e+00
1312
8
TraesCS7B01G273200
chr5B
98.774
734
9
0
1856
2589
253176817
253177550
0.000000e+00
1306
9
TraesCS7B01G273200
chr5A
99.042
731
7
0
1859
2589
180307202
180307932
0.000000e+00
1312
10
TraesCS7B01G273200
chr4A
99.042
731
7
0
1859
2589
16029670
16028940
0.000000e+00
1312
11
TraesCS7B01G273200
chr4A
98.906
731
8
0
1859
2589
423443174
423442444
0.000000e+00
1306
12
TraesCS7B01G273200
chr6A
98.906
731
8
0
1859
2589
384878618
384879348
0.000000e+00
1306
13
TraesCS7B01G273200
chr2A
98.645
738
8
2
1852
2589
456651274
456650539
0.000000e+00
1306
14
TraesCS7B01G273200
chr4D
78.693
352
27
20
1460
1803
329666582
329666893
9.460000e-45
191
15
TraesCS7B01G273200
chr4D
79.137
278
36
12
518
790
329665291
329665551
3.430000e-39
172
16
TraesCS7B01G273200
chr4D
83.824
136
12
7
741
876
329665545
329665670
1.260000e-23
121
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
TraesCS7B01G273200
chr7B
501318737
501321325
2588
True
4782.0
4782
100.000
1
2589
1
chr7B.!!$R1
2588
1
TraesCS7B01G273200
chr7D
476758093
476759940
1847
True
2796.0
2796
93.983
1
1858
1
chr7D.!!$R1
1857
2
TraesCS7B01G273200
chr4B
661635436
661636168
732
False
1315.0
1315
99.045
1857
2589
1
chr4B.!!$F1
732
3
TraesCS7B01G273200
chr7A
317173449
317174179
730
True
1312.0
1312
99.042
1859
2589
1
chr7A.!!$R1
730
4
TraesCS7B01G273200
chr7A
519091144
519093035
1891
False
876.5
1184
86.281
6
1847
2
chr7A.!!$F1
1841
5
TraesCS7B01G273200
chr5B
224613901
224614631
730
True
1312.0
1312
99.042
1859
2589
1
chr5B.!!$R1
730
6
TraesCS7B01G273200
chr5B
253176817
253177550
733
False
1306.0
1306
98.774
1856
2589
1
chr5B.!!$F1
733
7
TraesCS7B01G273200
chr5A
180307202
180307932
730
False
1312.0
1312
99.042
1859
2589
1
chr5A.!!$F1
730
8
TraesCS7B01G273200
chr4A
16028940
16029670
730
True
1312.0
1312
99.042
1859
2589
1
chr4A.!!$R1
730
9
TraesCS7B01G273200
chr4A
423442444
423443174
730
True
1306.0
1306
98.906
1859
2589
1
chr4A.!!$R2
730
10
TraesCS7B01G273200
chr6A
384878618
384879348
730
False
1306.0
1306
98.906
1859
2589
1
chr6A.!!$F1
730
11
TraesCS7B01G273200
chr2A
456650539
456651274
735
True
1306.0
1306
98.645
1852
2589
1
chr2A.!!$R1
737
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.
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.