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
TraesCS4B01G146400
chr4B
100.000
2303
0
0
1
2303
209117175
209114873
0.000000e+00
4253
1
TraesCS4B01G146400
chr4B
97.509
2248
44
1
68
2303
495577652
495579899
0.000000e+00
3831
2
TraesCS4B01G146400
chr2B
97.999
2249
32
2
68
2303
449208733
449210981
0.000000e+00
3892
3
TraesCS4B01G146400
chr2B
97.865
2248
36
1
68
2303
234530565
234532812
0.000000e+00
3875
4
TraesCS4B01G146400
chr3A
97.865
2248
36
1
68
2303
495091945
495094192
0.000000e+00
3875
5
TraesCS4B01G146400
chr3A
98.571
70
1
0
1
70
495091811
495091880
8.640000e-25
124
6
TraesCS4B01G146400
chr7A
97.575
2268
39
5
51
2303
60220151
60222417
0.000000e+00
3869
7
TraesCS4B01G146400
chr3B
97.777
2249
37
2
68
2303
6000171
6002419
0.000000e+00
3864
8
TraesCS4B01G146400
chr3B
98.751
881
11
0
1423
2303
101914993
101915873
0.000000e+00
1567
9
TraesCS4B01G146400
chr1B
97.374
2247
47
1
68
2302
619184736
619186982
0.000000e+00
3812
10
TraesCS4B01G146400
chr2D
95.687
2249
89
5
61
2303
377991109
377988863
0.000000e+00
3609
11
TraesCS4B01G146400
chr2D
98.571
70
1
0
1
70
18022931
18022862
8.640000e-25
124
12
TraesCS4B01G146400
chrUn
97.433
1714
31
2
68
1768
231559555
231561268
0.000000e+00
2909
13
TraesCS4B01G146400
chrUn
97.791
1313
17
1
1003
2303
403938465
403937153
0.000000e+00
2254
14
TraesCS4B01G146400
chrUn
98.571
70
1
0
1
70
231559421
231559490
8.640000e-25
124
15
TraesCS4B01G146400
chrUn
98.571
70
1
0
1
70
273328706
273328637
8.640000e-25
124
16
TraesCS4B01G146400
chr7D
97.371
1141
29
1
1163
2303
307137134
307138273
0.000000e+00
1940
17
TraesCS4B01G146400
chr7D
98.571
70
1
0
1
70
6942803
6942734
8.640000e-25
124
18
TraesCS4B01G146400
chr7D
98.571
70
1
0
1
70
307131317
307131386
8.640000e-25
124
19
TraesCS4B01G146400
chr6D
98.571
70
1
0
1
70
458917617
458917686
8.640000e-25
124
20
TraesCS4B01G146400
chr6B
98.571
70
1
0
1
70
311356762
311356693
8.640000e-25
124
21
TraesCS4B01G146400
chr3D
98.571
70
1
0
1
70
48694895
48694826
8.640000e-25
124
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
TraesCS4B01G146400
chr4B
209114873
209117175
2302
True
4253.0
4253
100.000
1
2303
1
chr4B.!!$R1
2302
1
TraesCS4B01G146400
chr4B
495577652
495579899
2247
False
3831.0
3831
97.509
68
2303
1
chr4B.!!$F1
2235
2
TraesCS4B01G146400
chr2B
449208733
449210981
2248
False
3892.0
3892
97.999
68
2303
1
chr2B.!!$F2
2235
3
TraesCS4B01G146400
chr2B
234530565
234532812
2247
False
3875.0
3875
97.865
68
2303
1
chr2B.!!$F1
2235
4
TraesCS4B01G146400
chr3A
495091811
495094192
2381
False
1999.5
3875
98.218
1
2303
2
chr3A.!!$F1
2302
5
TraesCS4B01G146400
chr7A
60220151
60222417
2266
False
3869.0
3869
97.575
51
2303
1
chr7A.!!$F1
2252
6
TraesCS4B01G146400
chr3B
6000171
6002419
2248
False
3864.0
3864
97.777
68
2303
1
chr3B.!!$F1
2235
7
TraesCS4B01G146400
chr3B
101914993
101915873
880
False
1567.0
1567
98.751
1423
2303
1
chr3B.!!$F2
880
8
TraesCS4B01G146400
chr1B
619184736
619186982
2246
False
3812.0
3812
97.374
68
2302
1
chr1B.!!$F1
2234
9
TraesCS4B01G146400
chr2D
377988863
377991109
2246
True
3609.0
3609
95.687
61
2303
1
chr2D.!!$R2
2242
10
TraesCS4B01G146400
chrUn
403937153
403938465
1312
True
2254.0
2254
97.791
1003
2303
1
chrUn.!!$R2
1300
11
TraesCS4B01G146400
chrUn
231559421
231561268
1847
False
1516.5
2909
98.002
1
1768
2
chrUn.!!$F1
1767
12
TraesCS4B01G146400
chr7D
307137134
307138273
1139
False
1940.0
1940
97.371
1163
2303
1
chr7D.!!$F2
1140
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.