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
TraesCS5D01G276000
chr5D
100.000
3486
0
0
1
3486
378821656
378818171
0.000000e+00
6438
1
TraesCS5D01G276000
chr2B
95.903
3490
130
8
1
3486
352036640
352040120
0.000000e+00
5640
2
TraesCS5D01G276000
chr2B
95.370
108
5
0
1
108
85868472
85868365
4.630000e-39
172
3
TraesCS5D01G276000
chr6B
95.757
3488
137
6
1
3486
628273441
628269963
0.000000e+00
5611
4
TraesCS5D01G276000
chr6B
98.000
150
3
0
3229
3378
360712037
360711888
9.600000e-66
261
5
TraesCS5D01G276000
chr6B
100.000
114
0
0
3373
3486
360712471
360712358
9.800000e-51
211
6
TraesCS5D01G276000
chr3B
95.300
3489
147
10
1
3486
355963559
355960085
0.000000e+00
5518
7
TraesCS5D01G276000
chr3B
95.737
3237
126
8
1
3234
402665454
402668681
0.000000e+00
5203
8
TraesCS5D01G276000
chr1B
96.753
3234
102
3
1
3231
425399402
425402635
0.000000e+00
5387
9
TraesCS5D01G276000
chr1B
95.269
3192
129
13
52
3234
555898136
555894958
0.000000e+00
5038
10
TraesCS5D01G276000
chr1B
99.333
150
1
0
3229
3378
112026348
112026497
4.430000e-69
272
11
TraesCS5D01G276000
chr1B
98.000
150
3
0
3229
3378
425402820
425402969
9.600000e-66
261
12
TraesCS5D01G276000
chr1B
99.123
114
1
0
3373
3486
425402387
425402500
4.560000e-49
206
13
TraesCS5D01G276000
chr7B
95.675
3237
127
9
1
3234
365271401
365268175
0.000000e+00
5190
14
TraesCS5D01G276000
chr7B
94.823
3187
148
10
56
3234
33969144
33972321
0.000000e+00
4955
15
TraesCS5D01G276000
chr7B
98.000
150
3
0
3229
3378
365267992
365267843
9.600000e-66
261
16
TraesCS5D01G276000
chr7B
99.123
114
1
0
3373
3486
214356694
214356807
4.560000e-49
206
17
TraesCS5D01G276000
chr4B
94.795
3189
154
8
50
3234
425954059
425950879
0.000000e+00
4959
18
TraesCS5D01G276000
chr4B
98.000
150
3
0
3229
3378
379331667
379331518
9.600000e-66
261
19
TraesCS5D01G276000
chr4B
99.123
114
1
0
3373
3486
379332104
379331991
4.560000e-49
206
20
TraesCS5D01G276000
chr4B
99.123
114
1
0
3373
3486
485280310
485280423
4.560000e-49
206
21
TraesCS5D01G276000
chr7D
98.000
150
3
0
3229
3378
341108938
341109087
9.600000e-66
261
22
TraesCS5D01G276000
chr3D
99.123
114
1
0
3373
3486
428374928
428375041
4.560000e-49
206
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
TraesCS5D01G276000
chr5D
378818171
378821656
3485
True
6438.000000
6438
100.000000
1
3486
1
chr5D.!!$R1
3485
1
TraesCS5D01G276000
chr2B
352036640
352040120
3480
False
5640.000000
5640
95.903000
1
3486
1
chr2B.!!$F1
3485
2
TraesCS5D01G276000
chr6B
628269963
628273441
3478
True
5611.000000
5611
95.757000
1
3486
1
chr6B.!!$R1
3485
3
TraesCS5D01G276000
chr6B
360711888
360712471
583
True
236.000000
261
99.000000
3229
3486
2
chr6B.!!$R2
257
4
TraesCS5D01G276000
chr3B
355960085
355963559
3474
True
5518.000000
5518
95.300000
1
3486
1
chr3B.!!$R1
3485
5
TraesCS5D01G276000
chr3B
402665454
402668681
3227
False
5203.000000
5203
95.737000
1
3234
1
chr3B.!!$F1
3233
6
TraesCS5D01G276000
chr1B
555894958
555898136
3178
True
5038.000000
5038
95.269000
52
3234
1
chr1B.!!$R1
3182
7
TraesCS5D01G276000
chr1B
425399402
425402969
3567
False
1951.333333
5387
97.958667
1
3486
3
chr1B.!!$F2
3485
8
TraesCS5D01G276000
chr7B
33969144
33972321
3177
False
4955.000000
4955
94.823000
56
3234
1
chr7B.!!$F1
3178
9
TraesCS5D01G276000
chr7B
365267843
365271401
3558
True
2725.500000
5190
96.837500
1
3378
2
chr7B.!!$R1
3377
10
TraesCS5D01G276000
chr4B
425950879
425954059
3180
True
4959.000000
4959
94.795000
50
3234
1
chr4B.!!$R1
3184
11
TraesCS5D01G276000
chr4B
379331518
379332104
586
True
233.500000
261
98.561500
3229
3486
2
chr4B.!!$R2
257
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.