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
TraesCS5D01G525600
chr5D
100.000
2861
0
0
1
2861
543816184
543819044
0.000000e+00
5284.0
1
TraesCS5D01G525600
chr5D
88.652
1269
133
4
731
1998
543771681
543772939
0.000000e+00
1535.0
2
TraesCS5D01G525600
chr5D
82.302
1147
158
27
742
1868
543830351
543831472
0.000000e+00
952.0
3
TraesCS5D01G525600
chr5D
89.889
722
61
4
731
1451
543803359
543804069
0.000000e+00
918.0
4
TraesCS5D01G525600
chr5D
88.732
213
19
5
1855
2065
543777982
543778191
3.660000e-64
255.0
5
TraesCS5D01G525600
chr5D
90.164
122
11
1
525
645
543801021
543801142
1.060000e-34
158.0
6
TraesCS5D01G525600
chr4A
97.416
2864
58
6
1
2861
625283120
625280270
0.000000e+00
4865.0
7
TraesCS5D01G525600
chr4A
87.579
1272
142
11
731
1998
625372987
625371728
0.000000e+00
1459.0
8
TraesCS5D01G525600
chr4A
84.267
1017
148
8
855
1863
625368253
625367241
0.000000e+00
981.0
9
TraesCS5D01G525600
chr4A
89.474
722
71
4
731
1451
625322518
625321801
0.000000e+00
907.0
10
TraesCS5D01G525600
chr4A
87.093
767
72
12
1485
2229
625321803
625321042
0.000000e+00
843.0
11
TraesCS5D01G525600
chr4A
84.088
861
130
7
990
1848
625265214
625264359
0.000000e+00
824.0
12
TraesCS5D01G525600
chr4A
85.714
210
20
7
742
951
625265421
625265222
2.230000e-51
213.0
13
TraesCS5D01G525600
chr4A
83.938
193
26
3
1876
2063
625264286
625264094
2.260000e-41
180.0
14
TraesCS5D01G525600
chr5B
92.841
1718
76
12
398
2075
685692429
685690719
0.000000e+00
2447.0
15
TraesCS5D01G525600
chr5B
82.753
1148
154
27
742
1868
685658028
685656904
0.000000e+00
983.0
16
TraesCS5D01G525600
chr5B
92.090
177
13
1
861
1036
685608009
685608185
6.120000e-62
248.0
17
TraesCS5D01G525600
chr5B
86.310
168
14
6
233
397
384587699
384587538
1.050000e-39
174.0
18
TraesCS5D01G525600
chr5B
84.884
172
21
3
229
398
294096437
294096605
4.900000e-38
169.0
19
TraesCS5D01G525600
chr3D
86.905
168
16
4
233
398
498263640
498263803
1.750000e-42
183.0
20
TraesCS5D01G525600
chr2D
86.826
167
17
3
233
397
73402885
73403048
6.300000e-42
182.0
21
TraesCS5D01G525600
chr2D
84.571
175
25
2
224
397
367502174
367502001
3.790000e-39
172.0
22
TraesCS5D01G525600
chr2D
85.714
168
13
8
233
397
532176554
532176713
1.760000e-37
167.0
23
TraesCS5D01G525600
chr2B
85.380
171
20
4
233
401
540729104
540729271
3.790000e-39
172.0
24
TraesCS5D01G525600
chr4D
85.629
167
19
3
233
397
498049953
498050116
1.360000e-38
171.0
25
TraesCS5D01G525600
chr1B
82.927
123
19
2
63
184
369544982
369545103
3.010000e-20
110.0
26
TraesCS5D01G525600
chr1A
94.118
51
1
2
96
145
333501653
333501702
3.060000e-10
76.8
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
TraesCS5D01G525600
chr5D
543816184
543819044
2860
False
5284.000000
5284
100.0000
1
2861
1
chr5D.!!$F3
2860
1
TraesCS5D01G525600
chr5D
543771681
543772939
1258
False
1535.000000
1535
88.6520
731
1998
1
chr5D.!!$F1
1267
2
TraesCS5D01G525600
chr5D
543830351
543831472
1121
False
952.000000
952
82.3020
742
1868
1
chr5D.!!$F4
1126
3
TraesCS5D01G525600
chr5D
543801021
543804069
3048
False
538.000000
918
90.0265
525
1451
2
chr5D.!!$F5
926
4
TraesCS5D01G525600
chr4A
625280270
625283120
2850
True
4865.000000
4865
97.4160
1
2861
1
chr4A.!!$R1
2860
5
TraesCS5D01G525600
chr4A
625367241
625372987
5746
True
1220.000000
1459
85.9230
731
1998
2
chr4A.!!$R4
1267
6
TraesCS5D01G525600
chr4A
625321042
625322518
1476
True
875.000000
907
88.2835
731
2229
2
chr4A.!!$R3
1498
7
TraesCS5D01G525600
chr4A
625264094
625265421
1327
True
405.666667
824
84.5800
742
2063
3
chr4A.!!$R2
1321
8
TraesCS5D01G525600
chr5B
685690719
685692429
1710
True
2447.000000
2447
92.8410
398
2075
1
chr5B.!!$R3
1677
9
TraesCS5D01G525600
chr5B
685656904
685658028
1124
True
983.000000
983
82.7530
742
1868
1
chr5B.!!$R2
1126
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.