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
TraesCS3B01G500300
chr3B
100.000
3172
0
0
1
3172
744590760
744593931
0.000000e+00
5858.0
1
TraesCS3B01G500300
chr3B
95.973
3203
60
18
1
3172
746856198
746853034
0.000000e+00
5136.0
2
TraesCS3B01G500300
chr3B
84.378
1197
138
28
1
1163
745203223
745202042
0.000000e+00
1129.0
3
TraesCS3B01G500300
chr3B
84.629
1158
128
31
1
1136
745540301
745541430
0.000000e+00
1107.0
4
TraesCS3B01G500300
chr3B
89.227
854
82
3
254
1098
746793772
746792920
0.000000e+00
1059.0
5
TraesCS3B01G500300
chr3B
88.631
862
90
4
1
856
745474688
745473829
0.000000e+00
1042.0
6
TraesCS3B01G500300
chr3B
88.235
833
92
4
1
830
744419687
744418858
0.000000e+00
990.0
7
TraesCS3B01G500300
chr3B
87.427
859
102
4
1
856
747493213
747494068
0.000000e+00
983.0
8
TraesCS3B01G500300
chr3B
89.446
578
51
5
1620
2191
746792905
746792332
0.000000e+00
721.0
9
TraesCS3B01G500300
chr3B
85.398
452
61
4
1736
2183
744339123
744338673
6.200000e-127
464.0
10
TraesCS3B01G500300
chr3B
83.463
514
69
8
1682
2180
746286471
746286983
6.200000e-127
464.0
11
TraesCS3B01G500300
chr3B
84.211
247
32
6
924
1163
745473740
745473494
1.900000e-57
233.0
12
TraesCS3B01G500300
chr3B
78.995
219
21
16
2824
3031
746853712
746853508
3.320000e-25
126.0
13
TraesCS3B01G500300
chr3B
77.778
207
28
13
2371
2565
746849093
746849293
9.300000e-21
111.0
14
TraesCS3B01G500300
chr3B
77.295
207
29
14
2371
2565
744597055
744596855
4.330000e-19
106.0
15
TraesCS3B01G500300
chr3B
89.655
58
6
0
2196
2253
744852436
744852379
1.220000e-09
75.0
16
TraesCS3B01G500300
chr3B
89.091
55
6
0
2199
2253
746295396
746295342
5.680000e-08
69.4
17
TraesCS3B01G500300
chr3D
92.072
1337
67
8
1
1316
560331311
560332629
0.000000e+00
1845.0
18
TraesCS3B01G500300
chr3D
93.970
879
27
4
1318
2191
560332722
560333579
0.000000e+00
1306.0
19
TraesCS3B01G500300
chr3D
87.805
1107
104
13
1
1098
560477972
560479056
0.000000e+00
1267.0
20
TraesCS3B01G500300
chr3D
84.027
1177
137
28
3
1133
560234937
560233766
0.000000e+00
1085.0
21
TraesCS3B01G500300
chr3D
87.239
862
104
3
1
856
560785697
560784836
0.000000e+00
977.0
22
TraesCS3B01G500300
chr3D
88.095
588
51
9
1617
2195
560479168
560479745
0.000000e+00
680.0
23
TraesCS3B01G500300
chr3D
94.545
330
17
1
2439
2768
560333839
560334167
2.820000e-140
508.0
24
TraesCS3B01G500300
chr3D
83.463
514
69
8
1682
2180
560553062
560553574
6.200000e-127
464.0
25
TraesCS3B01G500300
chr3D
90.521
211
19
1
2193
2403
560333629
560333838
8.670000e-71
278.0
26
TraesCS3B01G500300
chr3D
84.644
267
33
7
914
1173
560784653
560784388
3.140000e-65
259.0
27
TraesCS3B01G500300
chr3D
89.017
173
14
1
2374
2546
560334178
560334345
3.210000e-50
209.0
28
TraesCS3B01G500300
chr3D
82.745
255
23
10
2379
2628
560754904
560755142
1.150000e-49
207.0
29
TraesCS3B01G500300
chr3D
80.916
131
15
5
2824
2950
560333892
560334016
9.370000e-16
95.3
30
TraesCS3B01G500300
chr3D
79.389
131
19
5
2824
2947
560480046
560480175
5.640000e-13
86.1
31
TraesCS3B01G500300
chr3D
89.091
55
6
0
2199
2253
560556237
560556183
5.680000e-08
69.4
32
TraesCS3B01G500300
chr3A
87.311
859
103
4
1
856
696332784
696331929
0.000000e+00
977.0
33
TraesCS3B01G500300
chr3A
87.194
859
104
4
1
856
629087181
629088036
0.000000e+00
972.0
34
TraesCS3B01G500300
chr3A
80.668
838
120
22
341
1138
629019536
629018701
2.090000e-171
612.0
35
TraesCS3B01G500300
chr3A
80.024
841
121
24
341
1138
696270292
696269456
2.120000e-161
579.0
36
TraesCS3B01G500300
chr3A
86.192
449
57
4
1736
2180
696288811
696288364
6.150000e-132
481.0
37
TraesCS3B01G500300
chr3A
84.289
471
64
9
1707
2170
629057938
629058405
4.820000e-123
451.0
38
TraesCS3B01G500300
chr3A
87.054
224
28
1
940
1163
696476928
696476706
5.250000e-63
252.0
39
TraesCS3B01G500300
chr1A
94.545
55
3
0
1292
1346
547376775
547376829
5.640000e-13
86.1
40
TraesCS3B01G500300
chr1B
97.297
37
1
0
3068
3104
638893351
638893315
2.640000e-06
63.9
41
TraesCS3B01G500300
chr6D
100.000
31
0
0
1232
1262
467193792
467193762
1.230000e-04
58.4
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
TraesCS3B01G500300
chr3B
744590760
744593931
3171
False
5858.000000
5858
100.000000
1
3172
1
chr3B.!!$F1
3171
1
TraesCS3B01G500300
chr3B
746853034
746856198
3164
True
2631.000000
5136
87.484000
1
3172
2
chr3B.!!$R9
3171
2
TraesCS3B01G500300
chr3B
745202042
745203223
1181
True
1129.000000
1129
84.378000
1
1163
1
chr3B.!!$R5
1162
3
TraesCS3B01G500300
chr3B
745540301
745541430
1129
False
1107.000000
1107
84.629000
1
1136
1
chr3B.!!$F2
1135
4
TraesCS3B01G500300
chr3B
744418858
744419687
829
True
990.000000
990
88.235000
1
830
1
chr3B.!!$R2
829
5
TraesCS3B01G500300
chr3B
747493213
747494068
855
False
983.000000
983
87.427000
1
856
1
chr3B.!!$F5
855
6
TraesCS3B01G500300
chr3B
746792332
746793772
1440
True
890.000000
1059
89.336500
254
2191
2
chr3B.!!$R8
1937
7
TraesCS3B01G500300
chr3B
745473494
745474688
1194
True
637.500000
1042
86.421000
1
1163
2
chr3B.!!$R7
1162
8
TraesCS3B01G500300
chr3B
746286471
746286983
512
False
464.000000
464
83.463000
1682
2180
1
chr3B.!!$F3
498
9
TraesCS3B01G500300
chr3D
560233766
560234937
1171
True
1085.000000
1085
84.027000
3
1133
1
chr3D.!!$R1
1130
10
TraesCS3B01G500300
chr3D
560331311
560334345
3034
False
706.883333
1845
90.173500
1
2950
6
chr3D.!!$F3
2949
11
TraesCS3B01G500300
chr3D
560477972
560480175
2203
False
677.700000
1267
85.096333
1
2947
3
chr3D.!!$F4
2946
12
TraesCS3B01G500300
chr3D
560784388
560785697
1309
True
618.000000
977
85.941500
1
1173
2
chr3D.!!$R3
1172
13
TraesCS3B01G500300
chr3D
560553062
560553574
512
False
464.000000
464
83.463000
1682
2180
1
chr3D.!!$F1
498
14
TraesCS3B01G500300
chr3A
696331929
696332784
855
True
977.000000
977
87.311000
1
856
1
chr3A.!!$R4
855
15
TraesCS3B01G500300
chr3A
629087181
629088036
855
False
972.000000
972
87.194000
1
856
1
chr3A.!!$F2
855
16
TraesCS3B01G500300
chr3A
629018701
629019536
835
True
612.000000
612
80.668000
341
1138
1
chr3A.!!$R1
797
17
TraesCS3B01G500300
chr3A
696269456
696270292
836
True
579.000000
579
80.024000
341
1138
1
chr3A.!!$R2
797
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.