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
TraesCS1A01G074000
chr1A
100.000
2948
0
0
1
2948
57641207
57638260
0.000000e+00
5445
1
TraesCS1A01G074000
chr1A
90.720
1541
129
8
1049
2583
57405806
57404274
0.000000e+00
2041
2
TraesCS1A01G074000
chr1A
82.073
1534
258
13
1059
2584
37512185
37510661
0.000000e+00
1293
3
TraesCS1A01G074000
chr1A
91.068
918
69
11
1
913
199940333
199939424
0.000000e+00
1229
4
TraesCS1A01G074000
chr1A
82.465
787
127
9
1097
1874
36188248
36187464
0.000000e+00
678
5
TraesCS1A01G074000
chr1A
83.840
724
100
13
1856
2573
36614129
36614841
0.000000e+00
673
6
TraesCS1A01G074000
chr1D
92.124
1676
118
10
916
2584
58764276
58762608
0.000000e+00
2351
7
TraesCS1A01G074000
chr1D
91.611
1645
114
10
959
2584
58628733
58627094
0.000000e+00
2252
8
TraesCS1A01G074000
chr1D
82.150
1535
240
25
1062
2583
58869887
58868374
0.000000e+00
1286
9
TraesCS1A01G074000
chr1D
82.270
846
136
9
1036
1871
50059264
50060105
0.000000e+00
719
10
TraesCS1A01G074000
chr1D
83.571
700
107
8
1889
2584
38367056
38366361
0.000000e+00
649
11
TraesCS1A01G074000
chr1D
83.357
697
113
3
1887
2582
36623637
36622943
2.480000e-180
641
12
TraesCS1A01G074000
chr1D
81.715
793
123
20
1088
1866
37964719
37963935
2.480000e-180
641
13
TraesCS1A01G074000
chr1D
83.051
708
112
6
1864
2569
37424787
37425488
1.150000e-178
636
14
TraesCS1A01G074000
chr1D
95.902
366
15
0
2583
2948
58761571
58761206
7.030000e-166
593
15
TraesCS1A01G074000
chr1B
92.101
1671
125
3
914
2584
94233360
94231697
0.000000e+00
2348
16
TraesCS1A01G074000
chr1B
82.333
1449
238
15
1062
2503
94327198
94325761
0.000000e+00
1242
17
TraesCS1A01G074000
chr1B
84.187
683
104
3
1904
2584
58115637
58114957
0.000000e+00
660
18
TraesCS1A01G074000
chr1B
93.817
372
17
1
2583
2948
94230702
94230331
3.320000e-154
555
19
TraesCS1A01G074000
chr2A
94.317
915
51
1
1
914
474686300
474687214
0.000000e+00
1400
20
TraesCS1A01G074000
chr2A
93.021
917
56
6
1
913
350187277
350186365
0.000000e+00
1332
21
TraesCS1A01G074000
chr2A
91.913
915
56
10
1
913
350179717
350178819
0.000000e+00
1264
22
TraesCS1A01G074000
chr2A
90.481
914
83
4
1
911
324739763
324740675
0.000000e+00
1203
23
TraesCS1A01G074000
chr2A
89.989
929
81
11
1
925
728223342
728222422
0.000000e+00
1190
24
TraesCS1A01G074000
chr2A
89.794
921
84
9
1
918
322057211
322058124
0.000000e+00
1171
25
TraesCS1A01G074000
chr6A
90.721
916
72
12
1
911
290137213
290136306
0.000000e+00
1208
26
TraesCS1A01G074000
chr3A
89.559
929
81
15
1
923
310419883
310420801
0.000000e+00
1164
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
TraesCS1A01G074000
chr1A
57638260
57641207
2947
True
5445.0
5445
100.000
1
2948
1
chr1A.!!$R4
2947
1
TraesCS1A01G074000
chr1A
57404274
57405806
1532
True
2041.0
2041
90.720
1049
2583
1
chr1A.!!$R3
1534
2
TraesCS1A01G074000
chr1A
37510661
37512185
1524
True
1293.0
1293
82.073
1059
2584
1
chr1A.!!$R2
1525
3
TraesCS1A01G074000
chr1A
199939424
199940333
909
True
1229.0
1229
91.068
1
913
1
chr1A.!!$R5
912
4
TraesCS1A01G074000
chr1A
36187464
36188248
784
True
678.0
678
82.465
1097
1874
1
chr1A.!!$R1
777
5
TraesCS1A01G074000
chr1A
36614129
36614841
712
False
673.0
673
83.840
1856
2573
1
chr1A.!!$F1
717
6
TraesCS1A01G074000
chr1D
58627094
58628733
1639
True
2252.0
2252
91.611
959
2584
1
chr1D.!!$R4
1625
7
TraesCS1A01G074000
chr1D
58761206
58764276
3070
True
1472.0
2351
94.013
916
2948
2
chr1D.!!$R6
2032
8
TraesCS1A01G074000
chr1D
58868374
58869887
1513
True
1286.0
1286
82.150
1062
2583
1
chr1D.!!$R5
1521
9
TraesCS1A01G074000
chr1D
50059264
50060105
841
False
719.0
719
82.270
1036
1871
1
chr1D.!!$F2
835
10
TraesCS1A01G074000
chr1D
38366361
38367056
695
True
649.0
649
83.571
1889
2584
1
chr1D.!!$R3
695
11
TraesCS1A01G074000
chr1D
36622943
36623637
694
True
641.0
641
83.357
1887
2582
1
chr1D.!!$R1
695
12
TraesCS1A01G074000
chr1D
37963935
37964719
784
True
641.0
641
81.715
1088
1866
1
chr1D.!!$R2
778
13
TraesCS1A01G074000
chr1D
37424787
37425488
701
False
636.0
636
83.051
1864
2569
1
chr1D.!!$F1
705
14
TraesCS1A01G074000
chr1B
94230331
94233360
3029
True
1451.5
2348
92.959
914
2948
2
chr1B.!!$R3
2034
15
TraesCS1A01G074000
chr1B
94325761
94327198
1437
True
1242.0
1242
82.333
1062
2503
1
chr1B.!!$R2
1441
16
TraesCS1A01G074000
chr1B
58114957
58115637
680
True
660.0
660
84.187
1904
2584
1
chr1B.!!$R1
680
17
TraesCS1A01G074000
chr2A
474686300
474687214
914
False
1400.0
1400
94.317
1
914
1
chr2A.!!$F3
913
18
TraesCS1A01G074000
chr2A
350186365
350187277
912
True
1332.0
1332
93.021
1
913
1
chr2A.!!$R2
912
19
TraesCS1A01G074000
chr2A
350178819
350179717
898
True
1264.0
1264
91.913
1
913
1
chr2A.!!$R1
912
20
TraesCS1A01G074000
chr2A
324739763
324740675
912
False
1203.0
1203
90.481
1
911
1
chr2A.!!$F2
910
21
TraesCS1A01G074000
chr2A
728222422
728223342
920
True
1190.0
1190
89.989
1
925
1
chr2A.!!$R3
924
22
TraesCS1A01G074000
chr2A
322057211
322058124
913
False
1171.0
1171
89.794
1
918
1
chr2A.!!$F1
917
23
TraesCS1A01G074000
chr6A
290136306
290137213
907
True
1208.0
1208
90.721
1
911
1
chr6A.!!$R1
910
24
TraesCS1A01G074000
chr3A
310419883
310420801
918
False
1164.0
1164
89.559
1
923
1
chr3A.!!$F1
922
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.