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
TraesCS1A01G092300
chr1A
100.000
2954
0
0
1
2954
84797676
84794723
0.000000e+00
5456.0
1
TraesCS1A01G092300
chr1A
94.860
1576
58
14
801
2368
85006766
85005206
0.000000e+00
2440.0
2
TraesCS1A01G092300
chr1A
87.066
518
36
16
786
1272
84056038
84056555
9.250000e-155
556.0
3
TraesCS1A01G092300
chr1A
81.450
593
56
30
8
591
85007601
85007054
1.260000e-118
436.0
4
TraesCS1A01G092300
chr1A
89.091
220
14
5
2185
2394
84622323
84622542
6.280000e-67
265.0
5
TraesCS1A01G092300
chr1A
88.636
220
15
5
2185
2394
84485125
84485344
2.920000e-65
259.0
6
TraesCS1A01G092300
chr1A
85.987
157
15
6
726
879
84621093
84621245
8.470000e-36
161.0
7
TraesCS1A01G092300
chr1A
82.474
97
10
6
786
879
84483941
84484033
8.780000e-11
78.7
8
TraesCS1A01G092300
chr1A
93.750
48
2
1
2503
2550
84485526
84485572
1.470000e-08
71.3
9
TraesCS1A01G092300
chr1A
93.750
48
2
1
2503
2550
84622727
84622773
1.470000e-08
71.3
10
TraesCS1A01G092300
chr4D
88.857
2441
150
62
569
2954
464798381
464796008
0.000000e+00
2889.0
11
TraesCS1A01G092300
chr1D
90.233
1720
92
23
726
2394
88282852
88281158
0.000000e+00
2176.0
12
TraesCS1A01G092300
chr1D
91.407
1443
66
15
1558
2953
88243854
88242423
0.000000e+00
1925.0
13
TraesCS1A01G092300
chr1D
91.628
1302
67
17
720
1991
87903381
87904670
0.000000e+00
1762.0
14
TraesCS1A01G092300
chr1D
91.034
948
62
11
732
1661
88208045
88208987
0.000000e+00
1258.0
15
TraesCS1A01G092300
chr1D
91.723
737
39
11
726
1444
88244584
88243852
0.000000e+00
1003.0
16
TraesCS1A01G092300
chr1D
86.872
617
60
10
1
611
88276213
88275612
0.000000e+00
671.0
17
TraesCS1A01G092300
chr1D
80.616
779
92
33
1
767
88283703
88282972
5.570000e-152
547.0
18
TraesCS1A01G092300
chr1D
85.965
228
11
13
2178
2394
88215804
88216021
1.070000e-54
224.0
19
TraesCS1A01G092300
chr1D
94.444
54
2
1
2342
2394
87905145
87905198
6.790000e-12
82.4
20
TraesCS1A01G092300
chr1B
89.263
1723
116
33
720
2391
141844702
141846406
0.000000e+00
2093.0
21
TraesCS1A01G092300
chr1B
84.179
2326
182
66
138
2394
142135322
142133114
0.000000e+00
2085.0
22
TraesCS1A01G092300
chr1B
92.587
1295
67
15
720
1989
142037213
142038503
0.000000e+00
1832.0
23
TraesCS1A01G092300
chr1B
92.046
1295
74
15
720
1989
142093473
142094763
0.000000e+00
1794.0
24
TraesCS1A01G092300
chr1B
91.470
1102
87
4
896
1991
142086341
142087441
0.000000e+00
1507.0
25
TraesCS1A01G092300
chr1B
90.847
590
30
6
2388
2954
142133063
142132475
0.000000e+00
769.0
26
TraesCS1A01G092300
chr1B
82.533
229
27
10
2178
2395
142102864
142103090
3.890000e-44
189.0
27
TraesCS1A01G092300
chr3B
93.983
964
58
0
1028
1991
535705558
535704595
0.000000e+00
1459.0
28
TraesCS1A01G092300
chr3B
83.111
225
14
15
2181
2394
535555350
535555139
1.810000e-42
183.0
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
TraesCS1A01G092300
chr1A
84794723
84797676
2953
True
5456.0
5456
100.0000
1
2954
1
chr1A.!!$R1
2953
1
TraesCS1A01G092300
chr1A
85005206
85007601
2395
True
1438.0
2440
88.1550
8
2368
2
chr1A.!!$R2
2360
2
TraesCS1A01G092300
chr1A
84056038
84056555
517
False
556.0
556
87.0660
786
1272
1
chr1A.!!$F1
486
3
TraesCS1A01G092300
chr4D
464796008
464798381
2373
True
2889.0
2889
88.8570
569
2954
1
chr4D.!!$R1
2385
4
TraesCS1A01G092300
chr1D
88242423
88244584
2161
True
1464.0
1925
91.5650
726
2953
2
chr1D.!!$R2
2227
5
TraesCS1A01G092300
chr1D
88281158
88283703
2545
True
1361.5
2176
85.4245
1
2394
2
chr1D.!!$R3
2393
6
TraesCS1A01G092300
chr1D
88208045
88208987
942
False
1258.0
1258
91.0340
732
1661
1
chr1D.!!$F1
929
7
TraesCS1A01G092300
chr1D
87903381
87905198
1817
False
922.2
1762
93.0360
720
2394
2
chr1D.!!$F3
1674
8
TraesCS1A01G092300
chr1D
88275612
88276213
601
True
671.0
671
86.8720
1
611
1
chr1D.!!$R1
610
9
TraesCS1A01G092300
chr1B
141844702
141846406
1704
False
2093.0
2093
89.2630
720
2391
1
chr1B.!!$F1
1671
10
TraesCS1A01G092300
chr1B
142037213
142038503
1290
False
1832.0
1832
92.5870
720
1989
1
chr1B.!!$F2
1269
11
TraesCS1A01G092300
chr1B
142093473
142094763
1290
False
1794.0
1794
92.0460
720
1989
1
chr1B.!!$F4
1269
12
TraesCS1A01G092300
chr1B
142086341
142087441
1100
False
1507.0
1507
91.4700
896
1991
1
chr1B.!!$F3
1095
13
TraesCS1A01G092300
chr1B
142132475
142135322
2847
True
1427.0
2085
87.5130
138
2954
2
chr1B.!!$R1
2816
14
TraesCS1A01G092300
chr3B
535704595
535705558
963
True
1459.0
1459
93.9830
1028
1991
1
chr3B.!!$R2
963
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.