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
TraesCS4A01G381200
chr4A
100.000
2871
0
0
1
2871
658896298
658899168
0.000000e+00
5302.0
1
TraesCS4A01G381200
chr4A
91.964
1008
53
18
911
1901
658343103
658344099
0.000000e+00
1387.0
2
TraesCS4A01G381200
chr4A
88.095
714
72
9
1420
2129
658108879
658108175
0.000000e+00
835.0
3
TraesCS4A01G381200
chr4A
87.955
714
73
9
1420
2129
658069899
658069195
0.000000e+00
830.0
4
TraesCS4A01G381200
chr4A
87.266
267
23
5
584
841
658342669
658342933
7.780000e-76
294.0
5
TraesCS4A01G381200
chr7A
88.132
2334
164
60
3
2262
47899192
47901486
0.000000e+00
2671.0
6
TraesCS4A01G381200
chr7A
89.778
450
46
0
1421
1870
47781102
47780653
6.900000e-161
577.0
7
TraesCS4A01G381200
chr7A
88.450
329
28
7
1874
2200
47780392
47780072
3.470000e-104
388.0
8
TraesCS4A01G381200
chr7A
93.333
75
4
1
2263
2337
47901800
47901873
3.020000e-20
110.0
9
TraesCS4A01G381200
chr7D
88.038
2232
168
56
165
2323
45702574
45704779
0.000000e+00
2551.0
10
TraesCS4A01G381200
chr7D
87.885
487
49
4
1715
2199
45605985
45605507
5.370000e-157
564.0
11
TraesCS4A01G381200
chr7D
91.803
61
4
1
839
898
45703242
45703302
1.830000e-12
84.2
12
TraesCS4A01G381200
chr6A
95.091
550
24
3
2324
2871
556298190
556297642
0.000000e+00
863.0
13
TraesCS4A01G381200
chr6A
94.374
551
27
4
2324
2871
457310981
457311530
0.000000e+00
843.0
14
TraesCS4A01G381200
chr6A
94.182
550
30
2
2324
2871
572769404
572769953
0.000000e+00
837.0
15
TraesCS4A01G381200
chr6B
94.255
557
28
4
2319
2871
591519597
591519041
0.000000e+00
848.0
16
TraesCS4A01G381200
chr6B
94.364
550
29
2
2324
2871
213156724
213156175
0.000000e+00
843.0
17
TraesCS4A01G381200
chr5D
93.907
558
31
3
2317
2871
384697693
384697136
0.000000e+00
839.0
18
TraesCS4A01G381200
chr7B
94.213
553
24
7
2323
2871
746727129
746726581
0.000000e+00
837.0
19
TraesCS4A01G381200
chr1D
94.182
550
28
2
2323
2871
462935622
462936168
0.000000e+00
835.0
20
TraesCS4A01G381200
chr3D
94.000
550
31
2
2324
2871
500829330
500828781
0.000000e+00
832.0
21
TraesCS4A01G381200
chr6D
87.127
536
58
6
1329
1857
9973289
9973820
5.290000e-167
597.0
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
TraesCS4A01G381200
chr4A
658896298
658899168
2870
False
5302.0
5302
100.0000
1
2871
1
chr4A.!!$F1
2870
1
TraesCS4A01G381200
chr4A
658342669
658344099
1430
False
840.5
1387
89.6150
584
1901
2
chr4A.!!$F2
1317
2
TraesCS4A01G381200
chr4A
658108175
658108879
704
True
835.0
835
88.0950
1420
2129
1
chr4A.!!$R2
709
3
TraesCS4A01G381200
chr4A
658069195
658069899
704
True
830.0
830
87.9550
1420
2129
1
chr4A.!!$R1
709
4
TraesCS4A01G381200
chr7A
47899192
47901873
2681
False
1390.5
2671
90.7325
3
2337
2
chr7A.!!$F1
2334
5
TraesCS4A01G381200
chr7A
47780072
47781102
1030
True
482.5
577
89.1140
1421
2200
2
chr7A.!!$R1
779
6
TraesCS4A01G381200
chr7D
45702574
45704779
2205
False
1317.6
2551
89.9205
165
2323
2
chr7D.!!$F1
2158
7
TraesCS4A01G381200
chr6A
556297642
556298190
548
True
863.0
863
95.0910
2324
2871
1
chr6A.!!$R1
547
8
TraesCS4A01G381200
chr6A
457310981
457311530
549
False
843.0
843
94.3740
2324
2871
1
chr6A.!!$F1
547
9
TraesCS4A01G381200
chr6A
572769404
572769953
549
False
837.0
837
94.1820
2324
2871
1
chr6A.!!$F2
547
10
TraesCS4A01G381200
chr6B
591519041
591519597
556
True
848.0
848
94.2550
2319
2871
1
chr6B.!!$R2
552
11
TraesCS4A01G381200
chr6B
213156175
213156724
549
True
843.0
843
94.3640
2324
2871
1
chr6B.!!$R1
547
12
TraesCS4A01G381200
chr5D
384697136
384697693
557
True
839.0
839
93.9070
2317
2871
1
chr5D.!!$R1
554
13
TraesCS4A01G381200
chr7B
746726581
746727129
548
True
837.0
837
94.2130
2323
2871
1
chr7B.!!$R1
548
14
TraesCS4A01G381200
chr1D
462935622
462936168
546
False
835.0
835
94.1820
2323
2871
1
chr1D.!!$F1
548
15
TraesCS4A01G381200
chr3D
500828781
500829330
549
True
832.0
832
94.0000
2324
2871
1
chr3D.!!$R1
547
16
TraesCS4A01G381200
chr6D
9973289
9973820
531
False
597.0
597
87.1270
1329
1857
1
chr6D.!!$F1
528
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.