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
TraesCS6A01G110900
chr6A
100.000
6246
0
0
1
6246
80058486
80052241
0.000000e+00
11535
1
TraesCS6A01G110900
chr6A
96.524
5150
151
16
953
6088
582863693
582858558
0.000000e+00
8493
2
TraesCS6A01G110900
chr6A
96.485
4837
133
16
950
5771
557899233
557904047
0.000000e+00
7956
3
TraesCS6A01G110900
chr6A
98.101
316
6
0
5770
6085
557905918
557906233
9.150000e-153
551
4
TraesCS6A01G110900
chr6A
97.605
167
3
1
6081
6246
557908339
557908505
1.020000e-72
285
5
TraesCS6A01G110900
chr7A
96.575
6278
158
24
1
6246
620444439
620438187
0.000000e+00
10349
6
TraesCS6A01G110900
chr7A
95.861
6282
172
29
1
6246
548012772
548019001
0.000000e+00
10080
7
TraesCS6A01G110900
chr7A
96.761
5311
138
16
950
6246
708405552
708400262
0.000000e+00
8824
8
TraesCS6A01G110900
chr7A
94.957
932
47
0
3
934
184072546
184073477
0.000000e+00
1461
9
TraesCS6A01G110900
chr7A
95.312
320
13
2
5770
6088
267448261
267447943
2.010000e-139
507
10
TraesCS6A01G110900
chr7A
98.193
166
3
0
6081
6246
267447202
267447037
2.200000e-74
291
11
TraesCS6A01G110900
chr1A
96.461
6104
157
27
1
6088
57988872
57982812
0.000000e+00
10021
12
TraesCS6A01G110900
chr1A
98.204
167
2
1
6081
6246
28821920
28821754
2.200000e-74
291
13
TraesCS6A01G110900
chr1A
97.590
166
4
0
6081
6246
57982019
57981854
1.020000e-72
285
14
TraesCS6A01G110900
chr3A
96.871
5146
130
14
950
6085
724442837
724447961
0.000000e+00
8582
15
TraesCS6A01G110900
chr3A
96.757
5149
150
11
950
6088
15651082
15645941
0.000000e+00
8567
16
TraesCS6A01G110900
chr3A
96.296
945
34
1
1
945
31887607
31888550
0.000000e+00
1550
17
TraesCS6A01G110900
chr3A
97.590
166
4
0
6081
6246
745159946
745160111
1.020000e-72
285
18
TraesCS6A01G110900
chr4A
96.325
5089
139
18
696
5771
31823989
31818936
0.000000e+00
8318
19
TraesCS6A01G110900
chr4A
97.152
316
9
0
5770
6085
573630164
573630479
9.220000e-148
534
20
TraesCS6A01G110900
chr4A
94.318
88
4
1
950
1036
594984647
594984560
3.930000e-27
134
21
TraesCS6A01G110900
chr1D
96.684
935
28
3
1
934
259729972
259730904
0.000000e+00
1552
22
TraesCS6A01G110900
chr1D
95.824
934
37
1
1
934
8588657
8589588
0.000000e+00
1507
23
TraesCS6A01G110900
chrUn
95.838
937
39
0
1
937
70481048
70480112
0.000000e+00
1515
24
TraesCS6A01G110900
chr6D
95.624
937
36
1
1
937
43980096
43979165
0.000000e+00
1498
25
TraesCS6A01G110900
chr7D
95.596
931
40
1
7
937
503891156
503890227
0.000000e+00
1491
26
TraesCS6A01G110900
chr3B
94.000
950
51
2
1
945
171005647
171004699
0.000000e+00
1434
27
TraesCS6A01G110900
chr2A
97.236
796
21
1
4977
5771
770754028
770753233
0.000000e+00
1347
28
TraesCS6A01G110900
chr5D
97.605
167
3
1
6081
6246
23792540
23792374
1.020000e-72
285
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
TraesCS6A01G110900
chr6A
80052241
80058486
6245
True
11535.000000
11535
100.0000
1
6246
1
chr6A.!!$R1
6245
1
TraesCS6A01G110900
chr6A
582858558
582863693
5135
True
8493.000000
8493
96.5240
953
6088
1
chr6A.!!$R2
5135
2
TraesCS6A01G110900
chr6A
557899233
557908505
9272
False
2930.666667
7956
97.3970
950
6246
3
chr6A.!!$F1
5296
3
TraesCS6A01G110900
chr7A
620438187
620444439
6252
True
10349.000000
10349
96.5750
1
6246
1
chr7A.!!$R1
6245
4
TraesCS6A01G110900
chr7A
548012772
548019001
6229
False
10080.000000
10080
95.8610
1
6246
1
chr7A.!!$F2
6245
5
TraesCS6A01G110900
chr7A
708400262
708405552
5290
True
8824.000000
8824
96.7610
950
6246
1
chr7A.!!$R2
5296
6
TraesCS6A01G110900
chr7A
184072546
184073477
931
False
1461.000000
1461
94.9570
3
934
1
chr7A.!!$F1
931
7
TraesCS6A01G110900
chr7A
267447037
267448261
1224
True
399.000000
507
96.7525
5770
6246
2
chr7A.!!$R3
476
8
TraesCS6A01G110900
chr1A
57981854
57988872
7018
True
5153.000000
10021
97.0255
1
6246
2
chr1A.!!$R2
6245
9
TraesCS6A01G110900
chr3A
724442837
724447961
5124
False
8582.000000
8582
96.8710
950
6085
1
chr3A.!!$F2
5135
10
TraesCS6A01G110900
chr3A
15645941
15651082
5141
True
8567.000000
8567
96.7570
950
6088
1
chr3A.!!$R1
5138
11
TraesCS6A01G110900
chr3A
31887607
31888550
943
False
1550.000000
1550
96.2960
1
945
1
chr3A.!!$F1
944
12
TraesCS6A01G110900
chr4A
31818936
31823989
5053
True
8318.000000
8318
96.3250
696
5771
1
chr4A.!!$R1
5075
13
TraesCS6A01G110900
chr1D
259729972
259730904
932
False
1552.000000
1552
96.6840
1
934
1
chr1D.!!$F2
933
14
TraesCS6A01G110900
chr1D
8588657
8589588
931
False
1507.000000
1507
95.8240
1
934
1
chr1D.!!$F1
933
15
TraesCS6A01G110900
chrUn
70480112
70481048
936
True
1515.000000
1515
95.8380
1
937
1
chrUn.!!$R1
936
16
TraesCS6A01G110900
chr6D
43979165
43980096
931
True
1498.000000
1498
95.6240
1
937
1
chr6D.!!$R1
936
17
TraesCS6A01G110900
chr7D
503890227
503891156
929
True
1491.000000
1491
95.5960
7
937
1
chr7D.!!$R1
930
18
TraesCS6A01G110900
chr3B
171004699
171005647
948
True
1434.000000
1434
94.0000
1
945
1
chr3B.!!$R1
944
19
TraesCS6A01G110900
chr2A
770753233
770754028
795
True
1347.000000
1347
97.2360
4977
5771
1
chr2A.!!$R1
794
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.