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
TraesCS5A01G249400
chr5A
100.000
3188
0
0
1
3188
464178215
464175028
0.000000e+00
5888.0
1
TraesCS5A01G249400
chr5A
83.367
2471
338
36
49
2505
464160697
464158286
0.000000e+00
2218.0
2
TraesCS5A01G249400
chr5A
80.527
1176
221
5
1011
2185
474928644
474929812
0.000000e+00
896.0
3
TraesCS5A01G249400
chr5D
93.849
1837
103
5
670
2503
362887119
362885290
0.000000e+00
2758.0
4
TraesCS5A01G249400
chr5D
89.886
1493
140
11
1015
2503
362869069
362867584
0.000000e+00
1910.0
5
TraesCS5A01G249400
chr5D
96.499
657
23
0
1
657
362887762
362887106
0.000000e+00
1086.0
6
TraesCS5A01G249400
chr5D
81.224
1209
202
16
1014
2211
362969322
362968128
0.000000e+00
952.0
7
TraesCS5A01G249400
chr5D
89.419
671
53
7
2521
3188
362884912
362884257
0.000000e+00
830.0
8
TraesCS5A01G249400
chr5D
83.866
719
64
33
2503
3188
362867093
362866394
3.470000e-179
638.0
9
TraesCS5A01G249400
chr5B
83.273
2475
329
48
49
2503
429069142
429066733
0.000000e+00
2198.0
10
TraesCS5A01G249400
chr5B
90.577
1560
133
8
928
2482
429094503
429092953
0.000000e+00
2054.0
11
TraesCS5A01G249400
chr5B
87.518
1378
166
5
1130
2505
429177628
429176255
0.000000e+00
1587.0
12
TraesCS5A01G249400
chr5B
86.975
691
53
18
2502
3188
429092510
429091853
0.000000e+00
743.0
13
TraesCS5A01G249400
chr5B
92.308
104
7
1
2502
2605
429175885
429175783
2.560000e-31
147.0
14
TraesCS5A01G249400
chr5B
90.291
103
9
1
2503
2605
429066356
429066255
2.000000e-27
134.0
15
TraesCS5A01G249400
chr7B
89.130
92
4
5
2772
2861
506228135
506228222
3.360000e-20
110.0
16
TraesCS5A01G249400
chr3B
79.874
159
20
11
2702
2857
4499065
4499214
4.350000e-19
106.0
17
TraesCS5A01G249400
chr6B
83.838
99
16
0
2876
2974
66737906
66738004
9.410000e-16
95.3
18
TraesCS5A01G249400
chr2B
87.719
57
7
0
373
429
793972432
793972488
2.050000e-07
67.6
19
TraesCS5A01G249400
chr1B
80.220
91
9
8
2590
2674
623457203
623457116
3.430000e-05
60.2
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
TraesCS5A01G249400
chr5A
464175028
464178215
3187
True
5888.0
5888
100.000000
1
3188
1
chr5A.!!$R2
3187
1
TraesCS5A01G249400
chr5A
464158286
464160697
2411
True
2218.0
2218
83.367000
49
2505
1
chr5A.!!$R1
2456
2
TraesCS5A01G249400
chr5A
474928644
474929812
1168
False
896.0
896
80.527000
1011
2185
1
chr5A.!!$F1
1174
3
TraesCS5A01G249400
chr5D
362884257
362887762
3505
True
1558.0
2758
93.255667
1
3188
3
chr5D.!!$R3
3187
4
TraesCS5A01G249400
chr5D
362866394
362869069
2675
True
1274.0
1910
86.876000
1015
3188
2
chr5D.!!$R2
2173
5
TraesCS5A01G249400
chr5D
362968128
362969322
1194
True
952.0
952
81.224000
1014
2211
1
chr5D.!!$R1
1197
6
TraesCS5A01G249400
chr5B
429091853
429094503
2650
True
1398.5
2054
88.776000
928
3188
2
chr5B.!!$R2
2260
7
TraesCS5A01G249400
chr5B
429066255
429069142
2887
True
1166.0
2198
86.782000
49
2605
2
chr5B.!!$R1
2556
8
TraesCS5A01G249400
chr5B
429175783
429177628
1845
True
867.0
1587
89.913000
1130
2605
2
chr5B.!!$R3
1475
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.