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
TraesCS3A01G492800
chr3A
100.000
1733
0
0
1
1733
719482115
719483847
0.000000e+00
3201
1
TraesCS3A01G492800
chr3A
85.287
1271
100
36
421
1655
719386547
719387766
0.000000e+00
1230
2
TraesCS3A01G492800
chr3A
85.093
483
71
1
947
1429
719461533
719462014
2.190000e-135
492
3
TraesCS3A01G492800
chr3A
89.441
322
25
7
1175
1490
719555481
719555799
4.900000e-107
398
4
TraesCS3A01G492800
chr3A
82.178
505
45
17
421
905
719534630
719535109
2.280000e-105
392
5
TraesCS3A01G492800
chr3A
100.000
190
0
0
2258
2447
719484372
719484561
3.870000e-93
351
6
TraesCS3A01G492800
chr3A
89.151
212
19
2
967
1174
719535138
719535349
6.710000e-66
261
7
TraesCS3A01G492800
chr3A
87.568
185
23
0
2262
2446
719393319
719393503
5.300000e-52
215
8
TraesCS3A01G492800
chr3A
86.400
125
17
0
2310
2434
412035674
412035550
1.180000e-28
137
9
TraesCS3A01G492800
chr3A
85.385
130
16
3
2307
2434
448008149
448008277
5.490000e-27
132
10
TraesCS3A01G492800
chr3A
83.333
126
21
0
71
196
639776047
639775922
1.540000e-22
117
11
TraesCS3A01G492800
chr3D
92.216
1002
51
7
508
1490
589607423
589608416
0.000000e+00
1393
12
TraesCS3A01G492800
chr3D
87.141
1252
78
30
421
1654
589579605
589580791
0.000000e+00
1343
13
TraesCS3A01G492800
chr3D
87.422
644
61
12
647
1283
589582589
589583219
0.000000e+00
723
14
TraesCS3A01G492800
chr3B
88.793
928
55
26
253
1161
788138062
788138959
0.000000e+00
1092
15
TraesCS3A01G492800
chr3B
81.637
1051
96
37
422
1450
788106436
788107411
0.000000e+00
782
16
TraesCS3A01G492800
chr3B
91.275
298
23
1
1175
1472
788153556
788153850
1.050000e-108
403
17
TraesCS3A01G492800
chr3B
92.430
251
19
0
1
251
788137351
788137601
2.310000e-95
359
18
TraesCS3A01G492800
chr3B
85.246
122
18
0
76
197
659705009
659705130
2.550000e-25
126
19
TraesCS3A01G492800
chr4A
86.719
128
17
0
2307
2434
89183260
89183387
2.540000e-30
143
20
TraesCS3A01G492800
chr2B
87.302
126
14
2
2310
2434
311217979
311217855
2.540000e-30
143
21
TraesCS3A01G492800
chr2B
86.364
132
17
1
2304
2434
311308159
311308028
2.540000e-30
143
22
TraesCS3A01G492800
chr2B
84.252
127
20
0
71
197
86326698
86326572
9.190000e-25
124
23
TraesCS3A01G492800
chr2B
82.677
127
22
0
71
197
275404503
275404377
1.990000e-21
113
24
TraesCS3A01G492800
chr5B
86.508
126
15
2
2310
2434
151383664
151383540
1.180000e-28
137
25
TraesCS3A01G492800
chr5B
86.508
126
15
2
2310
2434
155018749
155018625
1.180000e-28
137
26
TraesCS3A01G492800
chr5B
85.965
114
16
0
87
200
276944773
276944660
3.300000e-24
122
27
TraesCS3A01G492800
chr6B
79.679
187
35
2
2260
2446
716227520
716227703
5.490000e-27
132
28
TraesCS3A01G492800
chr7B
84.127
126
20
0
72
197
559995595
559995470
3.300000e-24
122
29
TraesCS3A01G492800
chr1A
83.465
127
21
0
71
197
396958324
396958450
4.270000e-23
119
30
TraesCS3A01G492800
chr1D
82.308
130
23
0
68
197
162348733
162348604
1.990000e-21
113
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
TraesCS3A01G492800
chr3A
719482115
719484561
2446
False
1776.0
3201
100.0000
1
2447
2
chr3A.!!$F6
2446
1
TraesCS3A01G492800
chr3A
719386547
719387766
1219
False
1230.0
1230
85.2870
421
1655
1
chr3A.!!$F2
1234
2
TraesCS3A01G492800
chr3A
719534630
719535349
719
False
326.5
392
85.6645
421
1174
2
chr3A.!!$F7
753
3
TraesCS3A01G492800
chr3D
589607423
589608416
993
False
1393.0
1393
92.2160
508
1490
1
chr3D.!!$F1
982
4
TraesCS3A01G492800
chr3D
589579605
589583219
3614
False
1033.0
1343
87.2815
421
1654
2
chr3D.!!$F2
1233
5
TraesCS3A01G492800
chr3B
788106436
788107411
975
False
782.0
782
81.6370
422
1450
1
chr3B.!!$F2
1028
6
TraesCS3A01G492800
chr3B
788137351
788138959
1608
False
725.5
1092
90.6115
1
1161
2
chr3B.!!$F4
1160
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.