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
TraesCS3B01G369500
chr3B
100.000
2318
0
0
1
2318
581640947
581638630
0.000000e+00
4281.0
1
TraesCS3B01G369500
chr3B
97.297
37
1
0
1668
1704
581639242
581639206
1.920000e-06
63.9
2
TraesCS3B01G369500
chr3B
97.297
37
1
0
1706
1742
581639280
581639244
1.920000e-06
63.9
3
TraesCS3B01G369500
chr3B
100.000
30
0
0
2266
2295
505993096
505993067
3.220000e-04
56.5
4
TraesCS3B01G369500
chr2A
97.844
1345
29
0
1
1345
770135505
770136849
0.000000e+00
2324.0
5
TraesCS3B01G369500
chr2B
97.976
1235
23
1
1
1233
22558252
22557018
0.000000e+00
2141.0
6
TraesCS3B01G369500
chr3A
94.862
1343
69
0
1
1343
703710700
703709358
0.000000e+00
2098.0
7
TraesCS3B01G369500
chr3A
91.667
240
17
3
1348
1586
584749079
584748842
1.720000e-86
329.0
8
TraesCS3B01G369500
chr3A
96.104
154
5
1
1788
1941
584748511
584748359
1.380000e-62
250.0
9
TraesCS3B01G369500
chr7A
93.299
1343
89
1
1
1343
110824165
110822824
0.000000e+00
1980.0
10
TraesCS3B01G369500
chr5B
90.089
1352
132
2
1
1350
543291291
543292642
0.000000e+00
1753.0
11
TraesCS3B01G369500
chr7B
89.673
1346
133
2
1
1346
504462858
504461519
0.000000e+00
1711.0
12
TraesCS3B01G369500
chr7B
97.143
35
1
0
2269
2303
373066104
373066138
2.490000e-05
60.2
13
TraesCS3B01G369500
chr7D
88.914
1344
148
1
2
1345
22720731
22719389
0.000000e+00
1655.0
14
TraesCS3B01G369500
chr7D
89.191
1286
138
1
59
1344
423401199
423399915
0.000000e+00
1604.0
15
TraesCS3B01G369500
chr7D
87.658
1345
165
1
2
1346
561612815
561611472
0.000000e+00
1563.0
16
TraesCS3B01G369500
chr7D
97.143
35
1
0
2262
2296
510874219
510874253
2.490000e-05
60.2
17
TraesCS3B01G369500
chr7D
96.875
32
0
1
2265
2296
517572217
517572247
4.000000e-03
52.8
18
TraesCS3B01G369500
chr3D
95.147
989
29
7
1348
2318
443590768
443589781
0.000000e+00
1543.0
19
TraesCS3B01G369500
chr3D
97.297
37
1
0
1706
1742
443590446
443590410
1.920000e-06
63.9
20
TraesCS3B01G369500
chr3D
97.222
36
1
0
1669
1704
443590407
443590372
6.920000e-06
62.1
21
TraesCS3B01G369500
chr6B
100.000
30
0
0
2266
2295
713473814
713473785
3.220000e-04
56.5
22
TraesCS3B01G369500
chr1A
100.000
30
0
0
2267
2296
178340297
178340268
3.220000e-04
56.5
23
TraesCS3B01G369500
chr1B
94.286
35
0
2
2262
2296
556267141
556267173
4.000000e-03
52.8
24
TraesCS3B01G369500
chr1B
94.286
35
0
2
2262
2296
556306688
556306720
4.000000e-03
52.8
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
TraesCS3B01G369500
chr3B
581638630
581640947
2317
True
1469.600000
4281
98.198000
1
2318
3
chr3B.!!$R2
2317
1
TraesCS3B01G369500
chr2A
770135505
770136849
1344
False
2324.000000
2324
97.844000
1
1345
1
chr2A.!!$F1
1344
2
TraesCS3B01G369500
chr2B
22557018
22558252
1234
True
2141.000000
2141
97.976000
1
1233
1
chr2B.!!$R1
1232
3
TraesCS3B01G369500
chr3A
703709358
703710700
1342
True
2098.000000
2098
94.862000
1
1343
1
chr3A.!!$R1
1342
4
TraesCS3B01G369500
chr3A
584748359
584749079
720
True
289.500000
329
93.885500
1348
1941
2
chr3A.!!$R2
593
5
TraesCS3B01G369500
chr7A
110822824
110824165
1341
True
1980.000000
1980
93.299000
1
1343
1
chr7A.!!$R1
1342
6
TraesCS3B01G369500
chr5B
543291291
543292642
1351
False
1753.000000
1753
90.089000
1
1350
1
chr5B.!!$F1
1349
7
TraesCS3B01G369500
chr7B
504461519
504462858
1339
True
1711.000000
1711
89.673000
1
1346
1
chr7B.!!$R1
1345
8
TraesCS3B01G369500
chr7D
22719389
22720731
1342
True
1655.000000
1655
88.914000
2
1345
1
chr7D.!!$R1
1343
9
TraesCS3B01G369500
chr7D
423399915
423401199
1284
True
1604.000000
1604
89.191000
59
1344
1
chr7D.!!$R2
1285
10
TraesCS3B01G369500
chr7D
561611472
561612815
1343
True
1563.000000
1563
87.658000
2
1346
1
chr7D.!!$R3
1344
11
TraesCS3B01G369500
chr3D
443589781
443590768
987
True
556.333333
1543
96.555333
1348
2318
3
chr3D.!!$R1
970
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.