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
TraesCS7D01G084000
chr7D
100.000
2375
0
0
1
2375
51238841
51236467
0
4386
1
TraesCS7D01G084000
chr7D
93.795
2353
91
10
1
2349
79226633
79228934
0
3485
2
TraesCS7D01G084000
chr5D
95.835
2353
81
8
1
2350
384512075
384509737
0
3786
3
TraesCS7D01G084000
chr5D
94.135
2370
111
17
1
2350
29767644
29765283
0
3581
4
TraesCS7D01G084000
chr5D
93.639
1682
87
9
686
2350
140952538
140950860
0
2495
5
TraesCS7D01G084000
chr5D
95.712
1516
57
7
834
2346
401783433
401784943
0
2433
6
TraesCS7D01G084000
chr5D
95.465
838
35
3
1
836
401780346
401781182
0
1334
7
TraesCS7D01G084000
chr1D
94.898
2352
88
8
1
2349
336730165
336727843
0
3650
8
TraesCS7D01G084000
chr6D
93.993
2364
89
17
4
2349
297171452
297169124
0
3530
9
TraesCS7D01G084000
chr6D
93.554
2358
92
33
1
2349
446364371
446362065
0
3458
10
TraesCS7D01G084000
chr3A
91.953
2361
141
31
1
2349
702240713
702243036
0
3262
11
TraesCS7D01G084000
chr3A
92.087
1428
72
12
925
2349
615135803
615134414
0
1973
12
TraesCS7D01G084000
chr3A
94.927
887
43
2
1
885
615136676
615135790
0
1387
13
TraesCS7D01G084000
chr2D
94.907
1551
52
2
1
1550
239256910
239258434
0
2401
14
TraesCS7D01G084000
chr2D
92.967
1436
73
21
925
2349
645235747
645234329
0
2067
15
TraesCS7D01G084000
chr2D
94.820
888
42
4
1
885
645236620
645235734
0
1382
16
TraesCS7D01G084000
chr2D
92.469
810
45
10
1549
2349
239258381
239259183
0
1144
17
TraesCS7D01G084000
chr2A
92.503
1454
59
17
901
2349
610790142
610791550
0
2036
18
TraesCS7D01G084000
chr4D
94.112
1019
39
7
857
1855
125802883
125801866
0
1530
19
TraesCS7D01G084000
chr4A
95.147
886
42
1
1
885
129030567
129031452
0
1397
20
TraesCS7D01G084000
chr5A
92.212
886
57
4
1
885
235675138
235676012
0
1243
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
TraesCS7D01G084000
chr7D
51236467
51238841
2374
True
4386.0
4386
100.0000
1
2375
1
chr7D.!!$R1
2374
1
TraesCS7D01G084000
chr7D
79226633
79228934
2301
False
3485.0
3485
93.7950
1
2349
1
chr7D.!!$F1
2348
2
TraesCS7D01G084000
chr5D
384509737
384512075
2338
True
3786.0
3786
95.8350
1
2350
1
chr5D.!!$R3
2349
3
TraesCS7D01G084000
chr5D
29765283
29767644
2361
True
3581.0
3581
94.1350
1
2350
1
chr5D.!!$R1
2349
4
TraesCS7D01G084000
chr5D
140950860
140952538
1678
True
2495.0
2495
93.6390
686
2350
1
chr5D.!!$R2
1664
5
TraesCS7D01G084000
chr5D
401780346
401784943
4597
False
1883.5
2433
95.5885
1
2346
2
chr5D.!!$F1
2345
6
TraesCS7D01G084000
chr1D
336727843
336730165
2322
True
3650.0
3650
94.8980
1
2349
1
chr1D.!!$R1
2348
7
TraesCS7D01G084000
chr6D
297169124
297171452
2328
True
3530.0
3530
93.9930
4
2349
1
chr6D.!!$R1
2345
8
TraesCS7D01G084000
chr6D
446362065
446364371
2306
True
3458.0
3458
93.5540
1
2349
1
chr6D.!!$R2
2348
9
TraesCS7D01G084000
chr3A
702240713
702243036
2323
False
3262.0
3262
91.9530
1
2349
1
chr3A.!!$F1
2348
10
TraesCS7D01G084000
chr3A
615134414
615136676
2262
True
1680.0
1973
93.5070
1
2349
2
chr3A.!!$R1
2348
11
TraesCS7D01G084000
chr2D
239256910
239259183
2273
False
1772.5
2401
93.6880
1
2349
2
chr2D.!!$F1
2348
12
TraesCS7D01G084000
chr2D
645234329
645236620
2291
True
1724.5
2067
93.8935
1
2349
2
chr2D.!!$R1
2348
13
TraesCS7D01G084000
chr2A
610790142
610791550
1408
False
2036.0
2036
92.5030
901
2349
1
chr2A.!!$F1
1448
14
TraesCS7D01G084000
chr4D
125801866
125802883
1017
True
1530.0
1530
94.1120
857
1855
1
chr4D.!!$R1
998
15
TraesCS7D01G084000
chr4A
129030567
129031452
885
False
1397.0
1397
95.1470
1
885
1
chr4A.!!$F1
884
16
TraesCS7D01G084000
chr5A
235675138
235676012
874
False
1243.0
1243
92.2120
1
885
1
chr5A.!!$F1
884
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.