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
TraesCS6B01G357100
chr6B
100.000
2447
0
0
1
2447
625538254
625535808
0
4519
1
TraesCS6B01G357100
chr7B
95.933
2459
86
6
1
2447
52952796
52950340
0
3975
2
TraesCS6B01G357100
chr7B
97.075
1607
46
1
842
2447
742965082
742966688
0
2706
3
TraesCS6B01G357100
chr7B
93.690
935
28
6
1
921
327258709
327259626
0
1371
4
TraesCS6B01G357100
chr1B
94.957
2459
110
7
1
2447
286076157
286078613
0
3842
5
TraesCS6B01G357100
chr1B
95.294
935
30
8
1
921
619179149
619178215
0
1471
6
TraesCS6B01G357100
chr1B
95.080
935
32
7
1
921
583575208
583574274
0
1459
7
TraesCS6B01G357100
chr3D
97.822
1607
34
1
842
2447
202625480
202623874
0
2772
8
TraesCS6B01G357100
chr6D
97.761
1608
34
2
842
2447
430466784
430465177
0
2769
9
TraesCS6B01G357100
chr5A
97.083
1611
46
1
838
2447
162145420
162143810
0
2713
10
TraesCS6B01G357100
chr5A
95.294
935
30
7
1
921
420172524
420173458
0
1471
11
TraesCS6B01G357100
chr3B
96.951
1607
48
1
842
2447
201583761
201582155
0
2695
12
TraesCS6B01G357100
chr3B
96.826
1607
49
2
842
2447
92226626
92225021
0
2684
13
TraesCS6B01G357100
chr4D
96.762
1606
52
0
842
2447
97361819
97363424
0
2678
14
TraesCS6B01G357100
chr4D
95.396
934
31
6
1
922
398051449
398050516
0
1476
15
TraesCS6B01G357100
chr5B
95.508
935
28
7
1
921
130584989
130584055
0
1482
16
TraesCS6B01G357100
chr3A
95.396
934
30
6
1
921
247671819
247672752
0
1474
17
TraesCS6B01G357100
chr3A
95.187
935
31
7
1
921
122210600
122209666
0
1465
18
TraesCS6B01G357100
chrUn
95.080
935
32
6
1
921
222870884
222871818
0
1459
19
TraesCS6B01G357100
chrUn
93.690
935
28
6
1
921
182441251
182442168
0
1371
20
TraesCS6B01G357100
chr7A
95.080
935
32
7
1
921
60196418
60195484
0
1459
21
TraesCS6B01G357100
chr2B
94.973
935
33
5
1
921
234506708
234505774
0
1454
22
TraesCS6B01G357100
chr2D
94.861
934
36
6
1
922
200950855
200949922
0
1448
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
TraesCS6B01G357100
chr6B
625535808
625538254
2446
True
4519
4519
100.000
1
2447
1
chr6B.!!$R1
2446
1
TraesCS6B01G357100
chr7B
52950340
52952796
2456
True
3975
3975
95.933
1
2447
1
chr7B.!!$R1
2446
2
TraesCS6B01G357100
chr7B
742965082
742966688
1606
False
2706
2706
97.075
842
2447
1
chr7B.!!$F2
1605
3
TraesCS6B01G357100
chr7B
327258709
327259626
917
False
1371
1371
93.690
1
921
1
chr7B.!!$F1
920
4
TraesCS6B01G357100
chr1B
286076157
286078613
2456
False
3842
3842
94.957
1
2447
1
chr1B.!!$F1
2446
5
TraesCS6B01G357100
chr1B
619178215
619179149
934
True
1471
1471
95.294
1
921
1
chr1B.!!$R2
920
6
TraesCS6B01G357100
chr1B
583574274
583575208
934
True
1459
1459
95.080
1
921
1
chr1B.!!$R1
920
7
TraesCS6B01G357100
chr3D
202623874
202625480
1606
True
2772
2772
97.822
842
2447
1
chr3D.!!$R1
1605
8
TraesCS6B01G357100
chr6D
430465177
430466784
1607
True
2769
2769
97.761
842
2447
1
chr6D.!!$R1
1605
9
TraesCS6B01G357100
chr5A
162143810
162145420
1610
True
2713
2713
97.083
838
2447
1
chr5A.!!$R1
1609
10
TraesCS6B01G357100
chr5A
420172524
420173458
934
False
1471
1471
95.294
1
921
1
chr5A.!!$F1
920
11
TraesCS6B01G357100
chr3B
201582155
201583761
1606
True
2695
2695
96.951
842
2447
1
chr3B.!!$R2
1605
12
TraesCS6B01G357100
chr3B
92225021
92226626
1605
True
2684
2684
96.826
842
2447
1
chr3B.!!$R1
1605
13
TraesCS6B01G357100
chr4D
97361819
97363424
1605
False
2678
2678
96.762
842
2447
1
chr4D.!!$F1
1605
14
TraesCS6B01G357100
chr4D
398050516
398051449
933
True
1476
1476
95.396
1
922
1
chr4D.!!$R1
921
15
TraesCS6B01G357100
chr5B
130584055
130584989
934
True
1482
1482
95.508
1
921
1
chr5B.!!$R1
920
16
TraesCS6B01G357100
chr3A
247671819
247672752
933
False
1474
1474
95.396
1
921
1
chr3A.!!$F1
920
17
TraesCS6B01G357100
chr3A
122209666
122210600
934
True
1465
1465
95.187
1
921
1
chr3A.!!$R1
920
18
TraesCS6B01G357100
chrUn
222870884
222871818
934
False
1459
1459
95.080
1
921
1
chrUn.!!$F2
920
19
TraesCS6B01G357100
chrUn
182441251
182442168
917
False
1371
1371
93.690
1
921
1
chrUn.!!$F1
920
20
TraesCS6B01G357100
chr7A
60195484
60196418
934
True
1459
1459
95.080
1
921
1
chr7A.!!$R1
920
21
TraesCS6B01G357100
chr2B
234505774
234506708
934
True
1454
1454
94.973
1
921
1
chr2B.!!$R1
920
22
TraesCS6B01G357100
chr2D
200949922
200950855
933
True
1448
1448
94.861
1
922
1
chr2D.!!$R1
921
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.