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
TraesCS3B01G363700
chr3B
100.000
1708
0
0
821
2528
575683304
575681597
0
3155
1
TraesCS3B01G363700
chr3B
97.121
903
24
2
1626
2527
201634131
201633230
0
1522
2
TraesCS3B01G363700
chr3B
97.017
905
23
4
1626
2527
92181081
92181984
0
1519
3
TraesCS3B01G363700
chr3B
100.000
515
0
0
1
515
575684124
575683610
0
952
4
TraesCS3B01G363700
chr5B
97.342
903
22
2
1626
2527
713044537
713043636
0
1533
5
TraesCS3B01G363700
chr3D
97.238
905
22
3
1626
2527
202613618
202614522
0
1530
6
TraesCS3B01G363700
chr2D
97.238
905
21
3
1626
2527
635038932
635039835
0
1530
7
TraesCS3B01G363700
chr2D
97.124
904
24
2
1626
2527
17965514
17964611
0
1524
8
TraesCS3B01G363700
chr2D
98.132
803
15
0
823
1625
635038081
635038883
0
1400
9
TraesCS3B01G363700
chr7A
97.231
903
23
2
1626
2527
120827176
120826275
0
1528
10
TraesCS3B01G363700
chr7A
97.013
904
25
2
1626
2527
120924168
120923265
0
1519
11
TraesCS3B01G363700
chr7A
97.864
515
10
1
1
515
671960282
671959769
0
889
12
TraesCS3B01G363700
chr7A
97.864
515
10
1
1
515
672005439
672005952
0
889
13
TraesCS3B01G363700
chr4D
97.017
905
24
3
1626
2527
123369315
123370219
0
1519
14
TraesCS3B01G363700
chr4D
98.137
805
14
1
821
1625
123368463
123369266
0
1402
15
TraesCS3B01G363700
chr4D
98.012
805
15
1
821
1625
123579413
123580216
0
1397
16
TraesCS3B01G363700
chr4D
98.252
515
8
1
1
515
123578878
123579391
0
900
17
TraesCS3B01G363700
chr4D
97.670
515
11
1
1
515
123367927
123368440
0
883
18
TraesCS3B01G363700
chr7B
98.261
805
14
0
821
1625
743067126
743067930
0
1410
19
TraesCS3B01G363700
chr7B
97.772
808
18
0
821
1628
743112498
743111691
0
1393
20
TraesCS3B01G363700
chr7B
97.864
515
10
1
1
515
743066591
743067104
0
889
21
TraesCS3B01G363700
chr5A
98.144
808
15
0
821
1628
16622452
16621645
0
1410
22
TraesCS3B01G363700
chr5A
98.137
805
15
0
821
1625
300049387
300050191
0
1404
23
TraesCS3B01G363700
chr5A
97.864
515
10
1
1
515
300048851
300049364
0
889
24
TraesCS3B01G363700
chr7D
98.141
807
15
0
822
1628
382014050
382013244
0
1408
25
TraesCS3B01G363700
chr7D
98.058
515
9
1
1
515
382014585
382014072
0
894
26
TraesCS3B01G363700
chr1B
98.261
805
13
1
821
1625
461453044
461453847
0
1408
27
TraesCS3B01G363700
chrUn
98.058
515
9
1
1
515
273239083
273239596
0
894
28
TraesCS3B01G363700
chr2A
97.864
515
10
1
1
515
735173085
735173598
0
889
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
TraesCS3B01G363700
chr3B
575681597
575684124
2527
True
2053.5
3155
100.0000
1
2528
2
chr3B.!!$R2
2527
1
TraesCS3B01G363700
chr3B
201633230
201634131
901
True
1522.0
1522
97.1210
1626
2527
1
chr3B.!!$R1
901
2
TraesCS3B01G363700
chr3B
92181081
92181984
903
False
1519.0
1519
97.0170
1626
2527
1
chr3B.!!$F1
901
3
TraesCS3B01G363700
chr5B
713043636
713044537
901
True
1533.0
1533
97.3420
1626
2527
1
chr5B.!!$R1
901
4
TraesCS3B01G363700
chr3D
202613618
202614522
904
False
1530.0
1530
97.2380
1626
2527
1
chr3D.!!$F1
901
5
TraesCS3B01G363700
chr2D
17964611
17965514
903
True
1524.0
1524
97.1240
1626
2527
1
chr2D.!!$R1
901
6
TraesCS3B01G363700
chr2D
635038081
635039835
1754
False
1465.0
1530
97.6850
823
2527
2
chr2D.!!$F1
1704
7
TraesCS3B01G363700
chr7A
120826275
120827176
901
True
1528.0
1528
97.2310
1626
2527
1
chr7A.!!$R1
901
8
TraesCS3B01G363700
chr7A
120923265
120924168
903
True
1519.0
1519
97.0130
1626
2527
1
chr7A.!!$R2
901
9
TraesCS3B01G363700
chr7A
671959769
671960282
513
True
889.0
889
97.8640
1
515
1
chr7A.!!$R3
514
10
TraesCS3B01G363700
chr7A
672005439
672005952
513
False
889.0
889
97.8640
1
515
1
chr7A.!!$F1
514
11
TraesCS3B01G363700
chr4D
123367927
123370219
2292
False
1268.0
1519
97.6080
1
2527
3
chr4D.!!$F1
2526
12
TraesCS3B01G363700
chr4D
123578878
123580216
1338
False
1148.5
1397
98.1320
1
1625
2
chr4D.!!$F2
1624
13
TraesCS3B01G363700
chr7B
743111691
743112498
807
True
1393.0
1393
97.7720
821
1628
1
chr7B.!!$R1
807
14
TraesCS3B01G363700
chr7B
743066591
743067930
1339
False
1149.5
1410
98.0625
1
1625
2
chr7B.!!$F1
1624
15
TraesCS3B01G363700
chr5A
16621645
16622452
807
True
1410.0
1410
98.1440
821
1628
1
chr5A.!!$R1
807
16
TraesCS3B01G363700
chr5A
300048851
300050191
1340
False
1146.5
1404
98.0005
1
1625
2
chr5A.!!$F1
1624
17
TraesCS3B01G363700
chr7D
382013244
382014585
1341
True
1151.0
1408
98.0995
1
1628
2
chr7D.!!$R1
1627
18
TraesCS3B01G363700
chr1B
461453044
461453847
803
False
1408.0
1408
98.2610
821
1625
1
chr1B.!!$F1
804
19
TraesCS3B01G363700
chrUn
273239083
273239596
513
False
894.0
894
98.0580
1
515
1
chrUn.!!$F1
514
20
TraesCS3B01G363700
chr2A
735173085
735173598
513
False
889.0
889
97.8640
1
515
1
chr2A.!!$F1
514
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.