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
TraesCS3B01G181800
chr3B
100.000
2632
0
0
1
2632
190889985
190887354
0.000000e+00
4861.0
1
TraesCS3B01G181800
chr3B
99.517
621
3
0
1
621
771437882
771438502
0.000000e+00
1131.0
2
TraesCS3B01G181800
chr5D
96.335
2019
47
6
621
2632
60243557
60241559
0.000000e+00
3293.0
3
TraesCS3B01G181800
chr5D
94.301
193
10
1
430
621
484995959
484995767
7.120000e-76
294.0
4
TraesCS3B01G181800
chr4B
98.712
621
8
0
1
621
77011726
77011106
0.000000e+00
1103.0
5
TraesCS3B01G181800
chr3D
82.609
1150
162
18
777
1894
331001091
331002234
0.000000e+00
981.0
6
TraesCS3B01G181800
chr3D
95.642
413
18
0
18
430
424222577
424222989
0.000000e+00
664.0
7
TraesCS3B01G181800
chr3D
84.314
102
16
0
659
760
569067854
569067955
1.670000e-17
100.0
8
TraesCS3B01G181800
chr7B
95.008
621
28
1
1
621
599105229
599105846
0.000000e+00
972.0
9
TraesCS3B01G181800
chrUn
100.000
390
0
0
196
585
479942914
479943303
0.000000e+00
721.0
10
TraesCS3B01G181800
chrUn
92.157
51
4
0
1821
1871
82409567
82409517
3.630000e-09
73.1
11
TraesCS3B01G181800
chr7D
96.126
413
15
1
18
430
638153066
638153477
0.000000e+00
673.0
12
TraesCS3B01G181800
chr1B
95.884
413
17
0
18
430
667635116
667635528
0.000000e+00
669.0
13
TraesCS3B01G181800
chr1B
89.956
229
16
5
397
621
13340869
13340644
3.310000e-74
289.0
14
TraesCS3B01G181800
chr1B
89.083
229
18
5
397
621
13300233
13300008
7.170000e-71
278.0
15
TraesCS3B01G181800
chr5A
95.652
414
17
1
18
430
326654919
326654506
0.000000e+00
664.0
16
TraesCS3B01G181800
chr5A
77.489
693
142
12
775
1463
6175945
6175263
1.130000e-108
403.0
17
TraesCS3B01G181800
chr1D
80.427
889
145
18
1187
2061
295856348
295855475
0.000000e+00
651.0
18
TraesCS3B01G181800
chr1D
75.982
1120
227
35
777
1878
229965352
229964257
8.290000e-150
540.0
19
TraesCS3B01G181800
chr1D
81.388
317
52
7
878
1191
295858260
295857948
4.350000e-63
252.0
20
TraesCS3B01G181800
chr4D
93.779
434
22
4
1
429
418512168
418512601
0.000000e+00
647.0
21
TraesCS3B01G181800
chr4D
75.603
1119
235
31
777
1878
428939014
428937917
1.080000e-143
520.0
22
TraesCS3B01G181800
chr1A
74.950
994
222
25
775
1754
50932357
50931377
5.200000e-117
431.0
23
TraesCS3B01G181800
chr1A
78.383
643
119
16
830
1464
426923930
426924560
1.470000e-107
399.0
24
TraesCS3B01G181800
chr6B
90.393
229
16
4
397
621
395689346
395689572
1.980000e-76
296.0
25
TraesCS3B01G181800
chr6B
78.355
231
49
1
799
1028
221421257
221421487
5.870000e-32
148.0
26
TraesCS3B01G181800
chr6D
90.000
230
17
4
397
622
58108556
58108329
2.560000e-75
292.0
27
TraesCS3B01G181800
chr5B
78.846
260
48
4
774
1032
526651928
526652181
4.510000e-38
169.0
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
TraesCS3B01G181800
chr3B
190887354
190889985
2631
True
4861.0
4861
100.0000
1
2632
1
chr3B.!!$R1
2631
1
TraesCS3B01G181800
chr3B
771437882
771438502
620
False
1131.0
1131
99.5170
1
621
1
chr3B.!!$F1
620
2
TraesCS3B01G181800
chr5D
60241559
60243557
1998
True
3293.0
3293
96.3350
621
2632
1
chr5D.!!$R1
2011
3
TraesCS3B01G181800
chr4B
77011106
77011726
620
True
1103.0
1103
98.7120
1
621
1
chr4B.!!$R1
620
4
TraesCS3B01G181800
chr3D
331001091
331002234
1143
False
981.0
981
82.6090
777
1894
1
chr3D.!!$F1
1117
5
TraesCS3B01G181800
chr7B
599105229
599105846
617
False
972.0
972
95.0080
1
621
1
chr7B.!!$F1
620
6
TraesCS3B01G181800
chr5A
6175263
6175945
682
True
403.0
403
77.4890
775
1463
1
chr5A.!!$R1
688
7
TraesCS3B01G181800
chr1D
229964257
229965352
1095
True
540.0
540
75.9820
777
1878
1
chr1D.!!$R1
1101
8
TraesCS3B01G181800
chr1D
295855475
295858260
2785
True
451.5
651
80.9075
878
2061
2
chr1D.!!$R2
1183
9
TraesCS3B01G181800
chr4D
428937917
428939014
1097
True
520.0
520
75.6030
777
1878
1
chr4D.!!$R1
1101
10
TraesCS3B01G181800
chr1A
50931377
50932357
980
True
431.0
431
74.9500
775
1754
1
chr1A.!!$R1
979
11
TraesCS3B01G181800
chr1A
426923930
426924560
630
False
399.0
399
78.3830
830
1464
1
chr1A.!!$F1
634
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.