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
TraesCS6B01G182400
chr6B
100.000
4254
0
0
1
4254
204329849
204334102
0.000000e+00
7856.0
1
TraesCS6B01G182400
chr6B
81.779
697
84
24
1302
1992
88718767
88719426
1.040000e-150
544.0
2
TraesCS6B01G182400
chr6A
93.701
3572
165
18
724
4254
143373977
143377529
0.000000e+00
5295.0
3
TraesCS6B01G182400
chr6A
75.877
713
99
37
2030
2704
608337046
608337723
3.220000e-76
296.0
4
TraesCS6B01G182400
chr6A
93.878
49
3
0
4104
4152
520869964
520869916
1.640000e-09
75.0
5
TraesCS6B01G182400
chr6D
94.936
2350
96
9
1910
4254
115018925
115021256
0.000000e+00
3659.0
6
TraesCS6B01G182400
chr6D
92.791
1193
60
13
716
1885
115017740
115018929
0.000000e+00
1703.0
7
TraesCS6B01G182400
chr6D
78.144
334
46
13
2036
2367
86739905
86739597
2.020000e-43
187.0
8
TraesCS6B01G182400
chr5B
93.194
720
43
5
1
716
648667244
648667961
0.000000e+00
1053.0
9
TraesCS6B01G182400
chr5B
90.529
718
62
5
2
715
33895910
33896625
0.000000e+00
944.0
10
TraesCS6B01G182400
chr5B
84.375
64
8
2
4084
4146
123760713
123760775
1.280000e-05
62.1
11
TraesCS6B01G182400
chr1B
91.771
717
52
6
3
715
575837787
575837074
0.000000e+00
990.0
12
TraesCS6B01G182400
chr1B
78.834
326
56
6
2250
2573
633192328
633192014
1.550000e-49
207.0
13
TraesCS6B01G182400
chr3B
91.389
720
57
4
1
715
704907168
704907887
0.000000e+00
981.0
14
TraesCS6B01G182400
chr3B
89.291
719
70
6
1
715
744229361
744228646
0.000000e+00
894.0
15
TraesCS6B01G182400
chr3B
76.641
518
93
19
2243
2753
735245353
735245849
1.170000e-65
261.0
16
TraesCS6B01G182400
chr3B
87.755
147
17
1
566
711
661661797
661661651
2.030000e-38
171.0
17
TraesCS6B01G182400
chr7B
90.694
720
62
4
1
715
449621005
449621724
0.000000e+00
953.0
18
TraesCS6B01G182400
chr7B
90.251
718
64
5
1
712
14161270
14161987
0.000000e+00
933.0
19
TraesCS6B01G182400
chr7B
77.629
523
88
17
2243
2757
113921597
113922098
1.500000e-74
291.0
20
TraesCS6B01G182400
chrUn
92.308
598
42
3
1
594
84379209
84378612
0.000000e+00
846.0
21
TraesCS6B01G182400
chr2B
88.889
684
71
4
36
715
747792865
747792183
0.000000e+00
837.0
22
TraesCS6B01G182400
chr1A
81.229
602
73
14
1400
1991
462129890
462129319
2.330000e-122
449.0
23
TraesCS6B01G182400
chr1A
77.652
443
67
16
2355
2783
548490025
548490449
1.530000e-59
241.0
24
TraesCS6B01G182400
chr7A
78.447
515
85
15
2250
2757
579013494
579012999
3.190000e-81
313.0
25
TraesCS6B01G182400
chr7A
86.567
134
17
1
2358
2490
643649383
643649250
3.430000e-31
147.0
26
TraesCS6B01G182400
chr5A
78.161
522
87
17
2243
2757
622374653
622375154
1.490000e-79
307.0
27
TraesCS6B01G182400
chr5A
84.375
64
8
2
4084
4146
118670754
118670816
1.280000e-05
62.1
28
TraesCS6B01G182400
chr2A
78.330
443
64
14
2355
2783
174456420
174456844
1.520000e-64
257.0
29
TraesCS6B01G182400
chr3A
80.272
294
44
8
2250
2541
40814594
40814313
4.310000e-50
209.0
30
TraesCS6B01G182400
chr5D
94.937
79
2
2
2335
2412
478728674
478728751
5.780000e-24
122.0
31
TraesCS6B01G182400
chr5D
84.375
64
8
2
4084
4146
113391529
113391591
1.280000e-05
62.1
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
TraesCS6B01G182400
chr6B
204329849
204334102
4253
False
7856
7856
100.0000
1
4254
1
chr6B.!!$F2
4253
1
TraesCS6B01G182400
chr6B
88718767
88719426
659
False
544
544
81.7790
1302
1992
1
chr6B.!!$F1
690
2
TraesCS6B01G182400
chr6A
143373977
143377529
3552
False
5295
5295
93.7010
724
4254
1
chr6A.!!$F1
3530
3
TraesCS6B01G182400
chr6A
608337046
608337723
677
False
296
296
75.8770
2030
2704
1
chr6A.!!$F2
674
4
TraesCS6B01G182400
chr6D
115017740
115021256
3516
False
2681
3659
93.8635
716
4254
2
chr6D.!!$F1
3538
5
TraesCS6B01G182400
chr5B
648667244
648667961
717
False
1053
1053
93.1940
1
716
1
chr5B.!!$F3
715
6
TraesCS6B01G182400
chr5B
33895910
33896625
715
False
944
944
90.5290
2
715
1
chr5B.!!$F1
713
7
TraesCS6B01G182400
chr1B
575837074
575837787
713
True
990
990
91.7710
3
715
1
chr1B.!!$R1
712
8
TraesCS6B01G182400
chr3B
704907168
704907887
719
False
981
981
91.3890
1
715
1
chr3B.!!$F1
714
9
TraesCS6B01G182400
chr3B
744228646
744229361
715
True
894
894
89.2910
1
715
1
chr3B.!!$R2
714
10
TraesCS6B01G182400
chr7B
449621005
449621724
719
False
953
953
90.6940
1
715
1
chr7B.!!$F3
714
11
TraesCS6B01G182400
chr7B
14161270
14161987
717
False
933
933
90.2510
1
712
1
chr7B.!!$F1
711
12
TraesCS6B01G182400
chr7B
113921597
113922098
501
False
291
291
77.6290
2243
2757
1
chr7B.!!$F2
514
13
TraesCS6B01G182400
chrUn
84378612
84379209
597
True
846
846
92.3080
1
594
1
chrUn.!!$R1
593
14
TraesCS6B01G182400
chr2B
747792183
747792865
682
True
837
837
88.8890
36
715
1
chr2B.!!$R1
679
15
TraesCS6B01G182400
chr1A
462129319
462129890
571
True
449
449
81.2290
1400
1991
1
chr1A.!!$R1
591
16
TraesCS6B01G182400
chr5A
622374653
622375154
501
False
307
307
78.1610
2243
2757
1
chr5A.!!$F2
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.