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
TraesCS5A01G333400
chr5A
100.000
4090
0
0
1
4090
542030150
542026061
0.000000e+00
7553.0
1
TraesCS5A01G333400
chr1A
97.086
3020
82
3
1
3018
394484551
394487566
0.000000e+00
5084.0
2
TraesCS5A01G333400
chr1A
96.750
2308
74
1
711
3018
394415106
394417412
0.000000e+00
3845.0
3
TraesCS5A01G333400
chr1A
94.333
1094
34
7
3016
4090
394418058
394419142
0.000000e+00
1652.0
4
TraesCS5A01G333400
chr1A
96.380
663
21
3
3016
3678
394488212
394488871
0.000000e+00
1088.0
5
TraesCS5A01G333400
chr1A
92.711
439
11
6
3672
4090
394506632
394507069
7.510000e-172
614.0
6
TraesCS5A01G333400
chr4D
95.206
2545
117
5
475
3018
502619229
502621769
0.000000e+00
4019.0
7
TraesCS5A01G333400
chr4D
88.075
1065
77
15
3018
4046
129501157
129500107
0.000000e+00
1218.0
8
TraesCS5A01G333400
chr3D
95.206
2545
117
5
475
3018
579345094
579347634
0.000000e+00
4019.0
9
TraesCS5A01G333400
chr2D
95.130
2546
118
5
475
3018
82250141
82247600
0.000000e+00
4010.0
10
TraesCS5A01G333400
chr2D
89.035
1067
68
14
3016
4046
607121350
607122403
0.000000e+00
1277.0
11
TraesCS5A01G333400
chrUn
95.128
2545
119
5
475
3018
134333280
134330740
0.000000e+00
4008.0
12
TraesCS5A01G333400
chrUn
83.766
616
74
15
3174
3767
71017183
71016572
9.930000e-156
560.0
13
TraesCS5A01G333400
chrUn
92.199
282
16
2
3765
4046
388007274
388007549
1.070000e-105
394.0
14
TraesCS5A01G333400
chr3B
94.536
2544
135
4
475
3018
728851773
728854312
0.000000e+00
3925.0
15
TraesCS5A01G333400
chr3B
92.962
1094
53
4
3016
4090
678822928
678824016
0.000000e+00
1572.0
16
TraesCS5A01G333400
chr3B
88.632
563
57
6
475
1033
685958131
685957572
0.000000e+00
678.0
17
TraesCS5A01G333400
chr3B
86.923
390
26
11
568
955
678819542
678819908
8.180000e-112
414.0
18
TraesCS5A01G333400
chr6B
93.176
2550
166
6
475
3018
646101433
646103980
0.000000e+00
3738.0
19
TraesCS5A01G333400
chr4B
92.042
2111
157
8
909
3017
524149752
524147651
0.000000e+00
2957.0
20
TraesCS5A01G333400
chr4B
92.949
1092
51
6
3019
4090
77616327
77615242
0.000000e+00
1567.0
21
TraesCS5A01G333400
chr2B
93.144
1094
47
5
3016
4090
238550302
238551386
0.000000e+00
1580.0
22
TraesCS5A01G333400
chr2B
81.210
777
111
13
3016
3767
37447935
37447169
9.790000e-166
593.0
23
TraesCS5A01G333400
chr2A
87.087
1030
57
29
3099
4090
27757429
27758420
0.000000e+00
1096.0
24
TraesCS5A01G333400
chr5D
86.680
1006
76
15
3087
4046
324731318
324730325
0.000000e+00
1062.0
25
TraesCS5A01G333400
chr5D
86.238
1010
76
15
3084
4046
133266529
133267522
0.000000e+00
1037.0
26
TraesCS5A01G333400
chr3A
92.857
490
28
4
1
490
562956940
562956458
0.000000e+00
704.0
27
TraesCS5A01G333400
chr3A
82.392
301
47
4
195
492
719094540
719094243
1.460000e-64
257.0
28
TraesCS5A01G333400
chr7A
90.447
492
36
5
1
492
8469822
8470302
4.460000e-179
638.0
29
TraesCS5A01G333400
chr4A
89.375
480
45
4
1
478
718658774
718659249
2.100000e-167
599.0
30
TraesCS5A01G333400
chr4A
88.235
476
50
4
1
475
718706023
718706493
7.670000e-157
564.0
31
TraesCS5A01G333400
chr4A
87.424
493
54
5
1
492
392505924
392505439
9.930000e-156
560.0
32
TraesCS5A01G333400
chr5B
87.018
493
53
7
3
492
50308195
50307711
2.780000e-151
545.0
33
TraesCS5A01G333400
chr5B
85.507
483
63
4
1
481
220878576
220878099
7.900000e-137
497.0
34
TraesCS5A01G333400
chr1B
84.988
413
39
9
3016
3411
62478422
62478016
8.240000e-107
398.0
35
TraesCS5A01G333400
chr7B
97.561
41
1
0
154
194
443398031
443398071
2.040000e-08
71.3
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
TraesCS5A01G333400
chr5A
542026061
542030150
4089
True
7553.0
7553
100.0000
1
4090
1
chr5A.!!$R1
4089
1
TraesCS5A01G333400
chr1A
394484551
394488871
4320
False
3086.0
5084
96.7330
1
3678
2
chr1A.!!$F3
3677
2
TraesCS5A01G333400
chr1A
394415106
394419142
4036
False
2748.5
3845
95.5415
711
4090
2
chr1A.!!$F2
3379
3
TraesCS5A01G333400
chr4D
502619229
502621769
2540
False
4019.0
4019
95.2060
475
3018
1
chr4D.!!$F1
2543
4
TraesCS5A01G333400
chr4D
129500107
129501157
1050
True
1218.0
1218
88.0750
3018
4046
1
chr4D.!!$R1
1028
5
TraesCS5A01G333400
chr3D
579345094
579347634
2540
False
4019.0
4019
95.2060
475
3018
1
chr3D.!!$F1
2543
6
TraesCS5A01G333400
chr2D
82247600
82250141
2541
True
4010.0
4010
95.1300
475
3018
1
chr2D.!!$R1
2543
7
TraesCS5A01G333400
chr2D
607121350
607122403
1053
False
1277.0
1277
89.0350
3016
4046
1
chr2D.!!$F1
1030
8
TraesCS5A01G333400
chrUn
134330740
134333280
2540
True
4008.0
4008
95.1280
475
3018
1
chrUn.!!$R2
2543
9
TraesCS5A01G333400
chrUn
71016572
71017183
611
True
560.0
560
83.7660
3174
3767
1
chrUn.!!$R1
593
10
TraesCS5A01G333400
chr3B
728851773
728854312
2539
False
3925.0
3925
94.5360
475
3018
1
chr3B.!!$F1
2543
11
TraesCS5A01G333400
chr3B
678819542
678824016
4474
False
993.0
1572
89.9425
568
4090
2
chr3B.!!$F2
3522
12
TraesCS5A01G333400
chr3B
685957572
685958131
559
True
678.0
678
88.6320
475
1033
1
chr3B.!!$R1
558
13
TraesCS5A01G333400
chr6B
646101433
646103980
2547
False
3738.0
3738
93.1760
475
3018
1
chr6B.!!$F1
2543
14
TraesCS5A01G333400
chr4B
524147651
524149752
2101
True
2957.0
2957
92.0420
909
3017
1
chr4B.!!$R2
2108
15
TraesCS5A01G333400
chr4B
77615242
77616327
1085
True
1567.0
1567
92.9490
3019
4090
1
chr4B.!!$R1
1071
16
TraesCS5A01G333400
chr2B
238550302
238551386
1084
False
1580.0
1580
93.1440
3016
4090
1
chr2B.!!$F1
1074
17
TraesCS5A01G333400
chr2B
37447169
37447935
766
True
593.0
593
81.2100
3016
3767
1
chr2B.!!$R1
751
18
TraesCS5A01G333400
chr2A
27757429
27758420
991
False
1096.0
1096
87.0870
3099
4090
1
chr2A.!!$F1
991
19
TraesCS5A01G333400
chr5D
324730325
324731318
993
True
1062.0
1062
86.6800
3087
4046
1
chr5D.!!$R1
959
20
TraesCS5A01G333400
chr5D
133266529
133267522
993
False
1037.0
1037
86.2380
3084
4046
1
chr5D.!!$F1
962
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.