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
TraesCS5B01G056000
chr5B
100.000
4164
0
0
1
4164
62030396
62026233
0.000000e+00
7690.0
1
TraesCS5B01G056000
chr5B
93.451
3283
134
29
136
3385
63542169
63545403
0.000000e+00
4796.0
2
TraesCS5B01G056000
chr5B
85.025
995
137
7
2050
3035
72098413
72099404
0.000000e+00
1002.0
3
TraesCS5B01G056000
chr5B
95.714
140
6
0
1
140
63536825
63536964
4.190000e-55
226.0
4
TraesCS5B01G056000
chr5B
85.057
174
23
3
2090
2260
70962123
70961950
1.540000e-39
174.0
5
TraesCS5B01G056000
chr5B
95.652
69
2
1
4096
4164
63546845
63546912
4.400000e-20
110.0
6
TraesCS5B01G056000
chr5A
94.783
3412
127
12
1
3385
46707853
46711240
0.000000e+00
5267.0
7
TraesCS5B01G056000
chr5A
84.857
1017
140
10
2032
3038
47540567
47539555
0.000000e+00
1013.0
8
TraesCS5B01G056000
chr5A
83.350
973
150
8
2073
3038
47460990
47460023
0.000000e+00
889.0
9
TraesCS5B01G056000
chr5A
83.023
483
58
19
3533
4011
46713456
46713918
2.320000e-112
416.0
10
TraesCS5B01G056000
chr5A
74.521
679
149
21
1106
1769
47461967
47461298
1.470000e-69
274.0
11
TraesCS5B01G056000
chr5A
79.167
96
19
1
3757
3851
466571089
466570994
9.660000e-07
65.8
12
TraesCS5B01G056000
chr5D
96.182
2724
74
6
678
3385
58500592
58503301
0.000000e+00
4427.0
13
TraesCS5B01G056000
chr5D
94.215
726
24
6
1
726
58499902
58500609
0.000000e+00
1092.0
14
TraesCS5B01G056000
chr5D
84.464
1017
144
9
2032
3038
59044253
59043241
0.000000e+00
990.0
15
TraesCS5B01G056000
chr5D
91.599
369
26
4
3385
3750
58504205
58504571
4.800000e-139
505.0
16
TraesCS5B01G056000
chr5D
84.000
350
41
9
3385
3722
507140314
507139968
5.190000e-84
322.0
17
TraesCS5B01G056000
chr5D
75.207
726
154
21
1111
1817
59045080
59044362
1.870000e-83
320.0
18
TraesCS5B01G056000
chr5D
80.609
361
53
10
3386
3734
487498933
487498578
3.190000e-66
263.0
19
TraesCS5B01G056000
chr6B
84.594
357
43
9
3385
3734
163224391
163224742
1.110000e-90
344.0
20
TraesCS5B01G056000
chr6A
84.615
338
40
9
3385
3712
103683026
103683361
4.010000e-85
326.0
21
TraesCS5B01G056000
chr1B
84.181
354
36
12
3385
3724
512180081
512179734
4.010000e-85
326.0
22
TraesCS5B01G056000
chr1B
85.185
135
15
4
3385
3516
572882924
572883056
2.610000e-27
134.0
23
TraesCS5B01G056000
chr4D
82.720
353
42
11
3385
3723
51290321
51290668
3.150000e-76
296.0
24
TraesCS5B01G056000
chr3A
82.849
344
42
11
3386
3724
701240677
701240346
4.070000e-75
292.0
25
TraesCS5B01G056000
chr4B
77.447
470
98
6
2464
2926
619364309
619363841
1.470000e-69
274.0
26
TraesCS5B01G056000
chr4B
76.424
509
108
11
2470
2972
42135357
42134855
8.880000e-67
265.0
27
TraesCS5B01G056000
chr1D
81.662
349
39
11
3385
3724
423305100
423305432
2.470000e-67
267.0
28
TraesCS5B01G056000
chr1D
80.556
360
52
12
3385
3734
11976022
11975671
1.150000e-65
261.0
29
TraesCS5B01G056000
chr2B
88.128
219
21
5
3517
3733
753832166
753831951
5.340000e-64
255.0
30
TraesCS5B01G056000
chr2B
76.035
459
98
11
2313
2765
793525816
793525364
1.160000e-55
228.0
31
TraesCS5B01G056000
chr7B
80.537
298
58
0
2464
2761
40887717
40888014
3.240000e-56
230.0
32
TraesCS5B01G056000
chr7A
84.862
218
30
3
3507
3723
101466942
101466727
2.520000e-52
217.0
33
TraesCS5B01G056000
chr7A
71.837
664
151
30
2301
2945
694330643
694329997
1.550000e-34
158.0
34
TraesCS5B01G056000
chr6D
79.006
362
39
13
3385
3734
363798296
363797960
3.260000e-51
213.0
35
TraesCS5B01G056000
chr4A
79.839
124
23
2
2079
2201
573743489
573743611
5.730000e-14
89.8
36
TraesCS5B01G056000
chr3D
82.143
84
14
1
3758
3840
516184036
516184119
2.080000e-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
TraesCS5B01G056000
chr5B
62026233
62030396
4163
True
7690.0
7690
100.000000
1
4164
1
chr5B.!!$R1
4163
1
TraesCS5B01G056000
chr5B
63542169
63546912
4743
False
2453.0
4796
94.551500
136
4164
2
chr5B.!!$F3
4028
2
TraesCS5B01G056000
chr5B
72098413
72099404
991
False
1002.0
1002
85.025000
2050
3035
1
chr5B.!!$F2
985
3
TraesCS5B01G056000
chr5A
46707853
46713918
6065
False
2841.5
5267
88.903000
1
4011
2
chr5A.!!$F1
4010
4
TraesCS5B01G056000
chr5A
47539555
47540567
1012
True
1013.0
1013
84.857000
2032
3038
1
chr5A.!!$R1
1006
5
TraesCS5B01G056000
chr5A
47460023
47461967
1944
True
581.5
889
78.935500
1106
3038
2
chr5A.!!$R3
1932
6
TraesCS5B01G056000
chr5D
58499902
58504571
4669
False
2008.0
4427
93.998667
1
3750
3
chr5D.!!$F1
3749
7
TraesCS5B01G056000
chr5D
59043241
59045080
1839
True
655.0
990
79.835500
1111
3038
2
chr5D.!!$R3
1927
8
TraesCS5B01G056000
chr4B
42134855
42135357
502
True
265.0
265
76.424000
2470
2972
1
chr4B.!!$R1
502
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.