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
TraesCS3B01G061100
chr3B
100.000
2471
0
0
1
2471
32992994
32990524
0.000000e+00
4564.0
1
TraesCS3B01G061100
chr3B
91.083
942
63
9
1000
1938
33096984
33096061
0.000000e+00
1254.0
2
TraesCS3B01G061100
chr3B
81.163
1083
136
39
843
1886
33299235
33298182
0.000000e+00
808.0
3
TraesCS3B01G061100
chr3B
81.845
336
28
17
2123
2457
33005725
33005422
4.080000e-63
252.0
4
TraesCS3B01G061100
chr3B
80.913
241
35
9
1625
1859
33332713
33332478
1.950000e-41
180.0
5
TraesCS3B01G061100
chr4A
95.110
818
29
5
18
826
722668461
722667646
0.000000e+00
1279.0
6
TraesCS3B01G061100
chr7B
94.909
825
27
4
18
832
131180090
131179271
0.000000e+00
1277.0
7
TraesCS3B01G061100
chr2B
95.098
816
29
6
20
826
664342127
664342940
0.000000e+00
1275.0
8
TraesCS3B01G061100
chr3D
89.867
977
83
8
973
1938
20708406
20707435
0.000000e+00
1242.0
9
TraesCS3B01G061100
chr3D
89.714
350
30
4
2109
2457
20704884
20704540
2.260000e-120
442.0
10
TraesCS3B01G061100
chr3D
95.210
167
8
0
1937
2103
20705288
20705122
5.240000e-67
265.0
11
TraesCS3B01G061100
chr3D
82.822
163
22
6
1624
1784
20205620
20205462
9.210000e-30
141.0
12
TraesCS3B01G061100
chr3D
89.109
101
6
3
1587
1683
20561994
20561895
1.200000e-23
121.0
13
TraesCS3B01G061100
chr3D
86.813
91
8
2
843
933
20708490
20708404
5.620000e-17
99.0
14
TraesCS3B01G061100
chr3D
93.023
43
2
1
2058
2100
20038878
20038837
7.380000e-06
62.1
15
TraesCS3B01G061100
chr3D
97.143
35
0
1
2058
2092
20208578
20208545
9.540000e-05
58.4
16
TraesCS3B01G061100
chr3D
97.143
35
0
1
2058
2092
20399555
20399522
9.540000e-05
58.4
17
TraesCS3B01G061100
chr4B
91.041
826
54
9
18
830
20229751
20228933
0.000000e+00
1098.0
18
TraesCS3B01G061100
chr3A
86.338
710
70
17
895
1589
28231505
28230808
0.000000e+00
749.0
19
TraesCS3B01G061100
chr3A
85.503
676
63
19
827
1478
28322950
28322286
0.000000e+00
673.0
20
TraesCS3B01G061100
chr3A
83.462
647
66
21
843
1474
28391458
28390838
4.610000e-157
564.0
21
TraesCS3B01G061100
chr3A
88.571
350
36
4
2122
2469
28302070
28301723
2.940000e-114
422.0
22
TraesCS3B01G061100
chr3A
88.034
234
21
6
1587
1818
28216357
28216129
1.130000e-68
270.0
23
TraesCS3B01G061100
chr3A
80.228
263
40
11
1588
1842
27876467
27876209
1.170000e-43
187.0
24
TraesCS3B01G061100
chr3A
92.593
81
6
0
1964
2044
28388566
28388486
1.550000e-22
117.0
25
TraesCS3B01G061100
chr3A
98.276
58
1
0
1949
2006
28302373
28302316
4.350000e-18
102.0
26
TraesCS3B01G061100
chr3A
97.143
35
0
1
2058
2092
27777349
27777316
9.540000e-05
58.4
27
TraesCS3B01G061100
chr3A
97.143
35
0
1
2058
2092
27880522
27880489
9.540000e-05
58.4
28
TraesCS3B01G061100
chr3A
97.143
35
0
1
2058
2092
28054773
28054740
9.540000e-05
58.4
29
TraesCS3B01G061100
chr1B
82.407
108
15
4
524
630
221267077
221267181
9.410000e-15
91.6
30
TraesCS3B01G061100
chr4D
82.000
100
16
2
532
630
499228305
499228207
1.570000e-12
84.2
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
TraesCS3B01G061100
chr3B
32990524
32992994
2470
True
4564.0
4564
100.0000
1
2471
1
chr3B.!!$R1
2470
1
TraesCS3B01G061100
chr3B
33096061
33096984
923
True
1254.0
1254
91.0830
1000
1938
1
chr3B.!!$R3
938
2
TraesCS3B01G061100
chr3B
33298182
33299235
1053
True
808.0
808
81.1630
843
1886
1
chr3B.!!$R4
1043
3
TraesCS3B01G061100
chr4A
722667646
722668461
815
True
1279.0
1279
95.1100
18
826
1
chr4A.!!$R1
808
4
TraesCS3B01G061100
chr7B
131179271
131180090
819
True
1277.0
1277
94.9090
18
832
1
chr7B.!!$R1
814
5
TraesCS3B01G061100
chr2B
664342127
664342940
813
False
1275.0
1275
95.0980
20
826
1
chr2B.!!$F1
806
6
TraesCS3B01G061100
chr3D
20704540
20708490
3950
True
512.0
1242
90.4010
843
2457
4
chr3D.!!$R5
1614
7
TraesCS3B01G061100
chr4B
20228933
20229751
818
True
1098.0
1098
91.0410
18
830
1
chr4B.!!$R1
812
8
TraesCS3B01G061100
chr3A
28230808
28231505
697
True
749.0
749
86.3380
895
1589
1
chr3A.!!$R6
694
9
TraesCS3B01G061100
chr3A
28322286
28322950
664
True
673.0
673
85.5030
827
1478
1
chr3A.!!$R7
651
10
TraesCS3B01G061100
chr3A
28388486
28391458
2972
True
340.5
564
88.0275
843
2044
2
chr3A.!!$R9
1201
11
TraesCS3B01G061100
chr3A
28301723
28302373
650
True
262.0
422
93.4235
1949
2469
2
chr3A.!!$R8
520
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.