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
TraesCS3D01G319900
chr3D
100.000
3173
0
0
1
3173
433420376
433423548
0.000000e+00
5860.0
1
TraesCS3D01G319900
chr3D
94.040
755
41
3
2420
3173
490979873
490979122
0.000000e+00
1142.0
2
TraesCS3D01G319900
chr3D
100.000
32
0
0
1
32
374938455
374938424
3.420000e-05
60.2
3
TraesCS3D01G319900
chr3A
90.724
2404
172
25
40
2419
571795028
571797404
0.000000e+00
3157.0
4
TraesCS3D01G319900
chr3A
100.000
32
0
0
1
32
497618921
497618890
3.420000e-05
60.2
5
TraesCS3D01G319900
chr3B
89.474
2337
169
34
114
2419
566182136
566184426
0.000000e+00
2881.0
6
TraesCS3D01G319900
chr2D
98.276
754
13
0
2420
3173
8995941
8996694
0.000000e+00
1321.0
7
TraesCS3D01G319900
chr2D
98.361
732
12
0
2417
3148
8999726
9000457
0.000000e+00
1286.0
8
TraesCS3D01G319900
chr7D
97.497
759
18
1
2416
3173
53416663
53417421
0.000000e+00
1295.0
9
TraesCS3D01G319900
chr7D
94.063
758
40
4
2417
3173
520369664
520370417
0.000000e+00
1146.0
10
TraesCS3D01G319900
chr1D
95.503
756
34
0
2417
3172
91905681
91906436
0.000000e+00
1208.0
11
TraesCS3D01G319900
chr1D
95.503
756
33
1
2418
3172
91901361
91902116
0.000000e+00
1206.0
12
TraesCS3D01G319900
chr6D
94.848
757
33
4
2420
3173
394249261
394248508
0.000000e+00
1177.0
13
TraesCS3D01G319900
chr6D
94.368
728
37
3
2447
3173
394253321
394252597
0.000000e+00
1114.0
14
TraesCS3D01G319900
chr7A
100.000
46
0
0
2419
2464
105446371
105446326
5.640000e-13
86.1
15
TraesCS3D01G319900
chr5D
87.719
57
7
0
806
862
128550369
128550313
2.040000e-07
67.6
16
TraesCS3D01G319900
chr5D
100.000
30
0
0
1
30
298688745
298688774
4.420000e-04
56.5
17
TraesCS3D01G319900
chr1B
100.000
32
0
0
1
32
645254136
645254167
3.420000e-05
60.2
18
TraesCS3D01G319900
chr1A
100.000
32
0
0
1
32
576320959
576320990
3.420000e-05
60.2
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
TraesCS3D01G319900
chr3D
433420376
433423548
3172
False
5860.0
5860
100.0000
1
3173
1
chr3D.!!$F1
3172
1
TraesCS3D01G319900
chr3D
490979122
490979873
751
True
1142.0
1142
94.0400
2420
3173
1
chr3D.!!$R2
753
2
TraesCS3D01G319900
chr3A
571795028
571797404
2376
False
3157.0
3157
90.7240
40
2419
1
chr3A.!!$F1
2379
3
TraesCS3D01G319900
chr3B
566182136
566184426
2290
False
2881.0
2881
89.4740
114
2419
1
chr3B.!!$F1
2305
4
TraesCS3D01G319900
chr2D
8995941
9000457
4516
False
1303.5
1321
98.3185
2417
3173
2
chr2D.!!$F1
756
5
TraesCS3D01G319900
chr7D
53416663
53417421
758
False
1295.0
1295
97.4970
2416
3173
1
chr7D.!!$F1
757
6
TraesCS3D01G319900
chr7D
520369664
520370417
753
False
1146.0
1146
94.0630
2417
3173
1
chr7D.!!$F2
756
7
TraesCS3D01G319900
chr1D
91901361
91906436
5075
False
1207.0
1208
95.5030
2417
3172
2
chr1D.!!$F1
755
8
TraesCS3D01G319900
chr6D
394248508
394253321
4813
True
1145.5
1177
94.6080
2420
3173
2
chr6D.!!$R1
753
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.