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
TraesCS1A01G230900
chr1A
100.000
2664
0
0
1
2664
403631277
403633940
0.000000e+00
4920.0
1
TraesCS1A01G230900
chr1B
88.533
2468
141
65
297
2664
432380110
432377685
0.000000e+00
2859.0
2
TraesCS1A01G230900
chr1B
94.030
134
7
1
130
262
432380251
432380118
4.500000e-48
202.0
3
TraesCS1A01G230900
chr1B
77.733
247
32
14
272
508
432379877
432380110
2.150000e-26
130.0
4
TraesCS1A01G230900
chr1B
91.954
87
7
0
54
140
432380611
432380525
3.600000e-24
122.0
5
TraesCS1A01G230900
chr1D
90.180
1110
55
18
860
1928
319618133
319617037
0.000000e+00
1397.0
6
TraesCS1A01G230900
chr1D
88.175
778
63
19
10
767
319618900
319618132
0.000000e+00
900.0
7
TraesCS1A01G230900
chr1D
93.415
410
19
6
2256
2664
319616051
319615649
3.790000e-168
601.0
8
TraesCS1A01G230900
chr1D
87.826
345
20
8
1931
2257
319616976
319616636
4.160000e-103
385.0
9
TraesCS1A01G230900
chr2B
80.526
1217
102
61
614
1719
7684514
7683322
0.000000e+00
809.0
10
TraesCS1A01G230900
chr2A
79.648
1194
122
61
642
1719
2709303
2708115
0.000000e+00
747.0
11
TraesCS1A01G230900
chr2D
78.901
1237
116
68
615
1719
3004302
3005525
0.000000e+00
704.0
12
TraesCS1A01G230900
chr7D
84.868
304
18
9
2381
2664
470227796
470227501
5.610000e-72
281.0
13
TraesCS1A01G230900
chr7D
89.177
231
14
5
2076
2296
470228025
470227796
7.260000e-71
278.0
14
TraesCS1A01G230900
chr7D
75.380
329
48
24
255
570
48362462
48362770
7.740000e-26
128.0
15
TraesCS1A01G230900
chr7D
97.222
36
1
0
2016
2051
470228059
470228024
7.960000e-06
62.1
16
TraesCS1A01G230900
chr3D
82.877
292
36
5
283
572
20693103
20692824
1.580000e-62
250.0
17
TraesCS1A01G230900
chr5D
78.361
305
48
14
271
571
517281373
517281663
5.860000e-42
182.0
18
TraesCS1A01G230900
chr5D
78.571
196
30
5
376
571
40181280
40181463
4.660000e-23
119.0
19
TraesCS1A01G230900
chr5D
82.258
124
15
4
409
532
72874682
72874566
1.690000e-17
100.0
20
TraesCS1A01G230900
chr5D
83.133
83
12
2
448
528
40919823
40919905
1.020000e-09
75.0
21
TraesCS1A01G230900
chr5A
79.851
268
35
16
271
533
644359551
644359804
7.580000e-41
178.0
22
TraesCS1A01G230900
chr3B
77.124
306
50
15
276
571
801157346
801157641
2.740000e-35
159.0
23
TraesCS1A01G230900
chr4D
77.288
295
40
22
272
550
357262663
357262946
5.940000e-32
148.0
24
TraesCS1A01G230900
chr4B
78.148
270
34
17
273
532
440583997
440584251
5.940000e-32
148.0
25
TraesCS1A01G230900
chr4A
73.288
292
41
24
271
550
625068603
625068337
3.680000e-09
73.1
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
TraesCS1A01G230900
chr1A
403631277
403633940
2663
False
4920.000000
4920
100.000000
1
2664
1
chr1A.!!$F1
2663
1
TraesCS1A01G230900
chr1B
432377685
432380611
2926
True
1061.000000
2859
91.505667
54
2664
3
chr1B.!!$R1
2610
2
TraesCS1A01G230900
chr1D
319615649
319618900
3251
True
820.750000
1397
89.899000
10
2664
4
chr1D.!!$R1
2654
3
TraesCS1A01G230900
chr2B
7683322
7684514
1192
True
809.000000
809
80.526000
614
1719
1
chr2B.!!$R1
1105
4
TraesCS1A01G230900
chr2A
2708115
2709303
1188
True
747.000000
747
79.648000
642
1719
1
chr2A.!!$R1
1077
5
TraesCS1A01G230900
chr2D
3004302
3005525
1223
False
704.000000
704
78.901000
615
1719
1
chr2D.!!$F1
1104
6
TraesCS1A01G230900
chr7D
470227501
470228059
558
True
207.033333
281
90.422333
2016
2664
3
chr7D.!!$R1
648
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.