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
TraesCS2A01G158000
chr2A
100.000
3730
0
0
1
3730
104969145
104972874
0.000000e+00
6889.0
1
TraesCS2A01G158000
chr2A
88.235
1122
116
10
862
1976
105032642
105033754
0.000000e+00
1327.0
2
TraesCS2A01G158000
chr2A
91.468
504
39
4
2523
3025
105045241
105045741
0.000000e+00
689.0
3
TraesCS2A01G158000
chr2A
94.118
289
17
0
1974
2262
105034105
105034393
1.230000e-119
440.0
4
TraesCS2A01G158000
chr2A
79.024
410
47
25
3341
3729
105046308
105046699
1.030000e-60
244.0
5
TraesCS2A01G158000
chr2A
91.329
173
14
1
2349
2520
105043393
105043565
6.230000e-58
235.0
6
TraesCS2A01G158000
chr2B
93.417
3175
138
24
590
3729
158642188
158645326
0.000000e+00
4639.0
7
TraesCS2A01G158000
chr2B
94.543
1576
81
5
1422
2996
158780761
158782332
0.000000e+00
2429.0
8
TraesCS2A01G158000
chr2B
93.345
556
21
6
37
584
158641602
158642149
0.000000e+00
808.0
9
TraesCS2A01G158000
chr2B
84.689
836
86
16
2197
3025
159007087
159007887
0.000000e+00
797.0
10
TraesCS2A01G158000
chr2B
83.250
597
46
18
3155
3730
158782332
158782895
2.000000e-137
499.0
11
TraesCS2A01G158000
chr2B
90.535
243
23
0
3060
3302
159012834
159013076
4.650000e-84
322.0
12
TraesCS2A01G158000
chr2B
87.440
207
18
4
3526
3730
159095801
159096001
8.060000e-57
231.0
13
TraesCS2A01G158000
chr2B
97.436
39
1
0
1
39
158641530
158641568
2.400000e-07
67.6
14
TraesCS2A01G158000
chr2D
90.903
2946
186
36
615
3517
109000517
109003423
0.000000e+00
3880.0
15
TraesCS2A01G158000
chr2D
93.275
1026
62
7
2003
3025
109120414
109121435
0.000000e+00
1506.0
16
TraesCS2A01G158000
chr2D
84.467
1294
150
27
928
2176
109043357
109044644
0.000000e+00
1229.0
17
TraesCS2A01G158000
chr2D
95.550
764
32
2
2172
2934
109046362
109047124
0.000000e+00
1221.0
18
TraesCS2A01G158000
chr2D
88.320
899
100
4
2124
3019
109392189
109393085
0.000000e+00
1074.0
19
TraesCS2A01G158000
chr2D
85.754
723
69
17
3024
3730
109121518
109122222
0.000000e+00
734.0
20
TraesCS2A01G158000
chr2D
94.670
469
21
3
37
501
109000008
109000476
0.000000e+00
725.0
21
TraesCS2A01G158000
chr2D
93.636
440
17
6
3299
3730
109070275
109070711
0.000000e+00
647.0
22
TraesCS2A01G158000
chr2D
96.154
390
13
2
2928
3316
109069667
109070055
1.460000e-178
636.0
23
TraesCS2A01G158000
chr2D
92.582
364
24
1
1260
1620
109107346
109107709
1.540000e-143
520.0
24
TraesCS2A01G158000
chr2D
91.518
224
18
1
1695
1917
109113269
109113492
1.300000e-79
307.0
25
TraesCS2A01G158000
chr2D
100.000
35
0
0
1
35
108999939
108999973
8.650000e-07
65.8
26
TraesCS2A01G158000
chr4A
93.182
88
4
2
528
614
539752740
539752826
1.090000e-25
128.0
27
TraesCS2A01G158000
chr6A
92.683
82
5
1
535
615
77887272
77887191
2.350000e-22
117.0
28
TraesCS2A01G158000
chr6A
92.683
82
5
1
535
615
78016785
78016704
2.350000e-22
117.0
29
TraesCS2A01G158000
chr6A
90.805
87
7
1
530
615
77986104
77986018
8.470000e-22
115.0
30
TraesCS2A01G158000
chr6A
90.909
88
5
3
530
615
78134881
78134795
8.470000e-22
115.0
31
TraesCS2A01G158000
chr1D
90.909
88
5
2
530
615
121773735
121773649
8.470000e-22
115.0
32
TraesCS2A01G158000
chr1D
89.011
91
7
1
528
615
268535952
268535862
3.940000e-20
110.0
33
TraesCS2A01G158000
chr6B
89.773
88
6
1
530
617
710004839
710004755
3.940000e-20
110.0
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
TraesCS2A01G158000
chr2A
104969145
104972874
3729
False
6889.000000
6889
100.000000
1
3730
1
chr2A.!!$F1
3729
1
TraesCS2A01G158000
chr2A
105032642
105034393
1751
False
883.500000
1327
91.176500
862
2262
2
chr2A.!!$F2
1400
2
TraesCS2A01G158000
chr2A
105043393
105046699
3306
False
389.333333
689
87.273667
2349
3729
3
chr2A.!!$F3
1380
3
TraesCS2A01G158000
chr2B
158641530
158645326
3796
False
1838.200000
4639
94.732667
1
3729
3
chr2B.!!$F4
3728
4
TraesCS2A01G158000
chr2B
158780761
158782895
2134
False
1464.000000
2429
88.896500
1422
3730
2
chr2B.!!$F5
2308
5
TraesCS2A01G158000
chr2B
159007087
159007887
800
False
797.000000
797
84.689000
2197
3025
1
chr2B.!!$F1
828
6
TraesCS2A01G158000
chr2D
108999939
109003423
3484
False
1556.933333
3880
95.191000
1
3517
3
chr2D.!!$F4
3516
7
TraesCS2A01G158000
chr2D
109043357
109047124
3767
False
1225.000000
1229
90.008500
928
2934
2
chr2D.!!$F5
2006
8
TraesCS2A01G158000
chr2D
109120414
109122222
1808
False
1120.000000
1506
89.514500
2003
3730
2
chr2D.!!$F7
1727
9
TraesCS2A01G158000
chr2D
109392189
109393085
896
False
1074.000000
1074
88.320000
2124
3019
1
chr2D.!!$F3
895
10
TraesCS2A01G158000
chr2D
109069667
109070711
1044
False
641.500000
647
94.895000
2928
3730
2
chr2D.!!$F6
802
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.