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
TraesCS1D01G096300
chr1D
100.000
3598
0
0
1
3598
81480790
81484387
0.000000e+00
6645.0
1
TraesCS1D01G096300
chr1D
87.520
2516
214
60
181
2635
81366117
81368593
0.000000e+00
2815.0
2
TraesCS1D01G096300
chr1D
90.062
161
14
2
1
159
81365969
81366129
1.310000e-49
207.0
3
TraesCS1D01G096300
chr1A
93.651
3654
134
47
2
3598
100038074
100041686
0.000000e+00
5373.0
4
TraesCS1D01G096300
chr1A
89.535
1204
105
13
654
1845
100001832
100003026
0.000000e+00
1506.0
5
TraesCS1D01G096300
chr1A
88.904
739
50
12
1890
2624
100003140
100003850
0.000000e+00
881.0
6
TraesCS1D01G096300
chr1B
88.813
2485
206
45
188
2624
136062772
136065232
0.000000e+00
2983.0
7
TraesCS1D01G096300
chr1B
91.730
2116
122
34
2
2082
136166715
136168812
0.000000e+00
2889.0
8
TraesCS1D01G096300
chr1B
85.343
1501
152
35
181
1628
134722684
134724169
0.000000e+00
1491.0
9
TraesCS1D01G096300
chr1B
94.565
920
36
8
2071
2985
136168832
136169742
0.000000e+00
1410.0
10
TraesCS1D01G096300
chr1B
88.767
1006
84
23
1641
2635
134731147
134732134
0.000000e+00
1205.0
11
TraesCS1D01G096300
chr6A
85.512
283
40
1
3118
3399
422776250
422775968
9.770000e-76
294.0
12
TraesCS1D01G096300
chr6A
84.300
293
40
6
3115
3402
46548852
46549143
7.610000e-72
281.0
13
TraesCS1D01G096300
chr7D
84.615
286
42
2
3118
3402
118874916
118875200
2.110000e-72
283.0
14
TraesCS1D01G096300
chr4D
84.321
287
43
2
3118
3402
45853026
45853312
2.740000e-71
279.0
15
TraesCS1D01G096300
chr3A
84.483
290
38
7
3118
3402
597888027
597887740
2.740000e-71
279.0
16
TraesCS1D01G096300
chr3D
84.452
283
41
3
3118
3398
527520543
527520262
3.540000e-70
276.0
17
TraesCS1D01G096300
chr2A
84.588
279
42
1
3118
3395
52051591
52051313
3.540000e-70
276.0
18
TraesCS1D01G096300
chrUn
84.028
288
41
5
3118
3402
329701517
329701232
4.580000e-69
272.0
19
TraesCS1D01G096300
chr7B
74.442
493
91
22
1522
1995
578403528
578404004
2.850000e-41
180.0
20
TraesCS1D01G096300
chr4B
91.045
67
6
0
1635
1701
483947371
483947437
1.380000e-14
91.6
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
TraesCS1D01G096300
chr1D
81480790
81484387
3597
False
6645.0
6645
100.0000
1
3598
1
chr1D.!!$F1
3597
1
TraesCS1D01G096300
chr1D
81365969
81368593
2624
False
1511.0
2815
88.7910
1
2635
2
chr1D.!!$F2
2634
2
TraesCS1D01G096300
chr1A
100038074
100041686
3612
False
5373.0
5373
93.6510
2
3598
1
chr1A.!!$F1
3596
3
TraesCS1D01G096300
chr1A
100001832
100003850
2018
False
1193.5
1506
89.2195
654
2624
2
chr1A.!!$F2
1970
4
TraesCS1D01G096300
chr1B
136062772
136065232
2460
False
2983.0
2983
88.8130
188
2624
1
chr1B.!!$F3
2436
5
TraesCS1D01G096300
chr1B
136166715
136169742
3027
False
2149.5
2889
93.1475
2
2985
2
chr1B.!!$F4
2983
6
TraesCS1D01G096300
chr1B
134722684
134724169
1485
False
1491.0
1491
85.3430
181
1628
1
chr1B.!!$F1
1447
7
TraesCS1D01G096300
chr1B
134731147
134732134
987
False
1205.0
1205
88.7670
1641
2635
1
chr1B.!!$F2
994
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.