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
TraesCS7A01G125700
chr7A
100.000
3794
0
0
1
3794
80861021
80864814
0.000000e+00
7007
1
TraesCS7A01G125700
chr7D
95.118
3503
97
12
329
3794
76742919
76746384
0.000000e+00
5454
2
TraesCS7A01G125700
chr7D
90.986
2940
212
23
881
3794
76919223
76922135
0.000000e+00
3912
3
TraesCS7A01G125700
chr7D
85.931
2971
370
35
855
3794
76784059
76787012
0.000000e+00
3127
4
TraesCS7A01G125700
chr7D
93.092
1520
100
2
2280
3794
77045885
77047404
0.000000e+00
2220
5
TraesCS7A01G125700
chr7D
86.284
1881
221
20
1942
3794
76973468
76975339
0.000000e+00
2010
6
TraesCS7A01G125700
chr7D
85.157
1974
267
17
1771
3727
76930700
76932664
0.000000e+00
1999
7
TraesCS7A01G125700
chr7D
83.739
1974
270
34
1775
3719
76624400
76622449
0.000000e+00
1820
8
TraesCS7A01G125700
chr7D
86.358
1642
182
28
2173
3794
76955728
76957347
0.000000e+00
1753
9
TraesCS7A01G125700
chr7D
84.220
1635
232
18
1004
2619
7548419
7550046
0.000000e+00
1567
10
TraesCS7A01G125700
chr7D
83.591
1682
250
18
955
2619
7561062
7562734
0.000000e+00
1554
11
TraesCS7A01G125700
chr7D
92.857
252
14
4
2
251
76742518
76742767
2.790000e-96
363
12
TraesCS7A01G125700
chr7B
86.172
3464
396
34
373
3794
23596114
23599536
0.000000e+00
3666
13
TraesCS7A01G125700
chr7B
86.669
2678
330
16
1133
3794
23958164
23960830
0.000000e+00
2942
14
TraesCS7A01G125700
chr7B
87.855
2009
210
21
1794
3777
23525380
23527379
0.000000e+00
2327
15
TraesCS7A01G125700
chr7B
84.986
1845
253
17
886
2719
23582227
23584058
0.000000e+00
1851
16
TraesCS7A01G125700
chr7B
86.151
1242
131
21
563
1784
23515693
23516913
0.000000e+00
1303
17
TraesCS7A01G125700
chr7B
91.667
288
21
3
2
287
23515209
23515495
2.750000e-106
396
18
TraesCS7A01G125700
chr7B
88.511
235
11
5
3
235
23595892
23596112
1.740000e-68
270
19
TraesCS7A01G125700
chr3B
84.086
1684
237
20
955
2619
741463155
741464826
0.000000e+00
1596
20
TraesCS7A01G125700
chr4A
84.198
1658
244
8
1004
2646
731616816
731615162
0.000000e+00
1594
21
TraesCS7A01G125700
chr5A
83.154
279
38
8
1
277
695553980
695554251
2.930000e-61
246
22
TraesCS7A01G125700
chr5A
80.687
233
33
9
401
626
546532017
546531790
1.810000e-38
171
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
TraesCS7A01G125700
chr7A
80861021
80864814
3793
False
7007.0
7007
100.0000
1
3794
1
chr7A.!!$F1
3793
1
TraesCS7A01G125700
chr7D
76919223
76922135
2912
False
3912.0
3912
90.9860
881
3794
1
chr7D.!!$F4
2913
2
TraesCS7A01G125700
chr7D
76784059
76787012
2953
False
3127.0
3127
85.9310
855
3794
1
chr7D.!!$F3
2939
3
TraesCS7A01G125700
chr7D
76742518
76746384
3866
False
2908.5
5454
93.9875
2
3794
2
chr7D.!!$F9
3792
4
TraesCS7A01G125700
chr7D
77045885
77047404
1519
False
2220.0
2220
93.0920
2280
3794
1
chr7D.!!$F8
1514
5
TraesCS7A01G125700
chr7D
76973468
76975339
1871
False
2010.0
2010
86.2840
1942
3794
1
chr7D.!!$F7
1852
6
TraesCS7A01G125700
chr7D
76930700
76932664
1964
False
1999.0
1999
85.1570
1771
3727
1
chr7D.!!$F5
1956
7
TraesCS7A01G125700
chr7D
76622449
76624400
1951
True
1820.0
1820
83.7390
1775
3719
1
chr7D.!!$R1
1944
8
TraesCS7A01G125700
chr7D
76955728
76957347
1619
False
1753.0
1753
86.3580
2173
3794
1
chr7D.!!$F6
1621
9
TraesCS7A01G125700
chr7D
7548419
7550046
1627
False
1567.0
1567
84.2200
1004
2619
1
chr7D.!!$F1
1615
10
TraesCS7A01G125700
chr7D
7561062
7562734
1672
False
1554.0
1554
83.5910
955
2619
1
chr7D.!!$F2
1664
11
TraesCS7A01G125700
chr7B
23958164
23960830
2666
False
2942.0
2942
86.6690
1133
3794
1
chr7B.!!$F3
2661
12
TraesCS7A01G125700
chr7B
23525380
23527379
1999
False
2327.0
2327
87.8550
1794
3777
1
chr7B.!!$F1
1983
13
TraesCS7A01G125700
chr7B
23595892
23599536
3644
False
1968.0
3666
87.3415
3
3794
2
chr7B.!!$F5
3791
14
TraesCS7A01G125700
chr7B
23582227
23584058
1831
False
1851.0
1851
84.9860
886
2719
1
chr7B.!!$F2
1833
15
TraesCS7A01G125700
chr7B
23515209
23516913
1704
False
849.5
1303
88.9090
2
1784
2
chr7B.!!$F4
1782
16
TraesCS7A01G125700
chr3B
741463155
741464826
1671
False
1596.0
1596
84.0860
955
2619
1
chr3B.!!$F1
1664
17
TraesCS7A01G125700
chr4A
731615162
731616816
1654
True
1594.0
1594
84.1980
1004
2646
1
chr4A.!!$R1
1642
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.