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
TraesCS3B01G223100
chr3B
100.000
2841
0
0
1
2841
289834808
289837648
0.000000e+00
5247
1
TraesCS3B01G223100
chr3B
90.785
1606
127
19
1
1593
533671880
533670283
0.000000e+00
2126
2
TraesCS3B01G223100
chr3B
90.050
1588
141
13
1
1578
453572008
453570428
0.000000e+00
2041
3
TraesCS3B01G223100
chr3B
89.409
1558
155
9
26
1576
81049924
81051478
0.000000e+00
1954
4
TraesCS3B01G223100
chr3B
88.311
1249
107
24
1630
2841
284885577
284884331
0.000000e+00
1461
5
TraesCS3B01G223100
chr4B
93.640
2846
155
23
12
2841
207928244
207925409
0.000000e+00
4229
6
TraesCS3B01G223100
chr4B
89.407
2851
239
43
39
2841
486848462
486845627
0.000000e+00
3533
7
TraesCS3B01G223100
chr4B
83.997
2662
347
62
34
2644
154113666
154111033
0.000000e+00
2483
8
TraesCS3B01G223100
chr1B
94.001
2684
118
23
198
2841
534467428
534470108
0.000000e+00
4024
9
TraesCS3B01G223100
chr1B
89.461
2875
228
45
27
2841
475662759
475665618
0.000000e+00
3561
10
TraesCS3B01G223100
chr7B
91.794
2815
210
19
39
2841
182947006
182944201
0.000000e+00
3899
11
TraesCS3B01G223100
chr7B
86.047
2924
308
60
1
2841
518290322
518287416
0.000000e+00
3048
12
TraesCS3B01G223100
chr7B
86.031
1353
131
36
1539
2841
360406475
360405131
0.000000e+00
1399
13
TraesCS3B01G223100
chr7B
85.344
1351
139
40
1539
2841
594476100
594474761
0.000000e+00
1343
14
TraesCS3B01G223100
chr7B
85.344
1351
139
40
1539
2841
594480487
594479148
0.000000e+00
1343
15
TraesCS3B01G223100
chr2B
90.157
2794
226
33
80
2841
575350886
575353662
0.000000e+00
3591
16
TraesCS3B01G223100
chr2B
90.018
2805
208
43
96
2841
405161439
405164230
0.000000e+00
3563
17
TraesCS3B01G223100
chr2B
94.801
1981
71
20
891
2841
279188892
279186914
0.000000e+00
3059
18
TraesCS3B01G223100
chr2B
85.000
240
31
5
1
237
272995398
272995161
3.660000e-59
239
19
TraesCS3B01G223100
chr2B
79.348
184
26
11
1
177
279185183
279185005
4.970000e-23
119
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
TraesCS3B01G223100
chr3B
289834808
289837648
2840
False
5247
5247
100.0000
1
2841
1
chr3B.!!$F2
2840
1
TraesCS3B01G223100
chr3B
533670283
533671880
1597
True
2126
2126
90.7850
1
1593
1
chr3B.!!$R3
1592
2
TraesCS3B01G223100
chr3B
453570428
453572008
1580
True
2041
2041
90.0500
1
1578
1
chr3B.!!$R2
1577
3
TraesCS3B01G223100
chr3B
81049924
81051478
1554
False
1954
1954
89.4090
26
1576
1
chr3B.!!$F1
1550
4
TraesCS3B01G223100
chr3B
284884331
284885577
1246
True
1461
1461
88.3110
1630
2841
1
chr3B.!!$R1
1211
5
TraesCS3B01G223100
chr4B
207925409
207928244
2835
True
4229
4229
93.6400
12
2841
1
chr4B.!!$R2
2829
6
TraesCS3B01G223100
chr4B
486845627
486848462
2835
True
3533
3533
89.4070
39
2841
1
chr4B.!!$R3
2802
7
TraesCS3B01G223100
chr4B
154111033
154113666
2633
True
2483
2483
83.9970
34
2644
1
chr4B.!!$R1
2610
8
TraesCS3B01G223100
chr1B
534467428
534470108
2680
False
4024
4024
94.0010
198
2841
1
chr1B.!!$F2
2643
9
TraesCS3B01G223100
chr1B
475662759
475665618
2859
False
3561
3561
89.4610
27
2841
1
chr1B.!!$F1
2814
10
TraesCS3B01G223100
chr7B
182944201
182947006
2805
True
3899
3899
91.7940
39
2841
1
chr7B.!!$R1
2802
11
TraesCS3B01G223100
chr7B
518287416
518290322
2906
True
3048
3048
86.0470
1
2841
1
chr7B.!!$R3
2840
12
TraesCS3B01G223100
chr7B
360405131
360406475
1344
True
1399
1399
86.0310
1539
2841
1
chr7B.!!$R2
1302
13
TraesCS3B01G223100
chr7B
594474761
594480487
5726
True
1343
1343
85.3440
1539
2841
2
chr7B.!!$R4
1302
14
TraesCS3B01G223100
chr2B
575350886
575353662
2776
False
3591
3591
90.1570
80
2841
1
chr2B.!!$F2
2761
15
TraesCS3B01G223100
chr2B
405161439
405164230
2791
False
3563
3563
90.0180
96
2841
1
chr2B.!!$F1
2745
16
TraesCS3B01G223100
chr2B
279185005
279188892
3887
True
1589
3059
87.0745
1
2841
2
chr2B.!!$R2
2840
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.