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
TraesCS3B01G434700
chr3B
100.000
3423
0
0
1
3423
672959970
672963392
0.000000e+00
6322.0
1
TraesCS3B01G434700
chr3B
98.575
1895
15
1
1541
3423
673061358
673063252
0.000000e+00
3339.0
2
TraesCS3B01G434700
chr3B
99.261
677
4
1
864
1539
673060514
673061190
0.000000e+00
1221.0
3
TraesCS3B01G434700
chr3B
83.129
1061
136
27
1223
2263
674280694
674279657
0.000000e+00
928.0
4
TraesCS3B01G434700
chr3B
92.308
195
12
3
944
1138
673011558
673011749
1.210000e-69
274.0
5
TraesCS3B01G434700
chr3B
92.308
195
12
3
944
1138
673057422
673057613
1.210000e-69
274.0
6
TraesCS3B01G434700
chr3B
97.436
39
1
0
834
872
673059074
673059112
2.200000e-07
67.6
7
TraesCS3B01G434700
chr3A
95.581
2082
77
4
1129
3199
647490696
647492773
0.000000e+00
3321.0
8
TraesCS3B01G434700
chr3A
80.592
979
131
33
1694
2634
647803014
647802057
0.000000e+00
701.0
9
TraesCS3B01G434700
chr3A
83.544
316
19
15
838
1127
647485422
647485730
7.280000e-67
265.0
10
TraesCS3B01G434700
chr3A
90.805
87
7
1
3337
3423
647493325
647493410
7.760000e-22
115.0
11
TraesCS3B01G434700
chr3D
96.639
952
32
0
1161
2112
511395904
511396855
0.000000e+00
1581.0
12
TraesCS3B01G434700
chr3D
82.852
1522
183
49
1223
2706
511941715
511940234
0.000000e+00
1293.0
13
TraesCS3B01G434700
chr3D
90.535
729
66
2
1
729
527521500
527520775
0.000000e+00
961.0
14
TraesCS3B01G434700
chr3D
96.339
437
12
2
2363
2798
511405579
511406012
0.000000e+00
715.0
15
TraesCS3B01G434700
chr3D
93.657
268
12
1
2797
3059
511406050
511406317
2.480000e-106
396.0
16
TraesCS3B01G434700
chr3D
92.627
217
6
1
2108
2324
511405373
511405579
1.540000e-78
303.0
17
TraesCS3B01G434700
chr3D
91.758
182
7
5
957
1138
511394351
511394524
2.640000e-61
246.0
18
TraesCS3B01G434700
chr3D
94.253
87
4
1
3337
3423
511421647
511421732
7.710000e-27
132.0
19
TraesCS3B01G434700
chr3D
100.000
44
0
0
1129
1172
511395759
511395802
7.870000e-12
82.4
20
TraesCS3B01G434700
chrUn
99.261
677
4
1
864
1539
386104297
386103621
0.000000e+00
1221.0
21
TraesCS3B01G434700
chrUn
91.245
731
61
2
1
730
94298025
94297297
0.000000e+00
992.0
22
TraesCS3B01G434700
chrUn
90.698
731
65
2
1
730
94262244
94261516
0.000000e+00
970.0
23
TraesCS3B01G434700
chr1D
92.170
728
52
4
4
729
426866273
426865549
0.000000e+00
1024.0
24
TraesCS3B01G434700
chr6D
91.495
729
59
2
1
728
386908596
386909322
0.000000e+00
1000.0
25
TraesCS3B01G434700
chr5D
90.822
730
64
2
1
729
66771666
66772393
0.000000e+00
974.0
26
TraesCS3B01G434700
chr4D
90.809
729
63
3
1
729
359114502
359113778
0.000000e+00
972.0
27
TraesCS3B01G434700
chr4D
90.535
729
66
2
1
729
13341634
13342359
0.000000e+00
961.0
28
TraesCS3B01G434700
chr2D
90.809
729
62
4
1
729
152877159
152877882
0.000000e+00
970.0
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
TraesCS3B01G434700
chr3B
672959970
672963392
3422
False
6322.000000
6322
100.000000
1
3423
1
chr3B.!!$F1
3422
1
TraesCS3B01G434700
chr3B
673057422
673063252
5830
False
1225.400000
3339
96.895000
834
3423
4
chr3B.!!$F3
2589
2
TraesCS3B01G434700
chr3B
674279657
674280694
1037
True
928.000000
928
83.129000
1223
2263
1
chr3B.!!$R1
1040
3
TraesCS3B01G434700
chr3A
647490696
647493410
2714
False
1718.000000
3321
93.193000
1129
3423
2
chr3A.!!$F2
2294
4
TraesCS3B01G434700
chr3A
647802057
647803014
957
True
701.000000
701
80.592000
1694
2634
1
chr3A.!!$R1
940
5
TraesCS3B01G434700
chr3D
511940234
511941715
1481
True
1293.000000
1293
82.852000
1223
2706
1
chr3D.!!$R1
1483
6
TraesCS3B01G434700
chr3D
527520775
527521500
725
True
961.000000
961
90.535000
1
729
1
chr3D.!!$R2
728
7
TraesCS3B01G434700
chr3D
511394351
511396855
2504
False
636.466667
1581
96.132333
957
2112
3
chr3D.!!$F2
1155
8
TraesCS3B01G434700
chr3D
511405373
511406317
944
False
471.333333
715
94.207667
2108
3059
3
chr3D.!!$F3
951
9
TraesCS3B01G434700
chrUn
386103621
386104297
676
True
1221.000000
1221
99.261000
864
1539
1
chrUn.!!$R3
675
10
TraesCS3B01G434700
chrUn
94297297
94298025
728
True
992.000000
992
91.245000
1
730
1
chrUn.!!$R2
729
11
TraesCS3B01G434700
chrUn
94261516
94262244
728
True
970.000000
970
90.698000
1
730
1
chrUn.!!$R1
729
12
TraesCS3B01G434700
chr1D
426865549
426866273
724
True
1024.000000
1024
92.170000
4
729
1
chr1D.!!$R1
725
13
TraesCS3B01G434700
chr6D
386908596
386909322
726
False
1000.000000
1000
91.495000
1
728
1
chr6D.!!$F1
727
14
TraesCS3B01G434700
chr5D
66771666
66772393
727
False
974.000000
974
90.822000
1
729
1
chr5D.!!$F1
728
15
TraesCS3B01G434700
chr4D
359113778
359114502
724
True
972.000000
972
90.809000
1
729
1
chr4D.!!$R1
728
16
TraesCS3B01G434700
chr4D
13341634
13342359
725
False
961.000000
961
90.535000
1
729
1
chr4D.!!$F1
728
17
TraesCS3B01G434700
chr2D
152877159
152877882
723
False
970.000000
970
90.809000
1
729
1
chr2D.!!$F1
728
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.