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
TraesCS5D01G539400
chr5D
100.000
2407
0
0
1
2407
551022902
551020496
0.000000e+00
4446.0
1
TraesCS5D01G539400
chr5D
95.304
1725
32
17
715
2407
254535455
254533748
0.000000e+00
2691.0
2
TraesCS5D01G539400
chr5D
97.357
719
17
2
1
717
254536572
254535854
0.000000e+00
1221.0
3
TraesCS5D01G539400
chr7D
96.928
1725
19
6
715
2407
509916107
509914385
0.000000e+00
2861.0
4
TraesCS5D01G539400
chr7D
96.932
717
20
1
1
717
509917138
509916424
0.000000e+00
1201.0
5
TraesCS5D01G539400
chr2A
97.048
1694
38
5
724
2407
721732797
721734488
0.000000e+00
2841.0
6
TraesCS5D01G539400
chr2A
95.317
961
14
11
1453
2407
195111437
195112372
0.000000e+00
1496.0
7
TraesCS5D01G539400
chr2A
96.234
717
25
1
1
717
721731674
721732388
0.000000e+00
1173.0
8
TraesCS5D01G539400
chr2A
96.979
629
18
1
715
1343
195110437
195111064
0.000000e+00
1055.0
9
TraesCS5D01G539400
chr7A
95.814
1696
33
7
724
2407
678173856
678172187
0.000000e+00
2704.0
10
TraesCS5D01G539400
chr7A
96.513
717
24
1
1
717
678174978
678174263
0.000000e+00
1184.0
11
TraesCS5D01G539400
chr1A
97.330
1086
15
6
1335
2407
14530328
14529244
0.000000e+00
1832.0
12
TraesCS5D01G539400
chr1A
97.297
629
16
1
715
1343
14530994
14530367
0.000000e+00
1066.0
13
TraesCS5D01G539400
chr1A
93.007
715
20
10
1
715
14532079
14531395
0.000000e+00
1016.0
14
TraesCS5D01G539400
chr4D
96.916
908
6
4
1508
2407
40829854
40830747
0.000000e+00
1502.0
15
TraesCS5D01G539400
chr4D
96.566
728
22
2
1
725
40828032
40828759
0.000000e+00
1203.0
16
TraesCS5D01G539400
chr4D
97.138
629
17
1
715
1343
40829149
40829776
0.000000e+00
1061.0
17
TraesCS5D01G539400
chr4D
86.084
618
73
6
716
1333
315816947
315817551
0.000000e+00
652.0
18
TraesCS5D01G539400
chr4D
87.324
71
8
1
645
715
197775302
197775371
1.980000e-11
80.5
19
TraesCS5D01G539400
chr1B
94.888
978
21
9
715
1665
154145566
154146541
0.000000e+00
1502.0
20
TraesCS5D01G539400
chr1B
95.213
961
15
11
1453
2407
154146541
154147476
0.000000e+00
1491.0
21
TraesCS5D01G539400
chr1B
89.327
431
26
7
1994
2407
55536878
55536451
7.620000e-145
523.0
22
TraesCS5D01G539400
chr3A
93.490
722
39
5
1
717
365957651
365956933
0.000000e+00
1066.0
23
TraesCS5D01G539400
chr2D
93.075
722
41
4
1
717
361711292
361712009
0.000000e+00
1048.0
24
TraesCS5D01G539400
chr1D
90.868
657
42
10
1332
1976
479501988
479502638
0.000000e+00
865.0
25
TraesCS5D01G539400
chrUn
90.152
660
47
11
1332
1979
260016889
260016236
0.000000e+00
843.0
26
TraesCS5D01G539400
chrUn
99.156
237
2
0
2171
2407
480831434
480831198
6.150000e-116
427.0
27
TraesCS5D01G539400
chr2B
87.117
652
69
7
1
640
131077500
131078148
0.000000e+00
725.0
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
TraesCS5D01G539400
chr5D
551020496
551022902
2406
True
4446.000000
4446
100.000000
1
2407
1
chr5D.!!$R1
2406
1
TraesCS5D01G539400
chr5D
254533748
254536572
2824
True
1956.000000
2691
96.330500
1
2407
2
chr5D.!!$R2
2406
2
TraesCS5D01G539400
chr7D
509914385
509917138
2753
True
2031.000000
2861
96.930000
1
2407
2
chr7D.!!$R1
2406
3
TraesCS5D01G539400
chr2A
721731674
721734488
2814
False
2007.000000
2841
96.641000
1
2407
2
chr2A.!!$F2
2406
4
TraesCS5D01G539400
chr2A
195110437
195112372
1935
False
1275.500000
1496
96.148000
715
2407
2
chr2A.!!$F1
1692
5
TraesCS5D01G539400
chr7A
678172187
678174978
2791
True
1944.000000
2704
96.163500
1
2407
2
chr7A.!!$R1
2406
6
TraesCS5D01G539400
chr1A
14529244
14532079
2835
True
1304.666667
1832
95.878000
1
2407
3
chr1A.!!$R1
2406
7
TraesCS5D01G539400
chr4D
40828032
40830747
2715
False
1255.333333
1502
96.873333
1
2407
3
chr4D.!!$F3
2406
8
TraesCS5D01G539400
chr4D
315816947
315817551
604
False
652.000000
652
86.084000
716
1333
1
chr4D.!!$F2
617
9
TraesCS5D01G539400
chr1B
154145566
154147476
1910
False
1496.500000
1502
95.050500
715
2407
2
chr1B.!!$F1
1692
10
TraesCS5D01G539400
chr3A
365956933
365957651
718
True
1066.000000
1066
93.490000
1
717
1
chr3A.!!$R1
716
11
TraesCS5D01G539400
chr2D
361711292
361712009
717
False
1048.000000
1048
93.075000
1
717
1
chr2D.!!$F1
716
12
TraesCS5D01G539400
chr1D
479501988
479502638
650
False
865.000000
865
90.868000
1332
1976
1
chr1D.!!$F1
644
13
TraesCS5D01G539400
chrUn
260016236
260016889
653
True
843.000000
843
90.152000
1332
1979
1
chrUn.!!$R1
647
14
TraesCS5D01G539400
chr2B
131077500
131078148
648
False
725.000000
725
87.117000
1
640
1
chr2B.!!$F1
639
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.