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
TraesCS7D01G209900
chr7D
100.000
3173
0
0
1
3173
168065552
168068724
0.000000e+00
5860.0
1
TraesCS7D01G209900
chr7D
95.455
44
2
0
817
860
534456414
534456371
1.580000e-08
71.3
2
TraesCS7D01G209900
chr7B
95.301
2341
48
15
866
3171
133242428
133244741
0.000000e+00
3657.0
3
TraesCS7D01G209900
chr7B
92.546
872
48
12
1
860
708728978
708729844
0.000000e+00
1234.0
4
TraesCS7D01G209900
chr7A
96.554
1480
39
2
869
2345
170188204
170189674
0.000000e+00
2440.0
5
TraesCS7D01G209900
chr7A
94.068
826
28
2
2346
3171
170189703
170190507
0.000000e+00
1234.0
6
TraesCS7D01G209900
chr3D
97.917
864
14
2
1
860
33361935
33361072
0.000000e+00
1493.0
7
TraesCS7D01G209900
chr3D
82.083
240
43
0
2511
2750
587422435
587422196
4.150000e-49
206.0
8
TraesCS7D01G209900
chr6D
97.912
862
15
3
1
860
344159289
344158429
0.000000e+00
1489.0
9
TraesCS7D01G209900
chr6D
97.680
862
17
3
1
860
42506029
42505169
0.000000e+00
1478.0
10
TraesCS7D01G209900
chr6D
96.756
863
24
3
1
860
233688478
233689339
0.000000e+00
1435.0
11
TraesCS7D01G209900
chr2D
96.065
864
29
3
1
860
212009229
212010091
0.000000e+00
1402.0
12
TraesCS7D01G209900
chr2D
83.333
144
10
3
731
860
35976400
35976543
1.550000e-23
121.0
13
TraesCS7D01G209900
chr1A
95.405
827
26
7
1
821
4656253
4657073
0.000000e+00
1306.0
14
TraesCS7D01G209900
chr3B
95.556
450
19
1
84
533
169688868
169689316
0.000000e+00
719.0
15
TraesCS7D01G209900
chr3B
83.830
235
36
2
2510
2743
784455617
784455384
4.120000e-54
222.0
16
TraesCS7D01G209900
chr3B
83.830
235
36
2
2510
2743
784526754
784526521
4.120000e-54
222.0
17
TraesCS7D01G209900
chr3B
81.106
217
36
2
1057
1268
784455975
784455759
5.440000e-38
169.0
18
TraesCS7D01G209900
chr1D
93.709
461
26
2
1
458
32720155
32719695
0.000000e+00
688.0
19
TraesCS7D01G209900
chr1D
91.270
126
8
2
445
567
32719750
32719625
5.440000e-38
169.0
20
TraesCS7D01G209900
chr1D
96.226
53
0
2
810
860
379870795
379870743
5.640000e-13
86.1
21
TraesCS7D01G209900
chr2B
87.676
284
25
9
534
809
553880572
553880291
3.950000e-84
322.0
22
TraesCS7D01G209900
chr4B
90.000
250
17
7
575
820
665900511
665900266
1.840000e-82
316.0
23
TraesCS7D01G209900
chr5A
86.348
293
26
13
537
819
310728464
310728752
1.110000e-79
307.0
24
TraesCS7D01G209900
chr5D
90.323
62
3
2
800
858
551015184
551015123
9.440000e-11
78.7
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
TraesCS7D01G209900
chr7D
168065552
168068724
3172
False
5860.0
5860
100.0000
1
3173
1
chr7D.!!$F1
3172
1
TraesCS7D01G209900
chr7B
133242428
133244741
2313
False
3657.0
3657
95.3010
866
3171
1
chr7B.!!$F1
2305
2
TraesCS7D01G209900
chr7B
708728978
708729844
866
False
1234.0
1234
92.5460
1
860
1
chr7B.!!$F2
859
3
TraesCS7D01G209900
chr7A
170188204
170190507
2303
False
1837.0
2440
95.3110
869
3171
2
chr7A.!!$F1
2302
4
TraesCS7D01G209900
chr3D
33361072
33361935
863
True
1493.0
1493
97.9170
1
860
1
chr3D.!!$R1
859
5
TraesCS7D01G209900
chr6D
344158429
344159289
860
True
1489.0
1489
97.9120
1
860
1
chr6D.!!$R2
859
6
TraesCS7D01G209900
chr6D
42505169
42506029
860
True
1478.0
1478
97.6800
1
860
1
chr6D.!!$R1
859
7
TraesCS7D01G209900
chr6D
233688478
233689339
861
False
1435.0
1435
96.7560
1
860
1
chr6D.!!$F1
859
8
TraesCS7D01G209900
chr2D
212009229
212010091
862
False
1402.0
1402
96.0650
1
860
1
chr2D.!!$F2
859
9
TraesCS7D01G209900
chr1A
4656253
4657073
820
False
1306.0
1306
95.4050
1
821
1
chr1A.!!$F1
820
10
TraesCS7D01G209900
chr1D
32719625
32720155
530
True
428.5
688
92.4895
1
567
2
chr1D.!!$R2
566
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.