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
TraesCS3A01G202400
chr3A
100.000
2435
0
0
1
2435
342256289
342253855
0
4497
1
TraesCS3A01G202400
chr3A
95.597
1817
76
4
622
2435
275869251
275871066
0
2909
2
TraesCS3A01G202400
chr3A
94.989
1816
86
5
622
2434
331240709
331238896
0
2844
3
TraesCS3A01G202400
chr3A
93.422
1809
114
5
629
2434
324217174
324215368
0
2676
4
TraesCS3A01G202400
chr3A
93.007
1816
117
10
622
2434
623207005
623208813
0
2641
5
TraesCS3A01G202400
chr3A
94.612
631
30
4
1
628
275868580
275869209
0
974
6
TraesCS3A01G202400
chr3A
94.304
632
32
4
1
628
331241381
331240750
0
965
7
TraesCS3A01G202400
chr3A
93.153
628
40
3
4
628
227378702
227379329
0
918
8
TraesCS3A01G202400
chr5A
94.001
1817
103
6
622
2435
86546020
86547833
0
2747
9
TraesCS3A01G202400
chr5A
93.286
1817
112
7
622
2434
47161184
47162994
0
2671
10
TraesCS3A01G202400
chr5A
92.675
628
43
3
4
628
320333363
320332736
0
902
11
TraesCS3A01G202400
chr5A
92.393
631
44
4
1
628
111357617
111358246
0
896
12
TraesCS3A01G202400
chr5A
92.417
633
41
6
1
628
551132202
551132832
0
896
13
TraesCS3A01G202400
chr1A
93.502
1816
114
4
622
2435
222295262
222297075
0
2697
14
TraesCS3A01G202400
chr1A
93.532
1809
107
6
629
2434
18193966
18192165
0
2684
15
TraesCS3A01G202400
chr1A
93.455
1803
107
8
635
2434
540098212
540096418
0
2665
16
TraesCS3A01G202400
chr7A
93.027
631
41
3
1
628
483243989
483243359
0
918
17
TraesCS3A01G202400
chr4A
92.800
625
43
2
4
626
69935322
69935946
0
904
18
TraesCS3A01G202400
chr2A
92.915
621
42
2
4
622
420087315
420087935
0
902
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
TraesCS3A01G202400
chr3A
342253855
342256289
2434
True
4497.0
4497
100.0000
1
2435
1
chr3A.!!$R2
2434
1
TraesCS3A01G202400
chr3A
324215368
324217174
1806
True
2676.0
2676
93.4220
629
2434
1
chr3A.!!$R1
1805
2
TraesCS3A01G202400
chr3A
623207005
623208813
1808
False
2641.0
2641
93.0070
622
2434
1
chr3A.!!$F2
1812
3
TraesCS3A01G202400
chr3A
275868580
275871066
2486
False
1941.5
2909
95.1045
1
2435
2
chr3A.!!$F3
2434
4
TraesCS3A01G202400
chr3A
331238896
331241381
2485
True
1904.5
2844
94.6465
1
2434
2
chr3A.!!$R3
2433
5
TraesCS3A01G202400
chr3A
227378702
227379329
627
False
918.0
918
93.1530
4
628
1
chr3A.!!$F1
624
6
TraesCS3A01G202400
chr5A
86546020
86547833
1813
False
2747.0
2747
94.0010
622
2435
1
chr5A.!!$F2
1813
7
TraesCS3A01G202400
chr5A
47161184
47162994
1810
False
2671.0
2671
93.2860
622
2434
1
chr5A.!!$F1
1812
8
TraesCS3A01G202400
chr5A
320332736
320333363
627
True
902.0
902
92.6750
4
628
1
chr5A.!!$R1
624
9
TraesCS3A01G202400
chr5A
111357617
111358246
629
False
896.0
896
92.3930
1
628
1
chr5A.!!$F3
627
10
TraesCS3A01G202400
chr5A
551132202
551132832
630
False
896.0
896
92.4170
1
628
1
chr5A.!!$F4
627
11
TraesCS3A01G202400
chr1A
222295262
222297075
1813
False
2697.0
2697
93.5020
622
2435
1
chr1A.!!$F1
1813
12
TraesCS3A01G202400
chr1A
18192165
18193966
1801
True
2684.0
2684
93.5320
629
2434
1
chr1A.!!$R1
1805
13
TraesCS3A01G202400
chr1A
540096418
540098212
1794
True
2665.0
2665
93.4550
635
2434
1
chr1A.!!$R2
1799
14
TraesCS3A01G202400
chr7A
483243359
483243989
630
True
918.0
918
93.0270
1
628
1
chr7A.!!$R1
627
15
TraesCS3A01G202400
chr4A
69935322
69935946
624
False
904.0
904
92.8000
4
626
1
chr4A.!!$F1
622
16
TraesCS3A01G202400
chr2A
420087315
420087935
620
False
902.0
902
92.9150
4
622
1
chr2A.!!$F1
618
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.