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
TraesCS3B01G058300
chr3B
100.000
2549
0
0
1
2549
30406157
30403609
0.000000e+00
4708.0
1
TraesCS3B01G058300
chr3B
93.803
355
12
3
228
572
30099543
30099897
2.250000e-145
525.0
2
TraesCS3B01G058300
chr3B
90.308
227
21
1
346
572
29638276
29638051
1.920000e-76
296.0
3
TraesCS3B01G058300
chr3B
93.421
152
10
0
210
361
29639986
29639835
2.550000e-55
226.0
4
TraesCS3B01G058300
chr3B
96.970
132
4
0
2
133
30098950
30099081
3.300000e-54
222.0
5
TraesCS3B01G058300
chr3B
98.947
95
1
0
39
133
29604608
29604702
1.210000e-38
171.0
6
TraesCS3B01G058300
chr3B
94.737
76
4
0
5
80
29640058
29639983
4.450000e-23
119.0
7
TraesCS3B01G058300
chr6B
99.644
1966
5
2
584
2549
713444661
713446624
0.000000e+00
3591.0
8
TraesCS3B01G058300
chr6B
88.119
101
10
2
121
219
551188211
551188311
4.450000e-23
119.0
9
TraesCS3B01G058300
chr6B
88.119
101
10
2
121
219
551443229
551443329
4.450000e-23
119.0
10
TraesCS3B01G058300
chr2B
99.039
1977
15
3
572
2548
53421420
53423392
0.000000e+00
3542.0
11
TraesCS3B01G058300
chr2B
98.887
1977
20
2
572
2548
776222961
776224935
0.000000e+00
3528.0
12
TraesCS3B01G058300
chr2B
98.837
1977
21
2
572
2548
781094240
781096214
0.000000e+00
3522.0
13
TraesCS3B01G058300
chr2B
90.526
95
7
2
120
214
206711372
206711464
9.580000e-25
124.0
14
TraesCS3B01G058300
chr6A
98.887
1976
21
1
573
2548
507719445
507721419
0.000000e+00
3526.0
15
TraesCS3B01G058300
chr6A
98.786
1977
22
2
572
2548
616131295
616133269
0.000000e+00
3517.0
16
TraesCS3B01G058300
chr7A
98.787
1978
22
2
571
2548
39015366
39017341
0.000000e+00
3518.0
17
TraesCS3B01G058300
chr3A
98.787
1978
21
1
571
2548
54951916
54953890
0.000000e+00
3517.0
18
TraesCS3B01G058300
chr3A
87.968
374
27
8
210
571
26192324
26191957
2.340000e-115
425.0
19
TraesCS3B01G058300
chr3A
91.262
103
9
0
25
127
26193446
26193344
9.510000e-30
141.0
20
TraesCS3B01G058300
chr3A
86.567
67
8
1
238
304
26189680
26189615
3.520000e-09
73.1
21
TraesCS3B01G058300
chr3A
84.507
71
10
1
234
304
26169460
26169391
4.550000e-08
69.4
22
TraesCS3B01G058300
chr5B
98.736
1978
24
1
571
2548
641128781
641126805
0.000000e+00
3513.0
23
TraesCS3B01G058300
chr3D
91.420
338
26
3
210
547
18653802
18653468
6.430000e-126
460.0
24
TraesCS3B01G058300
chr3D
94.253
87
5
0
130
216
24062696
24062610
1.590000e-27
134.0
25
TraesCS3B01G058300
chrUn
90.526
95
9
0
128
222
17148597
17148691
2.660000e-25
126.0
26
TraesCS3B01G058300
chr7D
92.135
89
7
0
128
216
49828774
49828862
2.660000e-25
126.0
27
TraesCS3B01G058300
chr7D
92.222
90
6
1
128
217
565123565
565123477
2.660000e-25
126.0
28
TraesCS3B01G058300
chr1A
92.222
90
6
1
129
217
507880714
507880803
2.660000e-25
126.0
29
TraesCS3B01G058300
chr6D
89.691
97
8
2
121
216
450890401
450890496
3.440000e-24
122.0
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
TraesCS3B01G058300
chr3B
30403609
30406157
2548
True
4708.000000
4708
100.0000
1
2549
1
chr3B.!!$R1
2548
1
TraesCS3B01G058300
chr3B
30098950
30099897
947
False
373.500000
525
95.3865
2
572
2
chr3B.!!$F2
570
2
TraesCS3B01G058300
chr3B
29638051
29640058
2007
True
213.666667
296
92.8220
5
572
3
chr3B.!!$R2
567
3
TraesCS3B01G058300
chr6B
713444661
713446624
1963
False
3591.000000
3591
99.6440
584
2549
1
chr6B.!!$F3
1965
4
TraesCS3B01G058300
chr2B
53421420
53423392
1972
False
3542.000000
3542
99.0390
572
2548
1
chr2B.!!$F1
1976
5
TraesCS3B01G058300
chr2B
776222961
776224935
1974
False
3528.000000
3528
98.8870
572
2548
1
chr2B.!!$F3
1976
6
TraesCS3B01G058300
chr2B
781094240
781096214
1974
False
3522.000000
3522
98.8370
572
2548
1
chr2B.!!$F4
1976
7
TraesCS3B01G058300
chr6A
507719445
507721419
1974
False
3526.000000
3526
98.8870
573
2548
1
chr6A.!!$F1
1975
8
TraesCS3B01G058300
chr6A
616131295
616133269
1974
False
3517.000000
3517
98.7860
572
2548
1
chr6A.!!$F2
1976
9
TraesCS3B01G058300
chr7A
39015366
39017341
1975
False
3518.000000
3518
98.7870
571
2548
1
chr7A.!!$F1
1977
10
TraesCS3B01G058300
chr3A
54951916
54953890
1974
False
3517.000000
3517
98.7870
571
2548
1
chr3A.!!$F1
1977
11
TraesCS3B01G058300
chr3A
26189615
26193446
3831
True
213.033333
425
88.5990
25
571
3
chr3A.!!$R2
546
12
TraesCS3B01G058300
chr5B
641126805
641128781
1976
True
3513.000000
3513
98.7360
571
2548
1
chr5B.!!$R1
1977
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.