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
TraesCS3A01G233500
chr3A
100.000
2477
0
0
1
2477
435815150
435817626
0.000000e+00
4575
1
TraesCS3A01G233500
chr2D
94.448
1513
80
4
3
1512
480564338
480562827
0.000000e+00
2326
2
TraesCS3A01G233500
chr2D
93.011
186
13
0
2292
2477
119891612
119891427
3.140000e-69
272
3
TraesCS3A01G233500
chr2D
92.857
182
13
0
2291
2472
206254126
206253945
5.250000e-67
265
4
TraesCS3A01G233500
chr2D
84.112
107
17
0
2122
2228
561221097
561220991
1.210000e-18
104
5
TraesCS3A01G233500
chrUn
94.157
1506
84
3
1
1504
200779660
200781163
0.000000e+00
2290
6
TraesCS3A01G233500
chrUn
94.145
1503
84
3
4
1504
234324850
234323350
0.000000e+00
2285
7
TraesCS3A01G233500
chrUn
94.079
1503
85
3
4
1504
200673526
200672026
0.000000e+00
2279
8
TraesCS3A01G233500
chrUn
94.024
1506
86
3
1
1504
200754725
200756228
0.000000e+00
2279
9
TraesCS3A01G233500
chr6B
94.024
1506
86
3
1
1504
8638566
8640069
0.000000e+00
2279
10
TraesCS3A01G233500
chr6B
94.024
1506
86
3
1
1504
8650736
8652239
0.000000e+00
2279
11
TraesCS3A01G233500
chr6B
93.958
1506
87
3
1
1504
8697058
8698561
0.000000e+00
2274
12
TraesCS3A01G233500
chr6B
93.958
1506
87
3
1
1504
8710190
8711693
0.000000e+00
2274
13
TraesCS3A01G233500
chr6B
91.099
191
16
1
2286
2476
186604591
186604780
8.790000e-65
257
14
TraesCS3A01G233500
chr3B
93.874
555
31
2
1926
2477
421241227
421241781
0.000000e+00
833
15
TraesCS3A01G233500
chr3B
88.192
271
22
1
1549
1809
421240733
421241003
5.140000e-82
315
16
TraesCS3A01G233500
chr3B
89.848
197
18
2
2280
2476
439002747
439002553
4.090000e-63
252
17
TraesCS3A01G233500
chr3B
96.748
123
0
1
1808
1926
421241059
421241181
4.180000e-48
202
18
TraesCS3A01G233500
chr3D
92.715
302
18
4
2011
2310
299900217
299899918
1.360000e-117
433
19
TraesCS3A01G233500
chr3D
87.544
281
24
5
1541
1811
299903010
299902731
5.140000e-82
315
20
TraesCS3A01G233500
chr3D
90.769
195
17
1
2282
2476
542229469
542229276
2.440000e-65
259
21
TraesCS3A01G233500
chr3D
94.382
89
1
1
1842
1926
299900402
299900314
1.550000e-27
134
22
TraesCS3A01G233500
chr3D
100.000
54
0
0
1929
1982
299900265
299900212
1.570000e-17
100
23
TraesCS3A01G233500
chr5D
92.513
187
12
2
2290
2476
413771746
413771930
1.460000e-67
267
24
TraesCS3A01G233500
chr5D
83.553
152
18
7
2099
2248
441793672
441793818
4.300000e-28
135
25
TraesCS3A01G233500
chr5A
91.979
187
13
2
2291
2476
118526227
118526042
6.790000e-66
261
26
TraesCS3A01G233500
chr5A
84.138
145
21
2
2099
2243
558241308
558241450
3.320000e-29
139
27
TraesCS3A01G233500
chr7A
88.725
204
22
1
2274
2477
606625457
606625659
5.290000e-62
248
28
TraesCS3A01G233500
chr4A
81.757
148
20
7
2101
2245
717969811
717969668
1.560000e-22
117
29
TraesCS3A01G233500
chr7D
81.295
139
23
3
2099
2236
16707208
16707344
2.600000e-20
110
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
TraesCS3A01G233500
chr3A
435815150
435817626
2476
False
4575.0
4575
100.00000
1
2477
1
chr3A.!!$F1
2476
1
TraesCS3A01G233500
chr2D
480562827
480564338
1511
True
2326.0
2326
94.44800
3
1512
1
chr2D.!!$R3
1509
2
TraesCS3A01G233500
chrUn
200779660
200781163
1503
False
2290.0
2290
94.15700
1
1504
1
chrUn.!!$F2
1503
3
TraesCS3A01G233500
chrUn
234323350
234324850
1500
True
2285.0
2285
94.14500
4
1504
1
chrUn.!!$R2
1500
4
TraesCS3A01G233500
chrUn
200672026
200673526
1500
True
2279.0
2279
94.07900
4
1504
1
chrUn.!!$R1
1500
5
TraesCS3A01G233500
chrUn
200754725
200756228
1503
False
2279.0
2279
94.02400
1
1504
1
chrUn.!!$F1
1503
6
TraesCS3A01G233500
chr6B
8638566
8640069
1503
False
2279.0
2279
94.02400
1
1504
1
chr6B.!!$F1
1503
7
TraesCS3A01G233500
chr6B
8650736
8652239
1503
False
2279.0
2279
94.02400
1
1504
1
chr6B.!!$F2
1503
8
TraesCS3A01G233500
chr6B
8697058
8698561
1503
False
2274.0
2274
93.95800
1
1504
1
chr6B.!!$F3
1503
9
TraesCS3A01G233500
chr6B
8710190
8711693
1503
False
2274.0
2274
93.95800
1
1504
1
chr6B.!!$F4
1503
10
TraesCS3A01G233500
chr3B
421240733
421241781
1048
False
450.0
833
92.93800
1549
2477
3
chr3B.!!$F1
928
11
TraesCS3A01G233500
chr3D
299899918
299903010
3092
True
245.5
433
93.66025
1541
2310
4
chr3D.!!$R2
769
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.