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
TraesCS1D01G015100
chr1D
100.000
2869
0
0
1
2869
7157709
7154841
0.000000e+00
5299.0
1
TraesCS1D01G015100
chr1D
97.053
2884
58
18
1
2860
4340665
4343545
0.000000e+00
4830.0
2
TraesCS1D01G015100
chr1D
88.259
1218
102
23
741
1933
99010
100211
0.000000e+00
1419.0
3
TraesCS1D01G015100
chr1D
82.807
1553
198
43
1238
2758
5139250
5140765
0.000000e+00
1325.0
4
TraesCS1D01G015100
chr1D
83.901
1410
155
42
1371
2758
5356899
5358258
0.000000e+00
1280.0
5
TraesCS1D01G015100
chr1D
83.103
1373
160
34
1394
2758
3710386
3709078
0.000000e+00
1184.0
6
TraesCS1D01G015100
chr1D
81.541
1376
173
36
1394
2758
3826163
3824858
0.000000e+00
1059.0
7
TraesCS1D01G015100
chr1D
84.726
838
91
27
742
1558
5138785
5139606
0.000000e+00
804.0
8
TraesCS1D01G015100
chr1D
84.127
819
93
10
1977
2788
100219
101007
0.000000e+00
758.0
9
TraesCS1D01G015100
chr1D
86.534
401
46
5
339
732
98696
99095
4.980000e-118
435.0
10
TraesCS1D01G015100
chr1D
100.000
159
0
0
3095
3253
7154615
7154457
8.830000e-76
294.0
11
TraesCS1D01G015100
chr1D
98.742
159
2
0
3095
3253
4343823
4343981
1.910000e-72
283.0
12
TraesCS1D01G015100
chr1D
91.667
96
7
1
742
836
4341312
4341407
7.320000e-27
132.0
13
TraesCS1D01G015100
chr1D
91.667
96
7
1
742
836
7157063
7156968
7.320000e-27
132.0
14
TraesCS1D01G015100
chr1B
94.120
2874
133
14
1
2869
22184643
22187485
0.000000e+00
4338.0
15
TraesCS1D01G015100
chr1B
93.289
2876
140
13
1
2869
6438565
6435736
0.000000e+00
4193.0
16
TraesCS1D01G015100
chr1B
87.407
1215
119
16
742
1936
5521102
5519902
0.000000e+00
1365.0
17
TraesCS1D01G015100
chr1B
85.942
1252
129
32
742
1954
5688038
5686795
0.000000e+00
1293.0
18
TraesCS1D01G015100
chr1B
88.636
660
53
13
742
1382
5585822
5585166
0.000000e+00
784.0
19
TraesCS1D01G015100
chr1B
83.902
820
94
10
1976
2788
5584365
5583577
0.000000e+00
749.0
20
TraesCS1D01G015100
chr1B
87.531
401
43
6
339
733
5688351
5687952
1.060000e-124
457.0
21
TraesCS1D01G015100
chr1B
92.453
159
12
0
3095
3253
22187539
22187697
9.080000e-56
228.0
22
TraesCS1D01G015100
chr1B
84.500
200
20
10
346
536
5586084
5585887
1.540000e-43
187.0
23
TraesCS1D01G015100
chr1B
96.460
113
4
0
3096
3208
6435680
6435568
1.540000e-43
187.0
24
TraesCS1D01G015100
chr1B
88.816
152
15
2
583
733
5585886
5585736
5.540000e-43
185.0
25
TraesCS1D01G015100
chr1B
89.362
94
6
4
3097
3189
7314331
7314241
7.380000e-22
115.0
26
TraesCS1D01G015100
chr1A
84.660
1382
152
30
1389
2758
6517588
6518921
0.000000e+00
1323.0
27
TraesCS1D01G015100
chr1A
83.413
1049
107
30
1368
2410
6561932
6562919
0.000000e+00
911.0
28
TraesCS1D01G015100
chr1A
84.414
802
85
15
1998
2788
4095906
4095134
0.000000e+00
752.0
29
TraesCS1D01G015100
chr1A
83.784
740
105
10
2
733
6516431
6517163
0.000000e+00
688.0
30
TraesCS1D01G015100
chr1A
84.685
666
80
16
742
1398
6561451
6562103
0.000000e+00
645.0
31
TraesCS1D01G015100
chr1A
84.987
393
50
7
347
733
4097476
4097087
1.090000e-104
390.0
32
TraesCS1D01G015100
chr1A
86.471
340
42
4
397
733
6561199
6561537
1.430000e-98
370.0
33
TraesCS1D01G015100
chrUn
100.000
385
0
0
2293
2677
480721449
480721833
0.000000e+00
712.0
34
TraesCS1D01G015100
chr3D
91.045
67
6
0
3187
3253
30038419
30038353
1.240000e-14
91.6
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
TraesCS1D01G015100
chr1D
7154457
7157709
3252
True
1908.333333
5299
97.222333
1
3253
3
chr1D.!!$R3
3252
1
TraesCS1D01G015100
chr1D
4340665
4343981
3316
False
1748.333333
4830
95.820667
1
3253
3
chr1D.!!$F3
3252
2
TraesCS1D01G015100
chr1D
5356899
5358258
1359
False
1280.000000
1280
83.901000
1371
2758
1
chr1D.!!$F1
1387
3
TraesCS1D01G015100
chr1D
3709078
3710386
1308
True
1184.000000
1184
83.103000
1394
2758
1
chr1D.!!$R1
1364
4
TraesCS1D01G015100
chr1D
5138785
5140765
1980
False
1064.500000
1325
83.766500
742
2758
2
chr1D.!!$F4
2016
5
TraesCS1D01G015100
chr1D
3824858
3826163
1305
True
1059.000000
1059
81.541000
1394
2758
1
chr1D.!!$R2
1364
6
TraesCS1D01G015100
chr1D
98696
101007
2311
False
870.666667
1419
86.306667
339
2788
3
chr1D.!!$F2
2449
7
TraesCS1D01G015100
chr1B
22184643
22187697
3054
False
2283.000000
4338
93.286500
1
3253
2
chr1B.!!$F1
3252
8
TraesCS1D01G015100
chr1B
6435568
6438565
2997
True
2190.000000
4193
94.874500
1
3208
2
chr1B.!!$R5
3207
9
TraesCS1D01G015100
chr1B
5519902
5521102
1200
True
1365.000000
1365
87.407000
742
1936
1
chr1B.!!$R1
1194
10
TraesCS1D01G015100
chr1B
5686795
5688351
1556
True
875.000000
1293
86.736500
339
1954
2
chr1B.!!$R4
1615
11
TraesCS1D01G015100
chr1B
5583577
5586084
2507
True
476.250000
784
86.463500
346
2788
4
chr1B.!!$R3
2442
12
TraesCS1D01G015100
chr1A
6516431
6518921
2490
False
1005.500000
1323
84.222000
2
2758
2
chr1A.!!$F1
2756
13
TraesCS1D01G015100
chr1A
6561199
6562919
1720
False
642.000000
911
84.856333
397
2410
3
chr1A.!!$F2
2013
14
TraesCS1D01G015100
chr1A
4095134
4097476
2342
True
571.000000
752
84.700500
347
2788
2
chr1A.!!$R1
2441
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.