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
TraesCS7D01G030000
chr7D
100.000
3440
0
0
1
3440
15783511
15780072
0.000000e+00
6353.0
1
TraesCS7D01G030000
chr7D
92.025
163
13
0
2665
2827
15860781
15860943
2.670000e-56
230.0
2
TraesCS7D01G030000
chr7A
96.520
2069
67
4
825
2891
56153967
56151902
0.000000e+00
3417.0
3
TraesCS7D01G030000
chr7A
94.001
2067
90
13
830
2881
5200259
5202306
0.000000e+00
3099.0
4
TraesCS7D01G030000
chr7A
93.792
1498
72
15
842
2321
5194441
5195935
0.000000e+00
2231.0
5
TraesCS7D01G030000
chr7A
93.703
1477
71
10
1
1473
5221713
5223171
0.000000e+00
2193.0
6
TraesCS7D01G030000
chr7A
92.228
579
33
7
1936
2509
14795807
14796378
0.000000e+00
809.0
7
TraesCS7D01G030000
chr7A
93.478
322
18
1
1
319
5225759
5226080
3.110000e-130
475.0
8
TraesCS7D01G030000
chr7A
93.515
293
18
1
2925
3216
56151811
56151519
5.270000e-118
435.0
9
TraesCS7D01G030000
chr7A
81.687
486
35
17
2431
2881
5099484
5099018
4.220000e-94
355.0
10
TraesCS7D01G030000
chr7A
92.342
222
17
0
2448
2669
56117842
56117621
1.990000e-82
316.0
11
TraesCS7D01G030000
chr7A
88.318
214
12
5
2666
2879
56117594
56117394
9.540000e-61
244.0
12
TraesCS7D01G030000
chr7A
90.083
121
5
3
2543
2663
14796376
14796489
2.140000e-32
150.0
13
TraesCS7D01G030000
chr7A
90.625
96
5
2
3344
3439
5207078
5207169
1.300000e-24
124.0
14
TraesCS7D01G030000
chr7A
95.918
49
2
0
2894
2942
56151860
56151812
2.850000e-11
80.5
15
TraesCS7D01G030000
chr3D
95.752
1954
70
9
866
2810
585084774
585086723
0.000000e+00
3136.0
16
TraesCS7D01G030000
chr4A
94.329
1922
80
9
970
2891
719178267
719180159
0.000000e+00
2918.0
17
TraesCS7D01G030000
chr4A
94.454
595
33
0
1755
2349
719204667
719205261
0.000000e+00
917.0
18
TraesCS7D01G030000
chr4A
92.391
552
25
3
2341
2891
719205742
719206277
0.000000e+00
771.0
19
TraesCS7D01G030000
chr4A
92.557
309
23
0
2940
3248
719180254
719180562
8.760000e-121
444.0
20
TraesCS7D01G030000
chr4A
85.470
351
20
9
2925
3272
719206376
719206698
1.530000e-88
337.0
21
TraesCS7D01G030000
chr4A
80.049
411
31
14
2506
2881
719094113
719093719
1.220000e-64
257.0
22
TraesCS7D01G030000
chr4A
96.203
158
5
1
3283
3440
719180554
719180710
1.220000e-64
257.0
23
TraesCS7D01G030000
chr4A
94.118
51
2
1
2893
2942
719180179
719180229
3.680000e-10
76.8
24
TraesCS7D01G030000
chr4A
100.000
36
0
0
3405
3440
719206698
719206733
2.220000e-07
67.6
25
TraesCS7D01G030000
chr3A
90.725
1779
115
20
912
2656
725268039
725266277
0.000000e+00
2326.0
26
TraesCS7D01G030000
chr3A
86.878
221
28
1
1802
2022
725322406
725322187
2.650000e-61
246.0
27
TraesCS7D01G030000
chr3A
97.222
36
1
0
3272
3307
725265843
725265808
1.030000e-05
62.1
28
TraesCS7D01G030000
chr3B
92.968
1550
97
3
914
2455
798166109
798164564
0.000000e+00
2248.0
29
TraesCS7D01G030000
chrUn
87.337
995
99
7
1143
2122
51176104
51175122
0.000000e+00
1114.0
30
TraesCS7D01G030000
chr5D
81.902
326
47
10
829
1147
506858070
506858390
7.320000e-67
265.0
31
TraesCS7D01G030000
chr1B
79.545
132
16
6
2582
2703
191709764
191709894
2.200000e-12
84.2
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
TraesCS7D01G030000
chr7D
15780072
15783511
3439
True
6353.000000
6353
100.000000
1
3440
1
chr7D.!!$R1
3439
1
TraesCS7D01G030000
chr7A
5200259
5202306
2047
False
3099.000000
3099
94.001000
830
2881
1
chr7A.!!$F2
2051
2
TraesCS7D01G030000
chr7A
5194441
5195935
1494
False
2231.000000
2231
93.792000
842
2321
1
chr7A.!!$F1
1479
3
TraesCS7D01G030000
chr7A
5221713
5226080
4367
False
1334.000000
2193
93.590500
1
1473
2
chr7A.!!$F4
1472
4
TraesCS7D01G030000
chr7A
56151519
56153967
2448
True
1310.833333
3417
95.317667
825
3216
3
chr7A.!!$R3
2391
5
TraesCS7D01G030000
chr7A
14795807
14796489
682
False
479.500000
809
91.155500
1936
2663
2
chr7A.!!$F5
727
6
TraesCS7D01G030000
chr3D
585084774
585086723
1949
False
3136.000000
3136
95.752000
866
2810
1
chr3D.!!$F1
1944
7
TraesCS7D01G030000
chr4A
719178267
719180710
2443
False
923.950000
2918
94.301750
970
3440
4
chr4A.!!$F1
2470
8
TraesCS7D01G030000
chr4A
719204667
719206733
2066
False
523.150000
917
93.078750
1755
3440
4
chr4A.!!$F2
1685
9
TraesCS7D01G030000
chr3A
725265808
725268039
2231
True
1194.050000
2326
93.973500
912
3307
2
chr3A.!!$R2
2395
10
TraesCS7D01G030000
chr3B
798164564
798166109
1545
True
2248.000000
2248
92.968000
914
2455
1
chr3B.!!$R1
1541
11
TraesCS7D01G030000
chrUn
51175122
51176104
982
True
1114.000000
1114
87.337000
1143
2122
1
chrUn.!!$R1
979
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.