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
TraesCS6B01G377600
chr6B
100.000
2369
0
0
1
2369
652698487
652696119
0.000000e+00
4375.0
1
TraesCS6B01G377600
chr3B
96.367
2367
84
2
2
2368
680396475
680394111
0.000000e+00
3893.0
2
TraesCS6B01G377600
chr3B
95.823
2370
93
6
2
2369
131914703
131912338
0.000000e+00
3823.0
3
TraesCS6B01G377600
chr3B
95.571
2371
87
7
1
2369
610990468
610992822
0.000000e+00
3781.0
4
TraesCS6B01G377600
chr3B
94.409
1556
74
5
809
2361
731968899
731967354
0.000000e+00
2379.0
5
TraesCS6B01G377600
chr3B
95.298
1425
64
3
1
1425
108523327
108521906
0.000000e+00
2257.0
6
TraesCS6B01G377600
chr4B
95.063
2370
87
7
1
2369
29155949
29158289
0.000000e+00
3701.0
7
TraesCS6B01G377600
chr4B
96.635
1367
45
1
1
1366
2417766
2416400
0.000000e+00
2268.0
8
TraesCS6B01G377600
chr4B
94.820
888
36
3
1483
2369
2416221
2415343
0.000000e+00
1376.0
9
TraesCS6B01G377600
chr2B
95.816
1434
59
1
1
1434
697785740
697787172
0.000000e+00
2314.0
10
TraesCS6B01G377600
chr2B
96.357
1400
50
1
1
1400
110633561
110632163
0.000000e+00
2302.0
11
TraesCS6B01G377600
chr2B
95.701
884
35
3
1487
2369
110631711
110630830
0.000000e+00
1419.0
12
TraesCS6B01G377600
chr2B
95.667
877
32
6
1496
2369
697787481
697788354
0.000000e+00
1404.0
13
TraesCS6B01G377600
chr7B
94.737
1406
69
5
1
1406
619813978
619812578
0.000000e+00
2182.0
14
TraesCS6B01G377600
chr1B
95.878
1310
51
2
2
1311
685388873
685390179
0.000000e+00
2117.0
15
TraesCS6B01G377600
chr1B
96.499
914
29
3
1457
2369
685400180
685401091
0.000000e+00
1507.0
16
TraesCS6B01G377600
chr1B
94.118
153
8
1
1310
1461
685391800
685391952
5.090000e-57
231.0
17
TraesCS6B01G377600
chr1D
91.443
1005
58
13
447
1432
266178810
266177815
0.000000e+00
1354.0
18
TraesCS6B01G377600
chr1D
95.665
346
14
1
94
439
266181516
266181172
2.660000e-154
555.0
19
TraesCS6B01G377600
chr6A
90.040
1004
70
8
447
1432
396917939
396918930
0.000000e+00
1273.0
20
TraesCS6B01G377600
chr1A
88.835
1030
77
13
427
1432
40279613
40280628
0.000000e+00
1230.0
21
TraesCS6B01G377600
chr1A
96.210
343
12
1
94
436
40278850
40279191
5.720000e-156
560.0
22
TraesCS6B01G377600
chr7A
97.455
393
10
0
1977
2369
14707878
14707486
0.000000e+00
671.0
23
TraesCS6B01G377600
chrUn
97.449
392
10
0
1978
2369
403682626
403683017
0.000000e+00
669.0
24
TraesCS6B01G377600
chr4D
94.752
343
17
1
94
436
17107586
17107927
1.250000e-147
532.0
25
TraesCS6B01G377600
chr4D
83.133
83
5
5
1436
1518
258736117
258736190
1.520000e-07
67.6
26
TraesCS6B01G377600
chr3A
89.855
69
6
1
1436
1504
623996158
623996225
1.170000e-13
87.9
27
TraesCS6B01G377600
chr3D
81.818
99
13
3
1436
1530
481278240
481278337
7.020000e-11
78.7
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
TraesCS6B01G377600
chr6B
652696119
652698487
2368
True
4375.0
4375
100.0000
1
2369
1
chr6B.!!$R1
2368
1
TraesCS6B01G377600
chr3B
680394111
680396475
2364
True
3893.0
3893
96.3670
2
2368
1
chr3B.!!$R3
2366
2
TraesCS6B01G377600
chr3B
131912338
131914703
2365
True
3823.0
3823
95.8230
2
2369
1
chr3B.!!$R2
2367
3
TraesCS6B01G377600
chr3B
610990468
610992822
2354
False
3781.0
3781
95.5710
1
2369
1
chr3B.!!$F1
2368
4
TraesCS6B01G377600
chr3B
731967354
731968899
1545
True
2379.0
2379
94.4090
809
2361
1
chr3B.!!$R4
1552
5
TraesCS6B01G377600
chr3B
108521906
108523327
1421
True
2257.0
2257
95.2980
1
1425
1
chr3B.!!$R1
1424
6
TraesCS6B01G377600
chr4B
29155949
29158289
2340
False
3701.0
3701
95.0630
1
2369
1
chr4B.!!$F1
2368
7
TraesCS6B01G377600
chr4B
2415343
2417766
2423
True
1822.0
2268
95.7275
1
2369
2
chr4B.!!$R1
2368
8
TraesCS6B01G377600
chr2B
110630830
110633561
2731
True
1860.5
2302
96.0290
1
2369
2
chr2B.!!$R1
2368
9
TraesCS6B01G377600
chr2B
697785740
697788354
2614
False
1859.0
2314
95.7415
1
2369
2
chr2B.!!$F1
2368
10
TraesCS6B01G377600
chr7B
619812578
619813978
1400
True
2182.0
2182
94.7370
1
1406
1
chr7B.!!$R1
1405
11
TraesCS6B01G377600
chr1B
685400180
685401091
911
False
1507.0
1507
96.4990
1457
2369
1
chr1B.!!$F1
912
12
TraesCS6B01G377600
chr1B
685388873
685391952
3079
False
1174.0
2117
94.9980
2
1461
2
chr1B.!!$F2
1459
13
TraesCS6B01G377600
chr1D
266177815
266181516
3701
True
954.5
1354
93.5540
94
1432
2
chr1D.!!$R1
1338
14
TraesCS6B01G377600
chr6A
396917939
396918930
991
False
1273.0
1273
90.0400
447
1432
1
chr6A.!!$F1
985
15
TraesCS6B01G377600
chr1A
40278850
40280628
1778
False
895.0
1230
92.5225
94
1432
2
chr1A.!!$F1
1338
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.