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
TraesCS5D01G539700
chr5D
100.000
3261
0
0
1
3261
551072787
551076047
0.000000e+00
6023.0
1
TraesCS5D01G539700
chr5D
88.124
421
41
8
237
654
324595264
324595678
2.920000e-135
492.0
2
TraesCS5D01G539700
chr5D
88.221
416
40
8
239
650
434423570
434423980
3.780000e-134
488.0
3
TraesCS5D01G539700
chr5D
77.903
620
92
27
991
1583
552422865
552422264
8.660000e-91
344.0
4
TraesCS5D01G539700
chr5D
78.717
343
62
9
1020
1358
543536886
543536551
5.480000e-53
219.0
5
TraesCS5D01G539700
chr5D
100.000
33
0
0
2664
2696
551075352
551075384
9.770000e-06
62.1
6
TraesCS5D01G539700
chr5D
100.000
33
0
0
2566
2598
551075450
551075482
9.770000e-06
62.1
7
TraesCS5D01G539700
chr4A
93.339
2297
71
23
1001
3261
616886030
616883780
0.000000e+00
3319.0
8
TraesCS5D01G539700
chr4A
100.000
33
0
0
2664
2696
616884477
616884445
9.770000e-06
62.1
9
TraesCS5D01G539700
chr4A
100.000
32
0
0
2566
2597
616884379
616884348
3.510000e-05
60.2
10
TraesCS5D01G539700
chr5B
94.524
1680
70
12
926
2598
703488334
703489998
0.000000e+00
2573.0
11
TraesCS5D01G539700
chr5B
93.738
1517
52
12
993
2490
699353985
699355477
0.000000e+00
2235.0
12
TraesCS5D01G539700
chr5B
89.825
973
46
20
1
955
699353047
699353984
0.000000e+00
1199.0
13
TraesCS5D01G539700
chr5B
97.997
599
11
1
2664
3261
703489966
703490564
0.000000e+00
1038.0
14
TraesCS5D01G539700
chr5B
96.675
421
14
0
2522
2942
699355478
699355898
0.000000e+00
701.0
15
TraesCS5D01G539700
chr5B
94.562
331
11
3
2937
3261
699357484
699357813
3.750000e-139
505.0
16
TraesCS5D01G539700
chr5B
95.652
184
8
0
701
884
703488077
703488260
2.460000e-76
296.0
17
TraesCS5D01G539700
chr5B
75.490
612
104
27
997
1585
698256494
698257082
1.160000e-64
257.0
18
TraesCS5D01G539700
chr5B
81.731
312
47
10
1054
1359
703716172
703716479
5.400000e-63
252.0
19
TraesCS5D01G539700
chr5B
80.968
310
51
8
1054
1358
685422922
685422616
4.210000e-59
239.0
20
TraesCS5D01G539700
chr5B
83.871
248
34
6
1019
1265
699430580
699430822
7.040000e-57
231.0
21
TraesCS5D01G539700
chr5B
84.615
234
28
6
1030
1261
703529332
703529559
3.270000e-55
226.0
22
TraesCS5D01G539700
chr5B
100.000
33
0
0
2566
2598
699355620
699355652
9.770000e-06
62.1
23
TraesCS5D01G539700
chr3D
88.942
416
41
4
242
653
25967187
25967601
2.900000e-140
508.0
24
TraesCS5D01G539700
chr3D
88.293
410
41
6
246
653
548731057
548731461
4.890000e-133
484.0
25
TraesCS5D01G539700
chr2D
88.647
414
36
10
244
654
344348247
344347842
8.130000e-136
494.0
26
TraesCS5D01G539700
chr2D
88.136
413
37
9
246
654
9577292
9577696
6.330000e-132
481.0
27
TraesCS5D01G539700
chr2D
87.715
407
43
6
246
650
622932541
622932942
4.930000e-128
468.0
28
TraesCS5D01G539700
chr7D
87.990
408
44
4
246
651
16320957
16321361
8.190000e-131
477.0
29
TraesCS5D01G539700
chr1D
81.646
316
47
9
1092
1405
22968923
22968617
5.400000e-63
252.0
30
TraesCS5D01G539700
chr1B
92.208
77
6
0
1492
1568
115749426
115749502
3.440000e-20
110.0
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
TraesCS5D01G539700
chr5D
551072787
551076047
3260
False
2049.066667
6023
100.000000
1
3261
3
chr5D.!!$F3
3260
1
TraesCS5D01G539700
chr5D
552422264
552422865
601
True
344.000000
344
77.903000
991
1583
1
chr5D.!!$R2
592
2
TraesCS5D01G539700
chr4A
616883780
616886030
2250
True
1147.100000
3319
97.779667
1001
3261
3
chr4A.!!$R1
2260
3
TraesCS5D01G539700
chr5B
703488077
703490564
2487
False
1302.333333
2573
96.057667
701
3261
3
chr5B.!!$F6
2560
4
TraesCS5D01G539700
chr5B
699353047
699357813
4766
False
940.420000
2235
94.960000
1
3261
5
chr5B.!!$F5
3260
5
TraesCS5D01G539700
chr5B
698256494
698257082
588
False
257.000000
257
75.490000
997
1585
1
chr5B.!!$F1
588
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.