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
TraesCS5A01G315600
chr5A
100.000
3178
0
0
1
3178
525918368
525921545
0.000000e+00
5869.0
1
TraesCS5A01G315600
chr5A
97.548
3181
72
5
2
3178
525829744
525832922
0.000000e+00
5437.0
2
TraesCS5A01G315600
chr5A
95.284
1675
64
8
2
1664
525724311
525725982
0.000000e+00
2641.0
3
TraesCS5A01G315600
chr5A
93.393
1120
64
7
1677
2789
525726248
525727364
0.000000e+00
1650.0
4
TraesCS5A01G315600
chr5A
88.322
1216
87
26
2
1192
526264940
526266125
0.000000e+00
1408.0
5
TraesCS5A01G315600
chr5A
82.229
332
38
14
2
313
525601032
525601362
1.880000e-67
267.0
6
TraesCS5A01G315600
chr5A
86.017
236
13
4
2877
3112
525727401
525727616
5.300000e-58
235.0
7
TraesCS5A01G315600
chr5D
93.909
1412
71
8
2
1400
413489739
413491148
0.000000e+00
2117.0
8
TraesCS5A01G315600
chr5D
94.161
1096
54
4
314
1400
413592674
413593768
0.000000e+00
1661.0
9
TraesCS5A01G315600
chr5D
87.965
914
70
22
2289
3178
413594568
413595465
0.000000e+00
1042.0
10
TraesCS5A01G315600
chr5D
87.678
633
47
18
2289
2899
413491975
413492598
0.000000e+00
708.0
11
TraesCS5A01G315600
chr5D
90.094
424
32
6
1360
1775
413593767
413594188
2.790000e-150
542.0
12
TraesCS5A01G315600
chr5D
79.349
799
124
20
897
1657
413286485
413287280
1.010000e-144
523.0
13
TraesCS5A01G315600
chr5D
91.716
338
26
2
1777
2112
413594242
413594579
4.800000e-128
468.0
14
TraesCS5A01G315600
chr5D
92.593
324
20
4
1360
1682
413491147
413491467
2.230000e-126
462.0
15
TraesCS5A01G315600
chr5D
90.882
340
26
4
1775
2112
413491650
413491986
4.830000e-123
451.0
16
TraesCS5A01G315600
chr5D
94.862
253
10
3
2
251
413592423
413592675
2.970000e-105
392.0
17
TraesCS5A01G315600
chr5D
88.448
277
23
3
2903
3178
413492681
413492949
3.060000e-85
326.0
18
TraesCS5A01G315600
chr5D
83.200
250
22
15
2
233
413285248
413285495
8.930000e-51
211.0
19
TraesCS5A01G315600
chr5B
88.545
1196
101
18
935
2112
498722815
498723992
0.000000e+00
1417.0
20
TraesCS5A01G315600
chr5B
87.353
767
84
8
1171
1929
498511900
498512661
0.000000e+00
867.0
21
TraesCS5A01G315600
chr5B
94.033
419
15
7
2
411
498511424
498511841
7.480000e-176
627.0
22
TraesCS5A01G315600
chr5B
88.998
409
34
6
2774
3178
498779251
498779652
2.200000e-136
496.0
23
TraesCS5A01G315600
chr5B
82.932
457
48
10
2648
3101
498698277
498698706
4.970000e-103
385.0
24
TraesCS5A01G315600
chr5B
81.321
530
49
20
2278
2777
498723969
498724478
4.970000e-103
385.0
25
TraesCS5A01G315600
chr5B
94.944
178
6
2
2
176
498722615
498722792
3.120000e-70
276.0
26
TraesCS5A01G315600
chr5B
88.442
199
16
3
2980
3178
498512660
498512851
1.910000e-57
233.0
27
TraesCS5A01G315600
chr7D
88.213
263
22
5
1858
2112
447078139
447078400
3.980000e-79
305.0
28
TraesCS5A01G315600
chr7D
75.829
211
35
6
2302
2497
30762397
30762606
3.380000e-15
93.5
29
TraesCS5A01G315600
chr3A
86.038
265
28
6
1856
2112
153928197
153927934
3.120000e-70
276.0
30
TraesCS5A01G315600
chr3A
87.736
106
9
3
2188
2290
175168557
175168453
1.550000e-23
121.0
31
TraesCS5A01G315600
chr1B
85.878
262
31
5
1856
2112
469025293
469025553
1.120000e-69
274.0
32
TraesCS5A01G315600
chr1B
85.792
183
16
5
2114
2291
643457042
643457219
5.410000e-43
185.0
33
TraesCS5A01G315600
chr6B
84.906
265
28
7
1856
2112
501111921
501112181
1.130000e-64
257.0
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
TraesCS5A01G315600
chr5A
525918368
525921545
3177
False
5869.000000
5869
100.000000
1
3178
1
chr5A.!!$F3
3177
1
TraesCS5A01G315600
chr5A
525829744
525832922
3178
False
5437.000000
5437
97.548000
2
3178
1
chr5A.!!$F2
3176
2
TraesCS5A01G315600
chr5A
525724311
525727616
3305
False
1508.666667
2641
91.564667
2
3112
3
chr5A.!!$F5
3110
3
TraesCS5A01G315600
chr5A
526264940
526266125
1185
False
1408.000000
1408
88.322000
2
1192
1
chr5A.!!$F4
1190
4
TraesCS5A01G315600
chr5D
413592423
413595465
3042
False
821.000000
1661
91.759600
2
3178
5
chr5D.!!$F3
3176
5
TraesCS5A01G315600
chr5D
413489739
413492949
3210
False
812.800000
2117
90.702000
2
3178
5
chr5D.!!$F2
3176
6
TraesCS5A01G315600
chr5D
413285248
413287280
2032
False
367.000000
523
81.274500
2
1657
2
chr5D.!!$F1
1655
7
TraesCS5A01G315600
chr5B
498722615
498724478
1863
False
692.666667
1417
88.270000
2
2777
3
chr5B.!!$F4
2775
8
TraesCS5A01G315600
chr5B
498511424
498512851
1427
False
575.666667
867
89.942667
2
3178
3
chr5B.!!$F3
3176
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.