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
TraesCS1D01G074700
chr1D
100.000
4150
0
0
1
4150
56431029
56426880
0.000000e+00
7664.0
1
TraesCS1D01G074700
chr1D
93.342
1517
80
12
1848
3357
56874417
56872915
0.000000e+00
2222.0
2
TraesCS1D01G074700
chr1D
92.527
1365
70
15
399
1735
56610981
56609621
0.000000e+00
1927.0
3
TraesCS1D01G074700
chr1D
92.819
1323
56
12
2396
3681
56529582
56528262
0.000000e+00
1881.0
4
TraesCS1D01G074700
chr1D
88.882
1556
104
33
223
1735
56531619
56530090
0.000000e+00
1851.0
5
TraesCS1D01G074700
chr1D
91.561
1339
64
11
1995
3323
56609460
56608161
0.000000e+00
1801.0
6
TraesCS1D01G074700
chr1D
88.735
1447
80
33
329
1735
56875897
56874494
0.000000e+00
1692.0
7
TraesCS1D01G074700
chr1D
94.647
411
20
2
3604
4013
56869027
56868618
1.630000e-178
636.0
8
TraesCS1D01G074700
chr1D
93.023
387
21
4
1
383
56618832
56618448
1.010000e-155
560.0
9
TraesCS1D01G074700
chr1D
86.157
484
47
10
135
602
56612821
56612342
4.790000e-139
505.0
10
TraesCS1D01G074700
chr1D
86.758
438
27
8
367
793
56618435
56618018
3.780000e-125
459.0
11
TraesCS1D01G074700
chr1D
94.636
261
14
0
3382
3642
56608151
56607891
5.000000e-109
405.0
12
TraesCS1D01G074700
chr1D
80.268
522
44
21
1905
2396
57073748
57073256
5.140000e-89
339.0
13
TraesCS1D01G074700
chr1D
83.554
377
41
11
1439
1811
57200749
57200390
2.390000e-87
333.0
14
TraesCS1D01G074700
chr1D
90.323
248
24
0
985
1232
57219350
57219103
4.000000e-85
326.0
15
TraesCS1D01G074700
chr1D
88.382
241
13
6
2090
2323
56529807
56529575
4.090000e-70
276.0
16
TraesCS1D01G074700
chr1D
96.835
158
5
0
3358
3515
56869542
56869385
8.850000e-67
265.0
17
TraesCS1D01G074700
chr1D
90.355
197
19
0
1245
1441
57212907
57212711
4.120000e-65
259.0
18
TraesCS1D01G074700
chr1D
88.406
138
11
3
206
338
56876310
56876173
1.190000e-35
161.0
19
TraesCS1D01G074700
chr1D
96.203
79
2
1
113
191
56612930
56612853
1.210000e-25
128.0
20
TraesCS1D01G074700
chr1D
92.045
88
7
0
1848
1935
56609544
56609457
1.570000e-24
124.0
21
TraesCS1D01G074700
chr1D
100.000
29
0
0
1758
1786
56530050
56530022
2.000000e-03
54.7
22
TraesCS1D01G074700
chr1A
96.047
2049
68
5
2091
4134
54459970
54462010
0.000000e+00
3323.0
23
TraesCS1D01G074700
chr1A
91.653
2432
128
26
1250
3642
56369549
56371944
0.000000e+00
3297.0
24
TraesCS1D01G074700
chr1A
88.146
1780
119
45
329
2044
56336704
56338455
0.000000e+00
2034.0
25
TraesCS1D01G074700
chr1A
87.698
1707
133
39
135
1785
54458050
54459735
0.000000e+00
1917.0
26
TraesCS1D01G074700
chr1A
94.278
1136
50
7
2090
3218
56338470
56339597
0.000000e+00
1724.0
27
TraesCS1D01G074700
chr1A
93.266
787
53
0
3217
4003
56340308
56341094
0.000000e+00
1160.0
28
TraesCS1D01G074700
chr1A
89.841
502
27
8
451
938
56368136
56368627
1.270000e-174
623.0
29
TraesCS1D01G074700
chr1A
89.097
321
29
3
135
449
56367776
56368096
1.080000e-105
394.0
30
TraesCS1D01G074700
chr1A
93.833
227
14
0
1010
1236
56369276
56369502
3.970000e-90
342.0
31
TraesCS1D01G074700
chr1A
85.517
290
25
11
64
338
56365270
56365557
1.890000e-73
287.0
32
TraesCS1D01G074700
chr1A
90.863
197
11
3
1
191
54457820
54458015
1.480000e-64
257.0
33
TraesCS1D01G074700
chr1A
92.727
165
10
2
27
191
56367581
56367743
1.930000e-58
237.0
34
TraesCS1D01G074700
chr1A
100.000
29
0
0
4122
4150
54462045
54462073
2.000000e-03
54.7
35
TraesCS1D01G074700
chr1B
93.443
2120
91
12
1902
4003
91881289
91879200
0.000000e+00
3101.0
36
TraesCS1D01G074700
chr1B
90.498
863
58
9
972
1824
91882368
91881520
0.000000e+00
1118.0
37
TraesCS1D01G074700
chr1B
84.906
583
37
17
325
892
91882938
91882392
3.650000e-150
542.0
38
TraesCS1D01G074700
chr1B
84.615
286
26
12
69
338
91883498
91883215
6.840000e-68
268.0
39
TraesCS1D01G074700
chr1B
87.379
103
11
2
1295
1396
608950044
608950145
2.620000e-22
117.0
40
TraesCS1D01G074700
chr7B
76.075
372
72
14
1295
1659
409712036
409711675
1.190000e-40
178.0
41
TraesCS1D01G074700
chr5D
85.135
74
9
2
1109
1181
315485471
315485399
1.600000e-09
75.0
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
TraesCS1D01G074700
chr1D
56426880
56431029
4149
True
7664.000000
7664
100.000000
1
4150
1
chr1D.!!$R1
4149
1
TraesCS1D01G074700
chr1D
56528262
56531619
3357
True
1015.675000
1881
92.520750
223
3681
4
chr1D.!!$R6
3458
2
TraesCS1D01G074700
chr1D
56868618
56876310
7692
True
995.200000
2222
92.393000
206
4013
5
chr1D.!!$R9
3807
3
TraesCS1D01G074700
chr1D
56607891
56612930
5039
True
815.000000
1927
92.188167
113
3642
6
chr1D.!!$R7
3529
4
TraesCS1D01G074700
chr1D
56618018
56618832
814
True
509.500000
560
89.890500
1
793
2
chr1D.!!$R8
792
5
TraesCS1D01G074700
chr1A
56336704
56341094
4390
False
1639.333333
2034
91.896667
329
4003
3
chr1A.!!$F2
3674
6
TraesCS1D01G074700
chr1A
54457820
54462073
4253
False
1387.925000
3323
93.652000
1
4150
4
chr1A.!!$F1
4149
7
TraesCS1D01G074700
chr1A
56365270
56371944
6674
False
863.333333
3297
90.444667
27
3642
6
chr1A.!!$F3
3615
8
TraesCS1D01G074700
chr1B
91879200
91883498
4298
True
1257.250000
3101
88.365500
69
4003
4
chr1B.!!$R1
3934
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.