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
TraesCS3A01G163600
chr3A
100.000
3186
0
0
1
3186
166922329
166925514
0.000000e+00
5884.0
1
TraesCS3A01G163600
chr3A
95.261
211
10
0
2976
3186
181107338
181107548
5.090000e-88
335.0
2
TraesCS3A01G163600
chr3A
90.066
151
8
2
848
998
177859727
177859870
4.200000e-44
189.0
3
TraesCS3A01G163600
chr3A
88.333
60
5
2
2363
2421
166924661
166924719
1.590000e-08
71.3
4
TraesCS3A01G163600
chr3A
88.333
60
5
2
2333
2391
166924691
166924749
1.590000e-08
71.3
5
TraesCS3A01G163600
chr3D
92.526
1512
59
7
926
2391
149544036
149545539
0.000000e+00
2117.0
6
TraesCS3A01G163600
chr3D
92.571
1373
65
10
926
2262
149204875
149206246
0.000000e+00
1936.0
7
TraesCS3A01G163600
chr3D
93.812
1115
40
11
926
2011
147336227
147335113
0.000000e+00
1650.0
8
TraesCS3A01G163600
chr3D
93.599
828
38
6
2363
3186
149545480
149546296
0.000000e+00
1221.0
9
TraesCS3A01G163600
chr3D
91.768
826
56
8
1099
1918
141410595
141411414
0.000000e+00
1138.0
10
TraesCS3A01G163600
chr3D
84.921
1008
120
15
1150
2139
360691527
360692520
0.000000e+00
990.0
11
TraesCS3A01G163600
chr3D
87.561
820
87
12
6
818
147425232
147424421
0.000000e+00
935.0
12
TraesCS3A01G163600
chr3D
96.209
211
8
0
2976
3186
149767523
149767313
2.350000e-91
346.0
13
TraesCS3A01G163600
chr3D
87.448
239
14
2
2043
2265
147334799
147334561
8.770000e-66
261.0
14
TraesCS3A01G163600
chr3D
87.736
212
13
6
2976
3186
149207004
149207203
5.310000e-58
235.0
15
TraesCS3A01G163600
chr3B
90.521
1287
72
24
1000
2269
221912358
221913611
0.000000e+00
1655.0
16
TraesCS3A01G163600
chr3B
89.821
1287
71
25
1000
2269
221979838
221981081
0.000000e+00
1596.0
17
TraesCS3A01G163600
chr3B
89.677
1269
72
20
1004
2259
215572008
215573230
0.000000e+00
1563.0
18
TraesCS3A01G163600
chr3B
93.678
1044
58
1
1000
2035
215104678
215105721
0.000000e+00
1555.0
19
TraesCS3A01G163600
chr3B
88.846
1291
90
27
1000
2269
215385072
215386329
0.000000e+00
1537.0
20
TraesCS3A01G163600
chr3B
88.259
1252
95
23
1000
2237
215310446
215311659
0.000000e+00
1450.0
21
TraesCS3A01G163600
chr3B
92.719
879
34
9
1534
2391
221749621
221750490
0.000000e+00
1242.0
22
TraesCS3A01G163600
chr3B
89.689
708
46
14
2506
3186
221981527
221982234
0.000000e+00
878.0
23
TraesCS3A01G163600
chr3B
89.548
708
46
14
2506
3186
221914043
221914749
0.000000e+00
872.0
24
TraesCS3A01G163600
chr3B
87.553
707
58
15
2505
3186
215386788
215387489
0.000000e+00
791.0
25
TraesCS3A01G163600
chr3B
90.000
450
41
4
2367
2813
215115108
215115556
2.130000e-161
579.0
26
TraesCS3A01G163600
chr3B
85.817
557
44
16
2505
3036
221467325
221467871
2.780000e-155
558.0
27
TraesCS3A01G163600
chr3B
93.503
354
20
3
2835
3186
221753057
221753409
1.010000e-144
523.0
28
TraesCS3A01G163600
chr3B
86.242
487
43
12
1533
2004
469631613
469632090
1.020000e-139
507.0
29
TraesCS3A01G163600
chr3B
92.330
352
23
1
2835
3186
215115615
215115962
6.140000e-137
497.0
30
TraesCS3A01G163600
chr3B
87.147
389
28
8
2355
2738
221750419
221750790
3.800000e-114
422.0
31
TraesCS3A01G163600
chr3B
85.752
379
23
13
2031
2391
215114800
215115165
3.880000e-99
372.0
32
TraesCS3A01G163600
chr3B
79.331
508
61
21
441
937
221911886
221912360
1.840000e-82
316.0
33
TraesCS3A01G163600
chr3B
79.331
508
61
22
441
937
221979366
221979840
1.840000e-82
316.0
34
TraesCS3A01G163600
chr3B
87.245
196
18
5
744
937
215104490
215104680
1.920000e-52
217.0
35
TraesCS3A01G163600
chr3B
96.063
127
5
0
3060
3186
221467864
221467990
1.160000e-49
207.0
36
TraesCS3A01G163600
chr3B
93.893
131
6
1
2139
2269
221466846
221466974
2.510000e-46
196.0
37
TraesCS3A01G163600
chr3B
92.453
106
8
0
2732
2837
221752849
221752954
5.500000e-33
152.0
38
TraesCS3A01G163600
chr6A
85.103
1168
118
32
1000
2141
146441722
146440585
0.000000e+00
1142.0
39
TraesCS3A01G163600
chr1D
76.136
176
25
9
133
307
440750414
440750573
3.410000e-10
76.8
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
TraesCS3A01G163600
chr3A
166922329
166925514
3185
False
2008.866667
5884
92.222000
1
3186
3
chr3A.!!$F3
3185
1
TraesCS3A01G163600
chr3D
149544036
149546296
2260
False
1669.000000
2117
93.062500
926
3186
2
chr3D.!!$F4
2260
2
TraesCS3A01G163600
chr3D
141410595
141411414
819
False
1138.000000
1138
91.768000
1099
1918
1
chr3D.!!$F1
819
3
TraesCS3A01G163600
chr3D
149204875
149207203
2328
False
1085.500000
1936
90.153500
926
3186
2
chr3D.!!$F3
2260
4
TraesCS3A01G163600
chr3D
360691527
360692520
993
False
990.000000
990
84.921000
1150
2139
1
chr3D.!!$F2
989
5
TraesCS3A01G163600
chr3D
147334561
147336227
1666
True
955.500000
1650
90.630000
926
2265
2
chr3D.!!$R3
1339
6
TraesCS3A01G163600
chr3D
147424421
147425232
811
True
935.000000
935
87.561000
6
818
1
chr3D.!!$R1
812
7
TraesCS3A01G163600
chr3B
215572008
215573230
1222
False
1563.000000
1563
89.677000
1004
2259
1
chr3B.!!$F2
1255
8
TraesCS3A01G163600
chr3B
215310446
215311659
1213
False
1450.000000
1450
88.259000
1000
2237
1
chr3B.!!$F1
1237
9
TraesCS3A01G163600
chr3B
215385072
215387489
2417
False
1164.000000
1537
88.199500
1000
3186
2
chr3B.!!$F6
2186
10
TraesCS3A01G163600
chr3B
221911886
221914749
2863
False
947.666667
1655
86.466667
441
3186
3
chr3B.!!$F9
2745
11
TraesCS3A01G163600
chr3B
221979366
221982234
2868
False
930.000000
1596
86.280333
441
3186
3
chr3B.!!$F10
2745
12
TraesCS3A01G163600
chr3B
215104490
215105721
1231
False
886.000000
1555
90.461500
744
2035
2
chr3B.!!$F4
1291
13
TraesCS3A01G163600
chr3B
221749621
221753409
3788
False
584.750000
1242
91.455500
1534
3186
4
chr3B.!!$F8
1652
14
TraesCS3A01G163600
chr3B
215114800
215115962
1162
False
482.666667
579
89.360667
2031
3186
3
chr3B.!!$F5
1155
15
TraesCS3A01G163600
chr3B
221466846
221467990
1144
False
320.333333
558
91.924333
2139
3186
3
chr3B.!!$F7
1047
16
TraesCS3A01G163600
chr6A
146440585
146441722
1137
True
1142.000000
1142
85.103000
1000
2141
1
chr6A.!!$R1
1141
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.