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
TraesCS4A01G331000
chr4A
100.000
4074
0
0
1
4074
615458337
615454264
0.000000e+00
7524.0
1
TraesCS4A01G331000
chr4A
80.190
2206
306
66
1
2144
616699819
616701955
0.000000e+00
1531.0
2
TraesCS4A01G331000
chr4A
80.491
1548
180
52
2605
4074
615374354
615372851
0.000000e+00
1074.0
3
TraesCS4A01G331000
chr4A
82.271
1286
165
36
998
2242
615376102
615374839
0.000000e+00
1053.0
4
TraesCS4A01G331000
chr4A
81.604
723
83
24
1
704
616687949
616688640
1.650000e-153
553.0
5
TraesCS4A01G331000
chr4A
87.786
262
18
8
2331
2592
615374781
615374534
1.110000e-75
294.0
6
TraesCS4A01G331000
chr5B
91.713
4115
251
42
2
4074
697870119
697866053
0.000000e+00
5627.0
7
TraesCS4A01G331000
chr5B
84.615
1261
170
13
990
2247
697832246
697831007
0.000000e+00
1232.0
8
TraesCS4A01G331000
chr5B
79.625
1600
243
51
599
2157
699282960
699281403
0.000000e+00
1072.0
9
TraesCS4A01G331000
chr5B
78.813
1331
219
37
845
2150
703805047
703803755
0.000000e+00
837.0
10
TraesCS4A01G331000
chr5B
85.921
483
59
6
2605
3084
697830521
697830045
1.310000e-139
507.0
11
TraesCS4A01G331000
chr5B
76.673
553
110
16
2520
3065
699790222
699789682
5.150000e-74
289.0
12
TraesCS4A01G331000
chr5B
85.556
270
23
7
3820
4074
697865369
697865101
6.710000e-68
268.0
13
TraesCS4A01G331000
chr5B
87.895
190
18
3
1978
2167
697820163
697820347
6.860000e-53
219.0
14
TraesCS4A01G331000
chr5B
77.778
369
55
17
1832
2176
703893995
703893630
6.900000e-48
202.0
15
TraesCS4A01G331000
chr5D
91.543
4127
241
54
1
4074
552682733
552686804
0.000000e+00
5589.0
16
TraesCS4A01G331000
chr5D
84.652
1264
167
16
990
2248
552728996
552730237
0.000000e+00
1234.0
17
TraesCS4A01G331000
chr5D
85.348
546
69
9
2602
3144
552730714
552731251
4.600000e-154
555.0
18
TraesCS4A01G331000
chr5D
75.215
1279
245
50
936
2176
552407625
552408869
1.290000e-149
540.0
19
TraesCS4A01G331000
chr5D
75.185
1213
235
46
980
2159
542411225
542410046
2.810000e-141
512.0
20
TraesCS4A01G331000
chr5D
75.467
1178
215
46
1003
2153
552129717
552128587
1.310000e-139
507.0
21
TraesCS4A01G331000
chr5D
89.394
264
22
1
999
1262
551409722
551409465
1.090000e-85
327.0
22
TraesCS4A01G331000
chr5D
76.630
552
112
15
2520
3065
551544400
551543860
5.150000e-74
289.0
23
TraesCS4A01G331000
chr5D
78.397
287
53
8
2685
2968
552069237
552069517
1.160000e-40
178.0
24
TraesCS4A01G331000
chr5D
94.118
51
3
0
690
740
552500292
552500342
1.210000e-10
78.7
25
TraesCS4A01G331000
chr2D
76.291
1181
223
39
999
2149
651431730
651432883
9.820000e-161
577.0
26
TraesCS4A01G331000
chr2B
76.254
1196
215
46
999
2157
781149700
781150863
4.570000e-159
571.0
27
TraesCS4A01G331000
chr2A
76.046
956
192
26
999
1943
776170804
776169875
2.870000e-126
462.0
28
TraesCS4A01G331000
chr6D
79.431
457
83
8
2642
3092
25613964
25613513
3.060000e-81
313.0
29
TraesCS4A01G331000
chr6B
78.431
459
87
8
2643
3093
41434192
41433738
5.150000e-74
289.0
30
TraesCS4A01G331000
chr4D
80.511
313
47
9
999
1307
280248945
280248643
1.140000e-55
228.0
31
TraesCS4A01G331000
chrUn
76.804
194
35
10
122
313
23399715
23399900
2.590000e-17
100.0
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
TraesCS4A01G331000
chr4A
615454264
615458337
4073
True
7524.0
7524
100.0000
1
4074
1
chr4A.!!$R1
4073
1
TraesCS4A01G331000
chr4A
616699819
616701955
2136
False
1531.0
1531
80.1900
1
2144
1
chr4A.!!$F2
2143
2
TraesCS4A01G331000
chr4A
615372851
615376102
3251
True
807.0
1074
83.5160
998
4074
3
chr4A.!!$R2
3076
3
TraesCS4A01G331000
chr4A
616687949
616688640
691
False
553.0
553
81.6040
1
704
1
chr4A.!!$F1
703
4
TraesCS4A01G331000
chr5B
697865101
697870119
5018
True
2947.5
5627
88.6345
2
4074
2
chr5B.!!$R6
4072
5
TraesCS4A01G331000
chr5B
699281403
699282960
1557
True
1072.0
1072
79.6250
599
2157
1
chr5B.!!$R1
1558
6
TraesCS4A01G331000
chr5B
697830045
697832246
2201
True
869.5
1232
85.2680
990
3084
2
chr5B.!!$R5
2094
7
TraesCS4A01G331000
chr5B
703803755
703805047
1292
True
837.0
837
78.8130
845
2150
1
chr5B.!!$R3
1305
8
TraesCS4A01G331000
chr5B
699789682
699790222
540
True
289.0
289
76.6730
2520
3065
1
chr5B.!!$R2
545
9
TraesCS4A01G331000
chr5D
552682733
552686804
4071
False
5589.0
5589
91.5430
1
4074
1
chr5D.!!$F4
4073
10
TraesCS4A01G331000
chr5D
552728996
552731251
2255
False
894.5
1234
85.0000
990
3144
2
chr5D.!!$F5
2154
11
TraesCS4A01G331000
chr5D
552407625
552408869
1244
False
540.0
540
75.2150
936
2176
1
chr5D.!!$F2
1240
12
TraesCS4A01G331000
chr5D
542410046
542411225
1179
True
512.0
512
75.1850
980
2159
1
chr5D.!!$R1
1179
13
TraesCS4A01G331000
chr5D
552128587
552129717
1130
True
507.0
507
75.4670
1003
2153
1
chr5D.!!$R4
1150
14
TraesCS4A01G331000
chr5D
551543860
551544400
540
True
289.0
289
76.6300
2520
3065
1
chr5D.!!$R3
545
15
TraesCS4A01G331000
chr2D
651431730
651432883
1153
False
577.0
577
76.2910
999
2149
1
chr2D.!!$F1
1150
16
TraesCS4A01G331000
chr2B
781149700
781150863
1163
False
571.0
571
76.2540
999
2157
1
chr2B.!!$F1
1158
17
TraesCS4A01G331000
chr2A
776169875
776170804
929
True
462.0
462
76.0460
999
1943
1
chr2A.!!$R1
944
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.