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
TraesCS1D01G319800
chr1D
100.000
6306
0
0
1
6306
413774440
413780745
0.000000e+00
11646.0
1
TraesCS1D01G319800
chr1D
85.626
1127
132
6
3038
4147
104294594
104293481
0.000000e+00
1157.0
2
TraesCS1D01G319800
chr1D
91.000
400
34
2
4318
4716
413731042
413731440
7.190000e-149
538.0
3
TraesCS1D01G319800
chr1D
89.535
86
9
0
4165
4250
413730918
413731003
6.680000e-20
110.0
4
TraesCS1D01G319800
chr3A
96.992
4155
108
6
7
4148
435361344
435357194
0.000000e+00
6964.0
5
TraesCS1D01G319800
chr3A
84.488
1992
302
7
5
1994
82462662
82460676
0.000000e+00
1960.0
6
TraesCS1D01G319800
chr2B
96.301
4109
133
8
1
4096
677673036
677677138
0.000000e+00
6728.0
7
TraesCS1D01G319800
chr2B
96.546
2519
80
5
117
2632
490797393
490794879
0.000000e+00
4163.0
8
TraesCS1D01G319800
chr2B
83.695
1981
311
11
1
1977
626299631
626301603
0.000000e+00
1858.0
9
TraesCS1D01G319800
chr2B
74.570
1164
248
29
3020
4148
8556596
8555446
3.440000e-127
466.0
10
TraesCS1D01G319800
chr4A
95.479
3605
155
6
1
3601
16257364
16260964
0.000000e+00
5747.0
11
TraesCS1D01G319800
chr4A
83.717
1953
305
11
1
1947
456464130
456466075
0.000000e+00
1832.0
12
TraesCS1D01G319800
chr4A
78.014
1128
184
42
4174
5279
710413397
710412312
0.000000e+00
651.0
13
TraesCS1D01G319800
chr4A
79.926
807
138
11
3266
4060
596975324
596976118
7.090000e-159
571.0
14
TraesCS1D01G319800
chr7B
96.992
2194
61
3
4
2194
221309960
221312151
0.000000e+00
3681.0
15
TraesCS1D01G319800
chr7B
86.667
135
18
0
3020
3154
64179799
64179933
3.940000e-32
150.0
16
TraesCS1D01G319800
chr1B
92.584
1645
85
6
4165
5801
558496144
558497759
0.000000e+00
2327.0
17
TraesCS1D01G319800
chr1B
87.979
574
58
4
4165
4729
558284945
558285516
0.000000e+00
667.0
18
TraesCS1D01G319800
chr1B
92.275
466
26
9
5841
6306
558499450
558499905
0.000000e+00
652.0
19
TraesCS1D01G319800
chr1B
86.335
483
54
5
4960
5431
558285510
558285991
3.370000e-142
516.0
20
TraesCS1D01G319800
chr1B
93.827
81
5
0
5848
5928
558497772
558497852
8.590000e-24
122.0
21
TraesCS1D01G319800
chr1B
100.000
38
0
0
5687
5724
558497854
558497891
3.150000e-08
71.3
22
TraesCS1D01G319800
chr1A
83.578
1979
313
11
1
1974
491997818
491999789
0.000000e+00
1844.0
23
TraesCS1D01G319800
chr1A
91.574
1163
78
15
4808
5962
510804335
510805485
0.000000e+00
1587.0
24
TraesCS1D01G319800
chr1A
84.716
1145
150
6
3019
4138
299263942
299265086
0.000000e+00
1122.0
25
TraesCS1D01G319800
chr1A
94.178
584
32
1
4165
4746
510803750
510804333
0.000000e+00
889.0
26
TraesCS1D01G319800
chr1A
86.063
574
53
11
4165
4729
510672980
510673535
5.440000e-165
592.0
27
TraesCS1D01G319800
chr1A
85.044
341
24
8
5980
6306
510805465
510805792
7.890000e-84
322.0
28
TraesCS1D01G319800
chr6D
83.608
909
121
7
3021
3913
456453353
456452457
0.000000e+00
828.0
29
TraesCS1D01G319800
chr3B
79.553
895
157
10
3266
4148
368933504
368934384
3.230000e-172
616.0
30
TraesCS1D01G319800
chr6B
79.106
895
157
13
3266
4148
613577030
613576154
1.960000e-164
590.0
31
TraesCS1D01G319800
chr4B
78.348
896
167
14
3266
4148
375397934
375397053
7.140000e-154
555.0
32
TraesCS1D01G319800
chr6A
79.814
644
110
11
3287
3920
603141389
603140756
9.640000e-123
451.0
33
TraesCS1D01G319800
chr5B
74.335
1165
247
32
3020
4149
637138385
637137238
1.250000e-121
448.0
34
TraesCS1D01G319800
chrUn
79.837
615
97
20
4165
4764
90118229
90117627
2.100000e-114
424.0
35
TraesCS1D01G319800
chr7A
78.613
519
97
10
4156
4673
24627390
24627895
1.310000e-86
331.0
36
TraesCS1D01G319800
chr7D
78.058
515
100
9
4159
4673
23510267
23510768
4.750000e-81
313.0
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
TraesCS1D01G319800
chr1D
413774440
413780745
6305
False
11646.000000
11646
100.000000
1
6306
1
chr1D.!!$F1
6305
1
TraesCS1D01G319800
chr1D
104293481
104294594
1113
True
1157.000000
1157
85.626000
3038
4147
1
chr1D.!!$R1
1109
2
TraesCS1D01G319800
chr1D
413730918
413731440
522
False
324.000000
538
90.267500
4165
4716
2
chr1D.!!$F2
551
3
TraesCS1D01G319800
chr3A
435357194
435361344
4150
True
6964.000000
6964
96.992000
7
4148
1
chr3A.!!$R2
4141
4
TraesCS1D01G319800
chr3A
82460676
82462662
1986
True
1960.000000
1960
84.488000
5
1994
1
chr3A.!!$R1
1989
5
TraesCS1D01G319800
chr2B
677673036
677677138
4102
False
6728.000000
6728
96.301000
1
4096
1
chr2B.!!$F2
4095
6
TraesCS1D01G319800
chr2B
490794879
490797393
2514
True
4163.000000
4163
96.546000
117
2632
1
chr2B.!!$R2
2515
7
TraesCS1D01G319800
chr2B
626299631
626301603
1972
False
1858.000000
1858
83.695000
1
1977
1
chr2B.!!$F1
1976
8
TraesCS1D01G319800
chr2B
8555446
8556596
1150
True
466.000000
466
74.570000
3020
4148
1
chr2B.!!$R1
1128
9
TraesCS1D01G319800
chr4A
16257364
16260964
3600
False
5747.000000
5747
95.479000
1
3601
1
chr4A.!!$F1
3600
10
TraesCS1D01G319800
chr4A
456464130
456466075
1945
False
1832.000000
1832
83.717000
1
1947
1
chr4A.!!$F2
1946
11
TraesCS1D01G319800
chr4A
710412312
710413397
1085
True
651.000000
651
78.014000
4174
5279
1
chr4A.!!$R1
1105
12
TraesCS1D01G319800
chr4A
596975324
596976118
794
False
571.000000
571
79.926000
3266
4060
1
chr4A.!!$F3
794
13
TraesCS1D01G319800
chr7B
221309960
221312151
2191
False
3681.000000
3681
96.992000
4
2194
1
chr7B.!!$F2
2190
14
TraesCS1D01G319800
chr1B
558496144
558499905
3761
False
793.075000
2327
94.671500
4165
6306
4
chr1B.!!$F2
2141
15
TraesCS1D01G319800
chr1B
558284945
558285991
1046
False
591.500000
667
87.157000
4165
5431
2
chr1B.!!$F1
1266
16
TraesCS1D01G319800
chr1A
491997818
491999789
1971
False
1844.000000
1844
83.578000
1
1974
1
chr1A.!!$F2
1973
17
TraesCS1D01G319800
chr1A
299263942
299265086
1144
False
1122.000000
1122
84.716000
3019
4138
1
chr1A.!!$F1
1119
18
TraesCS1D01G319800
chr1A
510803750
510805792
2042
False
932.666667
1587
90.265333
4165
6306
3
chr1A.!!$F4
2141
19
TraesCS1D01G319800
chr1A
510672980
510673535
555
False
592.000000
592
86.063000
4165
4729
1
chr1A.!!$F3
564
20
TraesCS1D01G319800
chr6D
456452457
456453353
896
True
828.000000
828
83.608000
3021
3913
1
chr6D.!!$R1
892
21
TraesCS1D01G319800
chr3B
368933504
368934384
880
False
616.000000
616
79.553000
3266
4148
1
chr3B.!!$F1
882
22
TraesCS1D01G319800
chr6B
613576154
613577030
876
True
590.000000
590
79.106000
3266
4148
1
chr6B.!!$R1
882
23
TraesCS1D01G319800
chr4B
375397053
375397934
881
True
555.000000
555
78.348000
3266
4148
1
chr4B.!!$R1
882
24
TraesCS1D01G319800
chr6A
603140756
603141389
633
True
451.000000
451
79.814000
3287
3920
1
chr6A.!!$R1
633
25
TraesCS1D01G319800
chr5B
637137238
637138385
1147
True
448.000000
448
74.335000
3020
4149
1
chr5B.!!$R1
1129
26
TraesCS1D01G319800
chrUn
90117627
90118229
602
True
424.000000
424
79.837000
4165
4764
1
chrUn.!!$R1
599
27
TraesCS1D01G319800
chr7A
24627390
24627895
505
False
331.000000
331
78.613000
4156
4673
1
chr7A.!!$F1
517
28
TraesCS1D01G319800
chr7D
23510267
23510768
501
False
313.000000
313
78.058000
4159
4673
1
chr7D.!!$F1
514
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.