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
TraesCS1B01G041100
chr1B
100.000
6333
0
0
1
6333
20569664
20575996
0.000000e+00
11695.0
1
TraesCS1B01G041100
chr1B
92.411
2319
147
13
3892
6199
20016705
20014405
0.000000e+00
3280.0
2
TraesCS1B01G041100
chr1B
92.711
1372
90
8
1
1370
20037372
20036009
0.000000e+00
1971.0
3
TraesCS1B01G041100
chr1B
93.375
1268
64
10
3077
4328
19552067
19550804
0.000000e+00
1858.0
4
TraesCS1B01G041100
chr1B
93.003
1272
71
3
3077
4333
19478987
19477719
0.000000e+00
1840.0
5
TraesCS1B01G041100
chr1B
85.572
1802
205
35
4552
6333
19439110
19437344
0.000000e+00
1836.0
6
TraesCS1B01G041100
chr1B
92.925
1272
72
3
3077
4333
19380060
19378792
0.000000e+00
1834.0
7
TraesCS1B01G041100
chr1B
85.524
1803
205
35
4552
6333
19537746
19535979
0.000000e+00
1832.0
8
TraesCS1B01G041100
chr1B
93.166
1156
61
3
3077
4217
19343314
19342162
0.000000e+00
1681.0
9
TraesCS1B01G041100
chr1B
92.993
1156
63
3
3077
4217
19442052
19440900
0.000000e+00
1670.0
10
TraesCS1B01G041100
chr1B
87.759
1111
100
21
4552
5658
19340380
19339302
0.000000e+00
1266.0
11
TraesCS1B01G041100
chr1B
88.129
994
113
5
277
1267
19913837
19912846
0.000000e+00
1177.0
12
TraesCS1B01G041100
chr1B
88.466
919
101
5
352
1267
19808668
19807752
0.000000e+00
1105.0
13
TraesCS1B01G041100
chr1B
88.165
921
101
7
352
1267
19688575
19687658
0.000000e+00
1090.0
14
TraesCS1B01G041100
chr1B
87.948
921
103
7
352
1267
19588235
19587318
0.000000e+00
1079.0
15
TraesCS1B01G041100
chr1B
86.967
821
74
4
1441
2249
19553488
19552689
0.000000e+00
893.0
16
TraesCS1B01G041100
chr1B
88.676
574
57
4
647
1218
19554079
19553512
0.000000e+00
693.0
17
TraesCS1B01G041100
chr1B
89.714
525
34
11
1626
2150
20017735
20017231
0.000000e+00
652.0
18
TraesCS1B01G041100
chr1B
88.189
508
58
2
2237
2744
20017211
20016706
7.020000e-169
604.0
19
TraesCS1B01G041100
chr1B
82.753
632
96
10
5712
6333
19339289
19338661
9.280000e-153
551.0
20
TraesCS1B01G041100
chr1B
82.726
631
97
10
5712
6333
19374041
19373414
9.280000e-153
551.0
21
TraesCS1B01G041100
chr1B
82.047
635
98
9
5712
6333
19472963
19472332
1.560000e-145
527.0
22
TraesCS1B01G041100
chr1B
83.951
567
71
6
2310
2873
19552695
19552146
5.620000e-145
525.0
23
TraesCS1B01G041100
chr1B
94.737
247
12
1
4315
4561
19475450
19475205
3.580000e-102
383.0
24
TraesCS1B01G041100
chr1B
94.332
247
13
1
4315
4561
19539953
19539708
1.670000e-100
377.0
25
TraesCS1B01G041100
chr1B
93.927
247
14
1
4315
4561
19376523
19376278
7.750000e-99
372.0
26
TraesCS1B01G041100
chr1B
89.140
221
19
5
4552
4770
19374309
19374092
2.910000e-68
270.0
27
TraesCS1B01G041100
chr1B
90.110
182
16
2
4552
4732
19473232
19473052
1.060000e-57
235.0
28
TraesCS1B01G041100
chr1B
93.976
83
5
0
1366
1448
20017822
20017740
6.670000e-25
126.0
29
TraesCS1B01G041100
chr1B
82.692
104
16
1
5759
5862
17765254
17765355
2.430000e-14
91.6
30
TraesCS1B01G041100
chr1B
94.444
54
3
0
4788
4841
19374101
19374048
4.070000e-12
84.2
31
TraesCS1B01G041100
chr1B
76.712
146
30
4
21
165
175603159
175603301
1.890000e-10
78.7
32
TraesCS1B01G041100
chr1D
91.888
6287
384
44
1
6199
13707505
13701257
0.000000e+00
8669.0
33
TraesCS1B01G041100
chr1D
90.692
3556
245
45
2172
5656
13801014
13797474
0.000000e+00
4654.0
34
TraesCS1B01G041100
chr1D
91.117
2139
171
4
1
2121
13803577
13801440
0.000000e+00
2880.0
35
TraesCS1B01G041100
chr1D
91.693
638
50
2
5699
6333
13797475
13796838
0.000000e+00
881.0
36
TraesCS1B01G041100
chr1D
82.143
168
27
3
2
168
9750527
9750692
2.380000e-29
141.0
37
TraesCS1B01G041100
chr1A
89.365
3404
260
41
2581
5897
14747069
14743681
0.000000e+00
4187.0
38
TraesCS1B01G041100
chr1A
88.646
1876
178
15
277
2121
14749313
14747442
0.000000e+00
2252.0
39
TraesCS1B01G041100
chr6B
81.471
340
61
2
2448
2786
25268012
25268350
1.740000e-70
278.0
40
TraesCS1B01G041100
chr6A
79.949
389
64
8
2399
2786
22437071
22436696
2.250000e-69
274.0
41
TraesCS1B01G041100
chr4A
79.639
388
72
4
2404
2786
236159317
236159702
8.090000e-69
272.0
42
TraesCS1B01G041100
chr4A
79.104
134
27
1
5
138
725738849
725738981
2.430000e-14
91.6
43
TraesCS1B01G041100
chr5D
78.261
368
74
6
2404
2770
14608395
14608033
1.370000e-56
231.0
44
TraesCS1B01G041100
chr7A
81.407
199
37
0
2173
2371
136449040
136449238
5.080000e-36
163.0
45
TraesCS1B01G041100
chr7A
85.345
116
17
0
2399
2514
91840531
91840416
3.100000e-23
121.0
46
TraesCS1B01G041100
chr6D
86.614
127
14
3
5967
6092
18378993
18379117
3.080000e-28
137.0
47
TraesCS1B01G041100
chr2D
82.963
135
20
3
5
138
70532475
70532607
1.120000e-22
119.0
48
TraesCS1B01G041100
chr7B
83.740
123
19
1
23
145
72283595
72283474
1.440000e-21
115.0
49
TraesCS1B01G041100
chr7B
80.769
130
21
4
9
138
99134616
99134741
1.450000e-16
99.0
50
TraesCS1B01G041100
chr7D
80.952
105
20
0
2407
2511
3649601
3649497
4.070000e-12
84.2
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
TraesCS1B01G041100
chr1B
20569664
20575996
6332
False
11695.00
11695
100.000000
1
6333
1
chr1B.!!$F2
6332
1
TraesCS1B01G041100
chr1B
20036009
20037372
1363
True
1971.00
1971
92.711000
1
1370
1
chr1B.!!$R5
1369
2
TraesCS1B01G041100
chr1B
19437344
19442052
4708
True
1753.00
1836
89.282500
3077
6333
2
chr1B.!!$R8
3256
3
TraesCS1B01G041100
chr1B
19912846
19913837
991
True
1177.00
1177
88.129000
277
1267
1
chr1B.!!$R4
990
4
TraesCS1B01G041100
chr1B
19338661
19343314
4653
True
1166.00
1681
87.892667
3077
6333
3
chr1B.!!$R6
3256
5
TraesCS1B01G041100
chr1B
20014405
20017822
3417
True
1165.50
3280
91.072500
1366
6199
4
chr1B.!!$R12
4833
6
TraesCS1B01G041100
chr1B
19807752
19808668
916
True
1105.00
1105
88.466000
352
1267
1
chr1B.!!$R3
915
7
TraesCS1B01G041100
chr1B
19535979
19539953
3974
True
1104.50
1832
89.928000
4315
6333
2
chr1B.!!$R10
2018
8
TraesCS1B01G041100
chr1B
19687658
19688575
917
True
1090.00
1090
88.165000
352
1267
1
chr1B.!!$R2
915
9
TraesCS1B01G041100
chr1B
19587318
19588235
917
True
1079.00
1079
87.948000
352
1267
1
chr1B.!!$R1
915
10
TraesCS1B01G041100
chr1B
19550804
19554079
3275
True
992.25
1858
88.242250
647
4328
4
chr1B.!!$R11
3681
11
TraesCS1B01G041100
chr1B
19472332
19478987
6655
True
746.25
1840
89.974250
3077
6333
4
chr1B.!!$R9
3256
12
TraesCS1B01G041100
chr1B
19373414
19380060
6646
True
622.24
1834
90.632400
3077
6333
5
chr1B.!!$R7
3256
13
TraesCS1B01G041100
chr1D
13701257
13707505
6248
True
8669.00
8669
91.888000
1
6199
1
chr1D.!!$R1
6198
14
TraesCS1B01G041100
chr1D
13796838
13803577
6739
True
2805.00
4654
91.167333
1
6333
3
chr1D.!!$R2
6332
15
TraesCS1B01G041100
chr1A
14743681
14749313
5632
True
3219.50
4187
89.005500
277
5897
2
chr1A.!!$R1
5620
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.