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
TraesCS3B01G489700
chr3B
100.000
4106
0
0
1
4106
736309632
736313737
0.000000e+00
7583.0
1
TraesCS3B01G489700
chr3B
93.946
1949
93
12
1386
3312
736325017
736326962
0.000000e+00
2922.0
2
TraesCS3B01G489700
chr3B
81.088
772
92
32
454
1194
736324091
736324839
5.960000e-158
568.0
3
TraesCS3B01G489700
chr3B
89.302
215
13
6
744
956
736304514
736304720
1.130000e-65
261.0
4
TraesCS3B01G489700
chr3B
83.621
116
9
6
531
637
736253604
736253718
2.610000e-17
100.0
5
TraesCS3B01G489700
chr3B
97.500
40
1
0
3403
3442
736312934
736312973
7.360000e-08
69.4
6
TraesCS3B01G489700
chr3B
97.500
40
1
0
3303
3342
736313034
736313073
7.360000e-08
69.4
7
TraesCS3B01G489700
chr3D
93.716
3342
156
31
788
4106
554216330
554219640
0.000000e+00
4959.0
8
TraesCS3B01G489700
chr3D
93.936
1979
99
12
1345
3304
554328749
554330725
0.000000e+00
2970.0
9
TraesCS3B01G489700
chr3D
83.889
720
57
29
405
1100
554317271
554317955
2.080000e-177
632.0
10
TraesCS3B01G489700
chr3D
92.523
214
14
2
744
956
554170121
554170333
5.160000e-79
305.0
11
TraesCS3B01G489700
chr3D
81.526
249
32
6
400
637
554169596
554169841
4.190000e-45
193.0
12
TraesCS3B01G489700
chr3A
95.110
3006
121
15
1116
4106
690784749
690787743
0.000000e+00
4713.0
13
TraesCS3B01G489700
chr3A
94.295
2261
102
9
1387
3645
690857627
690859862
0.000000e+00
3435.0
14
TraesCS3B01G489700
chr3A
91.378
2111
127
30
1209
3304
690896500
690898570
0.000000e+00
2839.0
15
TraesCS3B01G489700
chr3A
92.715
1153
45
10
1
1144
690783623
690784745
0.000000e+00
1628.0
16
TraesCS3B01G489700
chr3A
84.424
764
84
23
405
1140
690856861
690857617
0.000000e+00
719.0
17
TraesCS3B01G489700
chr3A
91.096
438
29
3
3679
4106
690860178
690860615
5.910000e-163
584.0
18
TraesCS3B01G489700
chr3A
83.871
434
43
13
761
1189
690896098
690896509
4.980000e-104
388.0
19
TraesCS3B01G489700
chr3A
84.810
316
37
10
650
956
690795986
690796299
1.430000e-79
307.0
20
TraesCS3B01G489700
chr3A
77.801
473
72
19
274
728
690895580
690896037
1.130000e-65
261.0
21
TraesCS3B01G489700
chr3A
88.263
213
16
5
744
956
690752830
690753033
3.170000e-61
246.0
22
TraesCS3B01G489700
chr3A
77.062
388
46
24
274
625
690751818
690752198
2.520000e-42
183.0
23
TraesCS3B01G489700
chr3A
95.455
44
1
1
3400
3442
690859516
690859559
7.360000e-08
69.4
24
TraesCS3B01G489700
chr1D
92.113
1699
134
0
1431
3129
78066947
78065249
0.000000e+00
2396.0
25
TraesCS3B01G489700
chr1D
88.652
141
12
4
1
139
139138474
139138612
7.060000e-38
169.0
26
TraesCS3B01G489700
chr1D
82.090
201
32
4
51
248
384467260
384467061
7.060000e-38
169.0
27
TraesCS3B01G489700
chr1D
84.286
70
7
3
1389
1458
78067039
78066974
9.530000e-07
65.8
28
TraesCS3B01G489700
chr1A
90.315
1714
156
6
1419
3129
105302965
105304671
0.000000e+00
2237.0
29
TraesCS3B01G489700
chr1A
88.406
1449
166
2
1681
3129
109416571
109415125
0.000000e+00
1744.0
30
TraesCS3B01G489700
chr1A
87.857
140
14
3
1
139
152406100
152405963
1.180000e-35
161.0
31
TraesCS3B01G489700
chr1A
85.246
122
16
2
128
248
258106098
258106218
1.550000e-24
124.0
32
TraesCS3B01G489700
chr2A
83.665
251
35
6
1
248
194664421
194664668
8.880000e-57
231.0
33
TraesCS3B01G489700
chr5B
83.200
250
37
5
1
247
524453021
524452774
1.490000e-54
224.0
34
TraesCS3B01G489700
chr5B
82.800
250
38
5
1
247
524554886
524554639
6.910000e-53
219.0
35
TraesCS3B01G489700
chr7D
82.386
176
27
4
72
244
151011544
151011370
2.560000e-32
150.0
36
TraesCS3B01G489700
chr4B
80.503
159
25
5
90
245
370982848
370982693
2.590000e-22
117.0
37
TraesCS3B01G489700
chr2D
78.022
182
34
6
51
228
543287898
543288077
4.340000e-20
110.0
38
TraesCS3B01G489700
chr2D
80.392
102
19
1
3822
3922
106142758
106142657
4.400000e-10
76.8
39
TraesCS3B01G489700
chr4D
78.431
153
30
3
94
245
298928884
298928734
3.380000e-16
97.1
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
TraesCS3B01G489700
chr3B
736309632
736313737
4105
False
2573.933333
7583
98.333333
1
4106
3
chr3B.!!$F3
4105
1
TraesCS3B01G489700
chr3B
736324091
736326962
2871
False
1745.000000
2922
87.517000
454
3312
2
chr3B.!!$F4
2858
2
TraesCS3B01G489700
chr3D
554216330
554219640
3310
False
4959.000000
4959
93.716000
788
4106
1
chr3D.!!$F1
3318
3
TraesCS3B01G489700
chr3D
554328749
554330725
1976
False
2970.000000
2970
93.936000
1345
3304
1
chr3D.!!$F3
1959
4
TraesCS3B01G489700
chr3D
554317271
554317955
684
False
632.000000
632
83.889000
405
1100
1
chr3D.!!$F2
695
5
TraesCS3B01G489700
chr3D
554169596
554170333
737
False
249.000000
305
87.024500
400
956
2
chr3D.!!$F4
556
6
TraesCS3B01G489700
chr3A
690783623
690787743
4120
False
3170.500000
4713
93.912500
1
4106
2
chr3A.!!$F3
4105
7
TraesCS3B01G489700
chr3A
690856861
690860615
3754
False
1201.850000
3435
91.317500
405
4106
4
chr3A.!!$F4
3701
8
TraesCS3B01G489700
chr3A
690895580
690898570
2990
False
1162.666667
2839
84.350000
274
3304
3
chr3A.!!$F5
3030
9
TraesCS3B01G489700
chr3A
690751818
690753033
1215
False
214.500000
246
82.662500
274
956
2
chr3A.!!$F2
682
10
TraesCS3B01G489700
chr1D
78065249
78067039
1790
True
1230.900000
2396
88.199500
1389
3129
2
chr1D.!!$R2
1740
11
TraesCS3B01G489700
chr1A
105302965
105304671
1706
False
2237.000000
2237
90.315000
1419
3129
1
chr1A.!!$F1
1710
12
TraesCS3B01G489700
chr1A
109415125
109416571
1446
True
1744.000000
1744
88.406000
1681
3129
1
chr1A.!!$R1
1448
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.