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
TraesCS2D01G437100
chr2D
100.000
2552
0
0
1
2552
547426179
547428730
0.000000e+00
4713.0
1
TraesCS2D01G437100
chr2D
91.061
1253
49
27
791
1992
547286282
547287522
0.000000e+00
1635.0
2
TraesCS2D01G437100
chr2D
92.703
836
30
12
920
1735
547278276
547279100
0.000000e+00
1177.0
3
TraesCS2D01G437100
chr2D
81.422
1238
136
41
800
1995
547450609
547451794
0.000000e+00
926.0
4
TraesCS2D01G437100
chr2D
81.291
1224
141
40
791
1972
547489048
547490225
0.000000e+00
911.0
5
TraesCS2D01G437100
chr2D
90.227
706
43
12
61
755
547488367
547489057
0.000000e+00
898.0
6
TraesCS2D01G437100
chr2D
94.659
543
28
1
2011
2552
547287815
547288357
0.000000e+00
841.0
7
TraesCS2D01G437100
chr2D
84.099
849
102
14
805
1631
547559292
547560129
0.000000e+00
789.0
8
TraesCS2D01G437100
chr2D
91.344
543
45
2
2011
2552
547279605
547280146
0.000000e+00
741.0
9
TraesCS2D01G437100
chr2D
81.333
750
94
20
906
1636
547574530
547575252
3.680000e-158
568.0
10
TraesCS2D01G437100
chr2D
88.406
414
35
8
355
755
547547695
547548108
1.060000e-133
486.0
11
TraesCS2D01G437100
chr2D
89.825
285
25
3
2011
2293
547490559
547490841
1.870000e-96
363.0
12
TraesCS2D01G437100
chr2D
87.981
208
17
4
1788
1991
547279108
547279311
3.280000e-59
239.0
13
TraesCS2D01G437100
chr2D
98.361
61
1
0
1
61
547488221
547488281
9.650000e-20
108.0
14
TraesCS2D01G437100
chr2D
95.349
43
2
0
755
797
538941086
538941128
4.560000e-08
69.4
15
TraesCS2D01G437100
chr2D
91.667
48
3
1
430
477
382172365
382172319
5.890000e-07
65.8
16
TraesCS2D01G437100
chr2B
88.390
1180
74
21
856
1992
653788261
653789420
0.000000e+00
1362.0
17
TraesCS2D01G437100
chr2B
94.280
542
30
1
2011
2551
653773701
653774242
0.000000e+00
828.0
18
TraesCS2D01G437100
chr2B
82.899
883
112
17
791
1657
653796073
653796932
0.000000e+00
758.0
19
TraesCS2D01G437100
chr2B
84.218
754
91
15
920
1657
653808271
653809012
0.000000e+00
708.0
20
TraesCS2D01G437100
chr2B
87.234
564
33
14
1452
1990
653772858
653773407
7.810000e-170
606.0
21
TraesCS2D01G437100
chr2B
91.558
308
14
3
2246
2552
653792363
653792659
5.080000e-112
414.0
22
TraesCS2D01G437100
chr2B
96.154
156
6
0
2011
2166
653789713
653789868
3.260000e-64
255.0
23
TraesCS2D01G437100
chr2A
87.840
1176
76
37
800
1924
690747279
690748438
0.000000e+00
1317.0
24
TraesCS2D01G437100
chr2A
81.084
1015
124
31
906
1884
690805346
690806328
0.000000e+00
749.0
25
TraesCS2D01G437100
chr2A
82.373
868
112
21
806
1657
691392185
691391343
0.000000e+00
717.0
26
TraesCS2D01G437100
chr2A
96.721
305
9
1
2011
2314
690748554
690748858
8.150000e-140
507.0
27
TraesCS2D01G437100
chr2A
91.743
218
18
0
61
278
691392426
691392209
1.150000e-78
303.0
28
TraesCS2D01G437100
chr2A
79.433
282
45
7
176
449
690796706
690796982
1.210000e-43
187.0
29
TraesCS2D01G437100
chr2A
86.364
154
9
3
800
946
690805067
690805215
9.450000e-35
158.0
30
TraesCS2D01G437100
chr2A
98.333
60
1
0
2395
2454
690772503
690772562
3.470000e-19
106.0
31
TraesCS2D01G437100
chr2A
96.226
53
2
0
2347
2399
690748856
690748908
1.260000e-13
87.9
32
TraesCS2D01G437100
chr5A
85.345
348
29
8
1431
1758
602413162
602413507
8.740000e-90
340.0
33
TraesCS2D01G437100
chr5A
85.714
98
8
2
1760
1853
602413615
602413710
5.810000e-17
99.0
34
TraesCS2D01G437100
chr1A
81.119
143
18
4
473
607
76485605
76485464
3.470000e-19
106.0
35
TraesCS2D01G437100
chr1A
80.597
134
19
5
477
604
49148682
49148550
2.090000e-16
97.1
36
TraesCS2D01G437100
chr1A
95.349
43
2
0
755
797
463032376
463032418
4.560000e-08
69.4
37
TraesCS2D01G437100
chr4D
79.856
139
20
4
473
603
449913691
449913829
7.520000e-16
95.3
38
TraesCS2D01G437100
chr7D
92.453
53
3
1
428
479
165862265
165862317
9.790000e-10
75.0
39
TraesCS2D01G437100
chr7D
95.349
43
2
0
755
797
8593276
8593234
4.560000e-08
69.4
40
TraesCS2D01G437100
chr7D
100.000
30
0
0
548
577
89218110
89218139
3.550000e-04
56.5
41
TraesCS2D01G437100
chr7B
92.453
53
3
1
428
479
129928976
129929028
9.790000e-10
75.0
42
TraesCS2D01G437100
chr5B
95.652
46
2
0
432
477
445553328
445553283
9.790000e-10
75.0
43
TraesCS2D01G437100
chr5B
97.619
42
1
0
758
799
405748061
405748020
3.520000e-09
73.1
44
TraesCS2D01G437100
chr1D
97.674
43
1
0
755
797
465993268
465993226
9.790000e-10
75.0
45
TraesCS2D01G437100
chr6B
95.349
43
2
0
755
797
690826202
690826160
4.560000e-08
69.4
46
TraesCS2D01G437100
chr5D
93.478
46
3
0
432
477
373935815
373935770
4.560000e-08
69.4
47
TraesCS2D01G437100
chr3D
95.349
43
2
0
755
797
9253413
9253371
4.560000e-08
69.4
48
TraesCS2D01G437100
chr3D
95.349
43
2
0
755
797
500408526
500408568
4.560000e-08
69.4
49
TraesCS2D01G437100
chr6A
93.333
45
3
0
433
477
764239
764195
1.640000e-07
67.6
50
TraesCS2D01G437100
chr4A
86.885
61
4
4
739
797
89677960
89677902
5.890000e-07
65.8
51
TraesCS2D01G437100
chr4A
89.362
47
4
1
432
477
271792331
271792285
9.860000e-05
58.4
52
TraesCS2D01G437100
chr6D
100.000
28
0
0
545
572
15661474
15661447
5.000000e-03
52.8
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
TraesCS2D01G437100
chr2D
547426179
547428730
2551
False
4713.00
4713
100.000000
1
2552
1
chr2D.!!$F2
2551
1
TraesCS2D01G437100
chr2D
547286282
547288357
2075
False
1238.00
1635
92.860000
791
2552
2
chr2D.!!$F8
1761
2
TraesCS2D01G437100
chr2D
547450609
547451794
1185
False
926.00
926
81.422000
800
1995
1
chr2D.!!$F3
1195
3
TraesCS2D01G437100
chr2D
547559292
547560129
837
False
789.00
789
84.099000
805
1631
1
chr2D.!!$F5
826
4
TraesCS2D01G437100
chr2D
547278276
547280146
1870
False
719.00
1177
90.676000
920
2552
3
chr2D.!!$F7
1632
5
TraesCS2D01G437100
chr2D
547488221
547490841
2620
False
570.00
911
89.926000
1
2293
4
chr2D.!!$F9
2292
6
TraesCS2D01G437100
chr2D
547574530
547575252
722
False
568.00
568
81.333000
906
1636
1
chr2D.!!$F6
730
7
TraesCS2D01G437100
chr2B
653772858
653774242
1384
False
717.00
828
90.757000
1452
2551
2
chr2B.!!$F2
1099
8
TraesCS2D01G437100
chr2B
653808271
653809012
741
False
708.00
708
84.218000
920
1657
1
chr2B.!!$F1
737
9
TraesCS2D01G437100
chr2B
653788261
653796932
8671
False
697.25
1362
89.750250
791
2552
4
chr2B.!!$F3
1761
10
TraesCS2D01G437100
chr2A
690747279
690748908
1629
False
637.30
1317
93.595667
800
2399
3
chr2A.!!$F3
1599
11
TraesCS2D01G437100
chr2A
691391343
691392426
1083
True
510.00
717
87.058000
61
1657
2
chr2A.!!$R1
1596
12
TraesCS2D01G437100
chr2A
690805067
690806328
1261
False
453.50
749
83.724000
800
1884
2
chr2A.!!$F4
1084
13
TraesCS2D01G437100
chr5A
602413162
602413710
548
False
219.50
340
85.529500
1431
1853
2
chr5A.!!$F1
422
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.