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
TraesCS3B01G223300
chr3B
100.000
3197
0
0
1
3197
292019655
292022851
0.000000e+00
5904.0
1
TraesCS3B01G223300
chr3B
100.000
1907
0
0
3437
5343
292023091
292024997
0.000000e+00
3522.0
2
TraesCS3B01G223300
chr3B
83.995
731
79
24
1
707
783089498
783090214
0.000000e+00
667.0
3
TraesCS3B01G223300
chr3B
81.395
688
82
30
98
749
6047131
6046454
2.210000e-143
520.0
4
TraesCS3B01G223300
chr3D
97.600
2458
41
6
751
3195
268143946
268141494
0.000000e+00
4196.0
5
TraesCS3B01G223300
chr3D
97.036
1282
24
5
3452
4725
268141236
268139961
0.000000e+00
2145.0
6
TraesCS3B01G223300
chr3D
90.845
568
27
6
4778
5343
268070701
268070157
0.000000e+00
737.0
7
TraesCS3B01G223300
chr3D
87.524
529
47
13
4
518
613585503
613584980
1.280000e-165
593.0
8
TraesCS3B01G223300
chr3D
82.439
205
27
8
2942
3143
570500795
570500597
2.560000e-38
171.0
9
TraesCS3B01G223300
chr3D
81.553
206
28
9
2942
3143
35710707
35710906
1.540000e-35
161.0
10
TraesCS3B01G223300
chr3A
97.085
1544
27
5
752
2279
343234136
343232595
0.000000e+00
2586.0
11
TraesCS3B01G223300
chr3A
93.858
1498
39
10
3454
4940
343230074
343228619
0.000000e+00
2207.0
12
TraesCS3B01G223300
chr3A
98.048
461
9
0
2592
3052
343231018
343230558
0.000000e+00
802.0
13
TraesCS3B01G223300
chr3A
83.165
790
81
30
1
748
691039277
691040056
0.000000e+00
675.0
14
TraesCS3B01G223300
chr3A
93.056
432
28
2
4910
5340
343228618
343228188
9.770000e-177
630.0
15
TraesCS3B01G223300
chr3A
96.639
357
9
3
2268
2622
343231539
343231184
1.660000e-164
590.0
16
TraesCS3B01G223300
chr3A
100.000
106
0
0
3054
3159
343230431
343230326
4.220000e-46
196.0
17
TraesCS3B01G223300
chr4D
84.585
772
84
22
1
748
8881787
8881027
0.000000e+00
734.0
18
TraesCS3B01G223300
chr4D
84.951
711
66
26
10
694
472499393
472498698
0.000000e+00
682.0
19
TraesCS3B01G223300
chr4D
81.951
205
28
8
2942
3143
23910481
23910283
1.190000e-36
165.0
20
TraesCS3B01G223300
chr7D
83.655
673
76
25
98
749
474699991
474700650
2.130000e-168
603.0
21
TraesCS3B01G223300
chr7D
82.070
686
67
30
99
748
126659382
126658717
7.880000e-148
534.0
22
TraesCS3B01G223300
chr7D
83.803
426
52
14
4924
5338
41696433
41696852
6.490000e-104
388.0
23
TraesCS3B01G223300
chr5D
87.743
514
47
12
1
502
9590703
9591212
2.140000e-163
586.0
24
TraesCS3B01G223300
chr5D
87.023
524
50
16
1
516
554848445
554847932
4.640000e-160
575.0
25
TraesCS3B01G223300
chr1A
83.183
666
83
23
97
748
448632975
448632325
2.770000e-162
582.0
26
TraesCS3B01G223300
chr1A
97.059
34
1
0
2942
2975
77099302
77099335
2.080000e-04
58.4
27
TraesCS3B01G223300
chr4B
84.577
603
72
17
154
749
658965287
658965875
3.590000e-161
579.0
28
TraesCS3B01G223300
chr1D
81.818
704
75
33
93
759
247134033
247133346
4.710000e-150
542.0
29
TraesCS3B01G223300
chr6D
82.029
690
73
28
93
749
324813651
324812980
1.690000e-149
540.0
30
TraesCS3B01G223300
chr6D
85.799
338
38
9
4927
5257
460390100
460389766
3.060000e-92
350.0
31
TraesCS3B01G223300
chr2D
83.411
428
52
17
4928
5343
30739284
30739704
3.910000e-101
379.0
32
TraesCS3B01G223300
chr7A
83.292
407
56
8
4940
5342
15711280
15710882
1.090000e-96
364.0
33
TraesCS3B01G223300
chr6B
85.938
320
34
11
5020
5336
185111549
185111860
1.110000e-86
331.0
34
TraesCS3B01G223300
chr4A
82.258
372
57
7
4975
5343
106338622
106338257
4.020000e-81
313.0
35
TraesCS3B01G223300
chrUn
80.101
397
67
9
4933
5320
320341650
320341257
8.760000e-73
285.0
36
TraesCS3B01G223300
chr5A
94.872
39
2
0
4928
4966
396382283
396382245
1.610000e-05
62.1
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
TraesCS3B01G223300
chr3B
292019655
292024997
5342
False
4713.0
5904
100.000000
1
5343
2
chr3B.!!$F2
5342
1
TraesCS3B01G223300
chr3B
783089498
783090214
716
False
667.0
667
83.995000
1
707
1
chr3B.!!$F1
706
2
TraesCS3B01G223300
chr3B
6046454
6047131
677
True
520.0
520
81.395000
98
749
1
chr3B.!!$R1
651
3
TraesCS3B01G223300
chr3D
268139961
268143946
3985
True
3170.5
4196
97.318000
751
4725
2
chr3D.!!$R4
3974
4
TraesCS3B01G223300
chr3D
268070157
268070701
544
True
737.0
737
90.845000
4778
5343
1
chr3D.!!$R1
565
5
TraesCS3B01G223300
chr3D
613584980
613585503
523
True
593.0
593
87.524000
4
518
1
chr3D.!!$R3
514
6
TraesCS3B01G223300
chr3A
343228188
343234136
5948
True
1168.5
2586
96.447667
752
5340
6
chr3A.!!$R1
4588
7
TraesCS3B01G223300
chr3A
691039277
691040056
779
False
675.0
675
83.165000
1
748
1
chr3A.!!$F1
747
8
TraesCS3B01G223300
chr4D
8881027
8881787
760
True
734.0
734
84.585000
1
748
1
chr4D.!!$R1
747
9
TraesCS3B01G223300
chr4D
472498698
472499393
695
True
682.0
682
84.951000
10
694
1
chr4D.!!$R3
684
10
TraesCS3B01G223300
chr7D
474699991
474700650
659
False
603.0
603
83.655000
98
749
1
chr7D.!!$F2
651
11
TraesCS3B01G223300
chr7D
126658717
126659382
665
True
534.0
534
82.070000
99
748
1
chr7D.!!$R1
649
12
TraesCS3B01G223300
chr5D
9590703
9591212
509
False
586.0
586
87.743000
1
502
1
chr5D.!!$F1
501
13
TraesCS3B01G223300
chr5D
554847932
554848445
513
True
575.0
575
87.023000
1
516
1
chr5D.!!$R1
515
14
TraesCS3B01G223300
chr1A
448632325
448632975
650
True
582.0
582
83.183000
97
748
1
chr1A.!!$R1
651
15
TraesCS3B01G223300
chr4B
658965287
658965875
588
False
579.0
579
84.577000
154
749
1
chr4B.!!$F1
595
16
TraesCS3B01G223300
chr1D
247133346
247134033
687
True
542.0
542
81.818000
93
759
1
chr1D.!!$R1
666
17
TraesCS3B01G223300
chr6D
324812980
324813651
671
True
540.0
540
82.029000
93
749
1
chr6D.!!$R1
656
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.