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
TraesCS6B01G030800
chr6B
100.000
3456
0
0
1
3456
18300906
18297451
0.000000e+00
6383.0
1
TraesCS6B01G030800
chr6B
93.802
2049
96
16
491
2508
18150172
18148124
0.000000e+00
3051.0
2
TraesCS6B01G030800
chr6B
91.057
369
19
6
2622
2984
18148125
18147765
1.440000e-133
486.0
3
TraesCS6B01G030800
chr6B
83.629
507
43
14
1
478
18150651
18150156
1.140000e-119
440.0
4
TraesCS6B01G030800
chr6D
92.499
2493
145
18
973
3456
9908038
9905579
0.000000e+00
3530.0
5
TraesCS6B01G030800
chr6D
93.333
45
3
0
3105
3149
159234482
159234526
2.230000e-07
67.6
6
TraesCS6B01G030800
chrUn
89.996
2579
154
34
1
2508
71218455
71221000
0.000000e+00
3238.0
7
TraesCS6B01G030800
chrUn
93.381
1390
80
6
1129
2508
321359139
321360526
0.000000e+00
2047.0
8
TraesCS6B01G030800
chrUn
88.342
995
103
9
1512
2500
71181591
71182578
0.000000e+00
1182.0
9
TraesCS6B01G030800
chrUn
89.332
928
63
15
497
1388
71265948
71265021
0.000000e+00
1133.0
10
TraesCS6B01G030800
chrUn
88.389
844
73
9
2622
3456
71263983
71263156
0.000000e+00
992.0
11
TraesCS6B01G030800
chrUn
96.082
485
19
0
1441
1925
71265024
71264540
0.000000e+00
791.0
12
TraesCS6B01G030800
chrUn
92.157
561
41
1
1951
2508
71264542
71263982
0.000000e+00
789.0
13
TraesCS6B01G030800
chrUn
82.340
889
102
31
754
1612
71180729
71181592
0.000000e+00
721.0
14
TraesCS6B01G030800
chrUn
88.683
486
41
8
2622
3098
71220999
71221479
6.430000e-162
580.0
15
TraesCS6B01G030800
chrUn
88.683
486
41
8
2622
3098
321360525
321361005
6.430000e-162
580.0
16
TraesCS6B01G030800
chrUn
88.084
428
20
8
19
419
423403553
423403976
2.410000e-131
479.0
17
TraesCS6B01G030800
chrUn
80.131
458
78
11
987
1439
172238050
172237601
2.570000e-86
329.0
18
TraesCS6B01G030800
chrUn
80.000
440
58
11
999
1422
423403753
423403328
7.250000e-77
298.0
19
TraesCS6B01G030800
chrUn
90.789
76
7
0
125
200
71184025
71183950
6.100000e-18
102.0
20
TraesCS6B01G030800
chr6A
86.743
1305
145
20
1085
2376
11434090
11432801
0.000000e+00
1426.0
21
TraesCS6B01G030800
chr6A
81.004
458
74
11
987
1439
11116375
11115926
5.490000e-93
351.0
22
TraesCS6B01G030800
chr6A
91.139
79
7
0
122
200
11116287
11116365
1.310000e-19
108.0
23
TraesCS6B01G030800
chr5D
79.885
348
54
15
3011
3350
539865372
539865033
1.240000e-59
241.0
24
TraesCS6B01G030800
chr2B
84.746
118
15
3
2507
2623
638269743
638269628
7.840000e-22
115.0
25
TraesCS6B01G030800
chr2B
89.583
48
4
1
2546
2592
709170624
709170671
3.720000e-05
60.2
26
TraesCS6B01G030800
chr3D
81.707
82
15
0
3066
3147
107439669
107439588
6.190000e-08
69.4
27
TraesCS6B01G030800
chr2A
92.157
51
0
2
261
310
646556592
646556545
6.190000e-08
69.4
28
TraesCS6B01G030800
chr7D
90.000
50
5
0
237
286
622195900
622195949
8.010000e-07
65.8
29
TraesCS6B01G030800
chr5A
76.000
125
26
4
3051
3172
14990142
14990265
1.040000e-05
62.1
30
TraesCS6B01G030800
chr1B
91.111
45
3
1
2549
2592
657665627
657665671
3.720000e-05
60.2
31
TraesCS6B01G030800
chr4B
87.500
48
5
1
2546
2592
511368077
511368030
2.000000e-03
54.7
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
TraesCS6B01G030800
chr6B
18297451
18300906
3455
True
6383.000000
6383
100.0000
1
3456
1
chr6B.!!$R1
3455
1
TraesCS6B01G030800
chr6B
18147765
18150651
2886
True
1325.666667
3051
89.4960
1
2984
3
chr6B.!!$R2
2983
2
TraesCS6B01G030800
chr6D
9905579
9908038
2459
True
3530.000000
3530
92.4990
973
3456
1
chr6D.!!$R1
2483
3
TraesCS6B01G030800
chrUn
71218455
71221479
3024
False
1909.000000
3238
89.3395
1
3098
2
chrUn.!!$F3
3097
4
TraesCS6B01G030800
chrUn
321359139
321361005
1866
False
1313.500000
2047
91.0320
1129
3098
2
chrUn.!!$F4
1969
5
TraesCS6B01G030800
chrUn
71180729
71182578
1849
False
951.500000
1182
85.3410
754
2500
2
chrUn.!!$F2
1746
6
TraesCS6B01G030800
chrUn
71263156
71265948
2792
True
926.250000
1133
91.4900
497
3456
4
chrUn.!!$R4
2959
7
TraesCS6B01G030800
chr6A
11432801
11434090
1289
True
1426.000000
1426
86.7430
1085
2376
1
chr6A.!!$R2
1291
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.