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
TraesCS4B01G194200
chr4B
100.000
2558
0
0
1
2558
417374484
417371927
0.000000e+00
4724.0
1
TraesCS4B01G194200
chr3A
98.603
2362
30
3
1
2362
667661444
667663802
0.000000e+00
4176.0
2
TraesCS4B01G194200
chr3A
93.126
902
49
10
25
920
708548772
708547878
0.000000e+00
1310.0
3
TraesCS4B01G194200
chr4A
98.269
2368
38
3
1
2368
146048031
146045667
0.000000e+00
4143.0
4
TraesCS4B01G194200
chr4A
93.178
1070
62
6
1
1067
53752619
53753680
0.000000e+00
1561.0
5
TraesCS4B01G194200
chr4A
93.167
922
54
6
1
919
12668689
12667774
0.000000e+00
1345.0
6
TraesCS4B01G194200
chr4A
95.699
186
8
0
2373
2558
677895709
677895524
1.490000e-77
300.0
7
TraesCS4B01G194200
chr4A
93.506
154
6
3
1979
2131
53753677
53753827
2.560000e-55
226.0
8
TraesCS4B01G194200
chr2D
90.783
1942
124
26
1
1907
299656997
299655076
0.000000e+00
2543.0
9
TraesCS4B01G194200
chr2D
90.498
1947
127
24
1
1907
327321913
327323841
0.000000e+00
2518.0
10
TraesCS4B01G194200
chr2D
100.000
35
0
0
2209
2243
299655069
299655035
5.910000e-07
65.8
11
TraesCS4B01G194200
chr2D
95.238
42
0
2
2202
2243
327323843
327323882
5.910000e-07
65.8
12
TraesCS4B01G194200
chr2D
100.000
30
0
0
2210
2239
299655037
299655008
3.560000e-04
56.5
13
TraesCS4B01G194200
chr2D
100.000
30
0
0
2210
2239
327323880
327323909
3.560000e-04
56.5
14
TraesCS4B01G194200
chr1D
90.577
1942
129
23
1
1907
319528119
319526197
0.000000e+00
2523.0
15
TraesCS4B01G194200
chr1D
91.780
1545
79
14
1
1507
242558735
242560269
0.000000e+00
2106.0
16
TraesCS4B01G194200
chr1D
95.626
846
28
4
1506
2343
242560431
242561275
0.000000e+00
1349.0
17
TraesCS4B01G194200
chr1D
86.331
139
10
6
2251
2385
319526018
319525885
2.650000e-30
143.0
18
TraesCS4B01G194200
chr1D
100.000
35
0
0
2209
2243
319526190
319526156
5.910000e-07
65.8
19
TraesCS4B01G194200
chr1D
100.000
30
0
0
2210
2239
319526158
319526129
3.560000e-04
56.5
20
TraesCS4B01G194200
chr6A
85.256
1933
203
41
1
1869
241738171
241740085
0.000000e+00
1916.0
21
TraesCS4B01G194200
chr6A
84.086
1527
178
35
1
1480
261024732
261026240
0.000000e+00
1413.0
22
TraesCS4B01G194200
chr6A
86.683
413
27
11
1482
1867
261026800
261027211
1.410000e-117
433.0
23
TraesCS4B01G194200
chr5A
93.384
922
53
6
1
919
280765201
280766117
0.000000e+00
1358.0
24
TraesCS4B01G194200
chr7A
93.167
922
53
7
1
919
2540885
2541799
0.000000e+00
1345.0
25
TraesCS4B01G194200
chr7A
93.167
922
54
6
1
919
67563567
67564482
0.000000e+00
1345.0
26
TraesCS4B01G194200
chr1A
93.059
922
55
6
1
919
502836972
502836057
0.000000e+00
1339.0
27
TraesCS4B01G194200
chr1B
96.774
186
5
1
2373
2558
420713918
420713734
2.470000e-80
309.0
28
TraesCS4B01G194200
chr1B
92.308
39
2
1
2330
2368
633755949
633755912
1.000000e-03
54.7
29
TraesCS4B01G194200
chr7B
95.055
182
8
1
2373
2554
524876575
524876395
4.170000e-73
285.0
30
TraesCS4B01G194200
chr7B
89.583
48
1
4
2330
2377
355849412
355849455
9.890000e-05
58.4
31
TraesCS4B01G194200
chr3B
93.158
190
9
2
2373
2558
237161845
237161656
2.510000e-70
276.0
32
TraesCS4B01G194200
chr3B
94.444
36
2
0
2330
2365
824185252
824185287
3.560000e-04
56.5
33
TraesCS4B01G194200
chr3B
96.970
33
0
1
2330
2362
762387066
762387097
1.000000e-03
54.7
34
TraesCS4B01G194200
chrUn
82.353
119
14
7
2373
2489
67066201
67066088
2.090000e-16
97.1
35
TraesCS4B01G194200
chr6B
81.967
122
15
7
2370
2489
126251710
126251594
2.090000e-16
97.1
36
TraesCS4B01G194200
chr5B
82.353
119
14
7
2373
2489
507034118
507034005
2.090000e-16
97.1
37
TraesCS4B01G194200
chr5B
79.832
119
17
7
2373
2489
507053937
507053824
2.110000e-11
80.5
38
TraesCS4B01G194200
chr5B
92.308
39
2
1
2330
2368
697961108
697961071
1.000000e-03
54.7
39
TraesCS4B01G194200
chr2B
92.308
39
2
1
2330
2368
792770397
792770360
1.000000e-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
TraesCS4B01G194200
chr4B
417371927
417374484
2557
True
4724.000000
4724
100.000000
1
2558
1
chr4B.!!$R1
2557
1
TraesCS4B01G194200
chr3A
667661444
667663802
2358
False
4176.000000
4176
98.603000
1
2362
1
chr3A.!!$F1
2361
2
TraesCS4B01G194200
chr3A
708547878
708548772
894
True
1310.000000
1310
93.126000
25
920
1
chr3A.!!$R1
895
3
TraesCS4B01G194200
chr4A
146045667
146048031
2364
True
4143.000000
4143
98.269000
1
2368
1
chr4A.!!$R2
2367
4
TraesCS4B01G194200
chr4A
12667774
12668689
915
True
1345.000000
1345
93.167000
1
919
1
chr4A.!!$R1
918
5
TraesCS4B01G194200
chr4A
53752619
53753827
1208
False
893.500000
1561
93.342000
1
2131
2
chr4A.!!$F1
2130
6
TraesCS4B01G194200
chr2D
299655008
299656997
1989
True
888.433333
2543
96.927667
1
2243
3
chr2D.!!$R1
2242
7
TraesCS4B01G194200
chr2D
327321913
327323909
1996
False
880.100000
2518
95.245333
1
2243
3
chr2D.!!$F1
2242
8
TraesCS4B01G194200
chr1D
242558735
242561275
2540
False
1727.500000
2106
93.703000
1
2343
2
chr1D.!!$F1
2342
9
TraesCS4B01G194200
chr1D
319525885
319528119
2234
True
697.075000
2523
94.227000
1
2385
4
chr1D.!!$R1
2384
10
TraesCS4B01G194200
chr6A
241738171
241740085
1914
False
1916.000000
1916
85.256000
1
1869
1
chr6A.!!$F1
1868
11
TraesCS4B01G194200
chr6A
261024732
261027211
2479
False
923.000000
1413
85.384500
1
1867
2
chr6A.!!$F2
1866
12
TraesCS4B01G194200
chr5A
280765201
280766117
916
False
1358.000000
1358
93.384000
1
919
1
chr5A.!!$F1
918
13
TraesCS4B01G194200
chr7A
2540885
2541799
914
False
1345.000000
1345
93.167000
1
919
1
chr7A.!!$F1
918
14
TraesCS4B01G194200
chr7A
67563567
67564482
915
False
1345.000000
1345
93.167000
1
919
1
chr7A.!!$F2
918
15
TraesCS4B01G194200
chr1A
502836057
502836972
915
True
1339.000000
1339
93.059000
1
919
1
chr1A.!!$R1
918
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.