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
TraesCS2D01G302300
chr2D
100.000
7366
0
0
1
7366
385392302
385384937
0.000000e+00
13603.0
1
TraesCS2D01G302300
chr2D
81.261
1110
162
19
2812
3887
385388388
385387291
0.000000e+00
856.0
2
TraesCS2D01G302300
chr2D
81.261
1110
162
19
3915
5012
385389491
385388416
0.000000e+00
856.0
3
TraesCS2D01G302300
chr2D
91.186
295
23
2
2525
2816
385389490
385389196
1.490000e-106
398.0
4
TraesCS2D01G302300
chr2D
91.186
295
23
2
2813
3107
385389778
385389487
1.490000e-106
398.0
5
TraesCS2D01G302300
chr2A
97.242
4314
60
9
2184
6474
520993397
520989120
0.000000e+00
7252.0
6
TraesCS2D01G302300
chr2A
97.081
925
25
2
6442
7366
520989089
520988167
0.000000e+00
1557.0
7
TraesCS2D01G302300
chr2A
97.666
857
16
4
1304
2158
520994233
520993379
0.000000e+00
1469.0
8
TraesCS2D01G302300
chr2A
82.793
1110
163
11
3915
5012
520992765
520991672
0.000000e+00
966.0
9
TraesCS2D01G302300
chr2A
81.532
1110
159
19
2812
3887
520991644
520990547
0.000000e+00
872.0
10
TraesCS2D01G302300
chr2A
92.203
295
23
0
2813
3107
520993055
520992761
1.140000e-112
418.0
11
TraesCS2D01G302300
chr2A
89.552
335
11
5
864
1198
520994851
520994541
3.200000e-108
403.0
12
TraesCS2D01G302300
chr2A
90.476
294
25
2
2525
2815
520992764
520992471
1.160000e-102
385.0
13
TraesCS2D01G302300
chr2B
94.245
3875
165
15
2083
5915
456344287
456340429
0.000000e+00
5867.0
14
TraesCS2D01G302300
chr2B
91.966
1170
49
16
885
2026
456345437
456344285
0.000000e+00
1598.0
15
TraesCS2D01G302300
chr2B
93.711
636
29
6
6734
7366
456339191
456338564
0.000000e+00
942.0
16
TraesCS2D01G302300
chr2B
81.558
1117
167
12
3915
5012
456343551
456342455
0.000000e+00
885.0
17
TraesCS2D01G302300
chr2B
88.114
387
25
9
5928
6306
456340389
456340016
2.440000e-119
440.0
18
TraesCS2D01G302300
chr2B
93.220
295
20
0
2813
3107
456343841
456343547
1.130000e-117
435.0
19
TraesCS2D01G302300
chr2B
76.238
808
183
8
7
809
109990665
109989862
3.180000e-113
420.0
20
TraesCS2D01G302300
chr2B
91.525
295
22
1
2525
2816
456343550
456343256
3.200000e-108
403.0
21
TraesCS2D01G302300
chr2B
92.115
279
13
4
6442
6717
456339726
456339454
1.160000e-102
385.0
22
TraesCS2D01G302300
chr4D
77.833
803
171
7
1
800
374629272
374630070
2.390000e-134
490.0
23
TraesCS2D01G302300
chr4D
76.125
800
185
6
1
797
417379179
417379975
1.480000e-111
414.0
24
TraesCS2D01G302300
chr5D
77.387
796
175
4
7
800
545820565
545821357
1.120000e-127
468.0
25
TraesCS2D01G302300
chr5D
76.413
814
180
12
1
808
214600813
214601620
5.280000e-116
429.0
26
TraesCS2D01G302300
chr5B
77.256
809
168
14
1
801
369623642
369624442
1.870000e-125
460.0
27
TraesCS2D01G302300
chr5B
75.342
803
189
9
1
800
396397396
396398192
1.940000e-100
377.0
28
TraesCS2D01G302300
chr7D
77.171
806
172
11
7
806
454926844
454926045
6.730000e-125
459.0
29
TraesCS2D01G302300
chr7D
80.059
341
50
12
1399
1729
413449088
413448756
3.440000e-58
237.0
30
TraesCS2D01G302300
chr6D
76.578
824
189
3
7
828
88681335
88682156
4.050000e-122
449.0
31
TraesCS2D01G302300
chr6D
93.878
49
3
0
1965
2013
237070210
237070162
2.850000e-09
75.0
32
TraesCS2D01G302300
chr1B
89.855
207
18
3
3681
3885
684001084
684000879
5.670000e-66
263.0
33
TraesCS2D01G302300
chr1B
85.784
204
28
1
4808
5010
684001082
684000879
1.610000e-51
215.0
34
TraesCS2D01G302300
chr1D
85.306
245
27
6
1348
1591
47848843
47849079
2.050000e-60
244.0
35
TraesCS2D01G302300
chr1D
90.909
55
5
0
1959
2013
47849115
47849169
2.850000e-09
75.0
36
TraesCS2D01G302300
chr3D
84.490
245
29
6
1348
1591
523247108
523247344
4.440000e-57
233.0
37
TraesCS2D01G302300
chr3D
89.091
55
6
0
1959
2013
523247380
523247434
1.330000e-07
69.4
38
TraesCS2D01G302300
chr7A
84.158
202
24
6
1394
1594
475191277
475191083
9.760000e-44
189.0
39
TraesCS2D01G302300
chr7B
85.795
176
23
2
1422
1596
427833611
427833437
1.260000e-42
185.0
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
TraesCS2D01G302300
chr2D
385384937
385392302
7365
True
13603.000
13603
100.000000
1
7366
1
chr2D.!!$R1
7365
1
TraesCS2D01G302300
chr2D
385387291
385389778
2487
True
627.000
856
86.223500
2525
5012
4
chr2D.!!$R2
2487
2
TraesCS2D01G302300
chr2A
520988167
520994851
6684
True
1665.250
7252
91.068125
864
7366
8
chr2A.!!$R1
6502
3
TraesCS2D01G302300
chr2B
456338564
456345437
6873
True
1369.375
5867
90.806750
885
7366
8
chr2B.!!$R2
6481
4
TraesCS2D01G302300
chr2B
109989862
109990665
803
True
420.000
420
76.238000
7
809
1
chr2B.!!$R1
802
5
TraesCS2D01G302300
chr4D
374629272
374630070
798
False
490.000
490
77.833000
1
800
1
chr4D.!!$F1
799
6
TraesCS2D01G302300
chr4D
417379179
417379975
796
False
414.000
414
76.125000
1
797
1
chr4D.!!$F2
796
7
TraesCS2D01G302300
chr5D
545820565
545821357
792
False
468.000
468
77.387000
7
800
1
chr5D.!!$F2
793
8
TraesCS2D01G302300
chr5D
214600813
214601620
807
False
429.000
429
76.413000
1
808
1
chr5D.!!$F1
807
9
TraesCS2D01G302300
chr5B
369623642
369624442
800
False
460.000
460
77.256000
1
801
1
chr5B.!!$F1
800
10
TraesCS2D01G302300
chr5B
396397396
396398192
796
False
377.000
377
75.342000
1
800
1
chr5B.!!$F2
799
11
TraesCS2D01G302300
chr7D
454926045
454926844
799
True
459.000
459
77.171000
7
806
1
chr7D.!!$R2
799
12
TraesCS2D01G302300
chr6D
88681335
88682156
821
False
449.000
449
76.578000
7
828
1
chr6D.!!$F1
821
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.