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
TraesCS2B01G124600
chr2B
100.000
3155
0
0
1
3155
93110977
93114131
0.000000e+00
5827.0
1
TraesCS2B01G124600
chr2B
86.381
2122
179
56
209
2310
94035103
94033072
0.000000e+00
2217.0
2
TraesCS2B01G124600
chr2B
86.591
2036
164
57
209
2206
94225746
94223782
0.000000e+00
2146.0
3
TraesCS2B01G124600
chr2B
90.738
1328
97
13
943
2251
93440449
93441769
0.000000e+00
1748.0
4
TraesCS2B01G124600
chr2B
89.726
438
29
9
186
622
93426172
93426594
2.140000e-151
545.0
5
TraesCS2B01G124600
chr2B
78.049
574
105
10
1587
2142
94202752
94202182
3.010000e-90
342.0
6
TraesCS2B01G124600
chr2B
79.218
486
72
21
1028
1506
93139344
93138881
8.500000e-81
311.0
7
TraesCS2B01G124600
chr2B
77.340
203
20
12
750
927
93439094
93439295
2.590000e-16
97.1
8
TraesCS2B01G124600
chr2B
90.323
62
5
1
868
928
93934713
93934652
2.610000e-11
80.5
9
TraesCS2B01G124600
chr2D
92.465
2402
112
39
1
2361
59726096
59728469
0.000000e+00
3369.0
10
TraesCS2B01G124600
chr2D
86.670
2153
143
68
197
2315
60139709
60137667
0.000000e+00
2254.0
11
TraesCS2B01G124600
chr2D
91.330
669
45
4
847
1515
59845414
59846069
0.000000e+00
902.0
12
TraesCS2B01G124600
chr2D
90.516
601
40
9
1
590
59837991
59838585
0.000000e+00
778.0
13
TraesCS2B01G124600
chr2D
86.427
722
51
21
2361
3053
615473349
615474052
0.000000e+00
747.0
14
TraesCS2B01G124600
chr2D
84.296
796
90
25
2367
3155
373765343
373764576
0.000000e+00
745.0
15
TraesCS2B01G124600
chr2D
85.714
735
58
22
2353
3056
36236921
36236203
0.000000e+00
732.0
16
TraesCS2B01G124600
chr2D
76.117
783
141
33
1390
2155
59724710
59725463
4.970000e-98
368.0
17
TraesCS2B01G124600
chr2D
97.674
129
2
1
707
835
59839930
59840057
1.470000e-53
220.0
18
TraesCS2B01G124600
chr2D
94.697
132
7
0
578
709
59839525
59839656
4.120000e-49
206.0
19
TraesCS2B01G124600
chr2D
91.935
62
4
1
868
928
60108898
60108837
5.610000e-13
86.1
20
TraesCS2B01G124600
chr2A
88.655
1569
103
35
754
2315
60712035
60710535
0.000000e+00
1842.0
21
TraesCS2B01G124600
chr2A
97.781
811
17
1
1551
2361
59724410
59725219
0.000000e+00
1397.0
22
TraesCS2B01G124600
chr2A
89.012
901
46
21
687
1557
59723179
59724056
0.000000e+00
1066.0
23
TraesCS2B01G124600
chr2A
87.946
589
41
11
1727
2315
60249051
60248493
0.000000e+00
667.0
24
TraesCS2B01G124600
chr2A
92.650
449
25
5
1
443
59721064
59721510
9.540000e-180
640.0
25
TraesCS2B01G124600
chr2A
89.535
258
17
7
448
698
59721677
59721931
5.080000e-83
318.0
26
TraesCS2B01G124600
chr2A
81.115
323
34
14
270
584
60712553
60712250
1.890000e-57
233.0
27
TraesCS2B01G124600
chr2A
80.702
228
39
5
1011
1235
60195804
60195579
4.180000e-39
172.0
28
TraesCS2B01G124600
chr2A
80.702
228
39
5
1011
1235
60609823
60609598
4.180000e-39
172.0
29
TraesCS2B01G124600
chr5B
97.000
800
21
3
2357
3154
572740143
572740941
0.000000e+00
1341.0
30
TraesCS2B01G124600
chr4B
96.115
798
24
3
2361
3155
650784080
650784873
0.000000e+00
1295.0
31
TraesCS2B01G124600
chr4B
96.779
652
19
2
2506
3155
540467237
540467888
0.000000e+00
1086.0
32
TraesCS2B01G124600
chr4B
84.820
527
42
21
2356
2871
11622462
11622961
2.190000e-136
496.0
33
TraesCS2B01G124600
chrUn
87.980
782
42
22
2402
3155
19785466
19786223
0.000000e+00
876.0
34
TraesCS2B01G124600
chrUn
85.656
488
43
13
2690
3155
92963704
92964186
3.660000e-134
488.0
35
TraesCS2B01G124600
chr1A
86.877
823
58
17
2361
3155
482330695
482331495
0.000000e+00
876.0
36
TraesCS2B01G124600
chr7D
85.435
817
67
33
2368
3155
631440622
631439829
0.000000e+00
802.0
37
TraesCS2B01G124600
chr4D
86.621
725
55
20
2361
3056
464169931
464169220
0.000000e+00
763.0
38
TraesCS2B01G124600
chr1D
83.438
797
92
33
2368
3155
397641316
397642081
0.000000e+00
704.0
39
TraesCS2B01G124600
chr7A
82.984
811
98
29
2361
3155
316012533
316011747
0.000000e+00
697.0
40
TraesCS2B01G124600
chr5D
85.448
536
43
15
2636
3146
398517024
398517549
2.790000e-145
525.0
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
TraesCS2B01G124600
chr2B
93110977
93114131
3154
False
5827.000000
5827
100.000000
1
3155
1
chr2B.!!$F1
3154
1
TraesCS2B01G124600
chr2B
94033072
94035103
2031
True
2217.000000
2217
86.381000
209
2310
1
chr2B.!!$R3
2101
2
TraesCS2B01G124600
chr2B
94223782
94225746
1964
True
2146.000000
2146
86.591000
209
2206
1
chr2B.!!$R5
1997
3
TraesCS2B01G124600
chr2B
93439094
93441769
2675
False
922.550000
1748
84.039000
750
2251
2
chr2B.!!$F3
1501
4
TraesCS2B01G124600
chr2B
94202182
94202752
570
True
342.000000
342
78.049000
1587
2142
1
chr2B.!!$R4
555
5
TraesCS2B01G124600
chr2D
60137667
60139709
2042
True
2254.000000
2254
86.670000
197
2315
1
chr2D.!!$R3
2118
6
TraesCS2B01G124600
chr2D
59724710
59728469
3759
False
1868.500000
3369
84.291000
1
2361
2
chr2D.!!$F3
2360
7
TraesCS2B01G124600
chr2D
59845414
59846069
655
False
902.000000
902
91.330000
847
1515
1
chr2D.!!$F1
668
8
TraesCS2B01G124600
chr2D
615473349
615474052
703
False
747.000000
747
86.427000
2361
3053
1
chr2D.!!$F2
692
9
TraesCS2B01G124600
chr2D
373764576
373765343
767
True
745.000000
745
84.296000
2367
3155
1
chr2D.!!$R4
788
10
TraesCS2B01G124600
chr2D
36236203
36236921
718
True
732.000000
732
85.714000
2353
3056
1
chr2D.!!$R1
703
11
TraesCS2B01G124600
chr2D
59837991
59840057
2066
False
401.333333
778
94.295667
1
835
3
chr2D.!!$F4
834
12
TraesCS2B01G124600
chr2A
60710535
60712553
2018
True
1037.500000
1842
84.885000
270
2315
2
chr2A.!!$R4
2045
13
TraesCS2B01G124600
chr2A
59721064
59725219
4155
False
855.250000
1397
92.244500
1
2361
4
chr2A.!!$F1
2360
14
TraesCS2B01G124600
chr2A
60248493
60249051
558
True
667.000000
667
87.946000
1727
2315
1
chr2A.!!$R2
588
15
TraesCS2B01G124600
chr5B
572740143
572740941
798
False
1341.000000
1341
97.000000
2357
3154
1
chr5B.!!$F1
797
16
TraesCS2B01G124600
chr4B
650784080
650784873
793
False
1295.000000
1295
96.115000
2361
3155
1
chr4B.!!$F3
794
17
TraesCS2B01G124600
chr4B
540467237
540467888
651
False
1086.000000
1086
96.779000
2506
3155
1
chr4B.!!$F2
649
18
TraesCS2B01G124600
chrUn
19785466
19786223
757
False
876.000000
876
87.980000
2402
3155
1
chrUn.!!$F1
753
19
TraesCS2B01G124600
chr1A
482330695
482331495
800
False
876.000000
876
86.877000
2361
3155
1
chr1A.!!$F1
794
20
TraesCS2B01G124600
chr7D
631439829
631440622
793
True
802.000000
802
85.435000
2368
3155
1
chr7D.!!$R1
787
21
TraesCS2B01G124600
chr4D
464169220
464169931
711
True
763.000000
763
86.621000
2361
3056
1
chr4D.!!$R1
695
22
TraesCS2B01G124600
chr1D
397641316
397642081
765
False
704.000000
704
83.438000
2368
3155
1
chr1D.!!$F1
787
23
TraesCS2B01G124600
chr7A
316011747
316012533
786
True
697.000000
697
82.984000
2361
3155
1
chr7A.!!$R1
794
24
TraesCS2B01G124600
chr5D
398517024
398517549
525
False
525.000000
525
85.448000
2636
3146
1
chr5D.!!$F1
510
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.