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
TraesCS2B01G577600
chr2B
100.000
2234
0
0
1
2234
765875478
765873245
0.000000e+00
4126.0
1
TraesCS2B01G577600
chr2B
100.000
38
0
0
345
382
765875020
765874983
1.110000e-08
71.3
2
TraesCS2B01G577600
chr1D
87.659
1021
106
15
1214
2221
146075680
146074667
0.000000e+00
1170.0
3
TraesCS2B01G577600
chr1D
92.807
709
49
2
505
1212
222406618
222407325
0.000000e+00
1026.0
4
TraesCS2B01G577600
chr1D
92.086
278
15
4
60
330
34529990
34529713
3.480000e-103
385.0
5
TraesCS2B01G577600
chr1D
96.491
57
2
0
431
487
34529638
34529582
6.570000e-16
95.3
6
TraesCS2B01G577600
chr7D
87.282
1030
114
14
1213
2234
481036949
481037969
0.000000e+00
1160.0
7
TraesCS2B01G577600
chr7D
86.686
1029
124
12
1212
2234
280960813
280961834
0.000000e+00
1129.0
8
TraesCS2B01G577600
chr7D
93.475
705
45
1
509
1212
166249332
166248628
0.000000e+00
1046.0
9
TraesCS2B01G577600
chr7D
92.713
494
33
3
1216
1707
54622103
54622595
0.000000e+00
710.0
10
TraesCS2B01G577600
chr7D
96.073
331
12
1
1
330
637921994
637921664
2.520000e-149
538.0
11
TraesCS2B01G577600
chr7D
95.770
331
13
1
1
330
637894996
637894666
1.170000e-147
532.0
12
TraesCS2B01G577600
chr7D
93.958
331
19
1
1
330
116833715
116834045
1.190000e-137
499.0
13
TraesCS2B01G577600
chr7D
87.798
336
31
4
1
330
511515271
511514940
3.480000e-103
385.0
14
TraesCS2B01G577600
chr7D
96.552
58
2
0
431
488
116834120
116834177
1.830000e-16
97.1
15
TraesCS2B01G577600
chr7D
95.082
61
3
0
431
491
637894591
637894531
1.830000e-16
97.1
16
TraesCS2B01G577600
chr7D
95.082
61
3
0
431
491
637921589
637921529
1.830000e-16
97.1
17
TraesCS2B01G577600
chr3D
93.470
781
42
3
1
772
485216859
485217639
0.000000e+00
1151.0
18
TraesCS2B01G577600
chr4D
93.680
712
43
2
505
1215
328178585
328177875
0.000000e+00
1064.0
19
TraesCS2B01G577600
chr4D
92.480
492
35
2
1216
1706
453194496
453194986
0.000000e+00
702.0
20
TraesCS2B01G577600
chr4D
89.097
321
30
4
13
330
450127052
450126734
5.780000e-106
394.0
21
TraesCS2B01G577600
chr4D
88.889
315
30
5
14
326
64227128
64227439
1.250000e-102
383.0
22
TraesCS2B01G577600
chr4D
93.750
64
4
0
431
494
450126659
450126596
1.830000e-16
97.1
23
TraesCS2B01G577600
chr4D
96.491
57
2
0
431
487
64227518
64227574
6.570000e-16
95.3
24
TraesCS2B01G577600
chr5D
93.653
709
43
2
505
1212
394096722
394096015
0.000000e+00
1059.0
25
TraesCS2B01G577600
chr5D
93.079
708
47
2
505
1211
538210813
538210107
0.000000e+00
1035.0
26
TraesCS2B01G577600
chr5D
93.306
493
31
2
1216
1706
322675449
322675941
0.000000e+00
726.0
27
TraesCS2B01G577600
chr5D
92.292
493
36
2
1216
1706
115336830
115337322
0.000000e+00
699.0
28
TraesCS2B01G577600
chr2D
92.797
708
51
0
505
1212
155168544
155169251
0.000000e+00
1026.0
29
TraesCS2B01G577600
chr2D
92.807
709
49
2
505
1212
170409858
170410565
0.000000e+00
1026.0
30
TraesCS2B01G577600
chr2D
92.797
708
51
0
505
1212
187061810
187062517
0.000000e+00
1026.0
31
TraesCS2B01G577600
chr2D
92.807
709
49
2
505
1212
324340894
324341601
0.000000e+00
1026.0
32
TraesCS2B01G577600
chr2D
94.769
325
16
1
7
330
18336352
18336028
2.560000e-139
505.0
33
TraesCS2B01G577600
chr2D
93.750
64
4
0
431
494
18335953
18335890
1.830000e-16
97.1
34
TraesCS2B01G577600
chr6A
83.559
1034
138
27
1212
2234
108842529
108841517
0.000000e+00
939.0
35
TraesCS2B01G577600
chr6A
90.120
334
25
5
3
330
463582816
463583147
5.700000e-116
427.0
36
TraesCS2B01G577600
chr3A
83.560
1028
135
26
1216
2234
451442421
451443423
0.000000e+00
931.0
37
TraesCS2B01G577600
chr3A
92.188
64
5
0
431
494
403507495
403507432
8.500000e-15
91.6
38
TraesCS2B01G577600
chr2A
83.431
1026
141
24
1216
2234
127407183
127408186
0.000000e+00
926.0
39
TraesCS2B01G577600
chr2A
83.268
1028
143
19
1214
2234
730467836
730466831
0.000000e+00
918.0
40
TraesCS2B01G577600
chr2A
82.735
1031
143
28
1216
2234
538142134
538143141
0.000000e+00
885.0
41
TraesCS2B01G577600
chr1B
83.236
1032
132
29
1216
2234
493302887
493303890
0.000000e+00
909.0
42
TraesCS2B01G577600
chr7A
83.037
1014
144
22
1216
2221
91433031
91432038
0.000000e+00
894.0
43
TraesCS2B01G577600
chr7A
92.713
494
33
3
1216
1708
227097909
227097418
0.000000e+00
710.0
44
TraesCS2B01G577600
chr4A
82.668
1027
147
25
1216
2234
155291944
155292947
0.000000e+00
881.0
45
TraesCS2B01G577600
chr6D
93.131
495
31
3
1216
1708
15428460
15427967
0.000000e+00
723.0
46
TraesCS2B01G577600
chr5B
94.864
331
16
1
1
330
474268851
474268521
1.180000e-142
516.0
47
TraesCS2B01G577600
chr5B
95.378
238
10
1
93
330
111896303
111896067
5.820000e-101
377.0
48
TraesCS2B01G577600
chr5B
86.875
320
38
4
13
330
234152297
234151980
2.730000e-94
355.0
49
TraesCS2B01G577600
chr5B
96.552
58
2
0
431
488
234151905
234151848
1.830000e-16
97.1
50
TraesCS2B01G577600
chr5A
84.736
511
50
14
3
512
307611602
307611119
9.270000e-134
486.0
51
TraesCS2B01G577600
chr3B
92.285
337
19
4
1
330
384884911
384884575
2.600000e-129
472.0
52
TraesCS2B01G577600
chr3B
92.683
82
5
1
431
512
384884500
384884420
1.400000e-22
117.0
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
TraesCS2B01G577600
chr2B
765873245
765875478
2233
True
2098.65
4126
100.000
1
2234
2
chr2B.!!$R1
2233
1
TraesCS2B01G577600
chr1D
146074667
146075680
1013
True
1170.00
1170
87.659
1214
2221
1
chr1D.!!$R1
1007
2
TraesCS2B01G577600
chr1D
222406618
222407325
707
False
1026.00
1026
92.807
505
1212
1
chr1D.!!$F1
707
3
TraesCS2B01G577600
chr7D
481036949
481037969
1020
False
1160.00
1160
87.282
1213
2234
1
chr7D.!!$F3
1021
4
TraesCS2B01G577600
chr7D
280960813
280961834
1021
False
1129.00
1129
86.686
1212
2234
1
chr7D.!!$F2
1022
5
TraesCS2B01G577600
chr7D
166248628
166249332
704
True
1046.00
1046
93.475
509
1212
1
chr7D.!!$R1
703
6
TraesCS2B01G577600
chr3D
485216859
485217639
780
False
1151.00
1151
93.470
1
772
1
chr3D.!!$F1
771
7
TraesCS2B01G577600
chr4D
328177875
328178585
710
True
1064.00
1064
93.680
505
1215
1
chr4D.!!$R1
710
8
TraesCS2B01G577600
chr5D
394096015
394096722
707
True
1059.00
1059
93.653
505
1212
1
chr5D.!!$R1
707
9
TraesCS2B01G577600
chr5D
538210107
538210813
706
True
1035.00
1035
93.079
505
1211
1
chr5D.!!$R2
706
10
TraesCS2B01G577600
chr2D
155168544
155169251
707
False
1026.00
1026
92.797
505
1212
1
chr2D.!!$F1
707
11
TraesCS2B01G577600
chr2D
170409858
170410565
707
False
1026.00
1026
92.807
505
1212
1
chr2D.!!$F2
707
12
TraesCS2B01G577600
chr2D
187061810
187062517
707
False
1026.00
1026
92.797
505
1212
1
chr2D.!!$F3
707
13
TraesCS2B01G577600
chr2D
324340894
324341601
707
False
1026.00
1026
92.807
505
1212
1
chr2D.!!$F4
707
14
TraesCS2B01G577600
chr6A
108841517
108842529
1012
True
939.00
939
83.559
1212
2234
1
chr6A.!!$R1
1022
15
TraesCS2B01G577600
chr3A
451442421
451443423
1002
False
931.00
931
83.560
1216
2234
1
chr3A.!!$F1
1018
16
TraesCS2B01G577600
chr2A
127407183
127408186
1003
False
926.00
926
83.431
1216
2234
1
chr2A.!!$F1
1018
17
TraesCS2B01G577600
chr2A
730466831
730467836
1005
True
918.00
918
83.268
1214
2234
1
chr2A.!!$R1
1020
18
TraesCS2B01G577600
chr2A
538142134
538143141
1007
False
885.00
885
82.735
1216
2234
1
chr2A.!!$F2
1018
19
TraesCS2B01G577600
chr1B
493302887
493303890
1003
False
909.00
909
83.236
1216
2234
1
chr1B.!!$F1
1018
20
TraesCS2B01G577600
chr7A
91432038
91433031
993
True
894.00
894
83.037
1216
2221
1
chr7A.!!$R1
1005
21
TraesCS2B01G577600
chr4A
155291944
155292947
1003
False
881.00
881
82.668
1216
2234
1
chr4A.!!$F1
1018
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.