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
TraesCS5B01G378500
chr5B
100.000
3161
0
0
1
3161
556796748
556793588
0.000000e+00
5838.0
1
TraesCS5B01G378500
chr5B
87.112
1645
189
15
940
2575
621238336
621236706
0.000000e+00
1842.0
2
TraesCS5B01G378500
chr5B
86.792
53
6
1
384
435
508364071
508364019
1.220000e-04
58.4
3
TraesCS5B01G378500
chr6B
89.305
2188
200
19
991
3161
15397956
15395786
0.000000e+00
2713.0
4
TraesCS5B01G378500
chr6B
87.563
2187
167
39
993
3159
670592702
670590601
0.000000e+00
2435.0
5
TraesCS5B01G378500
chr6B
94.373
1564
84
2
1013
2575
15381521
15379961
0.000000e+00
2398.0
6
TraesCS5B01G378500
chr6B
91.223
319
22
3
2849
3161
16238726
16239044
2.250000e-116
429.0
7
TraesCS5B01G378500
chr6B
80.164
610
69
16
2384
2948
15215462
15214860
2.930000e-110
409.0
8
TraesCS5B01G378500
chr6B
94.737
114
6
0
3027
3140
16340582
16340695
9.010000e-41
178.0
9
TraesCS5B01G378500
chr6B
95.890
73
3
0
1
73
187263594
187263666
5.540000e-23
119.0
10
TraesCS5B01G378500
chr6B
94.667
75
2
2
1
74
664243687
664243760
7.160000e-22
115.0
11
TraesCS5B01G378500
chr6B
92.405
79
6
0
1
79
597487742
597487820
2.580000e-21
113.0
12
TraesCS5B01G378500
chr1B
93.713
1702
73
13
894
2575
662037207
662038894
0.000000e+00
2519.0
13
TraesCS5B01G378500
chr1B
94.013
785
41
4
62
841
662035008
662035791
0.000000e+00
1184.0
14
TraesCS5B01G378500
chr1B
90.110
91
3
6
1
88
41377850
41377763
2.580000e-21
113.0
15
TraesCS5B01G378500
chr6A
88.873
2058
177
25
1121
3159
9355310
9357334
0.000000e+00
2484.0
16
TraesCS5B01G378500
chr6A
87.202
1680
172
22
923
2575
9461362
9463025
0.000000e+00
1871.0
17
TraesCS5B01G378500
chr6A
95.833
72
3
0
1
72
141347117
141347046
1.990000e-22
117.0
18
TraesCS5B01G378500
chr2B
86.277
2055
234
28
1124
3159
709569633
709567608
0.000000e+00
2189.0
19
TraesCS5B01G378500
chr2B
82.864
1634
228
31
953
2575
54016705
54015113
0.000000e+00
1419.0
20
TraesCS5B01G378500
chr2B
83.031
1597
216
31
991
2575
54044022
54042469
0.000000e+00
1397.0
21
TraesCS5B01G378500
chr2B
80.990
1252
173
26
1756
2963
89491367
89492597
0.000000e+00
933.0
22
TraesCS5B01G378500
chr6D
86.355
2008
228
27
982
2969
33895034
33897015
0.000000e+00
2148.0
23
TraesCS5B01G378500
chr6D
89.364
818
38
12
2371
3161
8567307
8566512
0.000000e+00
983.0
24
TraesCS5B01G378500
chr6D
89.712
729
46
13
62
785
379560128
379559424
0.000000e+00
904.0
25
TraesCS5B01G378500
chr6D
98.039
51
1
0
2961
3011
33897023
33897073
4.340000e-14
89.8
26
TraesCS5B01G378500
chr5D
86.062
1643
194
16
940
2573
499865132
499863516
0.000000e+00
1733.0
27
TraesCS5B01G378500
chr5D
81.188
606
77
21
2575
3159
42077645
42078234
1.340000e-123
453.0
28
TraesCS5B01G378500
chr5D
83.032
442
54
10
2717
3140
499863241
499862803
6.400000e-102
381.0
29
TraesCS5B01G378500
chr5D
77.695
269
49
7
476
740
175780643
175780904
1.520000e-33
154.0
30
TraesCS5B01G378500
chr4D
88.798
732
71
5
62
785
446103335
446104063
0.000000e+00
887.0
31
TraesCS5B01G378500
chr7A
89.655
696
64
6
93
782
28154547
28155240
0.000000e+00
880.0
32
TraesCS5B01G378500
chr7A
76.608
342
71
4
406
744
706267463
706267128
2.500000e-41
180.0
33
TraesCS5B01G378500
chr7B
85.114
833
104
12
997
1828
32348068
32347255
0.000000e+00
833.0
34
TraesCS5B01G378500
chr2D
84.802
658
69
6
121
775
76881649
76881020
1.600000e-177
632.0
35
TraesCS5B01G378500
chr2A
87.311
331
39
1
121
448
77743631
77743301
2.980000e-100
375.0
36
TraesCS5B01G378500
chr7D
81.124
249
44
3
383
629
610563981
610564228
2.490000e-46
196.0
37
TraesCS5B01G378500
chr4A
77.286
339
65
10
406
743
698512839
698513166
4.160000e-44
189.0
38
TraesCS5B01G378500
chr3B
94.690
113
6
0
3031
3143
778341289
778341177
3.240000e-40
176.0
39
TraesCS5B01G378500
chr3B
95.890
73
2
1
1
72
77515628
77515556
1.990000e-22
117.0
40
TraesCS5B01G378500
chr3D
93.860
114
7
0
3027
3140
582881500
582881613
4.190000e-39
172.0
41
TraesCS5B01G378500
chr3A
98.551
69
1
0
1
69
420889878
420889810
4.280000e-24
122.0
42
TraesCS5B01G378500
chr3A
95.833
72
3
0
1
72
571359983
571360054
1.990000e-22
117.0
43
TraesCS5B01G378500
chr1A
94.737
76
3
1
1
76
79096251
79096177
1.990000e-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
TraesCS5B01G378500
chr5B
556793588
556796748
3160
True
5838.0
5838
100.000
1
3161
1
chr5B.!!$R2
3160
1
TraesCS5B01G378500
chr5B
621236706
621238336
1630
True
1842.0
1842
87.112
940
2575
1
chr5B.!!$R3
1635
2
TraesCS5B01G378500
chr6B
15395786
15397956
2170
True
2713.0
2713
89.305
991
3161
1
chr6B.!!$R3
2170
3
TraesCS5B01G378500
chr6B
670590601
670592702
2101
True
2435.0
2435
87.563
993
3159
1
chr6B.!!$R4
2166
4
TraesCS5B01G378500
chr6B
15379961
15381521
1560
True
2398.0
2398
94.373
1013
2575
1
chr6B.!!$R2
1562
5
TraesCS5B01G378500
chr6B
15214860
15215462
602
True
409.0
409
80.164
2384
2948
1
chr6B.!!$R1
564
6
TraesCS5B01G378500
chr1B
662035008
662038894
3886
False
1851.5
2519
93.863
62
2575
2
chr1B.!!$F1
2513
7
TraesCS5B01G378500
chr6A
9355310
9357334
2024
False
2484.0
2484
88.873
1121
3159
1
chr6A.!!$F1
2038
8
TraesCS5B01G378500
chr6A
9461362
9463025
1663
False
1871.0
1871
87.202
923
2575
1
chr6A.!!$F2
1652
9
TraesCS5B01G378500
chr2B
709567608
709569633
2025
True
2189.0
2189
86.277
1124
3159
1
chr2B.!!$R3
2035
10
TraesCS5B01G378500
chr2B
54015113
54016705
1592
True
1419.0
1419
82.864
953
2575
1
chr2B.!!$R1
1622
11
TraesCS5B01G378500
chr2B
54042469
54044022
1553
True
1397.0
1397
83.031
991
2575
1
chr2B.!!$R2
1584
12
TraesCS5B01G378500
chr2B
89491367
89492597
1230
False
933.0
933
80.990
1756
2963
1
chr2B.!!$F1
1207
13
TraesCS5B01G378500
chr6D
33895034
33897073
2039
False
1118.9
2148
92.197
982
3011
2
chr6D.!!$F1
2029
14
TraesCS5B01G378500
chr6D
8566512
8567307
795
True
983.0
983
89.364
2371
3161
1
chr6D.!!$R1
790
15
TraesCS5B01G378500
chr6D
379559424
379560128
704
True
904.0
904
89.712
62
785
1
chr6D.!!$R2
723
16
TraesCS5B01G378500
chr5D
499862803
499865132
2329
True
1057.0
1733
84.547
940
3140
2
chr5D.!!$R1
2200
17
TraesCS5B01G378500
chr5D
42077645
42078234
589
False
453.0
453
81.188
2575
3159
1
chr5D.!!$F1
584
18
TraesCS5B01G378500
chr4D
446103335
446104063
728
False
887.0
887
88.798
62
785
1
chr4D.!!$F1
723
19
TraesCS5B01G378500
chr7A
28154547
28155240
693
False
880.0
880
89.655
93
782
1
chr7A.!!$F1
689
20
TraesCS5B01G378500
chr7B
32347255
32348068
813
True
833.0
833
85.114
997
1828
1
chr7B.!!$R1
831
21
TraesCS5B01G378500
chr2D
76881020
76881649
629
True
632.0
632
84.802
121
775
1
chr2D.!!$R1
654
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.