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
TraesCS1B01G066100
chr1B
100.000
2816
0
0
1
2816
50272523
50275338
0.000000e+00
5201.0
1
TraesCS1B01G066100
chr1B
96.429
644
23
0
2173
2816
50300685
50301328
0.000000e+00
1062.0
2
TraesCS1B01G066100
chr1B
89.922
645
59
4
2174
2816
221890584
221891224
0.000000e+00
826.0
3
TraesCS1B01G066100
chr1B
87.283
346
37
6
57
396
436690913
436691257
3.400000e-104
388.0
4
TraesCS1B01G066100
chr1B
97.368
38
1
0
403
440
436691286
436691323
6.510000e-07
65.8
5
TraesCS1B01G066100
chr5B
92.703
1110
76
4
1062
2171
590998819
590999923
0.000000e+00
1596.0
6
TraesCS1B01G066100
chr5B
91.047
1117
90
7
1062
2173
35772715
35771604
0.000000e+00
1500.0
7
TraesCS1B01G066100
chr5B
90.528
644
55
3
2174
2816
155570087
155569449
0.000000e+00
846.0
8
TraesCS1B01G066100
chr5B
93.671
474
26
3
580
1051
10419548
10419077
0.000000e+00
706.0
9
TraesCS1B01G066100
chr5B
92.585
472
31
3
2345
2816
485300420
485299953
0.000000e+00
675.0
10
TraesCS1B01G066100
chr5B
88.690
336
33
3
423
753
35773325
35772990
3.380000e-109
405.0
11
TraesCS1B01G066100
chr5B
89.950
199
17
2
57
252
10419751
10419553
1.290000e-63
254.0
12
TraesCS1B01G066100
chr5B
88.439
173
19
1
57
228
35773498
35773326
1.020000e-49
207.0
13
TraesCS1B01G066100
chr5B
98.276
58
1
0
1
58
35773871
35773814
4.960000e-18
102.0
14
TraesCS1B01G066100
chr2D
92.183
1113
83
3
1062
2173
340329757
340328648
0.000000e+00
1570.0
15
TraesCS1B01G066100
chr2D
92.537
469
31
4
581
1046
340332618
340332151
0.000000e+00
669.0
16
TraesCS1B01G066100
chr2D
91.327
196
16
1
559
753
2169749
2169944
1.660000e-67
267.0
17
TraesCS1B01G066100
chr2D
89.944
179
12
3
749
927
2170094
2170266
2.820000e-55
226.0
18
TraesCS1B01G066100
chr2D
92.857
140
8
2
124
262
340332752
340332614
4.760000e-48
202.0
19
TraesCS1B01G066100
chr4D
91.868
1119
82
5
1062
2173
216246872
216245756
0.000000e+00
1554.0
20
TraesCS1B01G066100
chr4D
91.778
1119
83
5
1062
2173
216211884
216210768
0.000000e+00
1548.0
21
TraesCS1B01G066100
chr4D
89.286
336
30
5
423
753
216212500
216212166
1.560000e-112
416.0
22
TraesCS1B01G066100
chr4D
89.286
336
31
4
423
753
216247489
216247154
1.560000e-112
416.0
23
TraesCS1B01G066100
chr4D
90.173
173
16
1
57
228
216212673
216212501
1.020000e-54
224.0
24
TraesCS1B01G066100
chr4D
89.474
171
17
1
57
226
216247662
216247492
6.110000e-52
215.0
25
TraesCS1B01G066100
chr4D
93.443
61
4
0
749
809
216247007
216246947
1.070000e-14
91.6
26
TraesCS1B01G066100
chr4B
91.824
1113
83
3
1062
2173
120260443
120259338
0.000000e+00
1544.0
27
TraesCS1B01G066100
chr4B
91.644
1113
84
4
1062
2173
40494940
40496044
0.000000e+00
1531.0
28
TraesCS1B01G066100
chr4B
91.105
1113
92
2
1062
2173
222597165
222598271
0.000000e+00
1500.0
29
TraesCS1B01G066100
chr4B
93.671
474
27
3
580
1051
222594300
222594772
0.000000e+00
706.0
30
TraesCS1B01G066100
chr4B
93.249
474
30
2
580
1051
120263306
120262833
0.000000e+00
697.0
31
TraesCS1B01G066100
chr4B
91.729
399
31
2
654
1051
268425096
268425493
1.140000e-153
553.0
32
TraesCS1B01G066100
chr4B
83.709
577
63
8
210
758
592246034
592246607
1.500000e-142
516.0
33
TraesCS1B01G066100
chr4B
91.089
303
20
5
749
1047
592246749
592247048
1.210000e-108
403.0
34
TraesCS1B01G066100
chr4B
88.995
209
20
2
57
262
120263509
120263301
3.600000e-64
255.0
35
TraesCS1B01G066100
chr4B
97.143
70
2
0
749
818
653934250
653934319
4.930000e-23
119.0
36
TraesCS1B01G066100
chr4B
100.000
33
0
0
1
33
120263672
120263640
8.420000e-06
62.1
37
TraesCS1B01G066100
chr7A
91.562
1114
85
4
1062
2173
492425248
492424142
0.000000e+00
1528.0
38
TraesCS1B01G066100
chr7A
93.038
474
28
5
580
1051
492428112
492427642
0.000000e+00
688.0
39
TraesCS1B01G066100
chr7A
85.781
647
78
10
2174
2816
68427661
68428297
0.000000e+00
673.0
40
TraesCS1B01G066100
chr2A
90.980
643
53
2
2174
2816
764180614
764179977
0.000000e+00
861.0
41
TraesCS1B01G066100
chr7D
91.008
645
46
8
2174
2816
578284964
578285598
0.000000e+00
859.0
42
TraesCS1B01G066100
chr7D
83.217
572
65
8
210
753
26329620
26330188
1.950000e-136
496.0
43
TraesCS1B01G066100
chr7D
91.722
302
20
4
749
1047
26330335
26330634
5.610000e-112
414.0
44
TraesCS1B01G066100
chr3D
90.108
647
56
7
2173
2816
470842513
470841872
0.000000e+00
833.0
45
TraesCS1B01G066100
chr3D
89.407
236
24
1
519
753
555156832
555156597
2.120000e-76
296.0
46
TraesCS1B01G066100
chr3D
95.833
72
3
0
749
820
555156450
555156379
1.770000e-22
117.0
47
TraesCS1B01G066100
chr6B
93.460
474
28
3
580
1051
706358209
706357737
0.000000e+00
701.0
48
TraesCS1B01G066100
chr6B
93.038
474
31
2
580
1051
706417357
706416884
0.000000e+00
691.0
49
TraesCS1B01G066100
chr6B
92.533
375
25
3
580
951
122827431
122827057
4.130000e-148
534.0
50
TraesCS1B01G066100
chr6B
89.952
209
18
2
57
262
706358412
706358204
1.660000e-67
267.0
51
TraesCS1B01G066100
chr6B
89.952
209
18
2
57
262
706417560
706417352
1.660000e-67
267.0
52
TraesCS1B01G066100
chr6B
90.955
199
15
2
57
252
122827634
122827436
5.980000e-67
265.0
53
TraesCS1B01G066100
chr6B
100.000
33
0
0
1
33
706358575
706358543
8.420000e-06
62.1
54
TraesCS1B01G066100
chr6B
100.000
33
0
0
1
33
706417723
706417691
8.420000e-06
62.1
55
TraesCS1B01G066100
chrUn
96.244
426
16
0
2174
2599
79052001
79051576
0.000000e+00
699.0
56
TraesCS1B01G066100
chr3A
93.249
474
29
3
580
1051
91837647
91838119
0.000000e+00
695.0
57
TraesCS1B01G066100
chr3A
94.118
51
3
0
1
51
198181727
198181777
8.360000e-11
78.7
58
TraesCS1B01G066100
chr2B
93.053
475
27
6
580
1051
758244627
758244156
0.000000e+00
689.0
59
TraesCS1B01G066100
chr2B
88.995
209
20
2
57
262
758244830
758244622
3.600000e-64
255.0
60
TraesCS1B01G066100
chr4A
91.772
474
35
4
580
1051
531951788
531952259
0.000000e+00
656.0
61
TraesCS1B01G066100
chr4A
90.452
199
15
3
57
252
531951586
531951783
2.780000e-65
259.0
62
TraesCS1B01G066100
chr3B
85.016
634
84
8
2183
2813
451756846
451757471
3.960000e-178
634.0
63
TraesCS1B01G066100
chr1A
83.160
576
62
17
205
753
60189786
60190353
7.010000e-136
494.0
64
TraesCS1B01G066100
chr1A
86.705
346
39
5
57
396
420515219
420514875
7.360000e-101
377.0
65
TraesCS1B01G066100
chr1D
86.705
346
39
6
57
396
324414181
324414525
7.360000e-101
377.0
66
TraesCS1B01G066100
chr1D
97.778
45
1
0
396
440
324414547
324414591
8.360000e-11
78.7
67
TraesCS1B01G066100
chr7B
89.474
209
19
2
57
262
504086518
504086310
7.740000e-66
261.0
68
TraesCS1B01G066100
chr5A
94.118
51
3
0
1
51
349134415
349134465
8.360000e-11
78.7
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
TraesCS1B01G066100
chr1B
50272523
50275338
2815
False
5201.000000
5201
100.000000
1
2816
1
chr1B.!!$F1
2815
1
TraesCS1B01G066100
chr1B
50300685
50301328
643
False
1062.000000
1062
96.429000
2173
2816
1
chr1B.!!$F2
643
2
TraesCS1B01G066100
chr1B
221890584
221891224
640
False
826.000000
826
89.922000
2174
2816
1
chr1B.!!$F3
642
3
TraesCS1B01G066100
chr5B
590998819
590999923
1104
False
1596.000000
1596
92.703000
1062
2171
1
chr5B.!!$F1
1109
4
TraesCS1B01G066100
chr5B
155569449
155570087
638
True
846.000000
846
90.528000
2174
2816
1
chr5B.!!$R1
642
5
TraesCS1B01G066100
chr5B
35771604
35773871
2267
True
553.500000
1500
91.613000
1
2173
4
chr5B.!!$R4
2172
6
TraesCS1B01G066100
chr5B
10419077
10419751
674
True
480.000000
706
91.810500
57
1051
2
chr5B.!!$R3
994
7
TraesCS1B01G066100
chr2D
340328648
340332752
4104
True
813.666667
1570
92.525667
124
2173
3
chr2D.!!$R1
2049
8
TraesCS1B01G066100
chr2D
2169749
2170266
517
False
246.500000
267
90.635500
559
927
2
chr2D.!!$F1
368
9
TraesCS1B01G066100
chr4D
216210768
216212673
1905
True
729.333333
1548
90.412333
57
2173
3
chr4D.!!$R1
2116
10
TraesCS1B01G066100
chr4D
216245756
216247662
1906
True
569.150000
1554
91.017750
57
2173
4
chr4D.!!$R2
2116
11
TraesCS1B01G066100
chr4B
40494940
40496044
1104
False
1531.000000
1531
91.644000
1062
2173
1
chr4B.!!$F1
1111
12
TraesCS1B01G066100
chr4B
222594300
222598271
3971
False
1103.000000
1500
92.388000
580
2173
2
chr4B.!!$F4
1593
13
TraesCS1B01G066100
chr4B
120259338
120263672
4334
True
639.525000
1544
93.517000
1
2173
4
chr4B.!!$R1
2172
14
TraesCS1B01G066100
chr4B
592246034
592247048
1014
False
459.500000
516
87.399000
210
1047
2
chr4B.!!$F5
837
15
TraesCS1B01G066100
chr7A
492424142
492428112
3970
True
1108.000000
1528
92.300000
580
2173
2
chr7A.!!$R1
1593
16
TraesCS1B01G066100
chr7A
68427661
68428297
636
False
673.000000
673
85.781000
2174
2816
1
chr7A.!!$F1
642
17
TraesCS1B01G066100
chr2A
764179977
764180614
637
True
861.000000
861
90.980000
2174
2816
1
chr2A.!!$R1
642
18
TraesCS1B01G066100
chr7D
578284964
578285598
634
False
859.000000
859
91.008000
2174
2816
1
chr7D.!!$F1
642
19
TraesCS1B01G066100
chr7D
26329620
26330634
1014
False
455.000000
496
87.469500
210
1047
2
chr7D.!!$F2
837
20
TraesCS1B01G066100
chr3D
470841872
470842513
641
True
833.000000
833
90.108000
2173
2816
1
chr3D.!!$R1
643
21
TraesCS1B01G066100
chr6B
122827057
122827634
577
True
399.500000
534
91.744000
57
951
2
chr6B.!!$R1
894
22
TraesCS1B01G066100
chr6B
706357737
706358575
838
True
343.366667
701
94.470667
1
1051
3
chr6B.!!$R2
1050
23
TraesCS1B01G066100
chr6B
706416884
706417723
839
True
340.033333
691
94.330000
1
1051
3
chr6B.!!$R3
1050
24
TraesCS1B01G066100
chr2B
758244156
758244830
674
True
472.000000
689
91.024000
57
1051
2
chr2B.!!$R1
994
25
TraesCS1B01G066100
chr4A
531951586
531952259
673
False
457.500000
656
91.112000
57
1051
2
chr4A.!!$F1
994
26
TraesCS1B01G066100
chr3B
451756846
451757471
625
False
634.000000
634
85.016000
2183
2813
1
chr3B.!!$F1
630
27
TraesCS1B01G066100
chr1A
60189786
60190353
567
False
494.000000
494
83.160000
205
753
1
chr1A.!!$F1
548
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.