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
TraesCS2D01G601600
chr2D
100.000
5539
0
0
1
5539
651695913
651701451
0.000000e+00
10229.0
1
TraesCS2D01G601600
chr2D
84.713
1027
106
28
2504
3515
651723707
651724697
0.000000e+00
979.0
2
TraesCS2D01G601600
chr2D
95.009
541
16
1
5010
5539
60174992
60175532
0.000000e+00
839.0
3
TraesCS2D01G601600
chr2D
83.219
876
115
26
2335
3198
651717432
651718287
0.000000e+00
774.0
4
TraesCS2D01G601600
chr2D
84.857
700
95
9
738
1428
651721023
651721720
0.000000e+00
695.0
5
TraesCS2D01G601600
chr2D
87.011
562
67
6
967
1525
651715663
651716221
3.640000e-176
628.0
6
TraesCS2D01G601600
chr2D
86.717
527
38
17
5010
5513
103064229
103063712
1.740000e-154
556.0
7
TraesCS2D01G601600
chr2D
86.235
494
56
10
3520
4009
651724812
651725297
4.920000e-145
525.0
8
TraesCS2D01G601600
chr2D
88.706
425
40
7
3196
3615
651719220
651719641
3.830000e-141
512.0
9
TraesCS2D01G601600
chr2D
84.469
367
40
7
3643
4009
651719725
651720074
4.110000e-91
346.0
10
TraesCS2D01G601600
chr2D
95.000
80
4
0
2139
2218
2461028
2461107
5.830000e-25
126.0
11
TraesCS2D01G601600
chr2D
92.647
68
5
0
657
724
651720916
651720983
1.270000e-16
99.0
12
TraesCS2D01G601600
chr2A
95.080
4390
172
16
1
4363
775978876
775974504
0.000000e+00
6870.0
13
TraesCS2D01G601600
chr2A
85.193
1344
161
25
2677
4009
775942143
775940827
0.000000e+00
1345.0
14
TraesCS2D01G601600
chr2A
80.196
1530
215
52
659
2133
775939984
775938488
0.000000e+00
1066.0
15
TraesCS2D01G601600
chr2A
84.455
817
89
16
2704
3515
775937842
775937059
0.000000e+00
771.0
16
TraesCS2D01G601600
chr2A
85.598
493
57
9
3522
4009
775936905
775936422
6.400000e-139
505.0
17
TraesCS2D01G601600
chr2A
90.541
296
24
4
1034
1327
775968762
775968469
6.730000e-104
388.0
18
TraesCS2D01G601600
chr2A
81.250
448
62
19
2243
2683
775968395
775967963
5.310000e-90
342.0
19
TraesCS2D01G601600
chr2A
82.428
313
26
5
4575
4883
775972501
775972214
4.290000e-61
246.0
20
TraesCS2D01G601600
chr2A
79.457
258
34
14
4101
4340
15610796
15611052
1.230000e-36
165.0
21
TraesCS2D01G601600
chr2B
91.268
2176
146
10
2724
4883
781579960
781577813
0.000000e+00
2926.0
22
TraesCS2D01G601600
chr2B
96.326
1633
53
5
1
1628
781582808
781581178
0.000000e+00
2676.0
23
TraesCS2D01G601600
chr2B
95.251
1116
47
5
1632
2743
781581084
781579971
0.000000e+00
1762.0
24
TraesCS2D01G601600
chr2B
81.506
1222
167
36
738
1928
781540130
781538937
0.000000e+00
950.0
25
TraesCS2D01G601600
chr2B
83.008
1024
127
32
2514
3515
781537614
781536616
0.000000e+00
883.0
26
TraesCS2D01G601600
chr2B
84.589
584
36
20
5010
5539
24026290
24025707
1.060000e-146
531.0
27
TraesCS2D01G601600
chr2B
86.515
482
53
8
3520
3997
781536504
781536031
2.290000e-143
520.0
28
TraesCS2D01G601600
chr2B
82.131
582
46
18
5010
5539
210670642
210671217
3.940000e-121
446.0
29
TraesCS2D01G601600
chr2B
90.551
254
20
4
5009
5260
438613145
438612894
3.200000e-87
333.0
30
TraesCS2D01G601600
chr2B
87.317
205
21
4
1933
2133
781538902
781538699
4.320000e-56
230.0
31
TraesCS2D01G601600
chr5A
82.634
1192
163
25
2821
3995
654167303
654166139
0.000000e+00
1014.0
32
TraesCS2D01G601600
chr5A
79.106
1431
197
52
738
2108
654157674
654156286
0.000000e+00
893.0
33
TraesCS2D01G601600
chr5A
82.885
818
111
19
738
1539
654169470
654168666
0.000000e+00
708.0
34
TraesCS2D01G601600
chr5A
82.597
747
105
17
3250
3990
654155038
654154311
2.180000e-178
636.0
35
TraesCS2D01G601600
chr5A
86.124
418
55
2
2821
3235
654155534
654155117
1.090000e-121
448.0
36
TraesCS2D01G601600
chr5A
82.863
461
35
16
5009
5438
328711035
328710588
1.880000e-99
374.0
37
TraesCS2D01G601600
chr5A
82.430
461
36
17
5010
5438
675499471
675499024
1.470000e-95
361.0
38
TraesCS2D01G601600
chr5A
90.598
234
19
2
5010
5241
644863183
644862951
1.940000e-79
307.0
39
TraesCS2D01G601600
chr5A
78.346
254
38
10
4096
4332
670398749
670399002
1.240000e-31
148.0
40
TraesCS2D01G601600
chr5A
75.072
345
60
20
108
432
654159474
654159136
2.690000e-28
137.0
41
TraesCS2D01G601600
chr5D
82.506
1189
165
21
2821
3989
527154988
527153823
0.000000e+00
1003.0
42
TraesCS2D01G601600
chr5D
79.404
1442
186
63
738
2108
527157094
527155693
0.000000e+00
915.0
43
TraesCS2D01G601600
chr5D
95.154
227
11
0
5010
5236
532654433
532654659
5.280000e-95
359.0
44
TraesCS2D01G601600
chr5B
79.262
1437
191
57
738
2108
663229119
663227724
0.000000e+00
904.0
45
TraesCS2D01G601600
chr5B
84.639
664
74
13
2821
3482
663227021
663226384
2.180000e-178
636.0
46
TraesCS2D01G601600
chr5B
91.860
86
7
0
2131
2216
27817221
27817306
2.710000e-23
121.0
47
TraesCS2D01G601600
chr4D
95.941
542
9
3
5010
5539
306427322
306427862
0.000000e+00
867.0
48
TraesCS2D01G601600
chr4D
91.765
85
7
0
2132
2216
320026968
320027052
9.750000e-23
119.0
49
TraesCS2D01G601600
chr4D
84.270
89
13
1
2129
2216
128674957
128675045
9.890000e-13
86.1
50
TraesCS2D01G601600
chr6D
93.601
547
21
5
5007
5539
454277070
454277616
0.000000e+00
804.0
51
TraesCS2D01G601600
chr6D
94.094
254
15
0
5007
5260
454293757
454293504
2.420000e-103
387.0
52
TraesCS2D01G601600
chr3D
91.103
562
18
8
5010
5539
519327490
519328051
0.000000e+00
732.0
53
TraesCS2D01G601600
chr3D
96.364
110
4
0
4900
5009
569501531
569501640
1.230000e-41
182.0
54
TraesCS2D01G601600
chr3D
90.566
106
10
0
3
108
77400426
77400321
2.080000e-29
141.0
55
TraesCS2D01G601600
chr3D
88.000
100
8
4
2132
2229
570105967
570105870
1.260000e-21
115.0
56
TraesCS2D01G601600
chr3D
88.764
89
10
0
2132
2220
86334305
86334217
5.870000e-20
110.0
57
TraesCS2D01G601600
chr3A
89.876
563
25
6
5009
5539
619069949
619070511
0.000000e+00
695.0
58
TraesCS2D01G601600
chr1D
89.336
572
19
8
5008
5539
359696547
359697116
0.000000e+00
680.0
59
TraesCS2D01G601600
chr1D
98.198
111
2
0
4899
5009
434426627
434426517
1.570000e-45
195.0
60
TraesCS2D01G601600
chr1D
97.619
42
1
0
2128
2169
223162269
223162310
7.700000e-09
73.1
61
TraesCS2D01G601600
chr4A
88.810
563
29
8
5010
5539
596138651
596139212
0.000000e+00
660.0
62
TraesCS2D01G601600
chr4A
90.909
88
8
0
2132
2219
618462258
618462171
9.750000e-23
119.0
63
TraesCS2D01G601600
chr4A
86.538
52
7
0
4289
4340
585391042
585391093
2.160000e-04
58.4
64
TraesCS2D01G601600
chr7A
84.362
486
51
8
5009
5472
13855476
13854994
2.350000e-123
453.0
65
TraesCS2D01G601600
chr7A
79.646
113
17
4
4100
4212
607907417
607907523
5.950000e-10
76.8
66
TraesCS2D01G601600
chr4B
86.133
375
28
7
5151
5513
651021419
651021057
3.130000e-102
383.0
67
TraesCS2D01G601600
chr4B
82.394
142
21
3
4205
4343
405339889
405339749
2.710000e-23
121.0
68
TraesCS2D01G601600
chr6B
82.900
462
34
17
5009
5438
698995444
698995892
1.880000e-99
374.0
69
TraesCS2D01G601600
chr6B
92.941
85
6
0
2132
2216
240546056
240546140
2.100000e-24
124.0
70
TraesCS2D01G601600
chr1B
90.171
234
20
2
5010
5241
83628868
83628636
9.020000e-78
302.0
71
TraesCS2D01G601600
chr1B
92.941
85
6
0
2132
2216
222194511
222194595
2.100000e-24
124.0
72
TraesCS2D01G601600
chr1A
94.545
110
6
0
4900
5009
16475415
16475524
2.650000e-38
171.0
73
TraesCS2D01G601600
chr1A
89.109
101
8
3
2128
2226
436259649
436259748
7.540000e-24
122.0
74
TraesCS2D01G601600
chr1A
91.011
89
8
0
2130
2218
57407821
57407733
2.710000e-23
121.0
75
TraesCS2D01G601600
chr1A
87.912
91
10
1
2132
2221
382550773
382550683
7.590000e-19
106.0
76
TraesCS2D01G601600
chr1A
87.640
89
10
1
2130
2217
449669511
449669423
9.820000e-18
102.0
77
TraesCS2D01G601600
chr1A
88.235
85
10
0
2132
2216
498666622
498666538
9.820000e-18
102.0
78
TraesCS2D01G601600
chr1A
89.024
82
8
1
2149
2229
105322650
105322569
3.530000e-17
100.0
79
TraesCS2D01G601600
chr3B
88.679
106
12
0
3
108
123633234
123633129
4.500000e-26
130.0
80
TraesCS2D01G601600
chr7B
93.902
82
5
0
2135
2216
625725340
625725259
2.100000e-24
124.0
81
TraesCS2D01G601600
chr7B
97.297
37
1
0
69
105
602554025
602554061
4.630000e-06
63.9
82
TraesCS2D01G601600
chr6A
90.000
90
9
0
2129
2218
356112243
356112332
3.510000e-22
117.0
83
TraesCS2D01G601600
chr6A
90.805
87
6
2
2131
2216
393802368
393802283
1.260000e-21
115.0
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
TraesCS2D01G601600
chr2D
651695913
651701451
5538
False
10229.000000
10229
100.000000
1
5539
1
chr2D.!!$F3
5538
1
TraesCS2D01G601600
chr2D
60174992
60175532
540
False
839.000000
839
95.009000
5010
5539
1
chr2D.!!$F2
529
2
TraesCS2D01G601600
chr2D
651715663
651725297
9634
False
569.750000
979
86.482125
657
4009
8
chr2D.!!$F4
3352
3
TraesCS2D01G601600
chr2D
103063712
103064229
517
True
556.000000
556
86.717000
5010
5513
1
chr2D.!!$R1
503
4
TraesCS2D01G601600
chr2A
775967963
775978876
10913
True
1961.500000
6870
87.324750
1
4883
4
chr2A.!!$R2
4882
5
TraesCS2D01G601600
chr2A
775936422
775942143
5721
True
921.750000
1345
83.860500
659
4009
4
chr2A.!!$R1
3350
6
TraesCS2D01G601600
chr2B
781577813
781582808
4995
True
2454.666667
2926
94.281667
1
4883
3
chr2B.!!$R4
4882
7
TraesCS2D01G601600
chr2B
781536031
781540130
4099
True
645.750000
950
84.586500
738
3997
4
chr2B.!!$R3
3259
8
TraesCS2D01G601600
chr2B
24025707
24026290
583
True
531.000000
531
84.589000
5010
5539
1
chr2B.!!$R1
529
9
TraesCS2D01G601600
chr2B
210670642
210671217
575
False
446.000000
446
82.131000
5010
5539
1
chr2B.!!$F1
529
10
TraesCS2D01G601600
chr5A
654166139
654169470
3331
True
861.000000
1014
82.759500
738
3995
2
chr5A.!!$R5
3257
11
TraesCS2D01G601600
chr5A
654154311
654159474
5163
True
528.500000
893
80.724750
108
3990
4
chr5A.!!$R4
3882
12
TraesCS2D01G601600
chr5D
527153823
527157094
3271
True
959.000000
1003
80.955000
738
3989
2
chr5D.!!$R1
3251
13
TraesCS2D01G601600
chr5B
663226384
663229119
2735
True
770.000000
904
81.950500
738
3482
2
chr5B.!!$R1
2744
14
TraesCS2D01G601600
chr4D
306427322
306427862
540
False
867.000000
867
95.941000
5010
5539
1
chr4D.!!$F2
529
15
TraesCS2D01G601600
chr6D
454277070
454277616
546
False
804.000000
804
93.601000
5007
5539
1
chr6D.!!$F1
532
16
TraesCS2D01G601600
chr3D
519327490
519328051
561
False
732.000000
732
91.103000
5010
5539
1
chr3D.!!$F1
529
17
TraesCS2D01G601600
chr3A
619069949
619070511
562
False
695.000000
695
89.876000
5009
5539
1
chr3A.!!$F1
530
18
TraesCS2D01G601600
chr1D
359696547
359697116
569
False
680.000000
680
89.336000
5008
5539
1
chr1D.!!$F2
531
19
TraesCS2D01G601600
chr4A
596138651
596139212
561
False
660.000000
660
88.810000
5010
5539
1
chr4A.!!$F2
529
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.