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
TraesCS2D01G168200
chr2D
100.000
4810
0
0
1
4810
112098325
112103134
0.000000e+00
8883.0
1
TraesCS2D01G168200
chr2D
85.532
1645
164
43
628
2225
111588299
111589916
0.000000e+00
1652.0
2
TraesCS2D01G168200
chr2D
89.116
1222
77
21
1781
2984
112180287
112179104
0.000000e+00
1469.0
3
TraesCS2D01G168200
chr2D
90.807
979
65
8
726
1686
112181350
112180379
0.000000e+00
1286.0
4
TraesCS2D01G168200
chr2D
79.050
1327
164
74
2935
4205
112178883
112177615
0.000000e+00
806.0
5
TraesCS2D01G168200
chr2D
83.062
738
87
23
2277
2984
111589931
111590660
1.890000e-178
636.0
6
TraesCS2D01G168200
chr2D
84.844
640
59
26
3442
4072
111591329
111591939
1.140000e-170
610.0
7
TraesCS2D01G168200
chr2D
90.795
239
18
1
1
235
112183584
112183346
2.790000e-82
316.0
8
TraesCS2D01G168200
chr2D
81.356
413
45
18
3000
3397
111590932
111591327
1.680000e-79
307.0
9
TraesCS2D01G168200
chr2D
90.805
174
11
1
4340
4513
111592354
111592522
1.350000e-55
228.0
10
TraesCS2D01G168200
chr2D
84.862
218
31
2
593
810
112187999
112187784
8.110000e-53
219.0
11
TraesCS2D01G168200
chr2D
83.636
220
33
2
593
810
112186881
112186663
2.270000e-48
204.0
12
TraesCS2D01G168200
chr2D
88.971
136
12
2
4060
4195
111591956
111592088
1.070000e-36
165.0
13
TraesCS2D01G168200
chr2D
92.405
79
3
1
252
327
112181846
112181768
5.090000e-20
110.0
14
TraesCS2D01G168200
chr2A
91.065
1813
66
37
246
1987
112744065
112745852
0.000000e+00
2362.0
15
TraesCS2D01G168200
chr2A
86.776
2019
174
47
628
2577
111921568
111923562
0.000000e+00
2163.0
16
TraesCS2D01G168200
chr2A
88.514
1454
106
22
593
1987
113312380
113310929
0.000000e+00
1703.0
17
TraesCS2D01G168200
chr2A
93.013
873
31
13
2051
2919
113310830
113309984
0.000000e+00
1247.0
18
TraesCS2D01G168200
chr2A
90.929
893
31
24
2051
2919
112745951
112746817
0.000000e+00
1155.0
19
TraesCS2D01G168200
chr2A
82.120
1236
134
58
3000
4195
111924197
111925385
0.000000e+00
977.0
20
TraesCS2D01G168200
chr2A
87.879
627
22
19
4205
4807
112748171
112748767
0.000000e+00
688.0
21
TraesCS2D01G168200
chr2A
92.774
429
25
3
2947
3373
113309983
113309559
2.460000e-172
616.0
22
TraesCS2D01G168200
chr2A
98.214
336
6
0
3745
4080
112747521
112747856
5.360000e-164
588.0
23
TraesCS2D01G168200
chr2A
90.868
438
31
6
2944
3377
112746815
112747247
3.230000e-161
579.0
24
TraesCS2D01G168200
chr2A
87.473
455
40
8
3752
4205
113309452
113309014
4.290000e-140
508.0
25
TraesCS2D01G168200
chr2A
90.202
347
33
1
2638
2983
111923579
111923925
7.340000e-123
451.0
26
TraesCS2D01G168200
chr2A
94.776
268
14
0
1
268
112743789
112744056
7.450000e-113
418.0
27
TraesCS2D01G168200
chr2A
83.203
256
38
3
324
575
640704748
640704494
3.740000e-56
230.0
28
TraesCS2D01G168200
chr2A
84.091
220
32
2
593
810
113319363
113319145
4.880000e-50
209.0
29
TraesCS2D01G168200
chr2A
91.270
126
4
3
4078
4196
112747959
112748084
1.070000e-36
165.0
30
TraesCS2D01G168200
chr2A
84.884
172
6
10
3442
3607
112747275
112747432
6.450000e-34
156.0
31
TraesCS2D01G168200
chr2A
92.405
79
3
2
252
327
113312488
113312410
5.090000e-20
110.0
32
TraesCS2D01G168200
chr2A
96.610
59
2
0
4342
4400
111925514
111925572
1.100000e-16
99.0
33
TraesCS2D01G168200
chr2A
86.842
76
4
2
4448
4523
111925575
111925644
3.990000e-11
80.5
34
TraesCS2D01G168200
chr2B
95.000
1040
31
8
723
1741
162007420
162008459
0.000000e+00
1613.0
35
TraesCS2D01G168200
chr2B
88.649
1295
70
27
1769
3032
162008548
162009796
0.000000e+00
1506.0
36
TraesCS2D01G168200
chr2B
91.967
1083
18
19
3745
4810
162010684
162011714
0.000000e+00
1454.0
37
TraesCS2D01G168200
chr2B
85.610
1237
107
32
593
1820
161722022
161723196
0.000000e+00
1232.0
38
TraesCS2D01G168200
chr2B
89.875
958
77
13
742
1686
162449043
162448093
0.000000e+00
1214.0
39
TraesCS2D01G168200
chr2B
89.834
905
55
11
2085
2984
162447668
162446796
0.000000e+00
1127.0
40
TraesCS2D01G168200
chr2B
85.889
1063
121
20
1935
2984
161723299
161724345
0.000000e+00
1105.0
41
TraesCS2D01G168200
chr2B
79.983
1184
118
62
3068
4205
162446481
162445371
0.000000e+00
763.0
42
TraesCS2D01G168200
chr2B
84.052
765
74
28
3442
4195
161725016
161725743
0.000000e+00
693.0
43
TraesCS2D01G168200
chr2B
89.049
347
21
6
1
331
162006797
162007142
9.630000e-112
414.0
44
TraesCS2D01G168200
chr2B
81.598
413
46
18
3000
3397
161724617
161725014
1.000000e-81
315.0
45
TraesCS2D01G168200
chr2B
90.678
236
19
3
1
235
162479373
162479140
1.300000e-80
311.0
46
TraesCS2D01G168200
chr2B
87.288
236
13
7
1781
1999
162447995
162447760
2.220000e-63
254.0
47
TraesCS2D01G168200
chr2B
87.442
215
26
1
594
808
162496509
162496296
3.720000e-61
246.0
48
TraesCS2D01G168200
chr2B
83.203
256
38
4
325
576
413085070
413084816
3.740000e-56
230.0
49
TraesCS2D01G168200
chr2B
85.321
218
31
1
593
810
162482976
162482760
1.740000e-54
224.0
50
TraesCS2D01G168200
chr2B
88.235
153
16
2
593
744
162449304
162449153
1.060000e-41
182.0
51
TraesCS2D01G168200
chr2B
88.158
152
7
4
4372
4513
161725909
161726059
2.300000e-38
171.0
52
TraesCS2D01G168200
chr2B
84.884
172
8
7
3442
3607
162010272
162010431
1.790000e-34
158.0
53
TraesCS2D01G168200
chr2B
87.963
108
7
2
223
327
162449437
162449333
6.540000e-24
122.0
54
TraesCS2D01G168200
chr4A
84.646
254
32
6
326
574
560904121
560903870
3.720000e-61
246.0
55
TraesCS2D01G168200
chr7A
84.314
255
34
5
328
577
206757205
206757458
1.340000e-60
244.0
56
TraesCS2D01G168200
chr7A
83.137
255
38
3
326
576
595822966
595822713
1.350000e-55
228.0
57
TraesCS2D01G168200
chr3B
83.465
254
35
6
326
574
571760210
571760461
3.740000e-56
230.0
58
TraesCS2D01G168200
chr1A
83.137
255
38
4
326
576
533465007
533464754
1.350000e-55
228.0
59
TraesCS2D01G168200
chr1A
83.071
254
36
6
326
574
510345796
510346047
1.740000e-54
224.0
60
TraesCS2D01G168200
chr6A
83.654
104
15
2
1394
1496
535154205
535154103
3.960000e-16
97.1
61
TraesCS2D01G168200
chr3A
100.000
42
0
0
4339
4380
23177335
23177294
1.440000e-10
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
TraesCS2D01G168200
chr2D
112098325
112103134
4809
False
8883.000000
8883
100.000000
1
4810
1
chr2D.!!$F1
4809
1
TraesCS2D01G168200
chr2D
112177615
112187999
10384
True
630.000000
1469
87.238714
1
4205
7
chr2D.!!$R1
4204
2
TraesCS2D01G168200
chr2D
111588299
111592522
4223
False
599.666667
1652
85.761667
628
4513
6
chr2D.!!$F2
3885
3
TraesCS2D01G168200
chr2A
113309014
113312488
3474
True
836.800000
1703
90.835800
252
4205
5
chr2A.!!$R3
3953
4
TraesCS2D01G168200
chr2A
112743789
112748767
4978
False
763.875000
2362
91.235625
1
4807
8
chr2A.!!$F2
4806
5
TraesCS2D01G168200
chr2A
111921568
111925644
4076
False
754.100000
2163
88.510000
628
4523
5
chr2A.!!$F1
3895
6
TraesCS2D01G168200
chr2B
162006797
162011714
4917
False
1029.000000
1613
89.909800
1
4810
5
chr2B.!!$F2
4809
7
TraesCS2D01G168200
chr2B
161722022
161726059
4037
False
703.200000
1232
85.061400
593
4513
5
chr2B.!!$F1
3920
8
TraesCS2D01G168200
chr2B
162445371
162449437
4066
True
610.333333
1214
87.196333
223
4205
6
chr2B.!!$R3
3982
9
TraesCS2D01G168200
chr2B
162479140
162482976
3836
True
267.500000
311
87.999500
1
810
2
chr2B.!!$R4
809
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.