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
TraesCS3A01G157600
chr3A
100.000
3218
0
0
1
3218
154743329
154740112
0.000000e+00
5943.0
1
TraesCS3A01G157600
chr3B
93.260
2626
105
26
626
3217
199928818
199926231
0.000000e+00
3803.0
2
TraesCS3A01G157600
chr3B
94.442
2339
93
20
888
3217
200365772
200368082
0.000000e+00
3565.0
3
TraesCS3A01G157600
chr3B
94.487
1451
52
11
626
2066
199704432
199703000
0.000000e+00
2211.0
4
TraesCS3A01G157600
chr3B
92.960
1179
44
12
2059
3217
199702520
199701361
0.000000e+00
1681.0
5
TraesCS3A01G157600
chr3B
91.589
214
14
2
693
902
200365544
200365757
3.140000e-75
292.0
6
TraesCS3A01G157600
chr3B
93.333
195
12
1
17
210
199704623
199704429
1.460000e-73
287.0
7
TraesCS3A01G157600
chr3B
91.795
195
15
1
17
210
199929009
199928815
1.470000e-68
270.0
8
TraesCS3A01G157600
chr3B
90.640
203
16
2
11
210
200365296
200365498
1.900000e-67
267.0
9
TraesCS3A01G157600
chr3B
85.043
234
26
3
201
433
167963879
167964104
2.500000e-56
230.0
10
TraesCS3A01G157600
chr3B
82.479
234
30
7
203
434
97732953
97732729
9.110000e-46
195.0
11
TraesCS3A01G157600
chr3D
95.985
1594
61
2
671
2261
136776381
136774788
0.000000e+00
2586.0
12
TraesCS3A01G157600
chr3D
94.650
972
25
11
2257
3217
136774621
136773666
0.000000e+00
1482.0
13
TraesCS3A01G157600
chr3D
86.063
696
67
11
12
685
136777082
136776395
0.000000e+00
721.0
14
TraesCS3A01G157600
chr1B
89.634
1640
122
13
840
2462
131789936
131788328
0.000000e+00
2043.0
15
TraesCS3A01G157600
chr1B
89.281
1642
127
17
838
2462
131505323
131503714
0.000000e+00
2012.0
16
TraesCS3A01G157600
chr1B
84.406
917
90
21
806
1711
131179862
131178988
0.000000e+00
852.0
17
TraesCS3A01G157600
chr1B
88.274
452
53
0
1811
2262
131670674
131670223
2.820000e-150
542.0
18
TraesCS3A01G157600
chr1B
89.919
248
14
7
2981
3217
130859579
130859332
3.120000e-80
309.0
19
TraesCS3A01G157600
chr1B
89.919
248
14
7
2981
3217
131380108
131379861
3.120000e-80
309.0
20
TraesCS3A01G157600
chr1B
89.558
249
14
8
2981
3217
130794038
130793790
4.030000e-79
305.0
21
TraesCS3A01G157600
chr1B
89.558
249
14
8
2981
3217
131583412
131583164
4.030000e-79
305.0
22
TraesCS3A01G157600
chr1B
78.618
304
47
12
803
1099
130742829
130742537
5.480000e-43
185.0
23
TraesCS3A01G157600
chr1B
93.069
101
7
0
2735
2835
131787364
131787264
7.190000e-32
148.0
24
TraesCS3A01G157600
chr1B
88.073
109
5
4
2735
2835
131129883
131129775
4.360000e-24
122.0
25
TraesCS3A01G157600
chr1B
97.059
68
1
1
2394
2461
130795270
130795204
2.620000e-21
113.0
26
TraesCS3A01G157600
chr1B
97.015
67
1
1
2394
2460
131602258
131602193
9.440000e-21
111.0
27
TraesCS3A01G157600
chr1B
94.521
73
2
2
2853
2924
345311161
345311232
9.440000e-21
111.0
28
TraesCS3A01G157600
chr1B
92.308
78
1
4
2854
2926
453344420
453344497
4.390000e-19
106.0
29
TraesCS3A01G157600
chr1D
88.856
1669
116
10
806
2461
80006138
80004527
0.000000e+00
1988.0
30
TraesCS3A01G157600
chr1D
88.646
1647
126
19
822
2462
79950146
79948555
0.000000e+00
1949.0
31
TraesCS3A01G157600
chr1D
90.400
375
24
6
2464
2835
79948222
79947857
1.740000e-132
483.0
32
TraesCS3A01G157600
chr1D
89.641
251
12
8
2981
3217
80001933
80001683
1.120000e-79
307.0
33
TraesCS3A01G157600
chr1D
95.050
101
5
0
2735
2835
79947000
79946900
3.320000e-35
159.0
34
TraesCS3A01G157600
chr1D
89.908
109
3
4
2735
2835
80002122
80002014
2.010000e-27
134.0
35
TraesCS3A01G157600
chr1A
87.856
1614
112
12
871
2462
98604580
98603029
0.000000e+00
1818.0
36
TraesCS3A01G157600
chr6B
86.087
230
25
1
206
435
8131965
8131743
1.150000e-59
241.0
37
TraesCS3A01G157600
chr2B
85.837
233
26
1
206
438
719971011
719970786
1.150000e-59
241.0
38
TraesCS3A01G157600
chr2B
94.118
85
5
0
2843
2927
173468231
173468315
2.610000e-26
130.0
39
TraesCS3A01G157600
chr2B
90.244
82
4
1
2843
2924
551551548
551551625
1.580000e-18
104.0
40
TraesCS3A01G157600
chr5A
85.169
236
28
1
207
442
129619224
129619452
5.370000e-58
235.0
41
TraesCS3A01G157600
chr2D
85.841
226
25
1
208
433
291400
291618
1.930000e-57
233.0
42
TraesCS3A01G157600
chr2A
85.841
226
24
2
208
433
217691
217474
1.930000e-57
233.0
43
TraesCS3A01G157600
chr7B
84.416
231
26
5
207
435
464555666
464555888
5.410000e-53
219.0
44
TraesCS3A01G157600
chr5B
82.143
224
32
4
210
433
317076657
317076872
5.480000e-43
185.0
45
TraesCS3A01G157600
chr4A
94.521
73
2
2
2853
2924
498697545
498697474
9.440000e-21
111.0
46
TraesCS3A01G157600
chr4A
94.521
73
2
2
2853
2924
498697492
498697563
9.440000e-21
111.0
47
TraesCS3A01G157600
chr4A
78.102
137
18
7
474
600
545619771
545619905
3.440000e-10
76.8
48
TraesCS3A01G157600
chr5D
81.600
125
14
5
455
571
532664520
532664397
9.500000e-16
95.3
49
TraesCS3A01G157600
chr4B
88.679
53
6
0
548
600
75189493
75189441
7.450000e-07
65.8
50
TraesCS3A01G157600
chr4B
97.297
37
1
0
452
488
115063001
115062965
2.680000e-06
63.9
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
TraesCS3A01G157600
chr3A
154740112
154743329
3217
True
5943.000000
5943
100.000000
1
3218
1
chr3A.!!$R1
3217
1
TraesCS3A01G157600
chr3B
199926231
199929009
2778
True
2036.500000
3803
92.527500
17
3217
2
chr3B.!!$R3
3200
2
TraesCS3A01G157600
chr3B
199701361
199704623
3262
True
1393.000000
2211
93.593333
17
3217
3
chr3B.!!$R2
3200
3
TraesCS3A01G157600
chr3B
200365296
200368082
2786
False
1374.666667
3565
92.223667
11
3217
3
chr3B.!!$F2
3206
4
TraesCS3A01G157600
chr3D
136773666
136777082
3416
True
1596.333333
2586
92.232667
12
3217
3
chr3D.!!$R1
3205
5
TraesCS3A01G157600
chr1B
131503714
131505323
1609
True
2012.000000
2012
89.281000
838
2462
1
chr1B.!!$R6
1624
6
TraesCS3A01G157600
chr1B
131787264
131789936
2672
True
1095.500000
2043
91.351500
840
2835
2
chr1B.!!$R11
1995
7
TraesCS3A01G157600
chr1B
131178988
131179862
874
True
852.000000
852
84.406000
806
1711
1
chr1B.!!$R4
905
8
TraesCS3A01G157600
chr1B
130793790
130795270
1480
True
209.000000
305
93.308500
2394
3217
2
chr1B.!!$R10
823
9
TraesCS3A01G157600
chr1D
79946900
79950146
3246
True
863.666667
1949
91.365333
822
2835
3
chr1D.!!$R1
2013
10
TraesCS3A01G157600
chr1D
80001683
80006138
4455
True
809.666667
1988
89.468333
806
3217
3
chr1D.!!$R2
2411
11
TraesCS3A01G157600
chr1A
98603029
98604580
1551
True
1818.000000
1818
87.856000
871
2462
1
chr1A.!!$R1
1591
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.