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
TraesCS3B01G006500
chr3B
100.000
3483
0
0
1
3483
3406299
3409781
0.000000e+00
6433.0
1
TraesCS3B01G006500
chr3B
90.273
1357
85
21
55
1379
5324512
5323171
0.000000e+00
1731.0
2
TraesCS3B01G006500
chr3B
87.628
1269
91
27
854
2108
3667380
3666164
0.000000e+00
1413.0
3
TraesCS3B01G006500
chr3B
89.003
1164
73
16
959
2108
5169064
5170186
0.000000e+00
1389.0
4
TraesCS3B01G006500
chr3B
91.088
965
64
13
1899
2862
5322652
5321709
0.000000e+00
1286.0
5
TraesCS3B01G006500
chr3B
82.579
442
69
7
106
543
3610485
3610922
1.960000e-102
383.0
6
TraesCS3B01G006500
chr3B
82.500
440
73
4
106
543
5226207
5225770
1.960000e-102
383.0
7
TraesCS3B01G006500
chr3B
92.647
204
15
0
3280
3483
5321306
5321103
9.450000e-76
294.0
8
TraesCS3B01G006500
chr3B
88.177
203
17
3
2414
2616
3625833
3626028
5.810000e-58
235.0
9
TraesCS3B01G006500
chr3B
83.475
236
23
14
2310
2538
3665866
3665640
4.560000e-49
206.0
10
TraesCS3B01G006500
chr3B
83.404
235
23
14
2311
2538
5170484
5170709
1.640000e-48
204.0
11
TraesCS3B01G006500
chr3B
83.408
223
28
4
540
762
3610958
3611171
7.630000e-47
198.0
12
TraesCS3B01G006500
chr3B
83.636
220
27
4
543
762
5225731
5225521
7.630000e-47
198.0
13
TraesCS3B01G006500
chr3B
81.250
288
15
11
2906
3184
5321594
5321337
2.740000e-46
196.0
14
TraesCS3B01G006500
chr3D
91.109
1136
74
12
937
2071
1337531
1338640
0.000000e+00
1513.0
15
TraesCS3B01G006500
chr3D
95.672
439
13
5
937
1374
1640646
1640213
0.000000e+00
701.0
16
TraesCS3B01G006500
chr3D
85.735
687
69
11
1422
2103
1591396
1592058
0.000000e+00
699.0
17
TraesCS3B01G006500
chr3D
93.925
428
25
1
2983
3409
1339816
1340243
0.000000e+00
645.0
18
TraesCS3B01G006500
chr3D
89.139
488
50
3
57
543
1641539
1641054
3.850000e-169
604.0
19
TraesCS3B01G006500
chr3D
89.234
483
49
3
62
543
1336629
1337109
4.970000e-168
601.0
20
TraesCS3B01G006500
chr3D
90.974
421
22
9
853
1273
1644239
1643835
1.410000e-153
553.0
21
TraesCS3B01G006500
chr3D
90.339
383
22
7
543
915
1641015
1640638
4.040000e-134
488.0
22
TraesCS3B01G006500
chr3D
89.421
397
19
4
540
915
1337145
1337539
2.430000e-131
479.0
23
TraesCS3B01G006500
chr3D
86.455
347
31
11
2215
2553
1338984
1339322
1.980000e-97
366.0
24
TraesCS3B01G006500
chr3D
87.687
268
22
3
2590
2857
1339323
1339579
5.650000e-78
302.0
25
TraesCS3B01G006500
chr3D
87.435
191
19
4
2351
2538
1639106
1638918
7.570000e-52
215.0
26
TraesCS3B01G006500
chr3D
82.353
221
30
1
543
763
1523587
1523798
2.140000e-42
183.0
27
TraesCS3B01G006500
chr3A
90.521
844
42
13
588
1422
7477206
7476392
0.000000e+00
1081.0
28
TraesCS3B01G006500
chr3A
92.926
311
19
3
224
532
7477528
7477219
1.910000e-122
449.0
29
TraesCS3B01G006500
chr3A
90.909
209
14
4
1899
2107
7475900
7475697
3.420000e-70
276.0
30
TraesCS3B01G006500
chr3A
85.864
191
22
4
2351
2538
7475373
7475185
7.630000e-47
198.0
31
TraesCS3B01G006500
chr7D
96.783
373
12
0
994
1366
7302269
7301897
1.060000e-174
623.0
32
TraesCS3B01G006500
chr7D
86.719
128
17
0
1939
2066
7301777
7301650
3.620000e-30
143.0
33
TraesCS3B01G006500
chr7D
93.333
90
6
0
2397
2486
7300734
7300645
2.180000e-27
134.0
34
TraesCS3B01G006500
chr7A
96.515
373
13
0
994
1366
8262589
8262217
4.940000e-173
617.0
35
TraesCS3B01G006500
chr7A
83.509
285
44
3
3111
3393
725193620
725193903
2.670000e-66
263.0
36
TraesCS3B01G006500
chr7A
87.500
128
16
0
1939
2066
8262112
8261985
7.790000e-32
148.0
37
TraesCS3B01G006500
chr4A
95.979
373
15
0
994
1366
732517265
732516893
1.070000e-169
606.0
38
TraesCS3B01G006500
chr5B
80.777
515
77
15
2980
3483
457081716
457082219
1.960000e-102
383.0
39
TraesCS3B01G006500
chr7B
88.189
127
15
0
1940
2066
150374241
150374115
6.020000e-33
152.0
40
TraesCS3B01G006500
chr7B
94.444
36
0
2
7
42
110687169
110687136
2.000000e-03
54.7
41
TraesCS3B01G006500
chr6B
93.333
90
6
0
2397
2486
265677438
265677349
2.180000e-27
134.0
42
TraesCS3B01G006500
chrUn
85.294
68
6
4
55
122
30189147
30189084
2.240000e-07
67.6
43
TraesCS3B01G006500
chr5D
100.000
34
0
0
1
34
259455764
259455797
2.900000e-06
63.9
44
TraesCS3B01G006500
chr2D
100.000
34
0
0
1
34
485994942
485994909
2.900000e-06
63.9
45
TraesCS3B01G006500
chr2B
100.000
33
0
0
2
34
474542100
474542068
1.040000e-05
62.1
46
TraesCS3B01G006500
chr2B
88.679
53
1
1
1
48
11321442
11321390
3.750000e-05
60.2
47
TraesCS3B01G006500
chr6A
88.462
52
2
3
1
48
101544304
101544253
3.750000e-05
60.2
48
TraesCS3B01G006500
chr6D
97.059
34
1
0
1
34
305186081
305186114
1.350000e-04
58.4
49
TraesCS3B01G006500
chr6D
97.059
34
1
0
1
34
377836886
377836853
1.350000e-04
58.4
50
TraesCS3B01G006500
chr6D
97.059
34
1
0
1
34
404335073
404335106
1.350000e-04
58.4
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
TraesCS3B01G006500
chr3B
3406299
3409781
3482
False
6433.00
6433
100.000000
1
3483
1
chr3B.!!$F1
3482
1
TraesCS3B01G006500
chr3B
5321103
5324512
3409
True
876.75
1731
88.814500
55
3483
4
chr3B.!!$R3
3428
2
TraesCS3B01G006500
chr3B
3665640
3667380
1740
True
809.50
1413
85.551500
854
2538
2
chr3B.!!$R1
1684
3
TraesCS3B01G006500
chr3B
5169064
5170709
1645
False
796.50
1389
86.203500
959
2538
2
chr3B.!!$F4
1579
4
TraesCS3B01G006500
chr3B
3610485
3611171
686
False
290.50
383
82.993500
106
762
2
chr3B.!!$F3
656
5
TraesCS3B01G006500
chr3B
5225521
5226207
686
True
290.50
383
83.068000
106
762
2
chr3B.!!$R2
656
6
TraesCS3B01G006500
chr3D
1591396
1592058
662
False
699.00
699
85.735000
1422
2103
1
chr3D.!!$F2
681
7
TraesCS3B01G006500
chr3D
1336629
1340243
3614
False
651.00
1513
89.638500
62
3409
6
chr3D.!!$F3
3347
8
TraesCS3B01G006500
chr3D
1638918
1644239
5321
True
512.20
701
90.711800
57
2538
5
chr3D.!!$R1
2481
9
TraesCS3B01G006500
chr3A
7475185
7477528
2343
True
501.00
1081
90.055000
224
2538
4
chr3A.!!$R1
2314
10
TraesCS3B01G006500
chr7D
7300645
7302269
1624
True
300.00
623
92.278333
994
2486
3
chr7D.!!$R1
1492
11
TraesCS3B01G006500
chr7A
8261985
8262589
604
True
382.50
617
92.007500
994
2066
2
chr7A.!!$R1
1072
12
TraesCS3B01G006500
chr5B
457081716
457082219
503
False
383.00
383
80.777000
2980
3483
1
chr5B.!!$F1
503
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.