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
TraesCS3D01G519900
chr3D
100.000
4700
0
0
1
4700
602451095
602446396
0.000000e+00
8680.0
1
TraesCS3D01G519900
chr3D
94.963
1350
57
7
7
1354
602359363
602358023
0.000000e+00
2106.0
2
TraesCS3D01G519900
chr3D
90.500
1379
91
18
1986
3346
603634243
603632887
0.000000e+00
1784.0
3
TraesCS3D01G519900
chr3D
79.929
1410
194
57
2285
3640
602751183
602749809
0.000000e+00
953.0
4
TraesCS3D01G519900
chr3D
90.868
668
56
4
2282
2947
568495324
568495988
0.000000e+00
891.0
5
TraesCS3D01G519900
chr3D
79.161
1406
201
54
2282
3628
603867650
603869022
0.000000e+00
889.0
6
TraesCS3D01G519900
chr3D
81.557
1079
152
26
2282
3341
602656118
602657168
0.000000e+00
846.0
7
TraesCS3D01G519900
chr3D
81.027
896
129
26
2282
3166
602428996
602429861
0.000000e+00
675.0
8
TraesCS3D01G519900
chr3D
76.508
1111
182
48
1145
2217
602752473
602751404
2.490000e-147
532.0
9
TraesCS3D01G519900
chr3D
76.508
1111
182
48
1145
2217
603866363
603867432
2.490000e-147
532.0
10
TraesCS3D01G519900
chr3D
89.970
329
27
2
1605
1931
603634561
603634237
2.020000e-113
420.0
11
TraesCS3D01G519900
chr3D
86.486
370
30
7
3351
3700
603632143
603631774
5.700000e-104
388.0
12
TraesCS3D01G519900
chr3D
83.173
416
55
8
1178
1593
603635013
603634613
2.670000e-97
366.0
13
TraesCS3D01G519900
chr3D
86.076
316
31
8
3038
3341
568496043
568496357
1.260000e-85
327.0
14
TraesCS3D01G519900
chr3D
77.801
482
72
23
902
1362
602378983
602378516
1.000000e-66
265.0
15
TraesCS3D01G519900
chr3D
84.058
276
40
3
73
347
114334491
114334763
3.610000e-66
263.0
16
TraesCS3D01G519900
chr3D
78.711
357
52
15
902
1238
602460693
602460341
2.850000e-52
217.0
17
TraesCS3D01G519900
chr3A
89.232
1523
106
22
2091
3563
732420967
732422481
0.000000e+00
1851.0
18
TraesCS3D01G519900
chr3A
89.850
1202
96
15
1615
2802
732427512
732428701
0.000000e+00
1520.0
19
TraesCS3D01G519900
chr3A
92.907
1001
70
1
3699
4698
596352854
596353854
0.000000e+00
1454.0
20
TraesCS3D01G519900
chr3A
81.748
1030
151
24
2339
3346
732082193
732083207
0.000000e+00
826.0
21
TraesCS3D01G519900
chr3A
85.216
832
60
27
2923
3701
732428713
732429534
0.000000e+00
797.0
22
TraesCS3D01G519900
chr3A
81.419
888
117
24
2472
3341
731991683
731990826
0.000000e+00
682.0
23
TraesCS3D01G519900
chr3A
86.117
497
30
14
1615
2100
732419647
732420115
2.530000e-137
499.0
24
TraesCS3D01G519900
chr3A
75.292
1198
196
60
1045
2202
732099163
732100300
9.150000e-132
481.0
25
TraesCS3D01G519900
chr3A
82.775
418
54
12
1178
1592
732427039
732427441
1.610000e-94
357.0
26
TraesCS3D01G519900
chr3A
80.717
446
40
15
931
1354
732069267
732068846
5.910000e-79
305.0
27
TraesCS3D01G519900
chr3A
80.288
416
67
11
1178
1593
732419005
732419405
2.750000e-77
300.0
28
TraesCS3D01G519900
chr3A
90.654
214
14
2
3493
3700
732422484
732422697
3.580000e-71
279.0
29
TraesCS3D01G519900
chr3B
87.161
1659
133
38
2111
3701
810251604
810253250
0.000000e+00
1810.0
30
TraesCS3D01G519900
chr3B
80.872
826
118
28
2282
3094
809627228
809628026
8.640000e-172
614.0
31
TraesCS3D01G519900
chr3B
88.190
525
45
9
348
857
810249940
810250462
1.120000e-170
610.0
32
TraesCS3D01G519900
chr3B
76.270
1319
211
50
956
2218
809625740
809627012
4.020000e-170
608.0
33
TraesCS3D01G519900
chr3B
81.846
661
70
25
952
1593
810250515
810251144
1.170000e-140
510.0
34
TraesCS3D01G519900
chr3B
90.691
376
27
4
1653
2020
810251232
810251607
1.170000e-135
494.0
35
TraesCS3D01G519900
chr3B
95.455
44
2
0
1556
1599
28699259
28699302
2.350000e-08
71.3
36
TraesCS3D01G519900
chr6D
94.721
1004
51
2
3699
4700
192102107
192103110
0.000000e+00
1559.0
37
TraesCS3D01G519900
chr6D
89.442
1004
104
2
3699
4700
28278159
28277156
0.000000e+00
1266.0
38
TraesCS3D01G519900
chr2D
93.021
1003
69
1
3699
4700
214054525
214055527
0.000000e+00
1463.0
39
TraesCS3D01G519900
chr2D
92.331
1004
75
2
3699
4700
181583127
181582124
0.000000e+00
1426.0
40
TraesCS3D01G519900
chr4D
94.249
939
53
1
3704
4641
177114002
177113064
0.000000e+00
1434.0
41
TraesCS3D01G519900
chr4D
85.315
286
33
8
71
349
445107911
445107628
2.140000e-73
287.0
42
TraesCS3D01G519900
chr5A
91.532
992
82
2
3699
4689
454200072
454201062
0.000000e+00
1365.0
43
TraesCS3D01G519900
chr5A
76.354
1108
187
47
1145
2218
31571618
31572684
4.170000e-145
525.0
44
TraesCS3D01G519900
chr5A
84.859
284
35
6
71
347
573816534
573816252
3.580000e-71
279.0
45
TraesCS3D01G519900
chr5A
82.230
287
32
10
72
351
573806738
573807012
3.660000e-56
230.0
46
TraesCS3D01G519900
chr5B
89.542
1004
103
2
3699
4700
77615136
77614133
0.000000e+00
1271.0
47
TraesCS3D01G519900
chr2A
89.154
1005
108
1
3697
4700
565380004
565379000
0.000000e+00
1251.0
48
TraesCS3D01G519900
chrUn
79.096
1416
202
56
2285
3640
276043093
276041712
0.000000e+00
889.0
49
TraesCS3D01G519900
chrUn
76.508
1111
182
48
1145
2217
276044383
276043314
2.490000e-147
532.0
50
TraesCS3D01G519900
chrUn
78.846
104
16
4
1485
1585
96548937
96549037
1.090000e-06
65.8
51
TraesCS3D01G519900
chr5D
85.461
282
34
5
72
347
533556714
533556994
2.140000e-73
287.0
52
TraesCS3D01G519900
chr1B
83.039
283
41
5
74
349
278707118
278707400
2.810000e-62
250.0
53
TraesCS3D01G519900
chr1B
86.364
110
13
1
241
350
637516209
637516102
8.260000e-23
119.0
54
TraesCS3D01G519900
chr1B
78.302
106
17
4
1485
1587
13965200
13965302
3.930000e-06
63.9
55
TraesCS3D01G519900
chr6B
79.252
294
53
5
62
347
52471570
52471863
1.030000e-46
198.0
56
TraesCS3D01G519900
chr1D
81.443
97
14
2
1491
1585
9646361
9646267
5.040000e-10
76.8
57
TraesCS3D01G519900
chr1A
79.381
97
16
2
1491
1585
10972188
10972094
1.090000e-06
65.8
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
TraesCS3D01G519900
chr3D
602446396
602451095
4699
True
8680.000000
8680
100.00000
1
4700
1
chr3D.!!$R3
4699
1
TraesCS3D01G519900
chr3D
602358023
602359363
1340
True
2106.000000
2106
94.96300
7
1354
1
chr3D.!!$R1
1347
2
TraesCS3D01G519900
chr3D
602656118
602657168
1050
False
846.000000
846
81.55700
2282
3341
1
chr3D.!!$F3
1059
3
TraesCS3D01G519900
chr3D
602749809
602752473
2664
True
742.500000
953
78.21850
1145
3640
2
chr3D.!!$R5
2495
4
TraesCS3D01G519900
chr3D
603631774
603635013
3239
True
739.500000
1784
87.53225
1178
3700
4
chr3D.!!$R6
2522
5
TraesCS3D01G519900
chr3D
603866363
603869022
2659
False
710.500000
889
77.83450
1145
3628
2
chr3D.!!$F5
2483
6
TraesCS3D01G519900
chr3D
602428996
602429861
865
False
675.000000
675
81.02700
2282
3166
1
chr3D.!!$F2
884
7
TraesCS3D01G519900
chr3D
568495324
568496357
1033
False
609.000000
891
88.47200
2282
3341
2
chr3D.!!$F4
1059
8
TraesCS3D01G519900
chr3A
596352854
596353854
1000
False
1454.000000
1454
92.90700
3699
4698
1
chr3A.!!$F1
999
9
TraesCS3D01G519900
chr3A
732427039
732429534
2495
False
891.333333
1520
85.94700
1178
3701
3
chr3A.!!$F5
2523
10
TraesCS3D01G519900
chr3A
732082193
732083207
1014
False
826.000000
826
81.74800
2339
3346
1
chr3A.!!$F2
1007
11
TraesCS3D01G519900
chr3A
732419005
732422697
3692
False
732.250000
1851
86.57275
1178
3700
4
chr3A.!!$F4
2522
12
TraesCS3D01G519900
chr3A
731990826
731991683
857
True
682.000000
682
81.41900
2472
3341
1
chr3A.!!$R1
869
13
TraesCS3D01G519900
chr3A
732099163
732100300
1137
False
481.000000
481
75.29200
1045
2202
1
chr3A.!!$F3
1157
14
TraesCS3D01G519900
chr3B
810249940
810253250
3310
False
856.000000
1810
86.97200
348
3701
4
chr3B.!!$F3
3353
15
TraesCS3D01G519900
chr3B
809625740
809628026
2286
False
611.000000
614
78.57100
956
3094
2
chr3B.!!$F2
2138
16
TraesCS3D01G519900
chr6D
192102107
192103110
1003
False
1559.000000
1559
94.72100
3699
4700
1
chr6D.!!$F1
1001
17
TraesCS3D01G519900
chr6D
28277156
28278159
1003
True
1266.000000
1266
89.44200
3699
4700
1
chr6D.!!$R1
1001
18
TraesCS3D01G519900
chr2D
214054525
214055527
1002
False
1463.000000
1463
93.02100
3699
4700
1
chr2D.!!$F1
1001
19
TraesCS3D01G519900
chr2D
181582124
181583127
1003
True
1426.000000
1426
92.33100
3699
4700
1
chr2D.!!$R1
1001
20
TraesCS3D01G519900
chr4D
177113064
177114002
938
True
1434.000000
1434
94.24900
3704
4641
1
chr4D.!!$R1
937
21
TraesCS3D01G519900
chr5A
454200072
454201062
990
False
1365.000000
1365
91.53200
3699
4689
1
chr5A.!!$F2
990
22
TraesCS3D01G519900
chr5A
31571618
31572684
1066
False
525.000000
525
76.35400
1145
2218
1
chr5A.!!$F1
1073
23
TraesCS3D01G519900
chr5B
77614133
77615136
1003
True
1271.000000
1271
89.54200
3699
4700
1
chr5B.!!$R1
1001
24
TraesCS3D01G519900
chr2A
565379000
565380004
1004
True
1251.000000
1251
89.15400
3697
4700
1
chr2A.!!$R1
1003
25
TraesCS3D01G519900
chrUn
276041712
276044383
2671
True
710.500000
889
77.80200
1145
3640
2
chrUn.!!$R1
2495
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.