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
TraesCS6D01G395900
chr6D
100.000
6367
0
0
1
6367
468186230
468179864
0.000000e+00
11758.0
1
TraesCS6D01G395900
chr6D
86.364
1254
157
11
107
1352
468100977
468099730
0.000000e+00
1356.0
2
TraesCS6D01G395900
chr6D
86.802
1038
136
1
4233
5269
468096641
468095604
0.000000e+00
1157.0
3
TraesCS6D01G395900
chr6D
85.095
1107
155
7
4193
5293
468168798
468167696
0.000000e+00
1122.0
4
TraesCS6D01G395900
chr6D
85.479
1033
149
1
4193
5224
468057329
468056297
0.000000e+00
1075.0
5
TraesCS6D01G395900
chr6D
84.040
990
104
28
1
969
468172544
468171588
0.000000e+00
904.0
6
TraesCS6D01G395900
chr6D
86.010
386
52
2
968
1353
468171427
468171044
4.590000e-111
412.0
7
TraesCS6D01G395900
chr6D
76.766
736
139
11
2013
2717
468152767
468152033
3.600000e-102
383.0
8
TraesCS6D01G395900
chr6D
81.450
469
61
12
940
1396
468060915
468060461
1.690000e-95
361.0
9
TraesCS6D01G395900
chr6D
93.074
231
16
0
3246
3476
26007083
26006853
7.910000e-89
339.0
10
TraesCS6D01G395900
chr6D
82.840
338
40
14
6039
6365
452702800
452703130
2.900000e-73
287.0
11
TraesCS6D01G395900
chr6D
82.687
335
43
12
6039
6365
332618602
332618929
3.760000e-72
283.0
12
TraesCS6D01G395900
chrUn
96.260
4305
108
23
1042
5329
211919524
211923792
0.000000e+00
7009.0
13
TraesCS6D01G395900
chrUn
96.553
3191
82
9
1874
5048
210239719
210236541
0.000000e+00
5258.0
14
TraesCS6D01G395900
chrUn
96.326
1116
26
4
764
1879
75283431
75284531
0.000000e+00
1820.0
15
TraesCS6D01G395900
chrUn
96.237
1116
27
4
764
1879
327314417
327313317
0.000000e+00
1814.0
16
TraesCS6D01G395900
chrUn
84.482
1379
154
30
1
1353
210220617
210219273
0.000000e+00
1306.0
17
TraesCS6D01G395900
chrUn
85.866
1033
142
3
4193
5224
346081747
346080718
0.000000e+00
1096.0
18
TraesCS6D01G395900
chrUn
96.928
586
14
3
5370
5951
210225648
210225063
0.000000e+00
979.0
19
TraesCS6D01G395900
chrUn
93.972
647
36
2
1
645
75282751
75283396
0.000000e+00
976.0
20
TraesCS6D01G395900
chrUn
93.972
647
36
2
1
645
327315097
327314452
0.000000e+00
976.0
21
TraesCS6D01G395900
chrUn
96.569
583
19
1
5370
5951
211923777
211924359
0.000000e+00
965.0
22
TraesCS6D01G395900
chrUn
98.091
419
8
0
5949
6367
211924482
211924900
0.000000e+00
730.0
23
TraesCS6D01G395900
chrUn
97.375
419
11
0
5949
6367
210224940
210224522
0.000000e+00
713.0
24
TraesCS6D01G395900
chrUn
95.985
274
9
1
574
845
211919251
211919524
1.630000e-120
444.0
25
TraesCS6D01G395900
chrUn
76.902
736
138
11
2013
2717
216381443
216382177
7.740000e-104
388.0
26
TraesCS6D01G395900
chrUn
97.906
191
4
0
655
845
479932506
479932316
1.320000e-86
331.0
27
TraesCS6D01G395900
chrUn
89.496
238
18
3
5642
5872
79237857
79237620
1.740000e-75
294.0
28
TraesCS6D01G395900
chrUn
93.333
75
5
0
5877
5951
45780349
45780423
1.880000e-20
111.0
29
TraesCS6D01G395900
chrUn
97.297
37
1
0
668
704
75283397
75283433
5.330000e-06
63.9
30
TraesCS6D01G395900
chr6B
96.240
4308
108
24
1042
5332
714410552
714406282
0.000000e+00
7009.0
31
TraesCS6D01G395900
chr6B
85.069
1085
155
7
4214
5293
714340738
714339656
0.000000e+00
1099.0
32
TraesCS6D01G395900
chr6B
84.003
1169
128
33
1
1146
714344027
714342895
0.000000e+00
1068.0
33
TraesCS6D01G395900
chr6B
96.741
583
18
1
5370
5951
714406300
714405718
0.000000e+00
970.0
34
TraesCS6D01G395900
chr6B
98.329
419
7
0
5949
6367
714405595
714405177
0.000000e+00
736.0
35
TraesCS6D01G395900
chr6B
95.620
274
10
1
574
845
714410825
714410552
7.580000e-119
438.0
36
TraesCS6D01G395900
chr6B
76.255
737
141
13
2013
2717
714336222
714335488
1.690000e-95
361.0
37
TraesCS6D01G395900
chr6B
92.083
240
18
1
3238
3476
279333154
279332915
2.840000e-88
337.0
38
TraesCS6D01G395900
chr6B
81.319
91
8
5
3171
3254
638497976
638497888
1.480000e-06
65.8
39
TraesCS6D01G395900
chr6A
90.983
1109
87
10
252
1352
614166575
614165472
0.000000e+00
1482.0
40
TraesCS6D01G395900
chr6A
86.239
1061
138
7
4213
5269
614162850
614161794
0.000000e+00
1144.0
41
TraesCS6D01G395900
chr6A
95.885
243
7
3
4
246
614167480
614167241
2.150000e-104
390.0
42
TraesCS6D01G395900
chr6A
88.519
270
28
3
3247
3516
572214939
572214673
2.210000e-84
324.0
43
TraesCS6D01G395900
chr6A
86.747
83
7
2
3171
3249
610122252
610122334
8.790000e-14
89.8
44
TraesCS6D01G395900
chr6A
83.146
89
10
3
3171
3254
59961231
59961319
6.850000e-10
76.8
45
TraesCS6D01G395900
chr6A
84.000
75
8
2
3171
3241
202356906
202356980
1.150000e-07
69.4
46
TraesCS6D01G395900
chr3B
89.329
328
33
2
6035
6360
2047097
2047424
1.650000e-110
411.0
47
TraesCS6D01G395900
chr3B
90.948
232
15
2
5647
5872
803061108
803061339
2.230000e-79
307.0
48
TraesCS6D01G395900
chr3B
89.030
237
20
6
5642
5872
345709825
345710061
8.080000e-74
289.0
49
TraesCS6D01G395900
chr3B
76.074
326
51
21
5996
6311
250404072
250404380
1.850000e-30
145.0
50
TraesCS6D01G395900
chr3B
84.416
77
4
4
3171
3241
799710342
799710416
1.150000e-07
69.4
51
TraesCS6D01G395900
chr4A
88.720
328
31
5
6039
6365
604355900
604356222
4.630000e-106
396.0
52
TraesCS6D01G395900
chr4A
88.720
328
31
5
6039
6365
604559859
604560181
4.630000e-106
396.0
53
TraesCS6D01G395900
chr4A
87.111
225
21
5
1596
1819
642598356
642598573
1.370000e-61
248.0
54
TraesCS6D01G395900
chr4A
93.333
75
5
0
5877
5951
537419651
537419577
1.880000e-20
111.0
55
TraesCS6D01G395900
chr4A
86.885
61
2
5
6004
6064
672315049
672315103
5.330000e-06
63.9
56
TraesCS6D01G395900
chr5D
93.506
231
15
0
3246
3476
383710555
383710785
1.700000e-90
344.0
57
TraesCS6D01G395900
chr5D
74.510
357
38
41
6004
6339
91996333
91996657
8.730000e-19
106.0
58
TraesCS6D01G395900
chr5D
85.366
82
11
1
3628
3709
453016396
453016476
4.090000e-12
84.2
59
TraesCS6D01G395900
chr2D
93.074
231
16
0
3246
3476
83172475
83172245
7.910000e-89
339.0
60
TraesCS6D01G395900
chr2D
93.074
231
16
0
3246
3476
389895463
389895233
7.910000e-89
339.0
61
TraesCS6D01G395900
chr2D
90.278
72
7
0
1735
1806
534412682
534412753
1.890000e-15
95.3
62
TraesCS6D01G395900
chr1D
89.744
234
18
2
5645
5872
233088288
233088055
1.740000e-75
294.0
63
TraesCS6D01G395900
chr4D
83.234
334
39
13
6041
6365
433946951
433946626
2.250000e-74
291.0
64
TraesCS6D01G395900
chr5B
89.316
234
17
3
5645
5872
594138699
594138930
2.900000e-73
287.0
65
TraesCS6D01G395900
chr5B
88.136
59
1
5
3489
3542
81210700
81210643
1.480000e-06
65.8
66
TraesCS6D01G395900
chr1A
88.608
237
21
2
5642
5872
425262641
425262405
3.760000e-72
283.0
67
TraesCS6D01G395900
chr4B
76.645
304
38
28
5988
6275
550625096
550625382
3.100000e-28
137.0
68
TraesCS6D01G395900
chr4B
74.923
323
61
17
6002
6315
507670501
507670190
5.180000e-26
130.0
69
TraesCS6D01G395900
chr3A
93.333
75
5
0
5877
5951
725052091
725052165
1.880000e-20
111.0
70
TraesCS6D01G395900
chr3A
92.000
75
6
0
5877
5951
351788075
351788149
8.730000e-19
106.0
71
TraesCS6D01G395900
chr3A
87.931
58
2
4
3489
3543
697758539
697758594
5.330000e-06
63.9
72
TraesCS6D01G395900
chr1B
93.243
74
5
0
5877
5950
603335074
603335001
6.750000e-20
110.0
73
TraesCS6D01G395900
chr1B
73.333
300
71
8
2422
2717
2356976
2356682
1.130000e-17
102.0
74
TraesCS6D01G395900
chr1B
73.038
293
66
10
2429
2717
22824279
22823996
2.440000e-14
91.6
75
TraesCS6D01G395900
chr7D
94.203
69
4
0
5877
5945
275969708
275969776
8.730000e-19
106.0
76
TraesCS6D01G395900
chr7D
88.571
70
7
1
3186
3254
210558409
210558340
4.090000e-12
84.2
77
TraesCS6D01G395900
chr7D
88.571
70
7
1
3186
3254
489164201
489164132
4.090000e-12
84.2
78
TraesCS6D01G395900
chr7B
88.571
70
7
1
3186
3254
226198924
226198855
4.090000e-12
84.2
79
TraesCS6D01G395900
chr7A
85.542
83
8
2
3171
3249
80986613
80986695
4.090000e-12
84.2
80
TraesCS6D01G395900
chr5A
77.953
127
20
5
2860
2982
625737573
625737451
8.850000e-09
73.1
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
TraesCS6D01G395900
chr6D
468179864
468186230
6366
True
11758.000000
11758
100.000000
1
6367
1
chr6D.!!$R3
6366
1
TraesCS6D01G395900
chr6D
468095604
468100977
5373
True
1256.500000
1356
86.583000
107
5269
2
chr6D.!!$R5
5162
2
TraesCS6D01G395900
chr6D
468167696
468172544
4848
True
812.666667
1122
85.048333
1
5293
3
chr6D.!!$R6
5292
3
TraesCS6D01G395900
chr6D
468056297
468060915
4618
True
718.000000
1075
83.464500
940
5224
2
chr6D.!!$R4
4284
4
TraesCS6D01G395900
chr6D
468152033
468152767
734
True
383.000000
383
76.766000
2013
2717
1
chr6D.!!$R2
704
5
TraesCS6D01G395900
chrUn
210236541
210239719
3178
True
5258.000000
5258
96.553000
1874
5048
1
chrUn.!!$R2
3174
6
TraesCS6D01G395900
chrUn
211919251
211924900
5649
False
2287.000000
7009
96.726250
574
6367
4
chrUn.!!$F4
5793
7
TraesCS6D01G395900
chrUn
327313317
327315097
1780
True
1395.000000
1814
95.104500
1
1879
2
chrUn.!!$R6
1878
8
TraesCS6D01G395900
chrUn
346080718
346081747
1029
True
1096.000000
1096
85.866000
4193
5224
1
chrUn.!!$R3
1031
9
TraesCS6D01G395900
chrUn
210219273
210225648
6375
True
999.333333
1306
92.928333
1
6367
3
chrUn.!!$R5
6366
10
TraesCS6D01G395900
chrUn
75282751
75284531
1780
False
953.300000
1820
95.865000
1
1879
3
chrUn.!!$F3
1878
11
TraesCS6D01G395900
chrUn
216381443
216382177
734
False
388.000000
388
76.902000
2013
2717
1
chrUn.!!$F2
704
12
TraesCS6D01G395900
chr6B
714405177
714410825
5648
True
2288.250000
7009
96.732500
574
6367
4
chr6B.!!$R4
5793
13
TraesCS6D01G395900
chr6B
714335488
714344027
8539
True
842.666667
1099
81.775667
1
5293
3
chr6B.!!$R3
5292
14
TraesCS6D01G395900
chr6A
614161794
614167480
5686
True
1005.333333
1482
91.035667
4
5269
3
chr6A.!!$R2
5265
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.