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
TraesCS6B01G398300
chr6B
100.000
4761
0
0
1
4761
673755500
673760260
0.000000e+00
8793.0
1
TraesCS6B01G398300
chr6B
91.574
985
71
8
2080
3063
672506937
672505964
0.000000e+00
1349.0
2
TraesCS6B01G398300
chr6B
86.802
1038
121
15
2083
3116
672894349
672895374
0.000000e+00
1144.0
3
TraesCS6B01G398300
chr6B
87.551
988
114
4
2080
3064
673365667
673364686
0.000000e+00
1134.0
4
TraesCS6B01G398300
chr6B
86.609
1038
124
14
2087
3121
672944929
672945954
0.000000e+00
1133.0
5
TraesCS6B01G398300
chr6B
86.570
1035
123
15
2086
3116
673608774
673607752
0.000000e+00
1127.0
6
TraesCS6B01G398300
chr6B
94.368
657
23
6
4118
4761
672502959
672502304
0.000000e+00
996.0
7
TraesCS6B01G398300
chr6B
93.725
494
25
5
1
493
672510221
672509733
0.000000e+00
736.0
8
TraesCS6B01G398300
chr6B
78.755
1012
123
33
3261
4212
673614634
673613655
1.140000e-165
593.0
9
TraesCS6B01G398300
chr6B
86.693
511
61
6
3207
3712
673607799
673607291
1.160000e-155
560.0
10
TraesCS6B01G398300
chr6B
86.180
521
65
6
3207
3722
672895327
672895845
1.500000e-154
556.0
11
TraesCS6B01G398300
chr6B
87.939
456
48
7
3238
3688
672619477
672619024
9.070000e-147
531.0
12
TraesCS6B01G398300
chr6B
87.692
455
51
5
3238
3688
673698568
673699021
4.220000e-145
525.0
13
TraesCS6B01G398300
chr6B
92.351
353
18
5
1024
1376
672507958
672507615
1.190000e-135
494.0
14
TraesCS6B01G398300
chr6B
88.537
410
44
2
1563
1969
673609342
673608933
1.190000e-135
494.0
15
TraesCS6B01G398300
chr6B
87.961
407
49
0
1563
1969
672883840
672884246
9.270000e-132
481.0
16
TraesCS6B01G398300
chr6B
83.838
495
67
8
1560
2049
672944356
672944842
4.340000e-125
459.0
17
TraesCS6B01G398300
chr6B
95.668
277
12
0
1
277
672534457
672534181
3.380000e-121
446.0
18
TraesCS6B01G398300
chr6B
85.870
368
43
5
1009
1376
672883328
672883686
2.690000e-102
383.0
19
TraesCS6B01G398300
chr6B
86.769
325
25
11
631
941
672508490
672508170
3.530000e-91
346.0
20
TraesCS6B01G398300
chr6B
84.943
352
41
8
1025
1376
673366778
673366439
3.530000e-91
346.0
21
TraesCS6B01G398300
chr6B
84.419
353
34
13
1024
1376
673696420
673696751
1.280000e-85
327.0
22
TraesCS6B01G398300
chr6B
83.662
355
33
19
1024
1376
672628592
672628261
1.290000e-80
311.0
23
TraesCS6B01G398300
chr6B
84.348
230
17
9
740
966
672509455
672509242
1.740000e-49
207.0
24
TraesCS6B01G398300
chr6B
77.961
363
47
18
4161
4513
672633446
672633107
3.760000e-46
196.0
25
TraesCS6B01G398300
chr6B
77.692
390
39
31
4338
4689
672947059
672947438
1.350000e-45
195.0
26
TraesCS6B01G398300
chr6B
75.208
480
78
24
3893
4353
672618839
672618382
6.290000e-44
189.0
27
TraesCS6B01G398300
chr6B
79.730
296
30
19
4359
4631
672896413
672896701
2.260000e-43
187.0
28
TraesCS6B01G398300
chr6B
79.000
300
32
18
4365
4636
673606718
673606422
4.900000e-40
176.0
29
TraesCS6B01G398300
chr6B
90.400
125
7
4
620
741
672509681
672509559
4.930000e-35
159.0
30
TraesCS6B01G398300
chr6B
81.560
141
24
2
4143
4282
672896254
672896393
1.080000e-21
115.0
31
TraesCS6B01G398300
chr6B
81.560
141
24
2
4143
4282
672946922
672947061
1.080000e-21
115.0
32
TraesCS6B01G398300
chr6B
81.560
141
24
2
4143
4282
673606883
673606744
1.080000e-21
115.0
33
TraesCS6B01G398300
chr6B
82.075
106
17
2
4249
4354
673699564
673699667
6.560000e-14
89.8
34
TraesCS6B01G398300
chr6B
84.000
75
11
1
4563
4636
672633087
672633013
2.380000e-08
71.3
35
TraesCS6B01G398300
chr6D
97.368
1596
27
3
1456
3051
445799525
445797945
0.000000e+00
2700.0
36
TraesCS6B01G398300
chr6D
94.872
741
26
6
638
1376
445800424
445799694
0.000000e+00
1147.0
37
TraesCS6B01G398300
chr6D
86.622
1039
118
19
2089
3121
445893803
445894826
0.000000e+00
1129.0
38
TraesCS6B01G398300
chr6D
86.698
857
57
18
3842
4661
445797111
445796275
0.000000e+00
898.0
39
TraesCS6B01G398300
chr6D
96.896
451
14
0
3243
3693
445797783
445797333
0.000000e+00
756.0
40
TraesCS6B01G398300
chr6D
82.958
710
98
16
3261
3954
445854357
445855059
1.880000e-173
619.0
41
TraesCS6B01G398300
chr6D
86.353
447
58
1
1545
1991
445852779
445853222
7.160000e-133
484.0
42
TraesCS6B01G398300
chr6D
91.843
331
20
4
54
384
445800746
445800423
5.620000e-124
455.0
43
TraesCS6B01G398300
chr6D
83.434
495
69
8
1560
2049
445893229
445893715
9.400000e-122
448.0
44
TraesCS6B01G398300
chr6D
85.366
410
57
2
1563
1969
445820119
445819710
5.700000e-114
422.0
45
TraesCS6B01G398300
chr6D
84.986
353
32
13
1024
1376
445812944
445812613
5.900000e-89
339.0
46
TraesCS6B01G398300
chr6D
82.776
389
41
20
989
1376
445820885
445820522
1.650000e-84
324.0
47
TraesCS6B01G398300
chr6D
88.889
270
21
6
1024
1293
445852273
445852533
1.650000e-84
324.0
48
TraesCS6B01G398300
chr6D
78.772
391
53
15
4131
4513
445822667
445822299
7.970000e-58
235.0
49
TraesCS6B01G398300
chr6D
75.688
436
65
27
3893
4308
445810145
445809731
3.790000e-41
180.0
50
TraesCS6B01G398300
chr6D
83.246
191
26
4
4109
4293
445855209
445855399
2.280000e-38
171.0
51
TraesCS6B01G398300
chr6D
81.538
130
14
9
4567
4690
445822281
445822156
1.090000e-16
99.0
52
TraesCS6B01G398300
chr6D
81.053
95
14
3
4001
4092
445840762
445840855
6.610000e-09
73.1
53
TraesCS6B01G398300
chr6D
84.507
71
10
1
4567
4636
445846704
445846774
8.550000e-08
69.4
54
TraesCS6B01G398300
chr6A
93.556
1614
94
4
2080
3693
592477383
592475780
0.000000e+00
2396.0
55
TraesCS6B01G398300
chr6A
86.551
1041
119
19
2087
3121
592549691
592550716
0.000000e+00
1127.0
56
TraesCS6B01G398300
chr6A
91.205
614
34
10
769
1376
592478820
592478221
0.000000e+00
817.0
57
TraesCS6B01G398300
chr6A
85.925
611
60
10
1374
1983
592478163
592477578
3.130000e-176
628.0
58
TraesCS6B01G398300
chr6A
85.595
597
67
16
3261
3846
592538722
592539310
4.070000e-170
608.0
59
TraesCS6B01G398300
chr6A
86.577
447
57
1
1545
1991
592537121
592537564
1.540000e-134
490.0
60
TraesCS6B01G398300
chr6A
91.060
302
21
3
667
967
592480178
592479882
2.060000e-108
403.0
61
TraesCS6B01G398300
chr6A
92.748
262
18
1
1
261
592482213
592481952
1.250000e-100
377.0
62
TraesCS6B01G398300
chr6A
94.606
241
11
1
245
485
592481740
592481502
5.820000e-99
372.0
63
TraesCS6B01G398300
chr6A
88.148
270
23
5
1024
1293
592536600
592536860
3.580000e-81
313.0
64
TraesCS6B01G398300
chr6A
90.667
225
15
3
4250
4472
592475159
592474939
1.300000e-75
294.0
65
TraesCS6B01G398300
chr6A
79.015
467
71
20
3842
4293
592539332
592539786
1.300000e-75
294.0
66
TraesCS6B01G398300
chr6A
86.617
269
27
6
3842
4109
592475558
592475298
6.030000e-74
289.0
67
TraesCS6B01G398300
chr6A
75.040
621
92
30
4041
4636
592499056
592498474
3.710000e-56
230.0
68
TraesCS6B01G398300
chr6A
81.818
220
26
5
3893
4109
592492294
592492086
6.330000e-39
172.0
69
TraesCS6B01G398300
chr6A
90.299
134
6
3
549
675
592481371
592481238
8.190000e-38
169.0
70
TraesCS6B01G398300
chr6A
89.167
120
13
0
4542
4661
592474910
592474791
2.970000e-32
150.0
71
TraesCS6B01G398300
chr6A
82.812
128
4
6
4105
4215
592475279
592475153
1.090000e-16
99.0
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
TraesCS6B01G398300
chr6B
673755500
673760260
4760
False
8793.000000
8793
100.000000
1
4761
1
chr6B.!!$F1
4760
1
TraesCS6B01G398300
chr6B
673364686
673366778
2092
True
740.000000
1134
86.247000
1025
3064
2
chr6B.!!$R7
2039
2
TraesCS6B01G398300
chr6B
672502304
672510221
7917
True
612.428571
1349
90.505000
1
4761
7
chr6B.!!$R4
4760
3
TraesCS6B01G398300
chr6B
673613655
673614634
979
True
593.000000
593
78.755000
3261
4212
1
chr6B.!!$R3
951
4
TraesCS6B01G398300
chr6B
672894349
672896701
2352
False
500.500000
1144
83.568000
2083
4631
4
chr6B.!!$F3
2548
5
TraesCS6B01G398300
chr6B
673606422
673609342
2920
True
494.400000
1127
84.472000
1563
4636
5
chr6B.!!$R8
3073
6
TraesCS6B01G398300
chr6B
672944356
672947438
3082
False
475.500000
1133
82.424750
1560
4689
4
chr6B.!!$F4
3129
7
TraesCS6B01G398300
chr6B
672883328
672884246
918
False
432.000000
481
86.915500
1009
1969
2
chr6B.!!$F2
960
8
TraesCS6B01G398300
chr6B
672618382
672619477
1095
True
360.000000
531
81.573500
3238
4353
2
chr6B.!!$R5
1115
9
TraesCS6B01G398300
chr6B
673696420
673699667
3247
False
313.933333
525
84.728667
1024
4354
3
chr6B.!!$F5
3330
10
TraesCS6B01G398300
chr6D
445796275
445800746
4471
True
1191.200000
2700
93.535400
54
4661
5
chr6D.!!$R1
4607
11
TraesCS6B01G398300
chr6D
445893229
445894826
1597
False
788.500000
1129
85.028000
1560
3121
2
chr6D.!!$F4
1561
12
TraesCS6B01G398300
chr6D
445852273
445855399
3126
False
399.500000
619
85.361500
1024
4293
4
chr6D.!!$F3
3269
13
TraesCS6B01G398300
chr6D
445819710
445822667
2957
True
270.000000
422
82.113000
989
4690
4
chr6D.!!$R3
3701
14
TraesCS6B01G398300
chr6D
445809731
445812944
3213
True
259.500000
339
80.337000
1024
4308
2
chr6D.!!$R2
3284
15
TraesCS6B01G398300
chr6A
592549691
592550716
1025
False
1127.000000
1127
86.551000
2087
3121
1
chr6A.!!$F1
1034
16
TraesCS6B01G398300
chr6A
592474791
592482213
7422
True
544.909091
2396
89.878364
1
4661
11
chr6A.!!$R3
4660
17
TraesCS6B01G398300
chr6A
592536600
592539786
3186
False
426.250000
608
84.833750
1024
4293
4
chr6A.!!$F2
3269
18
TraesCS6B01G398300
chr6A
592498474
592499056
582
True
230.000000
230
75.040000
4041
4636
1
chr6A.!!$R2
595
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.