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
TraesCS6D01G238000
chr6D
100.000
3647
0
0
1
3647
338138551
338134905
0.000000e+00
6735.0
1
TraesCS6D01G238000
chr6D
94.998
3159
87
29
3
3125
197263403
197266526
0.000000e+00
4892.0
2
TraesCS6D01G238000
chr6D
95.810
525
17
3
3121
3645
189258306
189258825
0.000000e+00
843.0
3
TraesCS6D01G238000
chr6D
95.619
525
19
2
3120
3644
331068964
331069484
0.000000e+00
839.0
4
TraesCS6D01G238000
chr2D
95.769
2671
70
9
461
3125
161651320
161648687
0.000000e+00
4266.0
5
TraesCS6D01G238000
chr2D
96.320
462
10
1
1
462
161651804
161651350
0.000000e+00
752.0
6
TraesCS6D01G238000
chr2D
88.312
77
9
0
5
81
298539152
298539228
3.880000e-15
93.5
7
TraesCS6D01G238000
chr2B
94.347
2671
117
15
461
3125
430822376
430819734
0.000000e+00
4065.0
8
TraesCS6D01G238000
chr2B
93.506
462
25
4
1
462
430822862
430822406
0.000000e+00
682.0
9
TraesCS6D01G238000
chr2B
89.713
418
17
2
2710
3126
602888718
602888326
9.030000e-141
510.0
10
TraesCS6D01G238000
chr2B
89.021
419
17
10
2710
3125
669355657
669356049
3.270000e-135
492.0
11
TraesCS6D01G238000
chr4A
93.968
2669
125
13
461
3125
418290634
418287998
0.000000e+00
4004.0
12
TraesCS6D01G238000
chr4A
93.506
462
23
1
1
462
418291118
418290664
0.000000e+00
680.0
13
TraesCS6D01G238000
chr3A
95.728
2458
88
6
461
2916
217012440
217014882
0.000000e+00
3941.0
14
TraesCS6D01G238000
chr3A
93.400
2682
124
18
461
3119
216936972
216939623
0.000000e+00
3923.0
15
TraesCS6D01G238000
chr3A
95.238
462
15
1
1
462
217011956
217012410
0.000000e+00
725.0
16
TraesCS6D01G238000
chr3A
93.939
462
20
2
1
462
216936489
216936942
0.000000e+00
691.0
17
TraesCS6D01G238000
chr3A
93.491
169
9
2
2960
3126
217015126
217015294
2.170000e-62
250.0
18
TraesCS6D01G238000
chr3B
96.240
1436
50
3
1365
2800
241261628
241260197
0.000000e+00
2350.0
19
TraesCS6D01G238000
chr6A
91.237
1746
108
16
469
2200
568172634
568174348
0.000000e+00
2335.0
20
TraesCS6D01G238000
chr4B
96.017
1431
54
3
1365
2794
199721268
199722696
0.000000e+00
2324.0
21
TraesCS6D01G238000
chr4B
93.558
1335
66
12
507
1829
527931247
527929921
0.000000e+00
1971.0
22
TraesCS6D01G238000
chr4B
89.516
372
11
3
2757
3125
199722697
199723043
2.580000e-121
446.0
23
TraesCS6D01G238000
chr4B
85.388
438
48
13
11
442
115709328
115708901
1.200000e-119
440.0
24
TraesCS6D01G238000
chr6B
92.759
1381
75
12
461
1822
129871403
129870029
0.000000e+00
1973.0
25
TraesCS6D01G238000
chr6B
89.286
84
7
2
11
92
353096126
353096043
1.790000e-18
104.0
26
TraesCS6D01G238000
chr7A
93.082
1301
61
11
1827
3125
276742033
276743306
0.000000e+00
1877.0
27
TraesCS6D01G238000
chr5B
91.996
912
31
5
1
879
357076115
357075213
0.000000e+00
1242.0
28
TraesCS6D01G238000
chr1D
96.205
527
16
2
3121
3647
143258445
143258967
0.000000e+00
859.0
29
TraesCS6D01G238000
chr5D
96.198
526
16
2
3122
3647
377379579
377380100
0.000000e+00
857.0
30
TraesCS6D01G238000
chr7D
95.833
528
18
2
3121
3647
334683605
334684129
0.000000e+00
850.0
31
TraesCS6D01G238000
chr7D
95.644
528
20
1
3120
3647
355379887
355379363
0.000000e+00
845.0
32
TraesCS6D01G238000
chr7D
95.627
526
20
1
3122
3647
245341410
245340888
0.000000e+00
841.0
33
TraesCS6D01G238000
chr4D
95.636
527
20
1
3121
3647
370833648
370833125
0.000000e+00
843.0
34
TraesCS6D01G238000
chr3D
95.636
527
19
2
3122
3647
123597814
123598337
0.000000e+00
843.0
35
TraesCS6D01G238000
chr1A
86.143
433
47
11
11
439
371317266
371317689
4.290000e-124
455.0
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
TraesCS6D01G238000
chr6D
338134905
338138551
3646
True
6735.000000
6735
100.0000
1
3647
1
chr6D.!!$R1
3646
1
TraesCS6D01G238000
chr6D
197263403
197266526
3123
False
4892.000000
4892
94.9980
3
3125
1
chr6D.!!$F2
3122
2
TraesCS6D01G238000
chr6D
189258306
189258825
519
False
843.000000
843
95.8100
3121
3645
1
chr6D.!!$F1
524
3
TraesCS6D01G238000
chr6D
331068964
331069484
520
False
839.000000
839
95.6190
3120
3644
1
chr6D.!!$F3
524
4
TraesCS6D01G238000
chr2D
161648687
161651804
3117
True
2509.000000
4266
96.0445
1
3125
2
chr2D.!!$R1
3124
5
TraesCS6D01G238000
chr2B
430819734
430822862
3128
True
2373.500000
4065
93.9265
1
3125
2
chr2B.!!$R2
3124
6
TraesCS6D01G238000
chr4A
418287998
418291118
3120
True
2342.000000
4004
93.7370
1
3125
2
chr4A.!!$R1
3124
7
TraesCS6D01G238000
chr3A
216936489
216939623
3134
False
2307.000000
3923
93.6695
1
3119
2
chr3A.!!$F1
3118
8
TraesCS6D01G238000
chr3A
217011956
217015294
3338
False
1638.666667
3941
94.8190
1
3126
3
chr3A.!!$F2
3125
9
TraesCS6D01G238000
chr3B
241260197
241261628
1431
True
2350.000000
2350
96.2400
1365
2800
1
chr3B.!!$R1
1435
10
TraesCS6D01G238000
chr6A
568172634
568174348
1714
False
2335.000000
2335
91.2370
469
2200
1
chr6A.!!$F1
1731
11
TraesCS6D01G238000
chr4B
527929921
527931247
1326
True
1971.000000
1971
93.5580
507
1829
1
chr4B.!!$R2
1322
12
TraesCS6D01G238000
chr4B
199721268
199723043
1775
False
1385.000000
2324
92.7665
1365
3125
2
chr4B.!!$F1
1760
13
TraesCS6D01G238000
chr6B
129870029
129871403
1374
True
1973.000000
1973
92.7590
461
1822
1
chr6B.!!$R1
1361
14
TraesCS6D01G238000
chr7A
276742033
276743306
1273
False
1877.000000
1877
93.0820
1827
3125
1
chr7A.!!$F1
1298
15
TraesCS6D01G238000
chr5B
357075213
357076115
902
True
1242.000000
1242
91.9960
1
879
1
chr5B.!!$R1
878
16
TraesCS6D01G238000
chr1D
143258445
143258967
522
False
859.000000
859
96.2050
3121
3647
1
chr1D.!!$F1
526
17
TraesCS6D01G238000
chr5D
377379579
377380100
521
False
857.000000
857
96.1980
3122
3647
1
chr5D.!!$F1
525
18
TraesCS6D01G238000
chr7D
334683605
334684129
524
False
850.000000
850
95.8330
3121
3647
1
chr7D.!!$F1
526
19
TraesCS6D01G238000
chr7D
355379363
355379887
524
True
845.000000
845
95.6440
3120
3647
1
chr7D.!!$R2
527
20
TraesCS6D01G238000
chr7D
245340888
245341410
522
True
841.000000
841
95.6270
3122
3647
1
chr7D.!!$R1
525
21
TraesCS6D01G238000
chr4D
370833125
370833648
523
True
843.000000
843
95.6360
3121
3647
1
chr4D.!!$R1
526
22
TraesCS6D01G238000
chr3D
123597814
123598337
523
False
843.000000
843
95.6360
3122
3647
1
chr3D.!!$F1
525
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.