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
TraesCS1A01G064300
chr1A
100.000
3405
0
0
1
3405
46203413
46200009
0.000000e+00
6288.0
1
TraesCS1A01G064300
chr1A
95.914
1811
36
9
1627
3405
46295091
46293287
0.000000e+00
2900.0
2
TraesCS1A01G064300
chr1A
98.241
1649
27
2
133
1781
46297240
46295594
0.000000e+00
2883.0
3
TraesCS1A01G064300
chr1A
91.811
1209
61
17
595
1787
45858405
45857219
0.000000e+00
1650.0
4
TraesCS1A01G064300
chr1A
88.335
1003
81
12
1463
2454
45857386
45856409
0.000000e+00
1171.0
5
TraesCS1A01G064300
chr1A
86.288
598
66
9
979
1571
46310430
46309844
1.330000e-178
636.0
6
TraesCS1A01G064300
chr1A
85.597
611
54
13
1783
2386
46309101
46308518
8.080000e-171
610.0
7
TraesCS1A01G064300
chr1A
85.434
611
55
12
1783
2386
46256794
46256211
3.760000e-169
604.0
8
TraesCS1A01G064300
chr1A
97.167
353
6
2
3056
3405
46252651
46252300
8.140000e-166
593.0
9
TraesCS1A01G064300
chr1A
98.571
210
3
0
1
210
46297450
46297241
4.150000e-99
372.0
10
TraesCS1A01G064300
chr1A
79.024
410
44
16
68
467
45859733
45859356
3.390000e-60
243.0
11
TraesCS1A01G064300
chr1A
77.460
315
60
9
2431
2741
46254469
46254162
9.710000e-41
178.0
12
TraesCS1A01G064300
chr1A
77.338
278
54
7
2431
2706
46305585
46305315
4.550000e-34
156.0
13
TraesCS1A01G064300
chr1A
93.478
46
3
0
496
541
46209455
46209410
6.100000e-08
69.4
14
TraesCS1A01G064300
chr1A
93.478
46
3
0
496
541
46258623
46258578
6.100000e-08
69.4
15
TraesCS1A01G064300
chr1A
93.478
46
3
0
496
541
46310909
46310864
6.100000e-08
69.4
16
TraesCS1A01G064300
chr1B
91.130
2875
162
52
588
3403
66376763
66373923
0.000000e+00
3810.0
17
TraesCS1A01G064300
chr1B
89.192
1906
131
36
596
2472
66125023
66123164
0.000000e+00
2309.0
18
TraesCS1A01G064300
chr1B
95.314
1195
51
4
588
1781
66501110
66499920
0.000000e+00
1892.0
19
TraesCS1A01G064300
chr1B
92.117
685
52
2
1459
2143
66499929
66499247
0.000000e+00
965.0
20
TraesCS1A01G064300
chr1B
94.636
522
25
3
2187
2707
66499248
66498729
0.000000e+00
806.0
21
TraesCS1A01G064300
chr1B
94.186
516
26
1
68
579
66501900
66501385
0.000000e+00
784.0
22
TraesCS1A01G064300
chr1B
93.407
364
18
1
222
579
66377401
66377038
5.000000e-148
534.0
23
TraesCS1A01G064300
chr1B
91.411
326
27
1
1459
1784
66500085
66499761
2.410000e-121
446.0
24
TraesCS1A01G064300
chr1B
87.569
362
19
12
2826
3184
66498672
66498334
2.460000e-106
396.0
25
TraesCS1A01G064300
chr1B
94.872
156
8
0
68
223
66377639
66377484
9.440000e-61
244.0
26
TraesCS1A01G064300
chr1B
79.508
366
38
15
109
468
66125513
66125179
3.420000e-55
226.0
27
TraesCS1A01G064300
chr1B
76.176
319
64
9
2428
2741
66510507
66510196
1.260000e-34
158.0
28
TraesCS1A01G064300
chr1B
90.667
75
5
2
1
73
47399611
47399537
7.780000e-17
99.0
29
TraesCS1A01G064300
chr1B
89.130
46
5
0
496
541
66515648
66515603
1.320000e-04
58.4
30
TraesCS1A01G064300
chr1D
91.275
1914
91
26
1538
3405
46449547
46447664
0.000000e+00
2540.0
31
TraesCS1A01G064300
chr1D
94.444
1602
70
10
68
1668
46451496
46449913
0.000000e+00
2447.0
32
TraesCS1A01G064300
chr1D
91.970
1208
59
19
596
1787
46397962
46396777
0.000000e+00
1659.0
33
TraesCS1A01G064300
chr1D
88.235
1003
83
11
1463
2454
46396944
46395966
0.000000e+00
1166.0
34
TraesCS1A01G064300
chr1D
85.574
610
58
11
1783
2386
46462567
46461982
2.250000e-171
612.0
35
TraesCS1A01G064300
chr1D
86.847
517
55
6
976
1488
46464091
46463584
1.770000e-157
566.0
36
TraesCS1A01G064300
chrUn
95.522
67
3
0
1
67
360089079
360089145
1.290000e-19
108.0
37
TraesCS1A01G064300
chrUn
95.522
67
3
0
1
67
416058131
416058197
1.290000e-19
108.0
38
TraesCS1A01G064300
chr7D
94.203
69
4
0
1
69
39202885
39202953
4.650000e-19
106.0
39
TraesCS1A01G064300
chr5D
92.105
76
3
1
1
76
474212348
474212276
1.670000e-18
104.0
40
TraesCS1A01G064300
chr4D
94.030
67
4
0
1
67
20231984
20231918
6.010000e-18
102.0
41
TraesCS1A01G064300
chr3A
94.030
67
4
0
1
67
421766983
421766917
6.010000e-18
102.0
42
TraesCS1A01G064300
chr2A
94.030
67
4
0
1
67
20199016
20198950
6.010000e-18
102.0
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
TraesCS1A01G064300
chr1A
46200009
46203413
3404
True
6288.000000
6288
100.000000
1
3405
1
chr1A.!!$R1
3404
1
TraesCS1A01G064300
chr1A
46293287
46297450
4163
True
2051.666667
2900
97.575333
1
3405
3
chr1A.!!$R5
3404
2
TraesCS1A01G064300
chr1A
45856409
45859733
3324
True
1021.333333
1650
86.390000
68
2454
3
chr1A.!!$R3
2386
3
TraesCS1A01G064300
chr1A
46305315
46310909
5594
True
367.850000
636
85.675250
496
2706
4
chr1A.!!$R6
2210
4
TraesCS1A01G064300
chr1A
46252300
46258623
6323
True
361.100000
604
88.384750
496
3405
4
chr1A.!!$R4
2909
5
TraesCS1A01G064300
chr1B
66373923
66377639
3716
True
1529.333333
3810
93.136333
68
3403
3
chr1B.!!$R5
3335
6
TraesCS1A01G064300
chr1B
66123164
66125513
2349
True
1267.500000
2309
84.350000
109
2472
2
chr1B.!!$R4
2363
7
TraesCS1A01G064300
chr1B
66498334
66501900
3566
True
881.500000
1892
92.538833
68
3184
6
chr1B.!!$R6
3116
8
TraesCS1A01G064300
chr1D
46447664
46451496
3832
True
2493.500000
2540
92.859500
68
3405
2
chr1D.!!$R2
3337
9
TraesCS1A01G064300
chr1D
46395966
46397962
1996
True
1412.500000
1659
90.102500
596
2454
2
chr1D.!!$R1
1858
10
TraesCS1A01G064300
chr1D
46461982
46464091
2109
True
589.000000
612
86.210500
976
2386
2
chr1D.!!$R3
1410
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.