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
TraesCS7A01G387300
chr7A
100.000
2455
0
0
1
2455
563493388
563495842
0.000000e+00
4534
1
TraesCS7A01G387300
chr7A
95.612
2461
65
27
1
2455
435733612
435731189
0.000000e+00
3906
2
TraesCS7A01G387300
chr7A
93.878
1568
57
14
888
2455
87693048
87691520
0.000000e+00
2327
3
TraesCS7A01G387300
chr7A
95.374
908
30
6
1
898
87693977
87693072
0.000000e+00
1434
4
TraesCS7A01G387300
chr7A
88.558
839
67
14
76
898
139135876
139135051
0.000000e+00
990
5
TraesCS7A01G387300
chr7A
86.580
924
86
23
1541
2453
139134425
139133529
0.000000e+00
985
6
TraesCS7A01G387300
chr7A
89.011
546
47
7
888
1432
139135027
139134494
0.000000e+00
664
7
TraesCS7A01G387300
chr5A
94.677
2273
79
16
189
2455
690643132
690640896
0.000000e+00
3489
8
TraesCS7A01G387300
chr5A
96.330
545
16
2
189
729
698853177
698853721
0.000000e+00
893
9
TraesCS7A01G387300
chr2B
96.058
1725
49
10
94
1813
338729380
338727670
0.000000e+00
2791
10
TraesCS7A01G387300
chr1D
94.770
1568
43
14
888
2455
34022524
34020996
0.000000e+00
2405
11
TraesCS7A01G387300
chr1D
96.476
908
20
6
1
898
34023453
34022548
0.000000e+00
1489
12
TraesCS7A01G387300
chr3B
96.131
1370
44
7
94
1458
395707738
395706373
0.000000e+00
2228
13
TraesCS7A01G387300
chr3B
92.746
965
32
13
1493
2455
395706372
395705444
0.000000e+00
1360
14
TraesCS7A01G387300
chr1A
85.193
1479
144
45
1
1432
291625851
291624401
0.000000e+00
1448
15
TraesCS7A01G387300
chr5D
88.584
911
77
14
1
895
448013340
448014239
0.000000e+00
1081
16
TraesCS7A01G387300
chr5D
87.079
921
80
25
1541
2450
448014875
448015767
0.000000e+00
1005
17
TraesCS7A01G387300
chr5D
88.577
534
48
9
900
1432
448014285
448014806
9.580000e-179
636
18
TraesCS7A01G387300
chr2A
85.946
925
90
27
1541
2455
148842079
148842973
0.000000e+00
952
19
TraesCS7A01G387300
chr4D
89.901
505
38
6
1541
2044
170688985
170688493
2.660000e-179
638
20
TraesCS7A01G387300
chr4D
89.703
505
39
6
1541
2044
170623130
170622638
1.240000e-177
632
21
TraesCS7A01G387300
chr4D
93.056
360
12
6
2107
2455
294681915
294682272
4.680000e-142
514
22
TraesCS7A01G387300
chr4D
92.000
100
4
3
1415
1511
414999564
414999662
1.180000e-28
137
23
TraesCS7A01G387300
chr5B
93.611
360
10
5
2107
2455
102916815
102917172
2.160000e-145
525
24
TraesCS7A01G387300
chr5B
91.176
102
6
2
1415
1514
166379180
166379080
4.260000e-28
135
25
TraesCS7A01G387300
chr4B
91.919
99
5
2
1415
1511
511163711
511163808
4.260000e-28
135
26
TraesCS7A01G387300
chr3A
91.919
99
5
2
1415
1511
470095776
470095679
4.260000e-28
135
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
TraesCS7A01G387300
chr7A
563493388
563495842
2454
False
4534.000000
4534
100.000000
1
2455
1
chr7A.!!$F1
2454
1
TraesCS7A01G387300
chr7A
435731189
435733612
2423
True
3906.000000
3906
95.612000
1
2455
1
chr7A.!!$R1
2454
2
TraesCS7A01G387300
chr7A
87691520
87693977
2457
True
1880.500000
2327
94.626000
1
2455
2
chr7A.!!$R2
2454
3
TraesCS7A01G387300
chr7A
139133529
139135876
2347
True
879.666667
990
88.049667
76
2453
3
chr7A.!!$R3
2377
4
TraesCS7A01G387300
chr5A
690640896
690643132
2236
True
3489.000000
3489
94.677000
189
2455
1
chr5A.!!$R1
2266
5
TraesCS7A01G387300
chr5A
698853177
698853721
544
False
893.000000
893
96.330000
189
729
1
chr5A.!!$F1
540
6
TraesCS7A01G387300
chr2B
338727670
338729380
1710
True
2791.000000
2791
96.058000
94
1813
1
chr2B.!!$R1
1719
7
TraesCS7A01G387300
chr1D
34020996
34023453
2457
True
1947.000000
2405
95.623000
1
2455
2
chr1D.!!$R1
2454
8
TraesCS7A01G387300
chr3B
395705444
395707738
2294
True
1794.000000
2228
94.438500
94
2455
2
chr3B.!!$R1
2361
9
TraesCS7A01G387300
chr1A
291624401
291625851
1450
True
1448.000000
1448
85.193000
1
1432
1
chr1A.!!$R1
1431
10
TraesCS7A01G387300
chr5D
448013340
448015767
2427
False
907.333333
1081
88.080000
1
2450
3
chr5D.!!$F1
2449
11
TraesCS7A01G387300
chr2A
148842079
148842973
894
False
952.000000
952
85.946000
1541
2455
1
chr2A.!!$F1
914
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.