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
TraesCS4A01G460600
chr4A
100.000
1908
0
0
1
1908
725837700
725839607
0.000000e+00
3524.0
1
TraesCS4A01G460600
chr4A
100.000
446
0
0
2398
2843
725840097
725840542
0.000000e+00
824.0
2
TraesCS4A01G460600
chr4A
75.117
213
39
9
2404
2611
390876555
390876352
1.400000e-13
87.9
3
TraesCS4A01G460600
chr7A
94.762
840
40
3
1011
1850
11789279
11788444
0.000000e+00
1304.0
4
TraesCS4A01G460600
chr7A
94.762
840
40
3
1011
1850
11792167
11791332
0.000000e+00
1304.0
5
TraesCS4A01G460600
chr7A
94.286
840
44
3
1011
1850
11877426
11876591
0.000000e+00
1282.0
6
TraesCS4A01G460600
chr7A
94.286
840
44
3
1011
1850
11923431
11922596
0.000000e+00
1282.0
7
TraesCS4A01G460600
chr7A
95.445
483
22
0
1426
1908
11982363
11981881
0.000000e+00
771.0
8
TraesCS4A01G460600
chr7A
93.567
342
15
3
3
337
11803189
11802848
1.180000e-138
503.0
9
TraesCS4A01G460600
chr7A
93.567
342
15
3
3
337
11829703
11829362
1.180000e-138
503.0
10
TraesCS4A01G460600
chr7A
92.982
342
17
3
3
337
11883194
11882853
2.540000e-135
492.0
11
TraesCS4A01G460600
chr7A
92.398
342
19
3
3
337
11930174
11929833
5.510000e-132
481.0
12
TraesCS4A01G460600
chr7A
88.594
377
21
11
657
1020
11828948
11828581
3.360000e-119
438.0
13
TraesCS4A01G460600
chr7A
94.035
285
16
1
337
620
11802812
11802528
5.630000e-117
431.0
14
TraesCS4A01G460600
chr7A
94.035
285
16
1
337
620
11829326
11829042
5.630000e-117
431.0
15
TraesCS4A01G460600
chr7A
88.556
367
18
12
667
1020
11802434
11802079
9.420000e-115
424.0
16
TraesCS4A01G460600
chr7A
92.982
285
18
2
337
620
11882817
11882534
5.670000e-112
414.0
17
TraesCS4A01G460600
chr7A
92.982
285
18
2
337
620
11929797
11929514
5.670000e-112
414.0
18
TraesCS4A01G460600
chr7A
88.623
334
22
9
690
1020
11929407
11929087
2.660000e-105
392.0
19
TraesCS4A01G460600
chr7A
87.395
357
23
13
667
1020
11882440
11882103
9.550000e-105
390.0
20
TraesCS4A01G460600
chr7A
90.726
248
21
1
2404
2651
11873554
11873309
2.110000e-86
329.0
21
TraesCS4A01G460600
chr7A
90.566
212
18
1
2440
2651
11919424
11919215
2.160000e-71
279.0
22
TraesCS4A01G460600
chr7A
85.124
242
28
4
2602
2843
11981673
11981440
1.020000e-59
241.0
23
TraesCS4A01G460600
chr7A
88.235
170
17
3
2675
2843
11981278
11981111
1.730000e-47
200.0
24
TraesCS4A01G460600
chr7A
78.161
174
30
6
2404
2575
686005469
686005302
1.390000e-18
104.0
25
TraesCS4A01G460600
chr7A
94.643
56
3
0
584
639
729297439
729297384
1.400000e-13
87.9
26
TraesCS4A01G460600
chrUn
93.567
342
15
3
3
337
341053088
341053429
1.180000e-138
503.0
27
TraesCS4A01G460600
chrUn
88.594
377
21
11
657
1020
341053843
341054210
3.360000e-119
438.0
28
TraesCS4A01G460600
chrUn
94.035
285
16
1
337
620
341053465
341053749
5.630000e-117
431.0
29
TraesCS4A01G460600
chr7D
83.607
183
26
4
584
766
636826553
636826731
4.870000e-38
169.0
30
TraesCS4A01G460600
chr5A
80.347
173
25
8
2404
2573
168240401
168240235
3.850000e-24
122.0
31
TraesCS4A01G460600
chr2D
76.364
220
40
10
2404
2619
16903812
16903601
1.080000e-19
108.0
32
TraesCS4A01G460600
chr7B
75.229
218
44
8
2398
2612
615662838
615663048
8.380000e-16
95.3
33
TraesCS4A01G460600
chr2A
84.615
91
12
2
2404
2493
756138425
756138336
3.900000e-14
89.8
34
TraesCS4A01G460600
chr3A
83.871
93
13
2
2404
2495
12149302
12149393
1.400000e-13
87.9
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
TraesCS4A01G460600
chr4A
725837700
725840542
2842
False
2174.000000
3524
100.000000
1
2843
2
chr4A.!!$F1
2842
1
TraesCS4A01G460600
chr7A
11788444
11792167
3723
True
1304.000000
1304
94.762000
1011
1850
2
chr7A.!!$R3
839
2
TraesCS4A01G460600
chr7A
11873309
11877426
4117
True
805.500000
1282
92.506000
1011
2651
2
chr7A.!!$R6
1640
3
TraesCS4A01G460600
chr7A
11919215
11923431
4216
True
780.500000
1282
92.426000
1011
2651
2
chr7A.!!$R8
1640
4
TraesCS4A01G460600
chr7A
11828581
11829703
1122
True
457.333333
503
92.065333
3
1020
3
chr7A.!!$R5
1017
5
TraesCS4A01G460600
chr7A
11802079
11803189
1110
True
452.666667
503
92.052667
3
1020
3
chr7A.!!$R4
1017
6
TraesCS4A01G460600
chr7A
11882103
11883194
1091
True
432.000000
492
91.119667
3
1020
3
chr7A.!!$R7
1017
7
TraesCS4A01G460600
chr7A
11929087
11930174
1087
True
429.000000
481
91.334333
3
1020
3
chr7A.!!$R9
1017
8
TraesCS4A01G460600
chr7A
11981111
11982363
1252
True
404.000000
771
89.601333
1426
2843
3
chr7A.!!$R10
1417
9
TraesCS4A01G460600
chrUn
341053088
341054210
1122
False
457.333333
503
92.065333
3
1020
3
chrUn.!!$F1
1017
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.