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
TraesCS4D01G255400
chr4D
100.000
3324
0
0
1
3324
424170647
424167324
0.000000e+00
6139.0
1
TraesCS4D01G255400
chr4D
95.949
3357
96
19
1
3324
424111640
424108291
0.000000e+00
5409.0
2
TraesCS4D01G255400
chr4D
93.148
2306
101
16
699
2958
423990217
423987923
0.000000e+00
3330.0
3
TraesCS4D01G255400
chr4D
93.861
1743
76
13
1606
3324
424196575
424194840
0.000000e+00
2597.0
4
TraesCS4D01G255400
chr4D
93.133
1762
108
4
699
2448
424323102
424321342
0.000000e+00
2571.0
5
TraesCS4D01G255400
chr4D
88.199
1771
129
37
804
2523
57840374
57842115
0.000000e+00
2039.0
6
TraesCS4D01G255400
chr4D
87.315
1419
135
28
955
2348
426870123
426871521
0.000000e+00
1581.0
7
TraesCS4D01G255400
chr4D
96.018
879
27
2
2452
3324
424309149
424308273
0.000000e+00
1423.0
8
TraesCS4D01G255400
chr4D
96.305
866
25
2
2463
3322
424194811
424193947
0.000000e+00
1415.0
9
TraesCS4D01G255400
chr4D
93.297
552
35
2
699
1249
424197767
424197217
0.000000e+00
813.0
10
TraesCS4D01G255400
chr4D
89.836
610
36
4
1
584
424447260
424446651
0.000000e+00
760.0
11
TraesCS4D01G255400
chr4D
89.180
610
33
6
1
585
424244418
424243817
0.000000e+00
730.0
12
TraesCS4D01G255400
chr4D
96.454
141
5
0
564
704
424446374
424446234
1.990000e-57
233.0
13
TraesCS4D01G255400
chr4D
92.199
141
10
1
564
704
424243541
424243402
7.270000e-47
198.0
14
TraesCS4D01G255400
chr4D
95.833
48
2
0
608
655
424243662
424243615
9.890000e-11
78.7
15
TraesCS4D01G255400
chr4A
93.792
2062
79
20
944
2958
40260686
40262745
0.000000e+00
3053.0
16
TraesCS4D01G255400
chr4A
85.583
1415
138
30
938
2334
38682956
38681590
0.000000e+00
1423.0
17
TraesCS4D01G255400
chr4A
89.716
282
20
4
2244
2523
539140504
539140778
5.280000e-93
351.0
18
TraesCS4D01G255400
chr4A
77.258
299
46
13
160
439
40255174
40255469
4.440000e-34
156.0
19
TraesCS4D01G255400
chr4B
93.999
2033
87
7
944
2962
520298421
520296410
0.000000e+00
3046.0
20
TraesCS4D01G255400
chr4B
90.186
1559
106
40
951
2485
86132213
86130678
0.000000e+00
1988.0
21
TraesCS4D01G255400
chr4B
85.003
1467
168
32
938
2375
522669258
522670701
0.000000e+00
1443.0
22
TraesCS4D01G255400
chr4B
85.852
1350
139
28
1046
2369
527644854
527643531
0.000000e+00
1387.0
23
TraesCS4D01G255400
chr4B
91.194
511
22
4
2085
2595
520289629
520289142
0.000000e+00
673.0
24
TraesCS4D01G255400
chr4B
94.355
372
21
0
2587
2958
520281360
520280989
3.720000e-159
571.0
25
TraesCS4D01G255400
chr4B
89.420
293
28
1
2967
3259
520296453
520296164
1.880000e-97
366.0
26
TraesCS4D01G255400
chr4B
89.100
211
18
2
2579
2788
86097025
86096819
1.180000e-64
257.0
27
TraesCS4D01G255400
chr4B
87.500
120
11
3
2810
2928
527747421
527747305
5.780000e-28
135.0
28
TraesCS4D01G255400
chrUn
92.320
612
36
5
1
603
60141253
60140644
0.000000e+00
859.0
29
TraesCS4D01G255400
chrUn
92.320
612
36
5
1
603
235655600
235654991
0.000000e+00
859.0
30
TraesCS4D01G255400
chrUn
94.194
310
12
3
944
1248
60140575
60140267
5.020000e-128
468.0
31
TraesCS4D01G255400
chr7A
89.062
192
16
2
3054
3243
545952681
545952493
1.990000e-57
233.0
32
TraesCS4D01G255400
chr5D
79.121
91
14
4
274
362
38735721
38735808
1.290000e-04
58.4
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
TraesCS4D01G255400
chr4D
424167324
424170647
3323
True
6139.000000
6139
100.000000
1
3324
1
chr4D.!!$R3
3323
1
TraesCS4D01G255400
chr4D
424108291
424111640
3349
True
5409.000000
5409
95.949000
1
3324
1
chr4D.!!$R2
3323
2
TraesCS4D01G255400
chr4D
423987923
423990217
2294
True
3330.000000
3330
93.148000
699
2958
1
chr4D.!!$R1
2259
3
TraesCS4D01G255400
chr4D
424321342
424323102
1760
True
2571.000000
2571
93.133000
699
2448
1
chr4D.!!$R5
1749
4
TraesCS4D01G255400
chr4D
57840374
57842115
1741
False
2039.000000
2039
88.199000
804
2523
1
chr4D.!!$F1
1719
5
TraesCS4D01G255400
chr4D
424193947
424197767
3820
True
1608.333333
2597
94.487667
699
3324
3
chr4D.!!$R6
2625
6
TraesCS4D01G255400
chr4D
426870123
426871521
1398
False
1581.000000
1581
87.315000
955
2348
1
chr4D.!!$F2
1393
7
TraesCS4D01G255400
chr4D
424308273
424309149
876
True
1423.000000
1423
96.018000
2452
3324
1
chr4D.!!$R4
872
8
TraesCS4D01G255400
chr4D
424446234
424447260
1026
True
496.500000
760
93.145000
1
704
2
chr4D.!!$R8
703
9
TraesCS4D01G255400
chr4D
424243402
424244418
1016
True
335.566667
730
92.404000
1
704
3
chr4D.!!$R7
703
10
TraesCS4D01G255400
chr4A
40260686
40262745
2059
False
3053.000000
3053
93.792000
944
2958
1
chr4A.!!$F2
2014
11
TraesCS4D01G255400
chr4A
38681590
38682956
1366
True
1423.000000
1423
85.583000
938
2334
1
chr4A.!!$R1
1396
12
TraesCS4D01G255400
chr4B
86130678
86132213
1535
True
1988.000000
1988
90.186000
951
2485
1
chr4B.!!$R2
1534
13
TraesCS4D01G255400
chr4B
520296164
520298421
2257
True
1706.000000
3046
91.709500
944
3259
2
chr4B.!!$R7
2315
14
TraesCS4D01G255400
chr4B
522669258
522670701
1443
False
1443.000000
1443
85.003000
938
2375
1
chr4B.!!$F1
1437
15
TraesCS4D01G255400
chr4B
527643531
527644854
1323
True
1387.000000
1387
85.852000
1046
2369
1
chr4B.!!$R5
1323
16
TraesCS4D01G255400
chrUn
235654991
235655600
609
True
859.000000
859
92.320000
1
603
1
chrUn.!!$R1
602
17
TraesCS4D01G255400
chrUn
60140267
60141253
986
True
663.500000
859
93.257000
1
1248
2
chrUn.!!$R2
1247
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.