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
TraesCS4D01G250600
chr4D
100.000
2612
0
0
1
2612
419245719
419248330
0.000000e+00
4824.0
1
TraesCS4D01G250600
chr4D
92.219
1812
88
16
201
1988
419207026
419205244
0.000000e+00
2516.0
2
TraesCS4D01G250600
chr4D
88.659
1693
113
24
521
2153
419232843
419231170
0.000000e+00
1989.0
3
TraesCS4D01G250600
chr4D
94.915
177
9
0
1
177
296754966
296754790
7.120000e-71
278.0
4
TraesCS4D01G250600
chr4D
85.075
134
18
2
2267
2400
419214419
419214288
4.530000e-28
135.0
5
TraesCS4D01G250600
chr4D
87.288
118
6
3
255
363
419233145
419233028
2.730000e-25
126.0
6
TraesCS4D01G250600
chr4B
91.009
1813
105
23
517
2309
517171408
517173182
0.000000e+00
2392.0
7
TraesCS4D01G250600
chr4B
90.746
1837
101
17
200
1997
517009023
517007217
0.000000e+00
2386.0
8
TraesCS4D01G250600
chr4B
88.704
1744
96
18
298
1997
517082055
517080369
0.000000e+00
2036.0
9
TraesCS4D01G250600
chr4B
90.007
1431
72
11
201
1611
517129656
517128277
0.000000e+00
1784.0
10
TraesCS4D01G250600
chr4B
87.651
413
28
5
1604
1997
517127232
517126824
2.370000e-125
459.0
11
TraesCS4D01G250600
chr4B
92.581
310
17
2
2307
2612
517173565
517173872
8.580000e-120
440.0
12
TraesCS4D01G250600
chr4B
97.297
111
3
0
201
311
517084417
517084307
3.430000e-44
189.0
13
TraesCS4D01G250600
chr4B
80.150
267
28
14
1997
2258
517126775
517126529
2.670000e-40
176.0
14
TraesCS4D01G250600
chr4B
87.681
138
9
4
232
363
517171128
517171263
1.250000e-33
154.0
15
TraesCS4D01G250600
chr4B
80.282
142
13
8
2117
2258
517060072
517059946
2.770000e-15
93.5
16
TraesCS4D01G250600
chr4B
93.750
48
3
0
2267
2314
517126493
517126446
3.610000e-09
73.1
17
TraesCS4D01G250600
chr4A
89.736
1705
89
31
303
1966
45735066
45736725
0.000000e+00
2100.0
18
TraesCS4D01G250600
chr4A
89.201
1565
103
30
443
1966
45469138
45467599
0.000000e+00
1893.0
19
TraesCS4D01G250600
chr4A
89.947
945
62
9
1070
1997
45366268
45365340
0.000000e+00
1188.0
20
TraesCS4D01G250600
chr4A
92.714
549
28
9
545
1084
45366977
45366432
0.000000e+00
782.0
21
TraesCS4D01G250600
chr4A
88.281
384
15
4
1993
2351
45411207
45410829
1.440000e-117
433.0
22
TraesCS4D01G250600
chr4A
93.548
248
11
2
1993
2239
45365300
45365057
5.310000e-97
364.0
23
TraesCS4D01G250600
chr4A
88.925
307
10
6
2137
2421
45411847
45411543
8.890000e-95
357.0
24
TraesCS4D01G250600
chr4A
89.531
277
22
3
2309
2585
45410327
45410058
6.920000e-91
344.0
25
TraesCS4D01G250600
chr4A
88.929
280
21
7
2309
2585
45364776
45364504
1.160000e-88
337.0
26
TraesCS4D01G250600
chr4A
83.624
287
26
10
1993
2272
45466261
45465989
1.550000e-62
250.0
27
TraesCS4D01G250600
chr4A
91.912
136
8
1
231
363
45376425
45376290
1.230000e-43
187.0
28
TraesCS4D01G250600
chr4A
94.643
112
5
1
201
312
45734566
45734676
3.460000e-39
172.0
29
TraesCS4D01G250600
chr4A
100.000
53
0
0
2267
2319
45410548
45410496
5.950000e-17
99.0
30
TraesCS4D01G250600
chr4A
98.000
50
1
0
2223
2272
45365050
45365001
1.290000e-13
87.9
31
TraesCS4D01G250600
chr4A
95.238
42
2
0
2306
2347
45410787
45410746
1.680000e-07
67.6
32
TraesCS4D01G250600
chr4A
100.000
35
0
0
2108
2142
45417635
45417601
6.030000e-07
65.8
33
TraesCS4D01G250600
chr7D
98.870
177
2
0
1
177
600893597
600893773
1.510000e-82
316.0
34
TraesCS4D01G250600
chr7D
94.350
177
10
0
1
177
456373189
456373365
3.310000e-69
272.0
35
TraesCS4D01G250600
chr7D
93.370
181
12
0
1
181
106417850
106417670
4.280000e-68
268.0
36
TraesCS4D01G250600
chr6D
95.480
177
8
0
4
180
404223316
404223140
1.530000e-72
283.0
37
TraesCS4D01G250600
chr3B
94.915
177
9
0
1
177
677855848
677856024
7.120000e-71
278.0
38
TraesCS4D01G250600
chr5D
94.915
177
8
1
1
177
228058427
228058602
2.560000e-70
276.0
39
TraesCS4D01G250600
chrUn
94.350
177
10
0
1
177
312499531
312499707
3.310000e-69
272.0
40
TraesCS4D01G250600
chr1B
93.820
178
10
1
1
177
349756537
349756360
1.540000e-67
267.0
41
TraesCS4D01G250600
chr7B
86.047
172
16
4
2439
2609
544452119
544451955
7.430000e-41
178.0
42
TraesCS4D01G250600
chr2D
84.756
164
20
3
2422
2583
33328178
33328018
2.690000e-35
159.0
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
TraesCS4D01G250600
chr4D
419245719
419248330
2611
False
4824.000000
4824
100.000000
1
2612
1
chr4D.!!$F1
2611
1
TraesCS4D01G250600
chr4D
419205244
419207026
1782
True
2516.000000
2516
92.219000
201
1988
1
chr4D.!!$R2
1787
2
TraesCS4D01G250600
chr4D
419231170
419233145
1975
True
1057.500000
1989
87.973500
255
2153
2
chr4D.!!$R4
1898
3
TraesCS4D01G250600
chr4B
517007217
517009023
1806
True
2386.000000
2386
90.746000
200
1997
1
chr4B.!!$R1
1797
4
TraesCS4D01G250600
chr4B
517080369
517084417
4048
True
1112.500000
2036
93.000500
201
1997
2
chr4B.!!$R3
1796
5
TraesCS4D01G250600
chr4B
517171128
517173872
2744
False
995.333333
2392
90.423667
232
2612
3
chr4B.!!$F1
2380
6
TraesCS4D01G250600
chr4B
517126446
517129656
3210
True
623.025000
1784
87.889500
201
2314
4
chr4B.!!$R4
2113
7
TraesCS4D01G250600
chr4A
45734566
45736725
2159
False
1136.000000
2100
92.189500
201
1966
2
chr4A.!!$F1
1765
8
TraesCS4D01G250600
chr4A
45465989
45469138
3149
True
1071.500000
1893
86.412500
443
2272
2
chr4A.!!$R5
1829
9
TraesCS4D01G250600
chr4A
45364504
45366977
2473
True
551.780000
1188
92.627600
545
2585
5
chr4A.!!$R3
2040
10
TraesCS4D01G250600
chr4A
45410058
45411847
1789
True
260.120000
433
92.395000
1993
2585
5
chr4A.!!$R4
592
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.