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
TraesCS3B01G249100
chr3B
100.000
3184
0
0
1
3184
397261246
397264429
0.000000e+00
5880
1
TraesCS3B01G249100
chr3B
92.978
1780
112
7
626
2399
245471673
245469901
0.000000e+00
2582
2
TraesCS3B01G249100
chr3B
92.415
936
66
3
4
934
422104427
422105362
0.000000e+00
1330
3
TraesCS3B01G249100
chr3B
93.434
792
47
3
2397
3184
245469760
245468970
0.000000e+00
1170
4
TraesCS3B01G249100
chr2A
92.139
2417
149
23
4
2399
302440239
302437843
0.000000e+00
3373
5
TraesCS3B01G249100
chr2A
93.467
796
40
8
2397
3184
259173909
259174700
0.000000e+00
1171
6
TraesCS3B01G249100
chr2A
93.342
796
41
7
2397
3184
348627166
348627957
0.000000e+00
1166
7
TraesCS3B01G249100
chr2A
94.150
547
29
3
4
548
348626129
348626674
0.000000e+00
830
8
TraesCS3B01G249100
chr2A
94.118
544
25
5
2646
3184
300547202
300547743
0.000000e+00
821
9
TraesCS3B01G249100
chr2A
91.900
321
23
1
2397
2714
300546881
300547201
2.250000e-121
446
10
TraesCS3B01G249100
chr7B
91.962
2426
158
26
1
2399
428787541
428785126
0.000000e+00
3365
11
TraesCS3B01G249100
chr7B
91.355
937
74
6
4
935
478020378
478021312
0.000000e+00
1275
12
TraesCS3B01G249100
chr7B
93.432
609
33
5
4
608
40703702
40704307
0.000000e+00
896
13
TraesCS3B01G249100
chr5B
91.660
2422
166
25
4
2399
291602043
291604454
0.000000e+00
3321
14
TraesCS3B01G249100
chr5B
92.290
428
26
6
2762
3184
496647323
496647748
4.540000e-168
601
15
TraesCS3B01G249100
chr5A
91.608
2419
159
28
4
2399
222766246
222768643
0.000000e+00
3302
16
TraesCS3B01G249100
chr6B
92.924
2247
130
18
164
2399
637183881
637181653
0.000000e+00
3241
17
TraesCS3B01G249100
chr6B
94.417
609
30
3
4
608
283253349
283253957
0.000000e+00
933
18
TraesCS3B01G249100
chr4B
90.961
2434
172
23
1
2399
360895360
360897780
0.000000e+00
3232
19
TraesCS3B01G249100
chr4B
94.264
2092
109
9
312
2399
205682161
205680077
0.000000e+00
3188
20
TraesCS3B01G249100
chr4B
94.892
646
24
4
2396
3032
205679935
205679290
0.000000e+00
1002
21
TraesCS3B01G249100
chr4B
91.866
627
46
4
2561
3184
360898197
360898821
0.000000e+00
870
22
TraesCS3B01G249100
chr4A
93.112
1539
86
13
871
2399
535944466
535942938
0.000000e+00
2237
23
TraesCS3B01G249100
chr2D
92.674
1324
68
8
4
1320
245569764
245571065
0.000000e+00
1881
24
TraesCS3B01G249100
chr6A
92.695
794
48
6
2397
3184
409744564
409745353
0.000000e+00
1136
25
TraesCS3B01G249100
chr3D
94.922
709
32
4
4
708
208626257
208626965
0.000000e+00
1107
26
TraesCS3B01G249100
chr1A
93.007
429
23
5
2762
3184
382776285
382776712
1.250000e-173
619
27
TraesCS3B01G249100
chr1B
91.803
427
30
4
2762
3184
82618043
82618468
9.840000e-165
590
28
TraesCS3B01G249100
chr1B
94.097
288
17
0
2427
2714
82617465
82617752
3.770000e-119
438
29
TraesCS3B01G249100
chr2B
94.097
288
17
0
2427
2714
93132999
93132712
3.770000e-119
438
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
TraesCS3B01G249100
chr3B
397261246
397264429
3183
False
5880.0
5880
100.0000
1
3184
1
chr3B.!!$F1
3183
1
TraesCS3B01G249100
chr3B
245468970
245471673
2703
True
1876.0
2582
93.2060
626
3184
2
chr3B.!!$R1
2558
2
TraesCS3B01G249100
chr3B
422104427
422105362
935
False
1330.0
1330
92.4150
4
934
1
chr3B.!!$F2
930
3
TraesCS3B01G249100
chr2A
302437843
302440239
2396
True
3373.0
3373
92.1390
4
2399
1
chr2A.!!$R1
2395
4
TraesCS3B01G249100
chr2A
259173909
259174700
791
False
1171.0
1171
93.4670
2397
3184
1
chr2A.!!$F1
787
5
TraesCS3B01G249100
chr2A
348626129
348627957
1828
False
998.0
1166
93.7460
4
3184
2
chr2A.!!$F3
3180
6
TraesCS3B01G249100
chr2A
300546881
300547743
862
False
633.5
821
93.0090
2397
3184
2
chr2A.!!$F2
787
7
TraesCS3B01G249100
chr7B
428785126
428787541
2415
True
3365.0
3365
91.9620
1
2399
1
chr7B.!!$R1
2398
8
TraesCS3B01G249100
chr7B
478020378
478021312
934
False
1275.0
1275
91.3550
4
935
1
chr7B.!!$F2
931
9
TraesCS3B01G249100
chr7B
40703702
40704307
605
False
896.0
896
93.4320
4
608
1
chr7B.!!$F1
604
10
TraesCS3B01G249100
chr5B
291602043
291604454
2411
False
3321.0
3321
91.6600
4
2399
1
chr5B.!!$F1
2395
11
TraesCS3B01G249100
chr5A
222766246
222768643
2397
False
3302.0
3302
91.6080
4
2399
1
chr5A.!!$F1
2395
12
TraesCS3B01G249100
chr6B
637181653
637183881
2228
True
3241.0
3241
92.9240
164
2399
1
chr6B.!!$R1
2235
13
TraesCS3B01G249100
chr6B
283253349
283253957
608
False
933.0
933
94.4170
4
608
1
chr6B.!!$F1
604
14
TraesCS3B01G249100
chr4B
205679290
205682161
2871
True
2095.0
3188
94.5780
312
3032
2
chr4B.!!$R1
2720
15
TraesCS3B01G249100
chr4B
360895360
360898821
3461
False
2051.0
3232
91.4135
1
3184
2
chr4B.!!$F1
3183
16
TraesCS3B01G249100
chr4A
535942938
535944466
1528
True
2237.0
2237
93.1120
871
2399
1
chr4A.!!$R1
1528
17
TraesCS3B01G249100
chr2D
245569764
245571065
1301
False
1881.0
1881
92.6740
4
1320
1
chr2D.!!$F1
1316
18
TraesCS3B01G249100
chr6A
409744564
409745353
789
False
1136.0
1136
92.6950
2397
3184
1
chr6A.!!$F1
787
19
TraesCS3B01G249100
chr3D
208626257
208626965
708
False
1107.0
1107
94.9220
4
708
1
chr3D.!!$F1
704
20
TraesCS3B01G249100
chr1B
82617465
82618468
1003
False
514.0
590
92.9500
2427
3184
2
chr1B.!!$F1
757
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.