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
TraesCS1D01G009900
chr1D
100.000
3068
0
0
1
3068
5355684
5358751
0.000000e+00
5666.0
1
TraesCS1D01G009900
chr1D
88.053
3097
248
64
3
3068
3711581
3708576
0.000000e+00
3557.0
2
TraesCS1D01G009900
chr1D
85.714
1904
187
45
1208
3068
5139396
5141257
0.000000e+00
1930.0
3
TraesCS1D01G009900
chr1D
86.159
1734
159
35
1013
2732
3826365
3824699
0.000000e+00
1797.0
4
TraesCS1D01G009900
chr1D
87.130
1352
108
24
480
1767
84072
85421
0.000000e+00
1472.0
5
TraesCS1D01G009900
chr1D
90.049
1025
76
20
3
1020
3842327
3841322
0.000000e+00
1304.0
6
TraesCS1D01G009900
chr1D
83.889
1409
157
39
1216
2575
7156339
7154952
0.000000e+00
1280.0
7
TraesCS1D01G009900
chr1D
83.031
1432
174
35
1193
2575
4342032
4343443
0.000000e+00
1234.0
8
TraesCS1D01G009900
chr1D
86.404
1015
102
24
430
1414
98698
99706
0.000000e+00
1077.0
9
TraesCS1D01G009900
chr1D
82.789
796
89
24
1786
2573
100219
100974
0.000000e+00
667.0
10
TraesCS1D01G009900
chr1D
83.475
587
59
20
1215
1767
99654
100236
2.110000e-141
512.0
11
TraesCS1D01G009900
chr1D
79.333
300
35
10
2795
3068
4347183
4347481
5.220000e-43
185.0
12
TraesCS1D01G009900
chr1D
100.000
31
0
0
2759
2789
4347036
4347066
1.190000e-04
58.4
13
TraesCS1D01G009900
chr1A
92.707
3099
172
20
5
3068
6516342
6519421
0.000000e+00
4421.0
14
TraesCS1D01G009900
chr1A
93.478
1748
76
14
486
2224
6561199
6562917
0.000000e+00
2562.0
15
TraesCS1D01G009900
chr1A
89.118
726
64
11
430
1142
4204250
4203527
0.000000e+00
889.0
16
TraesCS1D01G009900
chr1A
88.703
717
69
6
435
1142
4097477
4096764
0.000000e+00
865.0
17
TraesCS1D01G009900
chr1A
94.661
487
23
2
5
488
6560632
6561118
0.000000e+00
752.0
18
TraesCS1D01G009900
chr1A
87.409
548
61
5
1777
2322
4095936
4095395
9.340000e-175
623.0
19
TraesCS1D01G009900
chr1B
84.577
1407
151
37
1215
2575
6437233
6435847
0.000000e+00
1336.0
20
TraesCS1D01G009900
chr1B
83.065
1429
162
35
1179
2575
22185993
22187373
0.000000e+00
1225.0
21
TraesCS1D01G009900
chr1B
85.918
980
114
16
430
1390
5688349
5687375
0.000000e+00
1024.0
22
TraesCS1D01G009900
chr1B
88.092
697
63
12
671
1348
5585887
5585192
0.000000e+00
809.0
23
TraesCS1D01G009900
chr1B
84.173
695
82
17
735
1414
22185385
22186066
0.000000e+00
649.0
24
TraesCS1D01G009900
chr1B
82.218
568
80
15
1215
1767
5584908
5584347
1.290000e-128
470.0
25
TraesCS1D01G009900
chr1B
96.154
208
6
2
240
446
8159462
8159668
3.790000e-89
339.0
26
TraesCS1D01G009900
chr1B
94.444
180
7
1
72
248
8156579
8156758
1.080000e-69
274.0
27
TraesCS1D01G009900
chr1B
83.959
293
27
13
2795
3068
7314097
7313806
2.350000e-66
263.0
28
TraesCS1D01G009900
chr1B
80.537
298
34
12
2795
3068
22191156
22191453
1.110000e-49
207.0
29
TraesCS1D01G009900
chr1B
100.000
31
0
0
2759
2789
22191009
22191039
1.190000e-04
58.4
30
TraesCS1D01G009900
chr1B
96.875
32
1
0
2661
2692
8159944
8159975
2.000000e-03
54.7
31
TraesCS1D01G009900
chrUn
93.985
399
21
1
5
400
374223862
374224260
4.380000e-168
601.0
32
TraesCS1D01G009900
chrUn
93.734
399
22
1
5
400
349408926
349409324
2.040000e-166
595.0
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
TraesCS1D01G009900
chr1D
5355684
5358751
3067
False
5666.000000
5666
100.000000
1
3068
1
chr1D.!!$F3
3067
1
TraesCS1D01G009900
chr1D
3708576
3711581
3005
True
3557.000000
3557
88.053000
3
3068
1
chr1D.!!$R1
3065
2
TraesCS1D01G009900
chr1D
5139396
5141257
1861
False
1930.000000
1930
85.714000
1208
3068
1
chr1D.!!$F2
1860
3
TraesCS1D01G009900
chr1D
3824699
3826365
1666
True
1797.000000
1797
86.159000
1013
2732
1
chr1D.!!$R2
1719
4
TraesCS1D01G009900
chr1D
84072
85421
1349
False
1472.000000
1472
87.130000
480
1767
1
chr1D.!!$F1
1287
5
TraesCS1D01G009900
chr1D
3841322
3842327
1005
True
1304.000000
1304
90.049000
3
1020
1
chr1D.!!$R3
1017
6
TraesCS1D01G009900
chr1D
7154952
7156339
1387
True
1280.000000
1280
83.889000
1216
2575
1
chr1D.!!$R4
1359
7
TraesCS1D01G009900
chr1D
98698
100974
2276
False
752.000000
1077
84.222667
430
2573
3
chr1D.!!$F4
2143
8
TraesCS1D01G009900
chr1D
4342032
4347481
5449
False
492.466667
1234
87.454667
1193
3068
3
chr1D.!!$F5
1875
9
TraesCS1D01G009900
chr1A
6516342
6519421
3079
False
4421.000000
4421
92.707000
5
3068
1
chr1A.!!$F1
3063
10
TraesCS1D01G009900
chr1A
6560632
6562917
2285
False
1657.000000
2562
94.069500
5
2224
2
chr1A.!!$F2
2219
11
TraesCS1D01G009900
chr1A
4203527
4204250
723
True
889.000000
889
89.118000
430
1142
1
chr1A.!!$R1
712
12
TraesCS1D01G009900
chr1A
4095395
4097477
2082
True
744.000000
865
88.056000
435
2322
2
chr1A.!!$R2
1887
13
TraesCS1D01G009900
chr1B
6435847
6437233
1386
True
1336.000000
1336
84.577000
1215
2575
1
chr1B.!!$R2
1360
14
TraesCS1D01G009900
chr1B
5687375
5688349
974
True
1024.000000
1024
85.918000
430
1390
1
chr1B.!!$R1
960
15
TraesCS1D01G009900
chr1B
5584347
5585887
1540
True
639.500000
809
85.155000
671
1767
2
chr1B.!!$R4
1096
16
TraesCS1D01G009900
chr1B
22185385
22191453
6068
False
534.850000
1225
86.943750
735
3068
4
chr1B.!!$F2
2333
17
TraesCS1D01G009900
chr1B
8156579
8159975
3396
False
222.566667
339
95.824333
72
2692
3
chr1B.!!$F1
2620
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.