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
TraesCS7B01G390800
chr7B
100.000
2550
0
0
1
2550
657478342
657480891
0.000000e+00
4710.0
1
TraesCS7B01G390800
chr7B
99.249
1998
13
1
1
1996
657495276
657497273
0.000000e+00
3605.0
2
TraesCS7B01G390800
chr7B
95.000
340
17
0
1228
1567
657500720
657501059
3.730000e-148
534.0
3
TraesCS7B01G390800
chr7B
98.104
211
4
0
2074
2284
657497273
657497483
4.010000e-98
368.0
4
TraesCS7B01G390800
chr7B
89.177
231
15
5
1853
2081
657532241
657532463
1.930000e-71
279.0
5
TraesCS7B01G390800
chr7B
87.342
79
3
1
1751
1829
657532116
657532187
1.630000e-12
84.2
6
TraesCS7B01G390800
chr7D
89.339
1013
48
23
637
1602
586783155
586784154
0.000000e+00
1218.0
7
TraesCS7B01G390800
chr7D
91.948
534
40
2
1
531
586782623
586782090
0.000000e+00
745.0
8
TraesCS7B01G390800
chr7D
91.418
536
24
12
1157
1682
586765838
586766361
0.000000e+00
715.0
9
TraesCS7B01G390800
chr7D
90.772
531
46
3
1
531
586764821
586764294
0.000000e+00
706.0
10
TraesCS7B01G390800
chr7D
89.423
520
30
8
637
1145
586765356
586765861
1.290000e-177
632.0
11
TraesCS7B01G390800
chr7D
98.165
109
2
0
2119
2227
586766740
586766848
9.310000e-45
191.0
12
TraesCS7B01G390800
chr7D
98.058
103
2
0
533
635
586764863
586764965
2.020000e-41
180.0
13
TraesCS7B01G390800
chr7D
97.087
103
3
0
533
635
586782665
586782767
9.380000e-40
174.0
14
TraesCS7B01G390800
chr7A
89.762
840
35
22
739
1561
677871128
677871933
0.000000e+00
1027.0
15
TraesCS7B01G390800
chr7A
84.518
394
29
14
1853
2225
677872457
677872839
6.710000e-96
361.0
16
TraesCS7B01G390800
chr5B
94.891
274
8
3
2278
2550
281571140
281570872
8.430000e-115
424.0
17
TraesCS7B01G390800
chr5B
94.203
276
10
4
2276
2550
63251589
63251859
1.410000e-112
416.0
18
TraesCS7B01G390800
chr5B
94.495
109
6
0
998
1106
445173802
445173910
4.360000e-38
169.0
19
TraesCS7B01G390800
chr6B
93.972
282
12
4
2269
2550
695731235
695730959
3.030000e-114
422.0
20
TraesCS7B01G390800
chr6B
94.545
275
10
1
2276
2550
165072590
165072321
1.090000e-113
420.0
21
TraesCS7B01G390800
chr1B
94.585
277
8
4
2275
2550
295769576
295769306
3.030000e-114
422.0
22
TraesCS7B01G390800
chr1B
94.505
273
9
2
2279
2550
104950820
104950553
1.410000e-112
416.0
23
TraesCS7B01G390800
chr1B
87.037
216
28
0
1228
1443
428801992
428802207
7.050000e-61
244.0
24
TraesCS7B01G390800
chr1B
85.294
102
13
2
1439
1539
428802292
428802392
1.250000e-18
104.0
25
TraesCS7B01G390800
chr3B
95.149
268
7
2
2283
2550
734166415
734166154
3.920000e-113
418.0
26
TraesCS7B01G390800
chr3B
93.310
284
10
5
2271
2550
401515636
401515358
6.570000e-111
411.0
27
TraesCS7B01G390800
chr2A
94.203
276
10
2
2275
2550
18195187
18195456
1.410000e-112
416.0
28
TraesCS7B01G390800
chr2A
94.118
34
2
0
7
40
779429657
779429690
5.000000e-03
52.8
29
TraesCS7B01G390800
chr2A
96.774
31
1
0
10
40
779526378
779526408
5.000000e-03
52.8
30
TraesCS7B01G390800
chr2A
96.774
31
1
0
10
40
779625884
779625914
5.000000e-03
52.8
31
TraesCS7B01G390800
chr1D
87.037
216
28
0
1228
1443
316678681
316678896
7.050000e-61
244.0
32
TraesCS7B01G390800
chr1D
85.484
186
25
2
948
1132
316678382
316678566
2.590000e-45
193.0
33
TraesCS7B01G390800
chr1A
87.037
216
28
0
1228
1443
397770015
397770230
7.050000e-61
244.0
34
TraesCS7B01G390800
chr1A
86.145
166
23
0
966
1131
397769736
397769901
2.020000e-41
180.0
35
TraesCS7B01G390800
chr4D
93.130
131
9
0
1229
1359
3588484
3588354
2.590000e-45
193.0
36
TraesCS7B01G390800
chr6A
95.327
107
5
0
999
1105
129316997
129317103
1.210000e-38
171.0
37
TraesCS7B01G390800
chr5D
92.920
113
8
0
998
1110
373763090
373763202
5.640000e-37
165.0
38
TraesCS7B01G390800
chr5D
82.524
103
17
1
4
106
406482600
406482499
3.490000e-14
89.8
39
TraesCS7B01G390800
chr5D
95.455
44
2
0
4
47
445190990
445191033
1.270000e-08
71.3
40
TraesCS7B01G390800
chr6D
93.519
108
7
0
999
1106
106048845
106048952
7.300000e-36
161.0
41
TraesCS7B01G390800
chr5A
93.478
46
3
0
2
47
562492702
562492747
4.550000e-08
69.4
42
TraesCS7B01G390800
chr4A
81.481
81
12
2
553
632
479421445
479421367
2.120000e-06
63.9
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
TraesCS7B01G390800
chr7B
657478342
657480891
2549
False
4710.000000
4710
100.0000
1
2550
1
chr7B.!!$F1
2549
1
TraesCS7B01G390800
chr7B
657495276
657501059
5783
False
1502.333333
3605
97.4510
1
2284
3
chr7B.!!$F2
2283
2
TraesCS7B01G390800
chr7D
586782090
586782623
533
True
745.000000
745
91.9480
1
531
1
chr7D.!!$R2
530
3
TraesCS7B01G390800
chr7D
586764294
586764821
527
True
706.000000
706
90.7720
1
531
1
chr7D.!!$R1
530
4
TraesCS7B01G390800
chr7D
586782665
586784154
1489
False
696.000000
1218
93.2130
533
1602
2
chr7D.!!$F2
1069
5
TraesCS7B01G390800
chr7D
586764863
586766848
1985
False
429.500000
715
94.2660
533
2227
4
chr7D.!!$F1
1694
6
TraesCS7B01G390800
chr7A
677871128
677872839
1711
False
694.000000
1027
87.1400
739
2225
2
chr7A.!!$F1
1486
7
TraesCS7B01G390800
chr1D
316678382
316678896
514
False
218.500000
244
86.2605
948
1443
2
chr1D.!!$F1
495
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.