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
TraesCS3B01G203900
chr3B
100.000
3495
0
0
1
3495
237735546
237732052
0.000000e+00
6455.0
1
TraesCS3B01G203900
chr3B
92.221
1774
90
18
1751
3495
237972968
237971214
0.000000e+00
2468.0
2
TraesCS3B01G203900
chr3B
86.469
2121
178
53
1230
3295
238113670
238111604
0.000000e+00
2226.0
3
TraesCS3B01G203900
chr3B
92.598
743
44
4
999
1730
237973767
237973025
0.000000e+00
1057.0
4
TraesCS3B01G203900
chr3B
88.554
830
70
8
1
806
237978166
237977338
0.000000e+00
983.0
5
TraesCS3B01G203900
chr3B
84.112
107
2
3
904
995
237977215
237977109
4.800000e-14
89.8
6
TraesCS3B01G203900
chr3B
97.500
40
1
0
3317
3356
238111608
238111569
6.260000e-08
69.4
7
TraesCS3B01G203900
chr3A
94.919
2539
85
13
999
3495
190094896
190092360
0.000000e+00
3934.0
8
TraesCS3B01G203900
chr3A
86.625
2056
175
53
1289
3295
190228970
190226966
0.000000e+00
2182.0
9
TraesCS3B01G203900
chr3A
86.768
2033
169
55
1289
3272
191253952
191251971
0.000000e+00
2172.0
10
TraesCS3B01G203900
chr3A
89.483
1759
128
25
1
1730
191008849
191007119
0.000000e+00
2170.0
11
TraesCS3B01G203900
chr3A
88.243
1582
114
36
1751
3293
191006604
191005056
0.000000e+00
1825.0
12
TraesCS3B01G203900
chr3A
95.221
1088
28
3
1480
2548
188112420
188113502
0.000000e+00
1700.0
13
TraesCS3B01G203900
chr3A
95.716
957
26
10
2541
3495
188113380
188114323
0.000000e+00
1526.0
14
TraesCS3B01G203900
chr3A
92.802
903
54
8
1
897
188100174
188101071
0.000000e+00
1297.0
15
TraesCS3B01G203900
chr3A
88.560
1014
79
18
1
997
190096169
190095176
0.000000e+00
1195.0
16
TraesCS3B01G203900
chr3A
92.962
611
23
7
897
1488
188101147
188101756
0.000000e+00
872.0
17
TraesCS3B01G203900
chr3A
85.374
294
40
2
1289
1582
190582899
190582609
5.670000e-78
302.0
18
TraesCS3B01G203900
chr3A
89.922
129
12
1
3367
3495
191004979
191004852
7.760000e-37
165.0
19
TraesCS3B01G203900
chr3A
89.922
129
12
1
3367
3495
191251764
191251637
7.760000e-37
165.0
20
TraesCS3B01G203900
chr3A
88.189
127
14
1
3369
3495
190226888
190226763
2.170000e-32
150.0
21
TraesCS3B01G203900
chr3A
93.651
63
3
1
1022
1084
190229119
190229058
3.710000e-15
93.5
22
TraesCS3B01G203900
chr3A
93.651
63
3
1
1022
1084
191254101
191254040
3.710000e-15
93.5
23
TraesCS3B01G203900
chr3A
89.231
65
6
1
3317
3381
191251846
191251783
2.890000e-11
80.5
24
TraesCS3B01G203900
chr3A
89.831
59
5
1
3323
3381
191005052
191004995
1.350000e-09
75.0
25
TraesCS3B01G203900
chr3D
96.749
2307
40
8
1223
3495
161401874
161399569
0.000000e+00
3812.0
26
TraesCS3B01G203900
chr3D
91.425
1761
109
19
1
1730
161499770
161498021
0.000000e+00
2377.0
27
TraesCS3B01G203900
chr3D
87.889
1866
155
36
1232
3049
161596742
161594900
0.000000e+00
2128.0
28
TraesCS3B01G203900
chr3D
88.980
1579
108
30
1751
3295
161497955
161496409
0.000000e+00
1892.0
29
TraesCS3B01G203900
chr3D
95.959
1163
37
7
1
1157
161403736
161402578
0.000000e+00
1879.0
30
TraesCS3B01G203900
chr3D
89.922
129
12
1
3367
3495
161496333
161496206
7.760000e-37
165.0
31
TraesCS3B01G203900
chr3D
88.372
129
13
2
3367
3495
161594605
161594479
1.680000e-33
154.0
32
TraesCS3B01G203900
chr3D
94.681
94
5
0
1
94
161438936
161438843
2.810000e-31
147.0
33
TraesCS3B01G203900
chr3D
90.476
63
5
1
1022
1084
161596819
161596758
8.040000e-12
82.4
34
TraesCS3B01G203900
chr3D
93.750
48
3
0
3317
3364
161496413
161496366
4.840000e-09
73.1
35
TraesCS3B01G203900
chr3D
97.500
40
1
0
3317
3356
161594684
161594645
6.260000e-08
69.4
36
TraesCS3B01G203900
chr6D
88.344
163
14
3
550
707
281926087
281926249
1.280000e-44
191.0
37
TraesCS3B01G203900
chr6D
100.000
34
0
0
864
897
452414539
452414572
2.910000e-06
63.9
38
TraesCS3B01G203900
chr7D
80.214
187
25
10
714
897
579794562
579794385
2.830000e-26
130.0
39
TraesCS3B01G203900
chr2D
80.588
170
21
10
730
897
124318470
124318311
1.700000e-23
121.0
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
TraesCS3B01G203900
chr3B
237732052
237735546
3494
True
6455.000
6455
100.000000
1
3495
1
chr3B.!!$R1
3494
1
TraesCS3B01G203900
chr3B
237971214
237978166
6952
True
1149.450
2468
89.371250
1
3495
4
chr3B.!!$R2
3494
2
TraesCS3B01G203900
chr3B
238111569
238113670
2101
True
1147.700
2226
91.984500
1230
3356
2
chr3B.!!$R3
2126
3
TraesCS3B01G203900
chr3A
190092360
190096169
3809
True
2564.500
3934
91.739500
1
3495
2
chr3A.!!$R2
3494
4
TraesCS3B01G203900
chr3A
188112420
188114323
1903
False
1613.000
1700
95.468500
1480
3495
2
chr3A.!!$F2
2015
5
TraesCS3B01G203900
chr3A
188100174
188101756
1582
False
1084.500
1297
92.882000
1
1488
2
chr3A.!!$F1
1487
6
TraesCS3B01G203900
chr3A
191004852
191008849
3997
True
1058.750
2170
89.369750
1
3495
4
chr3A.!!$R4
3494
7
TraesCS3B01G203900
chr3A
190226763
190229119
2356
True
808.500
2182
89.488333
1022
3495
3
chr3A.!!$R3
2473
8
TraesCS3B01G203900
chr3A
191251637
191254101
2464
True
627.750
2172
89.893000
1022
3495
4
chr3A.!!$R5
2473
9
TraesCS3B01G203900
chr3D
161399569
161403736
4167
True
2845.500
3812
96.354000
1
3495
2
chr3D.!!$R2
3494
10
TraesCS3B01G203900
chr3D
161496206
161499770
3564
True
1126.775
2377
91.019250
1
3495
4
chr3D.!!$R3
3494
11
TraesCS3B01G203900
chr3D
161594479
161596819
2340
True
608.450
2128
91.059250
1022
3495
4
chr3D.!!$R4
2473
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.