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
TraesCS2D01G056600
chr2D
100.000
4917
0
0
1
4917
22512305
22507389
0.000000e+00
9081.0
1
TraesCS2D01G056600
chr2D
82.442
2973
442
51
990
3919
30449632
30446697
0.000000e+00
2525.0
2
TraesCS2D01G056600
chr2D
82.403
1398
235
10
1850
3243
22820228
22818838
0.000000e+00
1208.0
3
TraesCS2D01G056600
chr2D
90.646
588
55
0
3333
3920
22818751
22818164
0.000000e+00
782.0
4
TraesCS2D01G056600
chr2D
78.278
778
140
21
982
1740
22440268
22441035
1.600000e-129
473.0
5
TraesCS2D01G056600
chr2D
83.373
415
59
6
1446
1852
22820500
22820088
4.650000e-100
375.0
6
TraesCS2D01G056600
chr2D
81.696
224
41
0
1017
1240
22820907
22820684
2.340000e-43
187.0
7
TraesCS2D01G056600
chr2D
80.519
154
21
5
275
420
22484414
22484262
5.200000e-20
110.0
8
TraesCS2D01G056600
chr2D
89.394
66
7
0
840
905
22440088
22440153
3.150000e-12
84.2
9
TraesCS2D01G056600
chr2D
100.000
31
0
0
611
641
22439782
22439812
1.910000e-04
58.4
10
TraesCS2D01G056600
chr2B
94.548
3008
118
23
1516
4506
39184434
39187412
0.000000e+00
4604.0
11
TraesCS2D01G056600
chr2B
85.572
2211
295
19
1711
3915
39339962
39337770
0.000000e+00
2294.0
12
TraesCS2D01G056600
chr2B
82.218
2092
336
23
1849
3919
38417220
38419296
0.000000e+00
1770.0
13
TraesCS2D01G056600
chr2B
84.478
1791
243
25
1711
3491
49900548
49898783
0.000000e+00
1735.0
14
TraesCS2D01G056600
chr2B
81.414
2093
345
36
1850
3920
37677759
37679829
0.000000e+00
1670.0
15
TraesCS2D01G056600
chr2B
81.334
2084
357
27
1850
3920
38034384
38036448
0.000000e+00
1664.0
16
TraesCS2D01G056600
chr2B
80.718
1644
289
23
2293
3920
39087024
39088655
0.000000e+00
1254.0
17
TraesCS2D01G056600
chr2B
81.903
1398
239
11
1850
3243
38074070
38075457
0.000000e+00
1168.0
18
TraesCS2D01G056600
chr2B
88.095
588
70
0
3333
3920
38075556
38076143
0.000000e+00
699.0
19
TraesCS2D01G056600
chr2B
76.243
1368
239
43
686
1990
39341303
39339959
0.000000e+00
647.0
20
TraesCS2D01G056600
chr2B
78.503
1042
176
29
984
1990
49901573
49900545
1.490000e-179
640.0
21
TraesCS2D01G056600
chr2B
79.496
595
104
14
1267
1852
37677314
37677899
1.650000e-109
407.0
22
TraesCS2D01G056600
chr2B
91.901
284
15
2
1171
1446
39184158
39184441
1.660000e-104
390.0
23
TraesCS2D01G056600
chr2B
92.417
211
11
5
4697
4905
39187612
39187819
3.720000e-76
296.0
24
TraesCS2D01G056600
chr2B
77.187
583
71
38
4232
4773
39335419
39334858
2.900000e-72
283.0
25
TraesCS2D01G056600
chr2B
80.645
248
48
0
990
1237
38073115
38073362
5.020000e-45
193.0
26
TraesCS2D01G056600
chr2B
80.242
248
49
0
990
1237
38033631
38033878
2.340000e-43
187.0
27
TraesCS2D01G056600
chr2B
97.059
34
1
0
611
644
39341425
39341392
1.910000e-04
58.4
28
TraesCS2D01G056600
chr2B
94.444
36
2
0
4508
4543
39187597
39187632
6.880000e-04
56.5
29
TraesCS2D01G056600
chr2A
98.032
1728
32
2
980
2707
24309389
24307664
0.000000e+00
3001.0
30
TraesCS2D01G056600
chr2A
85.507
2208
299
16
1711
3913
24174241
24176432
0.000000e+00
2285.0
31
TraesCS2D01G056600
chr2A
82.609
2093
326
28
1850
3920
24411822
24409746
0.000000e+00
1814.0
32
TraesCS2D01G056600
chr2A
91.774
778
46
5
129
891
24310228
24309454
0.000000e+00
1066.0
33
TraesCS2D01G056600
chr2A
81.164
584
89
16
1281
1852
24412256
24411682
2.700000e-122
449.0
34
TraesCS2D01G056600
chr2A
88.356
146
13
4
4632
4773
24180252
24180397
6.540000e-39
172.0
35
TraesCS2D01G056600
chr2A
86.614
127
17
0
3938
4064
24176423
24176549
1.850000e-29
141.0
36
TraesCS2D01G056600
chr2A
83.974
156
11
7
4632
4773
24275748
24275903
2.390000e-28
137.0
37
TraesCS2D01G056600
chr2A
96.104
77
3
0
1
77
24310305
24310229
5.170000e-25
126.0
38
TraesCS2D01G056600
chr2A
81.379
145
18
6
4312
4452
24179976
24180115
5.200000e-20
110.0
39
TraesCS2D01G056600
chr7B
86.209
1414
174
14
982
2385
744137109
744138511
0.000000e+00
1511.0
40
TraesCS2D01G056600
chr7B
82.008
1534
232
31
2394
3919
744138571
744140068
0.000000e+00
1264.0
41
TraesCS2D01G056600
chr7B
82.623
305
40
8
6
301
744134718
744135018
1.760000e-64
257.0
42
TraesCS2D01G056600
chr7B
84.892
139
9
4
770
896
744136912
744137050
3.990000e-26
130.0
43
TraesCS2D01G056600
chr7B
79.048
210
27
9
4427
4627
744140759
744140960
1.440000e-25
128.0
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
TraesCS2D01G056600
chr2D
22507389
22512305
4916
True
9081.000000
9081
100.000000
1
4917
1
chr2D.!!$R2
4916
1
TraesCS2D01G056600
chr2D
30446697
30449632
2935
True
2525.000000
2525
82.442000
990
3919
1
chr2D.!!$R3
2929
2
TraesCS2D01G056600
chr2D
22818164
22820907
2743
True
638.000000
1208
84.529500
1017
3920
4
chr2D.!!$R4
2903
3
TraesCS2D01G056600
chr2D
22439782
22441035
1253
False
205.200000
473
89.224000
611
1740
3
chr2D.!!$F1
1129
4
TraesCS2D01G056600
chr2B
38417220
38419296
2076
False
1770.000000
1770
82.218000
1849
3919
1
chr2B.!!$F1
2070
5
TraesCS2D01G056600
chr2B
39184158
39187819
3661
False
1336.625000
4604
93.327500
1171
4905
4
chr2B.!!$F6
3734
6
TraesCS2D01G056600
chr2B
39087024
39088655
1631
False
1254.000000
1254
80.718000
2293
3920
1
chr2B.!!$F2
1627
7
TraesCS2D01G056600
chr2B
49898783
49901573
2790
True
1187.500000
1735
81.490500
984
3491
2
chr2B.!!$R2
2507
8
TraesCS2D01G056600
chr2B
37677314
37679829
2515
False
1038.500000
1670
80.455000
1267
3920
2
chr2B.!!$F3
2653
9
TraesCS2D01G056600
chr2B
38033631
38036448
2817
False
925.500000
1664
80.788000
990
3920
2
chr2B.!!$F4
2930
10
TraesCS2D01G056600
chr2B
39334858
39341425
6567
True
820.600000
2294
84.015250
611
4773
4
chr2B.!!$R1
4162
11
TraesCS2D01G056600
chr2B
38073115
38076143
3028
False
686.666667
1168
83.547667
990
3920
3
chr2B.!!$F5
2930
12
TraesCS2D01G056600
chr2A
24307664
24310305
2641
True
1397.666667
3001
95.303333
1
2707
3
chr2A.!!$R1
2706
13
TraesCS2D01G056600
chr2A
24409746
24412256
2510
True
1131.500000
1814
81.886500
1281
3920
2
chr2A.!!$R2
2639
14
TraesCS2D01G056600
chr2A
24174241
24180397
6156
False
677.000000
2285
85.464000
1711
4773
4
chr2A.!!$F2
3062
15
TraesCS2D01G056600
chr7B
744134718
744140960
6242
False
658.000000
1511
82.956000
6
4627
5
chr7B.!!$F1
4621
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.