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
TraesCS7A01G130800
chr7A
100.000
4879
0
0
1
4879
84249235
84244357
0.000000e+00
9010.0
1
TraesCS7A01G130800
chr7A
78.243
979
139
42
719
1664
78217301
78218238
1.190000e-155
560.0
2
TraesCS7A01G130800
chr7A
76.273
864
132
41
778
1615
78387964
78388780
4.580000e-105
392.0
3
TraesCS7A01G130800
chr7A
75.299
668
109
30
1859
2501
84026351
84025715
8.050000e-68
268.0
4
TraesCS7A01G130800
chr7A
100.000
36
0
0
1825
1860
84026406
84026371
3.150000e-07
67.6
5
TraesCS7A01G130800
chr7D
93.365
2984
106
23
411
3370
82449896
82446981
0.000000e+00
4329.0
6
TraesCS7A01G130800
chr7D
94.703
1548
45
10
3366
4879
82446947
82445403
0.000000e+00
2370.0
7
TraesCS7A01G130800
chr7D
79.529
552
85
17
1069
1612
82349141
82348610
7.720000e-98
368.0
8
TraesCS7A01G130800
chr7D
75.888
676
119
23
1859
2501
82348553
82347889
6.140000e-79
305.0
9
TraesCS7A01G130800
chr7D
81.786
280
29
12
3387
3659
82347819
82347555
1.060000e-51
215.0
10
TraesCS7A01G130800
chr7D
82.949
217
23
5
3401
3617
74393772
74393974
3.000000e-42
183.0
11
TraesCS7A01G130800
chr7D
82.911
158
20
5
2097
2250
73180287
73180441
8.520000e-28
135.0
12
TraesCS7A01G130800
chr7D
83.168
101
12
5
2381
2476
73180527
73180627
2.420000e-13
87.9
13
TraesCS7A01G130800
chr7D
88.525
61
7
0
157
217
388967249
388967189
1.880000e-09
75.0
14
TraesCS7A01G130800
chr7B
91.287
2835
155
40
578
3368
29830479
29827693
0.000000e+00
3783.0
15
TraesCS7A01G130800
chr7B
91.052
2671
148
31
199
2840
31448975
31446367
0.000000e+00
3524.0
16
TraesCS7A01G130800
chr7B
94.675
1521
69
4
1861
3370
30765400
30763881
0.000000e+00
2350.0
17
TraesCS7A01G130800
chr7B
90.464
1552
80
22
3366
4879
30763847
30762326
0.000000e+00
1984.0
18
TraesCS7A01G130800
chr7B
92.703
1069
35
11
3366
4392
31441774
31440707
0.000000e+00
1502.0
19
TraesCS7A01G130800
chr7B
92.596
986
31
10
3923
4879
29827005
29826033
0.000000e+00
1378.0
20
TraesCS7A01G130800
chr7B
90.164
1098
51
9
761
1836
30766456
30765394
0.000000e+00
1376.0
21
TraesCS7A01G130800
chr7B
89.410
1067
66
19
2327
3370
31442850
31441808
0.000000e+00
1301.0
22
TraesCS7A01G130800
chr7B
89.581
979
59
14
2221
3189
31444966
31444021
0.000000e+00
1203.0
23
TraesCS7A01G130800
chr7B
94.241
573
18
3
3366
3925
29827657
29827087
0.000000e+00
861.0
24
TraesCS7A01G130800
chr7B
96.705
516
14
2
2857
3370
31446379
31445865
0.000000e+00
856.0
25
TraesCS7A01G130800
chr7B
87.683
682
29
14
1295
1976
31445681
31445055
0.000000e+00
743.0
26
TraesCS7A01G130800
chr7B
80.182
661
93
20
1012
1664
16950969
16951599
1.240000e-125
460.0
27
TraesCS7A01G130800
chr7B
94.218
294
16
1
4587
4879
31440698
31440405
9.630000e-122
448.0
28
TraesCS7A01G130800
chr7B
79.537
562
87
17
1063
1616
29608521
29607980
4.610000e-100
375.0
29
TraesCS7A01G130800
chr7B
84.521
407
32
10
199
602
30770206
30769828
1.660000e-99
374.0
30
TraesCS7A01G130800
chr7B
75.706
531
86
22
1859
2354
29607933
29607411
4.910000e-55
226.0
31
TraesCS7A01G130800
chr7B
91.975
162
5
2
3366
3527
31445831
31445678
2.290000e-53
220.0
32
TraesCS7A01G130800
chr7B
84.158
101
12
3
3989
4086
30763151
30763052
1.450000e-15
95.3
33
TraesCS7A01G130800
chr7B
100.000
39
0
0
75
113
31449069
31449031
6.770000e-09
73.1
34
TraesCS7A01G130800
chr7B
97.436
39
1
0
75
113
30770300
30770262
3.150000e-07
67.6
35
TraesCS7A01G130800
chr7B
100.000
28
0
0
1012
1039
29608558
29608531
9.000000e-03
52.8
36
TraesCS7A01G130800
chr2B
79.127
733
95
38
2596
3302
601733596
601734296
2.070000e-123
453.0
37
TraesCS7A01G130800
chr2B
78.104
749
112
32
2596
3321
675713760
675714479
1.250000e-115
427.0
38
TraesCS7A01G130800
chr2B
78.738
301
39
18
3366
3662
55201808
55201529
1.400000e-40
178.0
39
TraesCS7A01G130800
chr2B
85.507
138
20
0
2105
2242
54786418
54786281
1.420000e-30
145.0
40
TraesCS7A01G130800
chr2B
83.544
158
22
4
2107
2262
122993563
122993718
1.420000e-30
145.0
41
TraesCS7A01G130800
chr2B
78.924
223
37
9
3367
3589
122928865
122929077
5.090000e-30
143.0
42
TraesCS7A01G130800
chr2B
81.250
96
16
2
128
222
701750068
701750162
5.240000e-10
76.8
43
TraesCS7A01G130800
chr2B
100.000
28
0
0
1588
1615
54887355
54887328
9.000000e-03
52.8
44
TraesCS7A01G130800
chr6A
78.075
748
108
36
2596
3317
561602197
561601480
5.840000e-114
422.0
45
TraesCS7A01G130800
chr6A
77.193
228
28
16
3366
3588
31741138
31741346
1.440000e-20
111.0
46
TraesCS7A01G130800
chr4A
77.064
654
97
27
858
1485
648880529
648881155
1.310000e-85
327.0
47
TraesCS7A01G130800
chr4A
88.710
62
3
3
169
227
646820609
646820549
6.770000e-09
73.1
48
TraesCS7A01G130800
chr3B
81.778
225
21
14
3366
3588
229463761
229463967
2.340000e-38
171.0
49
TraesCS7A01G130800
chr2A
83.735
166
26
1
2105
2269
36399233
36399068
6.540000e-34
156.0
50
TraesCS7A01G130800
chr2A
82.822
163
25
3
2105
2265
36410900
36410739
5.090000e-30
143.0
51
TraesCS7A01G130800
chr2A
100.000
28
0
0
1588
1615
36202236
36202209
9.000000e-03
52.8
52
TraesCS7A01G130800
chr2D
76.821
302
40
21
3366
3662
33313608
33313332
5.090000e-30
143.0
53
TraesCS7A01G130800
chr1D
85.859
99
12
2
125
222
28185735
28185638
2.400000e-18
104.0
54
TraesCS7A01G130800
chr5B
86.364
66
9
0
168
233
89029098
89029163
6.770000e-09
73.1
55
TraesCS7A01G130800
chr5B
85.075
67
7
3
173
238
391143620
391143684
1.130000e-06
65.8
56
TraesCS7A01G130800
chr5D
88.333
60
6
1
173
231
420882189
420882130
2.440000e-08
71.3
57
TraesCS7A01G130800
chr5D
85.938
64
9
0
153
216
375409241
375409304
8.760000e-08
69.4
58
TraesCS7A01G130800
chr5D
86.885
61
8
0
157
217
423328400
423328460
8.760000e-08
69.4
59
TraesCS7A01G130800
chr6D
97.222
36
1
0
3582
3617
54481445
54481410
1.470000e-05
62.1
60
TraesCS7A01G130800
chr4D
97.222
36
1
0
3582
3617
459211643
459211608
1.470000e-05
62.1
61
TraesCS7A01G130800
chr3D
97.222
36
1
0
3582
3617
231936362
231936397
1.470000e-05
62.1
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
TraesCS7A01G130800
chr7A
84244357
84249235
4878
True
9010.000000
9010
100.000000
1
4879
1
chr7A.!!$R1
4878
1
TraesCS7A01G130800
chr7A
78217301
78218238
937
False
560.000000
560
78.243000
719
1664
1
chr7A.!!$F1
945
2
TraesCS7A01G130800
chr7A
78387964
78388780
816
False
392.000000
392
76.273000
778
1615
1
chr7A.!!$F2
837
3
TraesCS7A01G130800
chr7D
82445403
82449896
4493
True
3349.500000
4329
94.034000
411
4879
2
chr7D.!!$R3
4468
4
TraesCS7A01G130800
chr7D
82347555
82349141
1586
True
296.000000
368
79.067667
1069
3659
3
chr7D.!!$R2
2590
5
TraesCS7A01G130800
chr7B
29826033
29830479
4446
True
2007.333333
3783
92.708000
578
4879
3
chr7B.!!$R2
4301
6
TraesCS7A01G130800
chr7B
31440405
31449069
8664
True
1096.677778
3524
92.591889
75
4879
9
chr7B.!!$R4
4804
7
TraesCS7A01G130800
chr7B
30762326
30770300
7974
True
1041.150000
2350
90.236333
75
4879
6
chr7B.!!$R3
4804
8
TraesCS7A01G130800
chr7B
16950969
16951599
630
False
460.000000
460
80.182000
1012
1664
1
chr7B.!!$F1
652
9
TraesCS7A01G130800
chr7B
29607411
29608558
1147
True
217.933333
375
85.081000
1012
2354
3
chr7B.!!$R1
1342
10
TraesCS7A01G130800
chr2B
601733596
601734296
700
False
453.000000
453
79.127000
2596
3302
1
chr2B.!!$F3
706
11
TraesCS7A01G130800
chr2B
675713760
675714479
719
False
427.000000
427
78.104000
2596
3321
1
chr2B.!!$F4
725
12
TraesCS7A01G130800
chr6A
561601480
561602197
717
True
422.000000
422
78.075000
2596
3317
1
chr6A.!!$R1
721
13
TraesCS7A01G130800
chr4A
648880529
648881155
626
False
327.000000
327
77.064000
858
1485
1
chr4A.!!$F1
627
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.