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
TraesCS3B01G431300
chr3B
100.000
3107
0
0
580
3686
670345916
670349022
0.000000e+00
5738.0
1
TraesCS3B01G431300
chr3B
90.221
1176
103
11
2514
3686
413565287
413564121
0.000000e+00
1524.0
2
TraesCS3B01G431300
chr3B
89.664
1190
116
6
2501
3686
461803121
461804307
0.000000e+00
1509.0
3
TraesCS3B01G431300
chr3B
82.267
344
44
13
2402
2738
495284139
495284472
7.790000e-72
281.0
4
TraesCS3B01G431300
chr3B
100.000
117
0
0
1
117
670345337
670345453
2.230000e-52
217.0
5
TraesCS3B01G431300
chr3B
92.958
142
8
2
2152
2292
498500278
498500418
4.830000e-49
206.0
6
TraesCS3B01G431300
chr3B
92.308
117
9
0
1
117
739186814
739186930
2.280000e-37
167.0
7
TraesCS3B01G431300
chr3B
86.364
154
11
7
2404
2552
495284815
495284963
3.810000e-35
159.0
8
TraesCS3B01G431300
chr3B
87.255
102
13
0
2002
2103
162317885
162317784
2.330000e-22
117.0
9
TraesCS3B01G431300
chr2B
96.855
1240
37
2
1279
2517
289631817
289633055
0.000000e+00
2073.0
10
TraesCS3B01G431300
chr2B
95.487
842
32
4
1279
2118
289633090
289633927
0.000000e+00
1339.0
11
TraesCS3B01G431300
chr2B
89.571
815
67
11
2001
2809
363238362
363239164
0.000000e+00
1018.0
12
TraesCS3B01G431300
chr2B
91.469
715
36
6
580
1294
289630818
289631507
0.000000e+00
959.0
13
TraesCS3B01G431300
chr2B
93.944
611
28
8
2192
2798
289633922
289634527
0.000000e+00
915.0
14
TraesCS3B01G431300
chr2B
87.472
447
47
8
1350
1790
107587639
107588082
1.180000e-139
507.0
15
TraesCS3B01G431300
chr2B
93.249
237
15
1
1051
1286
772257389
772257625
7.580000e-92
348.0
16
TraesCS3B01G431300
chr5B
89.589
1191
112
10
2501
3686
708404470
708405653
0.000000e+00
1502.0
17
TraesCS3B01G431300
chr5B
86.217
341
22
10
2001
2335
620049054
620049375
2.720000e-91
346.0
18
TraesCS3B01G431300
chrUn
88.992
1181
103
11
2512
3686
324100296
324101455
0.000000e+00
1435.0
19
TraesCS3B01G431300
chrUn
88.960
933
94
7
2758
3686
243888142
243887215
0.000000e+00
1144.0
20
TraesCS3B01G431300
chrUn
90.909
264
20
4
782
1043
342002615
342002354
5.860000e-93
351.0
21
TraesCS3B01G431300
chrUn
90.909
264
20
4
782
1043
358505888
358505627
5.860000e-93
351.0
22
TraesCS3B01G431300
chrUn
90.152
264
22
4
782
1043
314193864
314194125
1.270000e-89
340.0
23
TraesCS3B01G431300
chrUn
90.152
264
22
4
782
1043
320966952
320966691
1.270000e-89
340.0
24
TraesCS3B01G431300
chrUn
89.773
264
23
4
782
1043
314190140
314190401
5.900000e-88
335.0
25
TraesCS3B01G431300
chrUn
93.162
117
8
0
1
117
229634771
229634887
4.890000e-39
172.0
26
TraesCS3B01G431300
chr4A
87.721
1189
133
12
2501
3686
25135462
25136640
0.000000e+00
1375.0
27
TraesCS3B01G431300
chr4A
90.639
876
73
8
2815
3686
93497146
93498016
0.000000e+00
1155.0
28
TraesCS3B01G431300
chr4A
96.330
109
4
0
9
117
715586815
715586707
2.920000e-41
180.0
29
TraesCS3B01G431300
chr4A
85.000
80
10
2
2029
2107
199922361
199922283
3.050000e-11
80.5
30
TraesCS3B01G431300
chr7D
88.673
1130
110
13
2501
3622
154587888
154586769
0.000000e+00
1362.0
31
TraesCS3B01G431300
chr7D
82.979
188
11
10
1051
1237
527923684
527923851
2.290000e-32
150.0
32
TraesCS3B01G431300
chr1B
95.495
777
30
5
2913
3686
143600759
143599985
0.000000e+00
1236.0
33
TraesCS3B01G431300
chr1B
94.074
810
41
6
2001
2809
403001776
403002579
0.000000e+00
1223.0
34
TraesCS3B01G431300
chr1B
87.926
323
19
5
2001
2320
416144750
416145055
2.710000e-96
363.0
35
TraesCS3B01G431300
chr1B
88.976
254
22
5
1350
1597
613236696
613236443
3.580000e-80
309.0
36
TraesCS3B01G431300
chr1B
93.277
119
6
1
1
117
205363849
205363731
1.360000e-39
174.0
37
TraesCS3B01G431300
chr7A
90.786
814
60
8
2001
2809
422575109
422574306
0.000000e+00
1074.0
38
TraesCS3B01G431300
chr5D
89.619
867
56
20
2002
2856
193970075
193969231
0.000000e+00
1072.0
39
TraesCS3B01G431300
chr6B
89.394
462
47
2
582
1043
154908759
154909218
6.860000e-162
580.0
40
TraesCS3B01G431300
chr7B
94.690
113
6
0
5
117
587928371
587928259
3.780000e-40
176.0
41
TraesCS3B01G431300
chr7B
93.913
115
7
0
1
115
700748675
700748789
1.360000e-39
174.0
42
TraesCS3B01G431300
chr7B
93.162
117
8
0
1
117
70947492
70947376
4.890000e-39
172.0
43
TraesCS3B01G431300
chr7B
93.860
114
7
0
1
114
741030325
741030438
4.890000e-39
172.0
44
TraesCS3B01G431300
chr7B
92.373
118
8
1
1
117
611169095
611168978
2.280000e-37
167.0
45
TraesCS3B01G431300
chr7B
79.832
238
37
11
601
835
579437979
579438208
2.950000e-36
163.0
46
TraesCS3B01G431300
chr4B
91.262
103
9
0
2001
2103
340789399
340789297
1.380000e-29
141.0
47
TraesCS3B01G431300
chr4B
77.830
212
35
7
1594
1805
47117022
47116823
1.800000e-23
121.0
48
TraesCS3B01G431300
chr2A
81.579
152
22
6
624
772
617936683
617936535
1.800000e-23
121.0
49
TraesCS3B01G431300
chr1A
90.000
90
9
0
1482
1571
543951532
543951443
2.330000e-22
117.0
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
TraesCS3B01G431300
chr3B
670345337
670349022
3685
False
2977.5
5738
100.00000
1
3686
2
chr3B.!!$F5
3685
1
TraesCS3B01G431300
chr3B
413564121
413565287
1166
True
1524.0
1524
90.22100
2514
3686
1
chr3B.!!$R2
1172
2
TraesCS3B01G431300
chr3B
461803121
461804307
1186
False
1509.0
1509
89.66400
2501
3686
1
chr3B.!!$F1
1185
3
TraesCS3B01G431300
chr3B
495284139
495284963
824
False
220.0
281
84.31550
2402
2738
2
chr3B.!!$F4
336
4
TraesCS3B01G431300
chr2B
289630818
289634527
3709
False
1321.5
2073
94.43875
580
2798
4
chr2B.!!$F4
2218
5
TraesCS3B01G431300
chr2B
363238362
363239164
802
False
1018.0
1018
89.57100
2001
2809
1
chr2B.!!$F2
808
6
TraesCS3B01G431300
chr5B
708404470
708405653
1183
False
1502.0
1502
89.58900
2501
3686
1
chr5B.!!$F2
1185
7
TraesCS3B01G431300
chrUn
324100296
324101455
1159
False
1435.0
1435
88.99200
2512
3686
1
chrUn.!!$F2
1174
8
TraesCS3B01G431300
chrUn
243887215
243888142
927
True
1144.0
1144
88.96000
2758
3686
1
chrUn.!!$R1
928
9
TraesCS3B01G431300
chrUn
314190140
314194125
3985
False
337.5
340
89.96250
782
1043
2
chrUn.!!$F3
261
10
TraesCS3B01G431300
chr4A
25135462
25136640
1178
False
1375.0
1375
87.72100
2501
3686
1
chr4A.!!$F1
1185
11
TraesCS3B01G431300
chr4A
93497146
93498016
870
False
1155.0
1155
90.63900
2815
3686
1
chr4A.!!$F2
871
12
TraesCS3B01G431300
chr7D
154586769
154587888
1119
True
1362.0
1362
88.67300
2501
3622
1
chr7D.!!$R1
1121
13
TraesCS3B01G431300
chr1B
143599985
143600759
774
True
1236.0
1236
95.49500
2913
3686
1
chr1B.!!$R1
773
14
TraesCS3B01G431300
chr1B
403001776
403002579
803
False
1223.0
1223
94.07400
2001
2809
1
chr1B.!!$F1
808
15
TraesCS3B01G431300
chr7A
422574306
422575109
803
True
1074.0
1074
90.78600
2001
2809
1
chr7A.!!$R1
808
16
TraesCS3B01G431300
chr5D
193969231
193970075
844
True
1072.0
1072
89.61900
2002
2856
1
chr5D.!!$R1
854
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.