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
TraesCS2D01G402300
chr2D
100.000
3989
0
0
1
3989
517085192
517089180
0.000000e+00
7367.0
1
TraesCS2D01G402300
chr2D
84.049
1235
126
26
1985
3196
516925468
516926654
0.000000e+00
1123.0
2
TraesCS2D01G402300
chr2D
82.622
1312
131
45
747
2002
516924152
516925422
0.000000e+00
1070.0
3
TraesCS2D01G402300
chr2D
86.658
757
71
18
1158
1906
517037468
517038202
0.000000e+00
811.0
4
TraesCS2D01G402300
chr2D
91.573
534
26
11
1990
2504
517038200
517038733
0.000000e+00
719.0
5
TraesCS2D01G402300
chr2D
85.466
633
53
12
2926
3527
517045911
517046535
1.220000e-174
623.0
6
TraesCS2D01G402300
chr2D
86.332
578
59
5
2092
2649
516863240
516863817
2.640000e-171
612.0
7
TraesCS2D01G402300
chr2D
81.669
731
95
19
211
936
516872112
516872808
4.470000e-159
571.0
8
TraesCS2D01G402300
chr2D
89.912
456
22
7
2497
2932
517045421
517045872
2.080000e-157
566.0
9
TraesCS2D01G402300
chr2D
83.775
604
61
12
294
886
517036584
517037161
4.540000e-149
538.0
10
TraesCS2D01G402300
chr2D
78.182
825
91
41
1164
1969
516862426
516863180
1.020000e-120
444.0
11
TraesCS2D01G402300
chr2D
92.115
279
21
1
1
278
516970117
516970395
3.740000e-105
392.0
12
TraesCS2D01G402300
chr2D
81.120
482
67
12
2724
3185
516863863
516864340
8.150000e-97
364.0
13
TraesCS2D01G402300
chr2D
83.146
356
43
12
109
464
516923548
516923886
3.870000e-80
309.0
14
TraesCS2D01G402300
chr2D
75.622
201
31
12
668
864
516861661
516861847
2.550000e-12
84.2
15
TraesCS2D01G402300
chr2D
92.500
40
3
0
908
947
516856649
516856688
1.550000e-04
58.4
16
TraesCS2D01G402300
chr2D
94.595
37
1
1
1058
1093
516862327
516862363
5.570000e-04
56.5
17
TraesCS2D01G402300
chr2A
95.035
1571
61
8
523
2079
661446240
661447807
0.000000e+00
2453.0
18
TraesCS2D01G402300
chr2A
93.548
1302
41
9
2070
3355
661448214
661449488
0.000000e+00
1899.0
19
TraesCS2D01G402300
chr2A
88.969
970
46
17
2011
2932
661395340
661396296
0.000000e+00
1142.0
20
TraesCS2D01G402300
chr2A
83.081
1188
121
39
864
2002
661151209
661152365
0.000000e+00
1007.0
21
TraesCS2D01G402300
chr2A
86.093
906
82
24
1
886
661393054
661393935
0.000000e+00
935.0
22
TraesCS2D01G402300
chr2A
85.375
841
79
20
1158
1975
661394536
661395355
0.000000e+00
832.0
23
TraesCS2D01G402300
chr2A
83.212
685
76
14
1985
2649
661152412
661153077
3.430000e-165
592.0
24
TraesCS2D01G402300
chr2A
85.269
577
63
6
2092
2647
661082678
661083253
3.460000e-160
575.0
25
TraesCS2D01G402300
chr2A
95.775
355
15
0
1
355
661436095
661436449
1.240000e-159
573.0
26
TraesCS2D01G402300
chr2A
92.365
406
24
3
3349
3751
661449520
661449921
4.470000e-159
571.0
27
TraesCS2D01G402300
chr2A
87.064
487
49
5
2718
3196
661153107
661153587
4.540000e-149
538.0
28
TraesCS2D01G402300
chr2A
82.121
660
79
22
3349
3989
661405060
661405699
2.730000e-146
529.0
29
TraesCS2D01G402300
chr2A
77.706
924
112
45
1064
1969
661081767
661082614
2.790000e-131
479.0
30
TraesCS2D01G402300
chr2A
90.529
359
29
4
2999
3352
661403477
661403835
1.680000e-128
470.0
31
TraesCS2D01G402300
chr2A
88.971
272
18
4
624
886
661394060
661394328
3.840000e-85
326.0
32
TraesCS2D01G402300
chr2A
90.837
251
12
6
3749
3989
661450044
661450293
3.840000e-85
326.0
33
TraesCS2D01G402300
chr2A
92.063
189
10
1
342
525
661436737
661436925
1.100000e-65
261.0
34
TraesCS2D01G402300
chr2A
86.413
184
12
5
779
950
661149031
661149213
5.260000e-44
189.0
35
TraesCS2D01G402300
chr2A
94.828
58
3
0
575
632
661151122
661151179
1.530000e-14
91.6
36
TraesCS2D01G402300
chr2B
89.235
994
52
20
1990
2932
608802723
608803712
0.000000e+00
1192.0
37
TraesCS2D01G402300
chr2B
83.225
1228
123
30
1989
3193
608668011
608669178
0.000000e+00
1050.0
38
TraesCS2D01G402300
chr2B
82.642
1181
120
42
864
2002
608666791
608667928
0.000000e+00
966.0
39
TraesCS2D01G402300
chr2B
85.809
909
101
13
1
891
608800721
608801619
0.000000e+00
939.0
40
TraesCS2D01G402300
chr2B
85.828
755
78
14
1158
1906
608801994
608802725
0.000000e+00
774.0
41
TraesCS2D01G402300
chr2B
86.183
579
59
6
2092
2649
608540838
608541416
1.230000e-169
606.0
42
TraesCS2D01G402300
chr2B
78.017
928
103
51
1064
1966
608539924
608540775
1.290000e-134
490.0
43
TraesCS2D01G402300
chr2B
90.997
311
23
3
2953
3260
608803770
608804078
7.980000e-112
414.0
44
TraesCS2D01G402300
chr2B
80.866
554
59
21
113
664
608666263
608666771
3.740000e-105
392.0
45
TraesCS2D01G402300
chr2B
80.658
486
69
14
2721
3186
608541458
608541938
1.760000e-93
353.0
46
TraesCS2D01G402300
chr2B
91.367
139
11
1
3349
3487
608804313
608804450
5.260000e-44
189.0
47
TraesCS2D01G402300
chr2B
75.714
210
33
10
659
864
608539172
608539367
5.490000e-14
89.8
48
TraesCS2D01G402300
chr1B
77.322
926
109
46
1064
1969
676246687
676247531
1.690000e-123
453.0
49
TraesCS2D01G402300
chr1B
78.040
551
75
28
1058
1601
491697484
491697995
5.010000e-79
305.0
50
TraesCS2D01G402300
chr1B
77.966
295
45
9
266
551
280168268
280167985
2.470000e-37
167.0
51
TraesCS2D01G402300
chr1B
76.923
273
44
13
282
545
62086847
62086585
1.930000e-28
137.0
52
TraesCS2D01G402300
chr1B
83.962
106
9
2
420
517
623838672
623838777
1.180000e-15
95.3
53
TraesCS2D01G402300
chr4A
78.309
544
73
21
1064
1601
541336927
541336423
3.870000e-80
309.0
54
TraesCS2D01G402300
chr4A
81.250
320
27
16
1664
1969
541336410
541336110
1.120000e-55
228.0
55
TraesCS2D01G402300
chr4A
77.917
240
29
15
315
545
66560410
66560634
1.160000e-25
128.0
56
TraesCS2D01G402300
chr5B
77.119
236
35
12
319
545
473899223
473899448
7.000000e-23
119.0
57
TraesCS2D01G402300
chr1A
75.801
281
40
16
282
548
356610857
356610591
2.520000e-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
TraesCS2D01G402300
chr2D
517085192
517089180
3988
False
7367.000000
7367
100.000000
1
3989
1
chr2D.!!$F4
3988
1
TraesCS2D01G402300
chr2D
516923548
516926654
3106
False
834.000000
1123
83.272333
109
3196
3
chr2D.!!$F6
3087
2
TraesCS2D01G402300
chr2D
517036584
517038733
2149
False
689.333333
811
87.335333
294
2504
3
chr2D.!!$F7
2210
3
TraesCS2D01G402300
chr2D
517045421
517046535
1114
False
594.500000
623
87.689000
2497
3527
2
chr2D.!!$F8
1030
4
TraesCS2D01G402300
chr2D
516872112
516872808
696
False
571.000000
571
81.669000
211
936
1
chr2D.!!$F2
725
5
TraesCS2D01G402300
chr2D
516861661
516864340
2679
False
312.140000
612
83.170200
668
3185
5
chr2D.!!$F5
2517
6
TraesCS2D01G402300
chr2A
661446240
661450293
4053
False
1312.250000
2453
92.946250
523
3989
4
chr2A.!!$F6
3466
7
TraesCS2D01G402300
chr2A
661393054
661396296
3242
False
808.750000
1142
87.352000
1
2932
4
chr2A.!!$F3
2931
8
TraesCS2D01G402300
chr2A
661081767
661083253
1486
False
527.000000
575
81.487500
1064
2647
2
chr2A.!!$F1
1583
9
TraesCS2D01G402300
chr2A
661403477
661405699
2222
False
499.500000
529
86.325000
2999
3989
2
chr2A.!!$F4
990
10
TraesCS2D01G402300
chr2A
661149031
661153587
4556
False
483.520000
1007
86.919600
575
3196
5
chr2A.!!$F2
2621
11
TraesCS2D01G402300
chr2A
661436095
661436925
830
False
417.000000
573
93.919000
1
525
2
chr2A.!!$F5
524
12
TraesCS2D01G402300
chr2B
608666263
608669178
2915
False
802.666667
1050
82.244333
113
3193
3
chr2B.!!$F2
3080
13
TraesCS2D01G402300
chr2B
608800721
608804450
3729
False
701.600000
1192
88.647200
1
3487
5
chr2B.!!$F3
3486
14
TraesCS2D01G402300
chr2B
608539172
608541938
2766
False
384.700000
606
80.143000
659
3186
4
chr2B.!!$F1
2527
15
TraesCS2D01G402300
chr1B
676246687
676247531
844
False
453.000000
453
77.322000
1064
1969
1
chr1B.!!$F3
905
16
TraesCS2D01G402300
chr1B
491697484
491697995
511
False
305.000000
305
78.040000
1058
1601
1
chr1B.!!$F1
543
17
TraesCS2D01G402300
chr4A
541336110
541336927
817
True
268.500000
309
79.779500
1064
1969
2
chr4A.!!$R1
905
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.