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
TraesCS2D01G367800
chr2D
100.000
2483
0
0
2646
5128
472446172
472443690
0.000000e+00
4586.0
1
TraesCS2D01G367800
chr2D
100.000
2283
0
0
1
2283
472448817
472446535
0.000000e+00
4217.0
2
TraesCS2D01G367800
chr2D
81.591
1358
143
67
956
2274
472233959
472232670
0.000000e+00
1024.0
3
TraesCS2D01G367800
chr2D
87.928
497
47
4
3559
4054
472230916
472230432
1.600000e-159
573.0
4
TraesCS2D01G367800
chr2D
88.112
429
41
7
3081
3508
472231649
472231230
7.670000e-138
501.0
5
TraesCS2D01G367800
chr2D
90.598
234
12
5
4900
5126
472230435
472230205
8.340000e-78
302.0
6
TraesCS2D01G367800
chr2B
90.740
1717
113
30
14
1706
551570544
551568850
0.000000e+00
2248.0
7
TraesCS2D01G367800
chr2B
92.857
588
32
8
3547
4128
551566806
551566223
0.000000e+00
845.0
8
TraesCS2D01G367800
chr2B
86.199
826
57
30
2724
3509
551567833
551567025
0.000000e+00
841.0
9
TraesCS2D01G367800
chr2B
89.116
588
52
8
3547
4128
551534621
551534040
0.000000e+00
721.0
10
TraesCS2D01G367800
chr2B
91.829
514
28
7
958
1471
551538523
551538024
0.000000e+00
704.0
11
TraesCS2D01G367800
chr2B
88.739
444
21
11
4683
5121
551566233
551565814
2.740000e-142
516.0
12
TraesCS2D01G367800
chr2B
87.879
429
42
6
3081
3508
551535256
551534837
3.570000e-136
496.0
13
TraesCS2D01G367800
chr2B
90.566
318
24
3
1702
2017
551568739
551568426
2.860000e-112
416.0
14
TraesCS2D01G367800
chr2B
93.585
265
16
1
2016
2279
551568357
551568093
1.340000e-105
394.0
15
TraesCS2D01G367800
chr2B
95.890
73
3
0
4694
4766
551534029
551533957
9.020000e-23
119.0
16
TraesCS2D01G367800
chr2B
74.490
196
39
10
1188
1376
551399549
551399358
1.980000e-09
75.0
17
TraesCS2D01G367800
chr2B
95.455
44
2
0
2935
2978
541012275
541012232
2.560000e-08
71.3
18
TraesCS2D01G367800
chr2B
91.304
46
4
0
2933
2978
338755874
338755919
4.290000e-06
63.9
19
TraesCS2D01G367800
chr2A
92.384
1510
88
21
528
2017
613881118
613879616
0.000000e+00
2126.0
20
TraesCS2D01G367800
chr2A
93.741
1422
64
12
2728
4128
613878902
613877485
0.000000e+00
2109.0
21
TraesCS2D01G367800
chr2A
81.557
1323
143
67
986
2272
613720763
613719506
0.000000e+00
998.0
22
TraesCS2D01G367800
chr2A
87.925
588
57
7
3550
4128
613703427
613702845
0.000000e+00
680.0
23
TraesCS2D01G367800
chr2A
86.712
444
21
17
4683
5121
613877495
613877085
4.680000e-125
459.0
24
TraesCS2D01G367800
chr2A
94.715
246
12
1
3081
3325
613714111
613713866
1.040000e-101
381.0
25
TraesCS2D01G367800
chr2A
83.180
434
37
24
1
425
613881479
613881073
1.050000e-96
364.0
26
TraesCS2D01G367800
chr2A
91.250
240
14
3
2042
2278
613879443
613879208
2.300000e-83
320.0
27
TraesCS2D01G367800
chr2A
91.414
198
11
3
4875
5068
613701060
613700865
3.040000e-67
267.0
28
TraesCS2D01G367800
chr2A
95.122
82
4
0
2646
2727
613879197
613879116
4.170000e-26
130.0
29
TraesCS2D01G367800
chr2A
95.714
70
3
0
4823
4892
613702760
613702691
4.200000e-21
113.0
30
TraesCS2D01G367800
chr4A
89.720
749
53
13
1554
2278
395804892
395805640
0.000000e+00
935.0
31
TraesCS2D01G367800
chr4A
91.549
71
6
0
2646
2716
395805651
395805721
1.180000e-16
99.0
32
TraesCS2D01G367800
chr4A
87.755
49
5
1
2884
2932
633353262
633353215
7.170000e-04
56.5
33
TraesCS2D01G367800
chr4A
100.000
29
0
0
2904
2932
472667634
472667662
3.000000e-03
54.7
34
TraesCS2D01G367800
chr4A
90.476
42
3
1
2891
2932
635932324
635932364
3.000000e-03
54.7
35
TraesCS2D01G367800
chr1D
96.403
556
20
0
4127
4682
250741385
250740830
0.000000e+00
917.0
36
TraesCS2D01G367800
chr1D
95.315
555
26
0
4127
4681
19875235
19874681
0.000000e+00
881.0
37
TraesCS2D01G367800
chr5D
96.558
552
19
0
4127
4678
342525686
342526237
0.000000e+00
915.0
38
TraesCS2D01G367800
chr5D
96.377
552
18
2
4127
4678
397029806
397030355
0.000000e+00
907.0
39
TraesCS2D01G367800
chr5D
93.478
46
1
2
2937
2981
550192076
550192120
3.310000e-07
67.6
40
TraesCS2D01G367800
chrUn
95.691
557
23
1
4127
4683
115109770
115110325
0.000000e+00
894.0
41
TraesCS2D01G367800
chr5B
95.652
552
23
1
4127
4678
318172801
318173351
0.000000e+00
885.0
42
TraesCS2D01G367800
chr4D
95.471
552
25
0
4127
4678
108101239
108101790
0.000000e+00
881.0
43
TraesCS2D01G367800
chr4D
90.385
52
4
1
2933
2983
404666199
404666250
3.310000e-07
67.6
44
TraesCS2D01G367800
chr4D
100.000
29
0
0
2904
2932
312868377
312868349
3.000000e-03
54.7
45
TraesCS2D01G367800
chr1B
95.018
562
26
1
4127
4686
305284870
305284309
0.000000e+00
881.0
46
TraesCS2D01G367800
chr1B
100.000
32
0
0
2903
2934
36260857
36260826
5.540000e-05
60.2
47
TraesCS2D01G367800
chr1B
100.000
32
0
0
2903
2934
36263599
36263568
5.540000e-05
60.2
48
TraesCS2D01G367800
chr1B
100.000
31
0
0
2904
2934
497275994
497276024
1.990000e-04
58.4
49
TraesCS2D01G367800
chr7D
95.315
555
25
1
4127
4681
136708145
136707592
0.000000e+00
880.0
50
TraesCS2D01G367800
chr7D
100.000
31
0
0
2904
2934
416626631
416626601
1.990000e-04
58.4
51
TraesCS2D01G367800
chr5A
91.837
49
3
1
2936
2983
449018249
449018297
3.310000e-07
67.6
52
TraesCS2D01G367800
chr5A
83.117
77
6
5
2904
2979
462150465
462150535
4.290000e-06
63.9
53
TraesCS2D01G367800
chr5A
92.683
41
2
1
2892
2932
536890399
536890438
1.990000e-04
58.4
54
TraesCS2D01G367800
chr5A
90.698
43
2
2
2890
2930
552064825
552064867
7.170000e-04
56.5
55
TraesCS2D01G367800
chr6B
93.182
44
3
0
2935
2978
26595592
26595635
1.190000e-06
65.8
56
TraesCS2D01G367800
chr6B
100.000
29
0
0
2904
2932
567471502
567471530
3.000000e-03
54.7
57
TraesCS2D01G367800
chr1A
100.000
33
0
0
2937
2969
259202115
259202147
1.540000e-05
62.1
58
TraesCS2D01G367800
chr1A
79.070
86
12
5
2903
2983
475458706
475458790
3.000000e-03
54.7
59
TraesCS2D01G367800
chr1A
79.310
87
10
5
2903
2983
475483799
475483715
3.000000e-03
54.7
60
TraesCS2D01G367800
chr3B
89.583
48
3
1
2887
2934
752800471
752800516
5.540000e-05
60.2
61
TraesCS2D01G367800
chr3B
94.444
36
2
0
2932
2967
18648456
18648421
7.170000e-04
56.5
62
TraesCS2D01G367800
chr7A
94.737
38
1
1
2893
2930
654781574
654781610
1.990000e-04
58.4
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
TraesCS2D01G367800
chr2D
472443690
472448817
5127
True
4401.500000
4586
100.000000
1
5128
2
chr2D.!!$R2
5127
1
TraesCS2D01G367800
chr2D
472230205
472233959
3754
True
600.000000
1024
87.057250
956
5126
4
chr2D.!!$R1
4170
2
TraesCS2D01G367800
chr2B
551565814
551570544
4730
True
876.666667
2248
90.447667
14
5121
6
chr2B.!!$R4
5107
3
TraesCS2D01G367800
chr2B
551533957
551538523
4566
True
510.000000
721
91.178500
958
4766
4
chr2B.!!$R3
3808
4
TraesCS2D01G367800
chr2A
613719506
613720763
1257
True
998.000000
998
81.557000
986
2272
1
chr2A.!!$R2
1286
5
TraesCS2D01G367800
chr2A
613877085
613881479
4394
True
918.000000
2126
90.398167
1
5121
6
chr2A.!!$R4
5120
6
TraesCS2D01G367800
chr2A
613700865
613703427
2562
True
353.333333
680
91.684333
3550
5068
3
chr2A.!!$R3
1518
7
TraesCS2D01G367800
chr4A
395804892
395805721
829
False
517.000000
935
90.634500
1554
2716
2
chr4A.!!$F3
1162
8
TraesCS2D01G367800
chr1D
250740830
250741385
555
True
917.000000
917
96.403000
4127
4682
1
chr1D.!!$R2
555
9
TraesCS2D01G367800
chr1D
19874681
19875235
554
True
881.000000
881
95.315000
4127
4681
1
chr1D.!!$R1
554
10
TraesCS2D01G367800
chr5D
342525686
342526237
551
False
915.000000
915
96.558000
4127
4678
1
chr5D.!!$F1
551
11
TraesCS2D01G367800
chr5D
397029806
397030355
549
False
907.000000
907
96.377000
4127
4678
1
chr5D.!!$F2
551
12
TraesCS2D01G367800
chrUn
115109770
115110325
555
False
894.000000
894
95.691000
4127
4683
1
chrUn.!!$F1
556
13
TraesCS2D01G367800
chr5B
318172801
318173351
550
False
885.000000
885
95.652000
4127
4678
1
chr5B.!!$F1
551
14
TraesCS2D01G367800
chr4D
108101239
108101790
551
False
881.000000
881
95.471000
4127
4678
1
chr4D.!!$F1
551
15
TraesCS2D01G367800
chr1B
305284309
305284870
561
True
881.000000
881
95.018000
4127
4686
1
chr1B.!!$R1
559
16
TraesCS2D01G367800
chr7D
136707592
136708145
553
True
880.000000
880
95.315000
4127
4681
1
chr7D.!!$R1
554
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.