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
TraesCS2D01G572500
chr2D
100.000
3488
0
0
1
3488
638328550
638332037
0.000000e+00
6442.0
1
TraesCS2D01G572500
chr2D
78.954
784
133
23
1599
2370
637385799
637385036
4.020000e-139
505.0
2
TraesCS2D01G572500
chr2D
95.862
290
7
5
1308
1597
500370980
500371264
6.820000e-127
464.0
3
TraesCS2D01G572500
chr2D
95.533
291
9
4
1307
1597
500368431
500368717
2.450000e-126
462.0
4
TraesCS2D01G572500
chr2D
80.269
446
59
13
2121
2544
638314511
638314949
3.380000e-80
309.0
5
TraesCS2D01G572500
chr2D
74.116
792
151
38
1605
2381
636923009
636922257
9.540000e-71
278.0
6
TraesCS2D01G572500
chr2D
74.717
530
111
13
1849
2370
637345394
637344880
7.580000e-52
215.0
7
TraesCS2D01G572500
chr2D
80.727
275
44
7
1033
1307
637354204
637353939
4.560000e-49
206.0
8
TraesCS2D01G572500
chr2D
78.906
256
42
7
1052
1307
636725846
636725603
2.790000e-36
163.0
9
TraesCS2D01G572500
chr2D
77.406
239
37
13
1074
1307
636728519
636728293
3.650000e-25
126.0
10
TraesCS2D01G572500
chr2B
95.984
996
38
2
1597
2591
797198827
797199821
0.000000e+00
1616.0
11
TraesCS2D01G572500
chr2B
95.833
936
31
6
2560
3488
797252732
797253666
0.000000e+00
1506.0
12
TraesCS2D01G572500
chr2B
95.146
927
31
7
2571
3488
797199830
797200751
0.000000e+00
1450.0
13
TraesCS2D01G572500
chr2B
90.058
865
66
12
331
1180
797197458
797198317
0.000000e+00
1103.0
14
TraesCS2D01G572500
chr2B
96.711
456
14
1
2136
2591
797252277
797252731
0.000000e+00
758.0
15
TraesCS2D01G572500
chr2B
75.327
993
184
34
1788
2757
797178161
797179115
1.500000e-113
420.0
16
TraesCS2D01G572500
chr2B
87.500
208
16
6
142
346
797197238
797197438
7.530000e-57
231.0
17
TraesCS2D01G572500
chr2B
96.296
135
5
0
1173
1307
797198698
797198832
4.530000e-54
222.0
18
TraesCS2D01G572500
chr2B
78.755
273
53
3
1033
1304
744201858
744201590
9.950000e-41
178.0
19
TraesCS2D01G572500
chr2B
78.088
251
52
2
1049
1299
794490212
794490459
4.660000e-34
156.0
20
TraesCS2D01G572500
chr2B
73.286
423
74
29
1973
2381
796165240
796165637
6.120000e-23
119.0
21
TraesCS2D01G572500
chr2A
94.668
919
36
6
2582
3488
763970752
763969835
0.000000e+00
1413.0
22
TraesCS2D01G572500
chr2A
96.131
672
25
1
1921
2591
763974273
763973602
0.000000e+00
1096.0
23
TraesCS2D01G572500
chr2A
88.902
829
74
11
4
820
763976126
763975304
0.000000e+00
1005.0
24
TraesCS2D01G572500
chr2A
94.700
283
9
2
1597
1878
763974819
763974542
5.350000e-118
435.0
25
TraesCS2D01G572500
chr2A
88.776
294
26
3
1014
1307
763975100
763974814
1.540000e-93
353.0
26
TraesCS2D01G572500
chr2A
80.645
279
43
8
1030
1307
762660017
762660285
4.560000e-49
206.0
27
TraesCS2D01G572500
chr2A
95.122
41
2
0
3056
3096
23881821
23881781
8.080000e-07
65.8
28
TraesCS2D01G572500
chr6D
96.207
290
9
2
1308
1597
253872098
253871811
1.130000e-129
473.0
29
TraesCS2D01G572500
chr6D
96.207
290
10
1
1308
1597
253877325
253877037
1.130000e-129
473.0
30
TraesCS2D01G572500
chr6D
95.517
290
9
4
1308
1597
193218978
193218693
8.820000e-126
460.0
31
TraesCS2D01G572500
chrUn
97.112
277
7
1
2139
2415
361191635
361191360
1.900000e-127
466.0
32
TraesCS2D01G572500
chrUn
97.112
277
7
1
2139
2415
428808094
428807819
1.900000e-127
466.0
33
TraesCS2D01G572500
chr3B
94.178
292
12
2
1308
1597
82400601
82400889
1.150000e-119
440.0
34
TraesCS2D01G572500
chr3B
92.808
292
16
2
1308
1597
82405829
82406117
5.380000e-113
418.0
35
TraesCS2D01G572500
chr1D
93.471
291
15
4
1308
1597
68657939
68657652
2.490000e-116
429.0
36
TraesCS2D01G572500
chr1D
93.471
291
15
4
1308
1597
68685479
68685192
2.490000e-116
429.0
37
TraesCS2D01G572500
chr1D
84.585
253
30
8
3097
3343
98735281
98735032
3.480000e-60
243.0
38
TraesCS2D01G572500
chr7D
86.220
254
26
8
3097
3344
14414620
14414870
2.060000e-67
267.0
39
TraesCS2D01G572500
chr7D
84.810
237
27
8
3112
3342
129251369
129251602
2.710000e-56
230.0
40
TraesCS2D01G572500
chr7D
72.914
779
160
37
1605
2370
29984696
29985436
4.530000e-54
222.0
41
TraesCS2D01G572500
chr7A
84.644
267
30
8
3097
3357
75859267
75859006
4.470000e-64
255.0
42
TraesCS2D01G572500
chr7A
74.793
484
91
21
1895
2370
439730413
439730873
4.600000e-44
189.0
43
TraesCS2D01G572500
chr5A
85.375
253
28
8
3097
3343
150012121
150011872
1.610000e-63
254.0
44
TraesCS2D01G572500
chr3A
84.980
253
29
8
3097
3343
60001807
60002056
7.480000e-62
248.0
45
TraesCS2D01G572500
chr3A
97.368
38
1
0
3059
3096
704027770
704027733
8.080000e-07
65.8
46
TraesCS2D01G572500
chr4A
71.954
788
176
36
1605
2381
699189054
699188301
4.600000e-44
189.0
47
TraesCS2D01G572500
chr4A
91.071
56
5
0
1249
1304
699189115
699189060
3.730000e-10
76.8
48
TraesCS2D01G572500
chr4A
97.368
38
1
0
3059
3096
620561873
620561836
8.080000e-07
65.8
49
TraesCS2D01G572500
chr4B
77.432
257
52
1
1048
1304
673253984
673253734
7.800000e-32
148.0
50
TraesCS2D01G572500
chr5B
97.500
40
1
0
3057
3096
704163540
704163501
6.250000e-08
69.4
51
TraesCS2D01G572500
chr6A
97.436
39
1
0
3058
3096
600906616
600906654
2.250000e-07
67.6
52
TraesCS2D01G572500
chr4D
97.368
38
1
0
3059
3096
137038448
137038411
8.080000e-07
65.8
53
TraesCS2D01G572500
chr4D
96.875
32
1
0
1653
1684
491369571
491369602
2.000000e-03
54.7
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
TraesCS2D01G572500
chr2D
638328550
638332037
3487
False
6442.0
6442
100.0000
1
3488
1
chr2D.!!$F2
3487
1
TraesCS2D01G572500
chr2D
637385036
637385799
763
True
505.0
505
78.9540
1599
2370
1
chr2D.!!$R4
771
2
TraesCS2D01G572500
chr2D
500368431
500371264
2833
False
463.0
464
95.6975
1307
1597
2
chr2D.!!$F3
290
3
TraesCS2D01G572500
chr2D
636922257
636923009
752
True
278.0
278
74.1160
1605
2381
1
chr2D.!!$R1
776
4
TraesCS2D01G572500
chr2D
637344880
637345394
514
True
215.0
215
74.7170
1849
2370
1
chr2D.!!$R2
521
5
TraesCS2D01G572500
chr2B
797252277
797253666
1389
False
1132.0
1506
96.2720
2136
3488
2
chr2B.!!$F5
1352
6
TraesCS2D01G572500
chr2B
797197238
797200751
3513
False
924.4
1616
92.9968
142
3488
5
chr2B.!!$F4
3346
7
TraesCS2D01G572500
chr2B
797178161
797179115
954
False
420.0
420
75.3270
1788
2757
1
chr2B.!!$F3
969
8
TraesCS2D01G572500
chr2A
763969835
763976126
6291
True
860.4
1413
92.6354
4
3488
5
chr2A.!!$R2
3484
9
TraesCS2D01G572500
chr7D
29984696
29985436
740
False
222.0
222
72.9140
1605
2370
1
chr7D.!!$F2
765
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.