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
TraesCS1D01G421300
chr1D
100.000
5383
0
0
1
5383
477275672
477270290
0.000000e+00
9941.0
1
TraesCS1D01G421300
chr1D
89.510
286
21
8
5100
5383
477265264
477264986
2.390000e-93
353.0
2
TraesCS1D01G421300
chr1D
95.000
80
4
0
1216
1295
116478902
116478823
5.660000e-25
126.0
3
TraesCS1D01G421300
chr1A
93.839
4139
181
32
843
4945
573506868
573502768
0.000000e+00
6163.0
4
TraesCS1D01G421300
chr1A
86.179
492
28
11
4924
5383
573502758
573502275
3.740000e-136
496.0
5
TraesCS1D01G421300
chr1A
78.144
334
43
20
513
823
573507318
573506992
9.210000e-43
185.0
6
TraesCS1D01G421300
chr1B
93.656
1655
72
18
3026
4654
664953861
664952214
0.000000e+00
2444.0
7
TraesCS1D01G421300
chr1B
92.634
991
32
17
852
1818
664955739
664954766
0.000000e+00
1387.0
8
TraesCS1D01G421300
chr1B
90.353
850
63
8
2395
3238
675712830
675711994
0.000000e+00
1098.0
9
TraesCS1D01G421300
chr1B
94.082
659
31
4
2394
3044
664954590
664953932
0.000000e+00
994.0
10
TraesCS1D01G421300
chr1B
83.312
785
94
25
2467
3241
504629284
504628527
0.000000e+00
689.0
11
TraesCS1D01G421300
chr1B
86.172
593
36
21
3240
3815
675711885
675711322
2.770000e-167
599.0
12
TraesCS1D01G421300
chr1B
90.466
451
35
6
4937
5383
664949957
664949511
6.010000e-164
588.0
13
TraesCS1D01G421300
chr1B
87.500
504
45
5
1
492
664957371
664956874
2.810000e-157
566.0
14
TraesCS1D01G421300
chr1B
85.326
368
28
13
494
838
664956530
664956166
1.840000e-94
357.0
15
TraesCS1D01G421300
chr1B
91.813
171
14
0
4659
4829
664950407
664950237
6.970000e-59
239.0
16
TraesCS1D01G421300
chr1B
77.854
438
34
27
1091
1491
675713525
675713114
4.220000e-51
213.0
17
TraesCS1D01G421300
chr1B
89.474
171
12
3
2192
2356
664954769
664954599
1.520000e-50
211.0
18
TraesCS1D01G421300
chr1B
82.645
242
20
8
1493
1728
675713075
675712850
1.530000e-45
195.0
19
TraesCS1D01G421300
chr1B
80.753
239
33
8
1730
1961
504630006
504629774
1.990000e-39
174.0
20
TraesCS1D01G421300
chr1B
90.323
62
3
3
965
1026
675713611
675713553
1.610000e-10
78.7
21
TraesCS1D01G421300
chr3A
83.597
823
93
29
2431
3238
699802542
699803337
0.000000e+00
734.0
22
TraesCS1D01G421300
chr3A
86.738
279
31
5
5102
5379
19021810
19022083
6.770000e-79
305.0
23
TraesCS1D01G421300
chr3A
80.833
240
32
9
1730
1961
699801859
699802092
5.540000e-40
176.0
24
TraesCS1D01G421300
chr2B
83.415
814
90
32
2444
3241
362584461
362583677
0.000000e+00
713.0
25
TraesCS1D01G421300
chr2B
82.545
825
102
29
2431
3241
514619976
514619180
0.000000e+00
688.0
26
TraesCS1D01G421300
chr2B
80.753
239
33
8
1730
1961
362585157
362584925
1.990000e-39
174.0
27
TraesCS1D01G421300
chr7B
82.332
832
106
26
2423
3238
593124348
593125154
0.000000e+00
684.0
28
TraesCS1D01G421300
chr7B
90.535
243
20
2
1053
1295
2312525
2312764
8.700000e-83
318.0
29
TraesCS1D01G421300
chr4A
78.690
840
112
40
2004
2824
658960311
658959520
1.040000e-136
497.0
30
TraesCS1D01G421300
chr4A
76.856
916
121
55
2004
2888
658582200
658581345
2.980000e-117
433.0
31
TraesCS1D01G421300
chr4A
85.563
284
37
4
5100
5383
722002755
722002476
1.470000e-75
294.0
32
TraesCS1D01G421300
chr4A
83.025
324
31
15
2431
2745
617120821
617121129
6.870000e-69
272.0
33
TraesCS1D01G421300
chr4A
81.148
366
45
15
3521
3863
658581065
658580701
6.870000e-69
272.0
34
TraesCS1D01G421300
chr4A
85.532
235
27
7
3521
3749
658959197
658958964
6.970000e-59
239.0
35
TraesCS1D01G421300
chr4A
80.312
320
31
19
1050
1344
658961999
658961687
4.220000e-51
213.0
36
TraesCS1D01G421300
chr4A
88.125
160
17
2
1730
1888
658960490
658960332
7.120000e-44
189.0
37
TraesCS1D01G421300
chr4A
82.000
200
29
7
1730
1924
617120145
617120342
4.310000e-36
163.0
38
TraesCS1D01G421300
chr7D
78.017
837
111
40
2004
2819
45805561
45804777
4.910000e-125
459.0
39
TraesCS1D01G421300
chr7D
84.255
470
51
14
2938
3390
45804726
45804263
2.300000e-118
436.0
40
TraesCS1D01G421300
chr7D
87.611
226
16
8
1011
1228
45807460
45807239
8.950000e-63
252.0
41
TraesCS1D01G421300
chr7D
79.508
366
41
20
3531
3872
45804182
45803827
4.190000e-56
230.0
42
TraesCS1D01G421300
chr7D
81.250
256
32
9
1730
1984
45805789
45805549
5.500000e-45
193.0
43
TraesCS1D01G421300
chr7D
86.207
58
3
1
1238
1295
2589217
2589165
2.090000e-04
58.4
44
TraesCS1D01G421300
chr7D
100.000
29
0
0
2860
2888
45804753
45804725
3.000000e-03
54.7
45
TraesCS1D01G421300
chr7A
77.482
826
117
38
2018
2824
48058111
48057336
1.070000e-116
431.0
46
TraesCS1D01G421300
chr7A
87.324
284
33
2
5100
5383
42033901
42033621
6.730000e-84
322.0
47
TraesCS1D01G421300
chr7A
88.940
217
19
5
3526
3738
48056821
48056606
4.130000e-66
263.0
48
TraesCS1D01G421300
chr7A
88.325
197
20
3
1730
1924
48058355
48058160
3.240000e-57
233.0
49
TraesCS1D01G421300
chr7A
86.667
165
20
2
195
358
3326738
3326901
1.190000e-41
182.0
50
TraesCS1D01G421300
chr3D
88.070
285
28
4
5101
5383
80910882
80911162
3.110000e-87
333.0
51
TraesCS1D01G421300
chr3D
87.324
284
29
6
5100
5379
557049610
557049890
8.700000e-83
318.0
52
TraesCS1D01G421300
chrUn
90.535
243
20
2
1053
1295
83991987
83992226
8.700000e-83
318.0
53
TraesCS1D01G421300
chrUn
90.535
243
20
2
1053
1295
232030266
232030505
8.700000e-83
318.0
54
TraesCS1D01G421300
chrUn
90.535
243
20
2
1053
1295
232038473
232038712
8.700000e-83
318.0
55
TraesCS1D01G421300
chrUn
86.620
284
35
3
5100
5383
112562893
112563173
1.460000e-80
311.0
56
TraesCS1D01G421300
chr2D
87.234
282
26
8
5101
5379
513542465
513542739
4.050000e-81
313.0
57
TraesCS1D01G421300
chr4D
84.426
244
13
9
1053
1295
216318259
216318478
3.260000e-52
217.0
58
TraesCS1D01G421300
chr4D
83.030
165
28
0
39
203
323095937
323096101
3.360000e-32
150.0
59
TraesCS1D01G421300
chr4D
72.927
410
101
9
42
444
474718337
474717931
3.380000e-27
134.0
60
TraesCS1D01G421300
chr6B
80.000
165
33
0
39
203
136451418
136451254
7.320000e-24
122.0
61
TraesCS1D01G421300
chr6B
79.452
146
28
1
60
203
204598016
204598161
9.540000e-18
102.0
62
TraesCS1D01G421300
chr6B
78.231
147
30
2
55
200
12978327
12978182
5.740000e-15
93.5
63
TraesCS1D01G421300
chr6D
78.788
165
35
0
39
203
115106543
115106707
1.580000e-20
111.0
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
TraesCS1D01G421300
chr1D
477270290
477275672
5382
True
9941.000000
9941
100.000000
1
5383
1
chr1D.!!$R3
5382
1
TraesCS1D01G421300
chr1A
573502275
573507318
5043
True
2281.333333
6163
86.054000
513
5383
3
chr1A.!!$R1
4870
2
TraesCS1D01G421300
chr1B
664949511
664957371
7860
True
848.250000
2444
90.618875
1
5383
8
chr1B.!!$R2
5382
3
TraesCS1D01G421300
chr1B
675711322
675713611
2289
True
436.740000
1098
85.469400
965
3815
5
chr1B.!!$R3
2850
4
TraesCS1D01G421300
chr1B
504628527
504630006
1479
True
431.500000
689
82.032500
1730
3241
2
chr1B.!!$R1
1511
5
TraesCS1D01G421300
chr3A
699801859
699803337
1478
False
455.000000
734
82.215000
1730
3238
2
chr3A.!!$F2
1508
6
TraesCS1D01G421300
chr2B
514619180
514619976
796
True
688.000000
688
82.545000
2431
3241
1
chr2B.!!$R1
810
7
TraesCS1D01G421300
chr2B
362583677
362585157
1480
True
443.500000
713
82.084000
1730
3241
2
chr2B.!!$R2
1511
8
TraesCS1D01G421300
chr7B
593124348
593125154
806
False
684.000000
684
82.332000
2423
3238
1
chr7B.!!$F2
815
9
TraesCS1D01G421300
chr4A
658580701
658582200
1499
True
352.500000
433
79.002000
2004
3863
2
chr4A.!!$R2
1859
10
TraesCS1D01G421300
chr4A
658958964
658961999
3035
True
284.500000
497
83.164750
1050
3749
4
chr4A.!!$R3
2699
11
TraesCS1D01G421300
chr4A
617120145
617121129
984
False
217.500000
272
82.512500
1730
2745
2
chr4A.!!$F1
1015
12
TraesCS1D01G421300
chr7D
45803827
45807460
3633
True
270.783333
459
85.106833
1011
3872
6
chr7D.!!$R2
2861
13
TraesCS1D01G421300
chr7A
48056606
48058355
1749
True
309.000000
431
84.915667
1730
3738
3
chr7A.!!$R2
2008
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.