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
TraesCS2A01G208600
chr2A
100.000
4996
0
0
1
4996
191624433
191619438
0.000000e+00
9226.0
1
TraesCS2A01G208600
chr2A
89.476
2423
193
46
1880
4267
316872177
316869782
0.000000e+00
3005.0
2
TraesCS2A01G208600
chr2A
87.171
2354
230
59
1950
4267
324314204
324316521
0.000000e+00
2608.0
3
TraesCS2A01G208600
chr2A
91.058
1342
84
19
1880
3198
317030980
317029652
0.000000e+00
1781.0
4
TraesCS2A01G208600
chr2A
86.981
699
79
6
1
698
427936674
427937361
0.000000e+00
776.0
5
TraesCS2A01G208600
chr2A
86.099
705
84
13
1
698
98444156
98444853
0.000000e+00
747.0
6
TraesCS2A01G208600
chr2A
82.065
736
112
12
4268
4991
287489873
287490600
1.190000e-170
610.0
7
TraesCS2A01G208600
chr2A
88.208
212
24
1
1296
1506
279647523
279647734
8.300000e-63
252.0
8
TraesCS2A01G208600
chr2A
89.157
83
8
1
1466
1548
435491748
435491829
8.850000e-18
102.0
9
TraesCS2A01G208600
chr2A
91.892
74
5
1
1475
1548
435499598
435499670
8.850000e-18
102.0
10
TraesCS2A01G208600
chr2A
92.453
53
3
1
1302
1353
366239685
366239633
1.930000e-09
75.0
11
TraesCS2A01G208600
chr5A
90.807
2393
167
33
1903
4267
151320356
151317989
0.000000e+00
3151.0
12
TraesCS2A01G208600
chr5A
87.396
2277
202
59
2015
4264
508035367
508037585
0.000000e+00
2536.0
13
TraesCS2A01G208600
chr5A
86.857
700
84
8
1
698
453047434
453048127
0.000000e+00
776.0
14
TraesCS2A01G208600
chr5A
86.286
700
88
8
1
698
453039644
453040337
0.000000e+00
754.0
15
TraesCS2A01G208600
chr5A
85.277
686
89
9
4
683
166670647
166669968
0.000000e+00
697.0
16
TraesCS2A01G208600
chr5A
90.643
171
16
0
1296
1466
139383187
139383017
1.400000e-55
228.0
17
TraesCS2A01G208600
chr5A
90.230
174
15
2
1296
1468
139407763
139407591
5.030000e-55
226.0
18
TraesCS2A01G208600
chr5A
84.971
173
24
2
1525
1696
301732891
301733062
1.850000e-39
174.0
19
TraesCS2A01G208600
chr5A
96.875
32
0
1
729
760
526464480
526464510
9.000000e-03
52.8
20
TraesCS2A01G208600
chr7A
90.492
2398
169
43
1901
4267
424696130
424698499
0.000000e+00
3110.0
21
TraesCS2A01G208600
chr7A
88.281
2210
195
52
2087
4267
381605777
381607951
0.000000e+00
2588.0
22
TraesCS2A01G208600
chr7A
85.887
2062
218
60
2244
4269
450454388
450452364
0.000000e+00
2128.0
23
TraesCS2A01G208600
chr7A
85.791
2048
211
65
2244
4255
450456070
450458073
0.000000e+00
2097.0
24
TraesCS2A01G208600
chr7A
86.838
699
81
5
1
698
615702388
615703076
0.000000e+00
771.0
25
TraesCS2A01G208600
chr7A
86.305
701
81
12
1
698
615710154
615710842
0.000000e+00
749.0
26
TraesCS2A01G208600
chr7A
87.879
198
14
6
1089
1284
180593206
180593395
1.810000e-54
224.0
27
TraesCS2A01G208600
chr7A
84.388
237
16
15
1056
1284
422809719
422809942
3.920000e-51
213.0
28
TraesCS2A01G208600
chr7A
94.231
52
3
0
1417
1468
432453405
432453354
4.150000e-11
80.5
29
TraesCS2A01G208600
chr7A
92.857
56
3
1
1671
1725
583320580
583320525
4.150000e-11
80.5
30
TraesCS2A01G208600
chr7A
90.909
55
5
0
1414
1468
572601238
572601292
1.930000e-09
75.0
31
TraesCS2A01G208600
chr6A
89.740
2388
183
40
1903
4267
425477417
425479765
0.000000e+00
2996.0
32
TraesCS2A01G208600
chr6A
83.534
2909
324
101
1475
4267
340060812
340057943
0.000000e+00
2575.0
33
TraesCS2A01G208600
chr6A
87.732
701
76
9
1
698
107852257
107852950
0.000000e+00
809.0
34
TraesCS2A01G208600
chr6A
87.055
703
81
8
1
698
425483823
425484520
0.000000e+00
785.0
35
TraesCS2A01G208600
chr6A
88.908
568
56
6
1
566
405546364
405545802
0.000000e+00
693.0
36
TraesCS2A01G208600
chr6A
88.556
568
58
6
1
566
405579521
405578959
0.000000e+00
682.0
37
TraesCS2A01G208600
chr6A
86.622
598
72
6
1
595
257963923
257963331
0.000000e+00
654.0
38
TraesCS2A01G208600
chr6A
86.039
616
74
11
1
612
417452696
417453303
0.000000e+00
651.0
39
TraesCS2A01G208600
chr6A
87.009
585
67
8
1
582
417477909
417478487
0.000000e+00
651.0
40
TraesCS2A01G208600
chr6A
84.029
695
85
22
1
684
85856651
85855972
0.000000e+00
645.0
41
TraesCS2A01G208600
chr6A
87.234
329
33
7
1475
1800
340068748
340068426
2.840000e-97
366.0
42
TraesCS2A01G208600
chr6A
90.213
235
15
4
827
1058
322039411
322039182
2.920000e-77
300.0
43
TraesCS2A01G208600
chr6A
90.751
173
16
0
1296
1468
250345141
250344969
1.080000e-56
231.0
44
TraesCS2A01G208600
chr6A
90.751
173
16
0
1296
1468
250366716
250366544
1.080000e-56
231.0
45
TraesCS2A01G208600
chr6A
78.507
335
67
5
365
698
336256084
336256414
1.090000e-51
215.0
46
TraesCS2A01G208600
chr6A
96.842
95
3
0
604
698
425476160
425476254
5.180000e-35
159.0
47
TraesCS2A01G208600
chr6A
89.431
123
11
2
827
948
322031104
322030983
2.410000e-33
154.0
48
TraesCS2A01G208600
chr6A
82.051
156
26
2
405
559
373871380
373871226
1.130000e-26
132.0
49
TraesCS2A01G208600
chr6A
97.826
46
1
0
1423
1468
457723855
457723900
4.150000e-11
80.5
50
TraesCS2A01G208600
chr6A
97.500
40
1
0
1427
1466
457715743
457715782
8.970000e-08
69.4
51
TraesCS2A01G208600
chr1A
84.593
2778
325
82
1557
4267
405936996
405934255
0.000000e+00
2663.0
52
TraesCS2A01G208600
chr1A
91.622
931
46
11
401
1300
291309495
291310424
0.000000e+00
1258.0
53
TraesCS2A01G208600
chr1A
88.214
560
61
5
2
559
482970755
482971311
0.000000e+00
664.0
54
TraesCS2A01G208600
chr1A
86.312
621
69
11
1
614
320916197
320916808
0.000000e+00
662.0
55
TraesCS2A01G208600
chr1A
88.036
560
63
4
1
559
70740651
70741207
0.000000e+00
660.0
56
TraesCS2A01G208600
chr1A
88.014
559
60
6
1
557
322089111
322088558
0.000000e+00
654.0
57
TraesCS2A01G208600
chr1A
86.500
600
71
8
1
596
144483035
144482442
0.000000e+00
651.0
58
TraesCS2A01G208600
chr1A
85.877
616
74
10
1
612
267378340
267378946
1.170000e-180
643.0
59
TraesCS2A01G208600
chr1A
87.411
564
61
8
1
559
536248408
536248966
1.520000e-179
640.0
60
TraesCS2A01G208600
chr1A
87.321
560
67
4
1
559
70733086
70733642
5.450000e-179
638.0
61
TraesCS2A01G208600
chr1A
86.957
575
64
8
1
573
229647997
229647432
1.960000e-178
636.0
62
TraesCS2A01G208600
chr1A
85.833
600
76
7
1
596
144475127
144474533
3.280000e-176
628.0
63
TraesCS2A01G208600
chr1A
85.366
615
81
7
2
612
181084169
181083560
3.280000e-176
628.0
64
TraesCS2A01G208600
chr1A
83.550
693
93
18
1
684
411279827
411279147
3.280000e-176
628.0
65
TraesCS2A01G208600
chr1A
89.062
192
17
4
1089
1277
158725034
158725224
8.360000e-58
235.0
66
TraesCS2A01G208600
chr1A
82.692
156
25
2
405
559
332029681
332029835
2.430000e-28
137.0
67
TraesCS2A01G208600
chr1A
97.778
45
1
0
691
735
193421924
193421968
1.490000e-10
78.7
68
TraesCS2A01G208600
chr1A
95.556
45
2
0
691
735
193414121
193414165
6.940000e-09
73.1
69
TraesCS2A01G208600
chr1A
85.965
57
3
5
1475
1527
405937036
405936981
6.990000e-04
56.5
70
TraesCS2A01G208600
chr3A
87.176
2394
229
62
1902
4267
239575392
239573049
0.000000e+00
2649.0
71
TraesCS2A01G208600
chr3A
86.984
2397
230
66
1902
4267
239583219
239580874
0.000000e+00
2623.0
72
TraesCS2A01G208600
chr3A
91.006
934
49
10
401
1300
255353820
255354752
0.000000e+00
1227.0
73
TraesCS2A01G208600
chr3A
89.696
922
54
15
401
1300
255376159
255377061
0.000000e+00
1138.0
74
TraesCS2A01G208600
chr3A
87.966
698
79
3
1
698
438872661
438871969
0.000000e+00
819.0
75
TraesCS2A01G208600
chr3A
89.408
321
30
4
1475
1795
373250283
373249967
7.790000e-108
401.0
76
TraesCS2A01G208600
chr3A
85.153
229
17
13
1063
1284
583141954
583141736
8.420000e-53
219.0
77
TraesCS2A01G208600
chr3A
87.629
194
15
5
1089
1280
583149867
583149681
3.030000e-52
217.0
78
TraesCS2A01G208600
chr3A
90.123
81
7
1
1475
1555
118515886
118515807
2.460000e-18
104.0
79
TraesCS2A01G208600
chr3A
94.231
52
3
0
1417
1468
500862217
500862166
4.150000e-11
80.5
80
TraesCS2A01G208600
chr3A
94.231
52
3
0
1417
1468
500870268
500870217
4.150000e-11
80.5
81
TraesCS2A01G208600
chr3A
100.000
35
0
0
1266
1300
140079194
140079228
1.160000e-06
65.8
82
TraesCS2A01G208600
chr3A
93.023
43
1
2
1257
1297
140087379
140087421
1.500000e-05
62.1
83
TraesCS2A01G208600
chr3D
84.755
2532
291
79
1776
4267
327290115
327292591
0.000000e+00
2449.0
84
TraesCS2A01G208600
chr3D
89.346
413
44
0
4268
4680
523439701
523439289
2.060000e-143
520.0
85
TraesCS2A01G208600
chr3D
88.889
414
45
1
4268
4680
287716034
287715621
4.460000e-140
508.0
86
TraesCS2A01G208600
chr7B
85.687
2082
217
61
2219
4265
386489995
386487960
0.000000e+00
2119.0
87
TraesCS2A01G208600
chr7B
82.416
745
93
21
4268
4996
368571939
368572661
2.560000e-172
616.0
88
TraesCS2A01G208600
chr4B
83.355
2289
265
93
1690
3900
127552076
127554326
0.000000e+00
2010.0
89
TraesCS2A01G208600
chr4B
83.246
2286
267
94
1690
3900
127560120
127562364
0.000000e+00
1993.0
90
TraesCS2A01G208600
chr4B
81.295
278
38
13
413
683
306390918
306391188
3.920000e-51
213.0
91
TraesCS2A01G208600
chr4B
79.655
290
42
15
401
682
173656889
173657169
5.100000e-45
193.0
92
TraesCS2A01G208600
chr4B
78.457
311
46
15
410
704
479933241
479932936
3.070000e-42
183.0
93
TraesCS2A01G208600
chr4B
74.419
344
63
22
411
738
195574606
195574940
1.890000e-24
124.0
94
TraesCS2A01G208600
chr4B
79.375
160
30
3
401
559
359812760
359812603
5.290000e-20
110.0
95
TraesCS2A01G208600
chr4B
80.851
141
23
4
421
558
195532175
195532314
1.900000e-19
108.0
96
TraesCS2A01G208600
chr4B
91.525
59
4
1
691
748
206435147
206435205
4.150000e-11
80.5
97
TraesCS2A01G208600
chr1B
82.780
2288
271
97
1690
3900
278840615
278838374
0.000000e+00
1929.0
98
TraesCS2A01G208600
chr1B
82.058
719
104
18
4299
4996
157223060
157223774
1.550000e-164
590.0
99
TraesCS2A01G208600
chr1B
96.203
79
2
1
606
683
502176365
502176287
1.460000e-25
128.0
100
TraesCS2A01G208600
chr1B
73.837
344
62
22
411
738
236970315
236970646
1.470000e-20
111.0
101
TraesCS2A01G208600
chr1B
91.525
59
4
1
691
748
185595069
185595127
4.150000e-11
80.5
102
TraesCS2A01G208600
chr1B
89.831
59
5
1
691
748
185588208
185588266
1.930000e-09
75.0
103
TraesCS2A01G208600
chr1B
92.500
40
2
1
1760
1799
259882504
259882542
6.990000e-04
56.5
104
TraesCS2A01G208600
chr1B
96.970
33
1
0
1760
1792
479858735
479858703
6.990000e-04
56.5
105
TraesCS2A01G208600
chr1B
92.500
40
2
1
1760
1799
479881114
479881076
6.990000e-04
56.5
106
TraesCS2A01G208600
chr4A
88.925
921
68
15
405
1300
355574199
355573288
0.000000e+00
1105.0
107
TraesCS2A01G208600
chr4A
89.231
910
58
20
419
1300
355554658
355553761
0.000000e+00
1101.0
108
TraesCS2A01G208600
chr4A
87.500
104
10
3
1365
1468
313685778
313685678
3.160000e-22
117.0
109
TraesCS2A01G208600
chrUn
85.575
617
79
9
1
612
764936
764325
5.450000e-179
638.0
110
TraesCS2A01G208600
chrUn
87.659
551
60
8
1
546
348399441
348399988
7.060000e-178
634.0
111
TraesCS2A01G208600
chrUn
87.818
550
55
8
1
547
448869773
448870313
7.060000e-178
634.0
112
TraesCS2A01G208600
chrUn
87.146
529
62
6
1
526
305486051
305485526
3.330000e-166
595.0
113
TraesCS2A01G208600
chrUn
85.409
562
74
7
1
559
47106215
47105659
1.210000e-160
577.0
114
TraesCS2A01G208600
chrUn
85.336
566
70
11
1
559
52908663
52909222
1.560000e-159
573.0
115
TraesCS2A01G208600
chrUn
85.310
565
71
11
1
559
380607724
380607166
1.560000e-159
573.0
116
TraesCS2A01G208600
chrUn
84.534
569
78
8
1
565
336293363
336293925
5.650000e-154
555.0
117
TraesCS2A01G208600
chrUn
87.247
494
52
8
1
492
429590412
429589928
2.030000e-153
553.0
118
TraesCS2A01G208600
chrUn
84.629
566
74
11
1
559
52916754
52917313
7.310000e-153
551.0
119
TraesCS2A01G208600
chrUn
84.348
575
77
12
1
572
279452078
279451514
7.310000e-153
551.0
120
TraesCS2A01G208600
chrUn
80.435
184
30
6
377
559
404294271
404294093
8.720000e-28
135.0
121
TraesCS2A01G208600
chrUn
96.875
32
0
1
729
760
62292434
62292464
9.000000e-03
52.8
122
TraesCS2A01G208600
chr5D
83.595
701
93
13
4298
4996
171173313
171173993
5.450000e-179
638.0
123
TraesCS2A01G208600
chr5D
96.178
314
12
0
4683
4996
122594267
122594580
9.590000e-142
514.0
124
TraesCS2A01G208600
chr5D
88.889
414
45
1
4268
4680
506069285
506069698
4.460000e-140
508.0
125
TraesCS2A01G208600
chr5D
79.443
287
47
11
401
683
30068616
30068338
5.100000e-45
193.0
126
TraesCS2A01G208600
chr5D
75.896
307
50
17
412
698
399020483
399020785
8.720000e-28
135.0
127
TraesCS2A01G208600
chr5D
75.649
308
52
14
410
698
399028147
399028450
1.130000e-26
132.0
128
TraesCS2A01G208600
chr2D
91.283
413
36
0
4268
4680
325860353
325859941
9.390000e-157
564.0
129
TraesCS2A01G208600
chr2D
90.097
414
39
2
4268
4680
441597616
441598028
2.050000e-148
536.0
130
TraesCS2A01G208600
chr2D
89.209
417
45
0
4268
4684
495636236
495636652
5.730000e-144
521.0
131
TraesCS2A01G208600
chr2D
88.729
417
46
1
4268
4683
325840515
325840099
4.460000e-140
508.0
132
TraesCS2A01G208600
chr2D
88.889
414
44
2
4268
4680
385974335
385974747
4.460000e-140
508.0
133
TraesCS2A01G208600
chr2D
80.139
287
45
11
401
683
438302593
438302871
2.360000e-48
204.0
134
TraesCS2A01G208600
chr2D
79.649
285
49
9
402
683
438295109
438295387
3.950000e-46
196.0
135
TraesCS2A01G208600
chr6D
96.166
313
12
0
4684
4996
93799599
93799911
3.450000e-141
512.0
136
TraesCS2A01G208600
chr6D
96.166
313
12
0
4684
4996
141310131
141309819
3.450000e-141
512.0
137
TraesCS2A01G208600
chr6D
96.166
313
12
0
4684
4996
276685604
276685292
3.450000e-141
512.0
138
TraesCS2A01G208600
chr5B
79.520
708
122
15
4295
4996
443092934
443092244
2.700000e-132
483.0
139
TraesCS2A01G208600
chr5B
91.525
59
4
1
691
748
443886743
443886685
4.150000e-11
80.5
140
TraesCS2A01G208600
chr7D
81.227
277
44
8
410
683
470535247
470535518
3.030000e-52
217.0
141
TraesCS2A01G208600
chr1D
80.866
277
45
8
410
683
144771701
144771430
1.410000e-50
211.0
142
TraesCS2A01G208600
chr1D
80.505
277
46
8
410
683
144779422
144779151
6.560000e-49
206.0
143
TraesCS2A01G208600
chr1D
78.041
296
43
15
419
698
386798769
386799058
3.090000e-37
167.0
144
TraesCS2A01G208600
chr1D
77.023
309
46
18
405
698
386806763
386807061
2.410000e-33
154.0
145
TraesCS2A01G208600
chr1D
80.435
184
30
6
377
559
246493272
246493094
8.720000e-28
135.0
146
TraesCS2A01G208600
chr1D
80.435
184
30
6
377
559
246504277
246504099
8.720000e-28
135.0
147
TraesCS2A01G208600
chr4D
92.308
78
6
0
606
683
154203666
154203743
1.470000e-20
111.0
148
TraesCS2A01G208600
chr4D
86.275
102
11
3
606
704
154221273
154221374
1.900000e-19
108.0
149
TraesCS2A01G208600
chr6B
80.132
151
26
4
411
558
262703386
262703535
5.290000e-20
110.0
150
TraesCS2A01G208600
chr6B
79.605
152
28
3
405
555
522256151
522256002
6.840000e-19
106.0
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
TraesCS2A01G208600
chr2A
191619438
191624433
4995
True
9226.00
9226
100.000
1
4996
1
chr2A.!!$R1
4995
1
TraesCS2A01G208600
chr2A
316869782
316872177
2395
True
3005.00
3005
89.476
1880
4267
1
chr2A.!!$R2
2387
2
TraesCS2A01G208600
chr2A
324314204
324316521
2317
False
2608.00
2608
87.171
1950
4267
1
chr2A.!!$F4
2317
3
TraesCS2A01G208600
chr2A
317029652
317030980
1328
True
1781.00
1781
91.058
1880
3198
1
chr2A.!!$R3
1318
4
TraesCS2A01G208600
chr2A
427936674
427937361
687
False
776.00
776
86.981
1
698
1
chr2A.!!$F5
697
5
TraesCS2A01G208600
chr2A
98444156
98444853
697
False
747.00
747
86.099
1
698
1
chr2A.!!$F1
697
6
TraesCS2A01G208600
chr2A
287489873
287490600
727
False
610.00
610
82.065
4268
4991
1
chr2A.!!$F3
723
7
TraesCS2A01G208600
chr5A
151317989
151320356
2367
True
3151.00
3151
90.807
1903
4267
1
chr5A.!!$R3
2364
8
TraesCS2A01G208600
chr5A
508035367
508037585
2218
False
2536.00
2536
87.396
2015
4264
1
chr5A.!!$F4
2249
9
TraesCS2A01G208600
chr5A
453047434
453048127
693
False
776.00
776
86.857
1
698
1
chr5A.!!$F3
697
10
TraesCS2A01G208600
chr5A
453039644
453040337
693
False
754.00
754
86.286
1
698
1
chr5A.!!$F2
697
11
TraesCS2A01G208600
chr5A
166669968
166670647
679
True
697.00
697
85.277
4
683
1
chr5A.!!$R4
679
12
TraesCS2A01G208600
chr7A
424696130
424698499
2369
False
3110.00
3110
90.492
1901
4267
1
chr7A.!!$F4
2366
13
TraesCS2A01G208600
chr7A
381605777
381607951
2174
False
2588.00
2588
88.281
2087
4267
1
chr7A.!!$F2
2180
14
TraesCS2A01G208600
chr7A
450452364
450454388
2024
True
2128.00
2128
85.887
2244
4269
1
chr7A.!!$R2
2025
15
TraesCS2A01G208600
chr7A
450456070
450458073
2003
False
2097.00
2097
85.791
2244
4255
1
chr7A.!!$F5
2011
16
TraesCS2A01G208600
chr7A
615702388
615703076
688
False
771.00
771
86.838
1
698
1
chr7A.!!$F7
697
17
TraesCS2A01G208600
chr7A
615710154
615710842
688
False
749.00
749
86.305
1
698
1
chr7A.!!$F8
697
18
TraesCS2A01G208600
chr6A
340057943
340060812
2869
True
2575.00
2575
83.534
1475
4267
1
chr6A.!!$R7
2792
19
TraesCS2A01G208600
chr6A
425476160
425479765
3605
False
1577.50
2996
93.291
604
4267
2
chr6A.!!$F8
3663
20
TraesCS2A01G208600
chr6A
107852257
107852950
693
False
809.00
809
87.732
1
698
1
chr6A.!!$F1
697
21
TraesCS2A01G208600
chr6A
425483823
425484520
697
False
785.00
785
87.055
1
698
1
chr6A.!!$F5
697
22
TraesCS2A01G208600
chr6A
405545802
405546364
562
True
693.00
693
88.908
1
566
1
chr6A.!!$R10
565
23
TraesCS2A01G208600
chr6A
405578959
405579521
562
True
682.00
682
88.556
1
566
1
chr6A.!!$R11
565
24
TraesCS2A01G208600
chr6A
257963331
257963923
592
True
654.00
654
86.622
1
595
1
chr6A.!!$R4
594
25
TraesCS2A01G208600
chr6A
417452696
417453303
607
False
651.00
651
86.039
1
612
1
chr6A.!!$F3
611
26
TraesCS2A01G208600
chr6A
417477909
417478487
578
False
651.00
651
87.009
1
582
1
chr6A.!!$F4
581
27
TraesCS2A01G208600
chr6A
85855972
85856651
679
True
645.00
645
84.029
1
684
1
chr6A.!!$R1
683
28
TraesCS2A01G208600
chr1A
405934255
405937036
2781
True
1359.75
2663
85.279
1475
4267
2
chr1A.!!$R7
2792
29
TraesCS2A01G208600
chr1A
291309495
291310424
929
False
1258.00
1258
91.622
401
1300
1
chr1A.!!$F7
899
30
TraesCS2A01G208600
chr1A
482970755
482971311
556
False
664.00
664
88.214
2
559
1
chr1A.!!$F10
557
31
TraesCS2A01G208600
chr1A
320916197
320916808
611
False
662.00
662
86.312
1
614
1
chr1A.!!$F8
613
32
TraesCS2A01G208600
chr1A
70740651
70741207
556
False
660.00
660
88.036
1
559
1
chr1A.!!$F2
558
33
TraesCS2A01G208600
chr1A
322088558
322089111
553
True
654.00
654
88.014
1
557
1
chr1A.!!$R5
556
34
TraesCS2A01G208600
chr1A
144482442
144483035
593
True
651.00
651
86.500
1
596
1
chr1A.!!$R2
595
35
TraesCS2A01G208600
chr1A
267378340
267378946
606
False
643.00
643
85.877
1
612
1
chr1A.!!$F6
611
36
TraesCS2A01G208600
chr1A
536248408
536248966
558
False
640.00
640
87.411
1
559
1
chr1A.!!$F11
558
37
TraesCS2A01G208600
chr1A
70733086
70733642
556
False
638.00
638
87.321
1
559
1
chr1A.!!$F1
558
38
TraesCS2A01G208600
chr1A
229647432
229647997
565
True
636.00
636
86.957
1
573
1
chr1A.!!$R4
572
39
TraesCS2A01G208600
chr1A
144474533
144475127
594
True
628.00
628
85.833
1
596
1
chr1A.!!$R1
595
40
TraesCS2A01G208600
chr1A
181083560
181084169
609
True
628.00
628
85.366
2
612
1
chr1A.!!$R3
610
41
TraesCS2A01G208600
chr1A
411279147
411279827
680
True
628.00
628
83.550
1
684
1
chr1A.!!$R6
683
42
TraesCS2A01G208600
chr3A
239573049
239575392
2343
True
2649.00
2649
87.176
1902
4267
1
chr3A.!!$R2
2365
43
TraesCS2A01G208600
chr3A
239580874
239583219
2345
True
2623.00
2623
86.984
1902
4267
1
chr3A.!!$R3
2365
44
TraesCS2A01G208600
chr3A
255353820
255354752
932
False
1227.00
1227
91.006
401
1300
1
chr3A.!!$F3
899
45
TraesCS2A01G208600
chr3A
255376159
255377061
902
False
1138.00
1138
89.696
401
1300
1
chr3A.!!$F4
899
46
TraesCS2A01G208600
chr3A
438871969
438872661
692
True
819.00
819
87.966
1
698
1
chr3A.!!$R5
697
47
TraesCS2A01G208600
chr3D
327290115
327292591
2476
False
2449.00
2449
84.755
1776
4267
1
chr3D.!!$F1
2491
48
TraesCS2A01G208600
chr7B
386487960
386489995
2035
True
2119.00
2119
85.687
2219
4265
1
chr7B.!!$R1
2046
49
TraesCS2A01G208600
chr7B
368571939
368572661
722
False
616.00
616
82.416
4268
4996
1
chr7B.!!$F1
728
50
TraesCS2A01G208600
chr4B
127552076
127554326
2250
False
2010.00
2010
83.355
1690
3900
1
chr4B.!!$F1
2210
51
TraesCS2A01G208600
chr4B
127560120
127562364
2244
False
1993.00
1993
83.246
1690
3900
1
chr4B.!!$F2
2210
52
TraesCS2A01G208600
chr1B
278838374
278840615
2241
True
1929.00
1929
82.780
1690
3900
1
chr1B.!!$R1
2210
53
TraesCS2A01G208600
chr1B
157223060
157223774
714
False
590.00
590
82.058
4299
4996
1
chr1B.!!$F1
697
54
TraesCS2A01G208600
chr4A
355573288
355574199
911
True
1105.00
1105
88.925
405
1300
1
chr4A.!!$R3
895
55
TraesCS2A01G208600
chr4A
355553761
355554658
897
True
1101.00
1101
89.231
419
1300
1
chr4A.!!$R2
881
56
TraesCS2A01G208600
chrUn
764325
764936
611
True
638.00
638
85.575
1
612
1
chrUn.!!$R1
611
57
TraesCS2A01G208600
chrUn
348399441
348399988
547
False
634.00
634
87.659
1
546
1
chrUn.!!$F5
545
58
TraesCS2A01G208600
chrUn
448869773
448870313
540
False
634.00
634
87.818
1
547
1
chrUn.!!$F6
546
59
TraesCS2A01G208600
chrUn
305485526
305486051
525
True
595.00
595
87.146
1
526
1
chrUn.!!$R4
525
60
TraesCS2A01G208600
chrUn
47105659
47106215
556
True
577.00
577
85.409
1
559
1
chrUn.!!$R2
558
61
TraesCS2A01G208600
chrUn
52908663
52909222
559
False
573.00
573
85.336
1
559
1
chrUn.!!$F1
558
62
TraesCS2A01G208600
chrUn
380607166
380607724
558
True
573.00
573
85.310
1
559
1
chrUn.!!$R5
558
63
TraesCS2A01G208600
chrUn
336293363
336293925
562
False
555.00
555
84.534
1
565
1
chrUn.!!$F4
564
64
TraesCS2A01G208600
chrUn
52916754
52917313
559
False
551.00
551
84.629
1
559
1
chrUn.!!$F2
558
65
TraesCS2A01G208600
chrUn
279451514
279452078
564
True
551.00
551
84.348
1
572
1
chrUn.!!$R3
571
66
TraesCS2A01G208600
chr5D
171173313
171173993
680
False
638.00
638
83.595
4298
4996
1
chr5D.!!$F2
698
67
TraesCS2A01G208600
chr5B
443092244
443092934
690
True
483.00
483
79.520
4295
4996
1
chr5B.!!$R1
701
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.