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
TraesCS6D01G018900
chr6D
100.000
8829
0
0
1
8829
7677753
7686581
0.000000e+00
16305.0
1
TraesCS6D01G018900
chr6D
88.177
1201
136
6
1009
2205
7961850
7963048
0.000000e+00
1426.0
2
TraesCS6D01G018900
chr6D
93.153
701
23
12
5301
5977
7655233
7655932
0.000000e+00
1005.0
3
TraesCS6D01G018900
chr6D
80.921
1216
153
30
3089
4263
7904270
7905447
0.000000e+00
887.0
4
TraesCS6D01G018900
chr6D
95.766
496
20
1
2391
2885
7654173
7654668
0.000000e+00
798.0
5
TraesCS6D01G018900
chr6D
77.984
1131
199
39
1106
2201
8249836
8250951
0.000000e+00
664.0
6
TraesCS6D01G018900
chr6D
87.366
467
32
13
2886
3330
24254545
24255006
2.200000e-140
510.0
7
TraesCS6D01G018900
chr6D
87.097
465
36
11
2886
3330
7654703
7655163
1.020000e-138
505.0
8
TraesCS6D01G018900
chr6D
87.273
440
52
4
5430
5866
7905226
7905664
4.760000e-137
499.0
9
TraesCS6D01G018900
chr6D
89.412
340
28
7
2541
2876
24253310
24253645
1.060000e-113
422.0
10
TraesCS6D01G018900
chr6D
84.348
345
44
6
5094
5430
7681416
7681758
6.610000e-86
329.0
11
TraesCS6D01G018900
chr6D
84.348
345
44
6
3664
4006
7682846
7683182
6.610000e-86
329.0
12
TraesCS6D01G018900
chr6D
80.556
396
37
12
4737
5104
7681003
7681386
1.460000e-67
268.0
13
TraesCS6D01G018900
chr6D
80.556
396
37
12
3251
3634
7682489
7682856
1.460000e-67
268.0
14
TraesCS6D01G018900
chr6D
81.818
297
25
14
4832
5101
24255076
24255370
1.150000e-53
222.0
15
TraesCS6D01G018900
chr6D
86.935
199
22
3
1013
1207
7874142
7874340
4.150000e-53
220.0
16
TraesCS6D01G018900
chr6D
94.928
138
7
0
8076
8213
7685685
7685822
5.370000e-52
217.0
17
TraesCS6D01G018900
chr6D
89.759
166
15
2
3983
4146
24260313
24260478
2.500000e-50
211.0
18
TraesCS6D01G018900
chr6D
83.333
228
27
4
5430
5656
7681803
7682020
5.410000e-47
200.0
19
TraesCS6D01G018900
chr6D
79.286
280
51
7
4266
4542
7655627
7655902
1.170000e-43
189.0
20
TraesCS6D01G018900
chr6D
89.928
139
8
1
4737
4869
7655084
7655222
3.280000e-39
174.0
21
TraesCS6D01G018900
chr6D
82.266
203
31
4
3113
3313
8251339
8251538
4.240000e-38
171.0
22
TraesCS6D01G018900
chr6D
76.974
304
55
9
3035
3328
8658273
8657975
9.170000e-35
159.0
23
TraesCS6D01G018900
chr6D
87.302
126
8
4
1009
1134
7695032
7695149
4.300000e-28
137.0
24
TraesCS6D01G018900
chr6D
80.503
159
25
5
4102
4254
8144952
8144794
5.600000e-22
117.0
25
TraesCS6D01G018900
chr6D
79.114
158
22
8
4108
4255
8989467
8989623
2.030000e-16
99.0
26
TraesCS6D01G018900
chr6D
98.182
55
1
0
7362
7416
112516106
112516052
7.300000e-16
97.1
27
TraesCS6D01G018900
chr6D
85.714
84
9
3
915
998
24251778
24251858
1.580000e-12
86.1
28
TraesCS6D01G018900
chr6D
90.566
53
5
0
3
55
216146288
216146340
4.420000e-08
71.3
29
TraesCS6D01G018900
chr6D
90.385
52
4
1
7367
7418
111181586
111181536
5.720000e-07
67.6
30
TraesCS6D01G018900
chr6D
97.222
36
1
0
893
928
7885588
7885623
2.660000e-05
62.1
31
TraesCS6D01G018900
chr6D
97.222
36
1
0
893
928
7961717
7961752
2.660000e-05
62.1
32
TraesCS6D01G018900
chr6B
92.885
3317
158
27
1004
4262
14303253
14306549
0.000000e+00
4747.0
33
TraesCS6D01G018900
chr6B
84.277
1889
151
54
2479
4268
54420671
54418830
0.000000e+00
1709.0
34
TraesCS6D01G018900
chr6B
85.140
1716
184
42
521
2202
14323016
14324694
0.000000e+00
1690.0
35
TraesCS6D01G018900
chr6B
86.595
1201
142
12
1013
2205
14399892
14398703
0.000000e+00
1308.0
36
TraesCS6D01G018900
chr6B
86.016
1230
147
13
997
2205
13934134
13932909
0.000000e+00
1295.0
37
TraesCS6D01G018900
chr6B
85.599
1236
155
14
989
2205
14311065
14312296
0.000000e+00
1275.0
38
TraesCS6D01G018900
chr6B
85.620
1217
146
23
1010
2205
14455067
14453859
0.000000e+00
1251.0
39
TraesCS6D01G018900
chr6B
85.098
1228
161
13
997
2205
39311025
39312249
0.000000e+00
1234.0
40
TraesCS6D01G018900
chr6B
82.271
1444
194
28
1328
2723
14318227
14319656
0.000000e+00
1192.0
41
TraesCS6D01G018900
chr6B
87.959
789
75
13
3487
4268
39328622
39329397
0.000000e+00
913.0
42
TraesCS6D01G018900
chr6B
77.545
1100
210
29
1119
2194
14333505
14334591
5.820000e-176
628.0
43
TraesCS6D01G018900
chr6B
86.832
524
15
25
4264
4742
39329559
39330073
3.630000e-148
536.0
44
TraesCS6D01G018900
chr6B
90.258
349
26
7
2541
2885
39327866
39328210
4.860000e-122
449.0
45
TraesCS6D01G018900
chr6B
87.597
387
22
13
2886
3251
39328245
39328626
8.190000e-115
425.0
46
TraesCS6D01G018900
chr6B
88.328
317
25
9
688
998
39310677
39310987
3.890000e-98
370.0
47
TraesCS6D01G018900
chr6B
91.710
193
15
1
273
465
39310678
39310487
5.250000e-67
267.0
48
TraesCS6D01G018900
chr6B
80.303
396
38
12
4737
5104
14305539
14305922
6.800000e-66
263.0
49
TraesCS6D01G018900
chr6B
75.706
531
81
26
2241
2746
79037655
79038162
1.150000e-53
222.0
50
TraesCS6D01G018900
chr6B
79.402
301
50
8
3035
3328
15749126
15748831
1.500000e-47
202.0
51
TraesCS6D01G018900
chr6B
77.303
304
47
16
3648
3948
52565764
52565480
9.170000e-35
159.0
52
TraesCS6D01G018900
chr6B
73.704
521
76
35
3748
4255
15712410
15711938
7.140000e-31
147.0
53
TraesCS6D01G018900
chr6B
78.981
157
23
8
4108
4255
16322862
16323017
2.030000e-16
99.0
54
TraesCS6D01G018900
chr6B
95.082
61
3
0
4195
4255
16426439
16426499
7.300000e-16
97.1
55
TraesCS6D01G018900
chr6B
91.111
45
4
0
893
937
14402571
14402527
2.660000e-05
62.1
56
TraesCS6D01G018900
chr4A
88.373
1875
169
31
999
2853
667425287
667427132
0.000000e+00
2209.0
57
TraesCS6D01G018900
chr4A
85.039
1945
215
34
989
2885
667379992
667381908
0.000000e+00
1910.0
58
TraesCS6D01G018900
chr4A
80.114
1398
193
52
2895
4268
667427226
667428562
0.000000e+00
963.0
59
TraesCS6D01G018900
chr4A
82.215
984
83
48
2895
3820
667381951
667382900
0.000000e+00
763.0
60
TraesCS6D01G018900
chr4A
87.113
582
40
16
5430
5977
667383099
667383679
2.090000e-175
627.0
61
TraesCS6D01G018900
chr4A
83.759
431
48
13
3858
4268
667382906
667383334
1.070000e-103
388.0
62
TraesCS6D01G018900
chr4A
81.849
292
28
7
6321
6591
667384432
667384719
1.150000e-53
222.0
63
TraesCS6D01G018900
chr4A
78.947
285
47
8
4266
4542
667428601
667428880
1.960000e-41
182.0
64
TraesCS6D01G018900
chr4A
82.609
184
18
8
5987
6165
667384009
667384183
5.520000e-32
150.0
65
TraesCS6D01G018900
chr4A
89.091
55
6
0
1
55
339445756
339445702
1.590000e-07
69.4
66
TraesCS6D01G018900
chr6A
86.132
1882
212
21
1008
2856
7977695
7979560
0.000000e+00
1984.0
67
TraesCS6D01G018900
chr6A
83.878
1929
230
35
1008
2885
12420349
12422247
0.000000e+00
1764.0
68
TraesCS6D01G018900
chr6A
87.253
1216
142
10
995
2205
8170441
8171648
0.000000e+00
1375.0
69
TraesCS6D01G018900
chr6A
86.991
761
70
15
3515
4262
7980478
7981222
0.000000e+00
830.0
70
TraesCS6D01G018900
chr6A
77.865
1152
206
34
1096
2212
8624464
8623327
0.000000e+00
669.0
71
TraesCS6D01G018900
chr6A
77.104
297
48
15
3648
3943
8802907
8802630
4.270000e-33
154.0
72
TraesCS6D01G018900
chr6A
76.569
239
40
12
4737
4968
7980018
7980247
5.600000e-22
117.0
73
TraesCS6D01G018900
chr6A
98.246
57
1
0
7362
7418
91891218
91891162
5.640000e-17
100.0
74
TraesCS6D01G018900
chr6A
92.647
68
5
0
7351
7418
145532359
145532426
2.030000e-16
99.0
75
TraesCS6D01G018900
chr6A
90.741
54
5
0
7365
7418
117285534
117285481
1.230000e-08
73.1
76
TraesCS6D01G018900
chr6A
89.091
55
6
0
1
55
270246501
270246447
1.590000e-07
69.4
77
TraesCS6D01G018900
chr6A
97.222
36
1
0
893
928
8170323
8170358
2.660000e-05
62.1
78
TraesCS6D01G018900
chr4D
93.963
1143
44
15
7705
8829
493748787
493747652
0.000000e+00
1705.0
79
TraesCS6D01G018900
chr4D
97.049
576
10
5
8261
8829
503116421
503115846
0.000000e+00
963.0
80
TraesCS6D01G018900
chr4D
96.095
589
16
5
8248
8829
508665722
508666310
0.000000e+00
953.0
81
TraesCS6D01G018900
chr4D
81.301
615
59
29
7709
8283
365415929
365416527
1.750000e-121
448.0
82
TraesCS6D01G018900
chr4D
96.479
142
5
0
7933
8074
493748409
493748268
1.480000e-57
235.0
83
TraesCS6D01G018900
chr4D
94.444
144
3
1
8075
8213
493748558
493748415
5.370000e-52
217.0
84
TraesCS6D01G018900
chr4D
91.753
97
8
0
8116
8212
365416228
365416324
1.550000e-27
135.0
85
TraesCS6D01G018900
chr4D
96.491
57
2
0
7362
7418
31262053
31261997
2.620000e-15
95.3
86
TraesCS6D01G018900
chr4D
96.491
57
2
0
7362
7418
36977172
36977116
2.620000e-15
95.3
87
TraesCS6D01G018900
chr4D
96.491
57
2
0
7362
7418
77528328
77528272
2.620000e-15
95.3
88
TraesCS6D01G018900
chr4D
96.491
57
2
0
7362
7418
207226123
207226179
2.620000e-15
95.3
89
TraesCS6D01G018900
chr4D
96.491
57
2
0
7362
7418
234956346
234956402
2.620000e-15
95.3
90
TraesCS6D01G018900
chr4D
96.491
57
2
0
7362
7418
289704151
289704095
2.620000e-15
95.3
91
TraesCS6D01G018900
chr4D
96.491
57
2
0
7362
7418
291161111
291161167
2.620000e-15
95.3
92
TraesCS6D01G018900
chr4D
96.491
57
2
0
7362
7418
316080957
316081013
2.620000e-15
95.3
93
TraesCS6D01G018900
chr4D
96.491
57
2
0
7362
7418
316081835
316081891
2.620000e-15
95.3
94
TraesCS6D01G018900
chr4D
100.000
43
0
0
8195
8237
365416324
365416366
7.350000e-11
80.5
95
TraesCS6D01G018900
chr7D
93.942
1139
45
14
7709
8829
316381645
316382777
0.000000e+00
1700.0
96
TraesCS6D01G018900
chr7D
96.284
592
13
4
8245
8829
10555853
10555264
0.000000e+00
963.0
97
TraesCS6D01G018900
chr7D
78.040
1102
211
24
1122
2204
161390721
161391810
0.000000e+00
665.0
98
TraesCS6D01G018900
chr7D
91.694
301
17
7
7709
8004
608434141
608434438
2.290000e-110
411.0
99
TraesCS6D01G018900
chr7D
96.479
142
5
0
7933
8074
316382020
316382161
1.480000e-57
235.0
100
TraesCS6D01G018900
chr7D
93.750
144
4
1
8075
8213
316381871
316382014
2.500000e-50
211.0
101
TraesCS6D01G018900
chr7D
88.079
151
16
1
5252
5402
486201475
486201327
2.530000e-40
178.0
102
TraesCS6D01G018900
chr7D
87.805
82
10
0
7337
7418
93229940
93230021
7.300000e-16
97.1
103
TraesCS6D01G018900
chr7D
96.226
53
2
0
3
55
335997267
335997215
4.390000e-13
87.9
104
TraesCS6D01G018900
chr7D
90.385
52
5
0
3
54
300189767
300189716
1.590000e-07
69.4
105
TraesCS6D01G018900
chr5D
93.761
1138
43
14
7714
8829
77001605
77002736
0.000000e+00
1683.0
106
TraesCS6D01G018900
chr5D
96.147
597
14
3
8242
8829
168500891
168501487
0.000000e+00
966.0
107
TraesCS6D01G018900
chr5D
95.238
273
9
3
7702
7971
121083759
121083488
6.330000e-116
429.0
108
TraesCS6D01G018900
chr5D
94.444
144
3
1
8075
8213
77001826
77001969
5.370000e-52
217.0
109
TraesCS6D01G018900
chr5D
89.873
158
14
1
5244
5401
446154226
446154071
1.500000e-47
202.0
110
TraesCS6D01G018900
chr5D
90.361
83
8
0
7336
7418
166750095
166750013
9.370000e-20
110.0
111
TraesCS6D01G018900
chr5D
95.082
61
3
0
7362
7422
463514560
463514620
7.300000e-16
97.1
112
TraesCS6D01G018900
chr5D
96.491
57
2
0
7362
7418
179013867
179013923
2.620000e-15
95.3
113
TraesCS6D01G018900
chr5D
92.157
51
3
1
7367
7417
342492583
342492632
4.420000e-08
71.3
114
TraesCS6D01G018900
chr7B
86.832
1086
83
23
4924
5977
640002867
640003924
0.000000e+00
1158.0
115
TraesCS6D01G018900
chr7B
78.636
1100
203
24
1123
2204
123655645
123656730
0.000000e+00
701.0
116
TraesCS6D01G018900
chr7B
80.915
634
107
12
63
690
300671857
300672482
1.030000e-133
488.0
117
TraesCS6D01G018900
chr7B
80.349
631
103
13
63
691
672910700
672911311
8.080000e-125
459.0
118
TraesCS6D01G018900
chr7B
79.283
642
105
19
63
696
500773731
500773110
2.950000e-114
424.0
119
TraesCS6D01G018900
chr7B
82.816
419
53
11
3037
3455
639999858
640000257
3.030000e-94
357.0
120
TraesCS6D01G018900
chr7B
83.784
222
30
4
4051
4268
640003375
640003594
1.160000e-48
206.0
121
TraesCS6D01G018900
chr7B
91.304
92
6
2
2882
2973
639999526
639999615
3.350000e-24
124.0
122
TraesCS6D01G018900
chr7B
87.156
109
7
2
4737
4839
640000070
640000177
5.600000e-22
117.0
123
TraesCS6D01G018900
chr1D
96.939
588
11
2
8248
8829
196484161
196483575
0.000000e+00
979.0
124
TraesCS6D01G018900
chr1D
97.391
575
9
1
8261
8829
460859192
460859766
0.000000e+00
974.0
125
TraesCS6D01G018900
chr1D
90.154
325
22
8
7712
8030
196484582
196484262
1.770000e-111
414.0
126
TraesCS6D01G018900
chr1D
92.000
75
4
1
7362
7434
395990533
395990459
4.360000e-18
104.0
127
TraesCS6D01G018900
chr1D
95.082
61
3
0
7362
7422
348604157
348604217
7.300000e-16
97.1
128
TraesCS6D01G018900
chr1D
96.491
57
2
0
7362
7418
329001486
329001542
2.620000e-15
95.3
129
TraesCS6D01G018900
chr1D
90.566
53
5
0
3
55
159535020
159535072
4.420000e-08
71.3
130
TraesCS6D01G018900
chr1D
91.489
47
4
0
7372
7418
262175019
262175065
2.060000e-06
65.8
131
TraesCS6D01G018900
chr2D
96.599
588
14
5
8248
8829
405625397
405624810
0.000000e+00
970.0
132
TraesCS6D01G018900
chr2D
95.987
598
15
6
8241
8829
421784445
421785042
0.000000e+00
963.0
133
TraesCS6D01G018900
chr2D
95.307
277
10
2
7709
7982
416392354
416392630
3.780000e-118
436.0
134
TraesCS6D01G018900
chr2D
96.721
61
2
0
7362
7422
649592283
649592223
1.570000e-17
102.0
135
TraesCS6D01G018900
chr2D
89.873
79
2
2
7362
7434
116214131
116214053
7.300000e-16
97.1
136
TraesCS6D01G018900
chr2D
88.158
76
4
4
8075
8147
416392580
416392653
1.580000e-12
86.1
137
TraesCS6D01G018900
chrUn
96.429
588
14
2
8248
8829
80049526
80050112
0.000000e+00
963.0
138
TraesCS6D01G018900
chrUn
100.000
425
0
0
3277
3701
476555064
476554640
0.000000e+00
785.0
139
TraesCS6D01G018900
chrUn
81.905
315
27
10
4818
5104
476555019
476554707
1.150000e-58
239.0
140
TraesCS6D01G018900
chrUn
75.379
528
87
26
2241
2746
27945108
27944602
1.930000e-51
215.0
141
TraesCS6D01G018900
chrUn
78.431
204
31
7
4339
4531
27943658
27943457
4.330000e-23
121.0
142
TraesCS6D01G018900
chrUn
98.214
56
1
0
7363
7418
50668550
50668495
2.030000e-16
99.0
143
TraesCS6D01G018900
chr7A
78.455
1100
208
21
1123
2204
162577916
162579004
0.000000e+00
691.0
144
TraesCS6D01G018900
chr3D
95.327
321
11
3
7709
8026
47789883
47790202
2.840000e-139
507.0
145
TraesCS6D01G018900
chr3D
80.351
285
35
16
7976
8250
47790230
47790503
6.990000e-46
196.0
146
TraesCS6D01G018900
chr3D
93.684
95
5
1
8075
8169
47790109
47790202
3.320000e-29
141.0
147
TraesCS6D01G018900
chr3D
84.058
69
6
5
3
67
288722649
288722582
2.660000e-05
62.1
148
TraesCS6D01G018900
chr5B
78.807
637
125
7
63
696
440264038
440264667
3.810000e-113
420.0
149
TraesCS6D01G018900
chr5B
94.118
68
3
1
7351
7418
346974610
346974544
1.570000e-17
102.0
150
TraesCS6D01G018900
chr5B
90.411
73
7
0
7362
7434
498639609
498639537
7.300000e-16
97.1
151
TraesCS6D01G018900
chr1B
80.899
534
94
7
161
691
15779251
15778723
1.770000e-111
414.0
152
TraesCS6D01G018900
chr1B
77.899
276
47
11
3648
3922
630652000
630652262
9.170000e-35
159.0
153
TraesCS6D01G018900
chr3B
78.445
566
114
8
117
680
501419111
501418552
6.520000e-96
363.0
154
TraesCS6D01G018900
chr3B
78.462
520
85
16
175
690
55045675
55046171
1.850000e-81
315.0
155
TraesCS6D01G018900
chr3B
78.596
285
54
7
415
696
73677507
73677227
1.960000e-41
182.0
156
TraesCS6D01G018900
chr2A
80.049
406
74
6
293
696
561263368
561262968
2.410000e-75
294.0
157
TraesCS6D01G018900
chr2A
85.938
64
4
5
2
62
345566710
345566649
7.400000e-06
63.9
158
TraesCS6D01G018900
chr5A
91.667
72
6
0
7362
7433
116217865
116217794
5.640000e-17
100.0
159
TraesCS6D01G018900
chr5A
92.647
68
5
0
7351
7418
176666750
176666683
2.030000e-16
99.0
160
TraesCS6D01G018900
chr5A
89.091
55
6
0
1
55
217644198
217644252
1.590000e-07
69.4
161
TraesCS6D01G018900
chr1A
98.182
55
1
0
7362
7416
550504633
550504687
7.300000e-16
97.1
162
TraesCS6D01G018900
chr1A
92.982
57
4
0
7362
7418
244686684
244686740
5.680000e-12
84.2
163
TraesCS6D01G018900
chr4B
91.304
69
6
0
7350
7418
83187468
83187536
2.620000e-15
95.3
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
TraesCS6D01G018900
chr6D
7677753
7686581
8828
False
16305.000000
16305
100.000000
1
8829
1
chr6D.!!$F1
8828
1
TraesCS6D01G018900
chr6D
7961717
7963048
1331
False
744.050000
1426
92.699500
893
2205
2
chr6D.!!$F11
1312
2
TraesCS6D01G018900
chr6D
7904270
7905664
1394
False
693.000000
887
84.097000
3089
5866
2
chr6D.!!$F10
2777
3
TraesCS6D01G018900
chr6D
7654173
7655932
1759
False
534.200000
1005
89.046000
2391
5977
5
chr6D.!!$F8
3586
4
TraesCS6D01G018900
chr6D
8249836
8251538
1702
False
417.500000
664
80.125000
1106
3313
2
chr6D.!!$F12
2207
5
TraesCS6D01G018900
chr6D
24251778
24255370
3592
False
310.025000
510
86.077500
915
5101
4
chr6D.!!$F13
4186
6
TraesCS6D01G018900
chr6D
7681003
7685822
4819
False
268.500000
329
84.678167
3251
8213
6
chr6D.!!$F9
4962
7
TraesCS6D01G018900
chr6B
14303253
14306549
3296
False
2505.000000
4747
86.594000
1004
5104
2
chr6B.!!$F6
4100
8
TraesCS6D01G018900
chr6B
54418830
54420671
1841
True
1709.000000
1709
84.277000
2479
4268
1
chr6B.!!$R7
1789
9
TraesCS6D01G018900
chr6B
14318227
14324694
6467
False
1441.000000
1690
83.705500
521
2723
2
chr6B.!!$F7
2202
10
TraesCS6D01G018900
chr6B
13932909
13934134
1225
True
1295.000000
1295
86.016000
997
2205
1
chr6B.!!$R1
1208
11
TraesCS6D01G018900
chr6B
14311065
14312296
1231
False
1275.000000
1275
85.599000
989
2205
1
chr6B.!!$F1
1216
12
TraesCS6D01G018900
chr6B
14453859
14455067
1208
True
1251.000000
1251
85.620000
1010
2205
1
chr6B.!!$R2
1195
13
TraesCS6D01G018900
chr6B
39310677
39312249
1572
False
802.000000
1234
86.713000
688
2205
2
chr6B.!!$F8
1517
14
TraesCS6D01G018900
chr6B
14398703
14402571
3868
True
685.050000
1308
88.853000
893
2205
2
chr6B.!!$R8
1312
15
TraesCS6D01G018900
chr6B
14333505
14334591
1086
False
628.000000
628
77.545000
1119
2194
1
chr6B.!!$F2
1075
16
TraesCS6D01G018900
chr6B
39327866
39330073
2207
False
580.750000
913
88.161500
2541
4742
4
chr6B.!!$F9
2201
17
TraesCS6D01G018900
chr6B
79037655
79038162
507
False
222.000000
222
75.706000
2241
2746
1
chr6B.!!$F5
505
18
TraesCS6D01G018900
chr4A
667425287
667428880
3593
False
1118.000000
2209
82.478000
999
4542
3
chr4A.!!$F2
3543
19
TraesCS6D01G018900
chr4A
667379992
667384719
4727
False
676.666667
1910
83.764000
989
6591
6
chr4A.!!$F1
5602
20
TraesCS6D01G018900
chr6A
12420349
12422247
1898
False
1764.000000
1764
83.878000
1008
2885
1
chr6A.!!$F1
1877
21
TraesCS6D01G018900
chr6A
7977695
7981222
3527
False
977.000000
1984
83.230667
1008
4968
3
chr6A.!!$F3
3960
22
TraesCS6D01G018900
chr6A
8170323
8171648
1325
False
718.550000
1375
92.237500
893
2205
2
chr6A.!!$F4
1312
23
TraesCS6D01G018900
chr6A
8623327
8624464
1137
True
669.000000
669
77.865000
1096
2212
1
chr6A.!!$R1
1116
24
TraesCS6D01G018900
chr4D
503115846
503116421
575
True
963.000000
963
97.049000
8261
8829
1
chr4D.!!$R5
568
25
TraesCS6D01G018900
chr4D
508665722
508666310
588
False
953.000000
953
96.095000
8248
8829
1
chr4D.!!$F4
581
26
TraesCS6D01G018900
chr4D
493747652
493748787
1135
True
719.000000
1705
94.962000
7705
8829
3
chr4D.!!$R6
1124
27
TraesCS6D01G018900
chr4D
365415929
365416527
598
False
221.166667
448
91.018000
7709
8283
3
chr4D.!!$F6
574
28
TraesCS6D01G018900
chr7D
10555264
10555853
589
True
963.000000
963
96.284000
8245
8829
1
chr7D.!!$R1
584
29
TraesCS6D01G018900
chr7D
316381645
316382777
1132
False
715.333333
1700
94.723667
7709
8829
3
chr7D.!!$F4
1120
30
TraesCS6D01G018900
chr7D
161390721
161391810
1089
False
665.000000
665
78.040000
1122
2204
1
chr7D.!!$F2
1082
31
TraesCS6D01G018900
chr5D
168500891
168501487
596
False
966.000000
966
96.147000
8242
8829
1
chr5D.!!$F1
587
32
TraesCS6D01G018900
chr5D
77001605
77002736
1131
False
950.000000
1683
94.102500
7714
8829
2
chr5D.!!$F5
1115
33
TraesCS6D01G018900
chr7B
123655645
123656730
1085
False
701.000000
701
78.636000
1123
2204
1
chr7B.!!$F1
1081
34
TraesCS6D01G018900
chr7B
300671857
300672482
625
False
488.000000
488
80.915000
63
690
1
chr7B.!!$F2
627
35
TraesCS6D01G018900
chr7B
672910700
672911311
611
False
459.000000
459
80.349000
63
691
1
chr7B.!!$F3
628
36
TraesCS6D01G018900
chr7B
500773110
500773731
621
True
424.000000
424
79.283000
63
696
1
chr7B.!!$R1
633
37
TraesCS6D01G018900
chr7B
639999526
640003924
4398
False
392.400000
1158
86.378400
2882
5977
5
chr7B.!!$F4
3095
38
TraesCS6D01G018900
chr1D
460859192
460859766
574
False
974.000000
974
97.391000
8261
8829
1
chr1D.!!$F5
568
39
TraesCS6D01G018900
chr1D
196483575
196484582
1007
True
696.500000
979
93.546500
7712
8829
2
chr1D.!!$R2
1117
40
TraesCS6D01G018900
chr2D
405624810
405625397
587
True
970.000000
970
96.599000
8248
8829
1
chr2D.!!$R2
581
41
TraesCS6D01G018900
chr2D
421784445
421785042
597
False
963.000000
963
95.987000
8241
8829
1
chr2D.!!$F1
588
42
TraesCS6D01G018900
chrUn
80049526
80050112
586
False
963.000000
963
96.429000
8248
8829
1
chrUn.!!$F1
581
43
TraesCS6D01G018900
chr7A
162577916
162579004
1088
False
691.000000
691
78.455000
1123
2204
1
chr7A.!!$F1
1081
44
TraesCS6D01G018900
chr3D
47789883
47790503
620
False
281.333333
507
89.787333
7709
8250
3
chr3D.!!$F1
541
45
TraesCS6D01G018900
chr5B
440264038
440264667
629
False
420.000000
420
78.807000
63
696
1
chr5B.!!$F1
633
46
TraesCS6D01G018900
chr1B
15778723
15779251
528
True
414.000000
414
80.899000
161
691
1
chr1B.!!$R1
530
47
TraesCS6D01G018900
chr3B
501418552
501419111
559
True
363.000000
363
78.445000
117
680
1
chr3B.!!$R2
563
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.