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
TraesCS6D01G064800
chr6D
100.000
6592
0
0
1
6592
31468888
31475479
0.000000e+00
12174.0
1
TraesCS6D01G064800
chr6D
93.201
1456
67
20
2833
4262
31269928
31268479
0.000000e+00
2111.0
2
TraesCS6D01G064800
chr6D
92.032
1255
71
15
4347
5595
31268399
31267168
0.000000e+00
1736.0
3
TraesCS6D01G064800
chr6D
88.971
1360
80
26
2940
4262
30097791
30096465
0.000000e+00
1616.0
4
TraesCS6D01G064800
chr6D
82.715
1267
167
31
4347
5595
29926518
29927750
0.000000e+00
1079.0
5
TraesCS6D01G064800
chr6D
86.961
974
61
21
1764
2690
31270879
31269925
0.000000e+00
1035.0
6
TraesCS6D01G064800
chr6D
80.469
1408
209
41
4347
5734
29852360
29853721
0.000000e+00
1016.0
7
TraesCS6D01G064800
chr6D
82.508
1292
97
45
1684
2908
30099023
30097794
0.000000e+00
1014.0
8
TraesCS6D01G064800
chr6D
90.846
721
57
7
1
718
31272731
31272017
0.000000e+00
957.0
9
TraesCS6D01G064800
chr6D
85.097
463
38
15
812
1267
29848972
29849410
1.690000e-120
444.0
10
TraesCS6D01G064800
chr6D
91.185
329
17
1
5467
5783
31267251
31266923
2.820000e-118
436.0
11
TraesCS6D01G064800
chr6D
85.446
426
31
8
789
1214
31271670
31271276
1.320000e-111
414.0
12
TraesCS6D01G064800
chr6D
82.816
419
38
22
813
1214
29922324
29922725
1.760000e-90
344.0
13
TraesCS6D01G064800
chr6D
82.410
415
34
19
815
1214
30099820
30099430
6.370000e-85
326.0
14
TraesCS6D01G064800
chr6D
94.118
102
6
0
5960
6061
221219409
221219308
8.850000e-34
156.0
15
TraesCS6D01G064800
chr6D
96.739
92
3
0
1257
1348
31470063
31470154
3.180000e-33
154.0
16
TraesCS6D01G064800
chr6D
96.739
92
3
0
1176
1267
31470144
31470235
3.180000e-33
154.0
17
TraesCS6D01G064800
chr6D
91.176
102
9
0
5879
5980
31266549
31266650
8.910000e-29
139.0
18
TraesCS6D01G064800
chr6D
95.000
60
3
0
4284
4343
31268487
31268428
1.960000e-15
95.3
19
TraesCS6D01G064800
chr6D
97.561
41
1
0
6421
6461
60481498
60481458
3.300000e-08
71.3
20
TraesCS6D01G064800
chr6A
96.398
3137
81
14
2473
5595
31753732
31750614
0.000000e+00
5138.0
21
TraesCS6D01G064800
chr6A
85.482
3010
308
60
2653
5602
46699569
46696629
0.000000e+00
3018.0
22
TraesCS6D01G064800
chr6A
88.821
1789
109
34
663
2435
31755441
31753728
0.000000e+00
2111.0
23
TraesCS6D01G064800
chr6A
89.068
1363
86
28
2940
4262
32741303
32742642
0.000000e+00
1633.0
24
TraesCS6D01G064800
chr6A
85.999
1457
119
41
4348
5783
32742720
32744112
0.000000e+00
1482.0
25
TraesCS6D01G064800
chr6A
83.281
1268
162
28
4347
5595
32811227
32809991
0.000000e+00
1122.0
26
TraesCS6D01G064800
chr6A
80.922
1389
204
39
4347
5717
32884590
32883245
0.000000e+00
1040.0
27
TraesCS6D01G064800
chr6A
83.932
1002
88
31
1684
2646
32740080
32741047
0.000000e+00
891.0
28
TraesCS6D01G064800
chr6A
95.804
429
18
0
5467
5895
31750697
31750269
0.000000e+00
693.0
29
TraesCS6D01G064800
chr6A
87.751
498
46
8
2754
3239
45353753
45354247
9.590000e-158
568.0
30
TraesCS6D01G064800
chr6A
87.366
467
48
8
1
459
31755904
31755441
5.860000e-145
525.0
31
TraesCS6D01G064800
chr6A
87.500
432
42
8
1
423
31796704
31796276
7.680000e-134
488.0
32
TraesCS6D01G064800
chr6A
79.140
791
67
55
1685
2426
46700632
46699891
2.170000e-124
457.0
33
TraesCS6D01G064800
chr6A
93.080
289
15
3
785
1073
31756781
31756498
1.020000e-112
418.0
34
TraesCS6D01G064800
chr6A
86.216
399
37
11
818
1214
32739288
32739670
3.680000e-112
416.0
35
TraesCS6D01G064800
chr6A
83.090
479
41
15
810
1267
32887970
32887511
3.700000e-107
399.0
36
TraesCS6D01G064800
chr6A
79.458
443
52
20
858
1282
46701065
46700644
1.810000e-70
278.0
37
TraesCS6D01G064800
chr6A
77.338
556
64
29
683
1214
32814463
32813946
8.420000e-69
272.0
38
TraesCS6D01G064800
chr6A
91.099
191
16
1
5939
6129
31750275
31750086
2.360000e-64
257.0
39
TraesCS6D01G064800
chr6A
96.190
105
4
0
5966
6070
463805433
463805329
8.790000e-39
172.0
40
TraesCS6D01G064800
chr6A
94.118
102
6
0
5960
6061
262052143
262052042
8.850000e-34
156.0
41
TraesCS6D01G064800
chr6A
88.333
120
14
0
663
782
31760450
31760331
1.920000e-30
145.0
42
TraesCS6D01G064800
chr6A
94.505
91
5
0
1257
1347
31754947
31754857
2.480000e-29
141.0
43
TraesCS6D01G064800
chr6A
90.000
50
5
0
5805
5854
46696019
46695970
1.530000e-06
65.8
44
TraesCS6D01G064800
chr6B
93.208
3416
135
31
2106
5469
56398309
56394939
0.000000e+00
4933.0
45
TraesCS6D01G064800
chr6B
96.010
2005
55
10
3597
5595
56378585
56376600
0.000000e+00
3236.0
46
TraesCS6D01G064800
chr6B
85.183
3010
314
61
2654
5595
79877174
79880119
0.000000e+00
2966.0
47
TraesCS6D01G064800
chr6B
97.224
1621
41
3
1982
3600
56380283
56378665
0.000000e+00
2741.0
48
TraesCS6D01G064800
chr6B
89.257
1359
88
22
2940
4262
57417260
57418596
0.000000e+00
1648.0
49
TraesCS6D01G064800
chr6B
86.259
1470
126
33
4347
5783
57418673
57420099
0.000000e+00
1526.0
50
TraesCS6D01G064800
chr6B
89.710
1137
80
16
244
1372
56382124
56381017
0.000000e+00
1417.0
51
TraesCS6D01G064800
chr6B
86.907
1222
103
22
1
1214
56400279
56399107
0.000000e+00
1317.0
52
TraesCS6D01G064800
chr6B
83.346
1267
164
27
4347
5595
57732753
57731516
0.000000e+00
1127.0
53
TraesCS6D01G064800
chr6B
90.793
858
48
12
3322
4157
50409585
50408737
0.000000e+00
1118.0
54
TraesCS6D01G064800
chr6B
82.855
1289
95
50
1685
2908
57416030
57417257
0.000000e+00
1040.0
55
TraesCS6D01G064800
chr6B
96.846
539
16
1
6055
6592
56376173
56375635
0.000000e+00
900.0
56
TraesCS6D01G064800
chr6B
92.599
581
27
9
1369
1944
56380845
56380276
0.000000e+00
821.0
57
TraesCS6D01G064800
chr6B
95.712
513
14
1
5467
5971
56376683
56376171
0.000000e+00
819.0
58
TraesCS6D01G064800
chr6B
91.597
357
21
3
1637
1990
56398690
56398340
9.940000e-133
484.0
59
TraesCS6D01G064800
chr6B
80.694
663
51
22
1946
2562
79876382
79877013
1.690000e-120
444.0
60
TraesCS6D01G064800
chr6B
84.048
420
41
17
813
1214
57737013
57736602
1.340000e-101
381.0
61
TraesCS6D01G064800
chr6B
82.725
411
49
12
811
1214
57415227
57415622
4.890000e-91
346.0
62
TraesCS6D01G064800
chr6B
83.920
199
17
11
6150
6341
56394236
56394046
6.790000e-40
176.0
63
TraesCS6D01G064800
chr6B
85.093
161
18
3
666
826
56382283
56382129
6.840000e-35
159.0
64
TraesCS6D01G064800
chr6B
96.703
91
3
0
1257
1347
56381216
56381126
1.140000e-32
152.0
65
TraesCS6D01G064800
chr6B
91.579
95
5
1
1176
1267
56381135
56381041
1.930000e-25
128.0
66
TraesCS6D01G064800
chr6B
90.000
50
5
0
5805
5854
79880685
79880734
1.530000e-06
65.8
67
TraesCS6D01G064800
chrUn
84.677
2493
229
65
3322
5734
137913395
137910976
0.000000e+00
2346.0
68
TraesCS6D01G064800
chrUn
88.160
1647
137
22
2653
4262
27472851
27474476
0.000000e+00
1908.0
69
TraesCS6D01G064800
chrUn
84.712
1269
147
25
4347
5595
27474556
27475797
0.000000e+00
1225.0
70
TraesCS6D01G064800
chrUn
87.174
499
48
8
2754
3239
137913906
137913411
2.690000e-153
553.0
71
TraesCS6D01G064800
chrUn
80.867
669
50
31
1946
2562
27472050
27472692
7.790000e-124
455.0
72
TraesCS6D01G064800
chrUn
82.778
540
58
14
1668
2188
68355763
68356286
3.630000e-122
449.0
73
TraesCS6D01G064800
chrUn
82.674
531
58
17
1668
2188
268239291
268239797
2.180000e-119
440.0
74
TraesCS6D01G064800
chrUn
82.674
531
58
17
1668
2188
312454620
312454114
2.180000e-119
440.0
75
TraesCS6D01G064800
chrUn
86.740
181
24
0
5467
5647
27475714
27475894
1.120000e-47
202.0
76
TraesCS6D01G064800
chrUn
85.047
107
11
4
6470
6575
95262297
95262195
3.250000e-18
104.0
77
TraesCS6D01G064800
chr2D
79.917
1454
195
59
4347
5734
48566433
48567855
0.000000e+00
977.0
78
TraesCS6D01G064800
chr2D
82.584
1068
104
32
1659
2661
48562867
48563917
0.000000e+00
867.0
79
TraesCS6D01G064800
chr2D
86.837
471
31
12
812
1267
48562243
48562697
1.280000e-136
497.0
80
TraesCS6D01G064800
chr2D
82.667
150
12
4
1257
1405
48562615
48562751
3.230000e-23
121.0
81
TraesCS6D01G064800
chr2B
87.171
608
55
12
4360
4947
96277722
96278326
0.000000e+00
669.0
82
TraesCS6D01G064800
chr4B
87.007
608
56
14
4360
4947
614205250
614204646
0.000000e+00
664.0
83
TraesCS6D01G064800
chr4B
93.396
106
6
1
5951
6056
403270795
403270691
8.850000e-34
156.0
84
TraesCS6D01G064800
chr4B
97.500
40
1
0
6422
6461
564902382
564902343
1.190000e-07
69.4
85
TraesCS6D01G064800
chr4B
88.889
54
4
2
6410
6461
167355495
167355548
1.530000e-06
65.8
86
TraesCS6D01G064800
chr3B
86.184
608
61
13
4360
4947
701122710
701122106
2.590000e-178
636.0
87
TraesCS6D01G064800
chr5A
84.259
432
42
14
1780
2190
655642348
655642774
1.330000e-106
398.0
88
TraesCS6D01G064800
chr5A
88.889
243
26
1
1946
2188
655640983
655641224
1.390000e-76
298.0
89
TraesCS6D01G064800
chr5A
89.744
117
9
2
5954
6070
9507996
9508109
5.330000e-31
147.0
90
TraesCS6D01G064800
chr5A
84.058
69
7
3
6391
6456
368561817
368561884
5.520000e-06
63.9
91
TraesCS6D01G064800
chr5B
81.391
532
58
19
1668
2188
664893064
664893565
4.790000e-106
396.0
92
TraesCS6D01G064800
chr5B
97.561
41
1
0
6422
6462
82475840
82475880
3.300000e-08
71.3
93
TraesCS6D01G064800
chr1A
98.901
91
1
0
5966
6056
498811735
498811645
5.290000e-36
163.0
94
TraesCS6D01G064800
chr1A
95.098
102
2
3
5965
6063
327008617
327008718
2.460000e-34
158.0
95
TraesCS6D01G064800
chr4D
92.453
106
7
1
5966
6070
436376804
436376699
4.120000e-32
150.0
96
TraesCS6D01G064800
chr4D
84.722
72
8
3
6494
6563
47500188
47500118
1.190000e-07
69.4
97
TraesCS6D01G064800
chr4D
97.500
40
1
0
6422
6461
486185382
486185343
1.190000e-07
69.4
98
TraesCS6D01G064800
chr2A
100.000
38
0
0
6422
6459
706204949
706204986
3.300000e-08
71.3
99
TraesCS6D01G064800
chr5D
97.500
40
1
0
6422
6461
533641527
533641488
1.190000e-07
69.4
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
TraesCS6D01G064800
chr6D
31468888
31475479
6591
False
12174.000000
12174
100.000000
1
6592
1
chr6D.!!$F2
6591
1
TraesCS6D01G064800
chr6D
30096465
30099820
3355
True
985.333333
1616
84.629667
815
4262
3
chr6D.!!$R3
3447
2
TraesCS6D01G064800
chr6D
31266923
31272731
5808
True
969.185714
2111
90.667286
1
5783
7
chr6D.!!$R4
5782
3
TraesCS6D01G064800
chr6D
29848972
29853721
4749
False
730.000000
1016
82.783000
812
5734
2
chr6D.!!$F3
4922
4
TraesCS6D01G064800
chr6D
29922324
29927750
5426
False
711.500000
1079
82.765500
813
5595
2
chr6D.!!$F4
4782
5
TraesCS6D01G064800
chr6A
31750086
31760450
10364
True
1178.500000
5138
91.925750
1
6129
8
chr6A.!!$R4
6128
6
TraesCS6D01G064800
chr6A
32739288
32744112
4824
False
1105.500000
1633
86.303750
818
5783
4
chr6A.!!$F2
4965
7
TraesCS6D01G064800
chr6A
46695970
46701065
5095
True
954.700000
3018
83.520000
858
5854
4
chr6A.!!$R7
4996
8
TraesCS6D01G064800
chr6A
32883245
32887970
4725
True
719.500000
1040
82.006000
810
5717
2
chr6A.!!$R6
4907
9
TraesCS6D01G064800
chr6A
32809991
32814463
4472
True
697.000000
1122
80.309500
683
5595
2
chr6A.!!$R5
4912
10
TraesCS6D01G064800
chr6B
56394046
56400279
6233
True
1727.500000
4933
88.908000
1
6341
4
chr6B.!!$R3
6340
11
TraesCS6D01G064800
chr6B
79876382
79880734
4352
False
1158.600000
2966
85.292333
1946
5854
3
chr6B.!!$F2
3908
12
TraesCS6D01G064800
chr6B
56375635
56382283
6648
True
1152.555556
3236
93.497333
244
6592
9
chr6B.!!$R2
6348
13
TraesCS6D01G064800
chr6B
57415227
57420099
4872
False
1140.000000
1648
85.274000
811
5783
4
chr6B.!!$F1
4972
14
TraesCS6D01G064800
chr6B
50408737
50409585
848
True
1118.000000
1118
90.793000
3322
4157
1
chr6B.!!$R1
835
15
TraesCS6D01G064800
chr6B
57731516
57737013
5497
True
754.000000
1127
83.697000
813
5595
2
chr6B.!!$R4
4782
16
TraesCS6D01G064800
chrUn
137910976
137913906
2930
True
1449.500000
2346
85.925500
2754
5734
2
chrUn.!!$R3
2980
17
TraesCS6D01G064800
chrUn
27472050
27475894
3844
False
947.500000
1908
85.119750
1946
5647
4
chrUn.!!$F3
3701
18
TraesCS6D01G064800
chrUn
68355763
68356286
523
False
449.000000
449
82.778000
1668
2188
1
chrUn.!!$F1
520
19
TraesCS6D01G064800
chrUn
268239291
268239797
506
False
440.000000
440
82.674000
1668
2188
1
chrUn.!!$F2
520
20
TraesCS6D01G064800
chrUn
312454114
312454620
506
True
440.000000
440
82.674000
1668
2188
1
chrUn.!!$R2
520
21
TraesCS6D01G064800
chr2D
48562243
48567855
5612
False
615.500000
977
83.001250
812
5734
4
chr2D.!!$F1
4922
22
TraesCS6D01G064800
chr2B
96277722
96278326
604
False
669.000000
669
87.171000
4360
4947
1
chr2B.!!$F1
587
23
TraesCS6D01G064800
chr4B
614204646
614205250
604
True
664.000000
664
87.007000
4360
4947
1
chr4B.!!$R3
587
24
TraesCS6D01G064800
chr3B
701122106
701122710
604
True
636.000000
636
86.184000
4360
4947
1
chr3B.!!$R1
587
25
TraesCS6D01G064800
chr5A
655640983
655642774
1791
False
348.000000
398
86.574000
1780
2190
2
chr5A.!!$F3
410
26
TraesCS6D01G064800
chr5B
664893064
664893565
501
False
396.000000
396
81.391000
1668
2188
1
chr5B.!!$F2
520
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.