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
TraesCS2A01G506700
chr2A
100.000
7734
0
0
1
7734
734524258
734516525
0.000000e+00
14283.0
1
TraesCS2A01G506700
chr2A
98.462
2405
35
1
4322
6724
734535515
734533111
0.000000e+00
4235.0
2
TraesCS2A01G506700
chr2A
91.767
2247
102
42
4278
6493
10258580
10256386
0.000000e+00
3048.0
3
TraesCS2A01G506700
chr2A
98.185
1543
18
5
946
2484
734624574
734626110
0.000000e+00
2686.0
4
TraesCS2A01G506700
chr2A
98.756
1367
17
0
3037
4403
734536764
734535398
0.000000e+00
2431.0
5
TraesCS2A01G506700
chr2A
95.278
953
35
4
1
949
734623562
734624508
0.000000e+00
1502.0
6
TraesCS2A01G506700
chr2A
99.630
540
2
0
2499
3038
734626292
734626831
0.000000e+00
987.0
7
TraesCS2A01G506700
chr2A
90.476
63
6
0
2743
2805
30182025
30182087
4.970000e-12
84.2
8
TraesCS2A01G506700
chr6A
97.783
3699
52
11
3037
6722
23599541
23595860
0.000000e+00
6349.0
9
TraesCS2A01G506700
chr6A
96.900
2452
56
11
4286
6722
268197959
268200405
0.000000e+00
4089.0
10
TraesCS2A01G506700
chr6A
96.573
2451
57
10
4286
6724
23052499
23054934
0.000000e+00
4036.0
11
TraesCS2A01G506700
chr6A
95.347
1569
44
13
3037
4605
268196676
268198215
0.000000e+00
2466.0
12
TraesCS2A01G506700
chr6A
95.883
1506
34
12
3100
4605
23051278
23052755
0.000000e+00
2412.0
13
TraesCS2A01G506700
chr6A
94.819
1023
36
9
6720
7734
584504328
584503315
0.000000e+00
1580.0
14
TraesCS2A01G506700
chr6A
95.898
707
26
3
7030
7734
97612052
97611347
0.000000e+00
1142.0
15
TraesCS2A01G506700
chr6A
96.392
194
3
4
6720
6910
97613291
97613099
4.500000e-82
316.0
16
TraesCS2A01G506700
chr6A
96.373
193
4
3
6721
6910
97613819
97613627
1.620000e-81
315.0
17
TraesCS2A01G506700
chr6A
89.076
119
5
2
6913
7029
97613589
97613477
2.910000e-29
141.0
18
TraesCS2A01G506700
chr6A
92.079
101
2
1
6913
7013
97613061
97612967
3.760000e-28
137.0
19
TraesCS2A01G506700
chr7A
97.141
2448
58
7
4286
6722
130651510
130653956
0.000000e+00
4122.0
20
TraesCS2A01G506700
chr7A
97.790
1403
31
0
3037
4439
130650225
130651627
0.000000e+00
2420.0
21
TraesCS2A01G506700
chr7A
94.283
997
42
8
6746
7734
66752972
66753961
0.000000e+00
1511.0
22
TraesCS2A01G506700
chr7A
96.450
169
6
0
7444
7612
63875239
63875407
5.910000e-71
279.0
23
TraesCS2A01G506700
chr2B
92.137
2658
113
21
3832
6414
155882954
155885590
0.000000e+00
3663.0
24
TraesCS2A01G506700
chr2B
88.939
1546
101
36
782
2297
731339831
731341336
0.000000e+00
1844.0
25
TraesCS2A01G506700
chr2B
89.714
700
70
2
2
699
731313087
731313786
0.000000e+00
893.0
26
TraesCS2A01G506700
chr2B
89.971
339
34
0
6384
6722
155885524
155885862
9.210000e-119
438.0
27
TraesCS2A01G506700
chr2B
80.272
147
24
3
2342
2484
181060281
181060136
1.060000e-18
106.0
28
TraesCS2A01G506700
chr2B
78.689
122
21
4
2729
2850
609961483
609961599
8.320000e-10
76.8
29
TraesCS2A01G506700
chr2D
91.805
2294
114
37
772
3038
601201503
601203749
0.000000e+00
3127.0
30
TraesCS2A01G506700
chr2D
96.424
1622
49
6
3037
4649
339727478
339729099
0.000000e+00
2665.0
31
TraesCS2A01G506700
chr2D
87.952
332
39
1
1
331
601184781
601185112
2.620000e-104
390.0
32
TraesCS2A01G506700
chr2D
90.411
219
17
2
555
773
601188905
601189119
1.270000e-72
285.0
33
TraesCS2A01G506700
chr1D
92.916
2188
80
30
4286
6426
200756426
200754267
0.000000e+00
3112.0
34
TraesCS2A01G506700
chr1D
93.266
297
19
1
6429
6725
200754360
200754065
3.310000e-118
436.0
35
TraesCS2A01G506700
chr1D
78.543
508
70
17
6978
7475
120656980
120656502
1.630000e-76
298.0
36
TraesCS2A01G506700
chr1D
79.255
188
31
4
2347
2527
218666019
218666205
2.930000e-24
124.0
37
TraesCS2A01G506700
chr1D
79.255
188
31
4
2347
2527
234149388
234149574
2.930000e-24
124.0
38
TraesCS2A01G506700
chr1D
78.756
193
32
6
2342
2527
373485541
373485351
3.790000e-23
121.0
39
TraesCS2A01G506700
chr1D
83.333
120
17
3
2728
2847
365430056
365429940
2.950000e-19
108.0
40
TraesCS2A01G506700
chr6B
92.183
2162
98
32
4358
6493
481015811
481013695
0.000000e+00
2990.0
41
TraesCS2A01G506700
chr6B
85.285
333
30
5
6390
6722
481013847
481013534
7.480000e-85
326.0
42
TraesCS2A01G506700
chr6B
79.235
183
26
4
6541
6723
453527152
453527322
4.900000e-22
117.0
43
TraesCS2A01G506700
chr1A
96.279
1747
55
6
3037
4773
540659184
540660930
0.000000e+00
2857.0
44
TraesCS2A01G506700
chr1A
93.894
999
51
4
6738
7734
192592613
192591623
0.000000e+00
1498.0
45
TraesCS2A01G506700
chr1A
96.364
825
22
5
6913
7734
574821766
574822585
0.000000e+00
1351.0
46
TraesCS2A01G506700
chr1A
92.821
195
6
5
6728
6917
574820945
574821136
7.650000e-70
276.0
47
TraesCS2A01G506700
chr3A
96.226
1749
48
10
3037
4773
41415161
41413419
0.000000e+00
2848.0
48
TraesCS2A01G506700
chr3A
93.882
899
28
13
5518
6414
723559555
723560428
0.000000e+00
1330.0
49
TraesCS2A01G506700
chr3A
89.349
338
31
2
6387
6724
723560365
723560697
3.340000e-113
420.0
50
TraesCS2A01G506700
chr4A
96.105
1746
56
6
3037
4773
449968517
449966775
0.000000e+00
2837.0
51
TraesCS2A01G506700
chr4A
95.652
46
2
0
4394
4439
253994461
253994416
2.990000e-09
75.0
52
TraesCS2A01G506700
chr4A
77.311
119
18
6
2733
2848
433056911
433056799
2.330000e-05
62.1
53
TraesCS2A01G506700
chr5A
92.701
822
25
10
6913
7734
138078111
138077325
0.000000e+00
1153.0
54
TraesCS2A01G506700
chr5A
94.240
434
15
5
6973
7404
694498392
694497967
0.000000e+00
654.0
55
TraesCS2A01G506700
chr5A
96.373
193
4
3
6721
6910
138078342
138078150
1.620000e-81
315.0
56
TraesCS2A01G506700
chr5A
90.811
185
4
7
6721
6895
694498784
694498603
1.300000e-57
235.0
57
TraesCS2A01G506700
chr5A
83.088
136
22
1
2733
2868
539071652
539071786
1.050000e-23
122.0
58
TraesCS2A01G506700
chr3D
87.551
972
84
14
5757
6722
89282010
89282950
0.000000e+00
1090.0
59
TraesCS2A01G506700
chr3D
87.179
78
7
1
6328
6402
89282708
89282785
1.380000e-12
86.1
60
TraesCS2A01G506700
chr7D
87.853
354
42
1
6380
6732
196448123
196448476
1.550000e-111
414.0
61
TraesCS2A01G506700
chr7D
79.459
185
29
5
2350
2527
115977632
115977450
1.050000e-23
122.0
62
TraesCS2A01G506700
chr7D
78.919
185
31
4
2350
2527
617858903
617858720
1.360000e-22
119.0
63
TraesCS2A01G506700
chr7D
81.295
139
21
3
2350
2484
225707209
225707072
2.950000e-19
108.0
64
TraesCS2A01G506700
chr7D
84.127
63
10
0
2742
2804
602074390
602074452
2.330000e-05
62.1
65
TraesCS2A01G506700
chr1B
77.996
509
73
20
6988
7487
114875659
114875181
4.570000e-72
283.0
66
TraesCS2A01G506700
chr1B
82.569
109
14
4
2735
2842
312555262
312555366
2.970000e-14
91.6
67
TraesCS2A01G506700
chr5B
78.756
193
33
4
2342
2527
506578723
506578532
1.050000e-23
122.0
68
TraesCS2A01G506700
chr5B
92.500
40
3
0
2733
2772
391925184
391925145
3.010000e-04
58.4
69
TraesCS2A01G506700
chr4B
78.238
193
34
5
2342
2527
106355830
106356021
4.900000e-22
117.0
70
TraesCS2A01G506700
chr4B
80.303
132
22
2
6429
6557
434187764
434187634
6.390000e-16
97.1
71
TraesCS2A01G506700
chr7B
77.949
195
35
4
2342
2529
268063834
268063641
1.760000e-21
115.0
72
TraesCS2A01G506700
chr7B
80.556
72
14
0
2744
2815
57270391
57270320
1.000000e-03
56.5
73
TraesCS2A01G506700
chr6D
80.952
147
23
3
2342
2484
339854023
339853878
2.280000e-20
111.0
74
TraesCS2A01G506700
chr6D
80.808
99
18
1
2729
2826
403660713
403660811
8.320000e-10
76.8
75
TraesCS2A01G506700
chr6D
82.500
80
14
0
2733
2812
2900492
2900571
3.870000e-08
71.3
76
TraesCS2A01G506700
chr6D
83.117
77
13
0
2729
2805
445612613
445612689
3.870000e-08
71.3
77
TraesCS2A01G506700
chr3B
81.481
108
20
0
2729
2836
758458922
758459029
1.070000e-13
89.8
78
TraesCS2A01G506700
chr3B
87.500
72
9
0
2729
2800
238319934
238320005
4.970000e-12
84.2
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
TraesCS2A01G506700
chr2A
734516525
734524258
7733
True
14283.00
14283
100.000000
1
7734
1
chr2A.!!$R2
7733
1
TraesCS2A01G506700
chr2A
734533111
734536764
3653
True
3333.00
4235
98.609000
3037
6724
2
chr2A.!!$R3
3687
2
TraesCS2A01G506700
chr2A
10256386
10258580
2194
True
3048.00
3048
91.767000
4278
6493
1
chr2A.!!$R1
2215
3
TraesCS2A01G506700
chr2A
734623562
734626831
3269
False
1725.00
2686
97.697667
1
3038
3
chr2A.!!$F2
3037
4
TraesCS2A01G506700
chr6A
23595860
23599541
3681
True
6349.00
6349
97.783000
3037
6722
1
chr6A.!!$R1
3685
5
TraesCS2A01G506700
chr6A
268196676
268200405
3729
False
3277.50
4089
96.123500
3037
6722
2
chr6A.!!$F2
3685
6
TraesCS2A01G506700
chr6A
23051278
23054934
3656
False
3224.00
4036
96.228000
3100
6724
2
chr6A.!!$F1
3624
7
TraesCS2A01G506700
chr6A
584503315
584504328
1013
True
1580.00
1580
94.819000
6720
7734
1
chr6A.!!$R2
1014
8
TraesCS2A01G506700
chr6A
97611347
97613819
2472
True
410.20
1142
93.963600
6720
7734
5
chr6A.!!$R3
1014
9
TraesCS2A01G506700
chr7A
130650225
130653956
3731
False
3271.00
4122
97.465500
3037
6722
2
chr7A.!!$F3
3685
10
TraesCS2A01G506700
chr7A
66752972
66753961
989
False
1511.00
1511
94.283000
6746
7734
1
chr7A.!!$F2
988
11
TraesCS2A01G506700
chr2B
155882954
155885862
2908
False
2050.50
3663
91.054000
3832
6722
2
chr2B.!!$F4
2890
12
TraesCS2A01G506700
chr2B
731339831
731341336
1505
False
1844.00
1844
88.939000
782
2297
1
chr2B.!!$F3
1515
13
TraesCS2A01G506700
chr2B
731313087
731313786
699
False
893.00
893
89.714000
2
699
1
chr2B.!!$F2
697
14
TraesCS2A01G506700
chr2D
601201503
601203749
2246
False
3127.00
3127
91.805000
772
3038
1
chr2D.!!$F2
2266
15
TraesCS2A01G506700
chr2D
339727478
339729099
1621
False
2665.00
2665
96.424000
3037
4649
1
chr2D.!!$F1
1612
16
TraesCS2A01G506700
chr2D
601184781
601189119
4338
False
337.50
390
89.181500
1
773
2
chr2D.!!$F3
772
17
TraesCS2A01G506700
chr1D
200754065
200756426
2361
True
1774.00
3112
93.091000
4286
6725
2
chr1D.!!$R4
2439
18
TraesCS2A01G506700
chr6B
481013534
481015811
2277
True
1658.00
2990
88.734000
4358
6722
2
chr6B.!!$R1
2364
19
TraesCS2A01G506700
chr1A
540659184
540660930
1746
False
2857.00
2857
96.279000
3037
4773
1
chr1A.!!$F1
1736
20
TraesCS2A01G506700
chr1A
192591623
192592613
990
True
1498.00
1498
93.894000
6738
7734
1
chr1A.!!$R1
996
21
TraesCS2A01G506700
chr1A
574820945
574822585
1640
False
813.50
1351
94.592500
6728
7734
2
chr1A.!!$F2
1006
22
TraesCS2A01G506700
chr3A
41413419
41415161
1742
True
2848.00
2848
96.226000
3037
4773
1
chr3A.!!$R1
1736
23
TraesCS2A01G506700
chr3A
723559555
723560697
1142
False
875.00
1330
91.615500
5518
6724
2
chr3A.!!$F1
1206
24
TraesCS2A01G506700
chr4A
449966775
449968517
1742
True
2837.00
2837
96.105000
3037
4773
1
chr4A.!!$R3
1736
25
TraesCS2A01G506700
chr5A
138077325
138078342
1017
True
734.00
1153
94.537000
6721
7734
2
chr5A.!!$R1
1013
26
TraesCS2A01G506700
chr5A
694497967
694498784
817
True
444.50
654
92.525500
6721
7404
2
chr5A.!!$R2
683
27
TraesCS2A01G506700
chr3D
89282010
89282950
940
False
588.05
1090
87.365000
5757
6722
2
chr3D.!!$F1
965
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.