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
TraesCS1D01G395500
chr1D
100.000
2552
0
0
1
2552
464036994
464039545
0.000000e+00
4713.0
1
TraesCS1D01G395500
chr1D
93.496
1891
78
17
594
2447
347252970
347251088
0.000000e+00
2769.0
2
TraesCS1D01G395500
chr1D
94.619
223
12
0
377
599
202683487
202683265
1.880000e-91
346.0
3
TraesCS1D01G395500
chr1D
92.202
218
14
3
377
593
191302445
191302230
3.190000e-79
305.0
4
TraesCS1D01G395500
chr1D
91.441
222
19
0
377
598
403264616
403264837
3.190000e-79
305.0
5
TraesCS1D01G395500
chr1D
77.564
312
49
11
6
296
423783488
423783799
4.370000e-38
169.0
6
TraesCS1D01G395500
chr1A
93.607
2581
124
15
1
2552
556201170
556203738
0.000000e+00
3814.0
7
TraesCS1D01G395500
chr1A
90.306
1733
101
29
596
2295
38372360
38374058
0.000000e+00
2207.0
8
TraesCS1D01G395500
chr6D
93.467
1990
87
9
596
2552
312544305
312542326
0.000000e+00
2915.0
9
TraesCS1D01G395500
chr6D
93.458
214
14
0
386
599
460914108
460913895
4.100000e-83
318.0
10
TraesCS1D01G395500
chr6D
90.435
230
21
1
370
599
178904269
178904497
4.130000e-78
302.0
11
TraesCS1D01G395500
chr3D
93.380
1979
84
19
599
2552
447973574
447971618
0.000000e+00
2885.0
12
TraesCS1D01G395500
chr3D
91.089
2020
79
21
600
2552
573731195
573733180
0.000000e+00
2639.0
13
TraesCS1D01G395500
chr3D
93.371
1056
53
9
600
1639
519945751
519944697
0.000000e+00
1546.0
14
TraesCS1D01G395500
chr4D
93.253
1986
78
20
597
2549
50776931
50778893
0.000000e+00
2874.0
15
TraesCS1D01G395500
chr4D
92.369
249
15
4
351
599
122143283
122143527
4.040000e-93
351.0
16
TraesCS1D01G395500
chr4D
93.243
222
14
1
378
599
122140532
122140312
2.450000e-85
326.0
17
TraesCS1D01G395500
chr4D
92.056
214
17
0
386
599
161154639
161154426
4.130000e-78
302.0
18
TraesCS1D01G395500
chr4D
91.705
217
17
1
378
594
500807990
500807775
1.480000e-77
300.0
19
TraesCS1D01G395500
chr4D
91.589
214
18
0
386
599
91613402
91613189
1.920000e-76
296.0
20
TraesCS1D01G395500
chr4D
91.589
214
18
0
386
599
119942061
119941848
1.920000e-76
296.0
21
TraesCS1D01G395500
chr4D
91.589
214
18
0
386
599
433946704
433946917
1.920000e-76
296.0
22
TraesCS1D01G395500
chr4D
90.090
222
21
1
378
599
469286999
469286779
1.160000e-73
287.0
23
TraesCS1D01G395500
chr3A
92.973
1978
105
16
599
2552
235187478
235189445
0.000000e+00
2852.0
24
TraesCS1D01G395500
chr7D
93.860
1873
87
8
600
2447
623570819
623572688
0.000000e+00
2796.0
25
TraesCS1D01G395500
chr7D
91.967
1718
83
23
596
2290
63995386
63997071
0.000000e+00
2357.0
26
TraesCS1D01G395500
chr7D
89.960
249
21
1
351
599
245561220
245561464
4.100000e-83
318.0
27
TraesCS1D01G395500
chr7A
90.986
2019
119
22
583
2552
30966331
30968335
0.000000e+00
2662.0
28
TraesCS1D01G395500
chr2A
90.868
1982
131
21
594
2552
742454762
742452808
0.000000e+00
2612.0
29
TraesCS1D01G395500
chr2A
90.862
1740
98
21
585
2295
677958483
677956776
0.000000e+00
2276.0
30
TraesCS1D01G395500
chr2A
82.682
179
26
2
181
354
334533844
334534022
1.220000e-33
154.0
31
TraesCS1D01G395500
chr6A
92.013
1878
115
9
600
2446
76046189
76048062
0.000000e+00
2604.0
32
TraesCS1D01G395500
chr5D
93.352
1399
56
14
580
1949
539819790
539818400
0.000000e+00
2034.0
33
TraesCS1D01G395500
chr5D
93.694
222
13
1
378
599
221737408
221737628
5.260000e-87
331.0
34
TraesCS1D01G395500
chr5D
92.857
224
16
0
376
599
339274940
339275163
2.450000e-85
326.0
35
TraesCS1D01G395500
chr5D
92.342
222
16
1
378
599
268688814
268688594
5.300000e-82
315.0
36
TraesCS1D01G395500
chr5D
92.593
216
15
1
378
593
197484351
197484565
2.470000e-80
309.0
37
TraesCS1D01G395500
chr2D
93.061
980
31
14
1491
2447
572813896
572814861
0.000000e+00
1399.0
38
TraesCS1D01G395500
chr2D
83.425
181
25
3
179
354
12466104
12465924
2.030000e-36
163.0
39
TraesCS1D01G395500
chr5B
93.519
216
14
0
378
593
153866273
153866058
3.170000e-84
322.0
40
TraesCS1D01G395500
chr5A
92.793
222
16
0
378
599
49243659
49243880
3.170000e-84
322.0
41
TraesCS1D01G395500
chr4A
90.361
249
18
6
351
599
473326168
473326410
3.170000e-84
322.0
42
TraesCS1D01G395500
chr7B
89.344
244
22
2
356
599
214932377
214932616
1.150000e-78
303.0
43
TraesCS1D01G395500
chr7B
98.256
172
2
1
2381
2552
663210112
663210282
1.480000e-77
300.0
44
TraesCS1D01G395500
chr7B
92.683
41
2
1
170
210
671423540
671423501
9.860000e-05
58.4
45
TraesCS1D01G395500
chr4B
90.991
222
20
0
378
599
491132068
491131847
1.480000e-77
300.0
46
TraesCS1D01G395500
chr4B
88.525
244
24
2
356
599
348255928
348255689
2.480000e-75
292.0
47
TraesCS1D01G395500
chr4B
87.395
119
13
2
180
297
4298660
4298777
4.430000e-28
135.0
48
TraesCS1D01G395500
chrUn
88.426
216
24
1
378
593
11254906
11255120
2.520000e-65
259.0
49
TraesCS1D01G395500
chrUn
88.318
214
25
0
386
599
233519082
233518869
9.060000e-65
257.0
50
TraesCS1D01G395500
chrUn
87.330
221
26
2
377
597
88191276
88191494
4.210000e-63
252.0
51
TraesCS1D01G395500
chrUn
87.500
216
26
1
378
593
218991731
218991945
5.450000e-62
248.0
52
TraesCS1D01G395500
chrUn
86.070
201
22
6
388
585
244763926
244764123
7.150000e-51
211.0
53
TraesCS1D01G395500
chrUn
93.939
132
8
0
377
508
110450583
110450452
1.550000e-47
200.0
54
TraesCS1D01G395500
chrUn
83.981
206
31
2
393
597
54337770
54337974
2.000000e-46
196.0
55
TraesCS1D01G395500
chrUn
93.182
132
9
0
377
508
110428224
110428093
7.200000e-46
195.0
56
TraesCS1D01G395500
chrUn
82.915
199
24
10
397
591
296904261
296904069
1.210000e-38
171.0
57
TraesCS1D01G395500
chrUn
81.106
217
33
7
388
599
128551367
128551154
1.570000e-37
167.0
58
TraesCS1D01G395500
chrUn
100.000
31
0
0
180
210
381317668
381317638
9.860000e-05
58.4
59
TraesCS1D01G395500
chr2B
83.060
183
25
4
177
353
748341869
748341687
7.310000e-36
161.0
60
TraesCS1D01G395500
chr1B
82.162
185
27
3
177
355
91297487
91297303
1.220000e-33
154.0
61
TraesCS1D01G395500
chr6B
87.288
118
15
0
179
296
632735417
632735534
4.430000e-28
135.0
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
TraesCS1D01G395500
chr1D
464036994
464039545
2551
False
4713
4713
100.000
1
2552
1
chr1D.!!$F3
2551
1
TraesCS1D01G395500
chr1D
347251088
347252970
1882
True
2769
2769
93.496
594
2447
1
chr1D.!!$R3
1853
2
TraesCS1D01G395500
chr1A
556201170
556203738
2568
False
3814
3814
93.607
1
2552
1
chr1A.!!$F2
2551
3
TraesCS1D01G395500
chr1A
38372360
38374058
1698
False
2207
2207
90.306
596
2295
1
chr1A.!!$F1
1699
4
TraesCS1D01G395500
chr6D
312542326
312544305
1979
True
2915
2915
93.467
596
2552
1
chr6D.!!$R1
1956
5
TraesCS1D01G395500
chr3D
447971618
447973574
1956
True
2885
2885
93.380
599
2552
1
chr3D.!!$R1
1953
6
TraesCS1D01G395500
chr3D
573731195
573733180
1985
False
2639
2639
91.089
600
2552
1
chr3D.!!$F1
1952
7
TraesCS1D01G395500
chr3D
519944697
519945751
1054
True
1546
1546
93.371
600
1639
1
chr3D.!!$R2
1039
8
TraesCS1D01G395500
chr4D
50776931
50778893
1962
False
2874
2874
93.253
597
2549
1
chr4D.!!$F1
1952
9
TraesCS1D01G395500
chr3A
235187478
235189445
1967
False
2852
2852
92.973
599
2552
1
chr3A.!!$F1
1953
10
TraesCS1D01G395500
chr7D
623570819
623572688
1869
False
2796
2796
93.860
600
2447
1
chr7D.!!$F3
1847
11
TraesCS1D01G395500
chr7D
63995386
63997071
1685
False
2357
2357
91.967
596
2290
1
chr7D.!!$F1
1694
12
TraesCS1D01G395500
chr7A
30966331
30968335
2004
False
2662
2662
90.986
583
2552
1
chr7A.!!$F1
1969
13
TraesCS1D01G395500
chr2A
742452808
742454762
1954
True
2612
2612
90.868
594
2552
1
chr2A.!!$R2
1958
14
TraesCS1D01G395500
chr2A
677956776
677958483
1707
True
2276
2276
90.862
585
2295
1
chr2A.!!$R1
1710
15
TraesCS1D01G395500
chr6A
76046189
76048062
1873
False
2604
2604
92.013
600
2446
1
chr6A.!!$F1
1846
16
TraesCS1D01G395500
chr5D
539818400
539819790
1390
True
2034
2034
93.352
580
1949
1
chr5D.!!$R2
1369
17
TraesCS1D01G395500
chr2D
572813896
572814861
965
False
1399
1399
93.061
1491
2447
1
chr2D.!!$F1
956
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.