Multiple sequence alignment - TraesCS1D01G257800
Loading Multiple Alignment...
BLAST Results
BLAST Results - Input Sequence
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
TraesCS1D01G257800
chr1D
100.000
2910
0
0
1
2910
350655056
350652147
0.000000e+00
5374
1
TraesCS1D01G257800
chr1A
92.044
2627
114
42
258
2831
451619709
451617125
0.000000e+00
3605
2
TraesCS1D01G257800
chr1A
96.629
89
3
0
2822
2910
451616548
451616460
6.500000e-32
148
3
TraesCS1D01G257800
chr1B
92.501
1947
78
34
991
2910
473286179
473284274
0.000000e+00
2724
4
TraesCS1D01G257800
chr1B
94.023
686
28
6
258
942
473286853
473286180
0.000000e+00
1027
5
TraesCS1D01G257800
chr1B
96.721
61
2
0
1
61
194531600
194531660
5.130000e-18
102
6
TraesCS1D01G257800
chr4D
95.238
252
12
0
1
252
373813275
373813024
1.620000e-107
399
7
TraesCS1D01G257800
chr6A
95.161
248
12
0
1
248
601959714
601959961
2.720000e-105
392
8
TraesCS1D01G257800
chr6A
86.420
243
33
0
1
243
447583851
447584093
1.720000e-67
267
9
TraesCS1D01G257800
chr6B
94.024
251
12
2
1
248
647845744
647845994
7.610000e-101
377
BLAST Results - HSPs grouped
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
TraesCS1D01G257800
chr1D
350652147
350655056
2909
True
5374.0
5374
100.0000
1
2910
1
chr1D.!!$R1
2909
1
TraesCS1D01G257800
chr1A
451616460
451619709
3249
True
1876.5
3605
94.3365
258
2910
2
chr1A.!!$R1
2652
2
TraesCS1D01G257800
chr1B
473284274
473286853
2579
True
1875.5
2724
93.2620
258
2910
2
chr1B.!!$R1
2652
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
750
770
0.333652
TCTCACCGTCTCCACCCATA
59.666
55.0
0.0
0.0
0.0
2.74
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2539
2589
0.0414
CAAACGCACGCACTGATGAA
60.041
50.0
0.0
0.0
0.0
2.57
R
All possible primers
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.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
18
19
4.373116
GGGAGAACGGCGACTGCA
62.373
66.667
16.62
0.00
45.35
4.41
19
20
2.811317
GGAGAACGGCGACTGCAG
60.811
66.667
16.62
13.48
45.35
4.41
20
21
3.482783
GAGAACGGCGACTGCAGC
61.483
66.667
16.62
5.81
45.35
5.25
21
22
4.299547
AGAACGGCGACTGCAGCA
62.300
61.111
16.62
0.00
45.35
4.41
22
23
3.782244
GAACGGCGACTGCAGCAG
61.782
66.667
21.54
21.54
45.35
4.24
31
32
3.429141
CTGCAGCAGCGGTGGAAG
61.429
66.667
17.54
0.15
46.23
3.46
32
33
3.889134
CTGCAGCAGCGGTGGAAGA
62.889
63.158
17.54
0.00
46.23
2.87
33
34
3.426568
GCAGCAGCGGTGGAAGAC
61.427
66.667
17.54
0.00
0.00
3.01
34
35
3.114616
CAGCAGCGGTGGAAGACG
61.115
66.667
17.54
0.00
0.00
4.18
35
36
3.303135
AGCAGCGGTGGAAGACGA
61.303
61.111
17.54
0.00
0.00
4.20
36
37
3.112709
GCAGCGGTGGAAGACGAC
61.113
66.667
17.54
0.00
0.00
4.34
37
38
2.805353
CAGCGGTGGAAGACGACG
60.805
66.667
6.74
0.00
0.00
5.12
39
40
4.719369
GCGGTGGAAGACGACGCT
62.719
66.667
0.00
0.00
46.02
5.07
40
41
2.805353
CGGTGGAAGACGACGCTG
60.805
66.667
0.00
0.00
0.00
5.18
41
42
2.432628
GGTGGAAGACGACGCTGG
60.433
66.667
0.00
0.00
0.00
4.85
42
43
2.649034
GTGGAAGACGACGCTGGA
59.351
61.111
0.00
0.00
0.00
3.86
43
44
1.215647
GTGGAAGACGACGCTGGAT
59.784
57.895
0.00
0.00
0.00
3.41
44
45
0.802607
GTGGAAGACGACGCTGGATC
60.803
60.000
0.00
0.00
0.00
3.36
45
46
1.586564
GGAAGACGACGCTGGATCG
60.587
63.158
0.00
0.00
45.17
3.69
46
47
1.586564
GAAGACGACGCTGGATCGG
60.587
63.158
0.00
0.00
43.95
4.18
72
73
4.122515
GCAGACGTTCGCGACAGC
62.123
66.667
9.15
1.43
44.71
4.40
82
83
3.857854
GCGACAGCGGCATCACTG
61.858
66.667
1.45
0.00
39.86
3.66
83
84
3.190849
CGACAGCGGCATCACTGG
61.191
66.667
1.45
0.00
38.25
4.00
84
85
2.821366
GACAGCGGCATCACTGGG
60.821
66.667
1.45
0.00
38.25
4.45
92
93
4.147449
CATCACTGGGCGAGCCGA
62.147
66.667
8.14
3.04
36.85
5.54
93
94
3.842923
ATCACTGGGCGAGCCGAG
61.843
66.667
21.84
21.84
45.71
4.63
95
96
4.504916
CACTGGGCGAGCCGAGAG
62.505
72.222
28.47
18.87
43.43
3.20
96
97
4.742649
ACTGGGCGAGCCGAGAGA
62.743
66.667
28.47
1.40
43.43
3.10
97
98
4.200283
CTGGGCGAGCCGAGAGAC
62.200
72.222
19.41
0.00
43.43
3.36
125
126
2.745100
CGAGTCCGTCGTGGGAGA
60.745
66.667
0.00
0.00
44.20
3.71
126
127
2.751913
CGAGTCCGTCGTGGGAGAG
61.752
68.421
0.00
0.00
44.20
3.20
127
128
3.053849
GAGTCCGTCGTGGGAGAGC
62.054
68.421
0.00
0.00
36.58
4.09
128
129
3.371063
GTCCGTCGTGGGAGAGCA
61.371
66.667
0.00
0.00
36.58
4.26
129
130
3.371063
TCCGTCGTGGGAGAGCAC
61.371
66.667
0.00
0.00
38.76
4.40
130
131
4.778415
CCGTCGTGGGAGAGCACG
62.778
72.222
0.00
0.00
45.09
5.34
148
149
4.292178
CCGCGGGGAGCTCAGATC
62.292
72.222
20.10
0.00
45.59
2.75
149
150
4.292178
CGCGGGGAGCTCAGATCC
62.292
72.222
17.19
0.00
45.59
3.36
150
151
4.292178
GCGGGGAGCTCAGATCCG
62.292
72.222
23.48
23.48
44.04
4.18
151
152
3.610669
CGGGGAGCTCAGATCCGG
61.611
72.222
17.19
7.93
37.75
5.14
152
153
2.444895
GGGGAGCTCAGATCCGGT
60.445
66.667
17.19
0.00
37.75
5.28
153
154
2.801631
GGGGAGCTCAGATCCGGTG
61.802
68.421
17.19
0.00
37.75
4.94
154
155
2.060980
GGGAGCTCAGATCCGGTGT
61.061
63.158
17.19
0.00
37.75
4.16
155
156
1.439644
GGAGCTCAGATCCGGTGTC
59.560
63.158
17.19
0.79
0.00
3.67
156
157
1.064946
GAGCTCAGATCCGGTGTCG
59.935
63.158
9.40
0.00
0.00
4.35
179
180
4.796231
CGCAACGGAGGTCGGAGG
62.796
72.222
0.00
0.00
44.45
4.30
191
192
3.610669
CGGAGGCCGGAGATCCAG
61.611
72.222
5.05
1.73
44.15
3.86
192
193
3.237741
GGAGGCCGGAGATCCAGG
61.238
72.222
5.05
2.86
35.14
4.45
198
199
4.598894
CGGAGATCCAGGCGGCAG
62.599
72.222
13.08
2.03
35.14
4.85
199
200
4.247380
GGAGATCCAGGCGGCAGG
62.247
72.222
14.79
14.79
35.64
4.85
200
201
4.247380
GAGATCCAGGCGGCAGGG
62.247
72.222
20.47
16.40
0.00
4.45
249
250
1.221414
GCAAGAGCGCCATAGTTAGG
58.779
55.000
2.29
0.00
0.00
2.69
250
251
1.871080
CAAGAGCGCCATAGTTAGGG
58.129
55.000
2.29
0.00
0.00
3.53
251
252
0.759346
AAGAGCGCCATAGTTAGGGG
59.241
55.000
2.29
0.00
41.62
4.79
256
257
3.095922
GCCATAGTTAGGGGCACAC
57.904
57.895
0.00
0.00
46.92
3.82
257
258
0.546598
GCCATAGTTAGGGGCACACT
59.453
55.000
0.00
0.00
46.92
3.55
258
259
1.064685
GCCATAGTTAGGGGCACACTT
60.065
52.381
0.00
0.00
46.92
3.16
259
260
2.643551
CCATAGTTAGGGGCACACTTG
58.356
52.381
0.00
0.00
0.00
3.16
260
261
2.026262
CCATAGTTAGGGGCACACTTGT
60.026
50.000
0.00
0.00
0.00
3.16
261
262
3.270877
CATAGTTAGGGGCACACTTGTC
58.729
50.000
0.00
0.00
0.00
3.18
262
263
1.435256
AGTTAGGGGCACACTTGTCT
58.565
50.000
0.00
0.00
0.00
3.41
263
264
2.616524
AGTTAGGGGCACACTTGTCTA
58.383
47.619
0.00
0.00
0.00
2.59
264
265
2.567615
AGTTAGGGGCACACTTGTCTAG
59.432
50.000
0.00
0.00
0.00
2.43
265
266
2.565834
GTTAGGGGCACACTTGTCTAGA
59.434
50.000
0.00
0.00
0.00
2.43
266
267
0.977395
AGGGGCACACTTGTCTAGAC
59.023
55.000
16.32
16.32
0.00
2.59
267
268
0.977395
GGGGCACACTTGTCTAGACT
59.023
55.000
23.01
0.58
0.00
3.24
297
298
8.504815
CATCTGTCATATTTCACCATCTTGATC
58.495
37.037
0.00
0.00
0.00
2.92
358
359
0.687757
TCTCCCCACCATTCTCTCCG
60.688
60.000
0.00
0.00
0.00
4.63
393
394
3.628646
GACCTGGCCGGATTGTGCT
62.629
63.158
15.09
0.00
36.31
4.40
749
769
0.972983
CTCTCACCGTCTCCACCCAT
60.973
60.000
0.00
0.00
0.00
4.00
750
770
0.333652
TCTCACCGTCTCCACCCATA
59.666
55.000
0.00
0.00
0.00
2.74
846
866
1.462432
TGGAGCCCACCTAACACCA
60.462
57.895
0.00
0.00
0.00
4.17
847
867
1.002502
GGAGCCCACCTAACACCAC
60.003
63.158
0.00
0.00
0.00
4.16
872
892
4.345854
CGCTCTATATAAACCCTCTCCCT
58.654
47.826
0.00
0.00
0.00
4.20
944
964
4.026640
CACTGCAAGCAACAATACAAACAC
60.027
41.667
0.00
0.00
37.60
3.32
947
967
3.245048
GCAAGCAACAATACAAACACCAC
59.755
43.478
0.00
0.00
0.00
4.16
948
968
4.681744
CAAGCAACAATACAAACACCACT
58.318
39.130
0.00
0.00
0.00
4.00
969
989
1.609072
CGAGCATCCTAAGATCGACCA
59.391
52.381
0.00
0.00
46.76
4.02
1029
1053
3.774702
GCGGAGAACGTTGACGCC
61.775
66.667
22.58
12.90
46.52
5.68
1197
1221
2.582436
CGCCACAACCCCGTCTAT
59.418
61.111
0.00
0.00
0.00
1.98
1371
1395
2.369629
CGACAAGGTACGCACACGG
61.370
63.158
0.00
0.00
46.04
4.94
1372
1396
1.300388
GACAAGGTACGCACACGGT
60.300
57.895
0.00
0.00
46.04
4.83
1374
1398
0.877213
ACAAGGTACGCACACGGTTC
60.877
55.000
0.00
0.00
46.04
3.62
1384
1414
2.590575
CACGGTTCCACGGCACTT
60.591
61.111
0.00
0.00
38.39
3.16
1397
1427
1.667724
CGGCACTTGTGATGATTCTCC
59.332
52.381
4.79
0.00
0.00
3.71
1444
1475
0.401356
TCTGTGGAATGCAGCTTGGA
59.599
50.000
0.00
0.00
34.21
3.53
1447
1478
1.304381
TGGAATGCAGCTTGGACCC
60.304
57.895
0.00
0.00
0.00
4.46
1912
1948
0.533032
TCGCCGTTGACATATGACCA
59.467
50.000
10.38
4.12
0.00
4.02
1913
1949
1.138069
TCGCCGTTGACATATGACCAT
59.862
47.619
10.38
0.00
0.00
3.55
2278
2319
3.181466
TGGATCACTAGTGCGCATTACAT
60.181
43.478
15.91
3.61
0.00
2.29
2279
2320
4.038642
TGGATCACTAGTGCGCATTACATA
59.961
41.667
15.91
0.00
0.00
2.29
2310
2351
2.582978
GGGTAACTCTGGCGGACC
59.417
66.667
0.00
0.00
0.00
4.46
2320
2361
0.176219
CTGGCGGACCGGTATTACAA
59.824
55.000
17.22
0.00
39.70
2.41
2456
2504
0.035820
TAAACGTGGGTCAGGATGGC
60.036
55.000
0.00
0.00
42.54
4.40
2494
2542
7.342581
TGGTAACCATTTAATGCTACTGATCA
58.657
34.615
0.00
0.00
0.00
2.92
2530
2580
8.276252
TGCTTCTGTTAAAGTGTAAACTTCTT
57.724
30.769
0.00
0.00
0.00
2.52
2531
2581
8.181573
TGCTTCTGTTAAAGTGTAAACTTCTTG
58.818
33.333
0.00
0.00
0.00
3.02
2532
2582
8.182227
GCTTCTGTTAAAGTGTAAACTTCTTGT
58.818
33.333
0.00
0.00
0.00
3.16
2534
2584
9.834628
TTCTGTTAAAGTGTAAACTTCTTGTTG
57.165
29.630
0.00
0.00
39.13
3.33
2536
2586
9.490663
CTGTTAAAGTGTAAACTTCTTGTTGAG
57.509
33.333
0.00
0.00
39.13
3.02
2537
2587
9.221933
TGTTAAAGTGTAAACTTCTTGTTGAGA
57.778
29.630
0.00
0.00
39.13
3.27
2689
2755
4.503910
TCCCTATCACAAAACACGATCAG
58.496
43.478
0.00
0.00
0.00
2.90
2709
2775
8.333908
CGATCAGAGAAACTTATCTCCAAAATG
58.666
37.037
0.90
0.00
45.70
2.32
2717
2783
9.358872
GAAACTTATCTCCAAAATGAATCCAAC
57.641
33.333
0.00
0.00
0.00
3.77
2722
2788
6.729690
TCTCCAAAATGAATCCAACAAACT
57.270
33.333
0.00
0.00
0.00
2.66
2728
2796
9.270640
CCAAAATGAATCCAACAAACTCAAATA
57.729
29.630
0.00
0.00
0.00
1.40
2736
2804
8.742554
ATCCAACAAACTCAAATATCGTTTTC
57.257
30.769
0.00
0.00
0.00
2.29
2738
2806
6.087555
CCAACAAACTCAAATATCGTTTTCCG
59.912
38.462
0.00
0.00
38.13
4.30
2740
2808
5.239963
ACAAACTCAAATATCGTTTTCCGGT
59.760
36.000
0.00
0.00
37.11
5.28
2813
2882
0.106918
AAGAGTGCACCGGGACAAAA
60.107
50.000
14.63
0.00
37.91
2.44
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
1
2
4.373116
TGCAGTCGCCGTTCTCCC
62.373
66.667
0.00
0.00
37.32
4.30
3
4
3.482783
GCTGCAGTCGCCGTTCTC
61.483
66.667
16.64
0.00
37.32
2.87
4
5
4.299547
TGCTGCAGTCGCCGTTCT
62.300
61.111
16.64
0.00
37.32
3.01
5
6
3.782244
CTGCTGCAGTCGCCGTTC
61.782
66.667
21.21
0.00
37.32
3.95
12
13
4.687215
TCCACCGCTGCTGCAGTC
62.687
66.667
28.50
19.70
39.64
3.51
13
14
4.254709
TTCCACCGCTGCTGCAGT
62.255
61.111
28.50
9.31
39.64
4.40
14
15
3.429141
CTTCCACCGCTGCTGCAG
61.429
66.667
24.80
24.80
39.64
4.41
15
16
3.939939
TCTTCCACCGCTGCTGCA
61.940
61.111
16.29
0.88
39.64
4.41
16
17
3.426568
GTCTTCCACCGCTGCTGC
61.427
66.667
5.34
5.34
0.00
5.25
17
18
3.114616
CGTCTTCCACCGCTGCTG
61.115
66.667
0.00
0.00
0.00
4.41
18
19
3.303135
TCGTCTTCCACCGCTGCT
61.303
61.111
0.00
0.00
0.00
4.24
19
20
3.112709
GTCGTCTTCCACCGCTGC
61.113
66.667
0.00
0.00
0.00
5.25
20
21
2.805353
CGTCGTCTTCCACCGCTG
60.805
66.667
0.00
0.00
0.00
5.18
21
22
4.719369
GCGTCGTCTTCCACCGCT
62.719
66.667
0.00
0.00
41.06
5.52
22
23
4.719369
AGCGTCGTCTTCCACCGC
62.719
66.667
0.00
0.00
44.35
5.68
23
24
2.805353
CAGCGTCGTCTTCCACCG
60.805
66.667
0.00
0.00
0.00
4.94
24
25
2.227089
ATCCAGCGTCGTCTTCCACC
62.227
60.000
0.00
0.00
0.00
4.61
25
26
0.802607
GATCCAGCGTCGTCTTCCAC
60.803
60.000
0.00
0.00
0.00
4.02
26
27
1.511305
GATCCAGCGTCGTCTTCCA
59.489
57.895
0.00
0.00
0.00
3.53
27
28
1.586564
CGATCCAGCGTCGTCTTCC
60.587
63.158
0.00
0.00
34.56
3.46
28
29
1.586564
CCGATCCAGCGTCGTCTTC
60.587
63.158
0.00
0.00
37.39
2.87
29
30
2.490217
CCGATCCAGCGTCGTCTT
59.510
61.111
0.00
0.00
37.39
3.01
30
31
4.194720
GCCGATCCAGCGTCGTCT
62.195
66.667
0.00
0.00
37.39
4.18
55
56
4.122515
GCTGTCGCGAACGTCTGC
62.123
66.667
12.06
10.62
42.52
4.26
65
66
3.857854
CAGTGATGCCGCTGTCGC
61.858
66.667
0.00
0.00
43.88
5.19
66
67
3.190849
CCAGTGATGCCGCTGTCG
61.191
66.667
0.00
0.00
46.61
4.35
67
68
2.821366
CCCAGTGATGCCGCTGTC
60.821
66.667
0.00
0.00
46.61
3.51
75
76
4.147449
TCGGCTCGCCCAGTGATG
62.147
66.667
1.72
0.00
0.00
3.07
76
77
3.842923
CTCGGCTCGCCCAGTGAT
61.843
66.667
1.72
0.00
0.00
3.06
78
79
4.504916
CTCTCGGCTCGCCCAGTG
62.505
72.222
1.72
0.00
0.00
3.66
79
80
4.742649
TCTCTCGGCTCGCCCAGT
62.743
66.667
1.72
0.00
0.00
4.00
80
81
4.200283
GTCTCTCGGCTCGCCCAG
62.200
72.222
1.72
0.00
0.00
4.45
109
110
3.053849
GCTCTCCCACGACGGACTC
62.054
68.421
0.00
0.00
36.56
3.36
110
111
3.063084
GCTCTCCCACGACGGACT
61.063
66.667
0.00
0.00
36.56
3.85
111
112
3.371063
TGCTCTCCCACGACGGAC
61.371
66.667
0.00
0.00
36.56
4.79
112
113
3.371063
GTGCTCTCCCACGACGGA
61.371
66.667
0.00
0.00
36.56
4.69
131
132
4.292178
GATCTGAGCTCCCCGCGG
62.292
72.222
21.04
21.04
45.59
6.46
132
133
4.292178
GGATCTGAGCTCCCCGCG
62.292
72.222
12.15
0.00
45.59
6.46
133
134
4.292178
CGGATCTGAGCTCCCCGC
62.292
72.222
12.15
0.00
39.57
6.13
134
135
3.610669
CCGGATCTGAGCTCCCCG
61.611
72.222
20.16
20.16
39.85
5.73
135
136
2.444895
ACCGGATCTGAGCTCCCC
60.445
66.667
9.46
6.38
0.00
4.81
136
137
2.022240
GACACCGGATCTGAGCTCCC
62.022
65.000
9.46
3.78
0.00
4.30
137
138
1.439644
GACACCGGATCTGAGCTCC
59.560
63.158
9.46
0.00
0.00
4.70
138
139
1.064946
CGACACCGGATCTGAGCTC
59.935
63.158
9.46
6.82
0.00
4.09
139
140
3.201494
CGACACCGGATCTGAGCT
58.799
61.111
9.46
0.00
0.00
4.09
162
163
4.796231
CCTCCGACCTCCGTTGCG
62.796
72.222
0.00
0.00
36.31
4.85
164
165
4.452733
GGCCTCCGACCTCCGTTG
62.453
72.222
0.00
0.00
36.31
4.10
175
176
3.237741
CCTGGATCTCCGGCCTCC
61.238
72.222
0.00
0.00
41.13
4.30
176
177
3.934962
GCCTGGATCTCCGGCCTC
61.935
72.222
16.45
0.00
44.35
4.70
181
182
4.598894
CTGCCGCCTGGATCTCCG
62.599
72.222
0.00
0.00
39.43
4.63
182
183
4.247380
CCTGCCGCCTGGATCTCC
62.247
72.222
0.00
0.00
37.49
3.71
183
184
4.247380
CCCTGCCGCCTGGATCTC
62.247
72.222
0.00
0.00
37.49
2.75
230
231
1.221414
CCTAACTATGGCGCTCTTGC
58.779
55.000
7.64
0.00
0.00
4.01
231
232
1.541233
CCCCTAACTATGGCGCTCTTG
60.541
57.143
7.64
0.00
0.00
3.02
232
233
0.759346
CCCCTAACTATGGCGCTCTT
59.241
55.000
7.64
0.00
0.00
2.85
233
234
1.759459
GCCCCTAACTATGGCGCTCT
61.759
60.000
7.64
0.00
35.08
4.09
234
235
1.301795
GCCCCTAACTATGGCGCTC
60.302
63.158
7.64
0.00
35.08
5.03
235
236
2.829592
GCCCCTAACTATGGCGCT
59.170
61.111
7.64
0.00
35.08
5.92
238
239
0.546598
AGTGTGCCCCTAACTATGGC
59.453
55.000
0.00
0.00
45.56
4.40
239
240
2.026262
ACAAGTGTGCCCCTAACTATGG
60.026
50.000
0.00
0.00
0.00
2.74
240
241
3.055094
AGACAAGTGTGCCCCTAACTATG
60.055
47.826
0.00
0.00
0.00
2.23
241
242
3.182152
AGACAAGTGTGCCCCTAACTAT
58.818
45.455
0.00
0.00
0.00
2.12
242
243
2.616524
AGACAAGTGTGCCCCTAACTA
58.383
47.619
0.00
0.00
0.00
2.24
243
244
1.435256
AGACAAGTGTGCCCCTAACT
58.565
50.000
0.00
0.00
0.00
2.24
244
245
2.565834
TCTAGACAAGTGTGCCCCTAAC
59.434
50.000
0.00
0.00
0.00
2.34
245
246
2.565834
GTCTAGACAAGTGTGCCCCTAA
59.434
50.000
18.20
0.00
0.00
2.69
246
247
2.176889
GTCTAGACAAGTGTGCCCCTA
58.823
52.381
18.20
0.00
0.00
3.53
247
248
0.977395
GTCTAGACAAGTGTGCCCCT
59.023
55.000
18.20
0.00
0.00
4.79
248
249
0.977395
AGTCTAGACAAGTGTGCCCC
59.023
55.000
24.44
0.00
0.00
5.80
249
250
2.841442
AAGTCTAGACAAGTGTGCCC
57.159
50.000
24.44
0.00
0.00
5.36
250
251
5.073311
TGATAAGTCTAGACAAGTGTGCC
57.927
43.478
24.44
6.03
0.00
5.01
251
252
6.475076
CAGATGATAAGTCTAGACAAGTGTGC
59.525
42.308
24.44
8.99
0.00
4.57
252
253
7.542890
ACAGATGATAAGTCTAGACAAGTGTG
58.457
38.462
24.44
13.70
0.00
3.82
253
254
7.394641
TGACAGATGATAAGTCTAGACAAGTGT
59.605
37.037
24.44
14.35
33.56
3.55
254
255
7.766283
TGACAGATGATAAGTCTAGACAAGTG
58.234
38.462
24.44
11.66
33.56
3.16
255
256
7.946381
TGACAGATGATAAGTCTAGACAAGT
57.054
36.000
24.44
11.63
33.56
3.16
263
264
8.708378
TGGTGAAATATGACAGATGATAAGTCT
58.292
33.333
0.00
0.00
33.56
3.24
264
265
8.893219
TGGTGAAATATGACAGATGATAAGTC
57.107
34.615
0.00
0.00
0.00
3.01
265
266
9.499479
GATGGTGAAATATGACAGATGATAAGT
57.501
33.333
0.00
0.00
0.00
2.24
266
267
9.722184
AGATGGTGAAATATGACAGATGATAAG
57.278
33.333
0.00
0.00
0.00
1.73
297
298
3.337358
TGATCACTGTACAATGCACTGG
58.663
45.455
0.00
0.00
0.00
4.00
358
359
1.812922
TCGGTAGTCTCGTCTCCGC
60.813
63.158
0.00
0.00
40.81
5.54
364
365
2.045131
GCCAGGTCGGTAGTCTCGT
61.045
63.158
0.00
0.00
36.97
4.18
366
367
2.772691
CGGCCAGGTCGGTAGTCTC
61.773
68.421
5.20
0.00
36.97
3.36
393
394
0.609957
ATACTGCTTGCTGGCTTGCA
60.610
50.000
10.94
10.94
41.65
4.08
404
405
1.355720
ACTTGCTCCCCAATACTGCTT
59.644
47.619
0.00
0.00
31.91
3.91
632
633
0.890996
CTGGAAGTGTGAACCTGCCC
60.891
60.000
0.00
0.00
0.00
5.36
694
714
1.619807
GCTTCCCCGGCAAGGTAGTA
61.620
60.000
12.08
0.00
38.74
1.82
695
715
2.967946
GCTTCCCCGGCAAGGTAGT
61.968
63.158
12.08
0.00
38.74
2.73
696
716
2.124695
GCTTCCCCGGCAAGGTAG
60.125
66.667
12.08
5.69
38.74
3.18
731
751
0.333652
TATGGGTGGAGACGGTGAGA
59.666
55.000
0.00
0.00
0.00
3.27
749
769
1.611977
CGGAGAAGGACAGTGTGTGTA
59.388
52.381
0.00
0.00
40.56
2.90
750
770
0.389391
CGGAGAAGGACAGTGTGTGT
59.611
55.000
0.00
0.00
44.49
3.72
846
866
3.171528
GAGGGTTTATATAGAGCGGGGT
58.828
50.000
0.00
0.00
0.00
4.95
847
867
3.442076
AGAGGGTTTATATAGAGCGGGG
58.558
50.000
0.00
0.00
0.00
5.73
872
892
1.229496
TGTGGCTTGGAGCTAGGGA
60.229
57.895
0.00
0.00
41.99
4.20
944
964
2.351253
CGATCTTAGGATGCTCGAGTGG
60.351
54.545
15.13
0.00
31.46
4.00
947
967
2.095466
GGTCGATCTTAGGATGCTCGAG
60.095
54.545
8.45
8.45
30.25
4.04
948
968
1.880675
GGTCGATCTTAGGATGCTCGA
59.119
52.381
0.00
0.00
31.46
4.04
969
989
2.300437
CGTGAAAGGAAGGAAGGACTCT
59.700
50.000
0.00
0.00
0.00
3.24
1370
1394
0.889186
ATCACAAGTGCCGTGGAACC
60.889
55.000
0.00
0.00
35.03
3.62
1371
1395
0.238289
CATCACAAGTGCCGTGGAAC
59.762
55.000
0.00
0.00
35.03
3.62
1372
1396
0.107643
TCATCACAAGTGCCGTGGAA
59.892
50.000
0.00
0.00
35.03
3.53
1374
1398
1.131126
GAATCATCACAAGTGCCGTGG
59.869
52.381
0.00
0.00
35.03
4.94
1381
1411
2.881074
CGTCGGAGAATCATCACAAGT
58.119
47.619
0.00
0.00
39.69
3.16
1384
1414
0.179111
GGCGTCGGAGAATCATCACA
60.179
55.000
0.00
0.00
39.69
3.58
1397
1427
2.478746
CATTTTCCACGGGCGTCG
59.521
61.111
0.00
0.00
45.88
5.12
1567
1598
4.345962
TCGTCGCCGCCGAAGAAA
62.346
61.111
1.21
0.00
46.19
2.52
1900
1931
3.494924
GCACAGCCTATGGTCATATGTCA
60.495
47.826
1.90
3.47
0.00
3.58
1912
1948
2.047274
AACGCGTGCACAGCCTAT
60.047
55.556
14.98
5.89
0.00
2.57
1913
1949
2.980213
TTCAACGCGTGCACAGCCTA
62.980
55.000
14.98
3.28
0.00
3.93
2100
2140
4.677584
ACAAACACACAACGCATAACAAT
58.322
34.783
0.00
0.00
0.00
2.71
2263
2304
9.370126
GTTAAAAGAATATGTAATGCGCACTAG
57.630
33.333
14.90
0.00
0.00
2.57
2278
2319
6.592607
CAGAGTTACCCGCAGTTAAAAGAATA
59.407
38.462
0.00
0.00
0.00
1.75
2279
2320
5.411669
CAGAGTTACCCGCAGTTAAAAGAAT
59.588
40.000
0.00
0.00
0.00
2.40
2310
2351
8.504812
AAAACCGTTGTTAAATTGTAATACCG
57.495
30.769
0.00
0.00
33.30
4.02
2320
2361
5.125739
TGTGAGGTGAAAACCGTTGTTAAAT
59.874
36.000
0.00
0.00
33.30
1.40
2456
2504
1.082117
GTTACCATGTCGCTGGACCG
61.082
60.000
5.63
0.00
42.73
4.79
2466
2514
7.116075
TCAGTAGCATTAAATGGTTACCATGT
58.884
34.615
18.48
15.22
44.40
3.21
2494
2542
6.604795
ACTTTAACAGAAGCAGGCATTGATAT
59.395
34.615
0.00
0.00
0.00
1.63
2502
2550
5.008712
AGTTTACACTTTAACAGAAGCAGGC
59.991
40.000
0.00
0.00
0.00
4.85
2530
2580
3.187022
CACGCACTGATGAATTCTCAACA
59.813
43.478
7.05
1.37
34.49
3.33
2531
2581
3.740590
CACGCACTGATGAATTCTCAAC
58.259
45.455
7.05
1.11
34.49
3.18
2532
2582
2.160219
GCACGCACTGATGAATTCTCAA
59.840
45.455
7.05
0.00
34.49
3.02
2533
2583
1.733912
GCACGCACTGATGAATTCTCA
59.266
47.619
7.05
7.14
35.56
3.27
2534
2584
1.267235
CGCACGCACTGATGAATTCTC
60.267
52.381
7.05
2.78
0.00
2.87
2536
2586
0.443869
ACGCACGCACTGATGAATTC
59.556
50.000
0.00
0.00
0.00
2.17
2537
2587
0.874390
AACGCACGCACTGATGAATT
59.126
45.000
0.00
0.00
0.00
2.17
2538
2588
0.874390
AAACGCACGCACTGATGAAT
59.126
45.000
0.00
0.00
0.00
2.57
2539
2589
0.041400
CAAACGCACGCACTGATGAA
60.041
50.000
0.00
0.00
0.00
2.57
2689
2755
8.960591
TGGATTCATTTTGGAGATAAGTTTCTC
58.039
33.333
6.55
6.55
41.21
2.87
2709
2775
8.742554
AAACGATATTTGAGTTTGTTGGATTC
57.257
30.769
0.00
0.00
36.81
2.52
2736
2804
1.750399
CTGGAAATGGAGCCACCGG
60.750
63.158
0.00
0.00
42.61
5.28
2738
2806
2.409870
CGCTGGAAATGGAGCCACC
61.410
63.158
0.00
0.00
39.54
4.61
2740
2808
2.045045
CCGCTGGAAATGGAGCCA
60.045
61.111
0.00
0.00
30.98
4.75
2787
2855
1.569493
CGGTGCACTCTTTGGTTCG
59.431
57.895
17.98
4.30
0.00
3.95
2813
2882
2.512974
CGCCCGCGGTAGGAATTT
60.513
61.111
26.12
0.00
35.56
1.82
2835
3490
0.308993
GCGTATGAAATCTGCAGGCC
59.691
55.000
15.13
0.00
0.00
5.19
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.