Multiple sequence alignment - TraesCS3A01G242100
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
TraesCS3A01G242100
chr3A
100.000
6991
0
0
1
6991
454510022
454517012
0.000000e+00
12911.0
1
TraesCS3A01G242100
chr3D
97.358
2839
46
13
4172
6991
337307525
337310353
0.000000e+00
4800.0
2
TraesCS3A01G242100
chr3D
92.657
3146
113
48
1
3063
337303197
337306307
0.000000e+00
4421.0
3
TraesCS3A01G242100
chr3D
95.819
1124
23
7
3055
4172
337306365
337307470
0.000000e+00
1794.0
4
TraesCS3A01G242100
chr3B
95.701
2861
72
27
4172
6991
434984602
434987452
0.000000e+00
4554.0
5
TraesCS3A01G242100
chr3B
90.148
2223
86
33
1
2129
434980008
434982191
0.000000e+00
2769.0
6
TraesCS3A01G242100
chr3B
95.463
1124
22
6
3055
4172
434983422
434984522
0.000000e+00
1766.0
7
TraesCS3A01G242100
chr3B
96.820
912
22
4
2155
3063
434982457
434983364
0.000000e+00
1517.0
8
TraesCS3A01G242100
chrUn
87.629
97
4
5
6729
6823
146902797
146902887
9.590000e-19
106.0
9
TraesCS3A01G242100
chrUn
87.629
97
4
5
6729
6823
146930260
146930350
9.590000e-19
106.0
10
TraesCS3A01G242100
chrUn
88.172
93
3
5
6733
6823
154087980
154088066
3.450000e-18
104.0
11
TraesCS3A01G242100
chrUn
86.598
97
5
5
6729
6823
147063450
147063540
4.460000e-17
100.0
12
TraesCS3A01G242100
chrUn
86.598
97
5
5
6729
6823
147088682
147088772
4.460000e-17
100.0
13
TraesCS3A01G242100
chrUn
87.234
94
4
5
6732
6823
210791169
210791082
4.460000e-17
100.0
14
TraesCS3A01G242100
chr6D
88.172
93
4
3
6732
6823
392273216
392273130
3.450000e-18
104.0
15
TraesCS3A01G242100
chr6D
84.158
101
6
4
3067
3166
41929132
41929041
9.660000e-14
89.8
16
TraesCS3A01G242100
chr6A
82.653
98
8
3
3067
3164
52399501
52399413
2.090000e-10
78.7
17
TraesCS3A01G242100
chr5B
88.136
59
7
0
3062
3120
74996098
74996156
3.500000e-08
71.3
18
TraesCS3A01G242100
chr1D
86.567
67
6
3
6917
6982
116907616
116907552
3.500000e-08
71.3
19
TraesCS3A01G242100
chr1D
100.000
33
0
0
3088
3120
283621941
283621973
2.110000e-05
62.1
20
TraesCS3A01G242100
chr2A
97.561
41
0
1
3081
3120
611102352
611102392
1.260000e-07
69.4
21
TraesCS3A01G242100
chr7D
86.667
60
6
2
6921
6979
551607828
551607770
1.630000e-06
65.8
22
TraesCS3A01G242100
chr5D
84.848
66
6
3
6922
6986
302169091
302169153
5.850000e-06
63.9
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
TraesCS3A01G242100
chr3A
454510022
454517012
6990
False
12911.000000
12911
100.000
1
6991
1
chr3A.!!$F1
6990
1
TraesCS3A01G242100
chr3D
337303197
337310353
7156
False
3671.666667
4800
95.278
1
6991
3
chr3D.!!$F1
6990
2
TraesCS3A01G242100
chr3B
434980008
434987452
7444
False
2651.500000
4554
94.533
1
6991
4
chr3B.!!$F1
6990
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
377
391
0.322648
CTGGCCATGTGACTGACTGA
59.677
55.000
5.51
0.00
0.0
3.41
F
714
786
0.467290
GCTCCTTGTGTTTGGGTGGA
60.467
55.000
0.00
0.00
0.0
4.02
F
1988
2121
1.132640
GCTACCTTCTTTGTGCGCG
59.867
57.895
0.00
0.00
0.0
6.86
F
1990
2123
0.716108
CTACCTTCTTTGTGCGCGAG
59.284
55.000
12.10
0.00
0.0
5.03
F
3223
3666
3.555966
AGAAACTTGTCCTTTGTCCCAG
58.444
45.455
0.00
0.00
0.0
4.45
F
3580
4027
2.084546
GATTTTGGGCTAGCACGAGTT
58.915
47.619
18.24
3.73
0.0
3.01
F
4134
4581
2.502130
GCAAACCCTTCTAGAGCCTACT
59.498
50.000
0.00
0.00
0.0
2.57
F
4136
4583
3.476485
AACCCTTCTAGAGCCTACTGT
57.524
47.619
0.00
0.00
0.0
3.55
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1308
1429
0.108615
CAGTTGGACTCCGTAGCTGG
60.109
60.000
0.00
0.0
0.00
4.85
R
1991
2124
0.173481
TTCCGTGAGCTTCTGGATCG
59.827
55.000
3.01
0.0
32.20
3.69
R
2962
3335
1.030488
AGCAAAGCATCAGCAGCGAT
61.030
50.000
0.00
0.0
45.49
4.58
R
3580
4027
2.161855
GTGGGAGTGTCATTGAATGCA
58.838
47.619
0.00
0.0
0.00
3.96
R
5064
5592
3.502119
CCTTCCCTCCATTTTCCTCCAAA
60.502
47.826
0.00
0.0
0.00
3.28
R
5357
5886
1.677576
TCAGCAAGCAAAGTTGAGTGG
59.322
47.619
0.00
0.0
0.00
4.00
R
5848
6378
0.679640
TGCTACATCGGCTTTTGGGG
60.680
55.000
0.00
0.0
0.00
4.96
R
6183
6716
2.996249
TCCTTGGCAGCTAGATCAAG
57.004
50.000
0.00
0.0
37.09
3.02
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
117
122
4.649692
ACCTTATCCTGCTGCTATGAATG
58.350
43.478
0.00
0.00
0.00
2.67
172
177
4.509970
CACCAACCGATAAGATAATTGCGA
59.490
41.667
0.00
0.00
0.00
5.10
173
178
4.510340
ACCAACCGATAAGATAATTGCGAC
59.490
41.667
0.00
0.00
0.00
5.19
246
255
3.680937
CGAACCGCCTACTCATTTTTACA
59.319
43.478
0.00
0.00
0.00
2.41
247
256
4.435121
CGAACCGCCTACTCATTTTTACAC
60.435
45.833
0.00
0.00
0.00
2.90
248
257
4.281898
ACCGCCTACTCATTTTTACACT
57.718
40.909
0.00
0.00
0.00
3.55
249
258
4.000988
ACCGCCTACTCATTTTTACACTG
58.999
43.478
0.00
0.00
0.00
3.66
250
259
3.181510
CCGCCTACTCATTTTTACACTGC
60.182
47.826
0.00
0.00
0.00
4.40
251
260
3.684788
CGCCTACTCATTTTTACACTGCT
59.315
43.478
0.00
0.00
0.00
4.24
252
261
4.436050
CGCCTACTCATTTTTACACTGCTG
60.436
45.833
0.00
0.00
0.00
4.41
253
262
4.455877
GCCTACTCATTTTTACACTGCTGT
59.544
41.667
0.00
0.00
0.00
4.40
254
263
5.642063
GCCTACTCATTTTTACACTGCTGTA
59.358
40.000
0.00
0.00
0.00
2.74
255
264
6.402226
GCCTACTCATTTTTACACTGCTGTAC
60.402
42.308
0.00
0.00
32.28
2.90
256
265
6.874134
CCTACTCATTTTTACACTGCTGTACT
59.126
38.462
0.00
0.00
32.28
2.73
257
266
8.033038
CCTACTCATTTTTACACTGCTGTACTA
58.967
37.037
0.00
0.00
32.28
1.82
258
267
7.653767
ACTCATTTTTACACTGCTGTACTAC
57.346
36.000
0.00
0.00
32.28
2.73
273
287
3.949754
TGTACTACTACTCCGTTGGGATG
59.050
47.826
0.00
0.00
42.83
3.51
275
289
2.024655
ACTACTACTCCGTTGGGATGGA
60.025
50.000
0.00
0.00
42.83
3.41
276
290
1.946984
ACTACTCCGTTGGGATGGAA
58.053
50.000
0.00
0.00
42.83
3.53
277
291
2.262637
ACTACTCCGTTGGGATGGAAA
58.737
47.619
0.00
0.00
42.83
3.13
278
292
2.640826
ACTACTCCGTTGGGATGGAAAA
59.359
45.455
0.00
0.00
42.83
2.29
279
293
2.668144
ACTCCGTTGGGATGGAAAAA
57.332
45.000
0.00
0.00
42.83
1.94
280
294
2.514803
ACTCCGTTGGGATGGAAAAAG
58.485
47.619
0.00
0.00
42.83
2.27
281
295
2.107552
ACTCCGTTGGGATGGAAAAAGA
59.892
45.455
0.00
0.00
42.83
2.52
349
363
2.050918
TCCACGCACATCCCCATATTA
58.949
47.619
0.00
0.00
0.00
0.98
350
364
2.642311
TCCACGCACATCCCCATATTAT
59.358
45.455
0.00
0.00
0.00
1.28
374
388
2.042831
GGCTGGCCATGTGACTGAC
61.043
63.158
5.51
0.00
35.81
3.51
375
389
1.002868
GCTGGCCATGTGACTGACT
60.003
57.895
5.51
0.00
0.00
3.41
376
390
1.303799
GCTGGCCATGTGACTGACTG
61.304
60.000
5.51
0.00
0.00
3.51
377
391
0.322648
CTGGCCATGTGACTGACTGA
59.677
55.000
5.51
0.00
0.00
3.41
378
392
0.986527
TGGCCATGTGACTGACTGAT
59.013
50.000
0.00
0.00
0.00
2.90
379
393
1.352017
TGGCCATGTGACTGACTGATT
59.648
47.619
0.00
0.00
0.00
2.57
380
394
2.224843
TGGCCATGTGACTGACTGATTT
60.225
45.455
0.00
0.00
0.00
2.17
422
436
2.731968
CGCAAGCTGAACAAAAGTGTGT
60.732
45.455
0.00
0.00
38.27
3.72
423
437
3.253230
GCAAGCTGAACAAAAGTGTGTT
58.747
40.909
0.00
0.00
44.38
3.32
424
438
4.420168
GCAAGCTGAACAAAAGTGTGTTA
58.580
39.130
0.00
0.00
41.78
2.41
564
581
2.408050
GGATCTCCACGAAATCATCCG
58.592
52.381
0.00
0.00
35.64
4.18
566
583
0.527600
TCTCCACGAAATCATCCGCG
60.528
55.000
0.00
0.00
0.00
6.46
570
587
2.242670
CGAAATCATCCGCGTCGC
59.757
61.111
7.29
7.29
0.00
5.19
572
589
2.882366
GAAATCATCCGCGTCGCCC
61.882
63.158
12.44
0.00
0.00
6.13
618
639
3.243068
GCGGCTGTCAAAAGAAAGAAAGA
60.243
43.478
0.00
0.00
0.00
2.52
684
729
2.874010
ATCGCTCGCACCAGACGAAG
62.874
60.000
0.00
0.00
39.39
3.79
688
733
2.125912
CGCACCAGACGAAGGAGG
60.126
66.667
0.00
0.00
0.00
4.30
712
784
0.954452
GAGCTCCTTGTGTTTGGGTG
59.046
55.000
0.87
0.00
0.00
4.61
713
785
0.468029
AGCTCCTTGTGTTTGGGTGG
60.468
55.000
0.00
0.00
0.00
4.61
714
786
0.467290
GCTCCTTGTGTTTGGGTGGA
60.467
55.000
0.00
0.00
0.00
4.02
715
787
1.823250
GCTCCTTGTGTTTGGGTGGAT
60.823
52.381
0.00
0.00
0.00
3.41
731
803
1.291184
GGATTTGCCCTTTGCGTTGC
61.291
55.000
0.00
0.00
45.60
4.17
1015
1087
4.147449
CGATGCAGCCGGACCAGA
62.147
66.667
5.05
0.00
0.00
3.86
1162
1251
2.017559
ATGAACCTACCTCGCCTCGC
62.018
60.000
0.00
0.00
0.00
5.03
1260
1377
3.055094
TGGTATCCTGCAACTTCTCTTCC
60.055
47.826
0.00
0.00
0.00
3.46
1308
1429
6.103997
TCCGTATAGTTGAGGTTGTTGATTC
58.896
40.000
0.00
0.00
0.00
2.52
1314
1435
4.072131
GTTGAGGTTGTTGATTCCAGCTA
58.928
43.478
0.00
0.00
0.00
3.32
1335
1456
3.665190
ACGGAGTCCAACTGAATTCTTC
58.335
45.455
10.49
0.00
29.74
2.87
1422
1543
8.561738
TCTCAATTATTAACACAAGGTTCTCC
57.438
34.615
0.00
0.00
40.96
3.71
1870
1997
9.077885
GATATAGATGGTTTTATGCCCAAGAAA
57.922
33.333
0.00
0.00
33.66
2.52
1908
2035
2.203625
TTGGGCCCTTTGTGCTCC
60.204
61.111
25.70
0.00
0.00
4.70
1936
2063
2.680339
GCTGTTTTCCTCATAGCTGGAC
59.320
50.000
0.00
0.00
31.24
4.02
1983
2116
4.262938
GGGAGTTGTAGCTACCTTCTTTGT
60.263
45.833
21.01
0.00
36.54
2.83
1988
2121
1.132640
GCTACCTTCTTTGTGCGCG
59.867
57.895
0.00
0.00
0.00
6.86
1989
2122
1.289109
GCTACCTTCTTTGTGCGCGA
61.289
55.000
12.10
0.00
0.00
5.87
1990
2123
0.716108
CTACCTTCTTTGTGCGCGAG
59.284
55.000
12.10
0.00
0.00
5.03
2029
2162
4.441792
GGAATCCAACTTTTTGTGCTGTT
58.558
39.130
0.00
0.00
0.00
3.16
2030
2163
4.507756
GGAATCCAACTTTTTGTGCTGTTC
59.492
41.667
0.00
0.00
0.00
3.18
2107
2240
5.232463
TGTTCGGTATGAAGTGACCTTTAC
58.768
41.667
0.00
0.00
37.23
2.01
2118
2251
7.038659
TGAAGTGACCTTTACACAAAATTTGG
58.961
34.615
10.71
2.05
40.25
3.28
2225
2598
7.441836
CCTATGTGGCTAGTATGTGTTATCAA
58.558
38.462
0.00
0.00
0.00
2.57
2386
2759
4.233789
TGTGTGTCTTTTGTTTCAGTTGC
58.766
39.130
0.00
0.00
0.00
4.17
2644
3017
4.956700
TCCTCCGTGAGATCAAATTACTCT
59.043
41.667
0.00
0.00
0.00
3.24
2906
3279
5.103000
GCATACAGTTCTCTATTGTCGTGT
58.897
41.667
0.00
0.00
0.00
4.49
3078
3521
3.623960
GGCACTATACGCACATTAACCAA
59.376
43.478
0.00
0.00
0.00
3.67
3083
3526
7.274686
GCACTATACGCACATTAACCAAAATTT
59.725
33.333
0.00
0.00
0.00
1.82
3124
3567
3.681909
CCTAGAGCCTAGGCCCTAG
57.318
63.158
34.45
34.45
45.34
3.02
3207
3650
3.630312
TGGCCGCCATATTTTAGAGAAAC
59.370
43.478
8.43
0.00
0.00
2.78
3223
3666
3.555966
AGAAACTTGTCCTTTGTCCCAG
58.444
45.455
0.00
0.00
0.00
4.45
3258
3701
6.564709
TCTTGTTGATCATTTGTCTTCTGG
57.435
37.500
0.00
0.00
0.00
3.86
3479
3926
9.685276
TTGTCTGTGATCTGACCAATATTTATT
57.315
29.630
10.10
0.00
40.31
1.40
3580
4027
2.084546
GATTTTGGGCTAGCACGAGTT
58.915
47.619
18.24
3.73
0.00
3.01
3838
4285
6.371548
TGTTGTGTTTGCTAGGATATCTTGTC
59.628
38.462
2.05
0.00
0.00
3.18
4134
4581
2.502130
GCAAACCCTTCTAGAGCCTACT
59.498
50.000
0.00
0.00
0.00
2.57
4135
4582
3.680196
GCAAACCCTTCTAGAGCCTACTG
60.680
52.174
0.00
0.00
0.00
2.74
4136
4583
3.476485
AACCCTTCTAGAGCCTACTGT
57.524
47.619
0.00
0.00
0.00
3.55
4137
4584
3.476485
ACCCTTCTAGAGCCTACTGTT
57.524
47.619
0.00
0.00
0.00
3.16
4138
4585
3.792515
ACCCTTCTAGAGCCTACTGTTT
58.207
45.455
0.00
0.00
0.00
2.83
4139
4586
3.515901
ACCCTTCTAGAGCCTACTGTTTG
59.484
47.826
0.00
0.00
0.00
2.93
4140
4587
3.769844
CCCTTCTAGAGCCTACTGTTTGA
59.230
47.826
0.00
0.00
0.00
2.69
4141
4588
4.142049
CCCTTCTAGAGCCTACTGTTTGAG
60.142
50.000
0.00
0.00
0.00
3.02
4425
4952
4.261197
GGGTACGCTTTTCCATTCATGATC
60.261
45.833
2.05
0.00
0.00
2.92
4664
5191
8.100508
AGGCAAGTGTTTCTAGATAAAACTTC
57.899
34.615
14.97
11.64
37.48
3.01
4966
5494
6.479331
GGTTTTTACCATAAGATCTCCTCGAC
59.521
42.308
0.00
0.00
0.00
4.20
5357
5886
4.577693
TGGCATGATAATTTCAGAGACTGC
59.422
41.667
0.00
0.00
37.89
4.40
5848
6378
2.362077
CCTATTACATGCCAAAGGGTGC
59.638
50.000
0.00
0.00
36.17
5.01
6183
6716
1.200948
GCAAAGACAACATCCTGCCTC
59.799
52.381
0.00
0.00
32.72
4.70
6577
7110
0.533308
GTTGGCTCAACCGTGGTACA
60.533
55.000
6.76
0.00
43.94
2.90
6589
7122
5.680594
ACCGTGGTACATATTAAACCAGA
57.319
39.130
0.00
0.00
43.73
3.86
6657
7190
9.309516
CTGATCATTTCCAAATTAACTGAATGG
57.690
33.333
0.00
0.00
0.00
3.16
6681
7227
6.127619
GGCTAGCCTTGTCATAAAAGTTTGAT
60.128
38.462
27.17
0.00
0.00
2.57
6682
7228
6.749118
GCTAGCCTTGTCATAAAAGTTTGATG
59.251
38.462
2.29
6.61
0.00
3.07
6712
7272
8.122330
TCAATATATCAACGTTTGCTTCATCAC
58.878
33.333
0.00
0.00
0.00
3.06
6719
7279
6.416455
TCAACGTTTGCTTCATCACAAAATAC
59.584
34.615
0.00
0.00
37.50
1.89
6737
7302
8.380743
CAAAATACATTTGGTATCTGTTCACG
57.619
34.615
0.00
0.00
43.85
4.35
6750
7315
9.477484
GGTATCTGTTCACGAATATAAGATGTT
57.523
33.333
0.00
0.00
0.00
2.71
6815
7381
6.561737
TGAGTGAACAAACACACTAAAACA
57.438
33.333
0.00
0.00
45.54
2.83
6890
7458
6.708949
GGGAGTAGAACTTGTATTTGTGAACA
59.291
38.462
0.00
0.00
0.00
3.18
6904
7472
2.622942
TGTGAACAAAGGGAGTGCATTC
59.377
45.455
0.00
0.00
0.00
2.67
6938
7507
0.396139
ATACTAGAACGGTGGGCGGA
60.396
55.000
0.00
0.00
0.00
5.54
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
6
7
6.017109
TCCATCTTCTTTTTCTTTCCTCGTTG
60.017
38.462
0.00
0.00
0.00
4.10
9
10
6.372659
TCATCCATCTTCTTTTTCTTTCCTCG
59.627
38.462
0.00
0.00
0.00
4.63
18
19
8.306761
GTGGTGTTAATCATCCATCTTCTTTTT
58.693
33.333
0.00
0.00
32.83
1.94
59
60
2.610374
TGACGCCAAATAACCTAATCGC
59.390
45.455
0.00
0.00
0.00
4.58
117
122
4.134379
TCTTCCATCTCATCTCAACAGC
57.866
45.455
0.00
0.00
0.00
4.40
172
177
2.029290
GGGCCGTGATACGATAAGATGT
60.029
50.000
2.52
0.00
46.05
3.06
173
178
2.607187
GGGCCGTGATACGATAAGATG
58.393
52.381
2.52
0.00
46.05
2.90
246
255
3.347077
ACGGAGTAGTAGTACAGCAGT
57.653
47.619
10.33
5.72
41.94
4.40
247
256
3.181499
CCAACGGAGTAGTAGTACAGCAG
60.181
52.174
10.33
5.16
45.00
4.24
248
257
2.751259
CCAACGGAGTAGTAGTACAGCA
59.249
50.000
10.33
0.00
45.00
4.41
249
258
2.098770
CCCAACGGAGTAGTAGTACAGC
59.901
54.545
10.33
1.85
45.00
4.40
250
259
3.614092
TCCCAACGGAGTAGTAGTACAG
58.386
50.000
10.33
3.88
45.00
2.74
251
260
3.719268
TCCCAACGGAGTAGTAGTACA
57.281
47.619
10.33
0.00
45.00
2.90
252
261
3.317430
CCATCCCAACGGAGTAGTAGTAC
59.683
52.174
0.00
0.00
45.00
2.73
253
262
3.202818
TCCATCCCAACGGAGTAGTAGTA
59.797
47.826
0.00
0.00
45.00
1.82
254
263
2.024655
TCCATCCCAACGGAGTAGTAGT
60.025
50.000
0.00
0.00
45.00
2.73
255
264
2.662866
TCCATCCCAACGGAGTAGTAG
58.337
52.381
0.00
0.00
45.00
2.57
256
265
2.832643
TCCATCCCAACGGAGTAGTA
57.167
50.000
0.00
0.00
45.00
1.82
257
266
1.946984
TTCCATCCCAACGGAGTAGT
58.053
50.000
0.00
0.00
45.00
2.73
258
267
3.343941
TTTTCCATCCCAACGGAGTAG
57.656
47.619
0.00
0.00
45.00
2.57
294
308
1.247567
ATCTCAACCCAACGGCTTTG
58.752
50.000
0.00
0.00
34.63
2.77
374
388
6.251376
GCTTATTTTGTGGCGACTTAAATCAG
59.749
38.462
12.92
12.64
0.00
2.90
375
389
6.090129
GCTTATTTTGTGGCGACTTAAATCA
58.910
36.000
12.92
5.36
0.00
2.57
376
390
6.033513
GTGCTTATTTTGTGGCGACTTAAATC
59.966
38.462
12.92
4.27
0.00
2.17
377
391
5.861787
GTGCTTATTTTGTGGCGACTTAAAT
59.138
36.000
13.66
13.66
0.00
1.40
378
392
5.216648
GTGCTTATTTTGTGGCGACTTAAA
58.783
37.500
0.00
1.61
0.00
1.52
379
393
4.611807
CGTGCTTATTTTGTGGCGACTTAA
60.612
41.667
0.00
0.00
0.00
1.85
380
394
3.120477
CGTGCTTATTTTGTGGCGACTTA
60.120
43.478
0.00
0.00
0.00
2.24
554
571
2.626455
GGCGACGCGGATGATTTC
59.374
61.111
14.61
0.00
0.00
2.17
564
581
3.576356
CCATGTGATGGGCGACGC
61.576
66.667
12.43
12.43
46.86
5.19
618
639
5.407502
ACGTTAAAAAGAAGTGCTTGCTTT
58.592
33.333
0.00
0.00
36.80
3.51
712
784
1.291184
GCAACGCAAAGGGCAAATCC
61.291
55.000
0.00
0.00
45.17
3.01
713
785
1.291184
GGCAACGCAAAGGGCAAATC
61.291
55.000
0.00
0.00
45.17
2.17
714
786
1.301637
GGCAACGCAAAGGGCAAAT
60.302
52.632
0.00
0.00
45.17
2.32
715
787
2.107953
GGCAACGCAAAGGGCAAA
59.892
55.556
0.00
0.00
45.17
3.68
916
988
1.956477
GAGGGAGAGATCTCTGTCTGC
59.044
57.143
29.81
14.29
42.48
4.26
1015
1087
2.348998
CTTCCTCCGCTGCTGGTT
59.651
61.111
9.66
0.00
0.00
3.67
1162
1251
6.084326
TCAAAAAGAAAAAGAATCCTCCCG
57.916
37.500
0.00
0.00
0.00
5.14
1215
1332
4.736126
TGGCAAGAGATAATTCTGACGA
57.264
40.909
0.00
0.00
30.30
4.20
1260
1377
0.249398
AGGAATTGTCGACGGAAGGG
59.751
55.000
11.62
0.00
0.00
3.95
1308
1429
0.108615
CAGTTGGACTCCGTAGCTGG
60.109
60.000
0.00
0.00
0.00
4.85
1314
1435
3.665190
GAAGAATTCAGTTGGACTCCGT
58.335
45.455
8.44
0.00
46.62
4.69
1335
1456
7.274250
CCTTTTTCGCAATAAGAAATGGAAGAG
59.726
37.037
0.00
0.00
37.43
2.85
1485
1606
8.472007
TTTATAGAGGGACAAAGCAAGAAAAA
57.528
30.769
0.00
0.00
0.00
1.94
1539
1660
7.265673
TGAGTATTCAACTACTAGCATGGAAC
58.734
38.462
0.00
0.00
39.07
3.62
1870
1997
7.068716
GCCCAAGAATGACTATTTAAGGATGTT
59.931
37.037
0.00
0.00
0.00
2.71
1908
2035
4.553547
GCTATGAGGAAAACAGCGCTTATG
60.554
45.833
7.50
0.00
0.00
1.90
1936
2063
0.454957
CGATGCAAAACTCCTTGGCG
60.455
55.000
0.00
0.00
0.00
5.69
1976
2109
1.955529
GATCGCTCGCGCACAAAGAA
61.956
55.000
8.75
0.00
39.59
2.52
1983
2116
4.128388
TTCTGGATCGCTCGCGCA
62.128
61.111
8.75
0.00
39.59
6.09
1989
2122
1.140589
CGTGAGCTTCTGGATCGCT
59.859
57.895
0.00
0.00
38.54
4.93
1990
2123
1.880340
CCGTGAGCTTCTGGATCGC
60.880
63.158
0.00
0.00
37.48
4.58
1991
2124
0.173481
TTCCGTGAGCTTCTGGATCG
59.827
55.000
3.01
0.00
32.20
3.69
2004
2137
2.794350
GCACAAAAAGTTGGATTCCGTG
59.206
45.455
0.00
0.00
39.22
4.94
2107
2240
6.073657
CCTCAATACAACAGCCAAATTTTGTG
60.074
38.462
8.26
3.72
34.15
3.33
2142
2275
4.293671
CCAGGTTTTCCGCCCCCA
62.294
66.667
0.00
0.00
46.35
4.96
2145
2278
0.540133
TAAACCCAGGTTTTCCGCCC
60.540
55.000
19.35
0.00
44.84
6.13
2148
2281
3.887110
AGAAGTTAAACCCAGGTTTTCCG
59.113
43.478
19.35
0.00
44.84
4.30
2218
2591
4.862371
TGGATAAACCCCAGGTTGATAAC
58.138
43.478
0.00
0.00
46.20
1.89
2225
2598
2.364190
TCCTTTGGATAAACCCCAGGT
58.636
47.619
0.00
0.00
37.81
4.00
2386
2759
0.447801
CGCAATGGAGAACCTTTCCG
59.552
55.000
0.00
0.00
37.54
4.30
2644
3017
6.956435
ACTATATCAGGATGTCTCAATAGGCA
59.044
38.462
0.00
0.00
42.75
4.75
2879
3252
7.649705
CACGACAATAGAGAACTGTATGCTAAT
59.350
37.037
0.00
0.00
0.00
1.73
2927
3300
8.694696
AGGGTATGGATAAAATACCTACTCCTA
58.305
37.037
11.35
0.00
46.01
2.94
2962
3335
1.030488
AGCAAAGCATCAGCAGCGAT
61.030
50.000
0.00
0.00
45.49
4.58
3078
3521
3.865164
GCAAAATGCCTAGCGCTAAATTT
59.135
39.130
19.37
19.25
37.42
1.82
3083
3526
2.613026
TAGCAAAATGCCTAGCGCTA
57.387
45.000
17.75
17.75
46.52
4.26
3207
3650
4.911390
ACTAATCTGGGACAAAGGACAAG
58.089
43.478
0.00
0.00
38.70
3.16
3258
3701
8.392612
CAATGAAAGGCCAAATATCAAAATCAC
58.607
33.333
5.01
0.00
0.00
3.06
3479
3926
7.134163
CGATGATAAACATTAGCTGCAATCAA
58.866
34.615
1.02
0.00
39.56
2.57
3580
4027
2.161855
GTGGGAGTGTCATTGAATGCA
58.838
47.619
0.00
0.00
0.00
3.96
3726
4173
6.283694
TCTAGTAGCAACATAATCCTGCAAG
58.716
40.000
0.00
0.00
38.58
4.01
3838
4285
4.730613
GCATGTTTATGTGGAAAGTAGCGG
60.731
45.833
0.00
0.00
36.65
5.52
4048
4495
8.969260
TCTAGTAGTCGTATGAACCTTGAATA
57.031
34.615
0.00
0.00
0.00
1.75
4134
4581
6.428465
TCTGTAGTTGTGAAAACACTCAAACA
59.572
34.615
0.00
0.00
0.00
2.83
4135
4582
6.837992
TCTGTAGTTGTGAAAACACTCAAAC
58.162
36.000
0.00
0.00
0.00
2.93
4136
4583
6.653320
ACTCTGTAGTTGTGAAAACACTCAAA
59.347
34.615
0.00
0.00
29.00
2.69
4137
4584
6.170506
ACTCTGTAGTTGTGAAAACACTCAA
58.829
36.000
0.00
0.00
29.00
3.02
4138
4585
5.730550
ACTCTGTAGTTGTGAAAACACTCA
58.269
37.500
0.00
0.00
29.00
3.41
4139
4586
7.948278
ATACTCTGTAGTTGTGAAAACACTC
57.052
36.000
0.00
0.00
37.15
3.51
4140
4587
9.424319
CATATACTCTGTAGTTGTGAAAACACT
57.576
33.333
0.00
0.00
37.15
3.55
4141
4588
8.169268
GCATATACTCTGTAGTTGTGAAAACAC
58.831
37.037
0.00
0.00
37.15
3.32
4425
4952
5.940617
TGGATACCTTACTTTGGATCATGG
58.059
41.667
0.00
0.00
0.00
3.66
4664
5191
9.150348
AGTTTTTAACACCTGTTTTTGAATCTG
57.850
29.630
0.00
0.00
39.31
2.90
4707
5234
6.569035
CGCCTGATTATGATGTGCACATAAAT
60.569
38.462
31.45
26.90
41.42
1.40
5064
5592
3.502119
CCTTCCCTCCATTTTCCTCCAAA
60.502
47.826
0.00
0.00
0.00
3.28
5357
5886
1.677576
TCAGCAAGCAAAGTTGAGTGG
59.322
47.619
0.00
0.00
0.00
4.00
5524
6053
8.996655
AGGATATATACATGTCATATTGGTGCT
58.003
33.333
0.00
3.46
0.00
4.40
5848
6378
0.679640
TGCTACATCGGCTTTTGGGG
60.680
55.000
0.00
0.00
0.00
4.96
6183
6716
2.996249
TCCTTGGCAGCTAGATCAAG
57.004
50.000
0.00
0.00
37.09
3.02
6589
7122
9.256228
TGTTTCTACTGTTCCTCTATATCAACT
57.744
33.333
0.00
0.00
0.00
3.16
6657
7190
6.254281
TCAAACTTTTATGACAAGGCTAGC
57.746
37.500
6.04
6.04
0.00
3.42
6681
7227
7.609760
AGCAAACGTTGATATATTGACTTCA
57.390
32.000
0.00
0.00
0.00
3.02
6682
7228
8.175069
TGAAGCAAACGTTGATATATTGACTTC
58.825
33.333
0.00
11.48
36.21
3.01
6712
7272
8.233868
TCGTGAACAGATACCAAATGTATTTTG
58.766
33.333
0.00
0.00
40.31
2.44
6862
7430
4.189231
CAAATACAAGTTCTACTCCCCGG
58.811
47.826
0.00
0.00
0.00
5.73
6890
7458
3.222603
AGTTTTCGAATGCACTCCCTTT
58.777
40.909
0.00
0.00
0.00
3.11
6904
7472
8.371053
CCGTTCTAGTATTTGACTAAGTTTTCG
58.629
37.037
0.00
0.00
40.23
3.46
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.