Multiple sequence alignment - TraesCS5A01G246500
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
TraesCS5A01G246500
chr5A
100.000
2894
0
0
1
2894
459777340
459774447
0.000000e+00
5345
1
TraesCS5A01G246500
chr5B
89.019
2978
123
86
1
2894
425092621
425095478
0.000000e+00
3500
2
TraesCS5A01G246500
chr5D
91.443
2501
83
54
435
2894
359474258
359476668
0.000000e+00
3312
3
TraesCS5A01G246500
chr5D
83.333
402
36
17
1
401
359473675
359474046
2.760000e-90
342
4
TraesCS5A01G246500
chr4A
82.653
196
34
0
1690
1885
535035691
535035886
1.070000e-39
174
5
TraesCS5A01G246500
chr4D
82.967
182
31
0
1690
1871
61852301
61852482
6.420000e-37
165
6
TraesCS5A01G246500
chr4B
81.538
195
36
0
1691
1885
90892349
90892155
8.300000e-36
161
7
TraesCS5A01G246500
chr6B
80.769
208
29
11
1664
1864
539195275
539195072
4.990000e-33
152
8
TraesCS5A01G246500
chr1B
80.925
173
31
2
1693
1864
667750250
667750421
5.030000e-28
135
9
TraesCS5A01G246500
chr1D
79.885
174
31
4
1693
1864
479540798
479540969
1.090000e-24
124
10
TraesCS5A01G246500
chr3A
79.191
173
32
4
1693
1863
423672120
423672290
1.820000e-22
117
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
TraesCS5A01G246500
chr5A
459774447
459777340
2893
True
5345
5345
100.000
1
2894
1
chr5A.!!$R1
2893
1
TraesCS5A01G246500
chr5B
425092621
425095478
2857
False
3500
3500
89.019
1
2894
1
chr5B.!!$F1
2893
2
TraesCS5A01G246500
chr5D
359473675
359476668
2993
False
1827
3312
87.388
1
2894
2
chr5D.!!$F1
2893
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
413
415
0.108992
ATTTGCTTGACGCTGCATGG
60.109
50.0
0.0
0.0
39.07
3.66
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2037
2279
0.039437
GCGAATGCGGTAGCTAGCTA
60.039
55.0
20.67
20.67
45.42
3.32
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
58
59
2.417719
GTCCTGCTTCAGTACTTGGTG
58.582
52.381
0.00
0.00
0.00
4.17
68
69
1.003580
AGTACTTGGTGTGCATGGAGG
59.996
52.381
0.00
0.00
33.54
4.30
69
70
0.322456
TACTTGGTGTGCATGGAGGC
60.322
55.000
0.00
0.00
0.00
4.70
70
71
1.303888
CTTGGTGTGCATGGAGGCT
60.304
57.895
0.00
0.00
34.04
4.58
71
72
0.896940
CTTGGTGTGCATGGAGGCTT
60.897
55.000
0.00
0.00
34.04
4.35
72
73
1.180456
TTGGTGTGCATGGAGGCTTG
61.180
55.000
0.00
0.00
34.04
4.01
73
74
2.345760
GGTGTGCATGGAGGCTTGG
61.346
63.158
0.00
0.00
34.04
3.61
74
75
2.036098
TGTGCATGGAGGCTTGGG
59.964
61.111
0.00
0.00
34.04
4.12
75
76
2.356278
GTGCATGGAGGCTTGGGA
59.644
61.111
0.00
0.00
34.04
4.37
76
77
1.304381
GTGCATGGAGGCTTGGGAA
60.304
57.895
0.00
0.00
34.04
3.97
77
78
1.000521
TGCATGGAGGCTTGGGAAG
60.001
57.895
0.00
0.00
34.04
3.46
78
79
1.000396
GCATGGAGGCTTGGGAAGT
60.000
57.895
0.00
0.00
0.00
3.01
79
80
1.318158
GCATGGAGGCTTGGGAAGTG
61.318
60.000
0.00
0.00
0.00
3.16
80
81
1.000396
ATGGAGGCTTGGGAAGTGC
60.000
57.895
0.00
0.00
0.00
4.40
81
82
2.747855
GGAGGCTTGGGAAGTGCG
60.748
66.667
0.00
0.00
0.00
5.34
82
83
2.347490
GAGGCTTGGGAAGTGCGA
59.653
61.111
0.00
0.00
0.00
5.10
83
84
1.743252
GAGGCTTGGGAAGTGCGAG
60.743
63.158
0.00
0.00
0.00
5.03
86
87
2.684843
GCTTGGGAAGTGCGAGCTG
61.685
63.158
0.00
0.00
0.00
4.24
95
96
1.026718
AGTGCGAGCTGGTTTATGGC
61.027
55.000
0.00
0.00
0.00
4.40
96
97
1.026718
GTGCGAGCTGGTTTATGGCT
61.027
55.000
0.00
0.00
39.16
4.75
98
99
1.723870
CGAGCTGGTTTATGGCTGC
59.276
57.895
0.00
0.00
36.37
5.25
99
100
1.723870
GAGCTGGTTTATGGCTGCG
59.276
57.895
0.00
0.00
36.37
5.18
104
105
0.250945
TGGTTTATGGCTGCGTCCAA
60.251
50.000
0.63
0.00
39.96
3.53
105
106
0.885196
GGTTTATGGCTGCGTCCAAA
59.115
50.000
0.63
0.00
39.96
3.28
106
107
1.271102
GGTTTATGGCTGCGTCCAAAA
59.729
47.619
0.63
1.87
39.96
2.44
107
108
2.324860
GTTTATGGCTGCGTCCAAAAC
58.675
47.619
0.63
9.00
39.96
2.43
117
118
0.306533
CGTCCAAAACGTGAACCTGG
59.693
55.000
0.00
0.00
46.42
4.45
140
141
0.167470
CGAGCGAGTGGTAGAAACGA
59.833
55.000
0.00
0.00
0.00
3.85
146
147
3.610114
GCGAGTGGTAGAAACGAACTGTA
60.610
47.826
0.00
0.00
0.00
2.74
147
148
4.730657
CGAGTGGTAGAAACGAACTGTAT
58.269
43.478
0.00
0.00
0.00
2.29
148
149
5.159209
CGAGTGGTAGAAACGAACTGTATT
58.841
41.667
0.00
0.00
0.00
1.89
149
150
6.317088
CGAGTGGTAGAAACGAACTGTATTA
58.683
40.000
0.00
0.00
0.00
0.98
156
157
8.811378
GGTAGAAACGAACTGTATTATTACCAC
58.189
37.037
0.00
0.00
0.00
4.16
168
169
2.375173
ATTACCACCCTCGACGTTTC
57.625
50.000
0.00
0.00
0.00
2.78
207
208
2.126734
ACGGACGGTAGAAACGCG
60.127
61.111
3.53
3.53
34.00
6.01
229
230
1.750930
CACAGTGTGCAGGAGGAGT
59.249
57.895
10.97
0.00
0.00
3.85
230
231
0.602106
CACAGTGTGCAGGAGGAGTG
60.602
60.000
10.97
0.00
0.00
3.51
231
232
1.670406
CAGTGTGCAGGAGGAGTGC
60.670
63.158
0.00
0.00
41.59
4.40
237
238
1.072159
GCAGGAGGAGTGCAACAGT
59.928
57.895
0.00
0.00
41.43
3.55
240
241
1.131638
AGGAGGAGTGCAACAGTGAA
58.868
50.000
0.00
0.00
41.43
3.18
250
251
4.102649
GTGCAACAGTGAAGGTTTTGTAC
58.897
43.478
0.00
0.00
36.32
2.90
258
259
1.262151
GAAGGTTTTGTACGCTTGCGA
59.738
47.619
22.03
2.66
0.00
5.10
274
275
2.510238
GAGCGGTGCAGGTGCTAG
60.510
66.667
7.20
0.00
39.49
3.42
275
276
4.767255
AGCGGTGCAGGTGCTAGC
62.767
66.667
8.10
8.10
42.66
3.42
288
289
3.713764
AGGTGCTAGCACTTAATCAGGAT
59.286
43.478
38.82
14.90
45.52
3.24
301
302
6.540189
ACTTAATCAGGATCTGAAAATGACGG
59.460
38.462
1.53
0.00
44.04
4.79
338
339
2.119495
CTCTGGGGAAAGGCTAGCTTA
58.881
52.381
15.72
0.00
0.00
3.09
368
369
3.309436
TTGCATCACTCGACCCGGG
62.309
63.158
22.25
22.25
0.00
5.73
379
380
1.026584
CGACCCGGGAAACAGTTTTT
58.973
50.000
32.02
0.00
0.00
1.94
383
384
1.067974
CCCGGGAAACAGTTTTTGGTC
59.932
52.381
18.48
0.00
0.00
4.02
387
389
2.946990
GGGAAACAGTTTTTGGTCGAGA
59.053
45.455
0.00
0.00
0.00
4.04
410
412
3.574284
ATAAATTTGCTTGACGCTGCA
57.426
38.095
0.00
0.00
40.11
4.41
411
413
2.443887
AAATTTGCTTGACGCTGCAT
57.556
40.000
0.00
0.00
39.07
3.96
413
415
0.108992
ATTTGCTTGACGCTGCATGG
60.109
50.000
0.00
0.00
39.07
3.66
414
416
2.752322
TTTGCTTGACGCTGCATGGC
62.752
55.000
0.00
0.00
39.07
4.40
415
417
4.487412
GCTTGACGCTGCATGGCC
62.487
66.667
0.00
0.00
35.14
5.36
416
418
2.749044
CTTGACGCTGCATGGCCT
60.749
61.111
3.32
0.00
0.00
5.19
423
453
1.143183
GCTGCATGGCCTTTCATGG
59.857
57.895
3.32
0.00
43.34
3.66
430
460
3.369681
GCATGGCCTTTCATGGATTTCAA
60.370
43.478
3.32
0.00
43.34
2.69
432
462
4.475051
TGGCCTTTCATGGATTTCAATG
57.525
40.909
3.32
0.00
0.00
2.82
448
646
0.606401
AATGCACCTCCTGGAACACG
60.606
55.000
0.00
0.00
37.04
4.49
478
676
3.560025
GGATCCTGTGTTGACCATGTTCT
60.560
47.826
3.84
0.00
0.00
3.01
479
677
3.576078
TCCTGTGTTGACCATGTTCTT
57.424
42.857
0.00
0.00
0.00
2.52
480
678
3.213506
TCCTGTGTTGACCATGTTCTTG
58.786
45.455
0.00
0.00
0.00
3.02
481
679
2.287788
CCTGTGTTGACCATGTTCTTGC
60.288
50.000
0.00
0.00
0.00
4.01
541
742
5.107337
CCAGATGTCACGATCAAATATTCCG
60.107
44.000
0.00
0.00
0.00
4.30
542
743
5.691754
CAGATGTCACGATCAAATATTCCGA
59.308
40.000
0.00
0.00
0.00
4.55
543
744
5.923114
AGATGTCACGATCAAATATTCCGAG
59.077
40.000
0.00
0.00
0.00
4.63
544
745
5.257082
TGTCACGATCAAATATTCCGAGA
57.743
39.130
0.00
0.00
0.00
4.04
564
765
3.509967
AGAGAACCCCAATTTAAAAGGCG
59.490
43.478
4.88
0.21
0.00
5.52
620
821
2.617274
GGACGGCCAGCAAAGACAC
61.617
63.158
0.00
0.00
0.00
3.67
623
824
2.034879
CGGCCAGCAAAGACACGAT
61.035
57.895
2.24
0.00
0.00
3.73
644
845
5.163953
CGATCACGAAGCAAAAGAACATACT
60.164
40.000
0.00
0.00
42.66
2.12
645
846
6.034577
CGATCACGAAGCAAAAGAACATACTA
59.965
38.462
0.00
0.00
42.66
1.82
646
847
6.462073
TCACGAAGCAAAAGAACATACTAC
57.538
37.500
0.00
0.00
0.00
2.73
661
862
3.792053
CTACATCACGCCTCGGCCC
62.792
68.421
0.00
0.00
37.98
5.80
675
876
4.722700
GCCCGGGCACACACAGAT
62.723
66.667
40.73
0.00
41.49
2.90
684
885
3.020274
GGCACACACAGATAGAGAGAGA
58.980
50.000
0.00
0.00
0.00
3.10
685
886
3.066621
GGCACACACAGATAGAGAGAGAG
59.933
52.174
0.00
0.00
0.00
3.20
686
887
3.066621
GCACACACAGATAGAGAGAGAGG
59.933
52.174
0.00
0.00
0.00
3.69
687
888
4.522114
CACACACAGATAGAGAGAGAGGA
58.478
47.826
0.00
0.00
0.00
3.71
691
892
4.103153
ACACAGATAGAGAGAGAGGAGAGG
59.897
50.000
0.00
0.00
0.00
3.69
693
894
3.652869
CAGATAGAGAGAGAGGAGAGGGT
59.347
52.174
0.00
0.00
0.00
4.34
728
929
3.213402
GCGACTCGAGAGGGAGGG
61.213
72.222
21.68
0.85
38.39
4.30
729
930
2.590645
CGACTCGAGAGGGAGGGA
59.409
66.667
21.68
0.00
38.39
4.20
730
931
1.525077
CGACTCGAGAGGGAGGGAG
60.525
68.421
21.68
0.00
38.39
4.30
731
932
1.152839
GACTCGAGAGGGAGGGAGG
60.153
68.421
21.68
0.00
38.39
4.30
812
1013
1.608283
GGTTACATCATCGCCTAGGCC
60.608
57.143
28.09
10.55
37.98
5.19
813
1014
0.317160
TTACATCATCGCCTAGGCCG
59.683
55.000
28.09
21.60
37.98
6.13
814
1015
2.154798
TACATCATCGCCTAGGCCGC
62.155
60.000
28.09
3.58
37.98
6.53
815
1016
2.919856
ATCATCGCCTAGGCCGCT
60.920
61.111
28.09
11.78
37.98
5.52
1647
1872
4.220413
CTGAGCAGCATGTCCCTG
57.780
61.111
0.00
0.00
39.31
4.45
1842
2067
2.432628
CGCCACGTCCTCAAGGTC
60.433
66.667
0.00
0.00
36.34
3.85
2034
2276
2.005451
GCATGTGCTTCTCTCGTTCAT
58.995
47.619
0.00
0.00
38.21
2.57
2037
2279
3.667497
TGTGCTTCTCTCGTTCATCTT
57.333
42.857
0.00
0.00
0.00
2.40
2038
2280
4.783764
TGTGCTTCTCTCGTTCATCTTA
57.216
40.909
0.00
0.00
0.00
2.10
2039
2281
4.738124
TGTGCTTCTCTCGTTCATCTTAG
58.262
43.478
0.00
0.00
0.00
2.18
2040
2282
3.549873
GTGCTTCTCTCGTTCATCTTAGC
59.450
47.826
0.00
0.00
0.00
3.09
2047
2289
5.467399
TCTCTCGTTCATCTTAGCTAGCTAC
59.533
44.000
24.09
12.35
0.00
3.58
2048
2290
4.515944
TCTCGTTCATCTTAGCTAGCTACC
59.484
45.833
24.09
5.60
0.00
3.18
2084
2326
4.222847
GTTCCCCTCCGCGGCTAG
62.223
72.222
23.51
14.27
0.00
3.42
2133
2375
0.109272
TCTGTAGCGAGCGTTCCTTG
60.109
55.000
0.00
0.00
0.00
3.61
2175
2417
9.547279
AATTTAGGTGGTCCTCTATTTTCATTT
57.453
29.630
0.00
0.00
43.94
2.32
2176
2418
8.575649
TTTAGGTGGTCCTCTATTTTCATTTC
57.424
34.615
0.00
0.00
43.94
2.17
2177
2419
6.139679
AGGTGGTCCTCTATTTTCATTTCA
57.860
37.500
0.00
0.00
40.58
2.69
2181
2423
7.976175
GGTGGTCCTCTATTTTCATTTCATTTC
59.024
37.037
0.00
0.00
0.00
2.17
2213
2455
3.668447
ACTGTTGCTCATGTAACTCCTG
58.332
45.455
0.00
0.00
39.12
3.86
2217
2459
2.466846
TGCTCATGTAACTCCTGGCTA
58.533
47.619
0.00
0.00
0.00
3.93
2353
2595
1.515088
CGTGCGTGCTCCTGAGTAG
60.515
63.158
0.00
0.00
0.00
2.57
2354
2596
1.153745
GTGCGTGCTCCTGAGTAGG
60.154
63.158
1.29
1.29
46.06
3.18
2452
2694
0.037232
GTCCAGGTTTGCTAGTCGCT
60.037
55.000
0.00
0.00
40.11
4.93
2453
2695
1.203994
GTCCAGGTTTGCTAGTCGCTA
59.796
52.381
0.00
0.00
40.11
4.26
2454
2696
1.203994
TCCAGGTTTGCTAGTCGCTAC
59.796
52.381
0.00
0.00
40.11
3.58
2459
2705
2.165030
GGTTTGCTAGTCGCTACTACCA
59.835
50.000
3.11
0.00
40.11
3.25
2475
2721
4.424566
CACCTGCGTGCCATTGCC
62.425
66.667
0.00
0.00
36.33
4.52
2478
2724
3.672447
CTGCGTGCCATTGCCACA
61.672
61.111
0.00
0.00
36.33
4.17
2537
2783
0.395173
TTAGCCATTTTCCTCCCCGC
60.395
55.000
0.00
0.00
0.00
6.13
2538
2784
2.279037
TAGCCATTTTCCTCCCCGCC
62.279
60.000
0.00
0.00
0.00
6.13
2539
2785
2.683475
CCATTTTCCTCCCCGCCT
59.317
61.111
0.00
0.00
0.00
5.52
2552
2798
1.216710
CCGCCTCCTCACTCACTTC
59.783
63.158
0.00
0.00
0.00
3.01
2568
2814
2.542211
CTTCGGGCATTTGTTCGGGC
62.542
60.000
0.00
0.00
0.00
6.13
2569
2815
3.369400
CGGGCATTTGTTCGGGCA
61.369
61.111
0.00
0.00
0.00
5.36
2570
2816
2.261361
GGGCATTTGTTCGGGCAC
59.739
61.111
0.00
0.00
0.00
5.01
2571
2817
2.126502
GGCATTTGTTCGGGCACG
60.127
61.111
0.00
0.00
42.74
5.34
2572
2818
2.126502
GCATTTGTTCGGGCACGG
60.127
61.111
9.32
0.00
41.39
4.94
2573
2819
2.566010
CATTTGTTCGGGCACGGG
59.434
61.111
9.32
0.00
41.39
5.28
2574
2820
2.675075
ATTTGTTCGGGCACGGGG
60.675
61.111
9.32
0.00
41.39
5.73
2575
2821
3.501040
ATTTGTTCGGGCACGGGGT
62.501
57.895
9.32
0.00
41.39
4.95
2576
2822
2.127027
ATTTGTTCGGGCACGGGGTA
62.127
55.000
9.32
0.00
41.39
3.69
2585
2831
1.683938
GGGCACGGGGTAGCTTAATTT
60.684
52.381
0.00
0.00
0.00
1.82
2606
2852
0.895100
GCACAGACCAATGCTTCCCA
60.895
55.000
0.00
0.00
38.84
4.37
2623
2869
0.037303
CCATCCCCTCCATTGATCCG
59.963
60.000
0.00
0.00
0.00
4.18
2628
2874
1.131638
CCCTCCATTGATCCGAGGAA
58.868
55.000
13.89
0.00
45.15
3.36
2660
2921
1.806461
GCCATGATCCATGCAGCAGG
61.806
60.000
0.00
0.00
40.20
4.85
2774
3037
1.613061
CCCCCGCATTTAACTCCCT
59.387
57.895
0.00
0.00
0.00
4.20
2813
3076
2.543037
AGGTTCTTCTCCTCCTCCTC
57.457
55.000
0.00
0.00
0.00
3.71
2814
3077
1.007842
AGGTTCTTCTCCTCCTCCTCC
59.992
57.143
0.00
0.00
0.00
4.30
2815
3078
1.007842
GGTTCTTCTCCTCCTCCTCCT
59.992
57.143
0.00
0.00
0.00
3.69
2816
3079
2.384828
GTTCTTCTCCTCCTCCTCCTC
58.615
57.143
0.00
0.00
0.00
3.71
2817
3080
0.930726
TCTTCTCCTCCTCCTCCTCC
59.069
60.000
0.00
0.00
0.00
4.30
2818
3081
0.933700
CTTCTCCTCCTCCTCCTCCT
59.066
60.000
0.00
0.00
0.00
3.69
2819
3082
0.930726
TTCTCCTCCTCCTCCTCCTC
59.069
60.000
0.00
0.00
0.00
3.71
2820
3083
0.996762
TCTCCTCCTCCTCCTCCTCC
60.997
65.000
0.00
0.00
0.00
4.30
2821
3084
0.998945
CTCCTCCTCCTCCTCCTCCT
60.999
65.000
0.00
0.00
0.00
3.69
2826
3089
1.219213
TCCTCCTCCTCCTCCTTGATC
59.781
57.143
0.00
0.00
0.00
2.92
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
58
59
1.304381
TTCCCAAGCCTCCATGCAC
60.304
57.895
0.00
0.00
0.00
4.57
68
69
2.359230
AGCTCGCACTTCCCAAGC
60.359
61.111
0.00
0.00
0.00
4.01
69
70
2.037136
CCAGCTCGCACTTCCCAAG
61.037
63.158
0.00
0.00
0.00
3.61
70
71
2.032528
CCAGCTCGCACTTCCCAA
59.967
61.111
0.00
0.00
0.00
4.12
71
72
2.337879
AAACCAGCTCGCACTTCCCA
62.338
55.000
0.00
0.00
0.00
4.37
72
73
0.321298
TAAACCAGCTCGCACTTCCC
60.321
55.000
0.00
0.00
0.00
3.97
73
74
1.398390
CATAAACCAGCTCGCACTTCC
59.602
52.381
0.00
0.00
0.00
3.46
74
75
1.398390
CCATAAACCAGCTCGCACTTC
59.602
52.381
0.00
0.00
0.00
3.01
75
76
1.453155
CCATAAACCAGCTCGCACTT
58.547
50.000
0.00
0.00
0.00
3.16
76
77
1.026718
GCCATAAACCAGCTCGCACT
61.027
55.000
0.00
0.00
0.00
4.40
77
78
1.026718
AGCCATAAACCAGCTCGCAC
61.027
55.000
0.00
0.00
28.40
5.34
78
79
1.026182
CAGCCATAAACCAGCTCGCA
61.026
55.000
0.00
0.00
33.70
5.10
79
80
1.723870
CAGCCATAAACCAGCTCGC
59.276
57.895
0.00
0.00
33.70
5.03
80
81
1.723870
GCAGCCATAAACCAGCTCG
59.276
57.895
0.00
0.00
33.70
5.03
81
82
1.026718
ACGCAGCCATAAACCAGCTC
61.027
55.000
0.00
0.00
33.70
4.09
82
83
1.002134
ACGCAGCCATAAACCAGCT
60.002
52.632
0.00
0.00
37.32
4.24
83
84
1.429423
GACGCAGCCATAAACCAGC
59.571
57.895
0.00
0.00
0.00
4.85
86
87
0.885196
TTTGGACGCAGCCATAAACC
59.115
50.000
0.00
0.00
37.86
3.27
99
100
1.602377
CTCCAGGTTCACGTTTTGGAC
59.398
52.381
0.00
0.00
34.42
4.02
104
105
1.597027
CGGCTCCAGGTTCACGTTT
60.597
57.895
0.00
0.00
0.00
3.60
105
106
2.030562
CGGCTCCAGGTTCACGTT
59.969
61.111
0.00
0.00
0.00
3.99
106
107
2.915659
TCGGCTCCAGGTTCACGT
60.916
61.111
0.00
0.00
0.00
4.49
107
108
2.125912
CTCGGCTCCAGGTTCACG
60.126
66.667
0.00
0.00
0.00
4.35
108
109
2.435059
GCTCGGCTCCAGGTTCAC
60.435
66.667
0.00
0.00
0.00
3.18
109
110
4.069232
CGCTCGGCTCCAGGTTCA
62.069
66.667
0.00
0.00
0.00
3.18
110
111
3.708220
CTCGCTCGGCTCCAGGTTC
62.708
68.421
0.00
0.00
0.00
3.62
117
118
1.654954
TTCTACCACTCGCTCGGCTC
61.655
60.000
0.00
0.00
0.00
4.70
129
130
8.530311
TGGTAATAATACAGTTCGTTTCTACCA
58.470
33.333
0.00
0.00
33.45
3.25
140
141
5.450965
CGTCGAGGGTGGTAATAATACAGTT
60.451
44.000
0.00
0.00
33.45
3.16
146
147
4.436332
GAAACGTCGAGGGTGGTAATAAT
58.564
43.478
10.27
0.00
0.00
1.28
147
148
3.368323
GGAAACGTCGAGGGTGGTAATAA
60.368
47.826
10.27
0.00
0.00
1.40
148
149
2.166254
GGAAACGTCGAGGGTGGTAATA
59.834
50.000
10.27
0.00
0.00
0.98
149
150
1.066645
GGAAACGTCGAGGGTGGTAAT
60.067
52.381
10.27
0.00
0.00
1.89
168
169
2.794981
CGACCATGTAGTGTAGCGAAGG
60.795
54.545
0.00
0.00
0.00
3.46
229
230
3.181505
CGTACAAAACCTTCACTGTTGCA
60.182
43.478
0.00
0.00
0.00
4.08
230
231
3.359654
CGTACAAAACCTTCACTGTTGC
58.640
45.455
0.00
0.00
0.00
4.17
231
232
3.064820
AGCGTACAAAACCTTCACTGTTG
59.935
43.478
0.00
0.00
0.00
3.33
232
233
3.275999
AGCGTACAAAACCTTCACTGTT
58.724
40.909
0.00
0.00
0.00
3.16
237
238
1.003331
CGCAAGCGTACAAAACCTTCA
60.003
47.619
6.25
0.00
34.35
3.02
240
241
0.865769
CTCGCAAGCGTACAAAACCT
59.134
50.000
14.57
0.00
40.74
3.50
258
259
4.767255
GCTAGCACCTGCACCGCT
62.767
66.667
10.63
5.23
45.16
5.52
268
269
4.749099
CAGATCCTGATTAAGTGCTAGCAC
59.251
45.833
35.56
35.56
39.30
4.40
269
270
4.651045
TCAGATCCTGATTAAGTGCTAGCA
59.349
41.667
14.93
14.93
35.39
3.49
270
271
5.207110
TCAGATCCTGATTAAGTGCTAGC
57.793
43.478
8.10
8.10
35.39
3.42
274
275
7.192232
GTCATTTTCAGATCCTGATTAAGTGC
58.808
38.462
0.00
0.00
40.39
4.40
275
276
7.404985
CGTCATTTTCAGATCCTGATTAAGTG
58.595
38.462
0.00
0.00
40.39
3.16
288
289
0.871722
CGCAACCCGTCATTTTCAGA
59.128
50.000
0.00
0.00
0.00
3.27
301
302
2.202349
GCATCGAAGTGCGCAACC
60.202
61.111
14.00
0.00
40.61
3.77
338
339
0.034767
TGATGCAAGCAAGGCTAGCT
60.035
50.000
15.72
0.00
45.97
3.32
345
346
0.445436
GGTCGAGTGATGCAAGCAAG
59.555
55.000
0.00
0.00
28.10
4.01
368
369
8.623310
TTATTTTCTCGACCAAAAACTGTTTC
57.377
30.769
6.20
0.00
0.00
2.78
379
380
6.861055
GTCAAGCAAATTTATTTTCTCGACCA
59.139
34.615
0.00
0.00
0.00
4.02
410
412
4.685030
GCATTGAAATCCATGAAAGGCCAT
60.685
41.667
5.01
0.00
0.00
4.40
411
413
3.369681
GCATTGAAATCCATGAAAGGCCA
60.370
43.478
5.01
0.00
0.00
5.36
413
415
3.619929
GTGCATTGAAATCCATGAAAGGC
59.380
43.478
0.00
0.00
0.00
4.35
414
416
4.081309
AGGTGCATTGAAATCCATGAAAGG
60.081
41.667
0.00
0.00
0.00
3.11
415
417
5.080969
AGGTGCATTGAAATCCATGAAAG
57.919
39.130
0.00
0.00
0.00
2.62
416
418
4.081531
GGAGGTGCATTGAAATCCATGAAA
60.082
41.667
0.00
0.00
0.00
2.69
423
453
2.726821
TCCAGGAGGTGCATTGAAATC
58.273
47.619
0.00
0.00
35.89
2.17
430
460
1.003355
CGTGTTCCAGGAGGTGCAT
60.003
57.895
0.00
0.00
35.89
3.96
432
462
1.374758
CTCGTGTTCCAGGAGGTGC
60.375
63.158
6.13
0.00
41.07
5.01
448
646
0.250513
AACACAGGATCCCGCTTCTC
59.749
55.000
8.55
0.00
0.00
2.87
461
659
2.620115
AGCAAGAACATGGTCAACACAG
59.380
45.455
14.46
0.00
0.00
3.66
478
676
5.593968
TCTTTTGTTACTCGTGTCTAGCAA
58.406
37.500
0.00
0.00
0.00
3.91
479
677
5.190992
TCTTTTGTTACTCGTGTCTAGCA
57.809
39.130
0.00
0.00
0.00
3.49
480
678
6.520792
TTTCTTTTGTTACTCGTGTCTAGC
57.479
37.500
0.00
0.00
0.00
3.42
481
679
8.348983
TCTTTTCTTTTGTTACTCGTGTCTAG
57.651
34.615
0.00
0.00
0.00
2.43
541
742
4.380550
CGCCTTTTAAATTGGGGTTCTCTC
60.381
45.833
13.25
0.00
0.00
3.20
542
743
3.509967
CGCCTTTTAAATTGGGGTTCTCT
59.490
43.478
13.25
0.00
0.00
3.10
543
744
3.257375
ACGCCTTTTAAATTGGGGTTCTC
59.743
43.478
18.33
0.39
43.06
2.87
544
745
3.236047
ACGCCTTTTAAATTGGGGTTCT
58.764
40.909
18.33
3.87
43.06
3.01
564
765
2.203437
ACCCGGTTTGGCTCCAAC
60.203
61.111
0.00
0.00
35.46
3.77
606
807
0.955428
TGATCGTGTCTTTGCTGGCC
60.955
55.000
0.00
0.00
0.00
5.36
620
821
3.519908
TGTTCTTTTGCTTCGTGATCG
57.480
42.857
0.00
0.00
38.55
3.69
623
824
5.986741
TGTAGTATGTTCTTTTGCTTCGTGA
59.013
36.000
0.00
0.00
0.00
4.35
644
845
3.845259
GGGCCGAGGCGTGATGTA
61.845
66.667
8.14
0.00
43.06
2.29
661
862
0.817654
TCTCTATCTGTGTGTGCCCG
59.182
55.000
0.00
0.00
0.00
6.13
664
865
3.066621
CCTCTCTCTCTATCTGTGTGTGC
59.933
52.174
0.00
0.00
0.00
4.57
674
875
2.716424
CCACCCTCTCCTCTCTCTCTAT
59.284
54.545
0.00
0.00
0.00
1.98
675
876
2.131854
CCACCCTCTCCTCTCTCTCTA
58.868
57.143
0.00
0.00
0.00
2.43
684
885
1.063266
GTCTGATCTCCACCCTCTCCT
60.063
57.143
0.00
0.00
0.00
3.69
685
886
1.342474
TGTCTGATCTCCACCCTCTCC
60.342
57.143
0.00
0.00
0.00
3.71
686
887
2.151502
TGTCTGATCTCCACCCTCTC
57.848
55.000
0.00
0.00
0.00
3.20
687
888
2.225496
ACTTGTCTGATCTCCACCCTCT
60.225
50.000
0.00
0.00
0.00
3.69
691
892
1.731720
GCACTTGTCTGATCTCCACC
58.268
55.000
0.00
0.00
0.00
4.61
693
894
0.390340
GCGCACTTGTCTGATCTCCA
60.390
55.000
0.30
0.00
0.00
3.86
728
929
1.216710
CTCTCCTGTTCACCGCCTC
59.783
63.158
0.00
0.00
0.00
4.70
729
930
0.832135
TTCTCTCCTGTTCACCGCCT
60.832
55.000
0.00
0.00
0.00
5.52
730
931
0.034896
TTTCTCTCCTGTTCACCGCC
59.965
55.000
0.00
0.00
0.00
6.13
731
932
1.433534
CTTTCTCTCCTGTTCACCGC
58.566
55.000
0.00
0.00
0.00
5.68
814
1015
4.834453
CCGAGGAGGCTGCTGCAG
62.834
72.222
24.80
24.80
41.91
4.41
955
1157
1.750780
GGCTAAGCCTCTGGGTTGC
60.751
63.158
10.82
11.24
46.69
4.17
1040
1259
2.205152
GGCATGGGCATGGACATCC
61.205
63.158
0.00
0.00
43.71
3.51
1127
1346
2.674380
CACCACCAGGAGGCTTGC
60.674
66.667
2.09
0.00
39.06
4.01
1429
1648
2.738521
CGAGAACTGGTGGTGCGG
60.739
66.667
0.00
0.00
0.00
5.69
1430
1649
3.414700
GCGAGAACTGGTGGTGCG
61.415
66.667
0.00
0.00
0.00
5.34
1431
1650
3.050275
GGCGAGAACTGGTGGTGC
61.050
66.667
0.00
0.00
0.00
5.01
1842
2067
1.067364
TGCTTGTTGTTGTGCATCCAG
59.933
47.619
0.00
0.00
0.00
3.86
1918
2143
4.101790
GGTTGCATGCGGACGGTG
62.102
66.667
14.09
0.00
0.00
4.94
2034
2276
2.031069
CGAATGCGGTAGCTAGCTAAGA
60.031
50.000
25.74
10.39
45.42
2.10
2037
2279
0.039437
GCGAATGCGGTAGCTAGCTA
60.039
55.000
20.67
20.67
45.42
3.32
2038
2280
1.300233
GCGAATGCGGTAGCTAGCT
60.300
57.895
23.12
23.12
45.42
3.32
2039
2281
3.235355
GCGAATGCGGTAGCTAGC
58.765
61.111
13.03
13.03
45.42
3.42
2081
2323
4.350620
CTAGCCATGCACCGCTAG
57.649
61.111
22.65
22.65
46.20
3.42
2082
2324
1.971505
AAGCTAGCCATGCACCGCTA
61.972
55.000
12.13
14.17
36.53
4.26
2083
2325
1.971505
TAAGCTAGCCATGCACCGCT
61.972
55.000
12.13
13.44
39.17
5.52
2084
2326
1.523711
TAAGCTAGCCATGCACCGC
60.524
57.895
12.13
0.00
0.00
5.68
2133
2375
5.656859
ACCTAAATTAATCCAGCCAAGAACC
59.343
40.000
0.00
0.00
0.00
3.62
2176
2418
9.844790
TGAGCAACAGTAAATAGAAATGAAATG
57.155
29.630
0.00
0.00
0.00
2.32
2226
2468
0.247185
ACCAAATCAGCAAATGGCCG
59.753
50.000
0.00
0.00
46.50
6.13
2243
2485
2.092323
GTACATTCCCCAGCAAGAACC
58.908
52.381
0.00
0.00
0.00
3.62
2402
2644
3.741830
TTGTCCCAACGCAGACGCA
62.742
57.895
0.00
0.00
45.53
5.24
2403
2645
1.852067
AATTGTCCCAACGCAGACGC
61.852
55.000
0.00
0.00
45.53
5.19
2405
2647
2.793278
AAAATTGTCCCAACGCAGAC
57.207
45.000
0.00
0.00
0.00
3.51
2406
2648
3.482436
AGTAAAATTGTCCCAACGCAGA
58.518
40.909
0.00
0.00
0.00
4.26
2407
2649
3.252215
TGAGTAAAATTGTCCCAACGCAG
59.748
43.478
0.00
0.00
0.00
5.18
2452
2694
1.261938
ATGGCACGCAGGTGGTAGTA
61.262
55.000
0.00
0.00
44.54
1.82
2453
2695
2.124507
AATGGCACGCAGGTGGTAGT
62.125
55.000
0.00
0.00
44.54
2.73
2454
2696
1.377202
AATGGCACGCAGGTGGTAG
60.377
57.895
0.00
0.00
44.54
3.18
2459
2705
4.972733
TGGCAATGGCACGCAGGT
62.973
61.111
5.05
0.00
43.71
4.00
2475
2721
7.155328
ACAGTTGTCTATCTTCTTTAGGTGTG
58.845
38.462
0.00
0.00
0.00
3.82
2478
2724
6.651225
GCAACAGTTGTCTATCTTCTTTAGGT
59.349
38.462
14.88
0.00
0.00
3.08
2537
2783
1.893786
CCCGAAGTGAGTGAGGAGG
59.106
63.158
0.00
0.00
0.00
4.30
2538
2784
1.216710
GCCCGAAGTGAGTGAGGAG
59.783
63.158
0.00
0.00
0.00
3.69
2539
2785
0.904865
ATGCCCGAAGTGAGTGAGGA
60.905
55.000
0.00
0.00
0.00
3.71
2552
2798
3.369400
TGCCCGAACAAATGCCCG
61.369
61.111
0.00
0.00
0.00
6.13
2568
2814
2.490115
TGCAAAATTAAGCTACCCCGTG
59.510
45.455
0.00
0.00
0.00
4.94
2569
2815
2.490509
GTGCAAAATTAAGCTACCCCGT
59.509
45.455
0.00
0.00
0.00
5.28
2570
2816
2.490115
TGTGCAAAATTAAGCTACCCCG
59.510
45.455
0.00
0.00
0.00
5.73
2571
2817
3.761752
TCTGTGCAAAATTAAGCTACCCC
59.238
43.478
0.00
0.00
0.00
4.95
2572
2818
4.380550
GGTCTGTGCAAAATTAAGCTACCC
60.381
45.833
0.00
0.00
0.00
3.69
2573
2819
4.217550
TGGTCTGTGCAAAATTAAGCTACC
59.782
41.667
0.00
6.56
0.00
3.18
2574
2820
5.371115
TGGTCTGTGCAAAATTAAGCTAC
57.629
39.130
0.00
2.19
0.00
3.58
2575
2821
6.389091
CATTGGTCTGTGCAAAATTAAGCTA
58.611
36.000
0.00
0.00
0.00
3.32
2576
2822
4.935352
TTGGTCTGTGCAAAATTAAGCT
57.065
36.364
0.00
0.00
0.00
3.74
2585
2831
0.961019
GGAAGCATTGGTCTGTGCAA
59.039
50.000
0.00
0.00
43.63
4.08
2606
2852
1.356124
CTCGGATCAATGGAGGGGAT
58.644
55.000
0.00
0.00
0.00
3.85
2636
2882
1.895231
GCATGGATCATGGCGCTCA
60.895
57.895
7.64
3.81
41.64
4.26
2637
2883
1.853114
CTGCATGGATCATGGCGCTC
61.853
60.000
7.64
0.00
41.64
5.03
2813
3076
2.419851
GCAGAACTGATCAAGGAGGAGG
60.420
54.545
5.97
0.00
0.00
4.30
2814
3077
2.419851
GGCAGAACTGATCAAGGAGGAG
60.420
54.545
5.97
0.00
0.00
3.69
2815
3078
1.556911
GGCAGAACTGATCAAGGAGGA
59.443
52.381
5.97
0.00
0.00
3.71
2816
3079
1.407989
GGGCAGAACTGATCAAGGAGG
60.408
57.143
5.97
0.00
0.00
4.30
2817
3080
1.741732
CGGGCAGAACTGATCAAGGAG
60.742
57.143
5.97
0.00
0.00
3.69
2818
3081
0.250234
CGGGCAGAACTGATCAAGGA
59.750
55.000
5.97
0.00
0.00
3.36
2819
3082
1.372087
GCGGGCAGAACTGATCAAGG
61.372
60.000
5.97
0.00
0.00
3.61
2820
3083
0.674581
TGCGGGCAGAACTGATCAAG
60.675
55.000
5.97
0.00
0.00
3.02
2821
3084
0.035152
ATGCGGGCAGAACTGATCAA
60.035
50.000
5.97
0.00
0.00
2.57
2826
3089
0.734889
CCTTAATGCGGGCAGAACTG
59.265
55.000
0.00
0.00
0.00
3.16
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.