Multiple sequence alignment - TraesCS3D01G544800
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
TraesCS3D01G544800
chr3D
100.000
6347
0
0
1
6347
614209818
614203472
0.000000e+00
11721.0
1
TraesCS3D01G544800
chr3D
82.558
430
39
10
2
428
614240267
614239871
4.710000e-91
346.0
2
TraesCS3D01G544800
chr3D
77.626
219
26
10
1230
1447
97985776
97985580
1.870000e-20
111.0
3
TraesCS3D01G544800
chr3A
94.169
2967
104
16
1991
4954
750508170
750505270
0.000000e+00
4457.0
4
TraesCS3D01G544800
chr3A
97.496
1358
18
4
4950
6298
750505176
750503826
0.000000e+00
2305.0
5
TraesCS3D01G544800
chr3A
86.068
768
89
12
3
761
750512123
750511365
0.000000e+00
809.0
6
TraesCS3D01G544800
chr3A
78.960
1212
117
57
840
2000
750509316
750508192
0.000000e+00
699.0
7
TraesCS3D01G544800
chr3A
85.358
642
66
13
10
646
750510060
750509442
1.930000e-179
640.0
8
TraesCS3D01G544800
chr3A
79.894
378
55
12
2032
2402
125400285
125399922
2.270000e-64
257.0
9
TraesCS3D01G544800
chr3A
85.081
248
31
5
2032
2277
705928395
705928152
1.370000e-61
248.0
10
TraesCS3D01G544800
chr3A
87.574
169
16
1
882
1045
748208020
748208188
2.340000e-44
191.0
11
TraesCS3D01G544800
chr3A
87.574
169
16
1
882
1045
748550754
748550922
2.340000e-44
191.0
12
TraesCS3D01G544800
chr3A
87.574
169
16
1
882
1045
748664268
748664436
2.340000e-44
191.0
13
TraesCS3D01G544800
chr3A
86.982
169
17
1
882
1045
748459531
748459699
1.090000e-42
185.0
14
TraesCS3D01G544800
chr3A
86.982
169
17
1
882
1045
748743733
748743901
1.090000e-42
185.0
15
TraesCS3D01G544800
chr3A
98.113
53
1
0
6295
6347
750503798
750503746
6.780000e-15
93.5
16
TraesCS3D01G544800
chr3A
92.308
52
4
0
4156
4207
387281500
387281551
2.450000e-09
75.0
17
TraesCS3D01G544800
chr3B
94.670
863
27
7
2414
3274
823581540
823580695
0.000000e+00
1321.0
18
TraesCS3D01G544800
chr3B
89.696
1087
22
24
4950
6016
823578840
823577824
0.000000e+00
1304.0
19
TraesCS3D01G544800
chr3B
90.329
972
33
17
4013
4952
823579863
823578921
0.000000e+00
1218.0
20
TraesCS3D01G544800
chr3B
87.984
749
63
12
20
761
823584446
823583718
0.000000e+00
859.0
21
TraesCS3D01G544800
chr3B
85.286
768
66
26
3273
4007
823580656
823579903
0.000000e+00
749.0
22
TraesCS3D01G544800
chr3B
93.750
416
20
3
1991
2400
823581936
823581521
2.510000e-173
619.0
23
TraesCS3D01G544800
chr3B
80.988
810
64
32
1230
1993
823582730
823581965
1.550000e-155
560.0
24
TraesCS3D01G544800
chr3B
84.680
359
50
4
2033
2389
704306049
704306404
2.810000e-93
353.0
25
TraesCS3D01G544800
chr3B
87.550
249
5
7
6056
6298
823577819
823577591
1.360000e-66
265.0
26
TraesCS3D01G544800
chr3B
79.487
234
25
12
820
1045
823583160
823582942
1.840000e-30
145.0
27
TraesCS3D01G544800
chr3B
98.113
53
1
0
6295
6347
823577566
823577514
6.780000e-15
93.5
28
TraesCS3D01G544800
chr3B
85.507
69
5
1
4581
4644
746342187
746342119
4.110000e-07
67.6
29
TraesCS3D01G544800
chr2B
93.622
392
21
2
2014
2401
397907528
397907919
3.300000e-162
582.0
30
TraesCS3D01G544800
chr2B
84.536
194
20
7
1578
1768
683768664
683768478
3.910000e-42
183.0
31
TraesCS3D01G544800
chr2B
89.796
98
10
0
5900
5997
55881137
55881234
6.680000e-25
126.0
32
TraesCS3D01G544800
chr2B
97.500
40
1
0
4613
4652
513468762
513468723
1.140000e-07
69.4
33
TraesCS3D01G544800
chr5B
93.367
392
22
2
2014
2401
587824650
587825041
1.530000e-160
577.0
34
TraesCS3D01G544800
chr5B
95.082
183
9
0
2421
2603
587825025
587825207
8.050000e-74
289.0
35
TraesCS3D01G544800
chr5B
89.655
58
2
4
4615
4670
701152572
701152627
3.170000e-08
71.3
36
TraesCS3D01G544800
chr1B
93.523
386
22
1
2020
2402
37102328
37101943
7.140000e-159
571.0
37
TraesCS3D01G544800
chr1B
94.764
191
8
2
2414
2603
37101964
37101775
4.810000e-76
296.0
38
TraesCS3D01G544800
chr1B
91.589
107
8
1
5890
5996
52903636
52903741
5.130000e-31
147.0
39
TraesCS3D01G544800
chr1B
95.000
40
2
0
4613
4652
213904178
213904217
5.310000e-06
63.9
40
TraesCS3D01G544800
chr4A
77.869
488
71
18
2029
2509
176615829
176616286
1.050000e-67
268.0
41
TraesCS3D01G544800
chr4A
97.500
40
1
0
1408
1447
427793378
427793417
1.140000e-07
69.4
42
TraesCS3D01G544800
chrUn
87.574
169
16
1
882
1045
320622058
320622226
2.340000e-44
191.0
43
TraesCS3D01G544800
chrUn
77.523
218
16
12
1230
1447
308666333
308666149
4.050000e-17
100.0
44
TraesCS3D01G544800
chr2A
83.505
194
22
7
1578
1768
710382412
710382226
8.460000e-39
172.0
45
TraesCS3D01G544800
chr2A
82.584
178
21
7
1641
1818
138521583
138521416
1.430000e-31
148.0
46
TraesCS3D01G544800
chr2A
89.691
97
10
0
5900
5996
36628193
36628289
2.400000e-24
124.0
47
TraesCS3D01G544800
chr1D
91.589
107
8
1
5890
5996
34622952
34623057
5.130000e-31
147.0
48
TraesCS3D01G544800
chr1D
95.000
40
2
0
4613
4652
133947979
133948018
5.310000e-06
63.9
49
TraesCS3D01G544800
chr7B
88.000
125
11
2
1694
1818
283103456
283103336
1.840000e-30
145.0
50
TraesCS3D01G544800
chr1A
90.909
99
9
0
5898
5996
32896088
32896186
3.990000e-27
134.0
51
TraesCS3D01G544800
chr6A
88.776
98
11
0
5900
5997
76578628
76578725
3.110000e-23
121.0
52
TraesCS3D01G544800
chr6A
97.500
40
1
0
1408
1447
9090754
9090793
1.140000e-07
69.4
53
TraesCS3D01G544800
chr6A
97.436
39
1
0
4613
4651
604890720
604890758
4.110000e-07
67.6
54
TraesCS3D01G544800
chr2D
88.776
98
11
0
5900
5997
33718817
33718914
3.110000e-23
121.0
55
TraesCS3D01G544800
chr5A
77.232
224
18
13
1224
1447
147101620
147101810
4.050000e-17
100.0
56
TraesCS3D01G544800
chr5A
77.232
224
18
13
1224
1447
147104640
147104830
4.050000e-17
100.0
57
TraesCS3D01G544800
chr7A
74.900
251
36
16
1563
1809
693018687
693018460
8.760000e-14
89.8
58
TraesCS3D01G544800
chr4D
75.217
230
30
14
1224
1447
10611454
10611662
4.080000e-12
84.2
59
TraesCS3D01G544800
chr5D
85.965
57
5
2
4614
4670
327056036
327056089
2.470000e-04
58.4
60
TraesCS3D01G544800
chr5D
83.582
67
6
1
4581
4642
549576646
549576580
2.470000e-04
58.4
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
TraesCS3D01G544800
chr3D
614203472
614209818
6346
True
11721.000000
11721
100.000000
1
6347
1
chr3D.!!$R2
6346
1
TraesCS3D01G544800
chr3A
750503746
750512123
8377
True
1500.583333
4457
90.027333
3
6347
6
chr3A.!!$R3
6344
2
TraesCS3D01G544800
chr3B
823577514
823584446
6932
True
713.350000
1321
88.785300
20
6347
10
chr3B.!!$R2
6327
3
TraesCS3D01G544800
chr5B
587824650
587825207
557
False
433.000000
577
94.224500
2014
2603
2
chr5B.!!$F2
589
4
TraesCS3D01G544800
chr1B
37101775
37102328
553
True
433.500000
571
94.143500
2020
2603
2
chr1B.!!$R1
583
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
445
448
0.036306
CCGGACTTAGGGTTGTGCTT
59.964
55.000
0.00
0.0
0.00
3.91
F
1163
3212
0.106519
CCAATCCCAATCCCTCGCTT
60.107
55.000
0.00
0.0
0.00
4.68
F
1481
3565
0.036164
ACGCTGCTGTATGTTCCCAA
59.964
50.000
0.00
0.0
0.00
4.12
F
1855
3981
1.052124
TGGAGGTACCGGCTTATGGG
61.052
60.000
6.18
0.0
42.61
4.00
F
2778
4944
0.250727
TTGAGAAGGCGACAAAGGGG
60.251
55.000
0.00
0.0
0.00
4.79
F
3831
6068
1.135083
AGCACCGTACTCCGAAATCTG
60.135
52.381
0.00
0.0
39.56
2.90
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1371
3455
0.829333
ACTAGTGAGGATGGCTGCTG
59.171
55.000
0.00
0.00
0.00
4.41
R
2397
4563
1.275010
ACACACACACACACACAGAGA
59.725
47.619
0.00
0.00
0.00
3.10
R
2401
4567
1.275010
AGAGACACACACACACACACA
59.725
47.619
0.00
0.00
0.00
3.72
R
3831
6068
1.566563
CAGAGCTGCACACGTGTTC
59.433
57.895
20.79
15.89
0.00
3.18
R
4596
6873
1.649171
CGCTGTACTAAAGCAGTGACG
59.351
52.381
0.00
0.00
43.58
4.35
R
5661
8088
1.376543
AGAACGCATGCAGAAGGATG
58.623
50.000
19.57
0.50
45.39
3.51
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
57
59
1.312815
ACTGAGCTTTTGTGGAGTGC
58.687
50.000
0.00
0.00
0.00
4.40
96
98
4.142609
AGTCATGCGATCATTACCAAGT
57.857
40.909
0.00
0.00
29.28
3.16
150
152
0.478072
ACTTCATGGTGACCAAGGCA
59.522
50.000
9.06
0.00
36.95
4.75
204
206
9.539825
TGATCTTATAGCAGAAAGAACTTGATC
57.460
33.333
0.00
0.00
35.47
2.92
208
210
3.949132
AGCAGAAAGAACTTGATCCCTC
58.051
45.455
0.00
0.00
0.00
4.30
209
211
3.013219
GCAGAAAGAACTTGATCCCTCC
58.987
50.000
0.00
0.00
0.00
4.30
210
212
3.615155
CAGAAAGAACTTGATCCCTCCC
58.385
50.000
0.00
0.00
0.00
4.30
211
213
3.009473
CAGAAAGAACTTGATCCCTCCCA
59.991
47.826
0.00
0.00
0.00
4.37
221
223
1.694696
GATCCCTCCCACCACTCATAC
59.305
57.143
0.00
0.00
0.00
2.39
269
271
3.806521
AGCAGCTGTTCGTGAATCATATC
59.193
43.478
16.64
0.00
0.00
1.63
322
325
1.575244
TGCGCTAAGTCAGATCATGC
58.425
50.000
9.73
0.00
0.00
4.06
366
369
1.034292
GGCTCTTCCACCATGAAGCC
61.034
60.000
0.00
0.00
41.23
4.35
369
372
1.002134
CTTCCACCATGAAGCCCGT
60.002
57.895
0.00
0.00
35.72
5.28
375
378
0.981183
ACCATGAAGCCCGTGACTTA
59.019
50.000
0.00
0.00
33.60
2.24
389
392
0.614134
GACTTAGGGGTGGAGTCGGT
60.614
60.000
0.00
0.00
31.54
4.69
405
408
3.324170
GGTGACGGTGTGATAGACG
57.676
57.895
0.00
0.00
0.00
4.18
423
426
4.103103
GCCTTTCGGTCGCCTTGC
62.103
66.667
0.00
0.00
0.00
4.01
445
448
0.036306
CCGGACTTAGGGTTGTGCTT
59.964
55.000
0.00
0.00
0.00
3.91
460
465
2.919971
GCTTGGAGCAGAACGAACT
58.080
52.632
0.00
0.00
41.89
3.01
469
474
1.429463
CAGAACGAACTAGTGGGTGC
58.571
55.000
0.00
0.00
0.00
5.01
481
486
1.609210
TGGGTGCGAGACAGATCCA
60.609
57.895
0.00
0.00
0.00
3.41
482
487
0.977627
TGGGTGCGAGACAGATCCAT
60.978
55.000
0.00
0.00
0.00
3.41
498
503
2.759355
TCCATCTTGGATAAGGGACGT
58.241
47.619
0.00
0.00
42.67
4.34
550
559
0.948623
CGCAAATGAGTCGGTGGTGA
60.949
55.000
0.00
0.00
0.00
4.02
566
575
0.674895
GTGAGCAAGGACCGAGCAAT
60.675
55.000
12.74
0.00
0.00
3.56
579
588
2.208431
CGAGCAATGAACTGGGAGATC
58.792
52.381
0.00
0.00
0.00
2.75
587
596
2.567169
TGAACTGGGAGATCGACACATT
59.433
45.455
0.00
0.00
0.00
2.71
588
597
3.767131
TGAACTGGGAGATCGACACATTA
59.233
43.478
0.00
0.00
0.00
1.90
597
606
6.239176
GGGAGATCGACACATTAGAGAGAAAT
60.239
42.308
0.00
0.00
0.00
2.17
610
619
3.051496
AGAGAGAAATGGGATCCAGGAGA
60.051
47.826
15.23
0.00
36.75
3.71
615
624
5.019470
AGAAATGGGATCCAGGAGAAAAAC
58.981
41.667
15.23
0.00
36.75
2.43
616
625
4.402616
AATGGGATCCAGGAGAAAAACA
57.597
40.909
15.23
0.00
36.75
2.83
617
626
3.439857
TGGGATCCAGGAGAAAAACAG
57.560
47.619
15.23
0.00
0.00
3.16
619
628
2.095461
GGATCCAGGAGAAAAACAGGC
58.905
52.381
6.95
0.00
0.00
4.85
654
663
4.374689
AAGAAGAAGGAAAAGGGAGGAC
57.625
45.455
0.00
0.00
0.00
3.85
668
677
0.663568
GAGGACACGACAGAACACCG
60.664
60.000
0.00
0.00
0.00
4.94
716
725
0.767375
TGGAGGCAAGTCTCAAAGCT
59.233
50.000
3.88
0.00
35.58
3.74
719
728
2.941720
GGAGGCAAGTCTCAAAGCTATG
59.058
50.000
3.88
0.00
35.58
2.23
763
2719
1.202348
GAAACCGAGCCAATCCCTTTG
59.798
52.381
0.00
0.00
34.93
2.77
804
2761
2.431601
GCTGCGCTCTGTCGAACT
60.432
61.111
9.73
0.00
0.00
3.01
806
2763
0.526524
GCTGCGCTCTGTCGAACTAT
60.527
55.000
9.73
0.00
0.00
2.12
808
2765
2.263077
CTGCGCTCTGTCGAACTATTT
58.737
47.619
9.73
0.00
0.00
1.40
882
2868
7.068103
TCCACACATCTTGTATGAACACTTTTT
59.932
33.333
0.00
0.00
35.67
1.94
930
2925
6.095377
GTGAAAAAGGATATTTCTGCACAGG
58.905
40.000
0.00
0.00
37.60
4.00
974
2969
2.101750
TCCTCGCTCTGTTTGTTGTACA
59.898
45.455
0.00
0.00
0.00
2.90
975
2970
2.476619
CCTCGCTCTGTTTGTTGTACAG
59.523
50.000
0.00
0.00
43.41
2.74
979
2983
2.872245
GCTCTGTTTGTTGTACAGCTGA
59.128
45.455
23.35
0.48
42.12
4.26
985
2989
2.620251
TGTTGTACAGCTGAAGCAGT
57.380
45.000
23.35
5.30
45.16
4.40
1084
3133
3.089838
CCATCCCCAAGGTGAGCA
58.910
61.111
0.00
0.00
0.00
4.26
1085
3134
1.383799
CCATCCCCAAGGTGAGCAA
59.616
57.895
0.00
0.00
0.00
3.91
1086
3135
0.682209
CCATCCCCAAGGTGAGCAAG
60.682
60.000
0.00
0.00
0.00
4.01
1087
3136
1.000396
ATCCCCAAGGTGAGCAAGC
60.000
57.895
0.00
0.00
0.00
4.01
1099
3148
1.690893
TGAGCAAGCTATCTGGGCTAG
59.309
52.381
0.00
0.00
39.30
3.42
1113
3162
4.157120
CTAGGGTTCACCGGCCGG
62.157
72.222
42.17
42.17
46.96
6.13
1129
3178
1.540267
GCCGGAAAGGAAGGAAGAAAC
59.460
52.381
5.05
0.00
45.00
2.78
1134
3183
1.541275
AAGGAAGGAAGAAACCCCCA
58.459
50.000
0.00
0.00
0.00
4.96
1135
3184
1.773541
AGGAAGGAAGAAACCCCCAT
58.226
50.000
0.00
0.00
0.00
4.00
1137
3186
2.043115
AGGAAGGAAGAAACCCCCATTC
59.957
50.000
0.00
0.00
0.00
2.67
1141
3190
1.008327
GGAAGAAACCCCCATTCCCAT
59.992
52.381
0.00
0.00
36.08
4.00
1146
3195
1.158963
AACCCCCATTCCCATTCCCA
61.159
55.000
0.00
0.00
0.00
4.37
1147
3196
1.158963
ACCCCCATTCCCATTCCCAA
61.159
55.000
0.00
0.00
0.00
4.12
1148
3197
0.268566
CCCCCATTCCCATTCCCAAT
59.731
55.000
0.00
0.00
0.00
3.16
1152
3201
1.062275
CCATTCCCATTCCCAATCCCA
60.062
52.381
0.00
0.00
0.00
4.37
1153
3202
2.629098
CCATTCCCATTCCCAATCCCAA
60.629
50.000
0.00
0.00
0.00
4.12
1154
3203
3.320129
CATTCCCATTCCCAATCCCAAT
58.680
45.455
0.00
0.00
0.00
3.16
1156
3205
1.220236
TCCCATTCCCAATCCCAATCC
59.780
52.381
0.00
0.00
0.00
3.01
1157
3206
1.720781
CCATTCCCAATCCCAATCCC
58.279
55.000
0.00
0.00
0.00
3.85
1158
3207
1.221265
CCATTCCCAATCCCAATCCCT
59.779
52.381
0.00
0.00
0.00
4.20
1159
3208
2.601905
CATTCCCAATCCCAATCCCTC
58.398
52.381
0.00
0.00
0.00
4.30
1162
3211
1.533711
CCAATCCCAATCCCTCGCT
59.466
57.895
0.00
0.00
0.00
4.93
1163
3212
0.106519
CCAATCCCAATCCCTCGCTT
60.107
55.000
0.00
0.00
0.00
4.68
1167
3232
2.193248
CCAATCCCTCGCTTCCCC
59.807
66.667
0.00
0.00
0.00
4.81
1168
3233
2.203070
CAATCCCTCGCTTCCCCG
60.203
66.667
0.00
0.00
0.00
5.73
1179
3244
4.676951
TTCCCCGCCCCTTTGCTG
62.677
66.667
0.00
0.00
0.00
4.41
1186
3251
1.678970
GCCCCTTTGCTGACCGAAT
60.679
57.895
0.00
0.00
0.00
3.34
1187
3252
1.657751
GCCCCTTTGCTGACCGAATC
61.658
60.000
0.00
0.00
0.00
2.52
1188
3253
1.369091
CCCCTTTGCTGACCGAATCG
61.369
60.000
0.00
0.00
0.00
3.34
1189
3254
0.391130
CCCTTTGCTGACCGAATCGA
60.391
55.000
3.36
0.00
0.00
3.59
1190
3255
1.438651
CCTTTGCTGACCGAATCGAA
58.561
50.000
3.36
0.00
0.00
3.71
1191
3256
2.009774
CCTTTGCTGACCGAATCGAAT
58.990
47.619
3.36
0.00
0.00
3.34
1192
3257
2.223112
CCTTTGCTGACCGAATCGAATG
60.223
50.000
3.36
0.00
0.00
2.67
1193
3258
0.726827
TTGCTGACCGAATCGAATGC
59.273
50.000
3.36
3.67
0.00
3.56
1195
3260
1.927210
CTGACCGAATCGAATGCCG
59.073
57.895
3.36
0.00
40.25
5.69
1197
3262
2.125310
ACCGAATCGAATGCCGCA
60.125
55.556
3.36
0.00
38.37
5.69
1198
3263
1.498865
GACCGAATCGAATGCCGCAT
61.499
55.000
3.36
0.00
38.37
4.73
1211
3280
2.821366
CGCATGCAGGTGGAGGAC
60.821
66.667
19.57
0.00
0.00
3.85
1214
3283
1.153489
CATGCAGGTGGAGGACGAG
60.153
63.158
0.00
0.00
0.00
4.18
1215
3284
3.023949
ATGCAGGTGGAGGACGAGC
62.024
63.158
0.00
0.00
0.00
5.03
1216
3285
4.459089
GCAGGTGGAGGACGAGCC
62.459
72.222
0.00
0.00
0.00
4.70
1217
3286
3.775654
CAGGTGGAGGACGAGCCC
61.776
72.222
0.00
0.00
37.37
5.19
1218
3287
3.999285
AGGTGGAGGACGAGCCCT
61.999
66.667
0.00
0.00
39.77
5.19
1219
3288
3.775654
GGTGGAGGACGAGCCCTG
61.776
72.222
0.00
0.00
36.49
4.45
1220
3289
4.459089
GTGGAGGACGAGCCCTGC
62.459
72.222
7.54
7.54
43.95
4.85
1221
3290
4.704103
TGGAGGACGAGCCCTGCT
62.704
66.667
13.39
0.00
44.01
4.24
1222
3291
4.154347
GGAGGACGAGCCCTGCTG
62.154
72.222
0.00
0.00
39.88
4.41
1315
3393
2.463441
CCTTGGGAAGGTCAGGTCA
58.537
57.895
0.00
0.00
43.95
4.02
1316
3394
0.771127
CCTTGGGAAGGTCAGGTCAA
59.229
55.000
0.00
0.00
43.95
3.18
1317
3395
1.355720
CCTTGGGAAGGTCAGGTCAAT
59.644
52.381
0.00
0.00
43.95
2.57
1318
3396
2.619074
CCTTGGGAAGGTCAGGTCAATC
60.619
54.545
0.00
0.00
43.95
2.67
1319
3397
2.044793
TGGGAAGGTCAGGTCAATCT
57.955
50.000
0.00
0.00
0.00
2.40
1320
3398
1.909302
TGGGAAGGTCAGGTCAATCTC
59.091
52.381
0.00
0.00
0.00
2.75
1321
3399
1.134670
GGGAAGGTCAGGTCAATCTCG
60.135
57.143
0.00
0.00
0.00
4.04
1322
3400
1.646189
GAAGGTCAGGTCAATCTCGC
58.354
55.000
0.00
0.00
0.00
5.03
1323
3401
1.205893
GAAGGTCAGGTCAATCTCGCT
59.794
52.381
0.00
0.00
0.00
4.93
1324
3402
0.820871
AGGTCAGGTCAATCTCGCTC
59.179
55.000
0.00
0.00
0.00
5.03
1325
3403
0.820871
GGTCAGGTCAATCTCGCTCT
59.179
55.000
0.00
0.00
0.00
4.09
1326
3404
1.205893
GGTCAGGTCAATCTCGCTCTT
59.794
52.381
0.00
0.00
0.00
2.85
1327
3405
2.535331
GTCAGGTCAATCTCGCTCTTC
58.465
52.381
0.00
0.00
0.00
2.87
1328
3406
2.165437
GTCAGGTCAATCTCGCTCTTCT
59.835
50.000
0.00
0.00
0.00
2.85
1329
3407
2.828520
TCAGGTCAATCTCGCTCTTCTT
59.171
45.455
0.00
0.00
0.00
2.52
1330
3408
2.928757
CAGGTCAATCTCGCTCTTCTTG
59.071
50.000
0.00
0.00
0.00
3.02
1331
3409
2.564947
AGGTCAATCTCGCTCTTCTTGT
59.435
45.455
0.00
0.00
0.00
3.16
1332
3410
3.007398
AGGTCAATCTCGCTCTTCTTGTT
59.993
43.478
0.00
0.00
0.00
2.83
1371
3455
2.903284
GCATAGAGCAGAGCAGAGC
58.097
57.895
0.00
0.00
44.79
4.09
1372
3456
0.104487
GCATAGAGCAGAGCAGAGCA
59.896
55.000
0.00
0.00
44.79
4.26
1375
3459
0.969409
TAGAGCAGAGCAGAGCAGCA
60.969
55.000
0.00
0.00
36.85
4.41
1377
3461
3.501548
GCAGAGCAGAGCAGCAGC
61.502
66.667
0.00
0.00
42.56
5.25
1379
3463
3.320014
AGAGCAGAGCAGCAGCCA
61.320
61.111
0.00
0.00
43.56
4.75
1380
3464
2.124653
GAGCAGAGCAGCAGCCAT
60.125
61.111
0.00
0.00
43.56
4.40
1381
3465
2.124653
AGCAGAGCAGCAGCCATC
60.125
61.111
0.00
0.00
43.56
3.51
1382
3466
3.210528
GCAGAGCAGCAGCCATCC
61.211
66.667
0.00
0.00
43.56
3.51
1383
3467
2.590645
CAGAGCAGCAGCCATCCT
59.409
61.111
0.00
0.00
43.56
3.24
1384
3468
1.524165
CAGAGCAGCAGCCATCCTC
60.524
63.158
0.00
0.00
43.56
3.71
1385
3469
1.993948
AGAGCAGCAGCCATCCTCA
60.994
57.895
0.00
0.00
43.56
3.86
1386
3470
1.818785
GAGCAGCAGCCATCCTCAC
60.819
63.158
0.00
0.00
43.56
3.51
1388
3472
0.979709
AGCAGCAGCCATCCTCACTA
60.980
55.000
0.00
0.00
43.56
2.74
1389
3473
0.532417
GCAGCAGCCATCCTCACTAG
60.532
60.000
0.00
0.00
33.58
2.57
1390
3474
0.829333
CAGCAGCCATCCTCACTAGT
59.171
55.000
0.00
0.00
0.00
2.57
1391
3475
2.034878
CAGCAGCCATCCTCACTAGTA
58.965
52.381
0.00
0.00
0.00
1.82
1392
3476
2.432146
CAGCAGCCATCCTCACTAGTAA
59.568
50.000
0.00
0.00
0.00
2.24
1393
3477
2.432510
AGCAGCCATCCTCACTAGTAAC
59.567
50.000
0.00
0.00
0.00
2.50
1394
3478
2.168521
GCAGCCATCCTCACTAGTAACA
59.831
50.000
0.00
0.00
0.00
2.41
1395
3479
3.739519
GCAGCCATCCTCACTAGTAACAG
60.740
52.174
0.00
0.00
0.00
3.16
1406
3490
4.818005
TCACTAGTAACAGTGTTCGTCAGA
59.182
41.667
12.82
2.55
45.11
3.27
1464
3548
0.723414
CATACTGCAACTGCCTCACG
59.277
55.000
0.00
0.00
41.18
4.35
1479
3563
0.391130
TCACGCTGCTGTATGTTCCC
60.391
55.000
0.00
0.00
0.00
3.97
1480
3564
0.673333
CACGCTGCTGTATGTTCCCA
60.673
55.000
0.00
0.00
0.00
4.37
1481
3565
0.036164
ACGCTGCTGTATGTTCCCAA
59.964
50.000
0.00
0.00
0.00
4.12
1482
3566
1.340017
ACGCTGCTGTATGTTCCCAAT
60.340
47.619
0.00
0.00
0.00
3.16
1483
3567
1.745087
CGCTGCTGTATGTTCCCAATT
59.255
47.619
0.00
0.00
0.00
2.32
1486
3570
4.199310
GCTGCTGTATGTTCCCAATTCTA
58.801
43.478
0.00
0.00
0.00
2.10
1488
3572
5.220931
GCTGCTGTATGTTCCCAATTCTAAG
60.221
44.000
0.00
0.00
0.00
2.18
1490
3574
4.640201
GCTGTATGTTCCCAATTCTAAGCA
59.360
41.667
0.00
0.00
0.00
3.91
1491
3575
5.125417
GCTGTATGTTCCCAATTCTAAGCAA
59.875
40.000
0.00
0.00
0.00
3.91
1500
3584
4.829492
CCCAATTCTAAGCAATCCCCTTAG
59.171
45.833
0.00
0.00
41.86
2.18
1554
3638
6.166279
CAGTATCCTGCAACTTTCTTCACTA
58.834
40.000
0.00
0.00
0.00
2.74
1561
3645
6.650807
CCTGCAACTTTCTTCACTACAAGATA
59.349
38.462
0.00
0.00
32.32
1.98
1565
3649
7.171678
GCAACTTTCTTCACTACAAGATACAGT
59.828
37.037
0.00
0.00
32.32
3.55
1573
3657
5.302059
TCACTACAAGATACAGTATCCTGCC
59.698
44.000
16.32
0.00
42.81
4.85
1578
3662
7.136822
ACAAGATACAGTATCCTGCCAATTA
57.863
36.000
16.32
0.00
42.81
1.40
1579
3663
7.573710
ACAAGATACAGTATCCTGCCAATTAA
58.426
34.615
16.32
0.00
42.81
1.40
1580
3664
8.220559
ACAAGATACAGTATCCTGCCAATTAAT
58.779
33.333
16.32
0.00
42.81
1.40
1581
3665
9.071276
CAAGATACAGTATCCTGCCAATTAATT
57.929
33.333
15.87
0.00
42.81
1.40
1583
3667
9.646522
AGATACAGTATCCTGCCAATTAATTTT
57.353
29.630
15.87
0.00
42.81
1.82
1589
3673
9.212593
AGTATCCTGCCAATTAATTTTTATGGT
57.787
29.630
0.00
0.00
33.63
3.55
1593
3677
7.120432
TCCTGCCAATTAATTTTTATGGTTTGC
59.880
33.333
0.00
0.00
33.63
3.68
1632
3716
4.889832
AATATGCAGCAGCTTACTCAAC
57.110
40.909
0.00
0.00
42.74
3.18
1687
3777
3.260483
CGATGCTGTCGCCAGAGC
61.260
66.667
0.00
0.00
44.33
4.09
1787
3905
2.850254
GCTTGCCGCATTTGTTTGTTTG
60.850
45.455
0.00
0.00
38.92
2.93
1808
3926
7.122650
TGTTTGTTCTGAAAGATTTCTCCTTGT
59.877
33.333
6.84
0.00
46.36
3.16
1855
3981
1.052124
TGGAGGTACCGGCTTATGGG
61.052
60.000
6.18
0.00
42.61
4.00
1863
3989
1.510844
CGGCTTATGGGTGTTTGCC
59.489
57.895
0.00
0.00
37.24
4.52
1933
4059
3.313526
GGATCAGATGCACAACATGGTAC
59.686
47.826
0.00
0.00
39.84
3.34
2148
4311
7.376335
AGGGGAATCCAAGTATAGTTCTTAC
57.624
40.000
0.09
0.00
38.24
2.34
2149
4312
6.906901
AGGGGAATCCAAGTATAGTTCTTACA
59.093
38.462
0.09
0.00
38.24
2.41
2226
4389
5.892686
TGAGCCCATGAATTATCACATTTGA
59.107
36.000
0.00
0.00
38.69
2.69
2252
4418
5.717119
ACTGAAAATATTTGAGGCAGCAAG
58.283
37.500
0.39
0.00
0.00
4.01
2265
4431
4.202441
AGGCAGCAAGTATGTAATTCCTG
58.798
43.478
0.00
0.00
0.00
3.86
2396
4562
3.367292
CCAGTTTGTGCTCTCTCTCTCTC
60.367
52.174
0.00
0.00
0.00
3.20
2397
4563
3.507233
CAGTTTGTGCTCTCTCTCTCTCT
59.493
47.826
0.00
0.00
0.00
3.10
2398
4564
3.758554
AGTTTGTGCTCTCTCTCTCTCTC
59.241
47.826
0.00
0.00
0.00
3.20
2399
4565
3.719268
TTGTGCTCTCTCTCTCTCTCT
57.281
47.619
0.00
0.00
0.00
3.10
2400
4566
3.266510
TGTGCTCTCTCTCTCTCTCTC
57.733
52.381
0.00
0.00
0.00
3.20
2401
4567
2.840038
TGTGCTCTCTCTCTCTCTCTCT
59.160
50.000
0.00
0.00
0.00
3.10
2402
4568
3.201290
GTGCTCTCTCTCTCTCTCTCTG
58.799
54.545
0.00
0.00
0.00
3.35
2403
4569
2.840038
TGCTCTCTCTCTCTCTCTCTGT
59.160
50.000
0.00
0.00
0.00
3.41
2404
4570
3.201290
GCTCTCTCTCTCTCTCTCTGTG
58.799
54.545
0.00
0.00
0.00
3.66
2405
4571
3.369892
GCTCTCTCTCTCTCTCTCTGTGT
60.370
52.174
0.00
0.00
0.00
3.72
2406
4572
4.186926
CTCTCTCTCTCTCTCTCTGTGTG
58.813
52.174
0.00
0.00
0.00
3.82
2407
4573
3.582647
TCTCTCTCTCTCTCTCTGTGTGT
59.417
47.826
0.00
0.00
0.00
3.72
2408
4574
3.673902
TCTCTCTCTCTCTCTGTGTGTG
58.326
50.000
0.00
0.00
0.00
3.82
2409
4575
3.072330
TCTCTCTCTCTCTCTGTGTGTGT
59.928
47.826
0.00
0.00
0.00
3.72
2410
4576
3.145286
TCTCTCTCTCTCTGTGTGTGTG
58.855
50.000
0.00
0.00
0.00
3.82
2411
4577
2.884012
CTCTCTCTCTCTGTGTGTGTGT
59.116
50.000
0.00
0.00
0.00
3.72
2412
4578
2.620585
TCTCTCTCTCTGTGTGTGTGTG
59.379
50.000
0.00
0.00
0.00
3.82
2413
4579
2.360483
CTCTCTCTCTGTGTGTGTGTGT
59.640
50.000
0.00
0.00
0.00
3.72
2414
4580
2.099756
TCTCTCTCTGTGTGTGTGTGTG
59.900
50.000
0.00
0.00
0.00
3.82
2415
4581
1.824852
TCTCTCTGTGTGTGTGTGTGT
59.175
47.619
0.00
0.00
0.00
3.72
2416
4582
1.929169
CTCTCTGTGTGTGTGTGTGTG
59.071
52.381
0.00
0.00
0.00
3.82
2428
4594
2.620585
TGTGTGTGTGTCTCTCTCTCTG
59.379
50.000
0.00
0.00
0.00
3.35
2532
4698
5.231991
CGTTTTCCACATTTGTTTGGAGAAG
59.768
40.000
0.00
0.00
42.93
2.85
2644
4810
8.484214
ACTAAATGATATCTTGGTAGCTGAGA
57.516
34.615
3.98
0.00
0.00
3.27
2741
4907
6.801539
TGACACAGTTGTATGATCCTTTTC
57.198
37.500
0.00
0.00
35.47
2.29
2778
4944
0.250727
TTGAGAAGGCGACAAAGGGG
60.251
55.000
0.00
0.00
0.00
4.79
3145
5312
9.489084
GGCACTTTACTTATTTTCCATTCTTTT
57.511
29.630
0.00
0.00
0.00
2.27
3242
5410
4.398044
GTGAACAGGTGAGTTTTGGAGAAA
59.602
41.667
0.00
0.00
0.00
2.52
3310
5518
3.981071
AAATGTCTCTGGGAATGACGA
57.019
42.857
0.00
0.00
33.81
4.20
3448
5662
5.905331
TCCAGAAACATATATGACCAGGTCT
59.095
40.000
20.82
8.75
33.15
3.85
3529
5761
4.425577
AATGAAGCATCGGAACTTGTTC
57.574
40.909
5.03
5.03
0.00
3.18
3695
5928
1.805254
CTCTTGAAGCATTGCCCCG
59.195
57.895
4.70
0.00
0.00
5.73
3764
5998
9.812347
TTTCAGGCACATATTTGGATAGATATT
57.188
29.630
0.00
0.00
0.00
1.28
3831
6068
1.135083
AGCACCGTACTCCGAAATCTG
60.135
52.381
0.00
0.00
39.56
2.90
3837
6074
2.592897
CGTACTCCGAAATCTGAACACG
59.407
50.000
0.00
0.00
39.56
4.49
3864
6101
1.478510
GCTCTGGCTGCACTAGAACTA
59.521
52.381
0.50
0.00
35.15
2.24
4122
6397
1.953686
TGTTTCAGGCCAGCTTTGTAC
59.046
47.619
5.01
0.00
0.00
2.90
4128
6404
2.030805
CAGGCCAGCTTTGTACTGTTTC
60.031
50.000
5.01
0.00
33.09
2.78
4132
6408
3.066760
GCCAGCTTTGTACTGTTTCTGTT
59.933
43.478
0.00
0.00
33.09
3.16
4190
6466
3.005155
AGTTTCTTGAAATCCAGCAGTGC
59.995
43.478
7.13
7.13
0.00
4.40
4429
6706
2.701951
TGCATGATGAGAGCATGGTCTA
59.298
45.455
26.54
12.24
42.53
2.59
4446
6723
5.056480
TGGTCTATGTTTTGTGTCACTGAG
58.944
41.667
4.27
0.00
0.00
3.35
4600
6877
7.827236
ACTTTTTCCCATTCATATTACTCGTCA
59.173
33.333
0.00
0.00
0.00
4.35
4605
6882
5.292765
CCATTCATATTACTCGTCACTGCT
58.707
41.667
0.00
0.00
0.00
4.24
4703
7007
6.638096
TCATTCAGTGACACAACAATGATT
57.362
33.333
16.79
4.07
42.73
2.57
5240
7653
2.180432
GCATCTAGGAGCATGCATCA
57.820
50.000
21.98
0.52
44.18
3.07
5381
7801
7.536895
CTAATTATAGGAGCATGCATGAGAC
57.463
40.000
30.64
17.40
0.00
3.36
5493
7920
3.996363
TGTGTAGTGTGCTGCTAGAAATG
59.004
43.478
0.00
0.00
0.00
2.32
5508
7935
6.015519
TGCTAGAAATGTTAGGCATGTTTGTT
60.016
34.615
0.00
0.00
37.96
2.83
5543
7970
7.065120
TGACATGATTTTTGGAGGTTTGATT
57.935
32.000
0.00
0.00
0.00
2.57
5586
8013
0.542467
TTCAACAGCCCCATGCATGT
60.542
50.000
24.58
4.09
44.83
3.21
5661
8088
1.808945
CCATCACTTCCACTGCACTTC
59.191
52.381
0.00
0.00
0.00
3.01
5783
8211
0.253207
TCCTCCCTCCCCCTTTCTTC
60.253
60.000
0.00
0.00
0.00
2.87
6298
8736
6.013725
TGGTACTTGATCAGTGTTAGTTCCAT
60.014
38.462
15.16
0.00
35.97
3.41
6300
8738
7.064728
GGTACTTGATCAGTGTTAGTTCCATTC
59.935
40.741
12.71
0.00
35.97
2.67
6301
8739
6.773638
ACTTGATCAGTGTTAGTTCCATTCT
58.226
36.000
0.00
0.00
32.83
2.40
6303
8741
6.114187
TGATCAGTGTTAGTTCCATTCTGT
57.886
37.500
0.00
0.00
0.00
3.41
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
35
37
3.699067
CACTCCACAAAAGCTCAGTTTG
58.301
45.455
7.64
7.64
40.95
2.93
57
59
2.812591
GACTTGCCTGGCATATCTCATG
59.187
50.000
24.03
7.85
38.76
3.07
96
98
3.500331
TCGAGGTATAGGCCGACAA
57.500
52.632
0.00
0.00
0.00
3.18
150
152
5.510430
GGAGAAACCTTGGGATTCTAATGT
58.490
41.667
8.67
0.00
43.28
2.71
204
206
0.686441
TCGTATGAGTGGTGGGAGGG
60.686
60.000
0.00
0.00
0.00
4.30
208
210
1.670811
GCAATTCGTATGAGTGGTGGG
59.329
52.381
1.25
0.00
0.00
4.61
209
211
2.632377
AGCAATTCGTATGAGTGGTGG
58.368
47.619
2.58
0.00
0.00
4.61
210
212
3.684305
TGAAGCAATTCGTATGAGTGGTG
59.316
43.478
3.88
0.00
0.00
4.17
211
213
3.937814
TGAAGCAATTCGTATGAGTGGT
58.062
40.909
0.00
0.00
0.00
4.16
221
223
3.369546
AAGGTGGTTTGAAGCAATTCG
57.630
42.857
0.00
0.00
38.25
3.34
269
271
3.125316
GTCGGCTACTCCATTTTTGTCTG
59.875
47.826
0.00
0.00
34.01
3.51
322
325
0.107508
AGGATGTCGTGATGCAAGGG
60.108
55.000
0.00
0.00
0.00
3.95
329
332
0.833287
CCTTGGGAGGATGTCGTGAT
59.167
55.000
0.00
0.00
46.74
3.06
330
333
1.899437
GCCTTGGGAGGATGTCGTGA
61.899
60.000
0.00
0.00
46.74
4.35
366
369
0.903454
ACTCCACCCCTAAGTCACGG
60.903
60.000
0.00
0.00
0.00
4.94
369
372
0.613853
CCGACTCCACCCCTAAGTCA
60.614
60.000
0.00
0.00
39.49
3.41
375
378
2.603776
GTCACCGACTCCACCCCT
60.604
66.667
0.00
0.00
0.00
4.79
379
382
2.049433
CACCGTCACCGACTCCAC
60.049
66.667
0.00
0.00
35.63
4.02
389
392
1.509463
GCCGTCTATCACACCGTCA
59.491
57.895
0.00
0.00
0.00
4.35
423
426
0.321298
CACAACCCTAAGTCCGGTGG
60.321
60.000
0.00
0.00
30.96
4.61
445
448
1.272490
CCACTAGTTCGTTCTGCTCCA
59.728
52.381
0.00
0.00
0.00
3.86
460
465
1.103803
GATCTGTCTCGCACCCACTA
58.896
55.000
0.00
0.00
0.00
2.74
481
486
1.687123
CCGACGTCCCTTATCCAAGAT
59.313
52.381
10.58
0.00
33.20
2.40
482
487
1.108776
CCGACGTCCCTTATCCAAGA
58.891
55.000
10.58
0.00
33.20
3.02
550
559
0.036732
TTCATTGCTCGGTCCTTGCT
59.963
50.000
4.90
0.00
0.00
3.91
566
575
1.627864
TGTGTCGATCTCCCAGTTCA
58.372
50.000
0.00
0.00
0.00
3.18
579
588
5.011090
TCCCATTTCTCTCTAATGTGTCG
57.989
43.478
0.00
0.00
32.38
4.35
587
596
4.170845
TCTCCTGGATCCCATTTCTCTCTA
59.829
45.833
9.90
0.00
30.82
2.43
588
597
3.051496
TCTCCTGGATCCCATTTCTCTCT
60.051
47.826
9.90
0.00
30.82
3.10
597
606
2.041620
CCTGTTTTTCTCCTGGATCCCA
59.958
50.000
9.90
0.00
0.00
4.37
610
619
0.698818
ATCTCCTCCCGCCTGTTTTT
59.301
50.000
0.00
0.00
0.00
1.94
615
624
1.274728
CTTATGATCTCCTCCCGCCTG
59.725
57.143
0.00
0.00
0.00
4.85
616
625
1.148027
TCTTATGATCTCCTCCCGCCT
59.852
52.381
0.00
0.00
0.00
5.52
617
626
1.633774
TCTTATGATCTCCTCCCGCC
58.366
55.000
0.00
0.00
0.00
6.13
619
628
4.021544
CCTTCTTCTTATGATCTCCTCCCG
60.022
50.000
0.00
0.00
0.00
5.14
654
663
2.014554
CGACCGGTGTTCTGTCGTG
61.015
63.158
14.63
0.00
33.50
4.35
668
677
2.649614
GGCTATAGTCCGGCGACC
59.350
66.667
9.30
0.00
40.12
4.79
711
720
3.440173
ACGCACAATACTTGCATAGCTTT
59.560
39.130
0.00
0.00
40.20
3.51
716
725
4.000325
ACTTCACGCACAATACTTGCATA
59.000
39.130
0.00
0.00
40.20
3.14
719
728
2.721797
CGACTTCACGCACAATACTTGC
60.722
50.000
0.00
0.00
36.57
4.01
882
2868
8.714179
CACAAGGATAAATTTCTACACACGTTA
58.286
33.333
0.00
0.00
0.00
3.18
906
2894
6.095377
CCTGTGCAGAAATATCCTTTTTCAC
58.905
40.000
0.02
0.00
35.90
3.18
930
2925
1.446272
CCGGAAACAGAGCGAGGAC
60.446
63.158
0.00
0.00
0.00
3.85
974
2969
1.265236
ACTCTGCTACTGCTTCAGCT
58.735
50.000
0.00
0.00
42.66
4.24
975
2970
2.481104
CCTACTCTGCTACTGCTTCAGC
60.481
54.545
0.00
0.00
40.48
4.26
979
2983
2.024846
TCCTCCTACTCTGCTACTGCTT
60.025
50.000
0.00
0.00
40.48
3.91
985
2989
1.819697
CGCCATCCTCCTACTCTGCTA
60.820
57.143
0.00
0.00
0.00
3.49
1060
3094
4.794648
CTTGGGGATGGCGGCGAA
62.795
66.667
12.98
0.00
0.00
4.70
1084
3133
2.050918
GAACCCTAGCCCAGATAGCTT
58.949
52.381
0.00
0.00
41.83
3.74
1085
3134
1.062121
TGAACCCTAGCCCAGATAGCT
60.062
52.381
0.00
0.00
44.49
3.32
1086
3135
1.070914
GTGAACCCTAGCCCAGATAGC
59.929
57.143
0.00
0.00
0.00
2.97
1087
3136
1.694696
GGTGAACCCTAGCCCAGATAG
59.305
57.143
0.00
0.00
0.00
2.08
1099
3148
4.646877
TTTCCGGCCGGTGAACCC
62.647
66.667
41.57
0.00
36.47
4.11
1113
3162
2.158370
TGGGGGTTTCTTCCTTCCTTTC
60.158
50.000
0.00
0.00
0.00
2.62
1117
3166
2.457598
GAATGGGGGTTTCTTCCTTCC
58.542
52.381
0.00
0.00
0.00
3.46
1118
3167
2.457598
GGAATGGGGGTTTCTTCCTTC
58.542
52.381
0.00
0.00
35.36
3.46
1129
3178
0.268566
ATTGGGAATGGGAATGGGGG
59.731
55.000
0.00
0.00
0.00
5.40
1134
3183
3.590714
GATTGGGATTGGGAATGGGAAT
58.409
45.455
0.00
0.00
0.00
3.01
1135
3184
2.360209
GGATTGGGATTGGGAATGGGAA
60.360
50.000
0.00
0.00
0.00
3.97
1137
3186
1.720781
GGATTGGGATTGGGAATGGG
58.279
55.000
0.00
0.00
0.00
4.00
1141
3190
0.550914
CGAGGGATTGGGATTGGGAA
59.449
55.000
0.00
0.00
0.00
3.97
1146
3195
0.183731
GGAAGCGAGGGATTGGGATT
59.816
55.000
0.00
0.00
0.00
3.01
1147
3196
1.709994
GGGAAGCGAGGGATTGGGAT
61.710
60.000
0.00
0.00
0.00
3.85
1148
3197
2.375345
GGGAAGCGAGGGATTGGGA
61.375
63.158
0.00
0.00
0.00
4.37
1152
3201
4.176752
GCGGGGAAGCGAGGGATT
62.177
66.667
0.00
0.00
0.00
3.01
1162
3211
4.676951
CAGCAAAGGGGCGGGGAA
62.677
66.667
0.00
0.00
39.27
3.97
1167
3232
4.697756
TCGGTCAGCAAAGGGGCG
62.698
66.667
0.00
0.00
39.27
6.13
1168
3233
1.657751
GATTCGGTCAGCAAAGGGGC
61.658
60.000
0.00
0.00
0.00
5.80
1179
3244
1.498865
ATGCGGCATTCGATTCGGTC
61.499
55.000
10.23
0.00
42.43
4.79
1181
3246
1.082561
CATGCGGCATTCGATTCGG
60.083
57.895
13.81
0.00
42.43
4.30
1182
3247
1.723542
GCATGCGGCATTCGATTCG
60.724
57.895
13.81
0.00
43.97
3.34
1183
3248
4.216963
GCATGCGGCATTCGATTC
57.783
55.556
13.81
0.00
43.97
2.52
1193
3258
4.100084
TCCTCCACCTGCATGCGG
62.100
66.667
20.13
20.13
0.00
5.69
1195
3260
2.821366
CGTCCTCCACCTGCATGC
60.821
66.667
11.82
11.82
0.00
4.06
1197
3262
3.023949
GCTCGTCCTCCACCTGCAT
62.024
63.158
0.00
0.00
0.00
3.96
1198
3263
3.695606
GCTCGTCCTCCACCTGCA
61.696
66.667
0.00
0.00
0.00
4.41
1206
3275
4.828925
GCAGCAGGGCTCGTCCTC
62.829
72.222
0.00
0.00
36.40
3.71
1217
3286
4.351054
AGGAAACCCCCGCAGCAG
62.351
66.667
0.00
0.00
34.66
4.24
1218
3287
4.344865
GAGGAAACCCCCGCAGCA
62.345
66.667
0.00
0.00
34.66
4.41
1220
3289
4.426313
GGGAGGAAACCCCCGCAG
62.426
72.222
0.00
0.00
43.81
5.18
1228
3306
2.361737
GCAGCCAGGGGAGGAAAC
60.362
66.667
0.00
0.00
0.00
2.78
1263
3341
4.862092
CAGCGCCGACGAGATGCT
62.862
66.667
2.29
0.00
43.93
3.79
1289
3367
2.757077
CTTCCCAAGGGCGAGGTT
59.243
61.111
0.00
0.00
34.68
3.50
1310
3388
2.564947
ACAAGAAGAGCGAGATTGACCT
59.435
45.455
0.00
0.00
0.00
3.85
1312
3390
4.999751
AAACAAGAAGAGCGAGATTGAC
57.000
40.909
0.00
0.00
0.00
3.18
1315
3393
3.503748
CCCAAAACAAGAAGAGCGAGATT
59.496
43.478
0.00
0.00
0.00
2.40
1316
3394
3.077359
CCCAAAACAAGAAGAGCGAGAT
58.923
45.455
0.00
0.00
0.00
2.75
1317
3395
2.158813
ACCCAAAACAAGAAGAGCGAGA
60.159
45.455
0.00
0.00
0.00
4.04
1318
3396
2.222027
ACCCAAAACAAGAAGAGCGAG
58.778
47.619
0.00
0.00
0.00
5.03
1319
3397
2.341846
ACCCAAAACAAGAAGAGCGA
57.658
45.000
0.00
0.00
0.00
4.93
1320
3398
3.058914
CAGTACCCAAAACAAGAAGAGCG
60.059
47.826
0.00
0.00
0.00
5.03
1321
3399
3.883489
ACAGTACCCAAAACAAGAAGAGC
59.117
43.478
0.00
0.00
0.00
4.09
1322
3400
4.211374
CGACAGTACCCAAAACAAGAAGAG
59.789
45.833
0.00
0.00
0.00
2.85
1323
3401
4.124238
CGACAGTACCCAAAACAAGAAGA
58.876
43.478
0.00
0.00
0.00
2.87
1324
3402
4.124238
TCGACAGTACCCAAAACAAGAAG
58.876
43.478
0.00
0.00
0.00
2.85
1325
3403
4.139859
TCGACAGTACCCAAAACAAGAA
57.860
40.909
0.00
0.00
0.00
2.52
1326
3404
3.823281
TCGACAGTACCCAAAACAAGA
57.177
42.857
0.00
0.00
0.00
3.02
1327
3405
5.212194
CAAATCGACAGTACCCAAAACAAG
58.788
41.667
0.00
0.00
0.00
3.16
1328
3406
4.498345
GCAAATCGACAGTACCCAAAACAA
60.498
41.667
0.00
0.00
0.00
2.83
1329
3407
3.003897
GCAAATCGACAGTACCCAAAACA
59.996
43.478
0.00
0.00
0.00
2.83
1330
3408
3.252458
AGCAAATCGACAGTACCCAAAAC
59.748
43.478
0.00
0.00
0.00
2.43
1331
3409
3.252215
CAGCAAATCGACAGTACCCAAAA
59.748
43.478
0.00
0.00
0.00
2.44
1332
3410
2.811431
CAGCAAATCGACAGTACCCAAA
59.189
45.455
0.00
0.00
0.00
3.28
1371
3455
0.829333
ACTAGTGAGGATGGCTGCTG
59.171
55.000
0.00
0.00
0.00
4.41
1372
3456
2.432510
GTTACTAGTGAGGATGGCTGCT
59.567
50.000
5.39
0.00
0.00
4.24
1375
3459
3.714144
ACTGTTACTAGTGAGGATGGCT
58.286
45.455
5.39
0.00
0.00
4.75
1385
3469
5.106237
GGATCTGACGAACACTGTTACTAGT
60.106
44.000
0.00
0.00
0.00
2.57
1386
3470
5.124138
AGGATCTGACGAACACTGTTACTAG
59.876
44.000
0.00
0.00
0.00
2.57
1388
3472
3.827302
AGGATCTGACGAACACTGTTACT
59.173
43.478
0.00
0.00
0.00
2.24
1389
3473
4.175787
AGGATCTGACGAACACTGTTAC
57.824
45.455
0.00
0.00
0.00
2.50
1390
3474
4.038763
ACAAGGATCTGACGAACACTGTTA
59.961
41.667
0.00
0.00
0.00
2.41
1391
3475
3.181465
ACAAGGATCTGACGAACACTGTT
60.181
43.478
0.00
0.00
0.00
3.16
1392
3476
2.365617
ACAAGGATCTGACGAACACTGT
59.634
45.455
0.00
0.00
0.00
3.55
1393
3477
3.032017
ACAAGGATCTGACGAACACTG
57.968
47.619
0.00
0.00
0.00
3.66
1394
3478
3.654414
GAACAAGGATCTGACGAACACT
58.346
45.455
0.00
0.00
0.00
3.55
1395
3479
2.408704
CGAACAAGGATCTGACGAACAC
59.591
50.000
0.00
0.00
0.00
3.32
1464
3548
3.019564
AGAATTGGGAACATACAGCAGC
58.980
45.455
0.00
0.00
42.32
5.25
1479
3563
7.410120
AAACTAAGGGGATTGCTTAGAATTG
57.590
36.000
0.00
0.00
35.39
2.32
1480
3564
8.435931
AAAAACTAAGGGGATTGCTTAGAATT
57.564
30.769
0.00
0.00
35.39
2.17
1597
3681
8.131100
GCTGCTGCATATTTACAAGAAGATAAA
58.869
33.333
11.11
0.00
39.41
1.40
1600
3684
5.826737
AGCTGCTGCATATTTACAAGAAGAT
59.173
36.000
18.42
0.00
42.74
2.40
1610
3694
4.701651
TGTTGAGTAAGCTGCTGCATATTT
59.298
37.500
18.42
5.73
42.74
1.40
1614
3698
1.808945
GTGTTGAGTAAGCTGCTGCAT
59.191
47.619
18.42
8.55
42.74
3.96
1632
3716
3.142174
GGACCTCTTGAGGAAGTTTGTG
58.858
50.000
22.10
0.00
0.00
3.33
1787
3905
6.260936
TGACACAAGGAGAAATCTTTCAGAAC
59.739
38.462
5.53
0.00
39.61
3.01
1855
3981
2.161609
CCGATTCCTACAAGGCAAACAC
59.838
50.000
0.00
0.00
34.61
3.32
1863
3989
1.543429
GCCCATCCCGATTCCTACAAG
60.543
57.143
0.00
0.00
0.00
3.16
1933
4059
3.358707
TCCATTGCATAGGTACGTACG
57.641
47.619
18.98
15.01
0.00
3.67
1942
4068
6.798476
CGCTATGTAACATTTCCATTGCATAG
59.202
38.462
14.16
14.16
46.16
2.23
2141
4304
8.888579
ATGGTGCATTACTACTATGTAAGAAC
57.111
34.615
0.00
0.00
36.10
3.01
2226
4389
6.523840
TGCTGCCTCAAATATTTTCAGTTTT
58.476
32.000
0.00
0.00
0.00
2.43
2252
4418
6.017605
CCAGAACATCTGCAGGAATTACATAC
60.018
42.308
15.13
0.00
42.98
2.39
2265
4431
1.487976
TCCAGATCCCAGAACATCTGC
59.512
52.381
1.79
0.00
42.98
4.26
2332
4498
3.926616
TCCTGATTCGTTCCTTCTGTTC
58.073
45.455
0.00
0.00
0.00
3.18
2396
4562
1.929169
CACACACACACACACAGAGAG
59.071
52.381
0.00
0.00
0.00
3.20
2397
4563
1.275010
ACACACACACACACACAGAGA
59.725
47.619
0.00
0.00
0.00
3.10
2398
4564
1.660607
GACACACACACACACACAGAG
59.339
52.381
0.00
0.00
0.00
3.35
2399
4565
1.275010
AGACACACACACACACACAGA
59.725
47.619
0.00
0.00
0.00
3.41
2400
4566
1.660607
GAGACACACACACACACACAG
59.339
52.381
0.00
0.00
0.00
3.66
2401
4567
1.275010
AGAGACACACACACACACACA
59.725
47.619
0.00
0.00
0.00
3.72
2402
4568
1.927174
GAGAGACACACACACACACAC
59.073
52.381
0.00
0.00
0.00
3.82
2403
4569
1.824852
AGAGAGACACACACACACACA
59.175
47.619
0.00
0.00
0.00
3.72
2404
4570
2.099921
AGAGAGAGACACACACACACAC
59.900
50.000
0.00
0.00
0.00
3.82
2405
4571
2.359214
GAGAGAGAGACACACACACACA
59.641
50.000
0.00
0.00
0.00
3.72
2406
4572
2.621055
AGAGAGAGAGACACACACACAC
59.379
50.000
0.00
0.00
0.00
3.82
2407
4573
2.620585
CAGAGAGAGAGACACACACACA
59.379
50.000
0.00
0.00
0.00
3.72
2408
4574
2.621055
ACAGAGAGAGAGACACACACAC
59.379
50.000
0.00
0.00
0.00
3.82
2409
4575
2.881513
GACAGAGAGAGAGACACACACA
59.118
50.000
0.00
0.00
0.00
3.72
2410
4576
3.146066
AGACAGAGAGAGAGACACACAC
58.854
50.000
0.00
0.00
0.00
3.82
2411
4577
3.072330
AGAGACAGAGAGAGAGACACACA
59.928
47.826
0.00
0.00
0.00
3.72
2412
4578
3.674997
AGAGACAGAGAGAGAGACACAC
58.325
50.000
0.00
0.00
0.00
3.82
2413
4579
3.582647
AGAGAGACAGAGAGAGAGACACA
59.417
47.826
0.00
0.00
0.00
3.72
2414
4580
4.184629
GAGAGAGACAGAGAGAGAGACAC
58.815
52.174
0.00
0.00
0.00
3.67
2415
4581
3.837731
TGAGAGAGACAGAGAGAGAGACA
59.162
47.826
0.00
0.00
0.00
3.41
2416
4582
4.471904
TGAGAGAGACAGAGAGAGAGAC
57.528
50.000
0.00
0.00
0.00
3.36
2532
4698
3.507233
TGCATGAAATCCTCCAGTTTGAC
59.493
43.478
0.00
0.00
0.00
3.18
2644
4810
4.787135
AAACCACCCAATTTCCAACATT
57.213
36.364
0.00
0.00
0.00
2.71
2741
4907
9.277565
CCTTCTCAAATAAAATCACACATAACG
57.722
33.333
0.00
0.00
0.00
3.18
3050
5217
5.794894
TGTACCTCTGAAACATCTTTCTCC
58.205
41.667
0.00
0.00
37.30
3.71
3081
5248
5.003804
CACTACTAGGCATTGAACCAAAGT
58.996
41.667
0.00
0.00
32.39
2.66
3145
5312
9.244292
AGAGCAGAGTATTGATCCGTATATAAA
57.756
33.333
0.00
0.00
34.10
1.40
3283
5491
6.012113
TCATTCCCAGAGACATTTTGTGAAT
58.988
36.000
0.00
0.00
0.00
2.57
3369
5583
5.352569
GGCATTCGAGTATTTCCCATATCTG
59.647
44.000
0.00
0.00
0.00
2.90
3448
5662
7.867305
TTGACCATCAAACTGTAGTTTTACA
57.133
32.000
7.25
0.00
45.07
2.41
3529
5761
6.436843
ACCAAGAAGCCATAATTTCTTACG
57.563
37.500
0.00
0.00
40.62
3.18
3545
5777
1.694150
CTGGTGTCAGAGGACCAAGAA
59.306
52.381
0.00
0.00
41.76
2.52
3764
5998
8.862325
TTTTATAAAGTGGATCTTGCTCTGAA
57.138
30.769
0.00
0.00
36.40
3.02
3831
6068
1.566563
CAGAGCTGCACACGTGTTC
59.433
57.895
20.79
15.89
0.00
3.18
3954
6191
7.394359
ACCTTAACTGTCTGATGTTTGCATTAT
59.606
33.333
0.00
0.00
35.07
1.28
3968
6206
4.993705
TTCCATTCCACCTTAACTGTCT
57.006
40.909
0.00
0.00
0.00
3.41
4122
6397
8.365399
TGTAAATCAGTAGACAACAGAAACAG
57.635
34.615
0.00
0.00
0.00
3.16
4128
6404
7.095060
ACTGCATTGTAAATCAGTAGACAACAG
60.095
37.037
0.00
0.00
37.94
3.16
4132
6408
6.463360
TCACTGCATTGTAAATCAGTAGACA
58.537
36.000
3.77
0.00
37.66
3.41
4190
6466
3.734293
GCGCTAGTAAGGTGGACAGTTAG
60.734
52.174
0.00
0.00
0.00
2.34
4429
6706
7.445096
TCATTCATACTCAGTGACACAAAACAT
59.555
33.333
8.59
0.00
0.00
2.71
4446
6723
5.888161
ACTTCCCTGTTTCCATCATTCATAC
59.112
40.000
0.00
0.00
0.00
2.39
4578
6855
6.761242
CAGTGACGAGTAATATGAATGGGAAA
59.239
38.462
0.00
0.00
0.00
3.13
4579
6856
6.280643
CAGTGACGAGTAATATGAATGGGAA
58.719
40.000
0.00
0.00
0.00
3.97
4596
6873
1.649171
CGCTGTACTAAAGCAGTGACG
59.351
52.381
0.00
0.00
43.58
4.35
4600
6877
3.380479
TTGTCGCTGTACTAAAGCAGT
57.620
42.857
4.74
0.00
40.86
4.40
4605
6882
9.772973
ATCCATATTAATTGTCGCTGTACTAAA
57.227
29.630
0.00
0.00
0.00
1.85
4676
6980
4.816786
TGTTGTGTCACTGAATGATGTG
57.183
40.909
4.27
0.00
40.28
3.21
4703
7007
5.762179
TCTCTTCCAATTCTAAAGAGGCA
57.238
39.130
15.73
1.98
43.94
4.75
5240
7653
7.823745
TTTTTAGCCATCTCTTTTCTGAACT
57.176
32.000
0.00
0.00
0.00
3.01
5381
7801
1.592669
CTGGCAATCCTACGCTCCG
60.593
63.158
0.00
0.00
0.00
4.63
5493
7920
5.493809
TCCTAGGTAACAAACATGCCTAAC
58.506
41.667
9.08
0.00
35.17
2.34
5508
7935
8.112822
TCCAAAAATCATGTCAATTCCTAGGTA
58.887
33.333
9.08
0.00
0.00
3.08
5586
8013
4.912586
TCCGGATGGTAATCAACTTTTCA
58.087
39.130
0.00
0.00
34.17
2.69
5661
8088
1.376543
AGAACGCATGCAGAAGGATG
58.623
50.000
19.57
0.50
45.39
3.51
5726
8154
4.261489
GCTGATAGCCAAGTCCATTCATTG
60.261
45.833
0.00
0.00
34.48
2.82
5783
8211
3.142174
GACAAGTGGGAGGTGAAAAGAG
58.858
50.000
0.00
0.00
0.00
2.85
5926
8358
0.980754
TCGCCCACCACCATGAGTAT
60.981
55.000
0.00
0.00
0.00
2.12
6038
8470
7.927629
CCGAAAATTCCCATTTGACATATTCAT
59.072
33.333
0.00
0.00
32.57
2.57
6048
8480
6.815089
TCCATAATCCGAAAATTCCCATTTG
58.185
36.000
0.00
0.00
32.57
2.32
6141
8573
7.669304
TGTCAATTTTGAGATGGGACTAATTCA
59.331
33.333
0.00
0.00
37.98
2.57
6298
8736
7.155655
TGCATAGCATTTTACATCAACAGAA
57.844
32.000
0.00
0.00
31.71
3.02
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.