Multiple sequence alignment - TraesCS1A01G061400
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
TraesCS1A01G061400
chr1A
100.000
2607
0
0
1
2607
41918117
41920723
0.000000e+00
4815.0
1
TraesCS1A01G061400
chr1A
90.566
53
5
0
2185
2237
41907816
41907868
1.290000e-08
71.3
2
TraesCS1A01G061400
chr1D
91.642
1675
91
23
842
2478
41914539
41916202
0.000000e+00
2272.0
3
TraesCS1A01G061400
chr1D
85.970
335
30
10
526
855
41913103
41913425
2.480000e-90
342.0
4
TraesCS1A01G061400
chr1D
80.861
418
58
16
61
459
41912187
41912601
2.520000e-80
309.0
5
TraesCS1A01G061400
chr1D
94.231
104
6
0
2504
2607
41922043
41922146
2.690000e-35
159.0
6
TraesCS1A01G061400
chr1D
83.133
166
22
5
2290
2455
41863376
41863535
2.090000e-31
147.0
7
TraesCS1A01G061400
chr1D
84.127
63
8
2
179
240
494341759
494341820
2.800000e-05
60.2
8
TraesCS1A01G061400
chr1B
94.616
1263
54
7
853
2111
62284286
62285538
0.000000e+00
1943.0
9
TraesCS1A01G061400
chr1B
93.385
514
19
4
2109
2607
62285699
62286212
0.000000e+00
747.0
10
TraesCS1A01G061400
chr1B
82.872
397
39
14
464
855
62281017
62281389
1.930000e-86
329.0
11
TraesCS1A01G061400
chr1B
81.250
304
41
11
2312
2607
62003027
62003322
5.610000e-57
231.0
12
TraesCS1A01G061400
chr1B
82.000
150
20
6
2285
2432
62059398
62059542
1.270000e-23
121.0
13
TraesCS1A01G061400
chr1B
91.304
46
4
0
1
46
35401584
35401539
2.170000e-06
63.9
14
TraesCS1A01G061400
chr1B
85.714
56
2
2
2396
2447
61965312
61965365
1.000000e-03
54.7
15
TraesCS1A01G061400
chr4D
76.238
202
37
11
181
375
11293804
11294001
2.140000e-16
97.1
16
TraesCS1A01G061400
chrUn
86.765
68
5
3
178
243
340042920
340042985
3.600000e-09
73.1
17
TraesCS1A01G061400
chrUn
86.765
68
5
3
178
243
340045473
340045538
3.600000e-09
73.1
18
TraesCS1A01G061400
chrUn
86.765
68
5
3
178
243
449632508
449632443
3.600000e-09
73.1
19
TraesCS1A01G061400
chr7D
87.500
64
6
2
1
63
454844236
454844174
3.600000e-09
73.1
20
TraesCS1A01G061400
chr2A
91.304
46
4
0
1
46
137925327
137925372
2.170000e-06
63.9
21
TraesCS1A01G061400
chr2A
89.362
47
3
2
1
46
56944739
56944694
1.010000e-04
58.4
22
TraesCS1A01G061400
chr2D
100.000
30
0
0
17
46
39439448
39439477
3.620000e-04
56.5
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
TraesCS1A01G061400
chr1A
41918117
41920723
2606
False
4815.000000
4815
100.000000
1
2607
1
chr1A.!!$F2
2606
1
TraesCS1A01G061400
chr1D
41912187
41916202
4015
False
974.333333
2272
86.157667
61
2478
3
chr1D.!!$F4
2417
2
TraesCS1A01G061400
chr1B
62281017
62286212
5195
False
1006.333333
1943
90.291000
464
2607
3
chr1B.!!$F4
2143
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
20
21
0.036306
ATGGTGTCTTCGTTGGACCC
59.964
55.0
0.0
0.0
33.22
4.46
F
318
341
0.099791
CGCGGGTTGCCGAAATATTT
59.900
50.0
0.0
0.0
42.08
1.40
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1506
5119
0.748450
CGGGTTAATCTACCTCGGCA
59.252
55.0
0.00
0.0
38.3
5.69
R
2168
5954
0.328258
ACTCTTTGGGCGTGCCTTAT
59.672
50.0
11.25
0.0
36.1
1.73
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
19
20
1.156736
CATGGTGTCTTCGTTGGACC
58.843
55.000
0.00
0.00
33.22
4.46
20
21
0.036306
ATGGTGTCTTCGTTGGACCC
59.964
55.000
0.00
0.00
33.22
4.46
21
22
1.338890
TGGTGTCTTCGTTGGACCCA
61.339
55.000
0.00
0.00
34.30
4.51
22
23
0.036306
GGTGTCTTCGTTGGACCCAT
59.964
55.000
0.00
0.00
33.22
4.00
23
24
1.156736
GTGTCTTCGTTGGACCCATG
58.843
55.000
0.00
0.00
33.22
3.66
24
25
0.762418
TGTCTTCGTTGGACCCATGT
59.238
50.000
0.00
0.00
33.22
3.21
25
26
1.972075
TGTCTTCGTTGGACCCATGTA
59.028
47.619
0.00
0.00
33.22
2.29
26
27
2.028476
TGTCTTCGTTGGACCCATGTAG
60.028
50.000
0.00
0.00
33.22
2.74
27
28
1.553248
TCTTCGTTGGACCCATGTAGG
59.447
52.381
0.00
0.00
37.03
3.18
41
42
5.993748
CCATGTAGGGTGTGGTAAAAATT
57.006
39.130
0.00
0.00
0.00
1.82
42
43
6.353404
CCATGTAGGGTGTGGTAAAAATTT
57.647
37.500
0.00
0.00
0.00
1.82
43
44
6.162777
CCATGTAGGGTGTGGTAAAAATTTG
58.837
40.000
0.00
0.00
0.00
2.32
44
45
6.015010
CCATGTAGGGTGTGGTAAAAATTTGA
60.015
38.462
0.00
0.00
0.00
2.69
45
46
6.642707
TGTAGGGTGTGGTAAAAATTTGAG
57.357
37.500
0.00
0.00
0.00
3.02
46
47
5.536916
TGTAGGGTGTGGTAAAAATTTGAGG
59.463
40.000
0.00
0.00
0.00
3.86
47
48
4.810345
AGGGTGTGGTAAAAATTTGAGGA
58.190
39.130
0.00
0.00
0.00
3.71
48
49
4.587262
AGGGTGTGGTAAAAATTTGAGGAC
59.413
41.667
0.00
0.00
0.00
3.85
49
50
4.587262
GGGTGTGGTAAAAATTTGAGGACT
59.413
41.667
0.00
0.00
0.00
3.85
50
51
5.069914
GGGTGTGGTAAAAATTTGAGGACTT
59.930
40.000
0.00
0.00
0.00
3.01
51
52
5.983118
GGTGTGGTAAAAATTTGAGGACTTG
59.017
40.000
0.00
0.00
0.00
3.16
52
53
6.183360
GGTGTGGTAAAAATTTGAGGACTTGA
60.183
38.462
0.00
0.00
0.00
3.02
53
54
7.433680
GTGTGGTAAAAATTTGAGGACTTGAT
58.566
34.615
0.00
0.00
0.00
2.57
54
55
7.382218
GTGTGGTAAAAATTTGAGGACTTGATG
59.618
37.037
0.00
0.00
0.00
3.07
55
56
6.868339
GTGGTAAAAATTTGAGGACTTGATGG
59.132
38.462
0.00
0.00
0.00
3.51
56
57
6.780031
TGGTAAAAATTTGAGGACTTGATGGA
59.220
34.615
0.00
0.00
0.00
3.41
57
58
7.288852
TGGTAAAAATTTGAGGACTTGATGGAA
59.711
33.333
0.00
0.00
0.00
3.53
58
59
8.147704
GGTAAAAATTTGAGGACTTGATGGAAA
58.852
33.333
0.00
0.00
0.00
3.13
59
60
9.541143
GTAAAAATTTGAGGACTTGATGGAAAA
57.459
29.630
0.00
0.00
0.00
2.29
83
84
1.344763
ACTCTCCGGTGAAGTTTCAGG
59.655
52.381
7.75
0.00
37.98
3.86
93
94
3.375922
GTGAAGTTTCAGGGTTTCGAACA
59.624
43.478
0.00
0.00
37.98
3.18
106
107
0.834612
TCGAACAGAAACCACCACCT
59.165
50.000
0.00
0.00
0.00
4.00
111
112
0.754957
CAGAAACCACCACCTGCCAA
60.755
55.000
0.00
0.00
0.00
4.52
113
114
0.104120
GAAACCACCACCTGCCAAAC
59.896
55.000
0.00
0.00
0.00
2.93
119
120
0.534873
ACCACCTGCCAAACACAAAC
59.465
50.000
0.00
0.00
0.00
2.93
128
129
5.355350
CCTGCCAAACACAAACCAATTTTTA
59.645
36.000
0.00
0.00
0.00
1.52
154
155
7.352079
ACATCATTTCAACTTCTTCAAACCT
57.648
32.000
0.00
0.00
0.00
3.50
234
256
8.514330
TTTTAAGCACTTTTCTGGACTTAAGA
57.486
30.769
10.09
0.00
32.84
2.10
248
270
1.873591
CTTAAGATATGTGTGGCGGGC
59.126
52.381
0.00
0.00
0.00
6.13
266
288
2.789249
GGCCGATACCGTTGCAAC
59.211
61.111
19.89
19.89
0.00
4.17
268
290
3.086309
CCGATACCGTTGCAACCG
58.914
61.111
23.42
19.08
0.00
4.44
269
291
1.738830
CCGATACCGTTGCAACCGT
60.739
57.895
23.62
23.62
0.00
4.83
274
297
2.237393
TACCGTTGCAACCGTAAAGT
57.763
45.000
22.92
13.95
0.00
2.66
283
306
4.174762
TGCAACCGTAAAGTTTTGGAAAC
58.825
39.130
12.17
0.00
0.00
2.78
288
311
6.519679
ACCGTAAAGTTTTGGAAACTTTCT
57.480
33.333
25.90
12.74
44.50
2.52
290
313
7.475015
ACCGTAAAGTTTTGGAAACTTTCTAC
58.525
34.615
25.90
20.18
44.50
2.59
293
316
9.511144
CGTAAAGTTTTGGAAACTTTCTACAAT
57.489
29.630
25.90
10.55
44.50
2.71
304
327
3.058501
ACTTTCTACAATTTTGACGCGGG
60.059
43.478
12.47
0.00
0.00
6.13
310
333
2.741116
AATTTTGACGCGGGTTGCCG
62.741
55.000
12.47
0.00
42.08
5.69
318
341
0.099791
CGCGGGTTGCCGAAATATTT
59.900
50.000
0.00
0.00
42.08
1.40
326
349
2.600731
TGCCGAAATATTTTTGTGGCG
58.399
42.857
20.28
11.60
42.11
5.69
328
351
1.923864
CCGAAATATTTTTGTGGCGGC
59.076
47.619
0.00
0.00
0.00
6.53
358
381
2.461110
CCCGCGACTGGTGCATAAC
61.461
63.158
8.23
0.00
0.00
1.89
370
393
2.817258
GGTGCATAACAAACCAGTAGCA
59.183
45.455
0.00
0.00
33.94
3.49
396
419
0.753479
TTTTCTTTGCCCGCCACTGA
60.753
50.000
0.00
0.00
0.00
3.41
399
422
1.973281
CTTTGCCCGCCACTGATGT
60.973
57.895
0.00
0.00
0.00
3.06
404
427
0.667184
GCCCGCCACTGATGTTTTTG
60.667
55.000
0.00
0.00
0.00
2.44
406
429
1.068434
CCCGCCACTGATGTTTTTGTT
59.932
47.619
0.00
0.00
0.00
2.83
407
430
2.482839
CCCGCCACTGATGTTTTTGTTT
60.483
45.455
0.00
0.00
0.00
2.83
411
434
4.432712
GCCACTGATGTTTTTGTTTCACT
58.567
39.130
0.00
0.00
0.00
3.41
416
439
7.543868
CCACTGATGTTTTTGTTTCACTTGTAA
59.456
33.333
0.00
0.00
0.00
2.41
438
461
9.719279
TGTAAATTTGTAAAAGTTTACGAGTGG
57.281
29.630
15.24
0.00
44.52
4.00
439
462
7.688478
AAATTTGTAAAAGTTTACGAGTGGC
57.312
32.000
8.90
0.00
44.52
5.01
440
463
5.814764
TTTGTAAAAGTTTACGAGTGGCA
57.185
34.783
8.90
0.00
44.52
4.92
459
482
3.552068
GGCAGGTTGTAATTTTTGCTCGT
60.552
43.478
0.00
0.00
0.00
4.18
461
484
3.906008
CAGGTTGTAATTTTTGCTCGTCG
59.094
43.478
0.00
0.00
0.00
5.12
500
577
3.138798
GCCTACTCGTCCTCGCCA
61.139
66.667
0.00
0.00
36.96
5.69
519
596
1.474077
CAGCCACTAAATTGAGCCCAC
59.526
52.381
0.00
0.00
0.00
4.61
520
597
1.075374
AGCCACTAAATTGAGCCCACA
59.925
47.619
0.00
0.00
0.00
4.17
521
598
1.202348
GCCACTAAATTGAGCCCACAC
59.798
52.381
0.00
0.00
0.00
3.82
529
606
4.862641
AATTGAGCCCACACCTATAAGT
57.137
40.909
0.00
0.00
0.00
2.24
535
999
4.844884
AGCCCACACCTATAAGTCTTTTC
58.155
43.478
0.00
0.00
0.00
2.29
537
1001
4.189231
CCCACACCTATAAGTCTTTTCCG
58.811
47.826
0.00
0.00
0.00
4.30
575
1039
8.789762
GGTCTTTGCCTAGTTTATTTAGTTTGA
58.210
33.333
0.00
0.00
0.00
2.69
577
1041
9.344772
TCTTTGCCTAGTTTATTTAGTTTGACA
57.655
29.630
0.00
0.00
0.00
3.58
596
1060
5.761003
TGACATGTACTTTTCACTTGCATG
58.239
37.500
0.00
0.00
38.41
4.06
617
1081
5.204409
TGTCGGTAATGTACTGTCTTTGT
57.796
39.130
0.00
0.00
36.45
2.83
630
1094
1.461127
GTCTTTGTCGTGCTCCATGTC
59.539
52.381
0.00
0.00
0.00
3.06
668
1132
0.179078
AGGGTACAACGCGTTTGTCA
60.179
50.000
24.21
4.53
46.05
3.58
670
1134
1.595246
GGGTACAACGCGTTTGTCAAC
60.595
52.381
24.21
17.47
46.05
3.18
731
1195
3.061697
GGCGTACAACGATTTTCCAGTAG
59.938
47.826
3.22
0.00
46.05
2.57
746
1210
3.964688
TCCAGTAGTGTTGAGGACAAAGA
59.035
43.478
0.00
0.00
40.65
2.52
757
1221
1.342174
AGGACAAAGACGAACCGCTAA
59.658
47.619
0.00
0.00
0.00
3.09
773
1238
3.488489
CGCTAACCGTTGGATTTGAAAG
58.512
45.455
0.00
0.00
0.00
2.62
787
1252
8.624367
TGGATTTGAAAGGTCGACTTATTTAA
57.376
30.769
16.46
8.29
38.85
1.52
788
1253
9.069082
TGGATTTGAAAGGTCGACTTATTTAAA
57.931
29.630
16.46
15.58
38.85
1.52
789
1254
9.902196
GGATTTGAAAGGTCGACTTATTTAAAA
57.098
29.630
16.46
17.51
38.85
1.52
837
1308
6.159751
AGGTGGCCCTCAATTTTATAGTCTTA
59.840
38.462
0.00
0.00
35.62
2.10
864
4453
9.959749
GAGAAAATTACAAATCTTACCAACACA
57.040
29.630
0.00
0.00
0.00
3.72
886
4475
5.878116
ACAACTTGTTCAACTGTACTAGCAA
59.122
36.000
0.00
0.00
0.00
3.91
899
4490
1.015109
CTAGCAATGCAGCACTGAGG
58.985
55.000
8.35
0.00
36.85
3.86
910
4501
2.046892
ACTGAGGTGCACCATCGC
60.047
61.111
36.39
22.04
38.89
4.58
990
4587
1.703438
GCGCAAGATCAGTCTGCCAG
61.703
60.000
0.30
0.00
43.02
4.85
1137
4740
2.344203
CGCAACCGAGGAGGAGTCT
61.344
63.158
0.00
0.00
45.00
3.24
1146
4749
1.985116
GGAGGAGTCTCGGTGGCTT
60.985
63.158
0.00
0.00
40.85
4.35
1344
4947
4.782019
TGTCCACATACTGAATTTTGCC
57.218
40.909
0.00
0.00
0.00
4.52
1348
4951
3.511146
CCACATACTGAATTTTGCCCTGT
59.489
43.478
0.00
0.00
0.00
4.00
1357
4969
1.044611
TTTTGCCCTGTTTGCTACCC
58.955
50.000
0.00
0.00
0.00
3.69
1360
4972
0.842905
TGCCCTGTTTGCTACCCCTA
60.843
55.000
0.00
0.00
0.00
3.53
1361
4973
0.393944
GCCCTGTTTGCTACCCCTAC
60.394
60.000
0.00
0.00
0.00
3.18
1363
4975
0.988832
CCTGTTTGCTACCCCTACCA
59.011
55.000
0.00
0.00
0.00
3.25
1364
4976
1.339727
CCTGTTTGCTACCCCTACCAC
60.340
57.143
0.00
0.00
0.00
4.16
1365
4977
1.628846
CTGTTTGCTACCCCTACCACT
59.371
52.381
0.00
0.00
0.00
4.00
1366
4978
2.835764
CTGTTTGCTACCCCTACCACTA
59.164
50.000
0.00
0.00
0.00
2.74
1367
4979
3.249752
TGTTTGCTACCCCTACCACTAA
58.750
45.455
0.00
0.00
0.00
2.24
1370
4982
2.905246
TGCTACCCCTACCACTAAACA
58.095
47.619
0.00
0.00
0.00
2.83
1371
4983
3.456842
TGCTACCCCTACCACTAAACAT
58.543
45.455
0.00
0.00
0.00
2.71
1372
4984
3.199071
TGCTACCCCTACCACTAAACATG
59.801
47.826
0.00
0.00
0.00
3.21
1373
4985
2.801077
ACCCCTACCACTAAACATGC
57.199
50.000
0.00
0.00
0.00
4.06
1375
4987
2.580783
ACCCCTACCACTAAACATGCAT
59.419
45.455
0.00
0.00
0.00
3.96
1376
4988
2.951642
CCCCTACCACTAAACATGCATG
59.048
50.000
25.09
25.09
0.00
4.06
1416
5029
0.389426
GCAGCTTTGGCAGAATGGTG
60.389
55.000
7.86
7.86
41.70
4.17
1443
5056
0.961358
CCTTCCACTCTCGACCTCGT
60.961
60.000
0.00
0.00
40.80
4.18
1495
5108
1.905894
AGAAGAAGAACCTGGAGGAGC
59.094
52.381
0.00
0.00
38.94
4.70
1506
5119
1.379309
GGAGGAGCCTCACTCTCGT
60.379
63.158
17.68
0.00
45.48
4.18
1522
5135
2.857592
TCGTGCCGAGGTAGATTAAC
57.142
50.000
0.00
0.00
0.00
2.01
1542
5155
1.153647
CGACCGGCACTGCATTAGA
60.154
57.895
0.00
0.00
0.00
2.10
1553
5166
5.586243
GGCACTGCATTAGAGATTCAACTTA
59.414
40.000
2.82
0.00
0.00
2.24
1695
5308
5.220815
GGAGTTCGTGTCGTCTATCATTAGT
60.221
44.000
0.00
0.00
0.00
2.24
1735
5348
4.211125
TCGGCTCAAGAGAGATTAGTCAT
58.789
43.478
0.32
0.00
44.98
3.06
1831
5449
7.393234
GCCCACCTAATATAAGTGATATGCAAA
59.607
37.037
0.00
0.00
33.21
3.68
1895
5514
5.478233
TGAAATCATGTAAAACGCGCTAT
57.522
34.783
5.73
0.00
0.00
2.97
1973
5593
2.923020
CAAACACAACAAGGACAACTGC
59.077
45.455
0.00
0.00
0.00
4.40
1980
5600
0.386352
CAAGGACAACTGCACATGCG
60.386
55.000
0.00
0.00
45.83
4.73
2144
5927
2.159128
TGCATTCAACACACACTTTGGG
60.159
45.455
0.00
0.00
33.17
4.12
2168
5954
3.827302
GGTGGTACTTCTCTTGAGACAGA
59.173
47.826
0.00
0.00
0.00
3.41
2170
5956
5.652891
GGTGGTACTTCTCTTGAGACAGATA
59.347
44.000
0.00
0.00
0.00
1.98
2478
6265
5.767670
AGACAATACAGGTAGCTAGGAGAA
58.232
41.667
0.00
0.00
0.00
2.87
2479
6266
6.377912
AGACAATACAGGTAGCTAGGAGAAT
58.622
40.000
0.00
0.00
0.00
2.40
2543
6344
5.050091
CCTCATGCTACAAATATCCACGAAC
60.050
44.000
0.00
0.00
0.00
3.95
2555
6356
3.134574
TCCACGAACAGCCTTTTACAT
57.865
42.857
0.00
0.00
0.00
2.29
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
0
1
1.156736
GGTCCAACGAAGACACCATG
58.843
55.000
0.00
0.00
35.89
3.66
1
2
0.036306
GGGTCCAACGAAGACACCAT
59.964
55.000
0.00
0.00
35.89
3.55
2
3
1.338890
TGGGTCCAACGAAGACACCA
61.339
55.000
0.00
0.27
36.80
4.17
3
4
0.036306
ATGGGTCCAACGAAGACACC
59.964
55.000
0.00
0.00
36.80
4.16
4
5
1.156736
CATGGGTCCAACGAAGACAC
58.843
55.000
0.00
0.00
38.19
3.67
5
6
0.762418
ACATGGGTCCAACGAAGACA
59.238
50.000
0.00
0.00
35.89
3.41
6
7
2.618053
CTACATGGGTCCAACGAAGAC
58.382
52.381
0.00
0.00
0.00
3.01
7
8
1.553248
CCTACATGGGTCCAACGAAGA
59.447
52.381
0.00
0.00
0.00
2.87
8
9
2.024176
CCTACATGGGTCCAACGAAG
57.976
55.000
0.00
0.00
0.00
3.79
19
20
5.993748
AATTTTTACCACACCCTACATGG
57.006
39.130
0.00
0.00
39.57
3.66
20
21
6.987386
TCAAATTTTTACCACACCCTACATG
58.013
36.000
0.00
0.00
0.00
3.21
21
22
6.210584
CCTCAAATTTTTACCACACCCTACAT
59.789
38.462
0.00
0.00
0.00
2.29
22
23
5.536916
CCTCAAATTTTTACCACACCCTACA
59.463
40.000
0.00
0.00
0.00
2.74
23
24
5.771165
TCCTCAAATTTTTACCACACCCTAC
59.229
40.000
0.00
0.00
0.00
3.18
24
25
5.771165
GTCCTCAAATTTTTACCACACCCTA
59.229
40.000
0.00
0.00
0.00
3.53
25
26
4.587262
GTCCTCAAATTTTTACCACACCCT
59.413
41.667
0.00
0.00
0.00
4.34
26
27
4.587262
AGTCCTCAAATTTTTACCACACCC
59.413
41.667
0.00
0.00
0.00
4.61
27
28
5.784578
AGTCCTCAAATTTTTACCACACC
57.215
39.130
0.00
0.00
0.00
4.16
28
29
6.801575
TCAAGTCCTCAAATTTTTACCACAC
58.198
36.000
0.00
0.00
0.00
3.82
29
30
7.432869
CATCAAGTCCTCAAATTTTTACCACA
58.567
34.615
0.00
0.00
0.00
4.17
30
31
6.868339
CCATCAAGTCCTCAAATTTTTACCAC
59.132
38.462
0.00
0.00
0.00
4.16
31
32
6.780031
TCCATCAAGTCCTCAAATTTTTACCA
59.220
34.615
0.00
0.00
0.00
3.25
32
33
7.227049
TCCATCAAGTCCTCAAATTTTTACC
57.773
36.000
0.00
0.00
0.00
2.85
33
34
9.541143
TTTTCCATCAAGTCCTCAAATTTTTAC
57.459
29.630
0.00
0.00
0.00
2.01
57
58
3.277142
ACTTCACCGGAGAGTGTTTTT
57.723
42.857
9.46
0.00
38.91
1.94
58
59
3.277142
AACTTCACCGGAGAGTGTTTT
57.723
42.857
9.46
0.00
38.91
2.43
59
60
3.203716
GAAACTTCACCGGAGAGTGTTT
58.796
45.455
23.76
23.76
38.91
2.83
72
73
3.611970
TGTTCGAAACCCTGAAACTTCA
58.388
40.909
0.00
0.00
35.57
3.02
93
94
0.032615
TTTGGCAGGTGGTGGTTTCT
60.033
50.000
0.00
0.00
0.00
2.52
103
104
1.270907
TTGGTTTGTGTTTGGCAGGT
58.729
45.000
0.00
0.00
0.00
4.00
106
107
7.552687
TGTATAAAAATTGGTTTGTGTTTGGCA
59.447
29.630
0.00
0.00
0.00
4.92
128
129
9.082313
AGGTTTGAAGAAGTTGAAATGATGTAT
57.918
29.630
0.00
0.00
0.00
2.29
159
160
6.533723
GTCTCAATGGTGTGTATTAATCGTGA
59.466
38.462
0.00
0.00
0.00
4.35
162
163
8.818141
ATAGTCTCAATGGTGTGTATTAATCG
57.182
34.615
0.00
0.00
0.00
3.34
213
235
7.885399
ACATATCTTAAGTCCAGAAAAGTGCTT
59.115
33.333
1.63
0.00
0.00
3.91
215
237
7.119846
ACACATATCTTAAGTCCAGAAAAGTGC
59.880
37.037
1.63
0.00
0.00
4.40
216
238
8.446273
CACACATATCTTAAGTCCAGAAAAGTG
58.554
37.037
1.63
0.00
0.00
3.16
217
239
7.607991
CCACACATATCTTAAGTCCAGAAAAGT
59.392
37.037
1.63
0.00
0.00
2.66
218
240
7.414540
GCCACACATATCTTAAGTCCAGAAAAG
60.415
40.741
1.63
0.00
0.00
2.27
223
245
3.804325
CGCCACACATATCTTAAGTCCAG
59.196
47.826
1.63
0.00
0.00
3.86
224
246
3.431626
CCGCCACACATATCTTAAGTCCA
60.432
47.826
1.63
0.00
0.00
4.02
227
249
2.745152
GCCCGCCACACATATCTTAAGT
60.745
50.000
1.63
0.00
0.00
2.24
252
274
1.348276
TTACGGTTGCAACGGTATCG
58.652
50.000
35.82
28.01
42.02
2.92
258
280
2.532317
CCAAAACTTTACGGTTGCAACG
59.468
45.455
22.67
19.11
37.36
4.10
260
282
4.451629
TTCCAAAACTTTACGGTTGCAA
57.548
36.364
0.00
0.00
0.00
4.08
261
283
4.082136
AGTTTCCAAAACTTTACGGTTGCA
60.082
37.500
0.00
0.00
0.00
4.08
262
284
4.426416
AGTTTCCAAAACTTTACGGTTGC
58.574
39.130
0.00
0.00
0.00
4.17
263
285
6.809689
AGAAAGTTTCCAAAACTTTACGGTTG
59.190
34.615
23.28
0.00
46.81
3.77
264
286
6.927416
AGAAAGTTTCCAAAACTTTACGGTT
58.073
32.000
23.28
7.35
46.81
4.44
265
287
6.519679
AGAAAGTTTCCAAAACTTTACGGT
57.480
33.333
23.28
7.93
46.81
4.83
266
288
7.474190
TGTAGAAAGTTTCCAAAACTTTACGG
58.526
34.615
23.28
0.00
46.81
4.02
274
297
8.865001
CGTCAAAATTGTAGAAAGTTTCCAAAA
58.135
29.630
12.05
0.35
0.00
2.44
283
306
3.058501
ACCCGCGTCAAAATTGTAGAAAG
60.059
43.478
4.92
0.00
0.00
2.62
288
311
1.335142
GCAACCCGCGTCAAAATTGTA
60.335
47.619
4.92
0.00
0.00
2.41
290
313
1.281566
GGCAACCCGCGTCAAAATTG
61.282
55.000
4.92
1.21
43.84
2.32
304
327
3.181535
CGCCACAAAAATATTTCGGCAAC
60.182
43.478
21.26
5.44
41.27
4.17
310
333
2.966050
TGGCCGCCACAAAAATATTTC
58.034
42.857
8.43
0.00
0.00
2.17
318
341
0.179000
AAAAACATGGCCGCCACAAA
59.821
45.000
16.16
0.00
35.80
2.83
348
371
2.817258
GCTACTGGTTTGTTATGCACCA
59.183
45.455
0.00
0.00
38.30
4.17
349
372
2.817258
TGCTACTGGTTTGTTATGCACC
59.183
45.455
0.00
0.00
0.00
5.01
358
381
1.609208
AAGTGCCTGCTACTGGTTTG
58.391
50.000
0.00
0.00
0.00
2.93
387
410
2.507339
AACAAAAACATCAGTGGCGG
57.493
45.000
0.00
0.00
0.00
6.13
389
412
4.432712
AGTGAAACAAAAACATCAGTGGC
58.567
39.130
0.00
0.00
41.43
5.01
416
439
6.797454
TGCCACTCGTAAACTTTTACAAATT
58.203
32.000
11.45
0.00
42.34
1.82
421
444
3.811497
ACCTGCCACTCGTAAACTTTTAC
59.189
43.478
2.29
2.29
39.62
2.01
433
456
3.740832
GCAAAAATTACAACCTGCCACTC
59.259
43.478
0.00
0.00
0.00
3.51
438
461
3.638484
ACGAGCAAAAATTACAACCTGC
58.362
40.909
0.00
0.00
0.00
4.85
439
462
3.906008
CGACGAGCAAAAATTACAACCTG
59.094
43.478
0.00
0.00
0.00
4.00
440
463
4.141855
CGACGAGCAAAAATTACAACCT
57.858
40.909
0.00
0.00
0.00
3.50
459
482
1.086696
GCCACTGCTATTTTGAGCGA
58.913
50.000
0.00
0.00
45.99
4.93
461
484
2.229784
ACTTGCCACTGCTATTTTGAGC
59.770
45.455
0.00
0.00
43.16
4.26
485
562
2.409651
GCTGGCGAGGACGAGTAG
59.590
66.667
0.00
0.00
42.66
2.57
488
565
4.803426
GTGGCTGGCGAGGACGAG
62.803
72.222
0.00
0.00
42.66
4.18
489
566
3.931190
TAGTGGCTGGCGAGGACGA
62.931
63.158
0.00
0.00
42.66
4.20
490
567
2.501223
TTTAGTGGCTGGCGAGGACG
62.501
60.000
0.00
0.00
42.93
4.79
500
577
1.075374
TGTGGGCTCAATTTAGTGGCT
59.925
47.619
0.00
0.00
0.00
4.75
519
596
6.973474
CACTACTCGGAAAAGACTTATAGGTG
59.027
42.308
0.00
0.00
0.00
4.00
520
597
6.888632
TCACTACTCGGAAAAGACTTATAGGT
59.111
38.462
0.00
0.00
0.00
3.08
521
598
7.194962
GTCACTACTCGGAAAAGACTTATAGG
58.805
42.308
0.00
0.00
0.00
2.57
535
999
0.964358
AAGACCCCGTCACTACTCGG
60.964
60.000
0.00
0.00
45.42
4.63
537
1001
1.672145
GCAAAGACCCCGTCACTACTC
60.672
57.143
0.00
0.00
34.60
2.59
575
1039
5.560760
CGACATGCAAGTGAAAAGTACATGT
60.561
40.000
2.69
2.69
46.67
3.21
577
1041
4.083324
CCGACATGCAAGTGAAAAGTACAT
60.083
41.667
0.00
0.00
0.00
2.29
578
1042
3.249799
CCGACATGCAAGTGAAAAGTACA
59.750
43.478
0.00
0.00
0.00
2.90
596
1060
4.322804
CGACAAAGACAGTACATTACCGAC
59.677
45.833
0.00
0.00
0.00
4.79
617
1081
1.375908
GGCAAGACATGGAGCACGA
60.376
57.895
0.00
0.00
0.00
4.35
668
1132
1.279271
AGAGCTAAATCACCGGCTGTT
59.721
47.619
0.00
0.00
35.01
3.16
670
1134
1.576356
GAGAGCTAAATCACCGGCTG
58.424
55.000
0.00
0.00
35.01
4.85
731
1195
2.287103
GGTTCGTCTTTGTCCTCAACAC
59.713
50.000
0.00
0.00
37.70
3.32
746
1210
1.665599
CCAACGGTTAGCGGTTCGT
60.666
57.895
9.04
0.00
36.25
3.85
757
1221
1.877443
CGACCTTTCAAATCCAACGGT
59.123
47.619
0.00
0.00
0.00
4.83
790
1255
8.458843
CACCTATTTATCAGTTGTCCGATTTTT
58.541
33.333
0.00
0.00
0.00
1.94
797
1265
3.883489
GGCCACCTATTTATCAGTTGTCC
59.117
47.826
0.00
0.00
0.00
4.02
864
4453
6.513393
GCATTGCTAGTACAGTTGAACAAGTT
60.513
38.462
0.16
0.00
0.00
2.66
899
4490
2.113860
ATATATGGGCGATGGTGCAC
57.886
50.000
8.80
8.80
39.27
4.57
910
4501
3.432186
CCGCCTGGATGTGTATATATGGG
60.432
52.174
0.00
0.00
37.49
4.00
990
4587
2.476320
GCGGGCCATCTTGCTTCTC
61.476
63.158
4.39
0.00
0.00
2.87
1272
4875
1.273455
GGTGGTCGTCGTCAAACTCG
61.273
60.000
0.00
0.00
0.00
4.18
1344
4947
0.988832
TGGTAGGGGTAGCAAACAGG
59.011
55.000
0.00
0.00
0.00
4.00
1348
4951
3.651904
TGTTTAGTGGTAGGGGTAGCAAA
59.348
43.478
0.00
0.00
0.00
3.68
1370
4982
4.171005
CAGAAGCGAAATTCAACATGCAT
58.829
39.130
0.00
0.00
0.00
3.96
1371
4983
3.567530
CAGAAGCGAAATTCAACATGCA
58.432
40.909
0.00
0.00
0.00
3.96
1372
4984
2.919229
CCAGAAGCGAAATTCAACATGC
59.081
45.455
0.00
0.00
0.00
4.06
1373
4985
4.083110
ACTCCAGAAGCGAAATTCAACATG
60.083
41.667
0.00
0.00
0.00
3.21
1375
4987
3.250762
CACTCCAGAAGCGAAATTCAACA
59.749
43.478
0.00
0.00
0.00
3.33
1376
4988
3.814945
CACTCCAGAAGCGAAATTCAAC
58.185
45.455
0.00
0.00
0.00
3.18
1443
5056
2.366480
TTTCGTTCGGCTTGGACGGA
62.366
55.000
9.83
0.00
37.39
4.69
1506
5119
0.748450
CGGGTTAATCTACCTCGGCA
59.252
55.000
0.00
0.00
38.30
5.69
1522
5135
3.673956
TAATGCAGTGCCGGTCGGG
62.674
63.158
13.72
2.06
39.58
5.14
1553
5166
5.362430
ACAATCACAAGGGTTAACACAACAT
59.638
36.000
11.16
0.00
0.00
2.71
1695
5308
4.888239
AGCCGAGCTACTAAATAAGACAGA
59.112
41.667
0.00
0.00
36.99
3.41
1711
5324
2.360801
ACTAATCTCTCTTGAGCCGAGC
59.639
50.000
0.00
0.00
40.03
5.03
1735
5348
4.826274
AGCCAGAATTACTGCTAGAACA
57.174
40.909
0.00
0.00
44.52
3.18
1831
5449
7.496346
TTAGATTGTAGAAGGAACAGGTGAT
57.504
36.000
0.00
0.00
0.00
3.06
1888
5507
2.707039
CGGGTTTTCCATAGCGCG
59.293
61.111
0.00
0.00
42.91
6.86
1994
5614
5.212745
TGAACCTAAACCATGTTTCCCTTT
58.787
37.500
0.00
0.00
0.00
3.11
1995
5615
4.810345
TGAACCTAAACCATGTTTCCCTT
58.190
39.130
0.00
0.00
0.00
3.95
1996
5616
4.463050
TGAACCTAAACCATGTTTCCCT
57.537
40.909
0.00
0.00
0.00
4.20
2066
5686
4.698780
ACAGCCCGTAAAATTCTTTACTCC
59.301
41.667
6.28
0.00
43.20
3.85
2117
5900
5.512753
AGTGTGTGTTGAATGCATGTAAA
57.487
34.783
0.00
0.00
0.00
2.01
2118
5901
5.512753
AAGTGTGTGTTGAATGCATGTAA
57.487
34.783
0.00
0.00
0.00
2.41
2144
5927
3.321111
TGTCTCAAGAGAAGTACCACCAC
59.679
47.826
0.57
0.00
39.48
4.16
2168
5954
0.328258
ACTCTTTGGGCGTGCCTTAT
59.672
50.000
11.25
0.00
36.10
1.73
2170
5956
1.152756
AACTCTTTGGGCGTGCCTT
60.153
52.632
11.25
0.00
36.10
4.35
2506
6307
2.985896
GCATGAGGCTTTGTACCTACA
58.014
47.619
0.00
0.00
37.77
2.74
2543
6344
2.618709
GGGGAATCGATGTAAAAGGCTG
59.381
50.000
0.00
0.00
0.00
4.85
2555
6356
2.546899
TCTCTCTTTTGGGGGAATCGA
58.453
47.619
0.00
0.00
0.00
3.59
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.