Multiple sequence alignment - TraesCS5D01G238300
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
TraesCS5D01G238300
chr5D
100.000
2985
0
0
1
2985
346635778
346638762
0.000000e+00
5513.0
1
TraesCS5D01G238300
chr5D
73.469
343
65
16
27
351
447202761
447202427
4.070000e-19
106.0
2
TraesCS5D01G238300
chr5B
90.998
1744
111
26
1
1720
404192187
404190466
0.000000e+00
2309.0
3
TraesCS5D01G238300
chr5B
90.701
1226
71
12
1795
2985
404190451
404189234
0.000000e+00
1592.0
4
TraesCS5D01G238300
chr5A
94.544
1173
46
11
559
1725
444945616
444944456
0.000000e+00
1796.0
5
TraesCS5D01G238300
chr5A
88.860
763
48
15
2256
2985
444944055
444943297
0.000000e+00
904.0
6
TraesCS5D01G238300
chr5A
95.833
456
13
3
1795
2249
444944440
444943990
0.000000e+00
732.0
7
TraesCS5D01G238300
chr3A
96.970
33
0
1
360
391
732615270
732615302
1.000000e-03
54.7
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
TraesCS5D01G238300
chr5D
346635778
346638762
2984
False
5513.0
5513
100.0000
1
2985
1
chr5D.!!$F1
2984
1
TraesCS5D01G238300
chr5B
404189234
404192187
2953
True
1950.5
2309
90.8495
1
2985
2
chr5B.!!$R1
2984
2
TraesCS5D01G238300
chr5A
444943297
444945616
2319
True
1144.0
1796
93.0790
559
2985
3
chr5A.!!$R1
2426
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
488
491
0.027194
CATCACCTTGCATCGCTTCG
59.973
55.0
0.00
0.00
0.00
3.79
F
1228
1244
0.248907
ATGCGCTTCATGCAAGATGC
60.249
50.0
17.14
17.14
46.87
3.91
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1773
1795
0.114560
AACCGAGGGTCCAGAAGAGA
59.885
55.000
0.0
0.0
33.12
3.10
R
2926
2984
1.818674
CACTGGTAAATCCTGTTGGCC
59.181
52.381
0.0
0.0
44.20
5.36
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
40
41
1.602327
GAGAACCCTAGCCCGTCGTT
61.602
60.000
0.00
0.00
0.00
3.85
50
51
2.581409
CCGTCGTTTCGGGATCGG
60.581
66.667
8.13
0.00
45.88
4.18
54
55
3.192922
CGTTTCGGGATCGGTGGC
61.193
66.667
0.00
0.00
36.95
5.01
55
56
2.046700
GTTTCGGGATCGGTGGCA
60.047
61.111
0.00
0.00
36.95
4.92
94
95
3.344703
CCTCTTGGGTGCATTGTCA
57.655
52.632
0.00
0.00
0.00
3.58
123
124
3.068165
TCAGGTATCATCTGGTTACAGCG
59.932
47.826
0.00
0.00
44.54
5.18
157
158
0.540133
TGCTTGCTTTGATCCTGGCA
60.540
50.000
0.00
0.00
0.00
4.92
183
184
1.880027
CTTCTTCGGTTTTGGGTGGAG
59.120
52.381
0.00
0.00
0.00
3.86
190
191
1.893137
GGTTTTGGGTGGAGTGGATTC
59.107
52.381
0.00
0.00
0.00
2.52
197
198
1.156736
GTGGAGTGGATTCGTTGGTG
58.843
55.000
0.00
0.00
0.00
4.17
199
200
1.142060
TGGAGTGGATTCGTTGGTGTT
59.858
47.619
0.00
0.00
0.00
3.32
212
213
4.748102
TCGTTGGTGTTCTCTCATTTACAC
59.252
41.667
0.00
0.00
40.01
2.90
231
234
0.029567
CGTATCCTCGCAGTCAGTCC
59.970
60.000
0.00
0.00
0.00
3.85
247
250
0.945813
GTCCTCGGTCCTCACTATCG
59.054
60.000
0.00
0.00
0.00
2.92
248
251
0.818445
TCCTCGGTCCTCACTATCGC
60.818
60.000
0.00
0.00
0.00
4.58
249
252
1.101635
CCTCGGTCCTCACTATCGCA
61.102
60.000
0.00
0.00
0.00
5.10
255
258
1.123077
TCCTCACTATCGCATTGGCT
58.877
50.000
0.00
0.00
38.10
4.75
262
265
0.678950
TATCGCATTGGCTGGATCGA
59.321
50.000
0.00
0.00
38.10
3.59
270
273
0.036388
TGGCTGGATCGAAACTCCAC
60.036
55.000
2.00
0.97
37.87
4.02
272
275
0.108804
GCTGGATCGAAACTCCACGA
60.109
55.000
2.00
0.00
37.87
4.35
303
306
2.052157
GAGGACATGCGCTTACGATAC
58.948
52.381
9.73
0.00
43.93
2.24
308
311
1.526887
CATGCGCTTACGATACCTTGG
59.473
52.381
9.73
0.00
43.93
3.61
318
321
1.337447
CGATACCTTGGTGTGTTCGGT
60.337
52.381
2.03
0.00
0.00
4.69
320
323
0.533308
TACCTTGGTGTGTTCGGTGC
60.533
55.000
2.03
0.00
0.00
5.01
321
324
1.821759
CCTTGGTGTGTTCGGTGCA
60.822
57.895
0.00
0.00
0.00
4.57
330
333
2.047655
TTCGGTGCATCGGTGTCC
60.048
61.111
21.08
0.00
0.00
4.02
331
334
3.599285
TTCGGTGCATCGGTGTCCC
62.599
63.158
21.08
0.00
0.00
4.46
347
350
2.125269
CCGTGGTTTCCCTAGGCG
60.125
66.667
2.05
0.00
0.00
5.52
362
365
2.354188
GCGGTGCCGTTTTGGTTC
60.354
61.111
12.46
0.00
41.21
3.62
396
399
1.359848
CCTCATGTTAGTGTGGCGAC
58.640
55.000
0.00
0.00
0.00
5.19
397
400
0.992072
CTCATGTTAGTGTGGCGACG
59.008
55.000
0.00
0.00
0.00
5.12
412
415
4.547406
GGCGACGCCTATTTTCTTATTT
57.453
40.909
31.30
0.00
46.69
1.40
417
420
5.235616
CGACGCCTATTTTCTTATTTGGCTA
59.764
40.000
0.00
0.00
37.01
3.93
418
421
6.564125
CGACGCCTATTTTCTTATTTGGCTAG
60.564
42.308
0.00
0.00
37.01
3.42
419
422
5.008712
ACGCCTATTTTCTTATTTGGCTAGC
59.991
40.000
6.04
6.04
37.01
3.42
420
423
5.239525
CGCCTATTTTCTTATTTGGCTAGCT
59.760
40.000
15.72
0.00
37.01
3.32
421
424
6.442112
GCCTATTTTCTTATTTGGCTAGCTG
58.558
40.000
15.72
0.00
36.32
4.24
422
425
6.442112
CCTATTTTCTTATTTGGCTAGCTGC
58.558
40.000
15.72
0.00
41.94
5.25
423
426
4.355543
TTTTCTTATTTGGCTAGCTGCG
57.644
40.909
15.72
0.00
44.05
5.18
429
432
2.404566
TTTGGCTAGCTGCGGGTTGA
62.405
55.000
15.72
0.00
44.05
3.18
467
470
2.110011
ACTGGCTTGTATGGGGTTCTTT
59.890
45.455
0.00
0.00
0.00
2.52
479
482
1.546029
GGGTTCTTTCCATCACCTTGC
59.454
52.381
0.00
0.00
0.00
4.01
484
487
0.810648
TTTCCATCACCTTGCATCGC
59.189
50.000
0.00
0.00
0.00
4.58
488
491
0.027194
CATCACCTTGCATCGCTTCG
59.973
55.000
0.00
0.00
0.00
3.79
489
492
1.091771
ATCACCTTGCATCGCTTCGG
61.092
55.000
0.00
0.00
0.00
4.30
498
501
2.677003
ATCGCTTCGGCCGTTTGTG
61.677
57.895
27.15
21.08
37.76
3.33
510
513
2.416162
GCCGTTTGTGTTTTGTTCAGGA
60.416
45.455
0.00
0.00
0.00
3.86
511
514
3.839293
CCGTTTGTGTTTTGTTCAGGAA
58.161
40.909
0.00
0.00
0.00
3.36
513
516
3.610677
CGTTTGTGTTTTGTTCAGGAACC
59.389
43.478
9.49
0.00
40.46
3.62
514
517
4.561105
GTTTGTGTTTTGTTCAGGAACCA
58.439
39.130
9.49
0.00
40.46
3.67
523
532
5.560722
TTGTTCAGGAACCAGTCTCATAA
57.439
39.130
9.49
0.00
40.46
1.90
607
617
1.106944
AAGCAAACAGACCAACCCGG
61.107
55.000
0.00
0.00
42.50
5.73
645
655
2.793278
TGTACATCATGTCGGATCGG
57.207
50.000
0.00
0.00
0.00
4.18
786
796
2.520120
TGGTCCATCTATCCAGTCTCCT
59.480
50.000
0.00
0.00
0.00
3.69
941
951
1.754745
GAGAGGCAGAACCACCACA
59.245
57.895
0.00
0.00
43.14
4.17
942
952
0.603975
GAGAGGCAGAACCACCACAC
60.604
60.000
0.00
0.00
43.14
3.82
995
1007
0.814410
CGCCGTACCTGCTCTCTAGA
60.814
60.000
0.00
0.00
0.00
2.43
1213
1229
6.414694
GGAACATAACAATAACACATGATGCG
59.585
38.462
0.00
0.00
0.00
4.73
1215
1231
5.066375
ACATAACAATAACACATGATGCGCT
59.934
36.000
9.73
0.00
0.00
5.92
1219
1235
4.096833
ACAATAACACATGATGCGCTTCAT
59.903
37.500
27.68
27.68
36.79
2.57
1223
1239
3.633573
CATGATGCGCTTCATGCAA
57.366
47.368
37.60
15.81
46.87
4.08
1224
1240
1.477105
CATGATGCGCTTCATGCAAG
58.523
50.000
37.60
23.11
46.87
4.01
1227
1243
1.064952
TGATGCGCTTCATGCAAGATG
59.935
47.619
20.86
0.00
46.87
2.90
1228
1244
0.248907
ATGCGCTTCATGCAAGATGC
60.249
50.000
17.14
17.14
46.87
3.91
1238
1254
1.723273
GCAAGATGCAGCGCACATA
59.277
52.632
11.47
0.00
43.04
2.29
1239
1255
0.590732
GCAAGATGCAGCGCACATAC
60.591
55.000
11.47
7.37
43.04
2.39
1240
1256
1.012086
CAAGATGCAGCGCACATACT
58.988
50.000
11.47
9.45
43.04
2.12
1270
1286
6.767902
TGCTAATACTCTTTGTTGGATGGATC
59.232
38.462
0.00
0.00
0.00
3.36
1295
1317
1.603455
CTTGGCGGGTGACAATGGT
60.603
57.895
0.00
0.00
43.73
3.55
1430
1452
4.785453
CTGACCAAGGCGGGGCTC
62.785
72.222
5.68
0.72
40.22
4.70
1493
1515
4.154347
GCCTCCTCCTCCACGCTG
62.154
72.222
0.00
0.00
0.00
5.18
1526
1548
3.444388
AGTTCATCCTCTTCCACTACGTC
59.556
47.826
0.00
0.00
0.00
4.34
1707
1729
2.385803
CCAACGGTACCTCCATAGTCT
58.614
52.381
10.90
0.00
35.57
3.24
1708
1730
2.361438
CCAACGGTACCTCCATAGTCTC
59.639
54.545
10.90
0.00
35.57
3.36
1711
1733
2.778850
ACGGTACCTCCATAGTCTCTCT
59.221
50.000
10.90
0.00
35.57
3.10
1713
1735
3.816523
CGGTACCTCCATAGTCTCTCTTC
59.183
52.174
10.90
0.00
35.57
2.87
1714
1736
4.445162
CGGTACCTCCATAGTCTCTCTTCT
60.445
50.000
10.90
0.00
35.57
2.85
1718
1740
5.837829
ACCTCCATAGTCTCTCTTCTTCTT
58.162
41.667
0.00
0.00
0.00
2.52
1722
1744
7.201821
CCTCCATAGTCTCTCTTCTTCTTCTTC
60.202
44.444
0.00
0.00
0.00
2.87
1723
1745
7.410174
TCCATAGTCTCTCTTCTTCTTCTTCT
58.590
38.462
0.00
0.00
0.00
2.85
1726
1748
9.927668
CATAGTCTCTCTTCTTCTTCTTCTTTT
57.072
33.333
0.00
0.00
0.00
2.27
1748
1770
6.639632
TTTTCAAATATCCAGCTAGATGGC
57.360
37.500
22.56
0.00
40.41
4.40
1749
1771
5.573380
TTCAAATATCCAGCTAGATGGCT
57.427
39.130
22.56
15.57
44.10
4.75
1759
1781
3.415457
GCTAGATGGCTGGCTTCTATT
57.585
47.619
21.63
5.29
44.39
1.73
1760
1782
3.749226
GCTAGATGGCTGGCTTCTATTT
58.251
45.455
21.63
4.99
44.39
1.40
1761
1783
3.750652
GCTAGATGGCTGGCTTCTATTTC
59.249
47.826
21.63
13.01
44.39
2.17
1762
1784
3.939740
AGATGGCTGGCTTCTATTTCA
57.060
42.857
16.42
0.00
0.00
2.69
1763
1785
4.450305
AGATGGCTGGCTTCTATTTCAT
57.550
40.909
16.42
0.00
0.00
2.57
1764
1786
4.142790
AGATGGCTGGCTTCTATTTCATG
58.857
43.478
16.42
0.00
0.00
3.07
1765
1787
3.650281
TGGCTGGCTTCTATTTCATGA
57.350
42.857
2.00
0.00
0.00
3.07
1766
1788
4.174704
TGGCTGGCTTCTATTTCATGAT
57.825
40.909
0.00
0.00
0.00
2.45
1767
1789
4.139786
TGGCTGGCTTCTATTTCATGATC
58.860
43.478
0.00
0.00
0.00
2.92
1768
1790
3.505293
GGCTGGCTTCTATTTCATGATCC
59.495
47.826
0.00
0.00
0.00
3.36
1769
1791
4.139786
GCTGGCTTCTATTTCATGATCCA
58.860
43.478
0.00
0.00
0.00
3.41
1770
1792
4.765856
GCTGGCTTCTATTTCATGATCCAT
59.234
41.667
0.00
0.00
0.00
3.41
1771
1793
5.106237
GCTGGCTTCTATTTCATGATCCATC
60.106
44.000
0.00
0.00
0.00
3.51
1772
1794
4.999311
TGGCTTCTATTTCATGATCCATCG
59.001
41.667
0.00
0.00
0.00
3.84
1773
1795
4.999950
GGCTTCTATTTCATGATCCATCGT
59.000
41.667
0.00
0.00
0.00
3.73
1774
1796
5.121454
GGCTTCTATTTCATGATCCATCGTC
59.879
44.000
0.00
0.00
0.00
4.20
1775
1797
5.931146
GCTTCTATTTCATGATCCATCGTCT
59.069
40.000
0.00
0.00
0.00
4.18
1776
1798
6.090628
GCTTCTATTTCATGATCCATCGTCTC
59.909
42.308
0.00
0.00
0.00
3.36
1777
1799
6.907853
TCTATTTCATGATCCATCGTCTCT
57.092
37.500
0.00
0.00
0.00
3.10
1778
1800
7.295322
TCTATTTCATGATCCATCGTCTCTT
57.705
36.000
0.00
0.00
0.00
2.85
1779
1801
7.374272
TCTATTTCATGATCCATCGTCTCTTC
58.626
38.462
0.00
0.00
0.00
2.87
1780
1802
5.604758
TTTCATGATCCATCGTCTCTTCT
57.395
39.130
0.00
0.00
0.00
2.85
1781
1803
4.581077
TCATGATCCATCGTCTCTTCTG
57.419
45.455
0.00
0.00
0.00
3.02
1782
1804
3.320256
TCATGATCCATCGTCTCTTCTGG
59.680
47.826
0.00
0.00
0.00
3.86
1783
1805
3.018423
TGATCCATCGTCTCTTCTGGA
57.982
47.619
0.00
0.00
41.76
3.86
1784
1806
2.690497
TGATCCATCGTCTCTTCTGGAC
59.310
50.000
0.00
0.00
40.43
4.02
1785
1807
1.475403
TCCATCGTCTCTTCTGGACC
58.525
55.000
0.00
0.00
32.92
4.46
1786
1808
0.461961
CCATCGTCTCTTCTGGACCC
59.538
60.000
0.00
0.00
0.00
4.46
1787
1809
1.479709
CATCGTCTCTTCTGGACCCT
58.520
55.000
0.00
0.00
0.00
4.34
1788
1810
1.407258
CATCGTCTCTTCTGGACCCTC
59.593
57.143
0.00
0.00
0.00
4.30
1789
1811
0.677098
TCGTCTCTTCTGGACCCTCG
60.677
60.000
0.00
0.00
0.00
4.63
1790
1812
1.658686
CGTCTCTTCTGGACCCTCGG
61.659
65.000
0.00
0.00
0.00
4.63
1793
1815
0.533032
CTCTTCTGGACCCTCGGTTC
59.467
60.000
0.00
0.00
35.25
3.62
1817
1839
2.754946
TCGGACGGCTCTTGTTAATT
57.245
45.000
0.00
0.00
0.00
1.40
1825
1847
6.096673
ACGGCTCTTGTTAATTTTTGGATT
57.903
33.333
0.00
0.00
0.00
3.01
1981
2003
2.503061
CAGACCATCTCCGGCCAG
59.497
66.667
2.24
0.00
0.00
4.85
2043
2065
6.209788
GTGGTCTGAATTGTTATTTTGGGGTA
59.790
38.462
0.00
0.00
0.00
3.69
2240
2263
9.302345
CTAGTTTGAAGCATTAGTCTCGAATTA
57.698
33.333
0.00
0.00
0.00
1.40
2271
2294
9.011095
TGATATCACCCGTGTTATTTTAAACAA
57.989
29.630
0.00
0.00
40.85
2.83
2298
2321
7.910683
GGCAAAATATAGTTTGAAGCACTAGTC
59.089
37.037
25.42
6.87
40.29
2.59
2304
2327
5.234466
AGTTTGAAGCACTAGTCCTGAAT
57.766
39.130
0.00
0.00
0.00
2.57
2319
2342
6.219473
AGTCCTGAATTCGATGTGATGATAC
58.781
40.000
0.04
0.00
0.00
2.24
2377
2403
1.737029
GCTCGCAGATGTAGAACAGCA
60.737
52.381
0.00
0.00
36.88
4.41
2401
2432
7.922811
GCAGAATCAAAGAAGAAGAAAAAGGAA
59.077
33.333
0.00
0.00
0.00
3.36
2411
2442
9.454859
AGAAGAAGAAAAAGGAACCAGTATATG
57.545
33.333
0.00
0.00
0.00
1.78
2424
2455
7.868415
GGAACCAGTATATGAAGTCACAGATAC
59.132
40.741
0.00
0.00
41.98
2.24
2437
2468
4.627467
GTCACAGATACACAACATCAGTCC
59.373
45.833
0.00
0.00
0.00
3.85
2449
2480
5.833131
ACAACATCAGTCCCAAAACTACAAT
59.167
36.000
0.00
0.00
0.00
2.71
2455
2486
5.591067
TCAGTCCCAAAACTACAATTTCGTT
59.409
36.000
0.00
0.00
0.00
3.85
2470
2501
4.837896
TTTCGTTGTATGGAATGTGCAA
57.162
36.364
0.00
0.00
0.00
4.08
2552
2584
3.760580
AAGATCCTATTGGAAGAGGCG
57.239
47.619
0.00
0.00
46.80
5.52
2619
2653
8.271458
TCCACATGAGTTTATCCTAATTAGCAA
58.729
33.333
6.99
0.00
0.00
3.91
2621
2655
8.892723
CACATGAGTTTATCCTAATTAGCAACA
58.107
33.333
6.99
0.00
0.00
3.33
2622
2656
9.461312
ACATGAGTTTATCCTAATTAGCAACAA
57.539
29.630
6.99
0.00
0.00
2.83
2624
2658
7.970384
TGAGTTTATCCTAATTAGCAACAACG
58.030
34.615
6.99
0.00
0.00
4.10
2696
2754
6.998112
TGGGGCAGGATAAGTATAGATAGAT
58.002
40.000
0.00
0.00
0.00
1.98
2819
2877
1.273048
TGGCCAAGCAATGTCATGTTC
59.727
47.619
0.61
0.00
0.00
3.18
2874
2932
2.243478
TGGGCCAGCTAAATCAACCATA
59.757
45.455
0.00
0.00
0.00
2.74
2882
2940
7.229506
GCCAGCTAAATCAACCATAATCTAGTT
59.770
37.037
0.00
0.00
0.00
2.24
2926
2984
2.414058
ATCTCGCGAATACAGCAGAG
57.586
50.000
11.33
0.00
36.95
3.35
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
40
41
3.000819
ACTGCCACCGATCCCGAA
61.001
61.111
0.00
0.00
38.22
4.30
65
66
2.677971
CCAAGAGGGTAATGACGCG
58.322
57.895
3.53
3.53
43.15
6.01
90
91
3.184382
TGATACCTGAGTTCCCTGACA
57.816
47.619
0.00
0.00
0.00
3.58
94
95
3.310954
ACCAGATGATACCTGAGTTCCCT
60.311
47.826
0.00
0.00
33.65
4.20
157
158
2.558359
CCCAAAACCGAAGAAGCTTCAT
59.442
45.455
27.57
17.00
0.00
2.57
183
184
2.737252
GAGAGAACACCAACGAATCCAC
59.263
50.000
0.00
0.00
0.00
4.02
190
191
4.376008
CGTGTAAATGAGAGAACACCAACG
60.376
45.833
0.00
0.00
39.20
4.10
197
198
5.681982
CGAGGATACGTGTAAATGAGAGAAC
59.318
44.000
0.00
0.00
46.39
3.01
199
200
4.261072
GCGAGGATACGTGTAAATGAGAGA
60.261
45.833
0.00
0.00
46.39
3.10
212
213
0.029567
GGACTGACTGCGAGGATACG
59.970
60.000
0.00
0.00
46.39
3.06
231
234
0.955178
ATGCGATAGTGAGGACCGAG
59.045
55.000
0.00
0.00
39.35
4.63
247
250
1.064654
GAGTTTCGATCCAGCCAATGC
59.935
52.381
0.00
0.00
37.95
3.56
248
251
1.672881
GGAGTTTCGATCCAGCCAATG
59.327
52.381
0.00
0.00
36.79
2.82
249
252
1.281867
TGGAGTTTCGATCCAGCCAAT
59.718
47.619
2.00
0.00
41.96
3.16
270
273
2.592001
TCCTCTCGCTCCGGATCG
60.592
66.667
21.30
21.30
0.00
3.69
272
275
1.152652
ATGTCCTCTCGCTCCGGAT
60.153
57.895
3.57
0.00
0.00
4.18
303
306
1.172180
ATGCACCGAACACACCAAGG
61.172
55.000
0.00
0.00
0.00
3.61
308
311
1.959226
ACCGATGCACCGAACACAC
60.959
57.895
0.00
0.00
0.00
3.82
347
350
2.333581
CCGAACCAAAACGGCACC
59.666
61.111
0.00
0.00
42.55
5.01
352
355
3.248266
CCTAGACTACCGAACCAAAACG
58.752
50.000
0.00
0.00
0.00
3.60
362
365
0.463295
TGAGGCGACCTAGACTACCG
60.463
60.000
0.00
0.00
31.76
4.02
396
399
5.239525
AGCTAGCCAAATAAGAAAATAGGCG
59.760
40.000
12.13
0.00
44.97
5.52
397
400
6.442112
CAGCTAGCCAAATAAGAAAATAGGC
58.558
40.000
12.13
0.00
40.85
3.93
409
412
1.000896
AACCCGCAGCTAGCCAAAT
60.001
52.632
12.13
0.00
41.38
2.32
412
415
2.669133
ATCAACCCGCAGCTAGCCA
61.669
57.895
12.13
0.00
41.38
4.75
419
422
3.499737
GACGCCATCAACCCGCAG
61.500
66.667
0.00
0.00
0.00
5.18
421
424
4.778143
AGGACGCCATCAACCCGC
62.778
66.667
0.00
0.00
0.00
6.13
422
425
2.511600
GAGGACGCCATCAACCCG
60.512
66.667
0.00
0.00
0.00
5.28
423
426
2.511600
CGAGGACGCCATCAACCC
60.512
66.667
0.00
0.00
0.00
4.11
444
447
1.004277
GAACCCCATACAAGCCAGTCA
59.996
52.381
0.00
0.00
0.00
3.41
467
470
0.035152
AAGCGATGCAAGGTGATGGA
60.035
50.000
0.00
0.00
0.00
3.41
479
482
2.098298
CAAACGGCCGAAGCGATG
59.902
61.111
35.90
16.26
41.24
3.84
484
487
1.196200
CAAAACACAAACGGCCGAAG
58.804
50.000
35.90
22.51
0.00
3.79
488
491
1.923864
CTGAACAAAACACAAACGGCC
59.076
47.619
0.00
0.00
0.00
6.13
489
492
1.923864
CCTGAACAAAACACAAACGGC
59.076
47.619
0.00
0.00
0.00
5.68
498
501
3.945285
TGAGACTGGTTCCTGAACAAAAC
59.055
43.478
11.78
1.60
42.85
2.43
556
565
0.107831
TCTTCCACACGAAACAGGGG
59.892
55.000
0.00
0.00
0.00
4.79
831
841
3.203442
TCCAGATGGACGGCGTAC
58.797
61.111
17.03
17.03
39.78
3.67
921
931
1.152030
TGGTGGTTCTGCCTCTCCT
60.152
57.895
0.00
0.00
38.35
3.69
941
951
2.335369
GAGAGTGCGTCGGTGTGT
59.665
61.111
0.00
0.00
0.00
3.72
942
952
2.016704
GTGAGAGTGCGTCGGTGTG
61.017
63.158
0.00
0.00
0.00
3.82
984
996
3.376859
ACGACATCTTGTCTAGAGAGCAG
59.623
47.826
0.00
0.00
44.85
4.24
995
1007
2.864097
GCACTGACTGACGACATCTTGT
60.864
50.000
0.00
0.00
0.00
3.16
1220
1236
0.590732
GTATGTGCGCTGCATCTTGC
60.591
55.000
18.37
0.00
41.91
4.01
1221
1237
1.012086
AGTATGTGCGCTGCATCTTG
58.988
50.000
18.37
0.00
41.91
3.02
1222
1238
1.399440
CAAGTATGTGCGCTGCATCTT
59.601
47.619
18.37
16.97
41.91
2.40
1223
1239
1.012086
CAAGTATGTGCGCTGCATCT
58.988
50.000
18.37
13.32
41.91
2.90
1224
1240
0.729116
ACAAGTATGTGCGCTGCATC
59.271
50.000
18.37
11.76
41.91
3.91
1227
1243
1.595489
GCATACAAGTATGTGCGCTGC
60.595
52.381
18.44
0.76
43.57
5.25
1228
1244
1.935873
AGCATACAAGTATGTGCGCTG
59.064
47.619
18.44
0.00
42.96
5.18
1229
1245
2.315925
AGCATACAAGTATGTGCGCT
57.684
45.000
18.44
8.88
43.57
5.92
1230
1246
4.732285
ATTAGCATACAAGTATGTGCGC
57.268
40.909
18.44
0.00
43.57
6.09
1231
1247
6.863645
AGAGTATTAGCATACAAGTATGTGCG
59.136
38.462
18.44
0.00
43.57
5.34
1232
1248
8.594881
AAGAGTATTAGCATACAAGTATGTGC
57.405
34.615
18.44
9.27
43.57
4.57
1238
1254
8.100791
TCCAACAAAGAGTATTAGCATACAAGT
58.899
33.333
0.00
0.00
38.24
3.16
1239
1255
8.492673
TCCAACAAAGAGTATTAGCATACAAG
57.507
34.615
0.00
0.00
38.24
3.16
1240
1256
8.892723
CATCCAACAAAGAGTATTAGCATACAA
58.107
33.333
0.00
0.00
38.24
2.41
1270
1286
3.726517
CACCCGCCAAGCTGAACG
61.727
66.667
0.00
0.00
0.00
3.95
1726
1748
5.945310
AGCCATCTAGCTGGATATTTGAAA
58.055
37.500
16.90
0.00
42.95
2.69
1727
1749
5.573380
AGCCATCTAGCTGGATATTTGAA
57.427
39.130
16.90
0.00
42.95
2.69
1738
1760
2.094100
TAGAAGCCAGCCATCTAGCT
57.906
50.000
0.00
0.00
46.45
3.32
1739
1761
3.415457
AATAGAAGCCAGCCATCTAGC
57.585
47.619
8.27
0.00
0.00
3.42
1740
1762
4.965814
TGAAATAGAAGCCAGCCATCTAG
58.034
43.478
8.27
0.00
0.00
2.43
1741
1763
5.072193
TCATGAAATAGAAGCCAGCCATCTA
59.928
40.000
0.00
5.53
0.00
1.98
1742
1764
3.939740
TGAAATAGAAGCCAGCCATCT
57.060
42.857
1.75
1.75
0.00
2.90
1743
1765
4.139786
TCATGAAATAGAAGCCAGCCATC
58.860
43.478
0.00
0.00
0.00
3.51
1744
1766
4.174704
TCATGAAATAGAAGCCAGCCAT
57.825
40.909
0.00
0.00
0.00
4.40
1745
1767
3.650281
TCATGAAATAGAAGCCAGCCA
57.350
42.857
0.00
0.00
0.00
4.75
1746
1768
3.505293
GGATCATGAAATAGAAGCCAGCC
59.495
47.826
0.00
0.00
0.00
4.85
1747
1769
4.139786
TGGATCATGAAATAGAAGCCAGC
58.860
43.478
0.00
0.00
0.00
4.85
1748
1770
5.121925
CGATGGATCATGAAATAGAAGCCAG
59.878
44.000
0.00
0.00
0.00
4.85
1749
1771
4.999311
CGATGGATCATGAAATAGAAGCCA
59.001
41.667
0.00
0.00
0.00
4.75
1750
1772
4.999950
ACGATGGATCATGAAATAGAAGCC
59.000
41.667
0.00
0.00
0.00
4.35
1751
1773
5.931146
AGACGATGGATCATGAAATAGAAGC
59.069
40.000
0.00
0.00
0.00
3.86
1752
1774
7.377398
AGAGACGATGGATCATGAAATAGAAG
58.623
38.462
0.00
0.00
0.00
2.85
1753
1775
7.295322
AGAGACGATGGATCATGAAATAGAA
57.705
36.000
0.00
0.00
0.00
2.10
1754
1776
6.907853
AGAGACGATGGATCATGAAATAGA
57.092
37.500
0.00
0.00
0.00
1.98
1755
1777
7.328982
CAGAAGAGACGATGGATCATGAAATAG
59.671
40.741
0.00
0.00
0.00
1.73
1756
1778
7.150640
CAGAAGAGACGATGGATCATGAAATA
58.849
38.462
0.00
0.00
0.00
1.40
1757
1779
5.990386
CAGAAGAGACGATGGATCATGAAAT
59.010
40.000
0.00
0.00
0.00
2.17
1758
1780
5.354767
CAGAAGAGACGATGGATCATGAAA
58.645
41.667
0.00
0.00
0.00
2.69
1759
1781
4.202192
CCAGAAGAGACGATGGATCATGAA
60.202
45.833
0.00
0.00
34.60
2.57
1760
1782
3.320256
CCAGAAGAGACGATGGATCATGA
59.680
47.826
0.00
0.00
34.60
3.07
1761
1783
3.320256
TCCAGAAGAGACGATGGATCATG
59.680
47.826
0.00
0.00
36.92
3.07
1762
1784
3.320541
GTCCAGAAGAGACGATGGATCAT
59.679
47.826
0.00
0.00
43.42
2.45
1763
1785
2.690497
GTCCAGAAGAGACGATGGATCA
59.310
50.000
0.00
0.00
43.42
2.92
1764
1786
2.035321
GGTCCAGAAGAGACGATGGATC
59.965
54.545
0.00
0.00
43.42
3.36
1765
1787
2.035632
GGTCCAGAAGAGACGATGGAT
58.964
52.381
0.00
0.00
43.42
3.41
1766
1788
1.475403
GGTCCAGAAGAGACGATGGA
58.525
55.000
0.00
0.00
39.50
3.41
1767
1789
0.461961
GGGTCCAGAAGAGACGATGG
59.538
60.000
0.00
0.00
34.97
3.51
1768
1790
1.407258
GAGGGTCCAGAAGAGACGATG
59.593
57.143
0.00
0.00
34.97
3.84
1769
1791
1.770294
GAGGGTCCAGAAGAGACGAT
58.230
55.000
0.00
0.00
34.97
3.73
1770
1792
0.677098
CGAGGGTCCAGAAGAGACGA
60.677
60.000
0.00
0.00
34.97
4.20
1771
1793
1.658686
CCGAGGGTCCAGAAGAGACG
61.659
65.000
0.00
0.00
34.97
4.18
1772
1794
0.612453
ACCGAGGGTCCAGAAGAGAC
60.612
60.000
0.00
0.00
0.00
3.36
1773
1795
0.114560
AACCGAGGGTCCAGAAGAGA
59.885
55.000
0.00
0.00
33.12
3.10
1774
1796
0.533032
GAACCGAGGGTCCAGAAGAG
59.467
60.000
0.00
0.00
33.12
2.85
1775
1797
0.903454
GGAACCGAGGGTCCAGAAGA
60.903
60.000
20.76
0.00
33.12
2.87
1776
1798
0.905337
AGGAACCGAGGGTCCAGAAG
60.905
60.000
26.49
0.00
33.12
2.85
1777
1799
0.410663
TAGGAACCGAGGGTCCAGAA
59.589
55.000
26.49
10.01
33.12
3.02
1778
1800
0.410663
TTAGGAACCGAGGGTCCAGA
59.589
55.000
26.49
12.29
33.12
3.86
1779
1801
1.413077
GATTAGGAACCGAGGGTCCAG
59.587
57.143
26.49
0.00
33.12
3.86
1780
1802
1.492764
GATTAGGAACCGAGGGTCCA
58.507
55.000
26.49
8.78
33.12
4.02
1781
1803
0.388294
CGATTAGGAACCGAGGGTCC
59.612
60.000
18.27
18.27
33.12
4.46
1782
1804
0.388294
CCGATTAGGAACCGAGGGTC
59.612
60.000
0.00
0.00
45.00
4.46
1783
1805
2.512973
CCGATTAGGAACCGAGGGT
58.487
57.895
0.00
0.00
45.00
4.34
1793
1815
0.460311
ACAAGAGCCGTCCGATTAGG
59.540
55.000
0.00
0.00
42.97
2.69
1831
1853
6.825213
CCAGTCTACCTGAATGAATGAATGAA
59.175
38.462
0.00
0.00
44.49
2.57
1832
1854
6.351711
CCAGTCTACCTGAATGAATGAATGA
58.648
40.000
0.00
0.00
44.49
2.57
1833
1855
5.008415
GCCAGTCTACCTGAATGAATGAATG
59.992
44.000
0.00
0.00
44.49
2.67
1834
1856
5.128919
GCCAGTCTACCTGAATGAATGAAT
58.871
41.667
0.00
0.00
44.49
2.57
1835
1857
4.517285
GCCAGTCTACCTGAATGAATGAA
58.483
43.478
0.00
0.00
44.49
2.57
1836
1858
3.430790
CGCCAGTCTACCTGAATGAATGA
60.431
47.826
0.00
0.00
44.49
2.57
1842
1864
1.202580
GCATCGCCAGTCTACCTGAAT
60.203
52.381
0.00
0.00
44.49
2.57
1849
1871
2.501128
GCCAGCATCGCCAGTCTA
59.499
61.111
0.00
0.00
0.00
2.59
1953
1975
1.773052
AGATGGTCTGGATGATGGTGG
59.227
52.381
0.00
0.00
0.00
4.61
2043
2065
3.646162
TCCACACTTTGTACATCCTCAGT
59.354
43.478
0.00
0.00
0.00
3.41
2271
2294
6.840780
AGTGCTTCAAACTATATTTTGCCT
57.159
33.333
9.98
0.53
36.56
4.75
2298
2321
5.299949
TGGTATCATCACATCGAATTCAGG
58.700
41.667
6.22
0.00
0.00
3.86
2304
2327
9.996554
ATTTACTATTGGTATCATCACATCGAA
57.003
29.630
0.00
0.00
0.00
3.71
2319
2342
8.514594
TGAAGTTCTGCTTTGATTTACTATTGG
58.485
33.333
4.17
0.00
37.59
3.16
2377
2403
8.417106
GGTTCCTTTTTCTTCTTCTTTGATTCT
58.583
33.333
0.00
0.00
0.00
2.40
2401
2432
7.342026
TGTGTATCTGTGACTTCATATACTGGT
59.658
37.037
0.00
0.00
0.00
4.00
2411
2442
5.928839
ACTGATGTTGTGTATCTGTGACTTC
59.071
40.000
0.00
0.00
36.01
3.01
2424
2455
4.578516
TGTAGTTTTGGGACTGATGTTGTG
59.421
41.667
0.00
0.00
0.00
3.33
2449
2480
4.036852
TGTTGCACATTCCATACAACGAAA
59.963
37.500
0.00
0.00
42.68
3.46
2455
2486
2.512705
TGCTGTTGCACATTCCATACA
58.487
42.857
0.00
0.00
45.31
2.29
2470
2501
4.284490
TGAAGGACTCTAATCTTGTGCTGT
59.716
41.667
0.00
0.00
32.89
4.40
2552
2584
5.055812
TGAATTTTGTTGAATCAGTTGGCC
58.944
37.500
0.00
0.00
0.00
5.36
2592
2626
8.439971
TGCTAATTAGGATAAACTCATGTGGAT
58.560
33.333
14.28
0.00
0.00
3.41
2593
2627
7.801104
TGCTAATTAGGATAAACTCATGTGGA
58.199
34.615
14.28
0.00
0.00
4.02
2603
2637
9.656040
TTACTCGTTGTTGCTAATTAGGATAAA
57.344
29.630
14.28
6.25
0.00
1.40
2619
2653
3.728076
TTCTGCTGAGTTACTCGTTGT
57.272
42.857
7.92
0.00
32.35
3.32
2621
2655
4.694339
AGTTTTCTGCTGAGTTACTCGTT
58.306
39.130
7.92
0.00
32.35
3.85
2622
2656
4.299978
GAGTTTTCTGCTGAGTTACTCGT
58.700
43.478
7.92
0.00
32.35
4.18
2624
2658
3.675698
CCGAGTTTTCTGCTGAGTTACTC
59.324
47.826
5.27
5.27
0.00
2.59
2696
2754
4.701663
CTGAGGAAGCCGAAGCAA
57.298
55.556
0.00
0.00
43.56
3.91
2819
2877
3.002348
GGAATTTGAAGACGATAAGGCCG
59.998
47.826
0.00
0.00
0.00
6.13
2863
2921
8.778059
TGGTCCTAACTAGATTATGGTTGATTT
58.222
33.333
0.00
0.00
34.05
2.17
2882
2940
7.808279
TTCTCCTCTTTCTTTATTGGTCCTA
57.192
36.000
0.00
0.00
0.00
2.94
2926
2984
1.818674
CACTGGTAAATCCTGTTGGCC
59.181
52.381
0.00
0.00
44.20
5.36
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.