Multiple sequence alignment - TraesCS4D01G213600
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
TraesCS4D01G213600
chr4D
100.000
3481
0
0
1
3481
366325129
366321649
0.000000e+00
6429.0
1
TraesCS4D01G213600
chr4A
95.242
1387
50
7
2105
3481
98600190
98601570
0.000000e+00
2182.0
2
TraesCS4D01G213600
chr4A
86.043
1390
85
44
668
1985
98598586
98599938
0.000000e+00
1391.0
3
TraesCS4D01G213600
chr4A
91.429
350
28
1
3134
3481
56482117
56482466
2.430000e-131
479.0
4
TraesCS4D01G213600
chr4A
98.507
67
1
0
33
99
98598217
98598283
6.100000e-23
119.0
5
TraesCS4D01G213600
chr4B
88.459
1525
69
47
526
1985
450916372
450914890
0.000000e+00
1742.0
6
TraesCS4D01G213600
chr4B
96.429
756
22
3
2117
2871
450914756
450914005
0.000000e+00
1242.0
7
TraesCS4D01G213600
chr4B
92.190
589
21
6
2902
3481
450913879
450913307
0.000000e+00
809.0
8
TraesCS4D01G213600
chr4B
87.023
524
33
14
15
505
450916877
450916356
3.030000e-155
558.0
9
TraesCS4D01G213600
chr3D
94.000
350
19
1
3134
3481
443673035
443673384
2.380000e-146
529.0
10
TraesCS4D01G213600
chr2A
89.459
370
37
1
3114
3481
578017344
578017713
1.890000e-127
466.0
11
TraesCS4D01G213600
chr2A
81.818
88
9
3
2031
2111
532043322
532043409
2.240000e-07
67.6
12
TraesCS4D01G213600
chr6B
92.683
205
14
1
3134
3337
101435522
101435318
9.450000e-76
294.0
13
TraesCS4D01G213600
chr2D
92.045
88
5
2
2027
2113
20663382
20663468
4.720000e-24
122.0
14
TraesCS4D01G213600
chr5A
83.562
73
9
3
2040
2110
448620316
448620245
8.060000e-07
65.8
15
TraesCS4D01G213600
chr3A
100.000
33
0
0
2033
2065
649820030
649820062
1.040000e-05
62.1
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
TraesCS4D01G213600
chr4D
366321649
366325129
3480
True
6429.000000
6429
100.00000
1
3481
1
chr4D.!!$R1
3480
1
TraesCS4D01G213600
chr4A
98598217
98601570
3353
False
1230.666667
2182
93.26400
33
3481
3
chr4A.!!$F2
3448
2
TraesCS4D01G213600
chr4B
450913307
450916877
3570
True
1087.750000
1742
91.02525
15
3481
4
chr4B.!!$R1
3466
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
970
1065
1.302431
CGTCACATCAACCAGGCCA
60.302
57.895
5.01
0.00
0.00
5.36
F
1206
1338
0.037975
TTACTTCCGGGAGACAACGC
60.038
55.000
19.39
0.00
0.00
4.84
F
1283
1415
0.319383
GCGATGTCAGATCTGCGGAT
60.319
55.000
18.36
8.05
34.45
4.18
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1896
2065
0.319383
CTAGCTATGCTGACGCCTGG
60.319
60.000
1.96
0.0
40.10
4.45
R
2176
2534
0.809385
CTGCATGTTCTGGAGGCTTG
59.191
55.000
0.00
0.0
39.51
4.01
R
3180
3643
1.003003
TCACTGGATTCCGTTGATGCA
59.997
47.619
0.00
0.0
0.00
3.96
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
209
219
1.340248
CGTACGCCCTCCATTCACTAT
59.660
52.381
0.52
0.00
0.00
2.12
210
220
2.223971
CGTACGCCCTCCATTCACTATT
60.224
50.000
0.52
0.00
0.00
1.73
211
221
2.332063
ACGCCCTCCATTCACTATTG
57.668
50.000
0.00
0.00
0.00
1.90
219
229
6.434028
GCCCTCCATTCACTATTGCATTATAA
59.566
38.462
0.00
0.00
0.00
0.98
285
298
8.828688
AGTAGGTTTGTACACTCATTTTAGTC
57.171
34.615
0.00
0.00
0.00
2.59
286
299
7.876582
AGTAGGTTTGTACACTCATTTTAGTCC
59.123
37.037
0.00
0.00
0.00
3.85
293
306
8.054152
TGTACACTCATTTTAGTCCGTATGTA
57.946
34.615
0.00
0.00
0.00
2.29
296
309
7.609056
ACACTCATTTTAGTCCGTATGTACTT
58.391
34.615
0.00
0.00
0.00
2.24
344
357
1.813513
ACAATGAACGGAAGGAGCAG
58.186
50.000
0.00
0.00
0.00
4.24
500
547
5.851517
CGAATACTAGTAGTCGTTGCTTG
57.148
43.478
33.34
12.81
45.15
4.01
501
548
5.330295
CGAATACTAGTAGTCGTTGCTTGT
58.670
41.667
33.34
1.98
45.15
3.16
502
549
5.227391
CGAATACTAGTAGTCGTTGCTTGTG
59.773
44.000
33.34
11.61
45.15
3.33
503
550
2.673833
ACTAGTAGTCGTTGCTTGTGC
58.326
47.619
0.00
0.00
40.20
4.57
504
551
2.296471
ACTAGTAGTCGTTGCTTGTGCT
59.704
45.455
0.00
0.00
40.48
4.40
505
552
2.240493
AGTAGTCGTTGCTTGTGCTT
57.760
45.000
0.00
0.00
40.48
3.91
506
553
2.561569
AGTAGTCGTTGCTTGTGCTTT
58.438
42.857
0.00
0.00
40.48
3.51
507
554
2.943033
AGTAGTCGTTGCTTGTGCTTTT
59.057
40.909
0.00
0.00
40.48
2.27
508
555
2.939460
AGTCGTTGCTTGTGCTTTTT
57.061
40.000
0.00
0.00
40.48
1.94
532
579
8.857694
TTTTTCTTTGAGGGATAATAGTCGTT
57.142
30.769
0.00
0.00
0.00
3.85
533
580
7.843490
TTTCTTTGAGGGATAATAGTCGTTG
57.157
36.000
0.00
0.00
0.00
4.10
534
581
5.357257
TCTTTGAGGGATAATAGTCGTTGC
58.643
41.667
0.00
0.00
0.00
4.17
535
582
5.128827
TCTTTGAGGGATAATAGTCGTTGCT
59.871
40.000
0.00
0.00
0.00
3.91
536
583
5.353394
TTGAGGGATAATAGTCGTTGCTT
57.647
39.130
0.00
0.00
0.00
3.91
562
609
2.507992
CTTCTCGCGCCAGTCAGG
60.508
66.667
0.00
0.00
41.84
3.86
698
773
2.032799
CACTCGCACAAAAGGCTGTAAA
59.967
45.455
0.00
0.00
0.00
2.01
733
808
2.610433
TCGTTAATGAGCAGAGCACTG
58.390
47.619
6.80
6.80
45.91
3.66
762
837
2.675583
CCTCACCCTCATCTCATCTCA
58.324
52.381
0.00
0.00
0.00
3.27
763
838
3.241156
CCTCACCCTCATCTCATCTCAT
58.759
50.000
0.00
0.00
0.00
2.90
764
839
3.258872
CCTCACCCTCATCTCATCTCATC
59.741
52.174
0.00
0.00
0.00
2.92
765
840
4.154176
CTCACCCTCATCTCATCTCATCT
58.846
47.826
0.00
0.00
0.00
2.90
766
841
4.151121
TCACCCTCATCTCATCTCATCTC
58.849
47.826
0.00
0.00
0.00
2.75
767
842
3.896272
CACCCTCATCTCATCTCATCTCA
59.104
47.826
0.00
0.00
0.00
3.27
768
843
3.896888
ACCCTCATCTCATCTCATCTCAC
59.103
47.826
0.00
0.00
0.00
3.51
769
844
3.258872
CCCTCATCTCATCTCATCTCACC
59.741
52.174
0.00
0.00
0.00
4.02
770
845
4.154176
CCTCATCTCATCTCATCTCACCT
58.846
47.826
0.00
0.00
0.00
4.00
771
846
4.219070
CCTCATCTCATCTCATCTCACCTC
59.781
50.000
0.00
0.00
0.00
3.85
881
956
2.429930
CCCCACGCACCTCAAGAA
59.570
61.111
0.00
0.00
0.00
2.52
970
1065
1.302431
CGTCACATCAACCAGGCCA
60.302
57.895
5.01
0.00
0.00
5.36
988
1083
2.490148
AAGATCAGATCGGCGGCGA
61.490
57.895
36.40
36.40
0.00
5.54
1162
1287
1.202952
TCCCCTCTCGCTCTCTTATCC
60.203
57.143
0.00
0.00
0.00
2.59
1174
1299
3.657727
CTCTCTTATCCCTCTCCCTCTCT
59.342
52.174
0.00
0.00
0.00
3.10
1177
1302
2.542257
TATCCCTCTCCCTCTCTCCT
57.458
55.000
0.00
0.00
0.00
3.69
1190
1322
4.404394
CCCTCTCTCCTCCTCTTCTTTTAC
59.596
50.000
0.00
0.00
0.00
2.01
1206
1338
0.037975
TTACTTCCGGGAGACAACGC
60.038
55.000
19.39
0.00
0.00
4.84
1223
1355
1.469308
ACGCGAGAAGAAGAAGATCGT
59.531
47.619
15.93
0.00
35.87
3.73
1232
1364
4.130286
AGAAGAAGATCGTTGGATGGAC
57.870
45.455
0.00
0.00
31.51
4.02
1243
1375
1.804326
GGATGGACGTCAACGGTCG
60.804
63.158
18.91
0.00
44.95
4.79
1245
1377
1.069378
GATGGACGTCAACGGTCGAC
61.069
60.000
18.91
7.13
44.95
4.20
1283
1415
0.319383
GCGATGTCAGATCTGCGGAT
60.319
55.000
18.36
8.05
34.45
4.18
1311
1443
3.197790
CACGGATCTGGCGCTTGG
61.198
66.667
7.64
0.00
0.00
3.61
1418
1559
7.148340
CCAAGAGAAATAACAATCTGTCTGGAC
60.148
40.741
0.00
0.00
0.00
4.02
1432
1573
4.713553
TGTCTGGACATCTTGTTTTGCTA
58.286
39.130
0.00
0.00
36.21
3.49
1461
1602
3.119424
AGTTTAGCAGCTACTCCTCGTTC
60.119
47.826
0.00
0.00
0.00
3.95
1536
1677
3.492102
AGCTACAACAAGAGCTTCCAA
57.508
42.857
0.00
0.00
46.99
3.53
1633
1792
2.535331
GTTTTGTTTCTTTCAGCCGCA
58.465
42.857
0.00
0.00
0.00
5.69
1700
1862
3.415457
AGCCTGCCTCTTTCTATATGC
57.585
47.619
0.00
0.00
0.00
3.14
1729
1893
2.855728
CTTTGCTGCCGTGCGATTCC
62.856
60.000
0.00
0.00
35.36
3.01
1860
2024
5.069251
ACCCTCTTGAGAAGGTAATATCACG
59.931
44.000
0.00
0.00
37.12
4.35
1893
2062
8.171840
ACCATATTTGTTTTGTTTTGTTTCGTG
58.828
29.630
0.00
0.00
0.00
4.35
1894
2063
8.383619
CCATATTTGTTTTGTTTTGTTTCGTGA
58.616
29.630
0.00
0.00
0.00
4.35
1895
2064
9.193602
CATATTTGTTTTGTTTTGTTTCGTGAC
57.806
29.630
0.00
0.00
0.00
3.67
1896
2065
5.577860
TTGTTTTGTTTTGTTTCGTGACC
57.422
34.783
0.00
0.00
0.00
4.02
1897
2066
3.988517
TGTTTTGTTTTGTTTCGTGACCC
59.011
39.130
0.00
0.00
0.00
4.46
1950
2119
7.439157
TCAGAATTCTGTCATTTCACGAAAT
57.561
32.000
29.80
0.00
44.12
2.17
1981
2150
3.100658
TCGGAATGTGAAAACTGTCGA
57.899
42.857
0.00
0.00
0.00
4.20
1982
2151
3.659786
TCGGAATGTGAAAACTGTCGAT
58.340
40.909
0.00
0.00
0.00
3.59
1984
2153
4.084066
TCGGAATGTGAAAACTGTCGATTG
60.084
41.667
0.00
0.00
0.00
2.67
1986
2155
4.023193
GGAATGTGAAAACTGTCGATTGGT
60.023
41.667
0.00
0.00
0.00
3.67
1987
2156
5.507315
GGAATGTGAAAACTGTCGATTGGTT
60.507
40.000
0.00
0.00
0.00
3.67
2006
2252
4.873827
TGGTTCGATATTTACTTGCACCTC
59.126
41.667
0.00
0.00
0.00
3.85
2009
2255
5.339008
TCGATATTTACTTGCACCTCTGT
57.661
39.130
0.00
0.00
0.00
3.41
2011
2257
7.050970
TCGATATTTACTTGCACCTCTGTAT
57.949
36.000
0.00
0.00
0.00
2.29
2013
2259
8.635328
TCGATATTTACTTGCACCTCTGTATAA
58.365
33.333
0.00
0.00
0.00
0.98
2014
2260
9.424319
CGATATTTACTTGCACCTCTGTATAAT
57.576
33.333
0.00
0.00
0.00
1.28
2018
2264
8.662781
TTTACTTGCACCTCTGTATAATGATC
57.337
34.615
0.00
0.00
0.00
2.92
2023
2269
6.749139
TGCACCTCTGTATAATGATCTGTAC
58.251
40.000
0.00
0.00
0.00
2.90
2024
2270
6.551227
TGCACCTCTGTATAATGATCTGTACT
59.449
38.462
0.00
0.00
0.00
2.73
2025
2271
6.865726
GCACCTCTGTATAATGATCTGTACTG
59.134
42.308
0.00
0.00
0.00
2.74
2026
2272
6.865726
CACCTCTGTATAATGATCTGTACTGC
59.134
42.308
0.00
0.00
0.00
4.40
2032
2285
7.652727
TGTATAATGATCTGTACTGCACTCTC
58.347
38.462
0.00
0.00
0.00
3.20
2045
2298
5.725362
ACTGCACTCTCTGTTCCTAAATAC
58.275
41.667
0.00
0.00
0.00
1.89
2050
2303
6.311690
GCACTCTCTGTTCCTAAATACAAGAC
59.688
42.308
0.00
0.00
0.00
3.01
2052
2305
6.208994
ACTCTCTGTTCCTAAATACAAGACGT
59.791
38.462
0.00
0.00
0.00
4.34
2065
2318
2.097466
ACAAGACGTTTTGGCAGTTCAG
59.903
45.455
21.34
0.00
32.32
3.02
2069
2322
3.942748
AGACGTTTTGGCAGTTCAGTTTA
59.057
39.130
0.00
0.00
0.00
2.01
2131
2489
1.200020
CTTTTAGGCAGCCAACTTCCG
59.800
52.381
15.80
0.00
33.88
4.30
2176
2534
9.620259
ATCAACTTCCTTTTCAGTTATATCCTC
57.380
33.333
0.00
0.00
31.78
3.71
2199
2557
1.681166
GCCTCCAGAACATGCAGATGT
60.681
52.381
0.00
0.00
45.24
3.06
2234
2592
6.322712
AGTTGTTAAACCAAATCTTGCAGGTA
59.677
34.615
0.00
0.00
36.94
3.08
2688
3046
5.772521
AGAAATTGTTGTGCATCAAGTACC
58.227
37.500
0.00
0.00
36.66
3.34
2724
3083
6.570692
TCTGTTCGTTGATATAAGGAGTTCC
58.429
40.000
0.00
0.00
0.00
3.62
2736
3095
0.951040
GGAGTTCCTTGTGTGCCTCG
60.951
60.000
0.00
0.00
0.00
4.63
2872
3233
6.990341
AAAAACACTTTGGACTAACTACGT
57.010
33.333
0.00
0.00
0.00
3.57
2882
3243
9.666626
CTTTGGACTAACTACGTATATCTGAAG
57.333
37.037
0.00
0.00
0.00
3.02
2883
3244
8.969260
TTGGACTAACTACGTATATCTGAAGA
57.031
34.615
0.00
0.00
0.00
2.87
2924
3380
6.636705
TGGAGTACATTGGAACTGTGTATAC
58.363
40.000
0.00
0.00
33.29
1.47
3057
3514
6.234177
CAACATCTCTCAAAGTAAAGTCCCT
58.766
40.000
0.00
0.00
0.00
4.20
3169
3630
6.751425
CAGCACAAAACACATTTCTACAGAAA
59.249
34.615
6.85
6.85
46.60
2.52
3262
3725
2.232399
GTAAACCCCTTCGCTTCCAAA
58.768
47.619
0.00
0.00
0.00
3.28
3318
3781
2.031682
GCACACAGTCATCAAAGACCAC
60.032
50.000
0.00
0.00
39.34
4.16
3337
3800
7.509546
AGACCACTCAAGACAAATTAAGAAGA
58.490
34.615
0.00
0.00
0.00
2.87
3392
3857
4.523083
ACCAATACTTCGGTGCATGTATT
58.477
39.130
0.00
0.00
36.43
1.89
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
176
184
5.467735
GGAGGGCGTACGTATTATTTTGATT
59.532
40.000
17.90
0.00
0.00
2.57
187
197
0.457035
GTGAATGGAGGGCGTACGTA
59.543
55.000
17.90
0.00
0.00
3.57
190
200
3.131396
CAATAGTGAATGGAGGGCGTAC
58.869
50.000
0.00
0.00
0.00
3.67
192
202
1.747206
GCAATAGTGAATGGAGGGCGT
60.747
52.381
0.00
0.00
0.00
5.68
194
204
2.057137
TGCAATAGTGAATGGAGGGC
57.943
50.000
0.00
0.00
0.00
5.19
318
331
5.007724
GCTCCTTCCGTTCATTGTTATAAGG
59.992
44.000
0.00
0.00
34.79
2.69
360
373
8.006298
TGGCATCTTAGACTCAAAAAGAAAAA
57.994
30.769
0.00
0.00
33.26
1.94
361
374
7.285401
ACTGGCATCTTAGACTCAAAAAGAAAA
59.715
33.333
0.00
0.00
33.26
2.29
362
375
6.772716
ACTGGCATCTTAGACTCAAAAAGAAA
59.227
34.615
0.00
0.00
33.26
2.52
364
377
5.869579
ACTGGCATCTTAGACTCAAAAAGA
58.130
37.500
0.00
0.00
34.00
2.52
394
431
7.251321
TGGGCAATCTGTTTTTATTGGTTAT
57.749
32.000
0.00
0.00
34.37
1.89
403
440
5.813513
ATTCTCTTGGGCAATCTGTTTTT
57.186
34.783
0.00
0.00
0.00
1.94
410
447
4.759183
GGTGAGATATTCTCTTGGGCAATC
59.241
45.833
6.13
0.00
43.73
2.67
476
517
3.376234
AGCAACGACTACTAGTATTCGCA
59.624
43.478
31.11
1.94
40.44
5.10
507
554
8.726988
CAACGACTATTATCCCTCAAAGAAAAA
58.273
33.333
0.00
0.00
0.00
1.94
508
555
7.148306
GCAACGACTATTATCCCTCAAAGAAAA
60.148
37.037
0.00
0.00
0.00
2.29
509
556
6.315393
GCAACGACTATTATCCCTCAAAGAAA
59.685
38.462
0.00
0.00
0.00
2.52
510
557
5.815740
GCAACGACTATTATCCCTCAAAGAA
59.184
40.000
0.00
0.00
0.00
2.52
511
558
5.128827
AGCAACGACTATTATCCCTCAAAGA
59.871
40.000
0.00
0.00
0.00
2.52
512
559
5.360591
AGCAACGACTATTATCCCTCAAAG
58.639
41.667
0.00
0.00
0.00
2.77
513
560
5.353394
AGCAACGACTATTATCCCTCAAA
57.647
39.130
0.00
0.00
0.00
2.69
514
561
5.128827
AGAAGCAACGACTATTATCCCTCAA
59.871
40.000
0.00
0.00
0.00
3.02
515
562
4.649674
AGAAGCAACGACTATTATCCCTCA
59.350
41.667
0.00
0.00
0.00
3.86
516
563
4.985409
CAGAAGCAACGACTATTATCCCTC
59.015
45.833
0.00
0.00
0.00
4.30
517
564
4.740934
GCAGAAGCAACGACTATTATCCCT
60.741
45.833
0.00
0.00
41.58
4.20
518
565
3.495001
GCAGAAGCAACGACTATTATCCC
59.505
47.826
0.00
0.00
41.58
3.85
519
566
4.210120
CAGCAGAAGCAACGACTATTATCC
59.790
45.833
0.00
0.00
45.49
2.59
520
567
4.318404
GCAGCAGAAGCAACGACTATTATC
60.318
45.833
0.00
0.00
45.49
1.75
521
568
3.557595
GCAGCAGAAGCAACGACTATTAT
59.442
43.478
0.00
0.00
45.49
1.28
522
569
2.930040
GCAGCAGAAGCAACGACTATTA
59.070
45.455
0.00
0.00
45.49
0.98
523
570
1.734465
GCAGCAGAAGCAACGACTATT
59.266
47.619
0.00
0.00
45.49
1.73
524
571
1.338105
TGCAGCAGAAGCAACGACTAT
60.338
47.619
0.00
0.00
45.49
2.12
525
572
0.033366
TGCAGCAGAAGCAACGACTA
59.967
50.000
0.00
0.00
45.49
2.59
526
573
1.227645
TGCAGCAGAAGCAACGACT
60.228
52.632
0.00
0.00
45.49
4.18
527
574
1.082496
GTGCAGCAGAAGCAACGAC
60.082
57.895
0.00
0.00
44.64
4.34
528
575
0.815213
AAGTGCAGCAGAAGCAACGA
60.815
50.000
0.00
0.00
44.64
3.85
529
576
0.385223
GAAGTGCAGCAGAAGCAACG
60.385
55.000
0.00
0.00
44.64
4.10
530
577
0.950116
AGAAGTGCAGCAGAAGCAAC
59.050
50.000
0.00
0.00
44.64
4.17
531
578
1.233019
GAGAAGTGCAGCAGAAGCAA
58.767
50.000
0.00
0.00
44.64
3.91
532
579
0.947660
CGAGAAGTGCAGCAGAAGCA
60.948
55.000
0.00
0.00
45.49
3.91
533
580
1.786582
CGAGAAGTGCAGCAGAAGC
59.213
57.895
0.00
0.00
42.56
3.86
534
581
1.786582
GCGAGAAGTGCAGCAGAAG
59.213
57.895
0.00
0.00
0.00
2.85
535
582
2.023771
CGCGAGAAGTGCAGCAGAA
61.024
57.895
0.00
0.00
0.00
3.02
536
583
2.431430
CGCGAGAAGTGCAGCAGA
60.431
61.111
0.00
0.00
0.00
4.26
574
639
1.733526
GGAGTGTGTTTGGTGGCAC
59.266
57.895
9.70
9.70
36.26
5.01
630
695
1.080093
GCTGCACGGCTGTACTGTA
60.080
57.895
0.00
0.00
35.54
2.74
631
696
2.357517
GCTGCACGGCTGTACTGT
60.358
61.111
0.00
0.00
38.94
3.55
632
697
3.121030
GGCTGCACGGCTGTACTG
61.121
66.667
0.00
0.00
34.85
2.74
633
698
4.742201
CGGCTGCACGGCTGTACT
62.742
66.667
0.00
0.00
35.72
2.73
677
742
1.225855
TACAGCCTTTTGTGCGAGTG
58.774
50.000
0.00
0.00
32.56
3.51
678
743
1.961793
TTACAGCCTTTTGTGCGAGT
58.038
45.000
0.00
0.00
32.56
4.18
680
745
3.784701
TTTTTACAGCCTTTTGTGCGA
57.215
38.095
0.00
0.00
32.56
5.10
698
773
8.953990
GCTCATTAACGAATACGCAATTAATTT
58.046
29.630
0.00
0.00
43.96
1.82
762
837
2.578480
GGAAAGGAAAGGGAGGTGAGAT
59.422
50.000
0.00
0.00
0.00
2.75
763
838
1.985895
GGAAAGGAAAGGGAGGTGAGA
59.014
52.381
0.00
0.00
0.00
3.27
764
839
1.988846
AGGAAAGGAAAGGGAGGTGAG
59.011
52.381
0.00
0.00
0.00
3.51
765
840
2.133858
AGGAAAGGAAAGGGAGGTGA
57.866
50.000
0.00
0.00
0.00
4.02
766
841
2.555448
GGAAGGAAAGGAAAGGGAGGTG
60.555
54.545
0.00
0.00
0.00
4.00
767
842
1.711375
GGAAGGAAAGGAAAGGGAGGT
59.289
52.381
0.00
0.00
0.00
3.85
768
843
1.006043
GGGAAGGAAAGGAAAGGGAGG
59.994
57.143
0.00
0.00
0.00
4.30
769
844
1.006043
GGGGAAGGAAAGGAAAGGGAG
59.994
57.143
0.00
0.00
0.00
4.30
770
845
1.081481
GGGGAAGGAAAGGAAAGGGA
58.919
55.000
0.00
0.00
0.00
4.20
771
846
0.041238
GGGGGAAGGAAAGGAAAGGG
59.959
60.000
0.00
0.00
0.00
3.95
794
869
2.292916
GGCAACGCACAAACGAAGC
61.293
57.895
0.00
0.00
36.70
3.86
863
938
2.690653
TTTCTTGAGGTGCGTGGGGG
62.691
60.000
0.00
0.00
0.00
5.40
864
939
1.228124
TTTCTTGAGGTGCGTGGGG
60.228
57.895
0.00
0.00
0.00
4.96
865
940
1.515521
GGTTTCTTGAGGTGCGTGGG
61.516
60.000
0.00
0.00
0.00
4.61
866
941
1.841663
CGGTTTCTTGAGGTGCGTGG
61.842
60.000
0.00
0.00
0.00
4.94
868
943
2.251642
GCGGTTTCTTGAGGTGCGT
61.252
57.895
0.00
0.00
0.00
5.24
870
945
1.244019
ATGGCGGTTTCTTGAGGTGC
61.244
55.000
0.00
0.00
0.00
5.01
877
952
3.636764
GGATGGAATTATGGCGGTTTCTT
59.363
43.478
0.00
0.00
0.00
2.52
881
956
2.746279
TGGATGGAATTATGGCGGTT
57.254
45.000
0.00
0.00
0.00
4.44
918
997
3.209097
CCCAAATGGCCGCGTAGG
61.209
66.667
4.92
0.00
44.97
3.18
919
998
3.209097
CCCCAAATGGCCGCGTAG
61.209
66.667
4.92
0.00
0.00
3.51
928
1007
3.814268
CCACGAGCGCCCCAAATG
61.814
66.667
2.29
0.00
0.00
2.32
950
1031
0.605319
GGCCTGGTTGATGTGACGAA
60.605
55.000
0.00
0.00
0.00
3.85
961
1042
1.134280
CGATCTGATCTTGGCCTGGTT
60.134
52.381
15.16
0.00
0.00
3.67
962
1043
0.467384
CGATCTGATCTTGGCCTGGT
59.533
55.000
15.16
0.00
0.00
4.00
970
1065
2.028190
CGCCGCCGATCTGATCTT
59.972
61.111
15.16
0.00
36.29
2.40
988
1083
2.431942
GAACATGGTCGCCGTCGT
60.432
61.111
0.00
0.00
36.96
4.34
1162
1287
0.478507
GAGGAGGAGAGAGGGAGAGG
59.521
65.000
0.00
0.00
0.00
3.69
1174
1299
3.514309
CCGGAAGTAAAAGAAGAGGAGGA
59.486
47.826
0.00
0.00
0.00
3.71
1177
1302
3.513517
TCCCGGAAGTAAAAGAAGAGGA
58.486
45.455
0.73
0.00
0.00
3.71
1190
1322
2.809601
CGCGTTGTCTCCCGGAAG
60.810
66.667
0.73
0.00
0.00
3.46
1206
1338
4.098055
TCCAACGATCTTCTTCTTCTCG
57.902
45.455
0.00
0.00
35.56
4.04
1223
1355
0.320073
GACCGTTGACGTCCATCCAA
60.320
55.000
14.12
0.00
37.74
3.53
1243
1375
4.084849
CGCATTTCATTCTACAGATCCGTC
60.085
45.833
0.00
0.00
0.00
4.79
1245
1377
4.051237
TCGCATTTCATTCTACAGATCCG
58.949
43.478
0.00
0.00
0.00
4.18
1311
1443
2.349886
GCACACGATTCTGACAGGAATC
59.650
50.000
1.81
9.45
44.62
2.52
1347
1480
3.557577
TGCGAATTGGACAAAGTCATG
57.442
42.857
0.00
0.00
32.29
3.07
1348
1481
4.789012
AATGCGAATTGGACAAAGTCAT
57.211
36.364
0.00
0.00
32.29
3.06
1418
1559
5.232463
ACTGCCAAATAGCAAAACAAGATG
58.768
37.500
0.00
0.00
43.52
2.90
1432
1573
3.690460
AGTAGCTGCTAAACTGCCAAAT
58.310
40.909
11.57
0.00
43.85
2.32
1536
1677
5.305585
ACTGAAAACCTACGTGATTGTGAT
58.694
37.500
0.00
0.00
0.00
3.06
1633
1792
2.227388
CAGCTTCTCCGTTGCAGATTTT
59.773
45.455
0.00
0.00
0.00
1.82
1682
1844
3.006323
AGACGCATATAGAAAGAGGCAGG
59.994
47.826
0.00
0.00
0.00
4.85
1700
1862
0.514691
GGCAGCAAAGAGACAAGACG
59.485
55.000
0.00
0.00
0.00
4.18
1729
1893
6.128553
ACAGCACATTTCACATAAGACTAACG
60.129
38.462
0.00
0.00
0.00
3.18
1888
2057
3.220999
CTGACGCCTGGGTCACGAA
62.221
63.158
12.40
0.00
41.76
3.85
1889
2058
3.680786
CTGACGCCTGGGTCACGA
61.681
66.667
12.40
0.00
41.76
4.35
1891
2060
2.238847
TATGCTGACGCCTGGGTCAC
62.239
60.000
12.40
10.24
41.76
3.67
1893
2062
1.227380
CTATGCTGACGCCTGGGTC
60.227
63.158
7.35
7.35
37.45
4.46
1894
2063
2.903357
CTATGCTGACGCCTGGGT
59.097
61.111
0.00
0.00
34.43
4.51
1895
2064
1.748329
TAGCTATGCTGACGCCTGGG
61.748
60.000
1.96
0.00
40.10
4.45
1896
2065
0.319383
CTAGCTATGCTGACGCCTGG
60.319
60.000
1.96
0.00
40.10
4.45
1897
2066
0.943359
GCTAGCTATGCTGACGCCTG
60.943
60.000
7.70
0.00
40.10
4.85
1914
2083
8.016301
TGACAGAATTCTGATACATCTTAGCT
57.984
34.615
36.15
13.34
46.59
3.32
1934
2103
8.900511
ACATCAATTATTTCGTGAAATGACAG
57.099
30.769
16.12
6.29
40.83
3.51
1950
2119
8.356657
AGTTTTCACATTCCGAAACATCAATTA
58.643
29.630
0.00
0.00
35.13
1.40
1981
2150
5.885912
AGGTGCAAGTAAATATCGAACCAAT
59.114
36.000
0.00
0.00
0.00
3.16
1982
2151
5.250200
AGGTGCAAGTAAATATCGAACCAA
58.750
37.500
0.00
0.00
0.00
3.67
1984
2153
5.006746
CAGAGGTGCAAGTAAATATCGAACC
59.993
44.000
0.00
0.00
0.00
3.62
1986
2155
5.730550
ACAGAGGTGCAAGTAAATATCGAA
58.269
37.500
0.00
0.00
0.00
3.71
1987
2156
5.339008
ACAGAGGTGCAAGTAAATATCGA
57.661
39.130
0.00
0.00
0.00
3.59
2006
2252
7.656412
AGAGTGCAGTACAGATCATTATACAG
58.344
38.462
0.00
0.00
0.00
2.74
2009
2255
7.503902
ACAGAGAGTGCAGTACAGATCATTATA
59.496
37.037
0.00
0.00
0.00
0.98
2011
2257
5.654209
ACAGAGAGTGCAGTACAGATCATTA
59.346
40.000
0.00
0.00
0.00
1.90
2013
2259
4.022603
ACAGAGAGTGCAGTACAGATCAT
58.977
43.478
0.00
0.00
0.00
2.45
2014
2260
3.425659
ACAGAGAGTGCAGTACAGATCA
58.574
45.455
0.00
0.00
0.00
2.92
2016
2262
3.194542
GGAACAGAGAGTGCAGTACAGAT
59.805
47.826
0.00
0.00
0.00
2.90
2018
2264
2.560542
AGGAACAGAGAGTGCAGTACAG
59.439
50.000
0.00
0.00
0.00
2.74
2023
2269
5.724328
TGTATTTAGGAACAGAGAGTGCAG
58.276
41.667
0.00
0.00
0.00
4.41
2024
2270
5.738619
TGTATTTAGGAACAGAGAGTGCA
57.261
39.130
0.00
0.00
0.00
4.57
2025
2271
6.311690
GTCTTGTATTTAGGAACAGAGAGTGC
59.688
42.308
0.00
0.00
0.00
4.40
2026
2272
6.528423
CGTCTTGTATTTAGGAACAGAGAGTG
59.472
42.308
0.00
0.00
0.00
3.51
2032
2285
7.075741
CCAAAACGTCTTGTATTTAGGAACAG
58.924
38.462
0.20
0.00
0.00
3.16
2045
2298
2.097466
ACTGAACTGCCAAAACGTCTTG
59.903
45.455
0.00
0.00
0.00
3.02
2050
2303
5.099575
AGTTTAAACTGAACTGCCAAAACG
58.900
37.500
19.94
0.00
37.98
3.60
2065
2318
4.850859
AAACGCTTTTGGCAGTTTAAAC
57.149
36.364
10.47
10.47
41.69
2.01
2069
2322
3.851098
TGTAAAACGCTTTTGGCAGTTT
58.149
36.364
0.00
0.00
43.54
2.66
2077
2330
9.233232
CTCTGTTTCTAAATGTAAAACGCTTTT
57.767
29.630
0.00
0.00
36.02
2.27
2081
2334
6.665465
ACCTCTGTTTCTAAATGTAAAACGC
58.335
36.000
0.00
0.00
36.02
4.84
2176
2534
0.809385
CTGCATGTTCTGGAGGCTTG
59.191
55.000
0.00
0.00
39.51
4.01
2199
2557
5.235850
TGGTTTAACAACTAGGCATGAGA
57.764
39.130
0.00
0.00
32.90
3.27
2234
2592
4.654262
TGGTAGGACTTCTCTTCAACTGTT
59.346
41.667
0.00
0.00
0.00
3.16
2435
2793
4.347453
GTTTGTGCTGCCGCCTGG
62.347
66.667
0.00
0.00
38.77
4.45
2724
3083
1.845809
GAAGCACCGAGGCACACAAG
61.846
60.000
1.23
0.00
35.83
3.16
2736
3095
1.661112
GTGCTGAAGTATCGAAGCACC
59.339
52.381
21.54
8.29
44.53
5.01
2850
3211
9.933723
ATATACGTAGTTAGTCCAAAGTGTTTT
57.066
29.630
0.08
0.00
37.78
2.43
2882
3243
8.671028
TGTACTCCAGTTTTACTTTTGAAGTTC
58.329
33.333
0.00
0.00
42.81
3.01
2883
3244
8.570068
TGTACTCCAGTTTTACTTTTGAAGTT
57.430
30.769
0.00
0.00
42.81
2.66
2888
3249
7.936584
TCCAATGTACTCCAGTTTTACTTTTG
58.063
34.615
0.00
0.00
0.00
2.44
2892
3253
6.710744
CAGTTCCAATGTACTCCAGTTTTACT
59.289
38.462
0.00
0.00
0.00
2.24
2894
3255
6.485313
CACAGTTCCAATGTACTCCAGTTTTA
59.515
38.462
0.00
0.00
0.00
1.52
3032
3488
5.412904
GGGACTTTACTTTGAGAGATGTTGG
59.587
44.000
0.00
0.00
0.00
3.77
3057
3514
1.488812
AGGTGTAGTGGTTGAACTGCA
59.511
47.619
0.00
0.00
39.99
4.41
3180
3643
1.003003
TCACTGGATTCCGTTGATGCA
59.997
47.619
0.00
0.00
0.00
3.96
3262
3725
7.147585
TGCAGCTTCTAAGAATAGAGGAAGAAT
60.148
37.037
0.00
0.00
39.29
2.40
3392
3857
2.237643
TGCTTGCTGCCTTTTATGTGA
58.762
42.857
0.00
0.00
42.00
3.58
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.