Multiple sequence alignment - TraesCS1A01G230200
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
TraesCS1A01G230200
chr1A
100.000
2669
0
0
1
2669
402937827
402940495
0.000000e+00
4929.0
1
TraesCS1A01G230200
chr1B
89.164
1855
117
38
584
2398
433112059
433110249
0.000000e+00
2235.0
2
TraesCS1A01G230200
chr1B
91.791
268
11
2
2398
2665
433110218
433109962
1.950000e-96
363.0
3
TraesCS1A01G230200
chr1D
88.929
1120
58
23
891
1998
320195517
320194452
0.000000e+00
1321.0
4
TraesCS1A01G230200
chr1D
88.520
331
13
10
583
898
320195868
320195548
6.970000e-101
377.0
5
TraesCS1A01G230200
chr5B
93.391
575
38
0
1
575
537609630
537609056
0.000000e+00
852.0
6
TraesCS1A01G230200
chr5B
94.286
35
1
1
2394
2428
549974311
549974278
5.000000e-03
52.8
7
TraesCS1A01G230200
chr2D
92.443
569
43
0
5
573
111223575
111224143
0.000000e+00
813.0
8
TraesCS1A01G230200
chr2D
100.000
28
0
0
2398
2425
302248035
302248008
5.000000e-03
52.8
9
TraesCS1A01G230200
chr3B
89.792
578
58
1
1
577
445156351
445156928
0.000000e+00
739.0
10
TraesCS1A01G230200
chr3B
87.215
571
73
0
5
575
816249121
816248551
0.000000e+00
651.0
11
TraesCS1A01G230200
chr3D
89.667
571
59
0
5
575
609356400
609356970
0.000000e+00
728.0
12
TraesCS1A01G230200
chr4A
88.328
574
63
3
2
575
706872458
706873027
0.000000e+00
686.0
13
TraesCS1A01G230200
chr3A
88.225
569
66
1
5
573
60196767
60196200
0.000000e+00
678.0
14
TraesCS1A01G230200
chr3A
87.698
569
70
0
5
573
747300572
747300004
0.000000e+00
664.0
15
TraesCS1A01G230200
chr5D
87.741
571
70
0
5
575
435799484
435798914
0.000000e+00
667.0
16
TraesCS1A01G230200
chr5D
100.000
28
0
0
2398
2425
324588075
324588102
5.000000e-03
52.8
17
TraesCS1A01G230200
chr6B
94.444
36
1
1
2388
2422
58320189
58320154
1.000000e-03
54.7
18
TraesCS1A01G230200
chr5A
96.774
31
1
0
2398
2428
588845516
588845486
5.000000e-03
52.8
19
TraesCS1A01G230200
chr4D
96.774
31
1
0
2398
2428
494787218
494787188
5.000000e-03
52.8
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
TraesCS1A01G230200
chr1A
402937827
402940495
2668
False
4929
4929
100.0000
1
2669
1
chr1A.!!$F1
2668
1
TraesCS1A01G230200
chr1B
433109962
433112059
2097
True
1299
2235
90.4775
584
2665
2
chr1B.!!$R1
2081
2
TraesCS1A01G230200
chr1D
320194452
320195868
1416
True
849
1321
88.7245
583
1998
2
chr1D.!!$R1
1415
3
TraesCS1A01G230200
chr5B
537609056
537609630
574
True
852
852
93.3910
1
575
1
chr5B.!!$R1
574
4
TraesCS1A01G230200
chr2D
111223575
111224143
568
False
813
813
92.4430
5
573
1
chr2D.!!$F1
568
5
TraesCS1A01G230200
chr3B
445156351
445156928
577
False
739
739
89.7920
1
577
1
chr3B.!!$F1
576
6
TraesCS1A01G230200
chr3B
816248551
816249121
570
True
651
651
87.2150
5
575
1
chr3B.!!$R1
570
7
TraesCS1A01G230200
chr3D
609356400
609356970
570
False
728
728
89.6670
5
575
1
chr3D.!!$F1
570
8
TraesCS1A01G230200
chr4A
706872458
706873027
569
False
686
686
88.3280
2
575
1
chr4A.!!$F1
573
9
TraesCS1A01G230200
chr3A
60196200
60196767
567
True
678
678
88.2250
5
573
1
chr3A.!!$R1
568
10
TraesCS1A01G230200
chr3A
747300004
747300572
568
True
664
664
87.6980
5
573
1
chr3A.!!$R2
568
11
TraesCS1A01G230200
chr5D
435798914
435799484
570
True
667
667
87.7410
5
575
1
chr5D.!!$R1
570
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
140
141
0.322322
CCAAACCATGCACATGCCTT
59.678
50.0
5.06
0.0
41.18
4.35
F
774
784
0.332972
ACCAAATCTCTTCCCCCAGC
59.667
55.0
0.00
0.0
0.00
4.85
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1179
1248
1.922220
GTCGTCGTCATCGTCGTCG
60.922
63.158
0.0
0.0
45.27
5.12
R
2435
2565
0.036164
TACAGATGTTGCCGCCAAGT
59.964
50.000
0.0
0.0
0.00
3.16
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
46
47
2.109126
GTGGTGATCTTGGCTCGGC
61.109
63.158
0.00
0.00
0.00
5.54
140
141
0.322322
CCAAACCATGCACATGCCTT
59.678
50.000
5.06
0.00
41.18
4.35
163
164
1.236616
CCAGAAGTGTTGCGCATGGA
61.237
55.000
17.05
0.00
0.00
3.41
281
282
0.978151
TCCGGAAGAATCCCACGAAA
59.022
50.000
0.00
0.00
43.37
3.46
288
289
4.519350
GGAAGAATCCCACGAAAAACTCTT
59.481
41.667
0.00
0.00
40.10
2.85
292
293
3.269538
TCCCACGAAAAACTCTTCACA
57.730
42.857
0.00
0.00
0.00
3.58
323
324
7.050377
ACTCTCATTTTCGGTATGACATTCAT
58.950
34.615
0.00
0.00
40.72
2.57
324
325
7.225538
ACTCTCATTTTCGGTATGACATTCATC
59.774
37.037
0.00
0.00
38.26
2.92
337
338
4.079844
TGACATTCATCTTCCATAAGGCCA
60.080
41.667
5.01
0.00
33.22
5.36
343
344
1.140852
TCTTCCATAAGGCCATCCACG
59.859
52.381
5.01
0.00
33.22
4.94
358
359
5.545588
CCATCCACGACTATTGATCATCTT
58.454
41.667
0.00
0.00
0.00
2.40
359
360
5.994054
CCATCCACGACTATTGATCATCTTT
59.006
40.000
0.00
0.00
0.00
2.52
427
429
4.401202
TCTGAATCATTAGAGCACGGTACA
59.599
41.667
0.00
0.00
0.00
2.90
449
451
3.069158
ACCGTCTTTACAGTGTAGTTGCT
59.931
43.478
2.68
0.00
0.00
3.91
469
471
3.367292
GCTTGATTTCTCGAATGCCCAAA
60.367
43.478
0.00
0.00
0.00
3.28
485
487
3.321968
GCCCAAACAAAAGAATCCTCACT
59.678
43.478
0.00
0.00
0.00
3.41
490
492
4.731313
ACAAAAGAATCCTCACTTCCCT
57.269
40.909
0.00
0.00
0.00
4.20
494
496
6.044404
ACAAAAGAATCCTCACTTCCCTCTTA
59.956
38.462
0.00
0.00
0.00
2.10
525
527
1.083489
TGTTTAGAATGGCTTCGGCG
58.917
50.000
0.00
0.00
42.91
6.46
531
533
2.852495
GAATGGCTTCGGCGTCTGGA
62.852
60.000
6.85
0.00
42.91
3.86
577
579
4.329545
GCCGCCAAGACCAGTCCA
62.330
66.667
0.00
0.00
0.00
4.02
578
580
2.046892
CCGCCAAGACCAGTCCAG
60.047
66.667
0.00
0.00
0.00
3.86
579
581
2.046892
CGCCAAGACCAGTCCAGG
60.047
66.667
0.00
0.00
0.00
4.45
580
582
2.360475
GCCAAGACCAGTCCAGGC
60.360
66.667
13.32
13.32
40.92
4.85
581
583
2.046892
CCAAGACCAGTCCAGGCG
60.047
66.667
0.00
0.00
0.00
5.52
582
584
2.743928
CAAGACCAGTCCAGGCGC
60.744
66.667
0.00
0.00
0.00
6.53
628
630
0.679960
TCTGAATCGTGGAGCGGAGA
60.680
55.000
0.00
0.00
41.72
3.71
629
631
0.526524
CTGAATCGTGGAGCGGAGAC
60.527
60.000
0.00
0.00
41.72
3.36
667
677
2.167487
CCTCTCTGCCCAGAAGAAGTAC
59.833
54.545
0.00
0.00
36.94
2.73
753
763
3.488489
CTTCCGTTCATTTAACCGCAAG
58.512
45.455
0.00
0.00
34.33
4.01
772
782
2.358258
AGAACCAAATCTCTTCCCCCA
58.642
47.619
0.00
0.00
0.00
4.96
774
784
0.332972
ACCAAATCTCTTCCCCCAGC
59.667
55.000
0.00
0.00
0.00
4.85
795
812
3.377172
GCAAAGTAATCCACCACGCTTAT
59.623
43.478
0.00
0.00
0.00
1.73
796
813
4.495844
GCAAAGTAATCCACCACGCTTATC
60.496
45.833
0.00
0.00
0.00
1.75
797
814
4.755266
AAGTAATCCACCACGCTTATCT
57.245
40.909
0.00
0.00
0.00
1.98
798
815
4.323553
AGTAATCCACCACGCTTATCTC
57.676
45.455
0.00
0.00
0.00
2.75
799
816
3.961408
AGTAATCCACCACGCTTATCTCT
59.039
43.478
0.00
0.00
0.00
3.10
830
847
2.305927
GACATCAAGGAAGGAAGGACCA
59.694
50.000
0.00
0.00
42.04
4.02
832
849
0.693049
TCAAGGAAGGAAGGACCAGC
59.307
55.000
0.00
0.00
42.04
4.85
833
850
0.695347
CAAGGAAGGAAGGACCAGCT
59.305
55.000
0.00
0.00
42.04
4.24
834
851
1.074566
CAAGGAAGGAAGGACCAGCTT
59.925
52.381
0.00
0.00
42.04
3.74
835
852
0.695347
AGGAAGGAAGGACCAGCTTG
59.305
55.000
0.00
0.00
42.04
4.01
932
995
1.240256
AGCGCTTATCTACCCGAGAG
58.760
55.000
2.64
0.00
37.70
3.20
941
1004
1.379977
TACCCGAGAGCCACTCCTG
60.380
63.158
3.46
0.00
42.18
3.86
964
1027
2.838693
GGAGGAGGGGCCGTAGTC
60.839
72.222
0.00
0.00
43.43
2.59
974
1037
0.452585
GGCCGTAGTCACAGAGAGAC
59.547
60.000
0.00
0.00
36.26
3.36
978
1041
1.823797
GTAGTCACAGAGAGACCGGT
58.176
55.000
6.92
6.92
36.68
5.28
982
1045
2.203640
ACAGAGAGACCGGTGCCA
60.204
61.111
14.63
0.00
0.00
4.92
1243
1312
3.060020
GCCATCGACTCGTTCCCGA
62.060
63.158
0.00
0.00
41.73
5.14
1609
1690
2.389715
AGGACTGGCTCATGTACTACC
58.610
52.381
0.00
0.00
0.00
3.18
1692
1773
3.342627
CGTTGCGAGCGTGGGAAA
61.343
61.111
0.00
0.00
0.00
3.13
1693
1774
2.251371
GTTGCGAGCGTGGGAAAC
59.749
61.111
0.00
0.00
0.00
2.78
1799
1887
1.818850
CAGTATAACTGTACGCGCGT
58.181
50.000
39.05
39.05
41.19
6.01
1818
1910
4.607336
CGCGTACACGTATACGGTATACAA
60.607
45.833
25.90
13.94
46.39
2.41
1869
1961
1.348036
GTACTGGAAAGTGAGCAGGGT
59.652
52.381
0.00
0.00
0.00
4.34
1871
1963
0.397941
CTGGAAAGTGAGCAGGGTGA
59.602
55.000
0.00
0.00
0.00
4.02
1887
1979
2.952310
GGGTGACTTTTCATGATAGGGC
59.048
50.000
0.00
0.00
33.11
5.19
1943
2042
5.786311
TCATGGAAAAGATTTTGAAGCTGG
58.214
37.500
0.00
0.00
0.00
4.85
1964
2063
4.103153
TGGAGTTTTGTCCAATGTCTCTCT
59.897
41.667
0.00
0.00
44.01
3.10
1965
2064
4.693095
GGAGTTTTGTCCAATGTCTCTCTC
59.307
45.833
0.00
0.00
36.51
3.20
1966
2065
5.296151
AGTTTTGTCCAATGTCTCTCTCA
57.704
39.130
0.00
0.00
0.00
3.27
1967
2066
5.059833
AGTTTTGTCCAATGTCTCTCTCAC
58.940
41.667
0.00
0.00
0.00
3.51
1993
2092
8.792830
TCACTTTTTCTCTTCTCTTTTCTTGA
57.207
30.769
0.00
0.00
0.00
3.02
2085
2184
9.990360
TGTTATGTCAGTATTTTGTTGAGAGTA
57.010
29.630
0.00
0.00
0.00
2.59
2089
2188
5.932303
GTCAGTATTTTGTTGAGAGTAGCCA
59.068
40.000
0.00
0.00
0.00
4.75
2106
2205
4.510038
AGCCAAAGATGAAACATCACAC
57.490
40.909
13.06
0.28
0.00
3.82
2113
2212
8.298854
CCAAAGATGAAACATCACACTCATAAA
58.701
33.333
13.06
0.00
0.00
1.40
2115
2214
9.850628
AAAGATGAAACATCACACTCATAAATG
57.149
29.630
13.06
0.00
0.00
2.32
2138
2237
7.727578
TGTATGAAGTACTAATCTTGGGTCA
57.272
36.000
0.00
0.00
34.27
4.02
2158
2257
6.410540
GGTCATGGATATAATTCTCCTCCAC
58.589
44.000
0.00
0.00
38.74
4.02
2162
2261
5.158141
TGGATATAATTCTCCTCCACTGCT
58.842
41.667
3.97
0.00
31.19
4.24
2171
2270
0.177604
CCTCCACTGCTCTGCCTTAG
59.822
60.000
0.00
0.00
0.00
2.18
2178
2277
0.174389
TGCTCTGCCTTAGCTCGAAG
59.826
55.000
0.00
0.00
40.73
3.79
2247
2346
5.011943
CAGAAGTTTTGGGGGATTTGAATCA
59.988
40.000
6.11
0.00
37.15
2.57
2252
2351
6.730507
AGTTTTGGGGGATTTGAATCATAAGT
59.269
34.615
6.11
0.00
37.15
2.24
2280
2379
8.950007
TTTATTTTATCTTTTCTGGTGGAGGT
57.050
30.769
0.00
0.00
0.00
3.85
2281
2380
8.575649
TTATTTTATCTTTTCTGGTGGAGGTC
57.424
34.615
0.00
0.00
0.00
3.85
2282
2381
5.576563
TTTATCTTTTCTGGTGGAGGTCA
57.423
39.130
0.00
0.00
0.00
4.02
2285
2384
4.453480
TCTTTTCTGGTGGAGGTCATTT
57.547
40.909
0.00
0.00
0.00
2.32
2286
2385
4.144297
TCTTTTCTGGTGGAGGTCATTTG
58.856
43.478
0.00
0.00
0.00
2.32
2287
2386
2.584835
TTCTGGTGGAGGTCATTTGG
57.415
50.000
0.00
0.00
0.00
3.28
2288
2387
1.444933
TCTGGTGGAGGTCATTTGGT
58.555
50.000
0.00
0.00
0.00
3.67
2289
2388
1.780309
TCTGGTGGAGGTCATTTGGTT
59.220
47.619
0.00
0.00
0.00
3.67
2290
2389
2.162681
CTGGTGGAGGTCATTTGGTTC
58.837
52.381
0.00
0.00
0.00
3.62
2291
2390
1.496857
TGGTGGAGGTCATTTGGTTCA
59.503
47.619
0.00
0.00
0.00
3.18
2292
2391
1.886542
GGTGGAGGTCATTTGGTTCAC
59.113
52.381
0.00
0.00
0.00
3.18
2293
2392
2.582052
GTGGAGGTCATTTGGTTCACA
58.418
47.619
0.00
0.00
0.00
3.58
2341
2440
7.952930
TGTCCTAAGGATTCTATATGAGCTCTT
59.047
37.037
16.19
11.54
32.73
2.85
2346
2445
8.600449
AAGGATTCTATATGAGCTCTTTTTCG
57.400
34.615
16.19
0.00
0.00
3.46
2351
2450
2.409948
ATGAGCTCTTTTTCGGAGGG
57.590
50.000
16.19
0.00
0.00
4.30
2383
2482
3.826157
CCAACCCAAATCTCTTGCTACAA
59.174
43.478
0.00
0.00
0.00
2.41
2388
2487
5.416952
ACCCAAATCTCTTGCTACAATTCTG
59.583
40.000
0.00
0.00
0.00
3.02
2430
2560
5.263872
ACGGAGGGAGTATTAGAGATCAT
57.736
43.478
0.00
0.00
0.00
2.45
2431
2561
5.646215
ACGGAGGGAGTATTAGAGATCATT
58.354
41.667
0.00
0.00
0.00
2.57
2432
2562
5.478679
ACGGAGGGAGTATTAGAGATCATTG
59.521
44.000
0.00
0.00
0.00
2.82
2433
2563
5.105554
CGGAGGGAGTATTAGAGATCATTGG
60.106
48.000
0.00
0.00
0.00
3.16
2434
2564
5.337975
GGAGGGAGTATTAGAGATCATTGGC
60.338
48.000
0.00
0.00
0.00
4.52
2435
2565
5.158141
AGGGAGTATTAGAGATCATTGGCA
58.842
41.667
0.00
0.00
0.00
4.92
2436
2566
5.012561
AGGGAGTATTAGAGATCATTGGCAC
59.987
44.000
0.00
0.00
0.00
5.01
2458
2588
0.727398
GGCGGCAACATCTGTAGTTC
59.273
55.000
3.07
0.00
0.00
3.01
2459
2589
1.676014
GGCGGCAACATCTGTAGTTCT
60.676
52.381
3.07
0.00
0.00
3.01
2460
2590
1.661112
GCGGCAACATCTGTAGTTCTC
59.339
52.381
0.00
0.00
0.00
2.87
2461
2591
2.675317
GCGGCAACATCTGTAGTTCTCT
60.675
50.000
0.00
0.00
0.00
3.10
2497
2627
9.717892
GATAGGATTTCAATTCTACGTTTTTCC
57.282
33.333
0.00
0.00
29.50
3.13
2546
2676
3.706086
AGAGGCCTTGAATTGTTTTGTGT
59.294
39.130
6.77
0.00
0.00
3.72
2569
2699
4.398044
TGGAACTCAAACAGAACCAACTTC
59.602
41.667
0.00
0.00
31.49
3.01
2588
2718
8.385849
CCAACTTCTGGTTTCTGAAAGAGATGA
61.386
40.741
20.53
8.48
42.17
2.92
2612
2742
1.272147
GGAGTTGCCTTCCACATTCCT
60.272
52.381
0.00
0.00
34.74
3.36
2617
2747
2.676748
TGCCTTCCACATTCCTTTTGT
58.323
42.857
0.00
0.00
0.00
2.83
2622
2752
4.262164
CCTTCCACATTCCTTTTGTCCAAG
60.262
45.833
0.00
0.00
0.00
3.61
2623
2753
2.627699
TCCACATTCCTTTTGTCCAAGC
59.372
45.455
0.00
0.00
0.00
4.01
2630
2760
5.675684
TTCCTTTTGTCCAAGCTTTTCTT
57.324
34.783
0.00
0.00
34.78
2.52
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
46
47
1.475751
CCCCCGTTTCTCTGATGATGG
60.476
57.143
0.00
0.00
0.00
3.51
140
141
1.891919
GCGCAACACTTCTGGGACA
60.892
57.895
0.30
0.00
0.00
4.02
163
164
4.142227
GGAGCATGCTCTCATTCATTGTTT
60.142
41.667
38.84
6.15
42.38
2.83
219
220
5.755861
TCGTCATATTGCACCAATTAATCGA
59.244
36.000
0.00
0.00
35.54
3.59
288
289
4.991056
CCGAAAATGAGAGTCTTCTTGTGA
59.009
41.667
0.00
0.00
32.53
3.58
292
293
6.814146
GTCATACCGAAAATGAGAGTCTTCTT
59.186
38.462
0.00
0.00
34.12
2.52
297
298
6.535150
TGAATGTCATACCGAAAATGAGAGTC
59.465
38.462
10.20
10.20
40.26
3.36
305
306
6.176896
TGGAAGATGAATGTCATACCGAAAA
58.823
36.000
0.00
0.00
37.20
2.29
323
324
1.140852
CGTGGATGGCCTTATGGAAGA
59.859
52.381
3.32
0.00
34.25
2.87
324
325
1.140852
TCGTGGATGGCCTTATGGAAG
59.859
52.381
3.32
0.00
34.57
3.46
337
338
7.275183
TCAAAAGATGATCAATAGTCGTGGAT
58.725
34.615
0.00
0.00
31.50
3.41
343
344
7.254590
CGGAACCTCAAAAGATGATCAATAGTC
60.255
40.741
0.00
0.00
37.44
2.59
358
359
1.294138
CGGCTACCGGAACCTCAAA
59.706
57.895
9.46
0.00
44.15
2.69
359
360
2.975536
CGGCTACCGGAACCTCAA
59.024
61.111
9.46
0.00
44.15
3.02
409
411
3.454371
GGTGTACCGTGCTCTAATGAT
57.546
47.619
0.00
0.00
0.00
2.45
427
429
3.069158
AGCAACTACACTGTAAAGACGGT
59.931
43.478
0.00
0.00
46.63
4.83
435
437
5.633601
CGAGAAATCAAGCAACTACACTGTA
59.366
40.000
0.00
0.00
0.00
2.74
449
451
3.571828
TGTTTGGGCATTCGAGAAATCAA
59.428
39.130
0.00
0.00
0.00
2.57
469
471
4.352298
AGAGGGAAGTGAGGATTCTTTTGT
59.648
41.667
0.00
0.00
0.00
2.83
485
487
8.401955
AAACATTCCTATTAGGTAAGAGGGAA
57.598
34.615
9.57
6.86
43.19
3.97
494
496
7.816411
AGCCATTCTAAACATTCCTATTAGGT
58.184
34.615
9.57
0.00
36.53
3.08
525
527
3.006247
GGAGACTTTCATTGCTCCAGAC
58.994
50.000
0.00
0.00
44.91
3.51
531
533
3.330701
TGGTTAGGGAGACTTTCATTGCT
59.669
43.478
0.00
0.00
0.00
3.91
577
579
4.711949
CAACTCTGCTGGGCGCCT
62.712
66.667
28.56
0.00
38.05
5.52
579
581
4.704833
TCCAACTCTGCTGGGCGC
62.705
66.667
0.00
0.00
34.46
6.53
580
582
2.743928
GTCCAACTCTGCTGGGCG
60.744
66.667
0.00
0.00
34.46
6.13
581
583
1.376553
GAGTCCAACTCTGCTGGGC
60.377
63.158
0.00
0.00
41.88
5.36
582
584
0.397941
TTGAGTCCAACTCTGCTGGG
59.602
55.000
8.44
0.00
45.27
4.45
594
596
5.242838
ACGATTCAGAGGATAGATTGAGTCC
59.757
44.000
0.00
0.00
0.00
3.85
600
602
4.021544
GCTCCACGATTCAGAGGATAGATT
60.022
45.833
0.00
0.00
30.74
2.40
628
630
3.364441
TGCGGCCTACACGTACGT
61.364
61.111
16.72
16.72
0.00
3.57
629
631
2.877582
GTGCGGCCTACACGTACG
60.878
66.667
15.01
15.01
37.22
3.67
630
632
2.507769
GGTGCGGCCTACACGTAC
60.508
66.667
16.80
5.94
44.40
3.67
651
657
0.895530
TCGGTACTTCTTCTGGGCAG
59.104
55.000
0.00
0.00
0.00
4.85
667
677
1.364171
CTTCGGCTGGGTAGATCGG
59.636
63.158
0.00
0.00
0.00
4.18
753
763
2.728007
CTGGGGGAAGAGATTTGGTTC
58.272
52.381
0.00
0.00
0.00
3.62
772
782
1.165270
GCGTGGTGGATTACTTTGCT
58.835
50.000
0.00
0.00
0.00
3.91
774
784
4.876107
AGATAAGCGTGGTGGATTACTTTG
59.124
41.667
0.00
0.00
0.00
2.77
795
812
4.081254
CCTTGATGTCATGTGGAGAAGAGA
60.081
45.833
0.00
0.00
0.00
3.10
796
813
4.081254
TCCTTGATGTCATGTGGAGAAGAG
60.081
45.833
0.00
0.00
0.00
2.85
797
814
3.840078
TCCTTGATGTCATGTGGAGAAGA
59.160
43.478
0.00
0.00
0.00
2.87
798
815
4.212143
TCCTTGATGTCATGTGGAGAAG
57.788
45.455
0.00
0.00
0.00
2.85
799
816
4.566278
CCTTCCTTGATGTCATGTGGAGAA
60.566
45.833
0.00
0.00
0.00
2.87
835
852
1.666580
GGTAGGTATGCGAGGAGGC
59.333
63.158
0.00
0.00
0.00
4.70
880
902
2.162809
GAGTGAAAGAGAGGGAGACGAC
59.837
54.545
0.00
0.00
0.00
4.34
955
1018
0.452585
GTCTCTCTGTGACTACGGCC
59.547
60.000
0.00
0.00
33.03
6.13
960
1023
1.822506
CACCGGTCTCTCTGTGACTA
58.177
55.000
2.59
0.00
35.04
2.59
964
1027
2.262915
GGCACCGGTCTCTCTGTG
59.737
66.667
2.59
0.00
0.00
3.66
1174
1243
2.943034
GTCATCGTCGTCGCCGTC
60.943
66.667
0.00
0.00
36.96
4.79
1175
1244
4.806481
CGTCATCGTCGTCGCCGT
62.806
66.667
0.00
0.00
36.96
5.68
1176
1245
4.509883
TCGTCATCGTCGTCGCCG
62.510
66.667
0.00
0.00
38.33
6.46
1177
1246
2.943034
GTCGTCATCGTCGTCGCC
60.943
66.667
0.00
0.00
38.33
5.54
1178
1247
3.295462
CGTCGTCATCGTCGTCGC
61.295
66.667
0.00
0.00
41.73
5.19
1179
1248
1.922220
GTCGTCGTCATCGTCGTCG
60.922
63.158
0.00
0.00
45.27
5.12
1180
1249
1.922220
CGTCGTCGTCATCGTCGTC
60.922
63.158
7.05
2.04
45.27
4.20
1181
1250
2.095282
CGTCGTCGTCATCGTCGT
59.905
61.111
7.05
0.00
45.27
4.34
1182
1251
1.922220
GTCGTCGTCGTCATCGTCG
60.922
63.158
1.33
1.62
46.06
5.12
1579
1660
2.125673
CCAGTCCTTGTACCGCCG
60.126
66.667
0.00
0.00
0.00
6.46
1692
1773
3.305744
GCGGTAAAACAAACATGGATGGT
60.306
43.478
0.00
0.00
0.00
3.55
1693
1774
3.249917
GCGGTAAAACAAACATGGATGG
58.750
45.455
0.00
0.00
0.00
3.51
1694
1775
2.914214
CGCGGTAAAACAAACATGGATG
59.086
45.455
0.00
0.00
0.00
3.51
1695
1776
2.814919
TCGCGGTAAAACAAACATGGAT
59.185
40.909
6.13
0.00
0.00
3.41
1696
1777
2.219458
TCGCGGTAAAACAAACATGGA
58.781
42.857
6.13
0.00
0.00
3.41
1798
1886
5.734311
ACGTTGTATACCGTATACGTGTAC
58.266
41.667
22.87
20.19
43.05
2.90
1799
1887
5.977171
ACGTTGTATACCGTATACGTGTA
57.023
39.130
22.87
21.80
43.05
2.90
1810
1902
5.569059
GTGTGTGTACAGTACGTTGTATACC
59.431
44.000
18.72
12.94
41.92
2.73
1818
1910
2.864882
GCATGGTGTGTGTACAGTACGT
60.865
50.000
6.23
0.00
37.52
3.57
1869
1961
2.238646
ACGGCCCTATCATGAAAAGTCA
59.761
45.455
0.00
0.00
38.41
3.41
1871
1963
2.238646
TCACGGCCCTATCATGAAAAGT
59.761
45.455
0.00
0.00
0.00
2.66
1943
2042
5.178438
GTGAGAGAGACATTGGACAAAACTC
59.822
44.000
0.00
0.00
0.00
3.01
1964
2063
8.043710
AGAAAAGAGAAGAGAAAAAGTGAGTGA
58.956
33.333
0.00
0.00
0.00
3.41
1965
2064
8.207521
AGAAAAGAGAAGAGAAAAAGTGAGTG
57.792
34.615
0.00
0.00
0.00
3.51
1966
2065
8.672815
CAAGAAAAGAGAAGAGAAAAAGTGAGT
58.327
33.333
0.00
0.00
0.00
3.41
1967
2066
8.887717
TCAAGAAAAGAGAAGAGAAAAAGTGAG
58.112
33.333
0.00
0.00
0.00
3.51
2039
2138
3.119637
ACAAAATAATCAAAGCGGGTCCG
60.120
43.478
4.85
4.85
43.09
4.79
2041
2140
7.033185
ACATAACAAAATAATCAAAGCGGGTC
58.967
34.615
0.00
0.00
0.00
4.46
2045
2144
8.673626
ACTGACATAACAAAATAATCAAAGCG
57.326
30.769
0.00
0.00
0.00
4.68
2085
2184
4.147321
AGTGTGATGTTTCATCTTTGGCT
58.853
39.130
10.40
1.26
33.56
4.75
2089
2188
9.850628
CATTTATGAGTGTGATGTTTCATCTTT
57.149
29.630
10.40
0.00
33.56
2.52
2113
2212
8.319057
TGACCCAAGATTAGTACTTCATACAT
57.681
34.615
0.00
0.00
36.09
2.29
2115
2214
7.657761
CCATGACCCAAGATTAGTACTTCATAC
59.342
40.741
0.00
0.00
0.00
2.39
2118
2217
5.724370
TCCATGACCCAAGATTAGTACTTCA
59.276
40.000
0.00
0.00
0.00
3.02
2124
2223
9.965902
GAATTATATCCATGACCCAAGATTAGT
57.034
33.333
0.00
0.00
0.00
2.24
2138
2237
5.789575
AGCAGTGGAGGAGAATTATATCCAT
59.210
40.000
9.13
0.00
41.81
3.41
2158
2257
0.174389
TTCGAGCTAAGGCAGAGCAG
59.826
55.000
12.44
6.62
42.69
4.24
2162
2261
1.335182
CGATCTTCGAGCTAAGGCAGA
59.665
52.381
0.00
0.00
43.74
4.26
2194
2293
8.970691
AATTCGTTTGAATCAAAGATCGAATT
57.029
26.923
30.51
30.51
44.74
2.17
2196
2295
8.795786
AAAATTCGTTTGAATCAAAGATCGAA
57.204
26.923
24.35
24.35
44.02
3.71
2198
2297
9.112789
TGTAAAATTCGTTTGAATCAAAGATCG
57.887
29.630
8.88
9.47
44.02
3.69
2205
2304
9.796120
AAACTTCTGTAAAATTCGTTTGAATCA
57.204
25.926
0.00
0.00
44.02
2.57
2258
2357
6.552008
TGACCTCCACCAGAAAAGATAAAAT
58.448
36.000
0.00
0.00
0.00
1.82
2266
2365
3.230134
CCAAATGACCTCCACCAGAAAA
58.770
45.455
0.00
0.00
0.00
2.29
2268
2367
1.780309
ACCAAATGACCTCCACCAGAA
59.220
47.619
0.00
0.00
0.00
3.02
2269
2368
1.444933
ACCAAATGACCTCCACCAGA
58.555
50.000
0.00
0.00
0.00
3.86
2270
2369
2.162681
GAACCAAATGACCTCCACCAG
58.837
52.381
0.00
0.00
0.00
4.00
2271
2370
1.496857
TGAACCAAATGACCTCCACCA
59.503
47.619
0.00
0.00
0.00
4.17
2272
2371
1.886542
GTGAACCAAATGACCTCCACC
59.113
52.381
0.00
0.00
0.00
4.61
2273
2372
2.554032
CTGTGAACCAAATGACCTCCAC
59.446
50.000
0.00
0.00
0.00
4.02
2274
2373
2.488891
CCTGTGAACCAAATGACCTCCA
60.489
50.000
0.00
0.00
0.00
3.86
2275
2374
2.162681
CCTGTGAACCAAATGACCTCC
58.837
52.381
0.00
0.00
0.00
4.30
2276
2375
3.140325
TCCTGTGAACCAAATGACCTC
57.860
47.619
0.00
0.00
0.00
3.85
2277
2376
3.814504
ATCCTGTGAACCAAATGACCT
57.185
42.857
0.00
0.00
0.00
3.85
2278
2377
4.280677
TCAAATCCTGTGAACCAAATGACC
59.719
41.667
0.00
0.00
0.00
4.02
2279
2378
5.452078
TCAAATCCTGTGAACCAAATGAC
57.548
39.130
0.00
0.00
0.00
3.06
2280
2379
6.669125
ATTCAAATCCTGTGAACCAAATGA
57.331
33.333
0.00
0.00
37.80
2.57
2281
2380
6.956299
GATTCAAATCCTGTGAACCAAATG
57.044
37.500
0.00
0.00
37.80
2.32
2327
2426
5.011125
CCCTCCGAAAAAGAGCTCATATAGA
59.989
44.000
17.77
2.79
0.00
1.98
2329
2428
4.899457
TCCCTCCGAAAAAGAGCTCATATA
59.101
41.667
17.77
0.00
0.00
0.86
2336
2435
2.186532
ACTTCCCTCCGAAAAAGAGC
57.813
50.000
0.00
0.00
0.00
4.09
2351
2450
3.641436
AGATTTGGGTTGGTGGAAACTTC
59.359
43.478
0.00
0.00
0.00
3.01
2388
2487
9.983804
CCTCCGTAAAGAAATATACAAGAAAAC
57.016
33.333
0.00
0.00
0.00
2.43
2406
2536
6.196918
TGATCTCTAATACTCCCTCCGTAA
57.803
41.667
0.00
0.00
0.00
3.18
2430
2560
3.910490
GTTGCCGCCAAGTGCCAA
61.910
61.111
0.00
0.00
36.24
4.52
2432
2562
3.631487
GATGTTGCCGCCAAGTGCC
62.631
63.158
0.00
0.00
36.24
5.01
2433
2563
2.126346
GATGTTGCCGCCAAGTGC
60.126
61.111
0.00
0.00
0.00
4.40
2434
2564
1.210931
CAGATGTTGCCGCCAAGTG
59.789
57.895
0.00
0.00
0.00
3.16
2435
2565
0.036164
TACAGATGTTGCCGCCAAGT
59.964
50.000
0.00
0.00
0.00
3.16
2436
2566
0.729116
CTACAGATGTTGCCGCCAAG
59.271
55.000
0.00
0.00
0.00
3.61
2486
2616
2.812011
CAGGGGAACAGGAAAAACGTAG
59.188
50.000
0.00
0.00
0.00
3.51
2497
2627
2.196595
TGTAGGATTCCAGGGGAACAG
58.803
52.381
5.29
0.00
45.07
3.16
2546
2676
3.963129
AGTTGGTTCTGTTTGAGTTCCA
58.037
40.909
0.00
0.00
0.00
3.53
2569
2699
5.125097
CCCAATCATCTCTTTCAGAAACCAG
59.875
44.000
0.00
0.00
33.62
4.00
2612
2742
5.675684
AGGAAAGAAAAGCTTGGACAAAA
57.324
34.783
0.00
0.00
36.80
2.44
2617
2747
4.709397
TCAACAAGGAAAGAAAAGCTTGGA
59.291
37.500
0.00
0.00
36.80
3.53
2622
2752
6.276091
ACAGAATCAACAAGGAAAGAAAAGC
58.724
36.000
0.00
0.00
0.00
3.51
2623
2753
8.840321
TCTACAGAATCAACAAGGAAAGAAAAG
58.160
33.333
0.00
0.00
0.00
2.27
2630
2760
4.997395
GTGCTCTACAGAATCAACAAGGAA
59.003
41.667
0.00
0.00
0.00
3.36
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.