Multiple sequence alignment - TraesCS5A01G354200
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
TraesCS5A01G354200
chr5A
100.000
2903
0
0
1
2903
556824296
556821394
0.000000e+00
5361.0
1
TraesCS5A01G354200
chr5A
94.702
2095
107
3
115
2206
572042963
572040870
0.000000e+00
3251.0
2
TraesCS5A01G354200
chr5A
94.423
2080
112
2
128
2207
514263440
514261365
0.000000e+00
3195.0
3
TraesCS5A01G354200
chr5A
83.569
1059
159
9
1152
2208
480822806
480823851
0.000000e+00
977.0
4
TraesCS5A01G354200
chr1A
96.228
2121
68
6
99
2207
96354678
96356798
0.000000e+00
3463.0
5
TraesCS5A01G354200
chr1A
95.349
43
2
0
594
636
96356006
96356048
5.190000e-08
69.4
6
TraesCS5A01G354200
chrUn
94.904
2080
106
0
126
2205
281038937
281041016
0.000000e+00
3254.0
7
TraesCS5A01G354200
chrUn
80.500
1400
224
32
773
2158
170190948
170189584
0.000000e+00
1027.0
8
TraesCS5A01G354200
chrUn
81.250
96
14
3
2783
2876
26732879
26732972
1.120000e-09
75.0
9
TraesCS5A01G354200
chrUn
92.000
50
4
0
2825
2874
143847038
143847087
1.440000e-08
71.3
10
TraesCS5A01G354200
chrUn
89.796
49
5
0
2828
2876
26525443
26525395
2.420000e-06
63.9
11
TraesCS5A01G354200
chr7A
93.986
2095
108
5
122
2211
675052012
675049931
0.000000e+00
3155.0
12
TraesCS5A01G354200
chr7D
93.580
2056
117
4
154
2209
610424860
610422820
0.000000e+00
3051.0
13
TraesCS5A01G354200
chr5B
90.058
865
70
11
1346
2205
711861957
711861104
0.000000e+00
1107.0
14
TraesCS5A01G354200
chr6B
83.664
1059
159
8
1152
2209
171212112
171213157
0.000000e+00
985.0
15
TraesCS5A01G354200
chr6B
76.431
594
132
7
773
1364
626609863
626610450
6.040000e-82
315.0
16
TraesCS5A01G354200
chr6B
93.617
47
3
0
2828
2874
82958143
82958097
1.440000e-08
71.3
17
TraesCS5A01G354200
chr6B
93.333
45
3
0
2828
2872
83127839
83127795
1.870000e-07
67.6
18
TraesCS5A01G354200
chr2A
83.396
1060
155
9
1154
2207
729062297
729063341
0.000000e+00
963.0
19
TraesCS5A01G354200
chr2A
83.286
1059
157
8
1154
2206
642222822
642223866
0.000000e+00
957.0
20
TraesCS5A01G354200
chr7B
85.714
798
98
9
1411
2207
115224908
115225690
0.000000e+00
828.0
21
TraesCS5A01G354200
chr5D
89.508
305
15
4
2602
2903
440797428
440797718
1.270000e-98
370.0
22
TraesCS5A01G354200
chr5D
83.539
243
17
10
2208
2447
440795926
440796148
3.790000e-49
206.0
23
TraesCS5A01G354200
chr5D
97.403
77
2
0
298
374
553476196
553476272
6.530000e-27
132.0
24
TraesCS5A01G354200
chr5D
96.875
32
1
0
2515
2546
440797339
440797370
1.000000e-03
54.7
25
TraesCS5A01G354200
chr6A
93.617
47
3
0
2828
2874
34956875
34956829
1.440000e-08
71.3
26
TraesCS5A01G354200
chr6A
80.851
94
14
3
2783
2874
47701988
47702079
1.440000e-08
71.3
27
TraesCS5A01G354200
chr6A
80.851
94
14
3
2783
2874
47884701
47884792
1.440000e-08
71.3
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
TraesCS5A01G354200
chr5A
556821394
556824296
2902
True
5361.000000
5361
100.0000
1
2903
1
chr5A.!!$R2
2902
1
TraesCS5A01G354200
chr5A
572040870
572042963
2093
True
3251.000000
3251
94.7020
115
2206
1
chr5A.!!$R3
2091
2
TraesCS5A01G354200
chr5A
514261365
514263440
2075
True
3195.000000
3195
94.4230
128
2207
1
chr5A.!!$R1
2079
3
TraesCS5A01G354200
chr5A
480822806
480823851
1045
False
977.000000
977
83.5690
1152
2208
1
chr5A.!!$F1
1056
4
TraesCS5A01G354200
chr1A
96354678
96356798
2120
False
1766.200000
3463
95.7885
99
2207
2
chr1A.!!$F1
2108
5
TraesCS5A01G354200
chrUn
281038937
281041016
2079
False
3254.000000
3254
94.9040
126
2205
1
chrUn.!!$F3
2079
6
TraesCS5A01G354200
chrUn
170189584
170190948
1364
True
1027.000000
1027
80.5000
773
2158
1
chrUn.!!$R2
1385
7
TraesCS5A01G354200
chr7A
675049931
675052012
2081
True
3155.000000
3155
93.9860
122
2211
1
chr7A.!!$R1
2089
8
TraesCS5A01G354200
chr7D
610422820
610424860
2040
True
3051.000000
3051
93.5800
154
2209
1
chr7D.!!$R1
2055
9
TraesCS5A01G354200
chr5B
711861104
711861957
853
True
1107.000000
1107
90.0580
1346
2205
1
chr5B.!!$R1
859
10
TraesCS5A01G354200
chr6B
171212112
171213157
1045
False
985.000000
985
83.6640
1152
2209
1
chr6B.!!$F1
1057
11
TraesCS5A01G354200
chr6B
626609863
626610450
587
False
315.000000
315
76.4310
773
1364
1
chr6B.!!$F2
591
12
TraesCS5A01G354200
chr2A
729062297
729063341
1044
False
963.000000
963
83.3960
1154
2207
1
chr2A.!!$F2
1053
13
TraesCS5A01G354200
chr2A
642222822
642223866
1044
False
957.000000
957
83.2860
1154
2206
1
chr2A.!!$F1
1052
14
TraesCS5A01G354200
chr7B
115224908
115225690
782
False
828.000000
828
85.7140
1411
2207
1
chr7B.!!$F1
796
15
TraesCS5A01G354200
chr5D
440795926
440797718
1792
False
210.233333
370
89.9740
2208
2903
3
chr5D.!!$F2
695
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
36
37
0.322456
GGCATGCCTACAACCACTGA
60.322
55.0
29.98
0.0
0.0
3.41
F
473
489
0.893727
GTTGGGGGACAGCATCGTTT
60.894
55.0
0.00
0.0
0.0
3.60
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1070
1086
0.655733
CGGCGAAGAAACAACACTGT
59.344
50.0
0.0
0.0
37.39
3.55
R
2047
2096
0.388649
CACACCCGACTAGCACTCAC
60.389
60.0
0.0
0.0
0.00
3.51
R
All possible primers
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
33
34
4.743018
AGGCATGCCTACAACCAC
57.257
55.556
37.99
7.11
46.14
4.16
34
35
2.078452
AGGCATGCCTACAACCACT
58.922
52.632
37.99
10.83
46.14
4.00
35
36
0.322816
AGGCATGCCTACAACCACTG
60.323
55.000
37.99
0.00
46.14
3.66
36
37
0.322456
GGCATGCCTACAACCACTGA
60.322
55.000
29.98
0.00
0.00
3.41
37
38
1.533625
GCATGCCTACAACCACTGAA
58.466
50.000
6.36
0.00
0.00
3.02
38
39
1.470098
GCATGCCTACAACCACTGAAG
59.530
52.381
6.36
0.00
0.00
3.02
39
40
2.783135
CATGCCTACAACCACTGAAGT
58.217
47.619
0.00
0.00
0.00
3.01
40
41
2.543777
TGCCTACAACCACTGAAGTC
57.456
50.000
0.00
0.00
0.00
3.01
41
42
1.071699
TGCCTACAACCACTGAAGTCC
59.928
52.381
0.00
0.00
0.00
3.85
42
43
1.071699
GCCTACAACCACTGAAGTCCA
59.928
52.381
0.00
0.00
0.00
4.02
43
44
2.486548
GCCTACAACCACTGAAGTCCAA
60.487
50.000
0.00
0.00
0.00
3.53
44
45
3.139077
CCTACAACCACTGAAGTCCAAC
58.861
50.000
0.00
0.00
0.00
3.77
45
46
2.052782
ACAACCACTGAAGTCCAACC
57.947
50.000
0.00
0.00
0.00
3.77
46
47
1.564348
ACAACCACTGAAGTCCAACCT
59.436
47.619
0.00
0.00
0.00
3.50
47
48
2.775384
ACAACCACTGAAGTCCAACCTA
59.225
45.455
0.00
0.00
0.00
3.08
48
49
3.201266
ACAACCACTGAAGTCCAACCTAA
59.799
43.478
0.00
0.00
0.00
2.69
49
50
4.204012
CAACCACTGAAGTCCAACCTAAA
58.796
43.478
0.00
0.00
0.00
1.85
50
51
4.513406
ACCACTGAAGTCCAACCTAAAA
57.487
40.909
0.00
0.00
0.00
1.52
51
52
4.862371
ACCACTGAAGTCCAACCTAAAAA
58.138
39.130
0.00
0.00
0.00
1.94
78
79
3.761481
GCAATCAGCAGTGTCACAC
57.239
52.632
0.00
0.00
44.79
3.82
79
80
0.946528
GCAATCAGCAGTGTCACACA
59.053
50.000
11.40
0.00
44.79
3.72
80
81
1.538512
GCAATCAGCAGTGTCACACAT
59.461
47.619
11.40
0.00
44.79
3.21
81
82
2.667448
GCAATCAGCAGTGTCACACATG
60.667
50.000
11.40
6.10
44.79
3.21
82
83
2.809696
CAATCAGCAGTGTCACACATGA
59.190
45.455
11.40
11.49
36.74
3.07
83
84
2.845363
TCAGCAGTGTCACACATGAT
57.155
45.000
11.40
1.38
37.14
2.45
84
85
2.691927
TCAGCAGTGTCACACATGATC
58.308
47.619
11.40
0.00
37.14
2.92
85
86
2.037511
TCAGCAGTGTCACACATGATCA
59.962
45.455
11.40
0.00
37.14
2.92
86
87
3.007635
CAGCAGTGTCACACATGATCAT
58.992
45.455
11.40
1.18
37.14
2.45
87
88
4.081531
TCAGCAGTGTCACACATGATCATA
60.082
41.667
11.40
0.00
37.14
2.15
88
89
4.814771
CAGCAGTGTCACACATGATCATAT
59.185
41.667
11.40
0.00
37.14
1.78
89
90
4.814771
AGCAGTGTCACACATGATCATATG
59.185
41.667
12.46
12.46
37.14
1.78
90
91
4.024302
GCAGTGTCACACATGATCATATGG
60.024
45.833
17.92
7.39
37.14
2.74
91
92
5.121105
CAGTGTCACACATGATCATATGGT
58.879
41.667
17.92
9.18
37.14
3.55
92
93
5.007332
CAGTGTCACACATGATCATATGGTG
59.993
44.000
17.92
18.15
37.14
4.17
93
94
5.104817
AGTGTCACACATGATCATATGGTGA
60.105
40.000
24.00
23.14
37.82
4.02
94
95
5.761726
GTGTCACACATGATCATATGGTGAT
59.238
40.000
25.98
12.92
41.09
3.06
95
96
6.293244
GTGTCACACATGATCATATGGTGATG
60.293
42.308
25.98
13.21
39.76
3.07
96
97
9.575777
GTGTCACACATGATCATATGGTGATGC
62.576
44.444
25.98
20.37
39.76
3.91
209
210
1.687493
CCTCCTCGGCTTCCTCCTT
60.687
63.158
0.00
0.00
0.00
3.36
473
489
0.893727
GTTGGGGGACAGCATCGTTT
60.894
55.000
0.00
0.00
0.00
3.60
486
502
1.942657
CATCGTTTGCGGATGGAGAAT
59.057
47.619
0.00
0.00
38.89
2.40
498
514
3.267860
GAGAATGCGCCTGCTCCG
61.268
66.667
9.42
0.00
43.34
4.63
811
827
4.154347
CCTCTCCGGCTGTGCTCC
62.154
72.222
0.00
0.00
0.00
4.70
884
900
2.289694
ACCTCGTCAAGTCTTCCATTGG
60.290
50.000
0.00
0.00
0.00
3.16
973
989
1.219124
CTGGCTGCCACTCGTACAT
59.781
57.895
19.30
0.00
0.00
2.29
1070
1086
1.395045
CGGCTGGAGGCTATCAGTGA
61.395
60.000
15.70
0.00
41.46
3.41
1090
1106
0.934496
CAGTGTTGTTTCTTCGCCGA
59.066
50.000
0.00
0.00
0.00
5.54
1143
1159
0.902531
GGACTTTGAGGATCGGTGGA
59.097
55.000
0.00
0.00
38.61
4.02
1148
1164
0.252057
TTGAGGATCGGTGGAGGACA
60.252
55.000
0.00
0.00
38.61
4.02
1291
1314
1.038280
GGTACTGGCTACTATGGCGT
58.962
55.000
0.00
0.00
35.06
5.68
1351
1374
4.519730
TGCACAAGATGATGATTCAACACA
59.480
37.500
0.00
0.00
34.96
3.72
1556
1603
2.124570
CATGCCTCAAGGTCCGGG
60.125
66.667
0.00
0.00
37.57
5.73
1605
1652
3.199880
AGTAGTTTCAGTTGCACAGCT
57.800
42.857
0.00
0.00
0.00
4.24
1715
1762
4.734398
AGAACAAAAGTTGCAACATCCA
57.266
36.364
30.11
0.00
0.00
3.41
1915
1964
8.806146
AGGTTAATGTGTGATAGCATTTTTCTT
58.194
29.630
0.00
0.00
36.75
2.52
2109
2159
3.620427
TGATTAACCGTGCCATGTACT
57.380
42.857
0.00
0.00
0.00
2.73
2121
2171
2.890945
GCCATGTACTGTTTTTGGGTCT
59.109
45.455
0.00
0.00
0.00
3.85
2226
2276
6.882610
AAAAAGCAGTGTCATACATCTTCA
57.117
33.333
0.00
0.00
0.00
3.02
2262
2315
0.964700
TTTGGAATCGTGCCATGCAA
59.035
45.000
0.00
0.00
41.47
4.08
2264
2317
1.314534
TGGAATCGTGCCATGCAAGG
61.315
55.000
2.86
2.86
41.47
3.61
2266
2319
0.527565
GAATCGTGCCATGCAAGGTT
59.472
50.000
10.15
0.16
43.24
3.50
2267
2320
0.968405
AATCGTGCCATGCAAGGTTT
59.032
45.000
10.15
0.00
38.07
3.27
2274
2327
2.754552
TGCCATGCAAGGTTTAGCTAAG
59.245
45.455
10.15
0.00
34.76
2.18
2389
2442
1.665679
GACTTGCATGTCACCGTATGG
59.334
52.381
23.72
0.00
42.84
2.74
2396
2449
2.022764
TGTCACCGTATGGAAGCATG
57.977
50.000
8.33
0.00
39.21
4.06
2398
2451
2.290008
TGTCACCGTATGGAAGCATGTT
60.290
45.455
8.33
0.00
39.21
2.71
2405
2458
5.417580
ACCGTATGGAAGCATGTTTGTATTT
59.582
36.000
8.33
0.00
39.21
1.40
2406
2459
5.971202
CCGTATGGAAGCATGTTTGTATTTC
59.029
40.000
0.00
0.00
37.49
2.17
2447
2500
3.359950
GCCAATTTCCTGGATCAGAGTT
58.640
45.455
0.00
0.00
38.96
3.01
2450
2503
5.595952
GCCAATTTCCTGGATCAGAGTTAAT
59.404
40.000
0.00
0.00
38.96
1.40
2452
2505
7.486647
CCAATTTCCTGGATCAGAGTTAATTG
58.513
38.462
14.76
14.76
38.96
2.32
2453
2506
7.340232
CCAATTTCCTGGATCAGAGTTAATTGA
59.660
37.037
20.00
0.00
38.96
2.57
2455
2508
8.688747
ATTTCCTGGATCAGAGTTAATTGATC
57.311
34.615
14.40
14.40
45.66
2.92
2509
2587
7.527568
TTCCGTAAAAGGGATGTTTTTATGT
57.472
32.000
8.18
0.00
36.19
2.29
2510
2588
7.527568
TCCGTAAAAGGGATGTTTTTATGTT
57.472
32.000
8.18
0.00
36.19
2.71
2511
2589
7.953752
TCCGTAAAAGGGATGTTTTTATGTTT
58.046
30.769
8.18
0.00
36.19
2.83
2512
2590
8.422566
TCCGTAAAAGGGATGTTTTTATGTTTT
58.577
29.630
8.18
0.00
36.19
2.43
2513
2591
8.705134
CCGTAAAAGGGATGTTTTTATGTTTTC
58.295
33.333
8.18
0.00
36.19
2.29
2557
3750
3.008049
ACGTATTCCAAAGTCTTGCTCCT
59.992
43.478
0.00
0.00
0.00
3.69
2560
3753
4.861102
ATTCCAAAGTCTTGCTCCTTTG
57.139
40.909
5.39
5.39
44.48
2.77
2584
3777
3.058457
GCACGAAGCGTTCAACTTC
57.942
52.632
0.00
0.00
38.32
3.01
2593
3786
2.510615
CGTTCAACTTCGCAGAATCC
57.489
50.000
0.00
0.00
45.90
3.01
2594
3787
1.798223
CGTTCAACTTCGCAGAATCCA
59.202
47.619
0.00
0.00
45.90
3.41
2595
3788
2.223144
CGTTCAACTTCGCAGAATCCAA
59.777
45.455
0.00
0.00
45.90
3.53
2596
3789
3.303725
CGTTCAACTTCGCAGAATCCAAA
60.304
43.478
0.00
0.00
45.90
3.28
2597
3790
4.606961
GTTCAACTTCGCAGAATCCAAAA
58.393
39.130
0.00
0.00
45.90
2.44
2598
3791
4.909696
TCAACTTCGCAGAATCCAAAAA
57.090
36.364
0.00
0.00
45.90
1.94
2647
3840
1.406065
CCATGGACGATCTGGAGGCT
61.406
60.000
5.56
0.00
31.38
4.58
2658
3851
3.534941
GGAGGCTTCCGTATCCGT
58.465
61.111
0.00
0.00
32.79
4.69
2659
3852
2.724520
GGAGGCTTCCGTATCCGTA
58.275
57.895
0.00
0.00
32.79
4.02
2660
3853
1.254954
GGAGGCTTCCGTATCCGTAT
58.745
55.000
0.00
0.00
32.79
3.06
2661
3854
1.201880
GGAGGCTTCCGTATCCGTATC
59.798
57.143
0.00
0.00
32.79
2.24
2670
3863
2.415857
CCGTATCCGTATCCGAGAAGAG
59.584
54.545
0.00
0.00
35.63
2.85
2677
3870
0.472898
TATCCGAGAAGAGGAGGCGA
59.527
55.000
0.00
0.00
41.66
5.54
2715
3911
1.287191
CGTCGGCGATCATGGATCT
59.713
57.895
14.79
0.00
41.33
2.75
2716
3912
0.319040
CGTCGGCGATCATGGATCTT
60.319
55.000
14.79
0.00
41.33
2.40
2747
3943
2.951745
GCGTCGACCTCATCAGCG
60.952
66.667
10.58
0.00
0.00
5.18
2767
3963
0.807667
CGCTCCCTGACGAAATCCTG
60.808
60.000
0.00
0.00
0.00
3.86
2780
3976
0.554305
AATCCTGGGCAGCATCATCA
59.446
50.000
0.00
0.00
0.00
3.07
2781
3977
0.110678
ATCCTGGGCAGCATCATCAG
59.889
55.000
0.00
0.00
0.00
2.90
2782
3978
0.984432
TCCTGGGCAGCATCATCAGA
60.984
55.000
0.00
0.00
0.00
3.27
2783
3979
0.110678
CCTGGGCAGCATCATCAGAT
59.889
55.000
0.00
0.00
33.87
2.90
2784
3980
1.524848
CTGGGCAGCATCATCAGATC
58.475
55.000
0.00
0.00
30.20
2.75
2785
3981
0.841289
TGGGCAGCATCATCAGATCA
59.159
50.000
0.00
0.00
30.20
2.92
2786
3982
1.423921
TGGGCAGCATCATCAGATCAT
59.576
47.619
0.00
0.00
30.20
2.45
2787
3983
2.085320
GGGCAGCATCATCAGATCATC
58.915
52.381
0.00
0.00
30.20
2.92
2809
4005
1.562475
CCCTTATCCCCGTCAAGGAAA
59.438
52.381
1.17
0.00
45.00
3.13
2838
4034
1.076192
AACCGTTCTCTCCTCCCGA
59.924
57.895
0.00
0.00
0.00
5.14
2894
4090
1.507174
CCGTCGACAAGGACCTCTC
59.493
63.158
17.16
0.00
33.30
3.20
2897
4093
0.528470
GTCGACAAGGACCTCTCCAG
59.472
60.000
11.55
0.00
39.39
3.86
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
12
13
2.037121
GTGGTTGTAGGCATGCCTTTTT
59.963
45.455
42.49
22.57
45.70
1.94
13
14
1.618343
GTGGTTGTAGGCATGCCTTTT
59.382
47.619
42.49
22.96
45.70
2.27
14
15
1.203050
AGTGGTTGTAGGCATGCCTTT
60.203
47.619
42.49
23.74
45.70
3.11
15
16
0.405585
AGTGGTTGTAGGCATGCCTT
59.594
50.000
42.49
26.18
45.70
4.35
17
18
0.322456
TCAGTGGTTGTAGGCATGCC
60.322
55.000
30.12
30.12
0.00
4.40
18
19
1.470098
CTTCAGTGGTTGTAGGCATGC
59.530
52.381
9.90
9.90
0.00
4.06
19
20
2.744202
GACTTCAGTGGTTGTAGGCATG
59.256
50.000
0.00
0.00
32.74
4.06
20
21
2.290323
GGACTTCAGTGGTTGTAGGCAT
60.290
50.000
0.00
0.00
34.07
4.40
21
22
1.071699
GGACTTCAGTGGTTGTAGGCA
59.928
52.381
0.00
0.00
34.07
4.75
22
23
1.071699
TGGACTTCAGTGGTTGTAGGC
59.928
52.381
0.00
0.00
31.74
3.93
23
24
3.139077
GTTGGACTTCAGTGGTTGTAGG
58.861
50.000
0.00
0.00
0.00
3.18
24
25
3.139077
GGTTGGACTTCAGTGGTTGTAG
58.861
50.000
0.00
0.00
0.00
2.74
25
26
2.775384
AGGTTGGACTTCAGTGGTTGTA
59.225
45.455
0.00
0.00
0.00
2.41
26
27
1.564348
AGGTTGGACTTCAGTGGTTGT
59.436
47.619
0.00
0.00
0.00
3.32
27
28
2.348411
AGGTTGGACTTCAGTGGTTG
57.652
50.000
0.00
0.00
0.00
3.77
28
29
4.513406
TTTAGGTTGGACTTCAGTGGTT
57.487
40.909
0.00
0.00
0.00
3.67
29
30
4.513406
TTTTAGGTTGGACTTCAGTGGT
57.487
40.909
0.00
0.00
0.00
4.16
60
61
0.946528
TGTGTGACACTGCTGATTGC
59.053
50.000
17.47
0.00
35.11
3.56
61
62
2.809696
TCATGTGTGACACTGCTGATTG
59.190
45.455
17.47
3.80
35.11
2.67
62
63
3.130280
TCATGTGTGACACTGCTGATT
57.870
42.857
17.47
0.00
35.11
2.57
63
64
2.845363
TCATGTGTGACACTGCTGAT
57.155
45.000
17.47
0.00
35.11
2.90
64
65
2.037511
TGATCATGTGTGACACTGCTGA
59.962
45.455
17.47
15.94
37.14
4.26
65
66
2.419667
TGATCATGTGTGACACTGCTG
58.580
47.619
17.47
11.43
37.14
4.41
66
67
2.845363
TGATCATGTGTGACACTGCT
57.155
45.000
17.47
4.45
37.14
4.24
67
68
4.024302
CCATATGATCATGTGTGACACTGC
60.024
45.833
25.29
2.56
37.14
4.40
68
69
5.007332
CACCATATGATCATGTGTGACACTG
59.993
44.000
25.29
12.20
37.14
3.66
69
70
5.104817
TCACCATATGATCATGTGTGACACT
60.105
40.000
25.29
0.00
37.14
3.55
70
71
5.118286
TCACCATATGATCATGTGTGACAC
58.882
41.667
25.29
9.14
37.14
3.67
71
72
5.356291
TCACCATATGATCATGTGTGACA
57.644
39.130
25.29
10.10
37.14
3.58
72
73
5.334646
GCATCACCATATGATCATGTGTGAC
60.335
44.000
25.87
16.77
45.52
3.67
73
74
4.758165
GCATCACCATATGATCATGTGTGA
59.242
41.667
25.29
25.51
45.52
3.58
74
75
4.517453
TGCATCACCATATGATCATGTGTG
59.483
41.667
25.29
22.30
45.52
3.82
75
76
4.721132
TGCATCACCATATGATCATGTGT
58.279
39.130
25.29
14.02
45.52
3.72
76
77
5.414454
TCATGCATCACCATATGATCATGTG
59.586
40.000
21.91
21.91
45.52
3.21
77
78
5.566469
TCATGCATCACCATATGATCATGT
58.434
37.500
18.72
8.98
45.52
3.21
78
79
6.699575
ATCATGCATCACCATATGATCATG
57.300
37.500
18.72
3.77
45.52
3.07
79
80
7.665974
GGATATCATGCATCACCATATGATCAT
59.334
37.037
13.81
13.81
45.52
2.45
80
81
6.996282
GGATATCATGCATCACCATATGATCA
59.004
38.462
3.65
0.00
45.52
2.92
81
82
7.225011
AGGATATCATGCATCACCATATGATC
58.775
38.462
3.65
0.00
45.52
2.92
83
84
6.570654
AGGATATCATGCATCACCATATGA
57.429
37.500
3.65
0.00
43.13
2.15
84
85
7.331193
CGATAGGATATCATGCATCACCATATG
59.669
40.741
4.83
0.00
0.00
1.78
85
86
7.384477
CGATAGGATATCATGCATCACCATAT
58.616
38.462
4.83
0.00
0.00
1.78
86
87
6.752168
CGATAGGATATCATGCATCACCATA
58.248
40.000
4.83
0.00
0.00
2.74
87
88
5.608449
CGATAGGATATCATGCATCACCAT
58.392
41.667
4.83
0.00
0.00
3.55
88
89
5.014808
CGATAGGATATCATGCATCACCA
57.985
43.478
4.83
0.00
0.00
4.17
209
210
3.092511
GGGCTGCTGGGGAGATGA
61.093
66.667
0.00
0.00
0.00
2.92
370
386
2.683933
GGGAAGGCGAGGTGGAGA
60.684
66.667
0.00
0.00
0.00
3.71
473
489
2.896854
GCGCATTCTCCATCCGCA
60.897
61.111
0.30
0.00
43.67
5.69
602
618
1.353394
ACCCAGGCACCTTATAGGGC
61.353
60.000
9.27
0.00
40.58
5.19
663
679
0.467290
AAGCTTGTTTGGCCGGAAGA
60.467
50.000
5.05
0.00
0.00
2.87
811
827
0.460987
CTACAAGGCGCCTCCTGAAG
60.461
60.000
32.93
18.55
46.94
3.02
884
900
1.980772
AGCAGCCCCAATTCAGCAC
60.981
57.895
0.00
0.00
0.00
4.40
1070
1086
0.655733
CGGCGAAGAAACAACACTGT
59.344
50.000
0.00
0.00
37.39
3.55
1090
1106
1.842562
CTCAGGAGACCCATTGATGGT
59.157
52.381
9.07
0.00
46.65
3.55
1143
1159
1.208293
GCCGAGGAAGAGAAATGTCCT
59.792
52.381
0.00
0.00
44.67
3.85
1148
1164
1.153349
GGCGCCGAGGAAGAGAAAT
60.153
57.895
12.58
0.00
0.00
2.17
1291
1314
3.795688
AGGAAGAACATCTGCAGGAAA
57.204
42.857
15.13
0.00
0.00
3.13
1351
1374
1.128188
ACCGTTCCTTGCTCCTCCTT
61.128
55.000
0.00
0.00
0.00
3.36
1684
1731
8.611757
GTTGCAACTTTTGTTCTTTTTATCCAT
58.388
29.630
22.36
0.00
41.35
3.41
1715
1762
2.665008
TTCAGCACGCTTGGCAGTCT
62.665
55.000
0.00
0.00
0.00
3.24
1915
1964
0.970640
TGCACTCACGCCTAACCTTA
59.029
50.000
0.00
0.00
0.00
2.69
2047
2096
0.388649
CACACCCGACTAGCACTCAC
60.389
60.000
0.00
0.00
0.00
3.51
2217
2267
7.285629
ACTTGTACTAGCTAGCATGAAGATGTA
59.714
37.037
20.91
5.02
31.50
2.29
2226
2276
5.677319
TCCAAACTTGTACTAGCTAGCAT
57.323
39.130
20.91
4.85
0.00
3.79
2262
2315
6.769512
TGACTCAACATTCTTAGCTAAACCT
58.230
36.000
7.74
0.00
0.00
3.50
2264
2317
9.899226
AAAATGACTCAACATTCTTAGCTAAAC
57.101
29.630
7.74
0.00
39.19
2.01
2309
2362
9.766277
GACTCAACATTGATCTAGAAAAATGAC
57.234
33.333
25.89
12.60
36.46
3.06
2345
2398
9.334693
GTCACTTAAAATGACTCAACATTGATC
57.665
33.333
10.82
0.00
42.68
2.92
2383
2436
6.785191
AGAAATACAAACATGCTTCCATACG
58.215
36.000
0.00
0.00
0.00
3.06
2384
2437
8.986477
AAAGAAATACAAACATGCTTCCATAC
57.014
30.769
0.00
0.00
0.00
2.39
2410
2463
8.627377
AGGAAATTGGCCCATCTTCTATATTAT
58.373
33.333
0.00
0.00
0.00
1.28
2413
2466
6.251471
CAGGAAATTGGCCCATCTTCTATAT
58.749
40.000
0.00
0.00
0.00
0.86
2416
2469
3.373001
CCAGGAAATTGGCCCATCTTCTA
60.373
47.826
0.00
0.00
0.00
2.10
2417
2470
2.625087
CCAGGAAATTGGCCCATCTTCT
60.625
50.000
0.00
0.00
0.00
2.85
2418
2471
1.758862
CCAGGAAATTGGCCCATCTTC
59.241
52.381
0.00
1.96
0.00
2.87
2424
2477
1.063717
TCTGATCCAGGAAATTGGCCC
60.064
52.381
0.00
0.00
38.16
5.80
2483
2561
9.245481
ACATAAAAACATCCCTTTTACGGAATA
57.755
29.630
0.00
0.00
32.56
1.75
2484
2562
8.129496
ACATAAAAACATCCCTTTTACGGAAT
57.871
30.769
0.00
0.00
32.56
3.01
2486
2564
7.527568
AACATAAAAACATCCCTTTTACGGA
57.472
32.000
0.00
0.00
32.56
4.69
2487
2565
8.596271
AAAACATAAAAACATCCCTTTTACGG
57.404
30.769
0.00
0.00
32.56
4.02
2488
2566
9.471084
AGAAAACATAAAAACATCCCTTTTACG
57.529
29.630
0.00
0.00
32.56
3.18
2506
2584
7.588488
CGGTTTATAACACGTGAAAGAAAACAT
59.412
33.333
25.01
4.04
0.00
2.71
2508
2586
6.357766
CCGGTTTATAACACGTGAAAGAAAAC
59.642
38.462
25.01
21.51
0.00
2.43
2509
2587
6.038050
ACCGGTTTATAACACGTGAAAGAAAA
59.962
34.615
25.01
12.36
0.00
2.29
2510
2588
5.526846
ACCGGTTTATAACACGTGAAAGAAA
59.473
36.000
25.01
15.46
0.00
2.52
2511
2589
5.055812
ACCGGTTTATAACACGTGAAAGAA
58.944
37.500
25.01
10.11
0.00
2.52
2512
2590
4.630111
ACCGGTTTATAACACGTGAAAGA
58.370
39.130
25.01
3.64
0.00
2.52
2513
2591
4.996062
ACCGGTTTATAACACGTGAAAG
57.004
40.909
25.01
3.35
0.00
2.62
2546
3722
0.394565
ACGAGCAAAGGAGCAAGACT
59.605
50.000
0.00
0.00
36.85
3.24
2547
3723
0.514691
CACGAGCAAAGGAGCAAGAC
59.485
55.000
0.00
0.00
36.85
3.01
2548
3724
1.230635
GCACGAGCAAAGGAGCAAGA
61.231
55.000
0.00
0.00
41.58
3.02
2574
3767
1.798223
TGGATTCTGCGAAGTTGAACG
59.202
47.619
0.00
0.00
0.00
3.95
2595
3788
6.091577
CGTAAAAAGGGTTCTGCAAAGTTTTT
59.908
34.615
0.00
0.00
32.16
1.94
2596
3789
5.579119
CGTAAAAAGGGTTCTGCAAAGTTTT
59.421
36.000
0.00
0.00
0.00
2.43
2597
3790
5.106442
CGTAAAAAGGGTTCTGCAAAGTTT
58.894
37.500
0.00
0.00
0.00
2.66
2598
3791
4.440940
CCGTAAAAAGGGTTCTGCAAAGTT
60.441
41.667
0.00
0.00
0.00
2.66
2599
3792
3.067601
CCGTAAAAAGGGTTCTGCAAAGT
59.932
43.478
0.00
0.00
0.00
2.66
2600
3793
3.638484
CCGTAAAAAGGGTTCTGCAAAG
58.362
45.455
0.00
0.00
0.00
2.77
2657
3850
0.594110
CGCCTCCTCTTCTCGGATAC
59.406
60.000
0.00
0.00
0.00
2.24
2658
3851
0.472898
TCGCCTCCTCTTCTCGGATA
59.527
55.000
0.00
0.00
0.00
2.59
2659
3852
0.821711
CTCGCCTCCTCTTCTCGGAT
60.822
60.000
0.00
0.00
0.00
4.18
2660
3853
1.452289
CTCGCCTCCTCTTCTCGGA
60.452
63.158
0.00
0.00
0.00
4.55
2661
3854
1.452289
TCTCGCCTCCTCTTCTCGG
60.452
63.158
0.00
0.00
0.00
4.63
2677
3870
3.537874
GTATGCCCCGGCTCGTCT
61.538
66.667
7.35
0.00
42.51
4.18
2747
3943
2.174319
GGATTTCGTCAGGGAGCGC
61.174
63.158
0.00
0.00
0.00
5.92
2767
3963
2.085320
GATGATCTGATGATGCTGCCC
58.915
52.381
0.00
0.00
32.19
5.36
2780
3976
2.112691
ACGGGGATAAGGGAGATGATCT
59.887
50.000
0.00
0.00
0.00
2.75
2781
3977
2.498078
GACGGGGATAAGGGAGATGATC
59.502
54.545
0.00
0.00
0.00
2.92
2782
3978
2.158158
TGACGGGGATAAGGGAGATGAT
60.158
50.000
0.00
0.00
0.00
2.45
2783
3979
1.219469
TGACGGGGATAAGGGAGATGA
59.781
52.381
0.00
0.00
0.00
2.92
2784
3980
1.717032
TGACGGGGATAAGGGAGATG
58.283
55.000
0.00
0.00
0.00
2.90
2785
3981
2.330216
CTTGACGGGGATAAGGGAGAT
58.670
52.381
0.00
0.00
0.00
2.75
2786
3982
1.691482
CCTTGACGGGGATAAGGGAGA
60.691
57.143
0.00
0.00
37.82
3.71
2787
3983
0.759346
CCTTGACGGGGATAAGGGAG
59.241
60.000
0.00
0.00
37.82
4.30
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.