Multiple sequence alignment - TraesCS2D01G432300
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
TraesCS2D01G432300
chr2D
100.000
3200
0
0
1
3200
544615111
544611912
0.000000e+00
5910.0
1
TraesCS2D01G432300
chr2D
85.650
223
20
7
1196
1418
544613679
544613469
1.160000e-54
224.0
2
TraesCS2D01G432300
chr2D
85.650
223
20
7
1433
1643
544613916
544613694
1.160000e-54
224.0
3
TraesCS2D01G432300
chr2B
92.680
1612
93
13
1
1608
650169793
650168203
0.000000e+00
2300.0
4
TraesCS2D01G432300
chr2B
89.507
934
56
18
1558
2452
650168211
650167281
0.000000e+00
1144.0
5
TraesCS2D01G432300
chr2B
89.971
349
34
1
2649
2997
650166893
650166546
1.750000e-122
449.0
6
TraesCS2D01G432300
chr2B
83.103
290
32
6
1367
1643
650168678
650168393
6.850000e-62
248.0
7
TraesCS2D01G432300
chr2B
93.976
83
3
2
3119
3200
650166096
650166015
1.210000e-24
124.0
8
TraesCS2D01G432300
chr2B
100.000
45
0
0
2610
2654
667802115
667802159
2.050000e-12
84.2
9
TraesCS2D01G432300
chr2A
91.816
1564
108
13
762
2311
686842974
686841417
0.000000e+00
2161.0
10
TraesCS2D01G432300
chr2A
82.440
746
82
26
140
843
686843675
686842937
9.820000e-170
606.0
11
TraesCS2D01G432300
chr2A
84.593
344
30
12
2708
3051
686841215
686840895
1.430000e-83
320.0
12
TraesCS2D01G432300
chr2A
84.375
224
21
9
1196
1418
686842299
686842089
1.160000e-49
207.0
13
TraesCS2D01G432300
chr2A
93.243
74
5
0
2649
2722
686841309
686841236
3.370000e-20
110.0
14
TraesCS2D01G432300
chr2A
97.500
40
1
0
691
730
621188586
621188625
5.730000e-08
69.4
15
TraesCS2D01G432300
chr2A
100.000
35
0
0
1
35
686843726
686843692
7.410000e-07
65.8
16
TraesCS2D01G432300
chr1D
91.667
60
5
0
268
327
392950919
392950978
2.050000e-12
84.2
17
TraesCS2D01G432300
chr1D
96.000
50
2
0
2605
2654
286930014
286929965
7.360000e-12
82.4
18
TraesCS2D01G432300
chr1A
80.870
115
15
5
268
375
492270630
492270516
2.050000e-12
84.2
19
TraesCS2D01G432300
chr7D
96.000
50
2
0
2605
2654
58624673
58624722
7.360000e-12
82.4
20
TraesCS2D01G432300
chr7D
96.000
50
2
0
2605
2654
550839679
550839630
7.360000e-12
82.4
21
TraesCS2D01G432300
chr5B
96.000
50
2
0
2605
2654
615005134
615005085
7.360000e-12
82.4
22
TraesCS2D01G432300
chr5B
90.323
62
4
2
2593
2652
290450237
290450298
2.650000e-11
80.5
23
TraesCS2D01G432300
chr4A
96.000
50
2
0
2605
2654
734874288
734874239
7.360000e-12
82.4
24
TraesCS2D01G432300
chr4A
96.000
50
2
0
2605
2654
736112583
736112534
7.360000e-12
82.4
25
TraesCS2D01G432300
chr5A
92.593
54
4
0
2601
2654
523751774
523751721
9.520000e-11
78.7
26
TraesCS2D01G432300
chr3A
88.462
52
5
1
268
319
584127174
584127124
9.580000e-06
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
TraesCS2D01G432300
chr2D
544611912
544615111
3199
True
2119.333333
5910
90.433333
1
3200
3
chr2D.!!$R1
3199
1
TraesCS2D01G432300
chr2B
650166015
650169793
3778
True
853.000000
2300
89.847400
1
3200
5
chr2B.!!$R1
3199
2
TraesCS2D01G432300
chr2A
686840895
686843726
2831
True
578.300000
2161
89.411167
1
3051
6
chr2A.!!$R1
3050
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
97
98
0.246910
TGTACGCGAACATGGCCTAA
59.753
50.0
15.93
0.0
0.00
2.69
F
144
145
1.216064
AGTCAATCTGGCCCATGCTA
58.784
50.0
0.00
0.0
37.74
3.49
F
1093
1186
1.295020
TGGATCCATTCCCCGTCTTT
58.705
50.0
11.44
0.0
44.77
2.52
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1459
1552
1.377725
GACGTACTCCGGGGACTCA
60.378
63.158
9.33
0.00
42.24
3.41
R
2026
2174
2.504681
GTGCAAAATCAGGCGCCG
60.505
61.111
23.20
16.49
34.58
6.46
R
2544
2943
0.243636
CGGGCCAACATTCAGTTTCC
59.756
55.000
4.39
0.00
38.74
3.13
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
49
50
0.545309
ACTAGCAGAGGCCCTGTGAA
60.545
55.000
12.91
0.00
44.71
3.18
57
58
3.809832
CAGAGGCCCTGTGAATTATAACG
59.190
47.826
0.52
0.00
38.10
3.18
67
68
5.795972
TGTGAATTATAACGGACAACCTGA
58.204
37.500
0.00
0.00
0.00
3.86
77
78
4.504858
ACGGACAACCTGATCTTTGTATC
58.495
43.478
7.61
4.24
36.06
2.24
84
85
4.683832
ACCTGATCTTTGTATCTGTACGC
58.316
43.478
0.00
0.00
33.36
4.42
85
86
3.731216
CCTGATCTTTGTATCTGTACGCG
59.269
47.826
3.53
3.53
33.36
6.01
87
88
4.989044
TGATCTTTGTATCTGTACGCGAA
58.011
39.130
15.93
0.00
33.36
4.70
88
89
4.796830
TGATCTTTGTATCTGTACGCGAAC
59.203
41.667
15.93
0.00
33.36
3.95
97
98
0.246910
TGTACGCGAACATGGCCTAA
59.753
50.000
15.93
0.00
0.00
2.69
144
145
1.216064
AGTCAATCTGGCCCATGCTA
58.784
50.000
0.00
0.00
37.74
3.49
164
165
4.534103
GCTAAGAGGAATGGGGAGATGTAT
59.466
45.833
0.00
0.00
0.00
2.29
186
187
8.141909
TGTATAGTTGTGAAGGATAGCACATAC
58.858
37.037
0.00
0.00
43.73
2.39
243
244
7.220030
AGAGAGAGCACTTTAATGACTCAAAA
58.780
34.615
14.08
0.00
31.47
2.44
406
440
3.560896
GCAAGTTTCATTGTGTTGCCATT
59.439
39.130
0.00
0.00
38.03
3.16
440
474
4.947645
TGTCCCAAGCTCAAAGAATTTTG
58.052
39.130
0.00
0.00
44.03
2.44
482
516
1.425066
TCACCCCAAGCTCATTCAAGT
59.575
47.619
0.00
0.00
0.00
3.16
494
528
4.633565
GCTCATTCAAGTTTGGGACTAGAG
59.366
45.833
0.00
0.00
37.72
2.43
496
530
4.019321
TCATTCAAGTTTGGGACTAGAGGG
60.019
45.833
0.00
0.00
37.72
4.30
501
535
2.561526
AGTTTGGGACTAGAGGGGTACC
60.562
54.545
2.17
2.17
43.10
3.34
503
537
5.579676
AGTTTGGGACTAGAGGGGTACCTA
61.580
50.000
12.72
0.00
43.31
3.08
539
573
9.573133
AAACACTTATGCATGAAATAGTTTAGC
57.427
29.630
10.16
0.00
0.00
3.09
592
628
7.088589
AGTTACAAAAGGCTAAGCACATATG
57.911
36.000
0.00
0.00
0.00
1.78
716
760
2.487762
ACGTGTGGCACTTATCATTTGG
59.512
45.455
19.83
0.00
31.34
3.28
717
761
2.731968
CGTGTGGCACTTATCATTTGGC
60.732
50.000
19.83
0.00
36.39
4.52
773
817
3.866356
GTCTTTGGACCCGTACGC
58.134
61.111
10.49
0.00
36.53
4.42
1060
1153
2.215196
GCGTCTCTCCCTAGACTACTG
58.785
57.143
0.00
0.00
43.11
2.74
1061
1154
2.215196
CGTCTCTCCCTAGACTACTGC
58.785
57.143
0.00
0.00
43.11
4.40
1093
1186
1.295020
TGGATCCATTCCCCGTCTTT
58.705
50.000
11.44
0.00
44.77
2.52
1162
1255
3.740397
CCGGAGTACGTGCCGTCA
61.740
66.667
19.95
0.00
45.85
4.35
1207
1300
4.719369
GACCTCGCGCCGTTGACT
62.719
66.667
0.00
0.00
0.00
3.41
1285
1378
3.986006
GTGACGGTCACGGGCAGA
61.986
66.667
23.92
0.00
46.48
4.26
1292
1385
4.293648
TCACGGGCAGACACCACG
62.294
66.667
0.00
0.00
0.00
4.94
1300
1393
2.842462
AGACACCACGCCAGGTCA
60.842
61.111
0.00
0.00
40.77
4.02
1389
1482
1.819288
CGTGGCATCTCCGGAGTATAT
59.181
52.381
30.17
14.64
37.80
0.86
1699
1834
2.507992
CTGGAGCAGCGACCTTCG
60.508
66.667
11.82
0.00
43.89
3.79
1709
1844
2.177778
GACCTTCGTCGTCGGACC
59.822
66.667
1.91
0.00
40.17
4.46
1710
1845
3.333898
GACCTTCGTCGTCGGACCC
62.334
68.421
1.91
0.00
40.17
4.46
1768
1906
2.866523
ATTACTCCCCGTCGGCCTCA
62.867
60.000
5.50
0.00
0.00
3.86
1876
2014
3.591254
GAGGGCGGCGACATATCCC
62.591
68.421
17.61
12.95
37.24
3.85
2068
2217
4.681074
TGTTATCGGATTCATAGGCACA
57.319
40.909
0.00
0.00
0.00
4.57
2070
2219
6.353404
TGTTATCGGATTCATAGGCACATA
57.647
37.500
0.00
0.00
0.00
2.29
2140
2289
3.991773
TGTTAGTAGTTGCCTAACTTGCG
59.008
43.478
10.59
0.00
44.57
4.85
2154
2303
6.459298
GCCTAACTTGCGATACTACTCACTTA
60.459
42.308
0.00
0.00
0.00
2.24
2311
2472
6.705825
AGGTTTACAAATGGCAAATTTCTGAC
59.294
34.615
0.00
0.00
0.00
3.51
2318
2479
9.171877
ACAAATGGCAAATTTCTGACTTTTAAA
57.828
25.926
0.00
0.00
31.72
1.52
2319
2480
9.437045
CAAATGGCAAATTTCTGACTTTTAAAC
57.563
29.630
0.00
0.00
31.72
2.01
2322
2483
6.257630
TGGCAAATTTCTGACTTTTAAACTGC
59.742
34.615
0.00
0.00
0.00
4.40
2325
2486
7.847564
GCAAATTTCTGACTTTTAAACTGCAAG
59.152
33.333
0.00
0.00
42.29
4.01
2326
2487
8.330302
CAAATTTCTGACTTTTAAACTGCAAGG
58.670
33.333
0.00
0.00
39.30
3.61
2328
2489
6.377327
TTCTGACTTTTAAACTGCAAGGAG
57.623
37.500
0.00
0.00
39.30
3.69
2354
2528
1.889454
TCCAATTTGGATGCGGTGC
59.111
52.632
14.24
0.00
42.67
5.01
2363
2537
2.361483
ATGCGGTGCTTGATGGCA
60.361
55.556
0.00
0.00
40.15
4.92
2366
2540
1.517694
GCGGTGCTTGATGGCATTG
60.518
57.895
0.00
0.00
44.34
2.82
2387
2561
4.394729
TGTTTGCCTTCTTATCGGTTCTT
58.605
39.130
0.00
0.00
0.00
2.52
2404
2578
6.206634
TCGGTTCTTGATCTTAGCAAAATGTT
59.793
34.615
0.00
0.00
0.00
2.71
2417
2591
3.597255
CAAAATGTTGCCCATGTATGCA
58.403
40.909
0.00
0.00
32.82
3.96
2446
2620
1.276138
GTGGGGGAGCCAGAAAAATTG
59.724
52.381
0.00
0.00
0.00
2.32
2449
2623
3.245948
TGGGGGAGCCAGAAAAATTGTAT
60.246
43.478
0.00
0.00
0.00
2.29
2450
2624
3.384789
GGGGGAGCCAGAAAAATTGTATC
59.615
47.826
0.00
0.00
0.00
2.24
2451
2625
3.066760
GGGGAGCCAGAAAAATTGTATCG
59.933
47.826
0.00
0.00
0.00
2.92
2452
2626
3.945285
GGGAGCCAGAAAAATTGTATCGA
59.055
43.478
0.00
0.00
0.00
3.59
2454
2628
4.394920
GGAGCCAGAAAAATTGTATCGACA
59.605
41.667
0.00
0.00
0.00
4.35
2455
2629
5.447818
GGAGCCAGAAAAATTGTATCGACAG
60.448
44.000
0.00
0.00
36.76
3.51
2456
2630
4.396166
AGCCAGAAAAATTGTATCGACAGG
59.604
41.667
0.00
0.00
36.76
4.00
2457
2631
4.438744
GCCAGAAAAATTGTATCGACAGGG
60.439
45.833
0.00
0.00
36.76
4.45
2458
2632
4.438744
CCAGAAAAATTGTATCGACAGGGC
60.439
45.833
0.00
0.00
36.76
5.19
2459
2633
4.155826
CAGAAAAATTGTATCGACAGGGCA
59.844
41.667
0.00
0.00
36.76
5.36
2482
2881
9.280174
GGCATATAGTGTTATTAAGCAAGGTTA
57.720
33.333
0.00
0.00
0.00
2.85
2494
2893
2.647802
AGCAAGGTTAAGGAGGGCTAAA
59.352
45.455
0.00
0.00
0.00
1.85
2495
2894
2.753452
GCAAGGTTAAGGAGGGCTAAAC
59.247
50.000
0.00
0.00
0.00
2.01
2497
2896
2.639487
AGGTTAAGGAGGGCTAAACCA
58.361
47.619
5.44
0.00
41.67
3.67
2499
2898
4.377134
AGGTTAAGGAGGGCTAAACCATA
58.623
43.478
5.44
0.00
41.67
2.74
2512
2911
6.254804
GGGCTAAACCATAAAATACGCTTTTG
59.745
38.462
6.57
0.00
42.05
2.44
2517
2916
3.551485
CCATAAAATACGCTTTTGGCAGC
59.449
43.478
6.57
0.00
41.91
5.25
2519
2918
5.449862
CCATAAAATACGCTTTTGGCAGCTA
60.450
40.000
6.57
0.00
41.91
3.32
2520
2919
4.513198
AAAATACGCTTTTGGCAGCTAA
57.487
36.364
0.00
0.00
41.91
3.09
2521
2920
4.513198
AAATACGCTTTTGGCAGCTAAA
57.487
36.364
0.00
0.00
41.91
1.85
2522
2921
4.513198
AATACGCTTTTGGCAGCTAAAA
57.487
36.364
15.21
15.21
41.91
1.52
2562
2961
1.632589
AGGAAACTGAATGTTGGCCC
58.367
50.000
0.00
0.00
41.13
5.80
2566
2965
3.451894
CTGAATGTTGGCCCGGGC
61.452
66.667
38.57
38.57
41.06
6.13
2597
2996
3.145551
CCCTGCCTCTGCCAATGC
61.146
66.667
0.00
0.00
36.33
3.56
2598
2997
3.515286
CCTGCCTCTGCCAATGCG
61.515
66.667
0.00
0.00
41.78
4.73
2613
3012
0.251073
ATGCGGGTGGTAGGTTGTAC
59.749
55.000
0.00
0.00
0.00
2.90
2615
3014
0.108472
GCGGGTGGTAGGTTGTACTC
60.108
60.000
0.00
0.00
0.00
2.59
2616
3015
0.533951
CGGGTGGTAGGTTGTACTCC
59.466
60.000
0.00
0.00
0.00
3.85
2617
3016
0.907486
GGGTGGTAGGTTGTACTCCC
59.093
60.000
0.00
0.00
0.00
4.30
2618
3017
1.554118
GGGTGGTAGGTTGTACTCCCT
60.554
57.143
8.63
8.63
32.93
4.20
2619
3018
1.829849
GGTGGTAGGTTGTACTCCCTC
59.170
57.143
7.11
1.43
32.08
4.30
2620
3019
2.559252
GGTGGTAGGTTGTACTCCCTCT
60.559
54.545
7.11
0.00
32.08
3.69
2621
3020
2.496470
GTGGTAGGTTGTACTCCCTCTG
59.504
54.545
7.11
0.00
32.08
3.35
2622
3021
2.111255
TGGTAGGTTGTACTCCCTCTGT
59.889
50.000
7.11
0.00
32.08
3.41
2623
3022
3.334581
TGGTAGGTTGTACTCCCTCTGTA
59.665
47.826
7.11
0.00
32.08
2.74
2624
3023
4.202706
TGGTAGGTTGTACTCCCTCTGTAA
60.203
45.833
7.11
0.00
32.08
2.41
2626
3025
4.886496
AGGTTGTACTCCCTCTGTAAAC
57.114
45.455
0.00
0.00
0.00
2.01
2627
3026
4.490706
AGGTTGTACTCCCTCTGTAAACT
58.509
43.478
0.00
0.00
0.00
2.66
2628
3027
5.648247
AGGTTGTACTCCCTCTGTAAACTA
58.352
41.667
0.00
0.00
0.00
2.24
2629
3028
6.080009
AGGTTGTACTCCCTCTGTAAACTAA
58.920
40.000
0.00
0.00
0.00
2.24
2631
3030
7.897565
AGGTTGTACTCCCTCTGTAAACTAATA
59.102
37.037
0.00
0.00
0.00
0.98
2638
3037
8.862085
ACTCCCTCTGTAAACTAATATAAGAGC
58.138
37.037
0.00
0.00
0.00
4.09
2640
3039
7.504911
TCCCTCTGTAAACTAATATAAGAGCGT
59.495
37.037
0.00
0.00
0.00
5.07
2641
3040
7.808856
CCCTCTGTAAACTAATATAAGAGCGTC
59.191
40.741
0.00
0.00
0.00
5.19
2642
3041
8.569641
CCTCTGTAAACTAATATAAGAGCGTCT
58.430
37.037
0.00
0.00
0.00
4.18
2656
3077
4.300803
AGAGCGTCTAGATCACTACTACG
58.699
47.826
0.00
0.00
37.82
3.51
2661
3082
5.006552
GCGTCTAGATCACTACTACGAGTTT
59.993
44.000
0.00
0.00
36.15
2.66
2665
3086
8.755018
GTCTAGATCACTACTACGAGTTTAGAC
58.245
40.741
0.00
0.00
0.00
2.59
2714
3170
0.467290
GTTGTTTGGCTCCACCTGGA
60.467
55.000
0.00
0.00
43.08
3.86
2722
3178
1.318158
GCTCCACCTGGAAAGCATGG
61.318
60.000
0.00
0.00
44.91
3.66
2744
3200
4.421948
GTGATGTCGGTCAACCTAACTAG
58.578
47.826
0.00
0.00
0.00
2.57
2749
3205
4.828939
TGTCGGTCAACCTAACTAGAAGAA
59.171
41.667
0.00
0.00
0.00
2.52
2752
3208
5.035443
CGGTCAACCTAACTAGAAGAATCG
58.965
45.833
0.00
0.00
0.00
3.34
2759
3215
7.274603
ACCTAACTAGAAGAATCGGATGTAC
57.725
40.000
0.00
0.00
0.00
2.90
2788
3244
7.692291
CGTTGGCAGAATACTTGTAGTTTATTG
59.308
37.037
0.00
0.00
0.00
1.90
2806
3262
9.206870
AGTTTATTGCTTGGTTAAATTCATGTG
57.793
29.630
0.00
0.00
0.00
3.21
2829
3285
3.900966
TGGATCTCATGAACACCTCAG
57.099
47.619
0.00
0.00
37.52
3.35
2835
3291
5.233083
TCTCATGAACACCTCAGAAACAT
57.767
39.130
0.00
0.00
37.52
2.71
2866
3322
3.484649
CCAACAACCGTCGTAATCTATCG
59.515
47.826
0.00
0.00
0.00
2.92
2878
3334
8.927721
CGTCGTAATCTATCGGATATCATATCT
58.072
37.037
4.83
0.00
33.71
1.98
2984
3440
5.492895
TGCGTTTTCAATACTCCCTTGATA
58.507
37.500
0.00
0.00
32.94
2.15
2986
3442
5.353123
GCGTTTTCAATACTCCCTTGATACA
59.647
40.000
0.00
0.00
32.94
2.29
3044
3761
4.325119
TGCGGTTTGGCTGTTAGTTATTA
58.675
39.130
0.00
0.00
0.00
0.98
3051
3768
7.541091
GGTTTGGCTGTTAGTTATTAGCTTTTC
59.459
37.037
0.00
0.00
36.45
2.29
3066
3783
5.757850
AGCTTTTCTTGAAATCACGAGTT
57.242
34.783
0.00
0.00
0.00
3.01
3075
3792
7.203218
TCTTGAAATCACGAGTTCGATGATAT
58.797
34.615
8.72
3.45
43.02
1.63
3082
3799
7.674471
TCACGAGTTCGATGATATAAGAGAT
57.326
36.000
8.72
0.00
43.02
2.75
3106
3823
8.871629
ATTGGACCACACAAACTAAATACATA
57.128
30.769
0.00
0.00
0.00
2.29
3107
3824
7.675962
TGGACCACACAAACTAAATACATAC
57.324
36.000
0.00
0.00
0.00
2.39
3108
3825
7.455058
TGGACCACACAAACTAAATACATACT
58.545
34.615
0.00
0.00
0.00
2.12
3194
3978
6.900568
TGCTTTAAAAATGCATTTATCCCG
57.099
33.333
24.35
13.92
0.00
5.14
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
49
50
7.110155
ACAAAGATCAGGTTGTCCGTTATAAT
58.890
34.615
0.00
0.00
39.05
1.28
57
58
5.491982
ACAGATACAAAGATCAGGTTGTCC
58.508
41.667
11.38
6.83
38.80
4.02
67
68
4.740268
TGTTCGCGTACAGATACAAAGAT
58.260
39.130
14.93
0.00
0.00
2.40
77
78
0.179121
TAGGCCATGTTCGCGTACAG
60.179
55.000
22.78
12.01
0.00
2.74
84
85
1.134699
TCTGAGCTTAGGCCATGTTCG
60.135
52.381
5.01
0.00
39.73
3.95
85
86
2.559440
CTCTGAGCTTAGGCCATGTTC
58.441
52.381
5.01
2.34
39.73
3.18
87
88
0.835941
CCTCTGAGCTTAGGCCATGT
59.164
55.000
5.01
0.00
39.73
3.21
88
89
1.126488
TCCTCTGAGCTTAGGCCATG
58.874
55.000
5.01
0.00
39.73
3.66
97
98
0.043940
ACTCCCCATTCCTCTGAGCT
59.956
55.000
0.00
0.00
0.00
4.09
144
145
5.731924
ACTATACATCTCCCCATTCCTCTT
58.268
41.667
0.00
0.00
0.00
2.85
164
165
5.126545
ACGTATGTGCTATCCTTCACAACTA
59.873
40.000
0.00
0.00
45.03
2.24
243
244
7.665559
TCCTTGTGTAGATAGCATTGTTTCTTT
59.334
33.333
0.00
0.00
0.00
2.52
258
259
6.174720
AGAAACTTCATGTCCTTGTGTAGA
57.825
37.500
0.00
0.00
0.00
2.59
406
440
6.480763
TGAGCTTGGGACATTTGTAGAATTA
58.519
36.000
0.00
0.00
39.30
1.40
454
488
2.152016
GAGCTTGGGGTGAACAGTAAC
58.848
52.381
0.00
0.00
0.00
2.50
469
503
3.837355
AGTCCCAAACTTGAATGAGCTT
58.163
40.909
0.00
0.00
33.03
3.74
482
516
1.726352
AGGTACCCCTCTAGTCCCAAA
59.274
52.381
8.74
0.00
35.62
3.28
494
528
0.684153
TGTGTAGGCGTAGGTACCCC
60.684
60.000
8.74
2.05
0.00
4.95
496
530
2.029110
TGTTTGTGTAGGCGTAGGTACC
60.029
50.000
2.73
2.73
0.00
3.34
501
535
4.201685
GCATAAGTGTTTGTGTAGGCGTAG
60.202
45.833
0.00
0.00
0.00
3.51
503
537
2.482721
GCATAAGTGTTTGTGTAGGCGT
59.517
45.455
0.00
0.00
0.00
5.68
539
573
9.636965
GCTTTCTTTGTTTAAATTGTTTAGCAG
57.363
29.630
0.00
0.00
0.00
4.24
556
590
7.203218
AGCCTTTTGTAACTAAGCTTTCTTTG
58.797
34.615
3.20
0.00
33.85
2.77
614
650
7.277319
GCTAAATACACGAAAAGGCTTAGTACT
59.723
37.037
0.00
0.00
0.00
2.73
625
661
8.673711
AGATGCTAAATGCTAAATACACGAAAA
58.326
29.630
0.00
0.00
43.37
2.29
679
715
0.387929
ACGTGTGACCGTTCTGACAT
59.612
50.000
0.00
0.00
37.96
3.06
1036
1125
3.955101
CTAGGGAGAGACGCCGCG
61.955
72.222
12.14
12.14
0.00
6.46
1222
1315
2.437359
ACGTACTCCGGGGACTCG
60.437
66.667
9.33
12.28
42.24
4.18
1285
1378
2.347490
GATGACCTGGCGTGGTGT
59.653
61.111
6.72
0.00
41.00
4.16
1459
1552
1.377725
GACGTACTCCGGGGACTCA
60.378
63.158
9.33
0.00
42.24
3.41
1709
1844
4.082523
AGGTGTCGATGTGGCGGG
62.083
66.667
0.00
0.00
0.00
6.13
1710
1845
2.509336
GAGGTGTCGATGTGGCGG
60.509
66.667
0.00
0.00
0.00
6.13
1715
1850
2.573869
CCGCAGAGGTGTCGATGT
59.426
61.111
0.00
0.00
34.51
3.06
1717
1852
4.498520
CGCCGCAGAGGTGTCGAT
62.499
66.667
0.00
0.00
45.30
3.59
1859
1997
3.626924
GGGATATGTCGCCGCCCT
61.627
66.667
0.00
0.00
35.86
5.19
1861
1999
3.986006
TCGGGATATGTCGCCGCC
61.986
66.667
12.42
0.00
37.79
6.13
2026
2174
2.504681
GTGCAAAATCAGGCGCCG
60.505
61.111
23.20
16.49
34.58
6.46
2070
2219
9.887629
CAATATCTCATACTATTCCAATCTGCT
57.112
33.333
0.00
0.00
0.00
4.24
2087
2236
5.571791
TGCATGAGGAATCCAATATCTCA
57.428
39.130
0.61
0.00
38.59
3.27
2140
2289
8.604890
GCAAACAGGAAATAAGTGAGTAGTATC
58.395
37.037
0.00
0.00
0.00
2.24
2154
2303
1.000274
GAAGCACGGCAAACAGGAAAT
60.000
47.619
0.00
0.00
0.00
2.17
2278
2430
4.464597
TGCCATTTGTAAACCTGGGAATAC
59.535
41.667
0.00
0.00
31.26
1.89
2283
2435
3.760580
TTTGCCATTTGTAAACCTGGG
57.239
42.857
0.00
0.00
31.26
4.45
2285
2437
6.705381
TCAGAAATTTGCCATTTGTAAACCTG
59.295
34.615
0.00
0.00
31.05
4.00
2292
2453
8.729805
TTAAAAGTCAGAAATTTGCCATTTGT
57.270
26.923
0.00
0.00
0.00
2.83
2311
2472
3.496331
TCCCCTCCTTGCAGTTTAAAAG
58.504
45.455
0.00
0.00
0.00
2.27
2318
2479
1.501582
GATACTCCCCTCCTTGCAGT
58.498
55.000
0.00
0.00
0.00
4.40
2319
2480
0.761802
GGATACTCCCCTCCTTGCAG
59.238
60.000
0.00
0.00
0.00
4.41
2322
2483
4.210331
CAAATTGGATACTCCCCTCCTTG
58.790
47.826
0.00
0.00
35.03
3.61
2325
2486
2.783510
TCCAAATTGGATACTCCCCTCC
59.216
50.000
11.23
0.00
42.67
4.30
2363
2537
5.010282
AGAACCGATAAGAAGGCAAACAAT
58.990
37.500
0.00
0.00
0.00
2.71
2366
2540
4.454504
TCAAGAACCGATAAGAAGGCAAAC
59.545
41.667
0.00
0.00
0.00
2.93
2374
2548
6.465439
TGCTAAGATCAAGAACCGATAAGA
57.535
37.500
0.00
0.00
0.00
2.10
2404
2578
1.076850
CCACCTGCATACATGGGCA
60.077
57.895
8.39
8.39
38.52
5.36
2417
2591
1.923909
GCTCCCCCACTAACCACCT
60.924
63.158
0.00
0.00
0.00
4.00
2446
2620
4.785511
ACACTATATGCCCTGTCGATAC
57.214
45.455
0.00
0.00
0.00
2.24
2449
2623
5.801531
AATAACACTATATGCCCTGTCGA
57.198
39.130
0.00
0.00
0.00
4.20
2450
2624
6.090898
GCTTAATAACACTATATGCCCTGTCG
59.909
42.308
0.00
0.00
0.00
4.35
2451
2625
6.934645
TGCTTAATAACACTATATGCCCTGTC
59.065
38.462
0.00
0.00
0.00
3.51
2452
2626
6.837312
TGCTTAATAACACTATATGCCCTGT
58.163
36.000
0.00
0.00
0.00
4.00
2454
2628
6.942576
CCTTGCTTAATAACACTATATGCCCT
59.057
38.462
0.00
0.00
0.00
5.19
2455
2629
6.715264
ACCTTGCTTAATAACACTATATGCCC
59.285
38.462
0.00
0.00
0.00
5.36
2456
2630
7.745620
ACCTTGCTTAATAACACTATATGCC
57.254
36.000
0.00
0.00
0.00
4.40
2482
2881
5.826208
CGTATTTTATGGTTTAGCCCTCCTT
59.174
40.000
0.00
0.00
36.04
3.36
2483
2882
5.374071
CGTATTTTATGGTTTAGCCCTCCT
58.626
41.667
0.00
0.00
36.04
3.69
2544
2943
0.243636
CGGGCCAACATTCAGTTTCC
59.756
55.000
4.39
0.00
38.74
3.13
2597
2996
0.533951
GGAGTACAACCTACCACCCG
59.466
60.000
0.00
0.00
0.00
5.28
2598
2997
0.907486
GGGAGTACAACCTACCACCC
59.093
60.000
8.59
0.00
35.30
4.61
2613
3012
8.024285
CGCTCTTATATTAGTTTACAGAGGGAG
58.976
40.741
4.76
0.00
40.49
4.30
2615
3014
7.659186
ACGCTCTTATATTAGTTTACAGAGGG
58.341
38.462
8.36
8.36
42.53
4.30
2616
3015
8.569641
AGACGCTCTTATATTAGTTTACAGAGG
58.430
37.037
0.00
0.00
0.00
3.69
2624
3023
9.509956
AGTGATCTAGACGCTCTTATATTAGTT
57.490
33.333
0.00
0.00
0.00
2.24
2629
3028
9.590451
GTAGTAGTGATCTAGACGCTCTTATAT
57.410
37.037
10.41
0.00
0.00
0.86
2631
3030
6.587226
CGTAGTAGTGATCTAGACGCTCTTAT
59.413
42.308
10.41
2.13
33.25
1.73
2633
3032
4.746115
CGTAGTAGTGATCTAGACGCTCTT
59.254
45.833
10.41
5.20
33.25
2.85
2634
3033
4.037803
TCGTAGTAGTGATCTAGACGCTCT
59.962
45.833
10.41
7.61
36.98
4.09
2635
3034
4.297510
TCGTAGTAGTGATCTAGACGCTC
58.702
47.826
10.41
0.00
36.98
5.03
2636
3035
4.202141
ACTCGTAGTAGTGATCTAGACGCT
60.202
45.833
0.00
4.20
36.98
5.07
2637
3036
4.050553
ACTCGTAGTAGTGATCTAGACGC
58.949
47.826
0.00
0.00
36.98
5.19
2638
3037
6.586868
AAACTCGTAGTAGTGATCTAGACG
57.413
41.667
0.00
0.00
37.71
4.18
2640
3039
8.694540
AGTCTAAACTCGTAGTAGTGATCTAGA
58.305
37.037
0.00
0.00
0.00
2.43
2641
3040
8.876275
AGTCTAAACTCGTAGTAGTGATCTAG
57.124
38.462
0.00
0.00
0.00
2.43
2642
3041
9.743057
GTAGTCTAAACTCGTAGTAGTGATCTA
57.257
37.037
0.00
0.00
36.92
1.98
2643
3042
8.477256
AGTAGTCTAAACTCGTAGTAGTGATCT
58.523
37.037
0.00
0.00
36.92
2.75
2644
3043
8.647143
AGTAGTCTAAACTCGTAGTAGTGATC
57.353
38.462
0.00
0.00
36.92
2.92
2672
3093
8.495949
CAACTCAAAACTAAGCTTTCTATTCGA
58.504
33.333
3.20
0.00
0.00
3.71
2714
3170
1.271325
TGACCGACATCACCATGCTTT
60.271
47.619
0.00
0.00
32.57
3.51
2722
3178
3.314541
AGTTAGGTTGACCGACATCAC
57.685
47.619
10.76
0.00
42.08
3.06
2752
3208
0.535335
TCTGCCAACGGAGTACATCC
59.465
55.000
0.00
0.00
45.00
3.51
2759
3215
2.699954
ACAAGTATTCTGCCAACGGAG
58.300
47.619
0.00
0.00
31.21
4.63
2788
3244
6.862209
TCCATACACATGAATTTAACCAAGC
58.138
36.000
0.00
0.00
33.67
4.01
2806
3262
5.069648
TCTGAGGTGTTCATGAGATCCATAC
59.930
44.000
12.38
0.84
34.68
2.39
2808
3264
4.035814
TCTGAGGTGTTCATGAGATCCAT
58.964
43.478
12.38
0.00
34.68
3.41
2829
3285
5.578776
GGTTGTTGGGATTATCGATGTTTC
58.421
41.667
8.54
1.92
0.00
2.78
2835
3291
2.736081
CGACGGTTGTTGGGATTATCGA
60.736
50.000
0.00
0.00
0.00
3.59
2958
3414
2.482721
AGGGAGTATTGAAAACGCAACG
59.517
45.455
0.00
0.00
0.00
4.10
2960
3416
4.138290
TCAAGGGAGTATTGAAAACGCAA
58.862
39.130
0.00
0.00
33.85
4.85
2984
3440
3.567397
AGCTAGGTCGTATCAAGGATGT
58.433
45.455
0.00
0.00
0.00
3.06
2986
3442
3.823873
CTGAGCTAGGTCGTATCAAGGAT
59.176
47.826
16.71
0.00
0.00
3.24
3044
3761
5.559035
CGAACTCGTGATTTCAAGAAAAGCT
60.559
40.000
0.00
0.00
34.32
3.74
3051
3768
5.709011
ATCATCGAACTCGTGATTTCAAG
57.291
39.130
9.76
0.00
37.05
3.02
3062
3779
7.757624
GGTCCAATCTCTTATATCATCGAACTC
59.242
40.741
0.00
0.00
0.00
3.01
3066
3783
6.493458
TGTGGTCCAATCTCTTATATCATCGA
59.507
38.462
0.00
0.00
0.00
3.59
3075
3792
5.304686
AGTTTGTGTGGTCCAATCTCTTA
57.695
39.130
0.00
0.00
0.00
2.10
3082
3799
7.940137
AGTATGTATTTAGTTTGTGTGGTCCAA
59.060
33.333
0.00
0.00
0.00
3.53
3106
3823
7.801716
TCAGTTAAGCATCAAGTTGTTTAGT
57.198
32.000
2.11
0.00
0.00
2.24
3137
3921
9.449719
AAGGATACGTTTGACTATTTTGAGAAT
57.550
29.630
0.00
0.00
46.39
2.40
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.