Multiple sequence alignment - TraesCS3D01G269700
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
TraesCS3D01G269700
chr3D
100.000
2468
0
0
2647
5114
374209586
374207119
0.000000e+00
4558.0
1
TraesCS3D01G269700
chr3D
100.000
2423
0
0
1
2423
374212232
374209810
0.000000e+00
4475.0
2
TraesCS3D01G269700
chr3D
89.583
48
1
4
5066
5111
339252958
339253003
1.990000e-04
58.4
3
TraesCS3D01G269700
chr3A
94.106
2477
89
23
2647
5114
496706015
496703587
0.000000e+00
3712.0
4
TraesCS3D01G269700
chr3A
89.742
2174
76
55
1
2086
496708389
496706275
0.000000e+00
2643.0
5
TraesCS3D01G269700
chr3A
87.786
131
15
1
2209
2339
496706273
496706144
8.870000e-33
152.0
6
TraesCS3D01G269700
chr3A
83.051
118
16
3
1168
1285
118566671
118566784
2.520000e-18
104.0
7
TraesCS3D01G269700
chr3A
96.552
58
2
0
2127
2184
496705634
496705691
4.210000e-16
97.1
8
TraesCS3D01G269700
chr3A
96.296
54
2
0
3270
3323
496705449
496705396
7.050000e-14
89.8
9
TraesCS3D01G269700
chr3A
94.872
39
2
0
2079
2117
657522656
657522618
1.540000e-05
62.1
10
TraesCS3D01G269700
chr3B
94.822
2047
70
12
3070
5114
487909227
487907215
0.000000e+00
3160.0
11
TraesCS3D01G269700
chr3B
91.170
2401
83
51
1
2309
487912377
487910014
0.000000e+00
3140.0
12
TraesCS3D01G269700
chr3B
93.484
399
19
5
2648
3043
487909818
487909424
2.050000e-163
586.0
13
TraesCS3D01G269700
chr3B
94.382
89
3
2
2337
2423
487909936
487909848
8.930000e-28
135.0
14
TraesCS3D01G269700
chr3B
94.444
54
2
1
3270
3323
487909079
487909027
1.180000e-11
82.4
15
TraesCS3D01G269700
chr3B
91.525
59
4
1
2127
2184
487909434
487909492
4.240000e-11
80.5
16
TraesCS3D01G269700
chr4A
82.161
768
103
21
3352
4113
658262254
658261515
3.360000e-176
628.0
17
TraesCS3D01G269700
chr4A
94.872
39
2
0
2079
2117
734367086
734367048
1.540000e-05
62.1
18
TraesCS3D01G269700
chr7B
82.213
759
103
20
3361
4113
164157811
164158543
4.350000e-175
625.0
19
TraesCS3D01G269700
chr7B
100.000
36
0
0
2082
2117
245991839
245991874
3.300000e-07
67.6
20
TraesCS3D01G269700
chr2D
80.749
774
91
23
3361
4103
596163728
596162982
7.480000e-153
551.0
21
TraesCS3D01G269700
chr2B
80.469
768
100
27
3352
4113
785240840
785240117
4.500000e-150
542.0
22
TraesCS3D01G269700
chr2B
79.793
772
105
30
3352
4113
793488137
793487407
9.820000e-142
514.0
23
TraesCS3D01G269700
chr4B
80.339
768
105
26
3352
4113
16557424
16558151
1.620000e-149
540.0
24
TraesCS3D01G269700
chr4B
97.368
38
1
0
2080
2117
73612787
73612824
1.190000e-06
65.8
25
TraesCS3D01G269700
chr6B
80.364
769
102
29
3352
4113
351224238
351224964
5.830000e-149
538.0
26
TraesCS3D01G269700
chr6B
97.297
37
1
0
2080
2116
647951537
647951573
4.270000e-06
63.9
27
TraesCS3D01G269700
chr2A
82.137
655
92
15
3463
4113
778619716
778620349
5.830000e-149
538.0
28
TraesCS3D01G269700
chr2A
97.297
37
1
0
2082
2118
769485829
769485865
4.270000e-06
63.9
29
TraesCS3D01G269700
chr2A
94.872
39
2
0
2079
2117
686781515
686781553
1.540000e-05
62.1
30
TraesCS3D01G269700
chr2A
100.000
30
0
0
2184
2213
221283441
221283412
7.150000e-04
56.5
31
TraesCS3D01G269700
chr1B
77.178
241
43
10
1419
1647
642392312
642392072
4.160000e-26
130.0
32
TraesCS3D01G269700
chr1B
85.870
92
12
1
1194
1285
433633671
433633581
4.210000e-16
97.1
33
TraesCS3D01G269700
chr1A
84.375
128
20
0
1520
1647
557935723
557935596
5.380000e-25
126.0
34
TraesCS3D01G269700
chr1D
76.763
241
44
10
1419
1647
465522431
465522191
1.930000e-24
124.0
35
TraesCS3D01G269700
chr7D
82.308
130
20
2
1520
1646
632756271
632756400
5.410000e-20
110.0
36
TraesCS3D01G269700
chr7D
100.000
30
0
0
2184
2213
610762727
610762698
7.150000e-04
56.5
37
TraesCS3D01G269700
chr6A
80.916
131
22
2
1520
1647
575589572
575589702
3.260000e-17
100.0
38
TraesCS3D01G269700
chr5A
97.368
38
1
0
2081
2118
287608236
287608199
1.190000e-06
65.8
39
TraesCS3D01G269700
chr5A
92.500
40
3
0
2951
2990
403876082
403876121
1.990000e-04
58.4
40
TraesCS3D01G269700
chr7A
100.000
30
0
0
2184
2213
700612450
700612421
7.150000e-04
56.5
41
TraesCS3D01G269700
chr7A
100.000
30
0
0
2184
2213
700635687
700635658
7.150000e-04
56.5
42
TraesCS3D01G269700
chr7A
100.000
30
0
0
2184
2213
700653311
700653282
7.150000e-04
56.5
43
TraesCS3D01G269700
chrUn
100.000
29
0
0
2184
2212
83375478
83375450
3.000000e-03
54.7
44
TraesCS3D01G269700
chr6D
100.000
29
0
0
2184
2212
178131351
178131379
3.000000e-03
54.7
45
TraesCS3D01G269700
chr4D
100.000
29
0
0
2184
2212
24864735
24864763
3.000000e-03
54.7
BLAST Results - HSPs grouped
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS3D01G269700
chr3D
374207119
374212232
5113
True
4516.50
4558
100.0000
1
5114
2
chr3D.!!$R1
5113
1
TraesCS3D01G269700
chr3A
496703587
496708389
4802
True
1649.20
3712
91.9825
1
5114
4
chr3A.!!$R2
5113
2
TraesCS3D01G269700
chr3B
487907215
487912377
5162
True
1420.68
3160
93.6604
1
5114
5
chr3B.!!$R1
5113
3
TraesCS3D01G269700
chr4A
658261515
658262254
739
True
628.00
628
82.1610
3352
4113
1
chr4A.!!$R1
761
4
TraesCS3D01G269700
chr7B
164157811
164158543
732
False
625.00
625
82.2130
3361
4113
1
chr7B.!!$F1
752
5
TraesCS3D01G269700
chr2D
596162982
596163728
746
True
551.00
551
80.7490
3361
4103
1
chr2D.!!$R1
742
6
TraesCS3D01G269700
chr2B
785240117
785240840
723
True
542.00
542
80.4690
3352
4113
1
chr2B.!!$R1
761
7
TraesCS3D01G269700
chr2B
793487407
793488137
730
True
514.00
514
79.7930
3352
4113
1
chr2B.!!$R2
761
8
TraesCS3D01G269700
chr4B
16557424
16558151
727
False
540.00
540
80.3390
3352
4113
1
chr4B.!!$F1
761
9
TraesCS3D01G269700
chr6B
351224238
351224964
726
False
538.00
538
80.3640
3352
4113
1
chr6B.!!$F1
761
10
TraesCS3D01G269700
chr2A
778619716
778620349
633
False
538.00
538
82.1370
3463
4113
1
chr2A.!!$F3
650
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
452
475
0.108992
TCGCGTTTATGTTCTCGGCT
60.109
50.000
5.77
0.0
0.00
5.52
F
1471
1593
0.243095
ACTACCGGAAGAACACGCTC
59.757
55.000
9.46
0.0
0.00
5.03
F
2340
2511
0.824759
ATCTACACGTCTTGCCTCCC
59.175
55.000
0.00
0.0
0.00
4.30
F
2343
2514
1.122632
TACACGTCTTGCCTCCCCAA
61.123
55.000
0.00
0.0
0.00
4.12
F
2344
2515
1.228124
CACGTCTTGCCTCCCCAAA
60.228
57.895
0.00
0.0
0.00
3.28
F
2996
3242
1.340088
TGCATGTGGCCTTGATGTTT
58.660
45.000
3.32
0.0
43.89
2.83
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2328
2499
0.250727
TTCTTTGGGGAGGCAAGACG
60.251
55.000
0.00
0.00
0.00
4.18
R
2933
3179
0.690762
AGGGGTCGGCGCATATAAAT
59.309
50.000
10.83
0.00
0.00
1.40
R
3572
3994
1.755179
ATGTGTTGGTAGCTGATGGC
58.245
50.000
0.00
0.00
42.19
4.40
R
3762
4191
5.704053
GGTTCATTTTCTTTACTCCGGAAGA
59.296
40.000
5.23
1.78
0.00
2.87
R
3934
4374
6.430000
ACATAAGCTTCCAAGTGAAAATACGT
59.570
34.615
0.00
0.00
31.06
3.57
R
4918
5386
0.040204
ACCATGGCAAAGAAGAGGGG
59.960
55.000
13.04
0.00
0.00
4.79
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
253
254
3.357079
CGGCACCCACAACTGCTC
61.357
66.667
0.00
0.00
33.63
4.26
254
255
2.985847
GGCACCCACAACTGCTCC
60.986
66.667
0.00
0.00
33.63
4.70
255
256
3.357079
GCACCCACAACTGCTCCG
61.357
66.667
0.00
0.00
0.00
4.63
256
257
3.357079
CACCCACAACTGCTCCGC
61.357
66.667
0.00
0.00
0.00
5.54
257
258
4.643387
ACCCACAACTGCTCCGCC
62.643
66.667
0.00
0.00
0.00
6.13
258
259
4.335647
CCCACAACTGCTCCGCCT
62.336
66.667
0.00
0.00
0.00
5.52
259
260
2.281761
CCACAACTGCTCCGCCTT
60.282
61.111
0.00
0.00
0.00
4.35
260
261
2.620112
CCACAACTGCTCCGCCTTG
61.620
63.158
0.00
0.00
0.00
3.61
261
262
2.980233
ACAACTGCTCCGCCTTGC
60.980
61.111
0.00
0.00
0.00
4.01
344
364
1.141858
GGGTGATTTTTGGCCCAACAA
59.858
47.619
0.00
0.00
40.76
2.83
345
365
2.493035
GGTGATTTTTGGCCCAACAAG
58.507
47.619
0.00
0.00
0.00
3.16
346
366
1.872952
GTGATTTTTGGCCCAACAAGC
59.127
47.619
3.70
3.70
0.00
4.01
391
413
0.391661
AGGTTTCGAGCGTGCATCAT
60.392
50.000
0.00
0.00
0.00
2.45
446
469
4.235382
ACGTAACATCGCGTTTATGTTC
57.765
40.909
22.98
15.29
44.36
3.18
447
470
3.922240
ACGTAACATCGCGTTTATGTTCT
59.078
39.130
22.98
8.02
44.36
3.01
448
471
4.030977
ACGTAACATCGCGTTTATGTTCTC
59.969
41.667
22.98
17.05
44.36
2.87
449
472
3.634730
AACATCGCGTTTATGTTCTCG
57.365
42.857
16.32
0.00
42.45
4.04
450
473
1.924524
ACATCGCGTTTATGTTCTCGG
59.075
47.619
5.77
0.00
33.83
4.63
451
474
0.928229
ATCGCGTTTATGTTCTCGGC
59.072
50.000
5.77
0.00
0.00
5.54
452
475
0.108992
TCGCGTTTATGTTCTCGGCT
60.109
50.000
5.77
0.00
0.00
5.52
454
477
1.076332
GCGTTTATGTTCTCGGCTGT
58.924
50.000
0.00
0.00
0.00
4.40
457
493
2.092211
CGTTTATGTTCTCGGCTGTCAC
59.908
50.000
0.00
0.00
0.00
3.67
483
519
5.107104
TGCAAGCATTTACTAGACAGTTTCG
60.107
40.000
0.00
0.00
36.14
3.46
509
545
2.811317
GGAAGCTGTCACCTCGCG
60.811
66.667
0.00
0.00
0.00
5.87
543
579
3.012518
CCATTAGCAGACAAGTCCCTTG
58.987
50.000
2.54
2.54
45.85
3.61
681
758
6.862469
TTAACTACAGCAGTACCCAACTAT
57.138
37.500
0.00
0.00
36.04
2.12
684
761
6.862469
ACTACAGCAGTACCCAACTATAAA
57.138
37.500
0.00
0.00
35.76
1.40
685
762
6.637657
ACTACAGCAGTACCCAACTATAAAC
58.362
40.000
0.00
0.00
35.76
2.01
686
763
4.501071
ACAGCAGTACCCAACTATAAACG
58.499
43.478
0.00
0.00
35.76
3.60
690
767
6.148150
CAGCAGTACCCAACTATAAACGAAAA
59.852
38.462
0.00
0.00
35.76
2.29
691
768
6.882678
AGCAGTACCCAACTATAAACGAAAAT
59.117
34.615
0.00
0.00
35.76
1.82
857
957
1.463674
AGGGCCACGCATAAAGAAAG
58.536
50.000
6.18
0.00
0.00
2.62
858
958
0.455815
GGGCCACGCATAAAGAAAGG
59.544
55.000
4.39
0.00
0.00
3.11
859
959
1.459450
GGCCACGCATAAAGAAAGGA
58.541
50.000
0.00
0.00
0.00
3.36
860
960
1.816224
GGCCACGCATAAAGAAAGGAA
59.184
47.619
0.00
0.00
0.00
3.36
861
961
2.230266
GGCCACGCATAAAGAAAGGAAA
59.770
45.455
0.00
0.00
0.00
3.13
862
962
3.242518
GCCACGCATAAAGAAAGGAAAC
58.757
45.455
0.00
0.00
0.00
2.78
863
963
3.488489
CCACGCATAAAGAAAGGAAACG
58.512
45.455
0.00
0.00
0.00
3.60
925
1025
2.283676
GTCGTCTCCCACTCCCCA
60.284
66.667
0.00
0.00
0.00
4.96
958
1068
2.774234
TCCCTCCAAAGCATAGAGAAGG
59.226
50.000
0.00
0.00
0.00
3.46
1350
1468
5.107837
CCAAGTAAGATTCGATTCGATTCGG
60.108
44.000
24.57
12.61
39.95
4.30
1369
1487
2.369394
GGTTCGCCTCTGAAATTGGAT
58.631
47.619
0.00
0.00
0.00
3.41
1371
1489
2.749621
GTTCGCCTCTGAAATTGGATGT
59.250
45.455
0.00
0.00
0.00
3.06
1372
1490
3.904800
TCGCCTCTGAAATTGGATGTA
57.095
42.857
0.00
0.00
0.00
2.29
1382
1500
2.489938
ATTGGATGTACGCTGTTGGT
57.510
45.000
0.00
0.00
0.00
3.67
1401
1519
4.819761
GGCCGCTGCTGATCGACA
62.820
66.667
0.00
0.00
37.74
4.35
1471
1593
0.243095
ACTACCGGAAGAACACGCTC
59.757
55.000
9.46
0.00
0.00
5.03
1543
1665
0.994247
TCAAGGTGAGCATGGATGGT
59.006
50.000
0.00
0.00
41.89
3.55
1688
1813
5.200368
ACTTTCCATCTTTGCGTTTGAAT
57.800
34.783
0.00
0.00
0.00
2.57
1704
1832
5.449041
CGTTTGAATGGATCCAGTGGTATTG
60.449
44.000
21.47
2.07
0.00
1.90
1809
1963
8.424918
ACTAGTAATAACATCCACCTCTGATTG
58.575
37.037
0.00
0.00
0.00
2.67
1964
2118
4.878397
GTGATCTTCCATGGGAGTAAGTTG
59.122
45.833
20.09
0.00
31.21
3.16
1977
2137
6.889722
TGGGAGTAAGTTGCTTTAATTGCTAT
59.110
34.615
0.00
0.00
0.00
2.97
1978
2138
8.050325
TGGGAGTAAGTTGCTTTAATTGCTATA
58.950
33.333
0.00
0.00
0.00
1.31
2031
2191
8.517323
AGGAGTAATCCCAGAATATCTTTGAT
57.483
34.615
5.39
0.00
0.00
2.57
2065
2225
6.404712
ACAAATCTCGTCGAACTTTAATCC
57.595
37.500
0.00
0.00
0.00
3.01
2106
2266
5.043762
ACTCCCTCCATCCCAAAATAAGTA
58.956
41.667
0.00
0.00
0.00
2.24
2134
2294
7.313646
TCAACTTTAATCGAAACCAACAACAA
58.686
30.769
0.00
0.00
0.00
2.83
2135
2295
7.273815
TCAACTTTAATCGAAACCAACAACAAC
59.726
33.333
0.00
0.00
0.00
3.32
2136
2296
6.622549
ACTTTAATCGAAACCAACAACAACA
58.377
32.000
0.00
0.00
0.00
3.33
2137
2297
6.528774
ACTTTAATCGAAACCAACAACAACAC
59.471
34.615
0.00
0.00
0.00
3.32
2138
2298
4.712122
AATCGAAACCAACAACAACACT
57.288
36.364
0.00
0.00
0.00
3.55
2139
2299
4.712122
ATCGAAACCAACAACAACACTT
57.288
36.364
0.00
0.00
0.00
3.16
2140
2300
5.821516
ATCGAAACCAACAACAACACTTA
57.178
34.783
0.00
0.00
0.00
2.24
2179
2339
5.111293
CCAATTTAACATCAAGGCCACATC
58.889
41.667
5.01
0.00
0.00
3.06
2285
2456
6.932356
ACTATGAACATGATGTCATTCACC
57.068
37.500
13.08
0.00
33.61
4.02
2288
2459
6.785337
ATGAACATGATGTCATTCACCATT
57.215
33.333
0.00
0.00
33.61
3.16
2310
2481
1.003696
GGCAGATATTAGGGCTCCACC
59.996
57.143
0.00
0.00
37.93
4.61
2317
2488
1.900245
TTAGGGCTCCACCGTTTTTC
58.100
50.000
0.00
0.00
40.62
2.29
2318
2489
1.061546
TAGGGCTCCACCGTTTTTCT
58.938
50.000
0.00
0.00
40.62
2.52
2328
2499
3.435671
CCACCGTTTTTCTCCATCTACAC
59.564
47.826
0.00
0.00
0.00
2.90
2331
2502
3.367025
CCGTTTTTCTCCATCTACACGTC
59.633
47.826
0.00
0.00
0.00
4.34
2339
2510
1.471676
CCATCTACACGTCTTGCCTCC
60.472
57.143
0.00
0.00
0.00
4.30
2340
2511
0.824759
ATCTACACGTCTTGCCTCCC
59.175
55.000
0.00
0.00
0.00
4.30
2341
2512
1.218316
CTACACGTCTTGCCTCCCC
59.782
63.158
0.00
0.00
0.00
4.81
2343
2514
1.122632
TACACGTCTTGCCTCCCCAA
61.123
55.000
0.00
0.00
0.00
4.12
2344
2515
1.228124
CACGTCTTGCCTCCCCAAA
60.228
57.895
0.00
0.00
0.00
3.28
2384
2626
4.879598
TCGAGGAAAAGAAGACTGTAACC
58.120
43.478
0.00
0.00
0.00
2.85
2403
2645
8.978874
TGTAACCGTAGATACTGGATAACTTA
57.021
34.615
7.54
0.00
0.00
2.24
2686
2930
5.819901
GCCTCACAATTGGGCTATATCTATC
59.180
44.000
14.80
0.00
42.31
2.08
2766
3011
6.744112
TGCCAAATTAACAATCCGGATTATC
58.256
36.000
28.76
4.52
0.00
1.75
2794
3039
5.411977
CCATTTGCAAACATTTGAGGCAATA
59.588
36.000
15.41
0.00
43.18
1.90
2795
3040
6.072618
CCATTTGCAAACATTTGAGGCAATAA
60.073
34.615
15.41
0.00
43.18
1.40
2796
3041
7.362229
CCATTTGCAAACATTTGAGGCAATAAT
60.362
33.333
15.41
0.00
43.18
1.28
2797
3042
7.507733
TTTGCAAACATTTGAGGCAATAATT
57.492
28.000
8.05
0.00
43.18
1.40
2821
3066
3.051581
ACATGGATCTTCACTGGCCTAT
58.948
45.455
3.32
0.00
0.00
2.57
2996
3242
1.340088
TGCATGTGGCCTTGATGTTT
58.660
45.000
3.32
0.00
43.89
2.83
3051
3298
8.333908
TGTTGGTGAATTTTCGAAATTGATTTG
58.666
29.630
12.12
0.00
0.00
2.32
3053
3300
6.008875
GGTGAATTTTCGAAATTGATTTGCG
58.991
36.000
12.12
0.00
0.00
4.85
3091
3508
6.867662
AGCTTTCATACATGTATTGGCTAC
57.132
37.500
15.85
4.81
0.00
3.58
3095
3512
5.134202
TCATACATGTATTGGCTACGGAG
57.866
43.478
15.85
0.00
32.61
4.63
3110
3527
4.560108
GCTACGGAGGTCAAGTTCTAACAA
60.560
45.833
0.00
0.00
0.00
2.83
3229
3646
9.301153
GAATAGGTATTTGCAGTTTTTACCATG
57.699
33.333
12.29
0.00
35.76
3.66
3318
3736
6.276847
TGTATTTGTGTTTCCCATTGTGTTC
58.723
36.000
0.00
0.00
0.00
3.18
3597
4024
4.882842
TCAGCTACCAACACATTGACTA
57.117
40.909
0.00
0.00
38.15
2.59
3636
4063
7.724061
ACCTGAACATTAGGTTTGTGTAGATTT
59.276
33.333
0.00
0.00
46.13
2.17
3637
4064
8.023128
CCTGAACATTAGGTTTGTGTAGATTTG
58.977
37.037
0.00
0.00
40.63
2.32
3638
4065
8.458573
TGAACATTAGGTTTGTGTAGATTTGT
57.541
30.769
0.00
0.00
40.63
2.83
3639
4066
8.349245
TGAACATTAGGTTTGTGTAGATTTGTG
58.651
33.333
0.00
0.00
40.63
3.33
3640
4067
7.817418
ACATTAGGTTTGTGTAGATTTGTGT
57.183
32.000
0.00
0.00
0.00
3.72
3641
4068
8.911918
ACATTAGGTTTGTGTAGATTTGTGTA
57.088
30.769
0.00
0.00
0.00
2.90
3642
4069
8.999431
ACATTAGGTTTGTGTAGATTTGTGTAG
58.001
33.333
0.00
0.00
0.00
2.74
3643
4070
9.214957
CATTAGGTTTGTGTAGATTTGTGTAGA
57.785
33.333
0.00
0.00
0.00
2.59
3644
4071
9.959721
ATTAGGTTTGTGTAGATTTGTGTAGAT
57.040
29.630
0.00
0.00
0.00
1.98
3762
4191
7.454260
GGTCAGAACAAATAAGATTGACCTT
57.546
36.000
12.22
0.00
45.93
3.50
3885
4323
4.133013
ACACGTGTTTCTTAGACCTGTT
57.867
40.909
17.22
0.00
0.00
3.16
3934
4374
5.029807
TGAGGTATCGCAATTATGGTTGA
57.970
39.130
0.00
0.00
0.00
3.18
4047
4512
4.803613
TGTTGCACTACGTATTATGCTCTG
59.196
41.667
20.63
0.85
38.90
3.35
4198
4666
4.786507
TGATCAAGTTGCTGAACGATTTG
58.213
39.130
0.00
0.00
37.15
2.32
4232
4700
7.464045
GCCAAGAAGTACAACAATTTGACAAAC
60.464
37.037
1.94
0.00
36.48
2.93
4234
4702
6.262601
AGAAGTACAACAATTTGACAAACCG
58.737
36.000
1.94
0.00
36.48
4.44
4238
4706
7.262048
AGTACAACAATTTGACAAACCGAAAT
58.738
30.769
1.94
0.00
36.48
2.17
4239
4707
6.343226
ACAACAATTTGACAAACCGAAATG
57.657
33.333
1.94
1.43
36.48
2.32
4240
4708
5.196825
CAACAATTTGACAAACCGAAATGC
58.803
37.500
1.94
0.00
34.24
3.56
4242
4710
4.057432
CAATTTGACAAACCGAAATGCCT
58.943
39.130
1.94
0.00
0.00
4.75
4243
4711
5.221342
ACAATTTGACAAACCGAAATGCCTA
60.221
36.000
1.94
0.00
0.00
3.93
4431
4899
5.465724
GTCAAATCTTGAACTGGTAGAACGT
59.534
40.000
0.00
0.00
42.15
3.99
4432
4900
5.694910
TCAAATCTTGAACTGGTAGAACGTC
59.305
40.000
0.00
0.00
36.59
4.34
4436
4904
1.000506
TGAACTGGTAGAACGTCCTGC
59.999
52.381
0.00
0.00
0.00
4.85
4442
4910
0.101759
GTAGAACGTCCTGCCGCATA
59.898
55.000
0.00
0.00
0.00
3.14
4460
4928
3.559242
GCATACTGAAGATTCACCTGCTC
59.441
47.826
10.02
0.00
32.44
4.26
4541
5009
1.096386
CGATCCGTCTTCCTCCTCGT
61.096
60.000
0.00
0.00
0.00
4.18
4548
5016
0.967887
TCTTCCTCCTCGTCAGCAGG
60.968
60.000
0.00
0.00
0.00
4.85
4604
5072
3.561213
CACAGCGAGCGCATGGAG
61.561
66.667
17.68
0.00
44.88
3.86
4605
5073
4.074526
ACAGCGAGCGCATGGAGT
62.075
61.111
17.68
0.00
44.88
3.85
4606
5074
3.561213
CAGCGAGCGCATGGAGTG
61.561
66.667
17.68
1.42
44.88
3.51
4837
5305
0.108329
TGTCGCCGGATTTCCTCTTC
60.108
55.000
5.05
0.00
0.00
2.87
4969
5437
2.039480
CTCAACCATGATCCATCCCGAT
59.961
50.000
0.00
0.00
34.37
4.18
5011
5479
2.716217
CCTTCCTCCTTGGTCATGAAC
58.284
52.381
2.98
2.98
37.07
3.18
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
115
116
2.384433
TTTCCCGTTCCCCACCACA
61.384
57.895
0.00
0.00
0.00
4.17
256
257
3.711842
TTTGACGAGCGCGCAAGG
61.712
61.111
35.10
23.13
42.48
3.61
257
258
2.497628
GTTTGACGAGCGCGCAAG
60.498
61.111
35.10
27.41
42.48
4.01
258
259
4.007940
GGTTTGACGAGCGCGCAA
62.008
61.111
35.10
15.93
42.48
4.85
263
264
2.203972
TAGTCCCGGTTTGACGAGCG
62.204
60.000
0.00
0.00
37.80
5.03
264
265
0.175073
ATAGTCCCGGTTTGACGAGC
59.825
55.000
0.00
0.00
37.80
5.03
344
364
2.620585
GCAAGTTTGTTCTCTTCTGGCT
59.379
45.455
0.00
0.00
0.00
4.75
345
365
2.287849
GGCAAGTTTGTTCTCTTCTGGC
60.288
50.000
0.00
0.00
0.00
4.85
346
366
3.217626
AGGCAAGTTTGTTCTCTTCTGG
58.782
45.455
0.00
0.00
0.00
3.86
441
464
0.036952
CAGGTGACAGCCGAGAACAT
60.037
55.000
0.00
0.00
0.00
2.71
442
465
1.367471
CAGGTGACAGCCGAGAACA
59.633
57.895
0.00
0.00
0.00
3.18
443
466
2.029844
GCAGGTGACAGCCGAGAAC
61.030
63.158
0.00
0.00
36.76
3.01
444
467
2.038814
TTGCAGGTGACAGCCGAGAA
62.039
55.000
0.00
0.00
43.15
2.87
446
469
2.031012
TTGCAGGTGACAGCCGAG
59.969
61.111
0.00
0.00
43.15
4.63
447
470
2.031012
CTTGCAGGTGACAGCCGA
59.969
61.111
0.00
0.00
43.15
5.54
448
471
3.730761
GCTTGCAGGTGACAGCCG
61.731
66.667
0.00
0.00
43.15
5.52
449
472
1.530013
AATGCTTGCAGGTGACAGCC
61.530
55.000
0.00
0.00
43.15
4.85
450
473
0.316204
AAATGCTTGCAGGTGACAGC
59.684
50.000
0.87
0.00
44.24
4.40
451
474
2.816087
AGTAAATGCTTGCAGGTGACAG
59.184
45.455
0.87
0.00
0.00
3.51
452
475
2.862541
AGTAAATGCTTGCAGGTGACA
58.137
42.857
0.87
0.00
0.00
3.58
454
477
4.253685
GTCTAGTAAATGCTTGCAGGTGA
58.746
43.478
0.87
0.00
0.00
4.02
457
493
4.256920
ACTGTCTAGTAAATGCTTGCAGG
58.743
43.478
0.87
0.00
34.74
4.85
483
519
3.959991
GACAGCTTCCCCGGCAGAC
62.960
68.421
0.00
0.00
0.00
3.51
506
542
4.577246
GGCTCCAGCTAGGACGCG
62.577
72.222
3.53
3.53
43.07
6.01
509
545
1.270571
GCTAATGGCTCCAGCTAGGAC
60.271
57.143
0.00
0.44
43.07
3.85
543
579
1.299541
CACTGGGTGTCACAACTCAC
58.700
55.000
5.12
0.00
0.00
3.51
544
580
0.180171
CCACTGGGTGTCACAACTCA
59.820
55.000
5.12
0.00
0.00
3.41
545
581
3.006672
CCACTGGGTGTCACAACTC
57.993
57.895
5.12
0.00
0.00
3.01
770
852
0.825010
CCTCTGCCTGCCTTGTTTGT
60.825
55.000
0.00
0.00
0.00
2.83
773
855
2.282745
GCCTCTGCCTGCCTTGTT
60.283
61.111
0.00
0.00
0.00
2.83
857
957
1.596895
TATTTTGCCCGGGCGTTTCC
61.597
55.000
39.00
14.07
45.51
3.13
858
958
0.244178
TTATTTTGCCCGGGCGTTTC
59.756
50.000
39.00
14.88
45.51
2.78
859
959
0.680061
TTTATTTTGCCCGGGCGTTT
59.320
45.000
39.00
25.32
45.51
3.60
860
960
0.899019
ATTTATTTTGCCCGGGCGTT
59.101
45.000
39.00
24.97
45.51
4.84
861
961
0.458260
GATTTATTTTGCCCGGGCGT
59.542
50.000
39.00
26.18
45.51
5.68
862
962
0.249280
GGATTTATTTTGCCCGGGCG
60.249
55.000
39.00
7.25
45.51
6.13
863
963
1.068588
GAGGATTTATTTTGCCCGGGC
59.931
52.381
39.40
39.40
42.35
6.13
1350
1468
2.749621
ACATCCAATTTCAGAGGCGAAC
59.250
45.455
0.00
0.00
0.00
3.95
1369
1487
1.894756
GGCCAACCAACAGCGTACA
60.895
57.895
0.00
0.00
35.26
2.90
1371
1489
2.666862
CGGCCAACCAACAGCGTA
60.667
61.111
2.24
0.00
34.57
4.42
1382
1500
4.081185
TCGATCAGCAGCGGCCAA
62.081
61.111
4.82
0.00
42.56
4.52
1543
1665
1.987855
CTTCCTGAGGTACGGGGCA
60.988
63.158
0.00
0.00
44.73
5.36
1564
1686
3.126831
GCTGGAATACATCTTGAGGTCG
58.873
50.000
0.00
0.00
0.00
4.79
1688
1813
1.595311
AGGCAATACCACTGGATCCA
58.405
50.000
15.27
15.27
43.14
3.41
1704
1832
4.705991
ACTAGTAGAACTGAACACCTAGGC
59.294
45.833
9.30
0.00
0.00
3.93
1800
1954
5.006386
AGCTTTGACCTTTACAATCAGAGG
58.994
41.667
0.00
0.00
35.39
3.69
1809
1963
1.135944
GCAGCGAGCTTTGACCTTTAC
60.136
52.381
0.00
0.00
41.15
2.01
1918
2072
0.390866
CAAGCATCCAGTCAGCGTCT
60.391
55.000
0.00
0.00
0.00
4.18
1977
2137
3.382546
GGCGTCCACAGTAAATAGGAGTA
59.617
47.826
0.00
0.00
0.00
2.59
1978
2138
2.167900
GGCGTCCACAGTAAATAGGAGT
59.832
50.000
0.00
0.00
0.00
3.85
2031
2191
8.430063
GTTCGACGAGATTTGTATTTAAGACAA
58.570
33.333
0.67
0.67
35.03
3.18
2065
2225
4.636249
GGAGTAGTTCCATCTGCAATAGG
58.364
47.826
0.00
0.00
46.01
2.57
2106
2266
7.504924
TGTTGGTTTCGATTAAAGTTGAGAT
57.495
32.000
0.00
0.00
0.00
2.75
2118
2278
4.712122
AAGTGTTGTTGTTGGTTTCGAT
57.288
36.364
0.00
0.00
0.00
3.59
2134
2294
5.720041
TGGCTACTGGAATCTACTTAAGTGT
59.280
40.000
18.56
7.23
0.00
3.55
2135
2295
6.222038
TGGCTACTGGAATCTACTTAAGTG
57.778
41.667
18.56
8.35
0.00
3.16
2136
2296
6.869206
TTGGCTACTGGAATCTACTTAAGT
57.131
37.500
13.68
13.68
0.00
2.24
2137
2297
8.738645
AAATTGGCTACTGGAATCTACTTAAG
57.261
34.615
0.00
0.00
0.00
1.85
2139
2299
9.609346
GTTAAATTGGCTACTGGAATCTACTTA
57.391
33.333
0.00
0.00
0.00
2.24
2140
2300
8.107095
TGTTAAATTGGCTACTGGAATCTACTT
58.893
33.333
0.00
0.00
0.00
2.24
2224
2395
4.642885
CCTCAGACCAACCTAACAACAAAA
59.357
41.667
0.00
0.00
0.00
2.44
2282
2453
3.256631
GCCCTAATATCTGCCAAATGGTG
59.743
47.826
0.71
0.00
37.57
4.17
2285
2456
3.760684
GGAGCCCTAATATCTGCCAAATG
59.239
47.826
0.00
0.00
0.00
2.32
2288
2459
2.106511
GTGGAGCCCTAATATCTGCCAA
59.893
50.000
0.00
0.00
0.00
4.52
2310
2481
4.235360
AGACGTGTAGATGGAGAAAAACG
58.765
43.478
0.00
0.00
35.98
3.60
2317
2488
1.478510
AGGCAAGACGTGTAGATGGAG
59.521
52.381
0.00
0.00
0.00
3.86
2318
2489
1.476891
GAGGCAAGACGTGTAGATGGA
59.523
52.381
0.00
0.00
0.00
3.41
2328
2499
0.250727
TTCTTTGGGGAGGCAAGACG
60.251
55.000
0.00
0.00
0.00
4.18
2331
2502
3.071457
ACAATTTTCTTTGGGGAGGCAAG
59.929
43.478
0.00
0.00
0.00
4.01
2339
2510
4.777366
AGGATGGGTACAATTTTCTTTGGG
59.223
41.667
0.00
0.00
0.00
4.12
2340
2511
5.393027
CGAGGATGGGTACAATTTTCTTTGG
60.393
44.000
0.00
0.00
0.00
3.28
2341
2512
5.414454
TCGAGGATGGGTACAATTTTCTTTG
59.586
40.000
0.00
0.00
0.00
2.77
2343
2514
5.174037
TCGAGGATGGGTACAATTTTCTT
57.826
39.130
0.00
0.00
0.00
2.52
2344
2515
4.384208
CCTCGAGGATGGGTACAATTTTCT
60.384
45.833
28.21
0.00
37.39
2.52
2686
2930
1.063616
CAGCAACCGAGATTGAGCATG
59.936
52.381
0.00
0.00
0.00
4.06
2766
3011
4.628333
CCTCAAATGTTTGCAAATGGCTAG
59.372
41.667
16.21
8.90
45.15
3.42
2794
3039
4.159135
GCCAGTGAAGATCCATGTGAAATT
59.841
41.667
0.00
0.00
0.00
1.82
2795
3040
3.698040
GCCAGTGAAGATCCATGTGAAAT
59.302
43.478
0.00
0.00
0.00
2.17
2796
3041
3.084039
GCCAGTGAAGATCCATGTGAAA
58.916
45.455
0.00
0.00
0.00
2.69
2797
3042
2.618816
GGCCAGTGAAGATCCATGTGAA
60.619
50.000
0.00
0.00
0.00
3.18
2933
3179
0.690762
AGGGGTCGGCGCATATAAAT
59.309
50.000
10.83
0.00
0.00
1.40
2936
3182
1.001181
GTAAAGGGGTCGGCGCATATA
59.999
52.381
10.83
0.00
0.00
0.86
2996
3242
7.567622
ACCTAAGTAGATTCCAGTAGCCAATTA
59.432
37.037
0.00
0.00
0.00
1.40
3051
3298
2.213499
AGCTAAGGCAATATGACACGC
58.787
47.619
0.00
0.00
41.70
5.34
3053
3300
5.818136
TGAAAGCTAAGGCAATATGACAC
57.182
39.130
0.00
0.00
41.70
3.67
3091
3508
4.392138
GGAATTGTTAGAACTTGACCTCCG
59.608
45.833
0.00
0.00
0.00
4.63
3229
3646
6.254281
ACACAAATATAAGCACTGTTCCAC
57.746
37.500
0.00
0.00
0.00
4.02
3318
3736
9.559732
TGACACTAGTGGAAATAAATCATATGG
57.440
33.333
26.12
0.00
34.19
2.74
3514
3936
6.763715
ACATATCCCAGCTATTGGTTTCTA
57.236
37.500
0.00
0.00
46.25
2.10
3572
3994
1.755179
ATGTGTTGGTAGCTGATGGC
58.245
50.000
0.00
0.00
42.19
4.40
3760
4189
7.298854
GTTCATTTTCTTTACTCCGGAAGAAG
58.701
38.462
14.34
13.42
41.40
2.85
3761
4190
6.206048
GGTTCATTTTCTTTACTCCGGAAGAA
59.794
38.462
11.48
11.48
39.42
2.52
3762
4191
5.704053
GGTTCATTTTCTTTACTCCGGAAGA
59.296
40.000
5.23
1.78
0.00
2.87
3885
4323
7.573656
GCAGATCACATTACAGACATTTGACAA
60.574
37.037
0.00
0.00
0.00
3.18
3934
4374
6.430000
ACATAAGCTTCCAAGTGAAAATACGT
59.570
34.615
0.00
0.00
31.06
3.57
4232
4700
9.477484
GATTAGGTACATATATAGGCATTTCGG
57.523
37.037
0.00
0.00
0.00
4.30
4234
4702
9.477484
CGGATTAGGTACATATATAGGCATTTC
57.523
37.037
0.00
0.00
0.00
2.17
4238
4706
7.783119
ACATCGGATTAGGTACATATATAGGCA
59.217
37.037
0.00
0.00
0.00
4.75
4239
4707
8.082852
CACATCGGATTAGGTACATATATAGGC
58.917
40.741
0.00
0.00
0.00
3.93
4240
4708
8.082852
GCACATCGGATTAGGTACATATATAGG
58.917
40.741
0.00
0.00
0.00
2.57
4242
4710
8.528044
TGCACATCGGATTAGGTACATATATA
57.472
34.615
0.00
0.00
0.00
0.86
4243
4711
7.418337
TGCACATCGGATTAGGTACATATAT
57.582
36.000
0.00
0.00
0.00
0.86
4431
4899
1.123077
ATCTTCAGTATGCGGCAGGA
58.877
50.000
9.25
0.46
34.76
3.86
4432
4900
1.869767
GAATCTTCAGTATGCGGCAGG
59.130
52.381
9.25
0.00
34.76
4.85
4436
4904
2.868583
CAGGTGAATCTTCAGTATGCGG
59.131
50.000
0.00
0.00
37.98
5.69
4442
4910
2.636893
ACAGAGCAGGTGAATCTTCAGT
59.363
45.455
0.00
0.00
37.98
3.41
4460
4928
3.751246
CGCACCCCATTGCCACAG
61.751
66.667
0.00
0.00
39.53
3.66
4495
4963
1.321074
ATCTTGACGAGGACGACCCC
61.321
60.000
0.00
0.00
42.66
4.95
4541
5009
3.371097
GAACGCCCGATCCTGCTGA
62.371
63.158
0.00
0.00
0.00
4.26
4611
5079
2.500183
GAAGAACAGCAGCGCGGAAC
62.500
60.000
13.03
0.00
0.00
3.62
4612
5080
2.280797
AAGAACAGCAGCGCGGAA
60.281
55.556
13.03
0.00
0.00
4.30
4622
5090
0.603707
TCTGGGCGCAAGAAGAACAG
60.604
55.000
10.83
4.11
43.02
3.16
4918
5386
0.040204
ACCATGGCAAAGAAGAGGGG
59.960
55.000
13.04
0.00
0.00
4.79
5011
5479
4.966005
TGGCGACAGTTCTTCTCG
57.034
55.556
0.00
0.00
35.01
4.04
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.