Multiple sequence alignment - TraesCS4D01G132600
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
TraesCS4D01G132600
chr4D
100.000
6584
0
0
1
6584
119411913
119405330
0.000000e+00
12159.0
1
TraesCS4D01G132600
chr4A
97.371
2206
43
6
2298
4489
449817724
449815520
0.000000e+00
3738.0
2
TraesCS4D01G132600
chr4A
95.652
2116
47
13
4485
6583
449815438
449813351
0.000000e+00
3356.0
3
TraesCS4D01G132600
chr4A
92.662
1608
56
28
711
2294
449819414
449817845
0.000000e+00
2259.0
4
TraesCS4D01G132600
chr4A
100.000
129
0
0
588
716
449820276
449820148
8.530000e-59
239.0
5
TraesCS4D01G132600
chr4A
79.848
263
16
13
1
259
449889787
449889558
2.460000e-34
158.0
6
TraesCS4D01G132600
chr4A
90.526
95
9
0
363
457
449889465
449889371
6.930000e-25
126.0
7
TraesCS4D01G132600
chr4A
88.158
76
2
5
258
333
449889526
449889458
4.230000e-12
84.2
8
TraesCS4D01G132600
chr4B
97.591
2159
39
6
2342
4489
181690178
181688022
0.000000e+00
3687.0
9
TraesCS4D01G132600
chr4B
96.056
2003
33
13
4485
6483
181687940
181685980
0.000000e+00
3219.0
10
TraesCS4D01G132600
chr4B
95.312
1728
39
11
583
2294
181692021
181690320
0.000000e+00
2704.0
11
TraesCS4D01G132600
chr4B
92.116
482
15
7
1
471
181692825
181692356
0.000000e+00
658.0
12
TraesCS4D01G132600
chr4B
97.368
38
1
0
2297
2334
181690203
181690240
1.530000e-06
65.8
13
TraesCS4D01G132600
chr3A
82.663
646
100
9
5435
6076
186846071
186845434
4.460000e-156
562.0
14
TraesCS4D01G132600
chr3A
85.742
519
68
5
2365
2880
186848732
186848217
1.610000e-150
544.0
15
TraesCS4D01G132600
chr3A
91.324
219
19
0
3028
3246
186848218
186848000
3.860000e-77
300.0
16
TraesCS4D01G132600
chr3A
86.466
266
25
7
4613
4877
186846664
186846409
1.400000e-71
281.0
17
TraesCS4D01G132600
chr3B
82.481
645
103
8
5435
6076
237292012
237291375
2.070000e-154
556.0
18
TraesCS4D01G132600
chr3B
85.192
520
70
6
2364
2880
237294685
237294170
1.630000e-145
527.0
19
TraesCS4D01G132600
chr3B
86.525
282
24
7
4613
4893
237292607
237292339
1.390000e-76
298.0
20
TraesCS4D01G132600
chr3B
90.868
219
20
0
3028
3246
237294171
237293953
1.800000e-75
294.0
21
TraesCS4D01G132600
chr3D
82.353
646
102
9
5435
6076
160613209
160612572
9.650000e-153
551.0
22
TraesCS4D01G132600
chr3D
85.207
507
67
7
2378
2880
160615856
160615354
1.270000e-141
514.0
23
TraesCS4D01G132600
chr3D
91.324
219
19
0
3028
3246
160615355
160615137
3.860000e-77
300.0
24
TraesCS4D01G132600
chr3D
86.466
266
25
7
4613
4877
160613802
160613547
1.400000e-71
281.0
25
TraesCS4D01G132600
chr1A
87.446
231
17
3
5865
6093
566584952
566584732
8.470000e-64
255.0
26
TraesCS4D01G132600
chr1A
89.820
167
7
8
6165
6327
566584728
566584568
8.650000e-49
206.0
27
TraesCS4D01G132600
chr1B
88.679
212
9
9
6088
6294
657280588
657280387
1.830000e-60
244.0
28
TraesCS4D01G132600
chrUn
100.000
28
0
0
2307
2334
94184206
94184179
1.200000e-02
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
TraesCS4D01G132600
chr4D
119405330
119411913
6583
True
12159.00
12159
100.00000
1
6584
1
chr4D.!!$R1
6583
1
TraesCS4D01G132600
chr4A
449813351
449820276
6925
True
2398.00
3738
96.42125
588
6583
4
chr4A.!!$R1
5995
2
TraesCS4D01G132600
chr4B
181685980
181692825
6845
True
2567.00
3687
95.26875
1
6483
4
chr4B.!!$R1
6482
3
TraesCS4D01G132600
chr3A
186845434
186848732
3298
True
421.75
562
86.54875
2365
6076
4
chr3A.!!$R1
3711
4
TraesCS4D01G132600
chr3B
237291375
237294685
3310
True
418.75
556
86.26650
2364
6076
4
chr3B.!!$R1
3712
5
TraesCS4D01G132600
chr3D
160612572
160615856
3284
True
411.50
551
86.33750
2378
6076
4
chr3D.!!$R1
3698
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
556
568
0.038166
TGCTGAAGACCACCATTCCC
59.962
55.000
0.00
0.0
0.00
3.97
F
561
573
0.178975
AAGACCACCATTCCCGCAAA
60.179
50.000
0.00
0.0
0.00
3.68
F
826
1800
0.193069
CCTCAGATCCAGATCCCCCT
59.807
60.000
4.01
0.0
38.58
4.79
F
1100
2087
0.381089
CCGTGCGCTTAGTAGTAGCT
59.619
55.000
9.73
0.0
36.49
3.32
F
1527
2519
0.893270
CCACCAACAATCCCTTCGCA
60.893
55.000
0.00
0.0
0.00
5.10
F
1925
2917
0.899019
AACTTTGGCGGTGGTTTGTT
59.101
45.000
0.00
0.0
0.00
2.83
F
2340
3459
1.042229
TATTATGGGACGGTCGTGGG
58.958
55.000
0.00
0.0
0.00
4.61
F
3963
5102
1.015609
TCACTGGAGGTGGAGGGATA
58.984
55.000
0.00
0.0
45.38
2.59
F
5001
6445
3.304257
CCGAGCAGAACATTATCAATGGC
60.304
47.826
4.09
0.0
43.21
4.40
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1963
2955
2.808244
ACAAATGTGTTCCAAGTTGCG
58.192
42.857
0.0
0.0
32.58
4.85
R
2335
3454
3.429207
ACGAAACAAAACAAAAACCCACG
59.571
39.130
0.0
0.0
0.00
4.94
R
2338
3457
4.142859
GGGAACGAAACAAAACAAAAACCC
60.143
41.667
0.0
0.0
0.00
4.11
R
2861
3988
3.933332
CCTACCGAATGGAGAAGTTTGTC
59.067
47.826
0.0
0.0
39.21
3.18
R
3439
4566
4.555262
ACAAGCAACAAAATAATGGGACG
58.445
39.130
0.0
0.0
0.00
4.79
R
3652
4779
0.446616
GATGAAAACGGGTTCGGAGC
59.553
55.000
0.0
0.0
41.39
4.70
R
4130
5273
2.093869
CAGGGGCAGATTGTTGAAATGG
60.094
50.000
0.0
0.0
0.00
3.16
R
5559
7004
1.442769
CACCCATCTTCTCAACGGTG
58.557
55.000
0.0
0.0
35.24
4.94
R
6134
7586
0.389948
CAGACCAGCTACCGACCAAC
60.390
60.000
0.0
0.0
0.00
3.77
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
3.988976
AGCTAGATTGGCAGAAAGTCA
57.011
42.857
0.00
0.00
0.00
3.41
35
36
4.260170
AGCTAGATTGGCAGAAAGTCAAG
58.740
43.478
0.00
0.00
46.51
3.02
41
42
1.214175
TGGCAGAAAGTCAAGGGTTGA
59.786
47.619
0.00
0.00
37.33
3.18
84
85
2.557924
TCCATGTGTTTGATGTTCTGCC
59.442
45.455
0.00
0.00
0.00
4.85
101
102
3.119459
TCTGCCGCTAACAAACAAACAAA
60.119
39.130
0.00
0.00
0.00
2.83
102
103
3.585862
TGCCGCTAACAAACAAACAAAA
58.414
36.364
0.00
0.00
0.00
2.44
103
104
3.368236
TGCCGCTAACAAACAAACAAAAC
59.632
39.130
0.00
0.00
0.00
2.43
104
105
3.368236
GCCGCTAACAAACAAACAAAACA
59.632
39.130
0.00
0.00
0.00
2.83
105
106
4.143094
GCCGCTAACAAACAAACAAAACAA
60.143
37.500
0.00
0.00
0.00
2.83
106
107
5.546434
CCGCTAACAAACAAACAAAACAAG
58.454
37.500
0.00
0.00
0.00
3.16
107
108
5.012613
CGCTAACAAACAAACAAAACAAGC
58.987
37.500
0.00
0.00
0.00
4.01
108
109
5.388890
CGCTAACAAACAAACAAAACAAGCA
60.389
36.000
0.00
0.00
0.00
3.91
109
110
6.014898
GCTAACAAACAAACAAAACAAGCAG
58.985
36.000
0.00
0.00
0.00
4.24
113
114
2.620242
ACAAACAAAACAAGCAGGCAG
58.380
42.857
0.00
0.00
0.00
4.85
186
187
5.509832
AAGGATTTAAGGGTTACCGTTCT
57.490
39.130
12.88
1.13
43.47
3.01
187
188
5.509832
AGGATTTAAGGGTTACCGTTCTT
57.490
39.130
12.88
4.71
43.47
2.52
188
189
5.494724
AGGATTTAAGGGTTACCGTTCTTC
58.505
41.667
12.88
8.42
43.47
2.87
249
250
1.153549
GCTACAGCTTAGGCGCACT
60.154
57.895
10.83
6.69
44.37
4.40
263
264
3.569210
CACTGCCACCCTCCACCA
61.569
66.667
0.00
0.00
0.00
4.17
264
265
2.776526
ACTGCCACCCTCCACCAA
60.777
61.111
0.00
0.00
0.00
3.67
266
267
3.099841
TGCCACCCTCCACCAACA
61.100
61.111
0.00
0.00
0.00
3.33
268
269
2.281484
CCACCCTCCACCAACACG
60.281
66.667
0.00
0.00
0.00
4.49
366
378
1.751351
TGAAGCACTCCTCTATGTCCG
59.249
52.381
0.00
0.00
0.00
4.79
482
494
2.629763
GCGACGGCGTTCAGTTTT
59.370
55.556
16.19
0.00
40.36
2.43
483
495
1.010462
GCGACGGCGTTCAGTTTTT
60.010
52.632
16.19
0.00
40.36
1.94
503
515
4.563404
TTTTTGAGGGAACGGCGT
57.437
50.000
6.77
6.77
0.00
5.68
504
516
2.796500
TTTTTGAGGGAACGGCGTT
58.204
47.368
27.15
27.15
0.00
4.84
505
517
0.664224
TTTTTGAGGGAACGGCGTTC
59.336
50.000
37.30
37.30
41.32
3.95
506
518
0.464013
TTTTGAGGGAACGGCGTTCA
60.464
50.000
42.13
27.24
43.54
3.18
507
519
0.882927
TTTGAGGGAACGGCGTTCAG
60.883
55.000
42.13
4.88
43.54
3.02
508
520
2.434359
GAGGGAACGGCGTTCAGG
60.434
66.667
42.13
4.09
43.54
3.86
509
521
3.236003
GAGGGAACGGCGTTCAGGT
62.236
63.158
42.13
29.91
43.54
4.00
510
522
1.880819
GAGGGAACGGCGTTCAGGTA
61.881
60.000
42.13
0.00
43.54
3.08
511
523
1.004679
GGGAACGGCGTTCAGGTAA
60.005
57.895
42.13
0.00
43.54
2.85
512
524
1.293963
GGGAACGGCGTTCAGGTAAC
61.294
60.000
42.13
28.08
43.54
2.50
528
540
2.488153
GGTAACTGAAGACCACCAATGC
59.512
50.000
0.00
0.00
35.65
3.56
529
541
2.664402
AACTGAAGACCACCAATGCT
57.336
45.000
0.00
0.00
0.00
3.79
530
542
3.788227
AACTGAAGACCACCAATGCTA
57.212
42.857
0.00
0.00
0.00
3.49
531
543
3.788227
ACTGAAGACCACCAATGCTAA
57.212
42.857
0.00
0.00
0.00
3.09
532
544
4.307032
ACTGAAGACCACCAATGCTAAT
57.693
40.909
0.00
0.00
0.00
1.73
533
545
4.012374
ACTGAAGACCACCAATGCTAATG
58.988
43.478
0.00
0.00
0.00
1.90
534
546
2.754552
TGAAGACCACCAATGCTAATGC
59.245
45.455
0.00
0.00
40.20
3.56
535
547
2.814805
AGACCACCAATGCTAATGCT
57.185
45.000
0.00
0.00
40.48
3.79
536
548
2.372264
AGACCACCAATGCTAATGCTG
58.628
47.619
0.00
0.00
40.48
4.41
537
549
2.094675
GACCACCAATGCTAATGCTGT
58.905
47.619
0.00
0.00
40.48
4.40
538
550
1.820519
ACCACCAATGCTAATGCTGTG
59.179
47.619
0.00
0.00
40.48
3.66
539
551
1.470285
CCACCAATGCTAATGCTGTGC
60.470
52.381
0.00
0.00
40.48
4.57
540
552
1.475280
CACCAATGCTAATGCTGTGCT
59.525
47.619
0.00
0.00
40.48
4.40
541
553
1.475280
ACCAATGCTAATGCTGTGCTG
59.525
47.619
0.00
0.00
40.48
4.41
542
554
1.746787
CCAATGCTAATGCTGTGCTGA
59.253
47.619
0.00
0.00
40.48
4.26
543
555
2.164827
CCAATGCTAATGCTGTGCTGAA
59.835
45.455
0.00
0.00
40.48
3.02
544
556
3.435566
CAATGCTAATGCTGTGCTGAAG
58.564
45.455
0.00
0.00
40.48
3.02
545
557
2.477845
TGCTAATGCTGTGCTGAAGA
57.522
45.000
0.00
0.00
40.48
2.87
546
558
2.079158
TGCTAATGCTGTGCTGAAGAC
58.921
47.619
0.00
0.00
40.48
3.01
547
559
1.399791
GCTAATGCTGTGCTGAAGACC
59.600
52.381
0.00
0.00
36.03
3.85
548
560
2.703416
CTAATGCTGTGCTGAAGACCA
58.297
47.619
0.00
0.00
0.00
4.02
549
561
1.242076
AATGCTGTGCTGAAGACCAC
58.758
50.000
0.00
0.00
0.00
4.16
550
562
0.607489
ATGCTGTGCTGAAGACCACC
60.607
55.000
0.00
0.00
0.00
4.61
551
563
1.227943
GCTGTGCTGAAGACCACCA
60.228
57.895
0.00
0.00
0.00
4.17
552
564
0.607489
GCTGTGCTGAAGACCACCAT
60.607
55.000
0.00
0.00
0.00
3.55
553
565
1.901591
CTGTGCTGAAGACCACCATT
58.098
50.000
0.00
0.00
0.00
3.16
554
566
1.808945
CTGTGCTGAAGACCACCATTC
59.191
52.381
0.00
0.00
0.00
2.67
555
567
1.168714
GTGCTGAAGACCACCATTCC
58.831
55.000
0.00
0.00
0.00
3.01
556
568
0.038166
TGCTGAAGACCACCATTCCC
59.962
55.000
0.00
0.00
0.00
3.97
557
569
1.026718
GCTGAAGACCACCATTCCCG
61.027
60.000
0.00
0.00
0.00
5.14
558
570
1.002624
TGAAGACCACCATTCCCGC
60.003
57.895
0.00
0.00
0.00
6.13
559
571
1.002624
GAAGACCACCATTCCCGCA
60.003
57.895
0.00
0.00
0.00
5.69
560
572
0.608035
GAAGACCACCATTCCCGCAA
60.608
55.000
0.00
0.00
0.00
4.85
561
573
0.178975
AAGACCACCATTCCCGCAAA
60.179
50.000
0.00
0.00
0.00
3.68
562
574
0.893727
AGACCACCATTCCCGCAAAC
60.894
55.000
0.00
0.00
0.00
2.93
563
575
1.873270
GACCACCATTCCCGCAAACC
61.873
60.000
0.00
0.00
0.00
3.27
564
576
2.566010
CACCATTCCCGCAAACCG
59.434
61.111
0.00
0.00
0.00
4.44
565
577
2.114411
ACCATTCCCGCAAACCGT
59.886
55.556
0.00
0.00
34.38
4.83
566
578
2.265182
ACCATTCCCGCAAACCGTG
61.265
57.895
0.00
0.00
34.38
4.94
577
589
2.331809
CAAACCGTGCTTTTAGGAGC
57.668
50.000
0.00
0.00
43.00
4.70
578
590
1.068541
CAAACCGTGCTTTTAGGAGCC
60.069
52.381
0.00
0.00
42.01
4.70
579
591
0.608308
AACCGTGCTTTTAGGAGCCC
60.608
55.000
0.00
0.00
42.01
5.19
580
592
1.002624
CCGTGCTTTTAGGAGCCCA
60.003
57.895
0.00
0.00
42.01
5.36
581
593
1.026718
CCGTGCTTTTAGGAGCCCAG
61.027
60.000
0.00
0.00
42.01
4.45
822
1796
0.686224
CCAGCCTCAGATCCAGATCC
59.314
60.000
4.01
0.00
38.58
3.36
823
1797
0.686224
CAGCCTCAGATCCAGATCCC
59.314
60.000
4.01
0.00
38.58
3.85
824
1798
0.473501
AGCCTCAGATCCAGATCCCC
60.474
60.000
4.01
0.00
38.58
4.81
825
1799
1.487850
GCCTCAGATCCAGATCCCCC
61.488
65.000
4.01
0.00
38.58
5.40
826
1800
0.193069
CCTCAGATCCAGATCCCCCT
59.807
60.000
4.01
0.00
38.58
4.79
864
1838
4.845387
TCGATTATCTTTTCGTCTCCTCG
58.155
43.478
0.00
0.00
36.74
4.63
877
1851
1.000060
TCTCCTCGTAAACCAACACCG
60.000
52.381
0.00
0.00
0.00
4.94
1100
2087
0.381089
CCGTGCGCTTAGTAGTAGCT
59.619
55.000
9.73
0.00
36.49
3.32
1217
2208
6.144854
CCCATTTGATGATGCGTTACTAATG
58.855
40.000
0.00
0.00
0.00
1.90
1241
2232
1.282248
TGCTTTCGCGCTACAGTGTC
61.282
55.000
5.56
0.00
39.65
3.67
1242
2233
1.009389
GCTTTCGCGCTACAGTGTCT
61.009
55.000
5.56
0.00
0.00
3.41
1258
2249
6.957631
ACAGTGTCTATAAACCATCCATCAA
58.042
36.000
0.00
0.00
0.00
2.57
1259
2250
7.402054
ACAGTGTCTATAAACCATCCATCAAA
58.598
34.615
0.00
0.00
0.00
2.69
1260
2251
7.888021
ACAGTGTCTATAAACCATCCATCAAAA
59.112
33.333
0.00
0.00
0.00
2.44
1261
2252
8.739039
CAGTGTCTATAAACCATCCATCAAAAA
58.261
33.333
0.00
0.00
0.00
1.94
1333
2324
4.621034
GCGGATTTCAGTTACCATTGTTTG
59.379
41.667
0.00
0.00
0.00
2.93
1337
2328
7.375053
GGATTTCAGTTACCATTGTTTGCTTA
58.625
34.615
0.00
0.00
0.00
3.09
1338
2329
8.034804
GGATTTCAGTTACCATTGTTTGCTTAT
58.965
33.333
0.00
0.00
0.00
1.73
1361
2352
9.998106
TTATATACTCTTCCAGTTTTGCCTATC
57.002
33.333
0.00
0.00
36.43
2.08
1527
2519
0.893270
CCACCAACAATCCCTTCGCA
60.893
55.000
0.00
0.00
0.00
5.10
1809
2801
2.676121
TTTGGCCAGCCATCCACG
60.676
61.111
13.10
0.00
46.64
4.94
1925
2917
0.899019
AACTTTGGCGGTGGTTTGTT
59.101
45.000
0.00
0.00
0.00
2.83
1926
2918
0.899019
ACTTTGGCGGTGGTTTGTTT
59.101
45.000
0.00
0.00
0.00
2.83
1963
2955
7.820648
TCTCAGCATTTAATTTCTGTTCTTCC
58.179
34.615
0.00
0.00
0.00
3.46
2148
3140
8.997621
TTTTAGGTTGTGTTATCTAGCACTAG
57.002
34.615
5.90
0.00
38.12
2.57
2294
3296
8.993424
AGACTTGAAATACTGTCACCCTATAAT
58.007
33.333
0.00
0.00
32.41
1.28
2296
3298
8.768397
ACTTGAAATACTGTCACCCTATAATCA
58.232
33.333
0.00
0.00
0.00
2.57
2334
3453
7.989947
ATAACATCCTATATTATGGGACGGT
57.010
36.000
10.65
4.54
43.12
4.83
2335
3454
5.934402
ACATCCTATATTATGGGACGGTC
57.066
43.478
10.65
0.00
43.12
4.79
2337
3456
4.038271
TCCTATATTATGGGACGGTCGT
57.962
45.455
4.74
0.00
34.71
4.34
2338
3457
3.760151
TCCTATATTATGGGACGGTCGTG
59.240
47.826
4.74
0.00
34.71
4.35
2340
3459
1.042229
TATTATGGGACGGTCGTGGG
58.958
55.000
0.00
0.00
0.00
4.61
2359
3483
5.375717
GTGGGTTTTTGTTTTGTTTCGTTC
58.624
37.500
0.00
0.00
0.00
3.95
2861
3988
2.364972
ACAACTTCACCCTTTGGAGG
57.635
50.000
0.00
0.00
43.15
4.30
3011
4138
9.534565
TGTAACTGCAGATTATCTTATCAGTTC
57.465
33.333
23.35
18.96
38.60
3.01
3343
4470
9.753674
AATGGTTCTTATTTTCTATGAACTGGA
57.246
29.630
0.00
0.00
37.66
3.86
3963
5102
1.015609
TCACTGGAGGTGGAGGGATA
58.984
55.000
0.00
0.00
45.38
2.59
4130
5273
8.694394
GTTGATCTTTGCTCATTTTTAAGTCAC
58.306
33.333
0.00
0.00
0.00
3.67
4205
5351
5.892119
CCTCAGACTCAACCAGGTTAGTATA
59.108
44.000
3.89
0.00
0.00
1.47
4239
5556
9.077885
ACTTAATGCTTCCTTCTCATTAACAAA
57.922
29.630
0.00
0.00
37.59
2.83
4811
6255
7.066645
GCCGGTTAGTATTTTCTTTACCATCTT
59.933
37.037
1.90
0.00
0.00
2.40
4812
6256
8.953313
CCGGTTAGTATTTTCTTTACCATCTTT
58.047
33.333
0.00
0.00
0.00
2.52
4880
6324
6.302269
AGATGAGCAAGGAGGGTATTATTTG
58.698
40.000
0.00
0.00
0.00
2.32
5001
6445
3.304257
CCGAGCAGAACATTATCAATGGC
60.304
47.826
4.09
0.00
43.21
4.40
5380
6825
9.832445
TGTTTAGAACTGTCTGTATTCTTTCTT
57.168
29.630
0.00
0.00
34.55
2.52
5559
7004
1.996786
CTCGGCATGTGAATGGTGCC
61.997
60.000
5.57
5.57
41.84
5.01
5574
7019
0.798776
GTGCCACCGTTGAGAAGATG
59.201
55.000
0.00
0.00
0.00
2.90
6080
7525
2.488153
GCCGATTCCTTGTAGCTTTGTT
59.512
45.455
0.00
0.00
0.00
2.83
6084
7536
5.584649
CCGATTCCTTGTAGCTTTGTTGATA
59.415
40.000
0.00
0.00
0.00
2.15
6085
7537
6.238211
CCGATTCCTTGTAGCTTTGTTGATAG
60.238
42.308
0.00
0.00
0.00
2.08
6086
7538
6.238211
CGATTCCTTGTAGCTTTGTTGATAGG
60.238
42.308
0.00
0.00
0.00
2.57
6087
7539
5.499004
TCCTTGTAGCTTTGTTGATAGGT
57.501
39.130
0.00
0.00
0.00
3.08
6088
7540
5.245531
TCCTTGTAGCTTTGTTGATAGGTG
58.754
41.667
0.00
0.00
0.00
4.00
6089
7541
4.142600
CCTTGTAGCTTTGTTGATAGGTGC
60.143
45.833
0.00
0.00
0.00
5.01
6090
7542
4.286297
TGTAGCTTTGTTGATAGGTGCT
57.714
40.909
0.00
0.00
0.00
4.40
6134
7586
2.120232
GACACTCGATTCCATGTAGCG
58.880
52.381
0.00
0.00
0.00
4.26
6228
7692
7.056635
CCTTCCCATGTTCTTCTGTACATATT
58.943
38.462
0.00
0.00
33.41
1.28
6366
7830
3.036091
CCTGGATGGAATGCATCCTTTT
58.964
45.455
29.35
0.00
46.12
2.27
6367
7831
3.181469
CCTGGATGGAATGCATCCTTTTG
60.181
47.826
29.35
17.90
46.12
2.44
6368
7832
3.181469
CTGGATGGAATGCATCCTTTTGG
60.181
47.826
29.35
13.54
46.12
3.28
6369
7833
6.772769
CTGGATGGAATGCATCCTTTTGGC
62.773
50.000
29.35
6.64
46.12
4.52
6371
7835
2.304751
GGAATGCATCCTTTTGGCAG
57.695
50.000
0.00
0.00
45.56
4.85
6372
7836
1.551883
GGAATGCATCCTTTTGGCAGT
59.448
47.619
0.00
0.00
45.56
4.40
6373
7837
2.027837
GGAATGCATCCTTTTGGCAGTT
60.028
45.455
0.00
0.00
45.56
3.16
6374
7838
3.557686
GGAATGCATCCTTTTGGCAGTTT
60.558
43.478
0.00
0.00
45.56
2.66
6375
7839
4.322650
GGAATGCATCCTTTTGGCAGTTTA
60.323
41.667
0.00
0.00
45.56
2.01
6457
7933
4.635765
TGATTAGCCAAGTGTCATAACAGC
59.364
41.667
0.00
0.00
35.64
4.40
6519
7995
4.192317
ACCTCTGCTCGGAATTAATTGTC
58.808
43.478
5.17
0.00
0.00
3.18
6528
8004
3.778718
CGGAATTAATTGTCGCTCAAACG
59.221
43.478
5.17
0.00
39.62
3.60
6534
8010
2.661504
TTGTCGCTCAAACGAATGTG
57.338
45.000
0.00
0.00
44.93
3.21
6583
8059
3.056322
GGCATTTCTGGCATTTCACTCTT
60.056
43.478
0.00
0.00
46.77
2.85
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
10
11
2.751806
ACTTTCTGCCAATCTAGCTTGC
59.248
45.455
0.59
0.00
0.00
4.01
11
12
4.005650
TGACTTTCTGCCAATCTAGCTTG
58.994
43.478
0.00
0.00
0.00
4.01
14
15
3.376546
CCTTGACTTTCTGCCAATCTAGC
59.623
47.826
0.00
0.00
0.00
3.42
22
23
1.981256
TCAACCCTTGACTTTCTGCC
58.019
50.000
0.00
0.00
34.08
4.85
26
27
6.151648
TGAATCATGATCAACCCTTGACTTTC
59.848
38.462
9.06
1.52
43.48
2.62
84
85
5.012613
GCTTGTTTTGTTTGTTTGTTAGCG
58.987
37.500
0.00
0.00
0.00
4.26
101
102
0.319405
GAATTGCCTGCCTGCTTGTT
59.681
50.000
0.00
0.00
0.00
2.83
102
103
0.828762
TGAATTGCCTGCCTGCTTGT
60.829
50.000
0.00
0.00
0.00
3.16
103
104
0.108804
CTGAATTGCCTGCCTGCTTG
60.109
55.000
0.00
0.00
0.00
4.01
104
105
0.541296
ACTGAATTGCCTGCCTGCTT
60.541
50.000
0.00
0.00
0.00
3.91
105
106
0.541296
AACTGAATTGCCTGCCTGCT
60.541
50.000
0.00
0.00
0.00
4.24
106
107
0.319405
AAACTGAATTGCCTGCCTGC
59.681
50.000
0.00
0.00
0.00
4.85
107
108
1.401931
CGAAACTGAATTGCCTGCCTG
60.402
52.381
0.00
0.00
0.00
4.85
108
109
0.883833
CGAAACTGAATTGCCTGCCT
59.116
50.000
0.00
0.00
0.00
4.75
109
110
0.598065
ACGAAACTGAATTGCCTGCC
59.402
50.000
0.00
0.00
0.00
4.85
113
114
3.049912
GTCCAAACGAAACTGAATTGCC
58.950
45.455
0.00
0.00
0.00
4.52
159
160
4.397103
CGGTAACCCTTAAATCCTTTGACC
59.603
45.833
0.00
0.00
0.00
4.02
249
250
3.099841
TGTTGGTGGAGGGTGGCA
61.100
61.111
0.00
0.00
0.00
4.92
260
261
2.031163
GGAGAGCTGCGTGTTGGT
59.969
61.111
0.00
0.00
0.00
3.67
261
262
1.739562
GAGGAGAGCTGCGTGTTGG
60.740
63.158
0.00
0.00
0.00
3.77
263
264
1.882989
GAGGAGGAGAGCTGCGTGTT
61.883
60.000
0.00
0.00
0.00
3.32
264
265
2.283532
AGGAGGAGAGCTGCGTGT
60.284
61.111
0.00
0.00
0.00
4.49
266
267
1.752694
GAGAGGAGGAGAGCTGCGT
60.753
63.158
0.00
0.00
0.00
5.24
268
269
1.076044
AGGAGAGGAGGAGAGCTGC
60.076
63.158
0.00
0.00
0.00
5.25
389
401
2.825836
GGGCTCTGATTGGTGCCG
60.826
66.667
0.00
0.00
45.75
5.69
486
498
0.664224
GAACGCCGTTCCCTCAAAAA
59.336
50.000
18.88
0.00
36.65
1.94
487
499
0.464013
TGAACGCCGTTCCCTCAAAA
60.464
50.000
25.56
3.70
41.35
2.44
488
500
0.882927
CTGAACGCCGTTCCCTCAAA
60.883
55.000
25.56
6.40
41.35
2.69
489
501
1.301401
CTGAACGCCGTTCCCTCAA
60.301
57.895
25.56
7.12
41.35
3.02
490
502
2.342279
CTGAACGCCGTTCCCTCA
59.658
61.111
25.56
8.30
41.35
3.86
491
503
1.880819
TACCTGAACGCCGTTCCCTC
61.881
60.000
25.56
3.50
41.35
4.30
492
504
1.474332
TTACCTGAACGCCGTTCCCT
61.474
55.000
25.56
11.19
41.35
4.20
493
505
1.004679
TTACCTGAACGCCGTTCCC
60.005
57.895
25.56
4.60
41.35
3.97
494
506
0.320160
AGTTACCTGAACGCCGTTCC
60.320
55.000
25.56
10.16
43.37
3.62
495
507
0.788391
CAGTTACCTGAACGCCGTTC
59.212
55.000
22.39
22.39
43.37
3.95
496
508
0.390124
TCAGTTACCTGAACGCCGTT
59.610
50.000
0.16
0.16
44.67
4.44
497
509
2.043625
TCAGTTACCTGAACGCCGT
58.956
52.632
0.00
0.00
44.67
5.68
498
510
4.979204
TCAGTTACCTGAACGCCG
57.021
55.556
0.00
0.00
44.67
6.46
504
516
2.684943
TGGTGGTCTTCAGTTACCTGA
58.315
47.619
0.00
0.00
45.95
3.86
505
517
3.485463
TTGGTGGTCTTCAGTTACCTG
57.515
47.619
0.00
0.00
40.25
4.00
506
518
3.810743
GCATTGGTGGTCTTCAGTTACCT
60.811
47.826
0.00
0.00
36.67
3.08
507
519
2.488153
GCATTGGTGGTCTTCAGTTACC
59.512
50.000
0.00
0.00
36.24
2.85
508
520
3.412386
AGCATTGGTGGTCTTCAGTTAC
58.588
45.455
0.00
0.00
0.00
2.50
509
521
3.788227
AGCATTGGTGGTCTTCAGTTA
57.212
42.857
0.00
0.00
0.00
2.24
510
522
2.664402
AGCATTGGTGGTCTTCAGTT
57.336
45.000
0.00
0.00
0.00
3.16
511
523
3.788227
TTAGCATTGGTGGTCTTCAGT
57.212
42.857
0.00
0.00
37.28
3.41
512
524
3.181493
GCATTAGCATTGGTGGTCTTCAG
60.181
47.826
0.00
0.00
41.58
3.02
513
525
2.754552
GCATTAGCATTGGTGGTCTTCA
59.245
45.455
0.00
0.00
41.58
3.02
514
526
3.019564
AGCATTAGCATTGGTGGTCTTC
58.980
45.455
0.00
0.00
45.49
2.87
515
527
2.756760
CAGCATTAGCATTGGTGGTCTT
59.243
45.455
0.00
0.00
45.49
3.01
516
528
2.291153
ACAGCATTAGCATTGGTGGTCT
60.291
45.455
14.48
0.00
44.70
3.85
517
529
2.094675
ACAGCATTAGCATTGGTGGTC
58.905
47.619
14.48
0.00
44.70
4.02
518
530
1.820519
CACAGCATTAGCATTGGTGGT
59.179
47.619
14.48
0.00
44.70
4.16
519
531
1.470285
GCACAGCATTAGCATTGGTGG
60.470
52.381
14.48
7.06
44.70
4.61
520
532
1.475280
AGCACAGCATTAGCATTGGTG
59.525
47.619
10.11
10.11
45.62
4.17
521
533
1.475280
CAGCACAGCATTAGCATTGGT
59.525
47.619
0.00
0.00
45.49
3.67
522
534
1.746787
TCAGCACAGCATTAGCATTGG
59.253
47.619
0.00
0.00
45.49
3.16
523
535
3.128068
TCTTCAGCACAGCATTAGCATTG
59.872
43.478
0.00
0.00
45.49
2.82
524
536
3.128242
GTCTTCAGCACAGCATTAGCATT
59.872
43.478
0.00
0.00
45.49
3.56
525
537
2.681848
GTCTTCAGCACAGCATTAGCAT
59.318
45.455
0.00
0.00
45.49
3.79
526
538
2.079158
GTCTTCAGCACAGCATTAGCA
58.921
47.619
0.00
0.00
45.49
3.49
527
539
1.399791
GGTCTTCAGCACAGCATTAGC
59.600
52.381
0.00
0.00
42.56
3.09
528
540
2.703416
TGGTCTTCAGCACAGCATTAG
58.297
47.619
0.00
0.00
0.00
1.73
529
541
2.857186
TGGTCTTCAGCACAGCATTA
57.143
45.000
0.00
0.00
0.00
1.90
530
542
3.731716
TGGTCTTCAGCACAGCATT
57.268
47.368
0.00
0.00
0.00
3.56
538
550
1.026718
CGGGAATGGTGGTCTTCAGC
61.027
60.000
0.00
0.00
43.68
4.26
539
551
1.026718
GCGGGAATGGTGGTCTTCAG
61.027
60.000
0.00
0.00
0.00
3.02
540
552
1.002624
GCGGGAATGGTGGTCTTCA
60.003
57.895
0.00
0.00
0.00
3.02
541
553
0.608035
TTGCGGGAATGGTGGTCTTC
60.608
55.000
0.00
0.00
0.00
2.87
542
554
0.178975
TTTGCGGGAATGGTGGTCTT
60.179
50.000
0.00
0.00
0.00
3.01
543
555
0.893727
GTTTGCGGGAATGGTGGTCT
60.894
55.000
0.00
0.00
0.00
3.85
544
556
1.584495
GTTTGCGGGAATGGTGGTC
59.416
57.895
0.00
0.00
0.00
4.02
545
557
1.906333
GGTTTGCGGGAATGGTGGT
60.906
57.895
0.00
0.00
0.00
4.16
546
558
2.969827
GGTTTGCGGGAATGGTGG
59.030
61.111
0.00
0.00
0.00
4.61
547
559
2.265182
ACGGTTTGCGGGAATGGTG
61.265
57.895
0.00
0.00
0.00
4.17
548
560
2.114411
ACGGTTTGCGGGAATGGT
59.886
55.556
0.00
0.00
0.00
3.55
549
561
2.566010
CACGGTTTGCGGGAATGG
59.434
61.111
0.00
0.00
0.00
3.16
550
562
2.126502
GCACGGTTTGCGGGAATG
60.127
61.111
0.00
0.00
42.79
2.67
558
570
1.068541
GGCTCCTAAAAGCACGGTTTG
60.069
52.381
0.00
0.00
44.35
2.93
559
571
1.244816
GGCTCCTAAAAGCACGGTTT
58.755
50.000
0.00
0.00
44.35
3.27
560
572
0.608308
GGGCTCCTAAAAGCACGGTT
60.608
55.000
0.00
0.00
44.35
4.44
561
573
1.002502
GGGCTCCTAAAAGCACGGT
60.003
57.895
0.00
0.00
44.35
4.83
562
574
3.905249
GGGCTCCTAAAAGCACGG
58.095
61.111
0.00
0.00
44.35
4.94
564
576
0.322906
AGCTGGGCTCCTAAAAGCAC
60.323
55.000
0.00
0.00
46.26
4.40
565
577
2.078452
AGCTGGGCTCCTAAAAGCA
58.922
52.632
0.00
0.00
44.35
3.91
575
587
2.270205
CGTGAATGGAGCTGGGCT
59.730
61.111
0.00
0.00
43.88
5.19
576
588
2.045926
ACGTGAATGGAGCTGGGC
60.046
61.111
0.00
0.00
0.00
5.36
577
589
0.249120
TACACGTGAATGGAGCTGGG
59.751
55.000
25.01
0.00
0.00
4.45
578
590
1.337728
TGTACACGTGAATGGAGCTGG
60.338
52.381
25.01
0.00
0.00
4.85
579
591
2.078849
TGTACACGTGAATGGAGCTG
57.921
50.000
25.01
0.00
0.00
4.24
580
592
2.621338
CATGTACACGTGAATGGAGCT
58.379
47.619
25.01
0.00
34.90
4.09
581
593
1.665679
CCATGTACACGTGAATGGAGC
59.334
52.381
29.40
12.17
41.84
4.70
824
1798
4.806339
AAGGCGGAGGAGGGGAGG
62.806
72.222
0.00
0.00
0.00
4.30
825
1799
2.689034
AAAGGCGGAGGAGGGGAG
60.689
66.667
0.00
0.00
0.00
4.30
826
1800
2.687566
GAAAGGCGGAGGAGGGGA
60.688
66.667
0.00
0.00
0.00
4.81
864
1838
1.331447
GTGGTGTCGGTGTTGGTTTAC
59.669
52.381
0.00
0.00
0.00
2.01
877
1851
1.550065
CTGTCGATCGATGTGGTGTC
58.450
55.000
22.50
6.11
0.00
3.67
990
1970
3.277133
CCGAACATGGCTGGTTGG
58.723
61.111
0.00
0.00
37.29
3.77
1100
2087
1.438651
CGACAGCAATCGAGGGAAAA
58.561
50.000
3.71
0.00
45.13
2.29
1258
2249
2.917933
GCCCAGGCAGAAAAACTTTTT
58.082
42.857
3.12
0.00
41.49
1.94
1259
2250
2.620251
GCCCAGGCAGAAAAACTTTT
57.380
45.000
3.12
0.00
41.49
2.27
1333
2324
6.768381
AGGCAAAACTGGAAGAGTATATAAGC
59.232
38.462
0.00
0.00
37.43
3.09
1337
2328
8.034313
TGATAGGCAAAACTGGAAGAGTATAT
57.966
34.615
0.00
0.00
37.43
0.86
1338
2329
7.432148
TGATAGGCAAAACTGGAAGAGTATA
57.568
36.000
0.00
0.00
37.43
1.47
1339
2330
6.313519
TGATAGGCAAAACTGGAAGAGTAT
57.686
37.500
0.00
0.00
37.43
2.12
1361
2352
3.840890
TGGCGGCAATAACTAACTTTG
57.159
42.857
10.22
0.00
0.00
2.77
1925
2917
6.829229
AAATGCTGAGATTGTGAGAATGAA
57.171
33.333
0.00
0.00
0.00
2.57
1926
2918
7.926674
TTAAATGCTGAGATTGTGAGAATGA
57.073
32.000
0.00
0.00
0.00
2.57
1963
2955
2.808244
ACAAATGTGTTCCAAGTTGCG
58.192
42.857
0.00
0.00
32.58
4.85
2334
3453
3.673809
CGAAACAAAACAAAAACCCACGA
59.326
39.130
0.00
0.00
0.00
4.35
2335
3454
3.429207
ACGAAACAAAACAAAAACCCACG
59.571
39.130
0.00
0.00
0.00
4.94
2337
3456
4.451435
GGAACGAAACAAAACAAAAACCCA
59.549
37.500
0.00
0.00
0.00
4.51
2338
3457
4.142859
GGGAACGAAACAAAACAAAAACCC
60.143
41.667
0.00
0.00
0.00
4.11
2340
3459
5.849357
AGGGAACGAAACAAAACAAAAAC
57.151
34.783
0.00
0.00
0.00
2.43
2359
3483
6.349033
CCACAAAACTATCGGTCTAAAAAGGG
60.349
42.308
0.00
0.00
0.00
3.95
2861
3988
3.933332
CCTACCGAATGGAGAAGTTTGTC
59.067
47.826
0.00
0.00
39.21
3.18
2990
4117
8.674263
AAAGGAACTGATAAGATAATCTGCAG
57.326
34.615
7.63
7.63
40.86
4.41
3236
4363
5.534654
CCAGACATTTCCTTTACCTTTGTCA
59.465
40.000
0.00
0.00
35.60
3.58
3343
4470
8.664079
ACCAGAAGCCAGAACATAATATCTATT
58.336
33.333
0.00
0.00
0.00
1.73
3439
4566
4.555262
ACAAGCAACAAAATAATGGGACG
58.445
39.130
0.00
0.00
0.00
4.79
3652
4779
0.446616
GATGAAAACGGGTTCGGAGC
59.553
55.000
0.00
0.00
41.39
4.70
3963
5102
3.299503
AGGTGAAGAAGTGTTGCCAAAT
58.700
40.909
0.00
0.00
0.00
2.32
3975
5114
6.151985
TGCTTACTGTTTGAAAAGGTGAAGAA
59.848
34.615
0.00
0.00
0.00
2.52
4130
5273
2.093869
CAGGGGCAGATTGTTGAAATGG
60.094
50.000
0.00
0.00
0.00
3.16
4205
5351
7.127339
TGAGAAGGAAGCATTAAGTATTAGGGT
59.873
37.037
0.00
0.00
0.00
4.34
4246
5563
2.472695
TGGCATACACACAGAACCTC
57.527
50.000
0.00
0.00
0.00
3.85
4373
5710
6.839657
TGTACTTCCACCCATAAAAAGGAAAA
59.160
34.615
0.00
0.00
37.86
2.29
4610
6052
6.313744
ACAGGCTGTTACAAACTTACAATC
57.686
37.500
15.88
0.00
0.00
2.67
4837
6281
6.916909
TCATCTCTACTATCCTTCCACTCTT
58.083
40.000
0.00
0.00
0.00
2.85
4901
6345
3.482436
CTTCCTCGTGGCTCTAGATACT
58.518
50.000
0.00
0.00
0.00
2.12
5001
6445
1.737793
GTGACAAATGCCTAGGAACCG
59.262
52.381
14.75
0.00
0.00
4.44
5108
6552
5.059404
ACGGCTTTCATAAAACTCCAATG
57.941
39.130
0.00
0.00
0.00
2.82
5380
6825
5.362430
ACAAACAATTTTGCAAGTCTAGGGA
59.638
36.000
0.00
0.00
45.32
4.20
5559
7004
1.442769
CACCCATCTTCTCAACGGTG
58.557
55.000
0.00
0.00
35.24
4.94
5574
7019
3.164977
GGGAGAGCCTAGGCACCC
61.165
72.222
32.59
32.59
44.88
4.61
5822
7267
1.962144
CAGCTTTGTTCAGGCCCTG
59.038
57.895
3.69
3.69
0.00
4.45
6080
7525
5.596361
TCCAAAAGAAAACAAGCACCTATCA
59.404
36.000
0.00
0.00
0.00
2.15
6084
7536
4.405358
TCATCCAAAAGAAAACAAGCACCT
59.595
37.500
0.00
0.00
0.00
4.00
6085
7537
4.692228
TCATCCAAAAGAAAACAAGCACC
58.308
39.130
0.00
0.00
0.00
5.01
6086
7538
5.276348
CGTTCATCCAAAAGAAAACAAGCAC
60.276
40.000
0.00
0.00
0.00
4.40
6087
7539
4.803088
CGTTCATCCAAAAGAAAACAAGCA
59.197
37.500
0.00
0.00
0.00
3.91
6088
7540
4.209080
CCGTTCATCCAAAAGAAAACAAGC
59.791
41.667
0.00
0.00
0.00
4.01
6089
7541
5.231991
CACCGTTCATCCAAAAGAAAACAAG
59.768
40.000
0.00
0.00
0.00
3.16
6090
7542
5.105752
CACCGTTCATCCAAAAGAAAACAA
58.894
37.500
0.00
0.00
0.00
2.83
6134
7586
0.389948
CAGACCAGCTACCGACCAAC
60.390
60.000
0.00
0.00
0.00
3.77
6368
7832
2.540361
CGCAGGCATCAAGATAAACTGC
60.540
50.000
16.34
16.34
44.52
4.40
6369
7833
2.032550
CCGCAGGCATCAAGATAAACTG
59.967
50.000
0.00
0.00
46.14
3.16
6370
7834
2.292267
CCGCAGGCATCAAGATAAACT
58.708
47.619
0.00
0.00
46.14
2.66
6371
7835
2.763249
CCGCAGGCATCAAGATAAAC
57.237
50.000
0.00
0.00
46.14
2.01
6457
7933
8.888579
AGGGAATATAATGTAAGTTCTTCGTG
57.111
34.615
0.00
0.00
0.00
4.35
6488
7964
2.093106
CCGAGCAGAGGTAGTACAACT
58.907
52.381
2.06
0.00
0.00
3.16
6489
7965
2.089980
TCCGAGCAGAGGTAGTACAAC
58.910
52.381
2.06
0.00
0.00
3.32
6519
7995
2.286125
TGTGAACACATTCGTTTGAGCG
60.286
45.455
3.39
0.00
37.69
5.03
6548
8024
1.678101
GAAATGCCTCATAGCCACACC
59.322
52.381
0.00
0.00
0.00
4.16
6549
8025
2.357009
CAGAAATGCCTCATAGCCACAC
59.643
50.000
0.00
0.00
0.00
3.82
6550
8026
2.646930
CAGAAATGCCTCATAGCCACA
58.353
47.619
0.00
0.00
0.00
4.17
6557
8033
3.101437
TGAAATGCCAGAAATGCCTCAT
58.899
40.909
0.00
0.00
0.00
2.90
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.