Multiple sequence alignment - TraesCS3D01G121600
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
TraesCS3D01G121600
chr3D
100.000
3314
0
0
1
3314
79422371
79419058
0.000000e+00
6120
1
TraesCS3D01G121600
chr3D
91.629
1338
97
6
1001
2323
79504251
79505588
0.000000e+00
1836
2
TraesCS3D01G121600
chr3D
89.986
1388
118
10
996
2371
79428062
79429440
0.000000e+00
1773
3
TraesCS3D01G121600
chr3A
91.003
3090
173
51
265
3314
93043607
93040583
0.000000e+00
4069
4
TraesCS3D01G121600
chr3A
91.239
1324
107
5
1001
2318
93263757
93265077
0.000000e+00
1794
5
TraesCS3D01G121600
chr3A
91.219
1321
110
4
1001
2318
93337359
93338676
0.000000e+00
1792
6
TraesCS3D01G121600
chr3A
93.208
265
18
0
2052
2316
93265663
93265927
1.120000e-104
390
7
TraesCS3D01G121600
chr3B
90.544
2940
166
50
1
2906
125525323
125522462
0.000000e+00
3786
8
TraesCS3D01G121600
chr3B
91.855
1326
102
3
996
2318
125551787
125553109
0.000000e+00
1845
9
TraesCS3D01G121600
chr3B
91.843
1324
96
7
1001
2318
125778975
125780292
0.000000e+00
1836
10
TraesCS3D01G121600
chr3B
96.825
63
2
0
2945
3007
125522133
125522071
4.520000e-19
106
11
TraesCS3D01G121600
chr1A
82.063
853
128
17
1445
2292
129004474
129003642
0.000000e+00
704
12
TraesCS3D01G121600
chr1A
74.371
437
81
22
1025
1449
129004984
129004567
1.230000e-34
158
13
TraesCS3D01G121600
chr1D
90.492
305
27
1
3009
3311
183080107
183079803
5.150000e-108
401
14
TraesCS3D01G121600
chr1B
89.968
309
31
0
3006
3314
643276190
643276498
1.850000e-107
399
15
TraesCS3D01G121600
chr4B
90.541
296
28
0
3016
3311
447108579
447108284
3.100000e-105
392
16
TraesCS3D01G121600
chr4B
88.571
315
35
1
3001
3314
488151026
488151340
6.710000e-102
381
17
TraesCS3D01G121600
chr2B
89.869
306
27
4
3009
3313
707268419
707268721
1.120000e-104
390
18
TraesCS3D01G121600
chr2A
89.389
311
31
1
3006
3314
34143053
34142743
1.120000e-104
390
19
TraesCS3D01G121600
chr5D
89.967
299
30
0
3016
3314
536935314
536935016
1.440000e-103
387
20
TraesCS3D01G121600
chr2D
89.068
311
32
1
3006
3314
340480909
340481219
5.190000e-103
385
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
TraesCS3D01G121600
chr3D
79419058
79422371
3313
True
6120
6120
100.0000
1
3314
1
chr3D.!!$R1
3313
1
TraesCS3D01G121600
chr3D
79504251
79505588
1337
False
1836
1836
91.6290
1001
2323
1
chr3D.!!$F2
1322
2
TraesCS3D01G121600
chr3D
79428062
79429440
1378
False
1773
1773
89.9860
996
2371
1
chr3D.!!$F1
1375
3
TraesCS3D01G121600
chr3A
93040583
93043607
3024
True
4069
4069
91.0030
265
3314
1
chr3A.!!$R1
3049
4
TraesCS3D01G121600
chr3A
93337359
93338676
1317
False
1792
1792
91.2190
1001
2318
1
chr3A.!!$F1
1317
5
TraesCS3D01G121600
chr3A
93263757
93265927
2170
False
1092
1794
92.2235
1001
2318
2
chr3A.!!$F2
1317
6
TraesCS3D01G121600
chr3B
125522071
125525323
3252
True
1946
3786
93.6845
1
3007
2
chr3B.!!$R1
3006
7
TraesCS3D01G121600
chr3B
125551787
125553109
1322
False
1845
1845
91.8550
996
2318
1
chr3B.!!$F1
1322
8
TraesCS3D01G121600
chr3B
125778975
125780292
1317
False
1836
1836
91.8430
1001
2318
1
chr3B.!!$F2
1317
9
TraesCS3D01G121600
chr1A
129003642
129004984
1342
True
431
704
78.2170
1025
2292
2
chr1A.!!$R1
1267
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
349
353
0.034089
GCTGCTCCCACCACCTTTAT
60.034
55.0
0.0
0.0
0.00
1.40
F
677
724
0.178935
CCTTTGGCTTTCTCCCCCAA
60.179
55.0
0.0
0.0
36.88
4.12
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1218
1285
1.076485
GGCGAGGGGGTAGTACTGA
60.076
63.158
5.39
0.0
0.0
3.41
R
2613
2927
0.665670
CGTGGATCTCAGCTATGCGG
60.666
60.000
0.00
0.0
0.0
5.69
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
35
36
1.958715
CACCGTGGAATGCGTCACA
60.959
57.895
0.00
0.00
33.83
3.58
38
39
0.389296
CCGTGGAATGCGTCACAGTA
60.389
55.000
0.00
0.00
33.83
2.74
43
44
3.991773
GTGGAATGCGTCACAGTAAACTA
59.008
43.478
0.00
0.00
34.32
2.24
104
105
1.199327
CGCATACCGATGGATAGACGT
59.801
52.381
0.00
0.00
40.02
4.34
111
112
2.481568
CCGATGGATAGACGTACGCTAA
59.518
50.000
16.72
0.17
0.00
3.09
121
122
5.385396
AGACGTACGCTAATTAAATGTGC
57.615
39.130
16.72
0.00
0.00
4.57
124
125
5.350633
ACGTACGCTAATTAAATGTGCCTA
58.649
37.500
16.72
0.00
0.00
3.93
131
132
6.472163
CGCTAATTAAATGTGCCTAAAACTGG
59.528
38.462
0.00
0.00
0.00
4.00
132
133
6.756542
GCTAATTAAATGTGCCTAAAACTGGG
59.243
38.462
0.00
0.00
0.00
4.45
141
142
3.007614
TGCCTAAAACTGGGTAGACAGAC
59.992
47.826
0.00
0.00
40.97
3.51
160
161
1.284657
CTGATAGTTCAGGCACGCAG
58.715
55.000
0.00
0.00
44.78
5.18
163
164
0.324943
ATAGTTCAGGCACGCAGGTT
59.675
50.000
0.00
0.00
0.00
3.50
165
166
0.324943
AGTTCAGGCACGCAGGTTAT
59.675
50.000
0.00
0.00
0.00
1.89
166
167
0.727398
GTTCAGGCACGCAGGTTATC
59.273
55.000
0.00
0.00
0.00
1.75
167
168
0.613260
TTCAGGCACGCAGGTTATCT
59.387
50.000
0.00
0.00
0.00
1.98
168
169
0.108186
TCAGGCACGCAGGTTATCTG
60.108
55.000
0.00
0.00
46.03
2.90
169
170
0.391661
CAGGCACGCAGGTTATCTGT
60.392
55.000
0.00
0.00
45.08
3.41
172
173
1.438651
GCACGCAGGTTATCTGTTCA
58.561
50.000
0.00
0.00
45.08
3.18
177
178
2.353704
CGCAGGTTATCTGTTCAGTCCA
60.354
50.000
0.00
0.00
45.08
4.02
191
192
5.534278
TGTTCAGTCCAAAGATGTGCAAATA
59.466
36.000
0.00
0.00
0.00
1.40
195
196
6.371548
TCAGTCCAAAGATGTGCAAATACTAC
59.628
38.462
0.00
0.00
0.00
2.73
201
202
8.458052
CCAAAGATGTGCAAATACTACAACATA
58.542
33.333
0.00
0.00
0.00
2.29
210
214
7.663905
TGCAAATACTACAACATATACATCCCC
59.336
37.037
0.00
0.00
0.00
4.81
213
217
5.228945
ACTACAACATATACATCCCCAGC
57.771
43.478
0.00
0.00
0.00
4.85
222
226
6.908593
ACATATACATCCCCAGCTAATATGGA
59.091
38.462
0.00
0.00
40.51
3.41
223
227
5.965033
ATACATCCCCAGCTAATATGGAG
57.035
43.478
0.00
0.00
40.51
3.86
224
228
3.602608
ACATCCCCAGCTAATATGGAGT
58.397
45.455
0.00
0.00
40.51
3.85
225
229
3.983410
ACATCCCCAGCTAATATGGAGTT
59.017
43.478
0.00
0.00
40.51
3.01
226
230
4.202503
ACATCCCCAGCTAATATGGAGTTG
60.203
45.833
0.00
0.00
40.51
3.16
227
231
3.664320
TCCCCAGCTAATATGGAGTTGA
58.336
45.455
0.00
0.00
40.51
3.18
228
232
4.044308
TCCCCAGCTAATATGGAGTTGAA
58.956
43.478
0.00
0.00
40.51
2.69
229
233
4.103153
TCCCCAGCTAATATGGAGTTGAAG
59.897
45.833
0.00
0.00
40.51
3.02
230
234
3.817647
CCCAGCTAATATGGAGTTGAAGC
59.182
47.826
0.00
0.00
40.51
3.86
231
235
3.496130
CCAGCTAATATGGAGTTGAAGCG
59.504
47.826
0.00
0.00
40.51
4.68
232
236
3.496130
CAGCTAATATGGAGTTGAAGCGG
59.504
47.826
0.00
0.00
33.80
5.52
233
237
2.808543
GCTAATATGGAGTTGAAGCGGG
59.191
50.000
0.00
0.00
0.00
6.13
234
238
1.680338
AATATGGAGTTGAAGCGGGC
58.320
50.000
0.00
0.00
0.00
6.13
235
239
0.532862
ATATGGAGTTGAAGCGGGCG
60.533
55.000
0.00
0.00
0.00
6.13
236
240
1.609635
TATGGAGTTGAAGCGGGCGA
61.610
55.000
0.00
0.00
0.00
5.54
270
274
3.127533
GTGGCACGGTGGCTGATC
61.128
66.667
30.89
16.77
44.10
2.92
280
284
1.079197
TGGCTGATCGATGCGTGTT
60.079
52.632
0.54
0.00
0.00
3.32
281
285
0.174617
TGGCTGATCGATGCGTGTTA
59.825
50.000
0.54
0.00
0.00
2.41
282
286
0.855349
GGCTGATCGATGCGTGTTAG
59.145
55.000
0.54
0.00
0.00
2.34
283
287
0.230769
GCTGATCGATGCGTGTTAGC
59.769
55.000
0.54
0.00
37.71
3.09
349
353
0.034089
GCTGCTCCCACCACCTTTAT
60.034
55.000
0.00
0.00
0.00
1.40
351
355
2.356741
GCTGCTCCCACCACCTTTATTA
60.357
50.000
0.00
0.00
0.00
0.98
352
356
3.545703
CTGCTCCCACCACCTTTATTAG
58.454
50.000
0.00
0.00
0.00
1.73
353
357
2.916934
TGCTCCCACCACCTTTATTAGT
59.083
45.455
0.00
0.00
0.00
2.24
354
358
3.332485
TGCTCCCACCACCTTTATTAGTT
59.668
43.478
0.00
0.00
0.00
2.24
355
359
3.945921
GCTCCCACCACCTTTATTAGTTC
59.054
47.826
0.00
0.00
0.00
3.01
364
368
3.776417
ACCTTTATTAGTTCCTACCGGCA
59.224
43.478
0.00
0.00
0.00
5.69
381
385
1.167851
GCATTTGCTGACACTAGCCA
58.832
50.000
0.00
0.00
43.02
4.75
406
437
7.750229
TGCCTGAATTAATGGACAGATTATC
57.250
36.000
14.82
0.00
32.90
1.75
408
439
7.779326
TGCCTGAATTAATGGACAGATTATCAA
59.221
33.333
14.82
0.00
32.90
2.57
423
454
8.959548
ACAGATTATCAAGATGTGCAAATACAA
58.040
29.630
0.00
0.00
33.69
2.41
437
468
5.092105
GCAAATACAACATTCATGCGTACA
58.908
37.500
0.00
0.00
0.00
2.90
438
469
5.003402
GCAAATACAACATTCATGCGTACAC
59.997
40.000
0.00
0.00
0.00
2.90
442
473
3.366724
ACAACATTCATGCGTACACGTAG
59.633
43.478
3.44
0.00
42.22
3.51
451
482
1.517276
GCGTACACGTAGCTGCTAATG
59.483
52.381
11.57
14.65
42.22
1.90
452
483
2.793933
CGTACACGTAGCTGCTAATGT
58.206
47.619
23.45
23.45
34.11
2.71
453
484
3.789791
GCGTACACGTAGCTGCTAATGTA
60.790
47.826
21.94
21.94
42.22
2.29
454
485
3.966844
CGTACACGTAGCTGCTAATGTAG
59.033
47.826
24.47
17.75
34.11
2.74
457
488
4.918037
ACACGTAGCTGCTAATGTAGTAC
58.082
43.478
20.41
5.65
0.00
2.73
459
490
5.206299
CACGTAGCTGCTAATGTAGTACTC
58.794
45.833
11.57
0.00
0.00
2.59
461
492
4.515944
CGTAGCTGCTAATGTAGTACTCCT
59.484
45.833
11.57
0.00
0.00
3.69
462
493
5.699915
CGTAGCTGCTAATGTAGTACTCCTA
59.300
44.000
11.57
0.00
0.00
2.94
495
531
5.221342
ACAGAGATACATTACCAGCTAGCAC
60.221
44.000
18.83
0.00
0.00
4.40
496
532
5.010516
CAGAGATACATTACCAGCTAGCACT
59.989
44.000
18.83
0.42
0.00
4.40
498
534
2.990066
ACATTACCAGCTAGCACTCC
57.010
50.000
18.83
0.00
0.00
3.85
500
536
2.093447
ACATTACCAGCTAGCACTCCAC
60.093
50.000
18.83
0.00
0.00
4.02
503
539
1.127567
ACCAGCTAGCACTCCACCAA
61.128
55.000
18.83
0.00
0.00
3.67
505
541
1.376543
CAGCTAGCACTCCACCAATG
58.623
55.000
18.83
0.00
0.00
2.82
506
542
1.065926
CAGCTAGCACTCCACCAATGA
60.066
52.381
18.83
0.00
0.00
2.57
507
543
1.842562
AGCTAGCACTCCACCAATGAT
59.157
47.619
18.83
0.00
0.00
2.45
508
544
1.945394
GCTAGCACTCCACCAATGATG
59.055
52.381
10.63
0.00
0.00
3.07
509
545
1.945394
CTAGCACTCCACCAATGATGC
59.055
52.381
0.00
0.00
32.29
3.91
510
546
0.330604
AGCACTCCACCAATGATGCT
59.669
50.000
0.00
0.00
35.64
3.79
512
548
1.100510
CACTCCACCAATGATGCTGG
58.899
55.000
0.00
0.00
40.05
4.85
513
549
0.682209
ACTCCACCAATGATGCTGGC
60.682
55.000
0.00
0.00
37.48
4.85
557
597
3.760151
CCGTGCCATGATAATTGATGGAT
59.240
43.478
14.17
0.00
41.63
3.41
566
606
5.687780
TGATAATTGATGGATGACTGCTGT
58.312
37.500
0.00
0.00
0.00
4.40
596
636
2.422939
AGCCTGCCTATCCTATGGAA
57.577
50.000
0.00
0.00
34.34
3.53
664
705
1.039856
CCACCACCTTTGTCCTTTGG
58.960
55.000
0.00
0.00
0.00
3.28
677
724
0.178935
CCTTTGGCTTTCTCCCCCAA
60.179
55.000
0.00
0.00
36.88
4.12
682
729
1.155155
GCTTTCTCCCCCAACCCAA
59.845
57.895
0.00
0.00
0.00
4.12
711
759
2.636893
AGCCTCGCAGAAATATCATCCT
59.363
45.455
0.00
0.00
34.09
3.24
714
762
3.007290
CCTCGCAGAAATATCATCCTGGA
59.993
47.826
0.00
0.00
34.09
3.86
717
765
4.040829
TCGCAGAAATATCATCCTGGACAT
59.959
41.667
0.00
0.00
0.00
3.06
718
766
4.758674
CGCAGAAATATCATCCTGGACATT
59.241
41.667
0.00
0.00
0.00
2.71
719
767
5.106791
CGCAGAAATATCATCCTGGACATTC
60.107
44.000
0.00
0.00
0.00
2.67
720
768
6.002704
GCAGAAATATCATCCTGGACATTCT
58.997
40.000
0.00
0.46
0.00
2.40
721
769
6.489361
GCAGAAATATCATCCTGGACATTCTT
59.511
38.462
0.00
0.00
0.00
2.52
722
770
7.308469
GCAGAAATATCATCCTGGACATTCTTC
60.308
40.741
0.00
0.00
0.00
2.87
723
771
7.718314
CAGAAATATCATCCTGGACATTCTTCA
59.282
37.037
0.00
0.00
0.00
3.02
724
772
7.937942
AGAAATATCATCCTGGACATTCTTCAG
59.062
37.037
0.00
0.00
0.00
3.02
725
773
7.384524
AATATCATCCTGGACATTCTTCAGA
57.615
36.000
0.00
0.00
0.00
3.27
726
774
5.705397
ATCATCCTGGACATTCTTCAGAA
57.295
39.130
0.00
0.00
38.56
3.02
727
775
5.095145
TCATCCTGGACATTCTTCAGAAG
57.905
43.478
3.45
3.45
37.48
2.85
728
776
4.779489
TCATCCTGGACATTCTTCAGAAGA
59.221
41.667
8.95
8.95
37.48
2.87
758
806
2.717639
AAAATCTCATCCCGGACAGG
57.282
50.000
0.73
0.00
40.63
4.00
761
809
0.833287
ATCTCATCCCGGACAGGTTG
59.167
55.000
0.73
0.00
38.74
3.77
770
818
0.888736
CGGACAGGTTGTGGCATTCA
60.889
55.000
0.00
0.00
34.74
2.57
800
848
0.179073
CACCCATCCTCGTCACCATC
60.179
60.000
0.00
0.00
0.00
3.51
813
863
0.374758
CACCATCAGACATTTCGCCG
59.625
55.000
0.00
0.00
0.00
6.46
814
864
0.249120
ACCATCAGACATTTCGCCGA
59.751
50.000
0.00
0.00
0.00
5.54
900
951
2.033448
CAGCCAGGCAACCGGTTA
59.967
61.111
21.79
0.00
37.17
2.85
1230
1297
1.201424
CCCTGGTTCAGTACTACCCC
58.799
60.000
11.54
4.94
33.34
4.95
2482
2658
5.412286
TGTGTAGTTTAACCGGAAATAAGCC
59.588
40.000
9.46
0.00
0.00
4.35
2496
2672
1.397390
TAAGCCCCTCGATTCGGGTC
61.397
60.000
5.04
0.00
41.85
4.46
2613
2927
7.802720
AGAGAAATTTTGTTTTGTTTGTGTTGC
59.197
29.630
0.00
0.00
0.00
4.17
2647
2961
4.579384
ACGGTGGTGGTGGCTTGG
62.579
66.667
0.00
0.00
0.00
3.61
2719
3038
2.267642
CGGCCGATTCAGTCCCAA
59.732
61.111
24.07
0.00
0.00
4.12
2725
3044
1.089920
CGATTCAGTCCCAAGCAAGG
58.910
55.000
0.00
0.00
0.00
3.61
2740
3059
1.898094
AAGGCAGTGATGCAACGCA
60.898
52.632
10.34
0.00
44.86
5.24
2742
3061
2.126734
GCAGTGATGCAACGCACC
60.127
61.111
10.34
0.00
43.04
5.01
2748
3067
0.039346
TGATGCAACGCACCACAATG
60.039
50.000
0.00
0.00
43.04
2.82
2752
3071
0.939106
GCAACGCACCACAATGTTCC
60.939
55.000
0.00
0.00
0.00
3.62
2757
3076
1.164411
GCACCACAATGTTCCGATCA
58.836
50.000
0.00
0.00
0.00
2.92
2759
3078
2.164219
GCACCACAATGTTCCGATCATT
59.836
45.455
0.00
0.00
36.16
2.57
2908
3547
6.705381
GGACATTGATAGGAATCTGACTTGAG
59.295
42.308
0.00
0.00
32.93
3.02
2909
3548
7.192852
ACATTGATAGGAATCTGACTTGAGT
57.807
36.000
0.00
0.00
32.93
3.41
2910
3549
7.046652
ACATTGATAGGAATCTGACTTGAGTG
58.953
38.462
0.00
0.00
32.93
3.51
2912
3551
2.777832
AGGAATCTGACTTGAGTGCC
57.222
50.000
0.00
0.00
0.00
5.01
2913
3552
1.066573
AGGAATCTGACTTGAGTGCCG
60.067
52.381
0.00
0.00
0.00
5.69
2915
3554
2.612972
GGAATCTGACTTGAGTGCCGAA
60.613
50.000
0.00
0.00
0.00
4.30
2930
3569
1.860078
CGAAGGAACTGTCGGTTGC
59.140
57.895
7.93
7.93
44.89
4.17
2931
3570
0.878523
CGAAGGAACTGTCGGTTGCA
60.879
55.000
17.26
0.00
46.57
4.08
2932
3571
1.523758
GAAGGAACTGTCGGTTGCAT
58.476
50.000
17.26
6.17
46.57
3.96
2933
3572
1.464997
GAAGGAACTGTCGGTTGCATC
59.535
52.381
17.26
11.47
46.57
3.91
2934
3573
0.396435
AGGAACTGTCGGTTGCATCA
59.604
50.000
17.26
0.00
46.57
3.07
2935
3574
1.202758
AGGAACTGTCGGTTGCATCAA
60.203
47.619
17.26
0.00
46.57
2.57
2936
3575
1.606668
GGAACTGTCGGTTGCATCAAA
59.393
47.619
10.91
0.00
44.14
2.69
2937
3576
2.034053
GGAACTGTCGGTTGCATCAAAA
59.966
45.455
10.91
0.00
44.14
2.44
2938
3577
3.490078
GGAACTGTCGGTTGCATCAAAAA
60.490
43.478
10.91
0.00
44.14
1.94
2939
3578
3.354089
ACTGTCGGTTGCATCAAAAAG
57.646
42.857
0.00
0.00
0.00
2.27
2940
3579
2.948979
ACTGTCGGTTGCATCAAAAAGA
59.051
40.909
0.00
0.00
0.00
2.52
2941
3580
3.380004
ACTGTCGGTTGCATCAAAAAGAA
59.620
39.130
0.00
0.00
0.00
2.52
2942
3581
4.142271
ACTGTCGGTTGCATCAAAAAGAAA
60.142
37.500
0.00
0.00
0.00
2.52
2943
3582
4.748892
TGTCGGTTGCATCAAAAAGAAAA
58.251
34.783
0.00
0.00
0.00
2.29
3008
3669
7.472334
ACAAATGATGAGCCTAAACAAAGAT
57.528
32.000
0.00
0.00
0.00
2.40
3013
3674
6.121590
TGATGAGCCTAAACAAAGATATGCA
58.878
36.000
0.00
0.00
0.00
3.96
3050
3711
8.253810
AGATGTGAAATCTCTACGAATGAAGAA
58.746
33.333
0.00
0.00
0.00
2.52
3052
3713
6.590292
TGTGAAATCTCTACGAATGAAGAACC
59.410
38.462
0.00
0.00
0.00
3.62
3055
3716
2.159282
TCTCTACGAATGAAGAACCGGC
60.159
50.000
0.00
0.00
0.00
6.13
3069
3730
4.950050
AGAACCGGCATTAACTCTATCAG
58.050
43.478
0.00
0.00
0.00
2.90
3119
3780
8.689251
TGTACTCTATTTTTGATGAACTCGAG
57.311
34.615
11.84
11.84
0.00
4.04
3123
3784
7.065216
TCTATTTTTGATGAACTCGAGCTTG
57.935
36.000
13.61
0.00
0.00
4.01
3128
3789
3.515630
TGATGAACTCGAGCTTGTCATC
58.484
45.455
26.40
26.40
34.73
2.92
3153
3814
9.601217
TCAAGATTACCATAAGCTCTAAAACTC
57.399
33.333
0.00
0.00
0.00
3.01
3159
3820
7.203255
ACCATAAGCTCTAAAACTCACAAAC
57.797
36.000
0.00
0.00
0.00
2.93
3170
3831
9.179909
TCTAAAACTCACAAACAGAAATACCAA
57.820
29.630
0.00
0.00
0.00
3.67
3172
3833
8.474006
AAAACTCACAAACAGAAATACCAAAC
57.526
30.769
0.00
0.00
0.00
2.93
3191
3852
6.324770
ACCAAACAAGAACCAAGAAAGATGAT
59.675
34.615
0.00
0.00
0.00
2.45
3217
3878
2.098770
GGATGCAATGGTTTGAGCTCTC
59.901
50.000
16.19
5.49
34.60
3.20
3247
3908
2.834574
ACGATCAAGCTACTCACTCG
57.165
50.000
0.00
0.00
0.00
4.18
3279
3940
4.917998
CCCTGATAGTACGACAATCAATCG
59.082
45.833
0.00
0.00
45.17
3.34
3294
3955
0.533951
AATCGTACAACCCGGTCTCC
59.466
55.000
0.00
0.00
0.00
3.71
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
8
9
1.000717
CATTCCACGGTGAAAACCCAC
60.001
52.381
10.28
0.00
36.37
4.61
35
36
2.088950
AATGCCACGCGTAGTTTACT
57.911
45.000
13.44
0.00
0.00
2.24
38
39
0.386731
GCAAATGCCACGCGTAGTTT
60.387
50.000
13.44
7.95
34.31
2.66
59
60
1.566018
GCCAAGACGGTTTCTCCACG
61.566
60.000
0.00
0.00
36.97
4.94
90
91
0.873054
AGCGTACGTCTATCCATCGG
59.127
55.000
17.90
0.00
0.00
4.18
104
105
8.178964
CAGTTTTAGGCACATTTAATTAGCGTA
58.821
33.333
0.00
0.00
0.00
4.42
111
112
7.122204
GTCTACCCAGTTTTAGGCACATTTAAT
59.878
37.037
0.00
0.00
0.00
1.40
121
122
4.527038
TCAGTCTGTCTACCCAGTTTTAGG
59.473
45.833
0.00
0.00
34.02
2.69
124
125
5.780793
ACTATCAGTCTGTCTACCCAGTTTT
59.219
40.000
0.00
0.00
34.02
2.43
160
161
5.940470
ACATCTTTGGACTGAACAGATAACC
59.060
40.000
8.87
6.90
0.00
2.85
163
164
4.937620
GCACATCTTTGGACTGAACAGATA
59.062
41.667
8.87
0.00
0.00
1.98
165
166
3.141398
GCACATCTTTGGACTGAACAGA
58.859
45.455
8.87
0.00
0.00
3.41
166
167
2.880268
TGCACATCTTTGGACTGAACAG
59.120
45.455
0.00
0.00
0.00
3.16
167
168
2.929641
TGCACATCTTTGGACTGAACA
58.070
42.857
0.00
0.00
0.00
3.18
168
169
3.988379
TTGCACATCTTTGGACTGAAC
57.012
42.857
0.00
0.00
0.00
3.18
169
170
5.769662
AGTATTTGCACATCTTTGGACTGAA
59.230
36.000
0.00
0.00
0.00
3.02
172
173
6.237901
TGTAGTATTTGCACATCTTTGGACT
58.762
36.000
0.00
0.00
0.00
3.85
191
192
4.907875
AGCTGGGGATGTATATGTTGTAGT
59.092
41.667
0.00
0.00
0.00
2.73
195
196
7.500227
CCATATTAGCTGGGGATGTATATGTTG
59.500
40.741
0.00
0.00
0.00
3.33
201
202
5.353986
ACTCCATATTAGCTGGGGATGTAT
58.646
41.667
0.00
0.00
36.24
2.29
210
214
3.496130
CCGCTTCAACTCCATATTAGCTG
59.504
47.826
0.00
0.00
0.00
4.24
213
217
2.808543
GCCCGCTTCAACTCCATATTAG
59.191
50.000
0.00
0.00
0.00
1.73
222
226
4.008933
AGCTCGCCCGCTTCAACT
62.009
61.111
0.00
0.00
36.74
3.16
223
227
3.793144
CAGCTCGCCCGCTTCAAC
61.793
66.667
0.00
0.00
38.41
3.18
224
228
3.315142
ATCAGCTCGCCCGCTTCAA
62.315
57.895
0.00
0.00
38.41
2.69
225
229
3.774528
ATCAGCTCGCCCGCTTCA
61.775
61.111
0.00
0.00
38.41
3.02
226
230
3.267860
CATCAGCTCGCCCGCTTC
61.268
66.667
0.00
0.00
38.41
3.86
227
231
3.612247
AACATCAGCTCGCCCGCTT
62.612
57.895
0.00
0.00
38.41
4.68
228
232
4.087892
AACATCAGCTCGCCCGCT
62.088
61.111
0.00
0.00
41.90
5.52
229
233
3.869272
CAACATCAGCTCGCCCGC
61.869
66.667
0.00
0.00
0.00
6.13
230
234
3.869272
GCAACATCAGCTCGCCCG
61.869
66.667
0.00
0.00
0.00
6.13
231
235
2.747460
TGCAACATCAGCTCGCCC
60.747
61.111
0.00
0.00
0.00
6.13
232
236
2.789917
CTGCAACATCAGCTCGCC
59.210
61.111
0.00
0.00
0.00
5.54
349
353
2.026636
AGCAAATGCCGGTAGGAACTAA
60.027
45.455
1.90
0.00
42.48
2.24
351
355
0.328258
AGCAAATGCCGGTAGGAACT
59.672
50.000
1.90
0.00
43.38
3.01
352
356
0.451783
CAGCAAATGCCGGTAGGAAC
59.548
55.000
1.90
0.00
43.38
3.62
353
357
0.326595
TCAGCAAATGCCGGTAGGAA
59.673
50.000
1.90
0.00
43.38
3.36
354
358
0.392461
GTCAGCAAATGCCGGTAGGA
60.392
55.000
1.90
0.00
43.38
2.94
355
359
0.676466
TGTCAGCAAATGCCGGTAGG
60.676
55.000
1.90
0.00
43.38
3.18
364
368
1.747355
GCATGGCTAGTGTCAGCAAAT
59.253
47.619
0.00
0.00
43.67
2.32
381
385
7.946219
TGATAATCTGTCCATTAATTCAGGCAT
59.054
33.333
10.29
0.00
0.00
4.40
406
437
7.671827
CATGAATGTTGTATTTGCACATCTTG
58.328
34.615
0.00
0.00
0.00
3.02
408
439
5.808540
GCATGAATGTTGTATTTGCACATCT
59.191
36.000
0.00
0.00
0.00
2.90
423
454
1.924524
GCTACGTGTACGCATGAATGT
59.075
47.619
7.29
0.00
44.43
2.71
427
458
0.800683
GCAGCTACGTGTACGCATGA
60.801
55.000
7.29
0.00
44.43
3.07
437
468
4.275443
GGAGTACTACATTAGCAGCTACGT
59.725
45.833
0.00
5.29
0.00
3.57
438
469
4.515944
AGGAGTACTACATTAGCAGCTACG
59.484
45.833
8.10
0.00
0.00
3.51
500
536
2.842256
GCCTCGCCAGCATCATTGG
61.842
63.158
0.00
0.00
38.78
3.16
503
539
3.804153
CTCGCCTCGCCAGCATCAT
62.804
63.158
0.00
0.00
0.00
2.45
509
545
4.218578
ATCAGCTCGCCTCGCCAG
62.219
66.667
0.00
0.00
0.00
4.85
510
546
4.519437
CATCAGCTCGCCTCGCCA
62.519
66.667
0.00
0.00
0.00
5.69
557
597
4.284860
AGCACGCGACAGCAGTCA
62.285
61.111
15.93
0.00
45.23
3.41
596
636
1.302033
CTTGCAGCCTCGTGTTCCT
60.302
57.895
0.00
0.00
0.00
3.36
664
705
1.155155
TTGGGTTGGGGGAGAAAGC
59.845
57.895
0.00
0.00
0.00
3.51
699
747
7.935755
TCTGAAGAATGTCCAGGATGATATTTC
59.064
37.037
0.00
0.00
39.69
2.17
711
759
7.880160
TTTCTTTTCTTCTGAAGAATGTCCA
57.120
32.000
27.93
13.85
46.15
4.02
741
789
1.210478
CAACCTGTCCGGGATGAGATT
59.790
52.381
0.00
0.00
36.97
2.40
743
791
0.544357
ACAACCTGTCCGGGATGAGA
60.544
55.000
0.00
0.00
36.97
3.27
758
806
1.069227
GGACGAGTTGAATGCCACAAC
60.069
52.381
0.00
0.00
45.15
3.32
761
809
0.669318
TCGGACGAGTTGAATGCCAC
60.669
55.000
0.00
0.00
0.00
5.01
770
818
1.590147
GATGGGTGTCGGACGAGTT
59.410
57.895
3.34
0.00
0.00
3.01
800
848
2.379634
TGCGTCGGCGAAATGTCTG
61.380
57.895
16.53
0.00
44.10
3.51
897
948
2.343544
AGCGCGTCGTATTCAACTTAAC
59.656
45.455
8.43
0.00
0.00
2.01
900
951
1.389106
GAAGCGCGTCGTATTCAACTT
59.611
47.619
7.77
0.00
0.00
2.66
934
986
2.484417
CGAGAGGGAGAATTGGTGGATG
60.484
54.545
0.00
0.00
0.00
3.51
936
988
1.195115
CGAGAGGGAGAATTGGTGGA
58.805
55.000
0.00
0.00
0.00
4.02
1218
1285
1.076485
GGCGAGGGGGTAGTACTGA
60.076
63.158
5.39
0.00
0.00
3.41
1829
2002
2.962569
CGAAGCAGAGGTGGACGA
59.037
61.111
0.00
0.00
0.00
4.20
2097
2270
2.047844
CAGTCCGACACCAGCAGG
60.048
66.667
0.40
0.00
42.21
4.85
2496
2672
1.366111
AATCCAATCGCGACCCAACG
61.366
55.000
12.93
0.00
0.00
4.10
2609
2923
0.864455
GATCTCAGCTATGCGGCAAC
59.136
55.000
6.82
0.00
34.17
4.17
2613
2927
0.665670
CGTGGATCTCAGCTATGCGG
60.666
60.000
0.00
0.00
0.00
5.69
2725
3044
2.906939
TGGTGCGTTGCATCACTGC
61.907
57.895
0.00
6.39
45.28
4.40
2740
3059
3.016736
GGAATGATCGGAACATTGTGGT
58.983
45.455
16.85
0.00
37.96
4.16
2742
3061
2.032054
CGGGAATGATCGGAACATTGTG
59.968
50.000
16.85
4.34
37.96
3.33
2748
3067
3.060602
GAGATTCGGGAATGATCGGAAC
58.939
50.000
0.00
0.00
0.00
3.62
2752
3071
2.320367
GACGAGATTCGGGAATGATCG
58.680
52.381
17.35
17.35
45.59
3.69
2757
3076
1.001597
GCTACGACGAGATTCGGGAAT
60.002
52.381
0.00
0.00
45.59
3.01
2759
3078
0.745486
TGCTACGACGAGATTCGGGA
60.745
55.000
0.00
0.00
45.59
5.14
2874
3199
5.808366
TCCTATCAATGTCCACTATCCAC
57.192
43.478
0.00
0.00
0.00
4.02
2908
3547
3.550656
CGACAGTTCCTTCGGCAC
58.449
61.111
0.00
0.00
0.00
5.01
2912
3551
0.878523
TGCAACCGACAGTTCCTTCG
60.879
55.000
0.00
0.00
36.18
3.79
2913
3552
1.464997
GATGCAACCGACAGTTCCTTC
59.535
52.381
0.00
0.00
36.18
3.46
2915
3554
0.396435
TGATGCAACCGACAGTTCCT
59.604
50.000
0.00
0.00
36.18
3.36
2917
3556
3.347958
TTTTGATGCAACCGACAGTTC
57.652
42.857
0.00
0.00
36.18
3.01
2918
3557
3.380004
TCTTTTTGATGCAACCGACAGTT
59.620
39.130
0.00
0.00
40.16
3.16
2919
3558
2.948979
TCTTTTTGATGCAACCGACAGT
59.051
40.909
0.00
0.00
0.00
3.55
2920
3559
3.624326
TCTTTTTGATGCAACCGACAG
57.376
42.857
0.00
0.00
0.00
3.51
2921
3560
4.377839
TTTCTTTTTGATGCAACCGACA
57.622
36.364
0.00
0.00
0.00
4.35
2922
3561
5.710613
TTTTTCTTTTTGATGCAACCGAC
57.289
34.783
0.00
0.00
0.00
4.79
2941
3580
5.414765
GGGATCAAGATAACCGACAGTTTTT
59.585
40.000
0.00
0.00
40.05
1.94
2942
3581
4.941873
GGGATCAAGATAACCGACAGTTTT
59.058
41.667
0.00
0.00
40.05
2.43
2943
3582
4.225267
AGGGATCAAGATAACCGACAGTTT
59.775
41.667
0.00
0.00
40.05
2.66
2956
3595
4.285003
TCTTGGTTAACGAAGGGATCAAGA
59.715
41.667
24.60
18.30
37.57
3.02
3034
3695
2.159282
GCCGGTTCTTCATTCGTAGAGA
60.159
50.000
1.90
0.00
38.43
3.10
3037
3698
2.004583
TGCCGGTTCTTCATTCGTAG
57.995
50.000
1.90
0.00
0.00
3.51
3050
3711
2.434336
TGCTGATAGAGTTAATGCCGGT
59.566
45.455
1.90
0.00
0.00
5.28
3052
3713
5.484173
TTTTGCTGATAGAGTTAATGCCG
57.516
39.130
0.00
0.00
0.00
5.69
3069
3730
9.858247
CATATGCATCTTTTATGATGTTTTTGC
57.142
29.630
0.19
0.00
44.02
3.68
3101
3762
6.426633
TGACAAGCTCGAGTTCATCAAAAATA
59.573
34.615
15.13
0.00
0.00
1.40
3107
3768
3.056607
TGATGACAAGCTCGAGTTCATCA
60.057
43.478
28.28
28.28
39.74
3.07
3123
3784
9.547753
TTTAGAGCTTATGGTAATCTTGATGAC
57.452
33.333
0.00
0.00
0.00
3.06
3128
3789
9.383519
TGAGTTTTAGAGCTTATGGTAATCTTG
57.616
33.333
0.00
0.00
0.00
3.02
3134
3795
7.934665
TGTTTGTGAGTTTTAGAGCTTATGGTA
59.065
33.333
0.00
0.00
0.00
3.25
3136
3797
7.173218
TCTGTTTGTGAGTTTTAGAGCTTATGG
59.827
37.037
0.00
0.00
0.00
2.74
3153
3814
7.010091
GGTTCTTGTTTGGTATTTCTGTTTGTG
59.990
37.037
0.00
0.00
0.00
3.33
3159
3820
7.038154
TCTTGGTTCTTGTTTGGTATTTCTG
57.962
36.000
0.00
0.00
0.00
3.02
3170
3831
5.302568
TGCATCATCTTTCTTGGTTCTTGTT
59.697
36.000
0.00
0.00
0.00
2.83
3172
3833
5.381174
TGCATCATCTTTCTTGGTTCTTG
57.619
39.130
0.00
0.00
0.00
3.02
3217
3878
3.874706
AGCTTGATCGTATCGTTCGTAG
58.125
45.455
0.00
0.00
0.00
3.51
3294
3955
2.403252
GGTCTCATGGTGGTAGTTGG
57.597
55.000
0.00
0.00
0.00
3.77
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.