Multiple sequence alignment - TraesCS4D01G224300
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
TraesCS4D01G224300
chr4D
100.000
3432
0
0
1
3432
381101219
381097788
0.000000e+00
6338
1
TraesCS4D01G224300
chr4B
92.926
2290
74
33
479
2742
468456095
468453868
0.000000e+00
3251
2
TraesCS4D01G224300
chr4B
94.262
366
14
5
1
363
468456569
468456208
1.390000e-153
553
3
TraesCS4D01G224300
chr4A
94.571
1713
56
7
1135
2836
82404567
82406253
0.000000e+00
2614
4
TraesCS4D01G224300
chr4A
83.358
679
24
35
450
1087
82403921
82404551
2.330000e-151
545
5
TraesCS4D01G224300
chr4A
92.183
371
15
7
1
363
82403545
82403909
2.360000e-141
512
6
TraesCS4D01G224300
chr5D
94.301
579
24
1
2854
3432
431559411
431559980
0.000000e+00
878
7
TraesCS4D01G224300
chr5D
93.448
580
37
1
2854
3432
464612344
464611765
0.000000e+00
859
8
TraesCS4D01G224300
chr2D
92.123
584
41
1
2854
3432
127267993
127267410
0.000000e+00
819
9
TraesCS4D01G224300
chr2D
92.295
584
33
5
2852
3432
562893168
562893742
0.000000e+00
819
10
TraesCS4D01G224300
chr7D
94.227
537
25
5
2854
3385
75313916
75313381
0.000000e+00
815
11
TraesCS4D01G224300
chr6D
91.938
583
43
4
2851
3432
139290593
139291172
0.000000e+00
813
12
TraesCS4D01G224300
chr6D
92.110
583
32
5
2852
3432
321120731
321120161
0.000000e+00
809
13
TraesCS4D01G224300
chr6D
91.394
581
47
2
2852
3432
363868863
363868286
0.000000e+00
793
14
TraesCS4D01G224300
chr3A
90.816
588
47
3
2852
3432
649825271
649824684
0.000000e+00
780
15
TraesCS4D01G224300
chr2B
88.158
304
14
3
1335
1638
682132221
682132502
3.280000e-90
342
16
TraesCS4D01G224300
chr1D
96.571
175
6
0
1539
1713
8012973
8012799
1.200000e-74
291
17
TraesCS4D01G224300
chr1D
90.000
100
10
0
1335
1434
8013077
8012978
2.780000e-26
130
18
TraesCS4D01G224300
chr1B
95.000
180
8
1
1539
1717
658481279
658481100
7.250000e-72
281
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
TraesCS4D01G224300
chr4D
381097788
381101219
3431
True
6338.000000
6338
100.000000
1
3432
1
chr4D.!!$R1
3431
1
TraesCS4D01G224300
chr4B
468453868
468456569
2701
True
1902.000000
3251
93.594000
1
2742
2
chr4B.!!$R1
2741
2
TraesCS4D01G224300
chr4A
82403545
82406253
2708
False
1223.666667
2614
90.037333
1
2836
3
chr4A.!!$F1
2835
3
TraesCS4D01G224300
chr5D
431559411
431559980
569
False
878.000000
878
94.301000
2854
3432
1
chr5D.!!$F1
578
4
TraesCS4D01G224300
chr5D
464611765
464612344
579
True
859.000000
859
93.448000
2854
3432
1
chr5D.!!$R1
578
5
TraesCS4D01G224300
chr2D
127267410
127267993
583
True
819.000000
819
92.123000
2854
3432
1
chr2D.!!$R1
578
6
TraesCS4D01G224300
chr2D
562893168
562893742
574
False
819.000000
819
92.295000
2852
3432
1
chr2D.!!$F1
580
7
TraesCS4D01G224300
chr7D
75313381
75313916
535
True
815.000000
815
94.227000
2854
3385
1
chr7D.!!$R1
531
8
TraesCS4D01G224300
chr6D
139290593
139291172
579
False
813.000000
813
91.938000
2851
3432
1
chr6D.!!$F1
581
9
TraesCS4D01G224300
chr6D
321120161
321120731
570
True
809.000000
809
92.110000
2852
3432
1
chr6D.!!$R1
580
10
TraesCS4D01G224300
chr6D
363868286
363868863
577
True
793.000000
793
91.394000
2852
3432
1
chr6D.!!$R2
580
11
TraesCS4D01G224300
chr3A
649824684
649825271
587
True
780.000000
780
90.816000
2852
3432
1
chr3A.!!$R1
580
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
468
503
0.035725
TGAGGACGGACGAGCTAGAA
60.036
55.0
0.00
0.0
0.0
2.10
F
1069
1191
0.100861
CTCGCGTCCCTTCTACCTTC
59.899
60.0
5.77
0.0
0.0
3.46
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2389
2523
1.876714
CTTCACCGCATCCGTACCG
60.877
63.158
0.0
0.0
0.00
4.02
R
2823
2963
0.095762
CGGTAAAACGAACATCCGCC
59.904
55.000
0.0
0.0
35.47
6.13
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
124
125
5.624967
CGGAGCCTCGTAATATCTCTCTCTA
60.625
48.000
0.00
0.00
0.00
2.43
125
126
5.583457
GGAGCCTCGTAATATCTCTCTCTAC
59.417
48.000
0.00
0.00
0.00
2.59
126
127
6.368779
AGCCTCGTAATATCTCTCTCTACT
57.631
41.667
0.00
0.00
0.00
2.57
127
128
6.170506
AGCCTCGTAATATCTCTCTCTACTG
58.829
44.000
0.00
0.00
0.00
2.74
128
129
5.935789
GCCTCGTAATATCTCTCTCTACTGT
59.064
44.000
0.00
0.00
0.00
3.55
129
130
7.038870
AGCCTCGTAATATCTCTCTCTACTGTA
60.039
40.741
0.00
0.00
0.00
2.74
189
198
1.597027
CAGTTCCACACACGGGACC
60.597
63.158
0.00
0.00
33.18
4.46
218
227
1.746760
GCCACGATTCGCAATTCATC
58.253
50.000
5.86
0.00
0.00
2.92
345
356
2.930040
CGCTCCAAAACTCATGATACGT
59.070
45.455
0.00
0.00
0.00
3.57
346
357
4.109766
CGCTCCAAAACTCATGATACGTA
58.890
43.478
0.00
0.00
0.00
3.57
347
358
4.026804
CGCTCCAAAACTCATGATACGTAC
60.027
45.833
0.00
0.00
0.00
3.67
363
374
2.159531
ACGTACTACGAGTATTTGCGCA
60.160
45.455
15.49
5.66
46.05
6.09
364
375
2.847717
CGTACTACGAGTATTTGCGCAA
59.152
45.455
21.02
21.02
46.05
4.85
365
376
3.301379
CGTACTACGAGTATTTGCGCAAA
59.699
43.478
35.19
35.19
46.05
3.68
367
378
4.735662
ACTACGAGTATTTGCGCAAAAA
57.264
36.364
36.42
18.42
33.56
1.94
368
379
4.460505
ACTACGAGTATTTGCGCAAAAAC
58.539
39.130
36.42
24.50
33.56
2.43
372
398
3.728718
CGAGTATTTGCGCAAAAACACTT
59.271
39.130
36.42
22.31
33.56
3.16
380
406
4.286910
TGCGCAAAAACACTTGTATCTTC
58.713
39.130
8.16
0.00
0.00
2.87
385
411
6.513393
CGCAAAAACACTTGTATCTTCCTCTT
60.513
38.462
0.00
0.00
0.00
2.85
387
413
7.379797
GCAAAAACACTTGTATCTTCCTCTTTC
59.620
37.037
0.00
0.00
0.00
2.62
390
416
4.184629
CACTTGTATCTTCCTCTTTCCGG
58.815
47.826
0.00
0.00
0.00
5.14
396
422
2.885616
TCTTCCTCTTTCCGGTGTACT
58.114
47.619
0.00
0.00
0.00
2.73
400
426
2.821969
TCCTCTTTCCGGTGTACTGTAC
59.178
50.000
10.98
10.98
0.00
2.90
401
427
2.824341
CCTCTTTCCGGTGTACTGTACT
59.176
50.000
17.98
0.00
0.00
2.73
402
428
3.257624
CCTCTTTCCGGTGTACTGTACTT
59.742
47.826
17.98
0.00
0.00
2.24
404
430
5.376854
TCTTTCCGGTGTACTGTACTTAC
57.623
43.478
17.98
9.25
0.00
2.34
405
431
3.829886
TTCCGGTGTACTGTACTTACG
57.170
47.619
17.98
17.16
0.00
3.18
407
433
3.932822
TCCGGTGTACTGTACTTACGTA
58.067
45.455
17.98
0.00
0.00
3.57
408
434
4.320023
TCCGGTGTACTGTACTTACGTAA
58.680
43.478
17.98
7.94
0.00
3.18
411
437
5.106712
CCGGTGTACTGTACTTACGTAAGAA
60.107
44.000
35.60
21.08
43.62
2.52
412
438
6.370593
CGGTGTACTGTACTTACGTAAGAAA
58.629
40.000
35.60
22.21
43.62
2.52
414
440
7.149128
CGGTGTACTGTACTTACGTAAGAAAAC
60.149
40.741
35.60
27.66
43.62
2.43
415
441
7.862873
GGTGTACTGTACTTACGTAAGAAAACT
59.137
37.037
35.60
18.82
43.62
2.66
416
442
8.896826
GTGTACTGTACTTACGTAAGAAAACTC
58.103
37.037
35.60
20.61
43.62
3.01
417
443
8.840321
TGTACTGTACTTACGTAAGAAAACTCT
58.160
33.333
35.60
17.52
43.62
3.24
418
444
9.323963
GTACTGTACTTACGTAAGAAAACTCTC
57.676
37.037
35.60
17.61
43.62
3.20
419
445
7.366513
ACTGTACTTACGTAAGAAAACTCTCC
58.633
38.462
35.60
14.00
43.62
3.71
420
446
7.230309
ACTGTACTTACGTAAGAAAACTCTCCT
59.770
37.037
35.60
15.58
43.62
3.69
422
448
6.023357
ACTTACGTAAGAAAACTCTCCTCC
57.977
41.667
35.60
0.00
43.62
4.30
423
449
3.572604
ACGTAAGAAAACTCTCCTCCG
57.427
47.619
0.00
0.00
43.62
4.63
424
450
2.889678
ACGTAAGAAAACTCTCCTCCGT
59.110
45.455
0.00
0.00
43.62
4.69
426
452
4.202192
ACGTAAGAAAACTCTCCTCCGTTT
60.202
41.667
0.00
0.00
43.62
3.60
427
453
5.010012
ACGTAAGAAAACTCTCCTCCGTTTA
59.990
40.000
0.00
0.00
43.62
2.01
428
454
5.922544
CGTAAGAAAACTCTCCTCCGTTTAA
59.077
40.000
0.00
0.00
43.02
1.52
429
455
6.128982
CGTAAGAAAACTCTCCTCCGTTTAAC
60.129
42.308
0.00
0.00
43.02
2.01
430
456
4.639334
AGAAAACTCTCCTCCGTTTAACC
58.361
43.478
0.00
0.00
33.36
2.85
431
457
4.102054
AGAAAACTCTCCTCCGTTTAACCA
59.898
41.667
0.00
0.00
33.36
3.67
434
469
2.280628
CTCTCCTCCGTTTAACCATGC
58.719
52.381
0.00
0.00
0.00
4.06
468
503
0.035725
TGAGGACGGACGAGCTAGAA
60.036
55.000
0.00
0.00
0.00
2.10
558
603
4.888325
CCCAGGGAGCCGAGGGAT
62.888
72.222
0.00
0.00
43.32
3.85
567
612
2.765807
CCGAGGGATGGCTGGAGT
60.766
66.667
0.00
0.00
0.00
3.85
634
718
3.609703
TCGAGAGAGGGAGCAAGC
58.390
61.111
0.00
0.00
34.84
4.01
635
719
2.103934
CGAGAGAGGGAGCAAGCG
59.896
66.667
0.00
0.00
0.00
4.68
636
720
2.410687
CGAGAGAGGGAGCAAGCGA
61.411
63.158
0.00
0.00
0.00
4.93
637
721
1.437160
GAGAGAGGGAGCAAGCGAG
59.563
63.158
0.00
0.00
0.00
5.03
638
722
1.000270
AGAGAGGGAGCAAGCGAGA
60.000
57.895
0.00
0.00
0.00
4.04
709
793
1.453155
GAACTGACCGGCATTCATGT
58.547
50.000
0.00
0.00
0.00
3.21
741
840
3.085947
CCTGCCTGCCTGCCTCTA
61.086
66.667
0.00
0.00
0.00
2.43
742
841
2.505006
CTGCCTGCCTGCCTCTAG
59.495
66.667
0.00
0.00
0.00
2.43
743
842
3.085947
TGCCTGCCTGCCTCTAGG
61.086
66.667
0.00
0.00
40.95
3.02
753
852
3.230245
CCTCTAGGCTGAGCGGGG
61.230
72.222
0.00
0.00
33.02
5.73
754
853
3.922640
CTCTAGGCTGAGCGGGGC
61.923
72.222
0.00
0.00
0.00
5.80
913
1035
3.062639
GCAAAAGCCAGCCACCAT
58.937
55.556
0.00
0.00
0.00
3.55
914
1036
1.079612
GCAAAAGCCAGCCACCATC
60.080
57.895
0.00
0.00
0.00
3.51
915
1037
1.593265
CAAAAGCCAGCCACCATCC
59.407
57.895
0.00
0.00
0.00
3.51
916
1038
1.610379
AAAAGCCAGCCACCATCCC
60.610
57.895
0.00
0.00
0.00
3.85
917
1039
2.097978
AAAAGCCAGCCACCATCCCT
62.098
55.000
0.00
0.00
0.00
4.20
918
1040
2.793317
AAAGCCAGCCACCATCCCTG
62.793
60.000
0.00
0.00
0.00
4.45
960
1082
1.064240
AGTCCCAACCGAACAAAAGGT
60.064
47.619
0.00
0.00
43.68
3.50
961
1083
1.335810
GTCCCAACCGAACAAAAGGTC
59.664
52.381
0.00
0.00
40.37
3.85
962
1084
0.309612
CCCAACCGAACAAAAGGTCG
59.690
55.000
0.00
0.00
40.37
4.79
963
1085
1.018910
CCAACCGAACAAAAGGTCGT
58.981
50.000
2.10
0.00
40.37
4.34
970
1092
2.106418
GAACAAAAGGTCGTTCGTTGC
58.894
47.619
0.00
0.00
32.87
4.17
1069
1191
0.100861
CTCGCGTCCCTTCTACCTTC
59.899
60.000
5.77
0.00
0.00
3.46
1078
1200
5.270794
GTCCCTTCTACCTTCTTCTCCTTA
58.729
45.833
0.00
0.00
0.00
2.69
1110
1235
2.550180
GTCTCTGTTCTTTGAGTTGGGC
59.450
50.000
0.00
0.00
0.00
5.36
1474
1608
4.710167
TCCTCGCCGTCTCCGACA
62.710
66.667
0.00
0.00
35.63
4.35
1612
1746
2.125350
CTGAAGCAGTCCCTCGCC
60.125
66.667
0.00
0.00
0.00
5.54
2389
2523
2.738846
CTGTAGCGATATGAATGGTGGC
59.261
50.000
0.00
0.00
0.00
5.01
2425
2559
1.473258
AGAGCTGTCAGAGTAGCAGG
58.527
55.000
3.32
0.00
42.29
4.85
2513
2648
3.417101
TGTGTGAATATGGGGTGTCAAC
58.583
45.455
0.00
0.00
0.00
3.18
2540
2675
4.512944
GCTCTTGTGAGTCACATTTCTTCA
59.487
41.667
25.97
8.94
44.16
3.02
2593
2728
5.954296
AGTGAAGTGATCATCTTTGGTTG
57.046
39.130
0.00
0.00
40.97
3.77
2594
2729
4.763793
AGTGAAGTGATCATCTTTGGTTGG
59.236
41.667
0.00
0.00
40.97
3.77
2595
2730
4.520492
GTGAAGTGATCATCTTTGGTTGGT
59.480
41.667
0.00
0.00
40.97
3.67
2596
2731
5.705441
GTGAAGTGATCATCTTTGGTTGGTA
59.295
40.000
0.00
0.00
40.97
3.25
2743
2883
2.317040
GTCATCGGATCCTTGGAGGTA
58.683
52.381
10.75
0.00
36.53
3.08
2758
2898
2.369394
GAGGTAAGGCCAACTCCAATG
58.631
52.381
5.01
0.00
40.61
2.82
2783
2923
2.493713
ACGCATCGTCTGTTAGGATC
57.506
50.000
0.00
0.00
33.69
3.36
2784
2924
1.067212
ACGCATCGTCTGTTAGGATCC
59.933
52.381
2.48
2.48
33.69
3.36
2785
2925
1.772182
GCATCGTCTGTTAGGATCCG
58.228
55.000
5.98
0.00
30.25
4.18
2786
2926
1.772182
CATCGTCTGTTAGGATCCGC
58.228
55.000
5.98
1.45
30.25
5.54
2787
2927
0.311165
ATCGTCTGTTAGGATCCGCG
59.689
55.000
5.98
0.00
0.00
6.46
2788
2928
1.944676
CGTCTGTTAGGATCCGCGC
60.945
63.158
5.98
0.00
0.00
6.86
2789
2929
1.141019
GTCTGTTAGGATCCGCGCA
59.859
57.895
8.75
5.60
0.00
6.09
2790
2930
1.141019
TCTGTTAGGATCCGCGCAC
59.859
57.895
8.75
2.48
0.00
5.34
2791
2931
1.153647
CTGTTAGGATCCGCGCACA
60.154
57.895
8.75
7.10
0.00
4.57
2792
2932
1.148157
CTGTTAGGATCCGCGCACAG
61.148
60.000
8.75
16.41
0.00
3.66
2793
2933
1.141019
GTTAGGATCCGCGCACAGA
59.859
57.895
8.75
0.19
0.00
3.41
2794
2934
0.459585
GTTAGGATCCGCGCACAGAA
60.460
55.000
8.75
0.00
0.00
3.02
2795
2935
0.248012
TTAGGATCCGCGCACAGAAA
59.752
50.000
8.75
0.00
0.00
2.52
2796
2936
0.248012
TAGGATCCGCGCACAGAAAA
59.752
50.000
8.75
0.00
0.00
2.29
2797
2937
0.392998
AGGATCCGCGCACAGAAAAT
60.393
50.000
8.75
0.00
0.00
1.82
2798
2938
1.134521
AGGATCCGCGCACAGAAAATA
60.135
47.619
8.75
0.00
0.00
1.40
2799
2939
1.003866
GGATCCGCGCACAGAAAATAC
60.004
52.381
8.75
0.00
0.00
1.89
2800
2940
1.663643
GATCCGCGCACAGAAAATACA
59.336
47.619
8.75
0.00
0.00
2.29
2801
2941
0.793861
TCCGCGCACAGAAAATACAC
59.206
50.000
8.75
0.00
0.00
2.90
2802
2942
0.518355
CCGCGCACAGAAAATACACG
60.518
55.000
8.75
0.00
0.00
4.49
2803
2943
0.436913
CGCGCACAGAAAATACACGA
59.563
50.000
8.75
0.00
0.00
4.35
2804
2944
1.060553
CGCGCACAGAAAATACACGAT
59.939
47.619
8.75
0.00
0.00
3.73
2805
2945
2.694043
GCGCACAGAAAATACACGATC
58.306
47.619
0.30
0.00
0.00
3.69
2806
2946
2.536928
GCGCACAGAAAATACACGATCC
60.537
50.000
0.30
0.00
0.00
3.36
2807
2947
2.670905
CGCACAGAAAATACACGATCCA
59.329
45.455
0.00
0.00
0.00
3.41
2808
2948
3.483574
CGCACAGAAAATACACGATCCAC
60.484
47.826
0.00
0.00
0.00
4.02
2809
2949
3.181510
GCACAGAAAATACACGATCCACC
60.182
47.826
0.00
0.00
0.00
4.61
2810
2950
3.062099
CACAGAAAATACACGATCCACCG
59.938
47.826
0.00
0.00
0.00
4.94
2811
2951
3.259064
CAGAAAATACACGATCCACCGT
58.741
45.455
0.00
0.00
44.43
4.83
2812
2952
3.306166
CAGAAAATACACGATCCACCGTC
59.694
47.826
0.00
0.00
41.29
4.79
2813
2953
2.304751
AAATACACGATCCACCGTCC
57.695
50.000
0.00
0.00
41.29
4.79
2814
2954
1.187974
AATACACGATCCACCGTCCA
58.812
50.000
0.00
0.00
41.29
4.02
2815
2955
0.458669
ATACACGATCCACCGTCCAC
59.541
55.000
0.00
0.00
41.29
4.02
2816
2956
0.894642
TACACGATCCACCGTCCACA
60.895
55.000
0.00
0.00
41.29
4.17
2817
2957
1.736645
CACGATCCACCGTCCACAC
60.737
63.158
0.00
0.00
41.29
3.82
2818
2958
2.204461
ACGATCCACCGTCCACACA
61.204
57.895
0.00
0.00
38.56
3.72
2819
2959
1.005512
CGATCCACCGTCCACACAA
60.006
57.895
0.00
0.00
0.00
3.33
2820
2960
0.601576
CGATCCACCGTCCACACAAA
60.602
55.000
0.00
0.00
0.00
2.83
2821
2961
1.821216
GATCCACCGTCCACACAAAT
58.179
50.000
0.00
0.00
0.00
2.32
2822
2962
1.468520
GATCCACCGTCCACACAAATG
59.531
52.381
0.00
0.00
0.00
2.32
2823
2963
0.536233
TCCACCGTCCACACAAATGG
60.536
55.000
0.00
0.00
41.57
3.16
2824
2964
1.523154
CCACCGTCCACACAAATGGG
61.523
60.000
0.00
0.00
40.49
4.00
2825
2965
1.901464
ACCGTCCACACAAATGGGC
60.901
57.895
0.00
0.00
41.28
5.36
2827
2967
2.961768
GTCCACACAAATGGGCGG
59.038
61.111
0.00
0.00
40.49
6.13
2828
2968
1.602323
GTCCACACAAATGGGCGGA
60.602
57.895
0.00
0.00
40.49
5.54
2829
2969
0.965363
GTCCACACAAATGGGCGGAT
60.965
55.000
0.00
0.00
40.49
4.18
2830
2970
0.964860
TCCACACAAATGGGCGGATG
60.965
55.000
0.00
0.00
40.49
3.51
2831
2971
1.250154
CCACACAAATGGGCGGATGT
61.250
55.000
0.00
0.00
35.95
3.06
2832
2972
0.602562
CACACAAATGGGCGGATGTT
59.397
50.000
0.00
0.00
0.00
2.71
2833
2973
0.887933
ACACAAATGGGCGGATGTTC
59.112
50.000
0.00
0.00
0.00
3.18
2834
2974
0.179166
CACAAATGGGCGGATGTTCG
60.179
55.000
0.00
0.00
0.00
3.95
2835
2975
0.608035
ACAAATGGGCGGATGTTCGT
60.608
50.000
0.00
0.00
0.00
3.85
2836
2976
0.525761
CAAATGGGCGGATGTTCGTT
59.474
50.000
0.00
0.00
0.00
3.85
2837
2977
1.067915
CAAATGGGCGGATGTTCGTTT
60.068
47.619
0.00
0.00
0.00
3.60
2838
2978
1.253100
AATGGGCGGATGTTCGTTTT
58.747
45.000
0.00
0.00
0.00
2.43
2839
2979
2.116827
ATGGGCGGATGTTCGTTTTA
57.883
45.000
0.00
0.00
0.00
1.52
2840
2980
1.158434
TGGGCGGATGTTCGTTTTAC
58.842
50.000
0.00
0.00
0.00
2.01
2841
2981
0.448990
GGGCGGATGTTCGTTTTACC
59.551
55.000
0.00
0.00
0.00
2.85
2842
2982
0.095762
GGCGGATGTTCGTTTTACCG
59.904
55.000
0.00
0.00
42.63
4.02
2843
2983
1.070038
GCGGATGTTCGTTTTACCGA
58.930
50.000
0.00
0.00
42.40
4.69
2844
2984
1.460359
GCGGATGTTCGTTTTACCGAA
59.540
47.619
0.00
0.00
43.96
4.30
2860
3000
7.328493
GTTTTACCGAAAAATGCTTAGAGCAAT
59.672
33.333
6.72
0.00
41.21
3.56
2926
3066
2.978010
CGGACAAAAGTGGCGGCT
60.978
61.111
11.43
0.00
31.03
5.52
3009
3149
2.612471
CCAATTTTGAGCCGGATTTGCA
60.612
45.455
5.05
0.00
0.00
4.08
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
124
125
6.017523
CGAGTCTGATGACATACAGATACAGT
60.018
42.308
15.87
2.97
45.20
3.55
125
126
6.369799
CGAGTCTGATGACATACAGATACAG
58.630
44.000
15.87
6.37
45.20
2.74
126
127
5.239525
CCGAGTCTGATGACATACAGATACA
59.760
44.000
15.87
0.00
45.20
2.29
127
128
5.470437
TCCGAGTCTGATGACATACAGATAC
59.530
44.000
15.87
12.80
45.20
2.24
128
129
5.621193
TCCGAGTCTGATGACATACAGATA
58.379
41.667
15.87
0.00
45.20
1.98
129
130
4.464947
TCCGAGTCTGATGACATACAGAT
58.535
43.478
15.87
8.79
45.20
2.90
218
227
2.096406
CGCTTCAACATGCCGTCG
59.904
61.111
0.00
0.00
0.00
5.12
345
356
5.177142
TGTTTTTGCGCAAATACTCGTAGTA
59.823
36.000
37.90
23.47
34.68
1.82
346
357
4.024725
TGTTTTTGCGCAAATACTCGTAGT
60.025
37.500
37.90
0.00
34.68
2.73
347
358
4.317291
GTGTTTTTGCGCAAATACTCGTAG
59.683
41.667
37.90
0.00
34.68
3.51
363
374
7.255139
CGGAAAGAGGAAGATACAAGTGTTTTT
60.255
37.037
0.00
0.00
0.00
1.94
364
375
6.204882
CGGAAAGAGGAAGATACAAGTGTTTT
59.795
38.462
0.00
0.00
0.00
2.43
365
376
5.701290
CGGAAAGAGGAAGATACAAGTGTTT
59.299
40.000
0.00
0.00
0.00
2.83
367
378
4.322801
CCGGAAAGAGGAAGATACAAGTGT
60.323
45.833
0.00
0.00
0.00
3.55
368
379
4.184629
CCGGAAAGAGGAAGATACAAGTG
58.815
47.826
0.00
0.00
0.00
3.16
372
398
3.170717
ACACCGGAAAGAGGAAGATACA
58.829
45.455
9.46
0.00
0.00
2.29
380
406
2.824341
AGTACAGTACACCGGAAAGAGG
59.176
50.000
9.46
0.00
0.00
3.69
385
411
3.829886
CGTAAGTACAGTACACCGGAA
57.170
47.619
9.46
0.00
0.00
4.30
400
426
5.094134
CGGAGGAGAGTTTTCTTACGTAAG
58.906
45.833
26.13
26.13
37.25
2.34
401
427
4.520492
ACGGAGGAGAGTTTTCTTACGTAA
59.480
41.667
7.94
7.94
32.53
3.18
402
428
4.074970
ACGGAGGAGAGTTTTCTTACGTA
58.925
43.478
0.00
0.00
32.53
3.57
404
430
3.572604
ACGGAGGAGAGTTTTCTTACG
57.427
47.619
0.00
0.00
32.53
3.18
405
431
6.146837
GGTTAAACGGAGGAGAGTTTTCTTAC
59.853
42.308
0.00
0.00
40.54
2.34
407
433
5.061853
GGTTAAACGGAGGAGAGTTTTCTT
58.938
41.667
0.00
0.00
40.54
2.52
408
434
4.102054
TGGTTAAACGGAGGAGAGTTTTCT
59.898
41.667
0.00
0.00
40.54
2.52
409
435
4.383173
TGGTTAAACGGAGGAGAGTTTTC
58.617
43.478
0.00
0.00
40.54
2.29
411
437
4.324267
CATGGTTAAACGGAGGAGAGTTT
58.676
43.478
0.00
0.00
42.43
2.66
412
438
3.868754
GCATGGTTAAACGGAGGAGAGTT
60.869
47.826
0.00
0.00
0.00
3.01
414
440
2.280628
GCATGGTTAAACGGAGGAGAG
58.719
52.381
0.00
0.00
0.00
3.20
415
441
1.065709
GGCATGGTTAAACGGAGGAGA
60.066
52.381
0.00
0.00
0.00
3.71
416
442
1.065418
AGGCATGGTTAAACGGAGGAG
60.065
52.381
0.00
0.00
0.00
3.69
417
443
0.988832
AGGCATGGTTAAACGGAGGA
59.011
50.000
0.00
0.00
0.00
3.71
418
444
1.094785
CAGGCATGGTTAAACGGAGG
58.905
55.000
0.00
0.00
0.00
4.30
419
445
1.821216
ACAGGCATGGTTAAACGGAG
58.179
50.000
2.31
0.00
0.00
4.63
420
446
1.883275
CAACAGGCATGGTTAAACGGA
59.117
47.619
2.31
0.00
0.00
4.69
422
448
2.346099
CCAACAGGCATGGTTAAACG
57.654
50.000
2.31
0.00
33.08
3.60
434
469
3.612247
CTCACCTCCGGCCAACAGG
62.612
68.421
2.24
6.83
0.00
4.00
499
534
1.797537
GTTTTGCGTCGCCATCTGC
60.798
57.895
15.88
0.00
0.00
4.26
558
603
2.230994
GATGAGACGCACTCCAGCCA
62.231
60.000
7.56
0.00
44.34
4.75
561
606
0.244721
TGTGATGAGACGCACTCCAG
59.755
55.000
7.56
0.00
44.34
3.86
565
610
2.224042
TGACTTTGTGATGAGACGCACT
60.224
45.455
0.00
0.00
36.05
4.40
566
611
2.096713
GTGACTTTGTGATGAGACGCAC
60.097
50.000
0.00
0.00
35.63
5.34
567
612
2.135139
GTGACTTTGTGATGAGACGCA
58.865
47.619
0.00
0.00
0.00
5.24
634
718
1.834822
GGACCATCTCCCCCTCTCG
60.835
68.421
0.00
0.00
31.83
4.04
635
719
0.762461
CTGGACCATCTCCCCCTCTC
60.762
65.000
0.00
0.00
38.49
3.20
636
720
1.231751
TCTGGACCATCTCCCCCTCT
61.232
60.000
0.00
0.00
38.49
3.69
637
721
1.051556
GTCTGGACCATCTCCCCCTC
61.052
65.000
0.00
0.00
38.49
4.30
638
722
1.003573
GTCTGGACCATCTCCCCCT
59.996
63.158
0.00
0.00
38.49
4.79
668
752
1.400500
GGTCGTTGGTGCGTTTAATGG
60.400
52.381
0.00
0.00
0.00
3.16
736
835
3.230245
CCCCGCTCAGCCTAGAGG
61.230
72.222
0.00
0.00
36.15
3.69
737
836
3.922640
GCCCCGCTCAGCCTAGAG
61.923
72.222
0.00
0.00
38.68
2.43
908
1030
2.590007
GCTAGCGCAGGGATGGTG
60.590
66.667
11.47
0.00
35.78
4.17
909
1031
4.227134
CGCTAGCGCAGGGATGGT
62.227
66.667
26.07
0.00
39.56
3.55
910
1032
4.227134
ACGCTAGCGCAGGGATGG
62.227
66.667
35.63
7.99
44.19
3.51
911
1033
2.659897
GACGCTAGCGCAGGGATG
60.660
66.667
35.63
8.77
44.19
3.51
912
1034
3.917760
GGACGCTAGCGCAGGGAT
61.918
66.667
35.63
16.46
44.19
3.85
919
1041
4.849329
GGTGGTCGGACGCTAGCG
62.849
72.222
34.27
34.27
46.03
4.26
939
1061
1.607148
CCTTTTGTTCGGTTGGGACTC
59.393
52.381
0.00
0.00
0.00
3.36
950
1072
2.106418
GCAACGAACGACCTTTTGTTC
58.894
47.619
0.14
0.00
41.28
3.18
960
1082
1.002576
TCTACGAACAGCAACGAACGA
60.003
47.619
0.14
0.00
0.00
3.85
961
1083
1.382419
CTCTACGAACAGCAACGAACG
59.618
52.381
0.00
0.00
0.00
3.95
962
1084
1.719780
CCTCTACGAACAGCAACGAAC
59.280
52.381
0.00
0.00
0.00
3.95
963
1085
1.336517
CCCTCTACGAACAGCAACGAA
60.337
52.381
0.00
0.00
0.00
3.85
970
1092
0.378962
CGAGCTCCCTCTACGAACAG
59.621
60.000
8.47
0.00
35.90
3.16
1069
1191
6.038825
AGAGACATACACATCGTAAGGAGAAG
59.961
42.308
0.00
0.00
32.59
2.85
1078
1200
5.392767
AAGAACAGAGACATACACATCGT
57.607
39.130
0.00
0.00
0.00
3.73
1122
1247
2.124903
CTCACAAGCAAGCAAAGCAAG
58.875
47.619
0.00
0.00
0.00
4.01
1471
1605
3.917760
CCCTCCGAGGCCGATGTC
61.918
72.222
9.17
0.00
38.22
3.06
2362
2496
5.098893
CCATTCATATCGCTACAGCTACTC
58.901
45.833
0.00
0.00
39.32
2.59
2363
2497
4.524714
ACCATTCATATCGCTACAGCTACT
59.475
41.667
0.00
0.00
39.32
2.57
2389
2523
1.876714
CTTCACCGCATCCGTACCG
60.877
63.158
0.00
0.00
0.00
4.02
2513
2648
0.315251
TGTGACTCACAAGAGCGGAG
59.685
55.000
9.54
0.00
46.09
4.63
2540
2675
1.662629
CGCAGAAATGCTGTTCGAGAT
59.337
47.619
0.00
0.00
46.62
2.75
2563
2698
2.677199
TGATCACTTCACTTCACGCTC
58.323
47.619
0.00
0.00
0.00
5.03
2593
2728
1.291877
CGGTGAAGTGTGCAGCTACC
61.292
60.000
0.00
0.00
0.00
3.18
2594
2729
0.600255
ACGGTGAAGTGTGCAGCTAC
60.600
55.000
0.00
0.00
0.00
3.58
2595
2730
0.319555
GACGGTGAAGTGTGCAGCTA
60.320
55.000
0.00
0.00
0.00
3.32
2596
2731
1.595382
GACGGTGAAGTGTGCAGCT
60.595
57.895
0.00
0.00
0.00
4.24
2743
2883
0.971386
CTTGCATTGGAGTTGGCCTT
59.029
50.000
3.32
0.00
0.00
4.35
2770
2910
1.944676
GCGCGGATCCTAACAGACG
60.945
63.158
8.83
3.38
0.00
4.18
2771
2911
1.141019
TGCGCGGATCCTAACAGAC
59.859
57.895
8.83
0.00
0.00
3.51
2772
2912
1.141019
GTGCGCGGATCCTAACAGA
59.859
57.895
8.83
0.00
0.00
3.41
2773
2913
1.148157
CTGTGCGCGGATCCTAACAG
61.148
60.000
8.83
13.21
0.00
3.16
2774
2914
1.153647
CTGTGCGCGGATCCTAACA
60.154
57.895
8.83
7.72
0.00
2.41
2775
2915
0.459585
TTCTGTGCGCGGATCCTAAC
60.460
55.000
10.13
3.26
0.00
2.34
2776
2916
0.248012
TTTCTGTGCGCGGATCCTAA
59.752
50.000
10.13
0.00
0.00
2.69
2777
2917
0.248012
TTTTCTGTGCGCGGATCCTA
59.752
50.000
10.13
0.00
0.00
2.94
2778
2918
0.392998
ATTTTCTGTGCGCGGATCCT
60.393
50.000
10.13
0.00
0.00
3.24
2779
2919
1.003866
GTATTTTCTGTGCGCGGATCC
60.004
52.381
10.13
0.00
0.00
3.36
2780
2920
1.663643
TGTATTTTCTGTGCGCGGATC
59.336
47.619
10.13
0.03
0.00
3.36
2781
2921
1.396996
GTGTATTTTCTGTGCGCGGAT
59.603
47.619
10.13
0.00
0.00
4.18
2782
2922
0.793861
GTGTATTTTCTGTGCGCGGA
59.206
50.000
8.83
4.21
0.00
5.54
2783
2923
0.518355
CGTGTATTTTCTGTGCGCGG
60.518
55.000
8.83
0.00
32.76
6.46
2784
2924
0.436913
TCGTGTATTTTCTGTGCGCG
59.563
50.000
0.00
0.00
36.70
6.86
2785
2925
2.536928
GGATCGTGTATTTTCTGTGCGC
60.537
50.000
0.00
0.00
0.00
6.09
2786
2926
2.670905
TGGATCGTGTATTTTCTGTGCG
59.329
45.455
0.00
0.00
0.00
5.34
2787
2927
3.181510
GGTGGATCGTGTATTTTCTGTGC
60.182
47.826
0.00
0.00
0.00
4.57
2788
2928
3.062099
CGGTGGATCGTGTATTTTCTGTG
59.938
47.826
0.00
0.00
0.00
3.66
2789
2929
3.259064
CGGTGGATCGTGTATTTTCTGT
58.741
45.455
0.00
0.00
0.00
3.41
2790
2930
3.259064
ACGGTGGATCGTGTATTTTCTG
58.741
45.455
0.00
0.00
42.21
3.02
2791
2931
3.518590
GACGGTGGATCGTGTATTTTCT
58.481
45.455
0.00
0.00
43.96
2.52
2792
2932
2.606272
GGACGGTGGATCGTGTATTTTC
59.394
50.000
0.00
0.00
43.96
2.29
2793
2933
2.027929
TGGACGGTGGATCGTGTATTTT
60.028
45.455
0.00
0.00
43.96
1.82
2794
2934
1.551430
TGGACGGTGGATCGTGTATTT
59.449
47.619
0.00
0.00
43.96
1.40
2795
2935
1.134907
GTGGACGGTGGATCGTGTATT
60.135
52.381
0.00
0.00
43.96
1.89
2796
2936
0.458669
GTGGACGGTGGATCGTGTAT
59.541
55.000
0.00
0.00
43.96
2.29
2797
2937
0.894642
TGTGGACGGTGGATCGTGTA
60.895
55.000
0.00
0.00
43.96
2.90
2798
2938
2.204461
TGTGGACGGTGGATCGTGT
61.204
57.895
0.00
0.00
43.96
4.49
2799
2939
1.736645
GTGTGGACGGTGGATCGTG
60.737
63.158
0.00
0.00
43.96
4.35
2800
2940
1.750341
TTGTGTGGACGGTGGATCGT
61.750
55.000
0.00
0.00
46.83
3.73
2801
2941
0.601576
TTTGTGTGGACGGTGGATCG
60.602
55.000
0.00
0.00
0.00
3.69
2802
2942
1.468520
CATTTGTGTGGACGGTGGATC
59.531
52.381
0.00
0.00
0.00
3.36
2803
2943
1.533625
CATTTGTGTGGACGGTGGAT
58.466
50.000
0.00
0.00
0.00
3.41
2804
2944
0.536233
CCATTTGTGTGGACGGTGGA
60.536
55.000
0.00
0.00
42.02
4.02
2805
2945
1.523154
CCCATTTGTGTGGACGGTGG
61.523
60.000
0.00
0.00
42.02
4.61
2806
2946
1.956043
CCCATTTGTGTGGACGGTG
59.044
57.895
0.00
0.00
42.02
4.94
2807
2947
1.901464
GCCCATTTGTGTGGACGGT
60.901
57.895
0.00
0.00
42.02
4.83
2808
2948
2.961768
GCCCATTTGTGTGGACGG
59.038
61.111
0.00
0.00
42.02
4.79
2809
2949
2.560861
CGCCCATTTGTGTGGACG
59.439
61.111
0.00
0.00
42.02
4.79
2810
2950
0.965363
ATCCGCCCATTTGTGTGGAC
60.965
55.000
0.00
0.00
43.46
4.02
2811
2951
0.964860
CATCCGCCCATTTGTGTGGA
60.965
55.000
0.00
0.00
44.66
4.02
2812
2952
1.250154
ACATCCGCCCATTTGTGTGG
61.250
55.000
0.00
0.00
39.05
4.17
2813
2953
0.602562
AACATCCGCCCATTTGTGTG
59.397
50.000
0.00
0.00
0.00
3.82
2814
2954
0.887933
GAACATCCGCCCATTTGTGT
59.112
50.000
0.00
0.00
0.00
3.72
2815
2955
0.179166
CGAACATCCGCCCATTTGTG
60.179
55.000
0.00
0.00
0.00
3.33
2816
2956
0.608035
ACGAACATCCGCCCATTTGT
60.608
50.000
0.00
0.00
0.00
2.83
2817
2957
0.525761
AACGAACATCCGCCCATTTG
59.474
50.000
0.00
0.00
0.00
2.32
2818
2958
1.253100
AAACGAACATCCGCCCATTT
58.747
45.000
0.00
0.00
0.00
2.32
2819
2959
1.253100
AAAACGAACATCCGCCCATT
58.747
45.000
0.00
0.00
0.00
3.16
2820
2960
1.741145
GTAAAACGAACATCCGCCCAT
59.259
47.619
0.00
0.00
0.00
4.00
2821
2961
1.158434
GTAAAACGAACATCCGCCCA
58.842
50.000
0.00
0.00
0.00
5.36
2822
2962
0.448990
GGTAAAACGAACATCCGCCC
59.551
55.000
0.00
0.00
0.00
6.13
2823
2963
0.095762
CGGTAAAACGAACATCCGCC
59.904
55.000
0.00
0.00
35.47
6.13
2824
2964
1.070038
TCGGTAAAACGAACATCCGC
58.930
50.000
0.00
0.00
40.34
5.54
2831
2971
8.250976
GCTCTAAGCATTTTTCGGTAAAACGAA
61.251
37.037
0.00
0.00
44.89
3.85
2832
2972
6.542574
TCTAAGCATTTTTCGGTAAAACGA
57.457
33.333
0.00
0.00
38.48
3.85
2833
2973
5.283012
GCTCTAAGCATTTTTCGGTAAAACG
59.717
40.000
0.00
0.00
41.89
3.60
2834
2974
6.612855
GCTCTAAGCATTTTTCGGTAAAAC
57.387
37.500
0.00
0.00
41.89
2.43
2846
2986
7.680587
CCGCATTGGAATTGCTCTAAGCATT
62.681
44.000
1.95
0.00
46.59
3.56
2847
2987
6.285829
CCGCATTGGAATTGCTCTAAGCAT
62.286
45.833
1.95
0.00
46.59
3.79
2848
2988
5.037457
CCGCATTGGAATTGCTCTAAGCA
62.037
47.826
0.00
0.00
45.97
3.91
2849
2989
2.542411
CCGCATTGGAATTGCTCTAAGC
60.542
50.000
0.00
0.00
42.00
3.09
2850
2990
2.542411
GCCGCATTGGAATTGCTCTAAG
60.542
50.000
0.00
0.00
42.00
2.18
2860
3000
3.636929
ATGGGTCGCCGCATTGGAA
62.637
57.895
0.00
0.00
41.05
3.53
2868
3008
3.192922
GGACGAAATGGGTCGCCG
61.193
66.667
0.00
0.00
45.00
6.46
2926
3066
4.912485
TTTGGGTCGGCGCGTTGA
62.912
61.111
8.43
2.59
0.00
3.18
2963
3103
2.587322
GAATGGGTCATCCGCGGACA
62.587
60.000
33.75
24.01
38.76
4.02
3037
3181
1.076923
GGGGAGAGGAGTAGACGCA
60.077
63.158
0.00
0.00
0.00
5.24
3041
3185
3.070987
GCCCGGGGAGAGGAGTAGA
62.071
68.421
25.28
0.00
0.00
2.59
3229
3389
3.042560
GCACGAGGCTTGCCTTTT
58.957
55.556
15.92
2.97
40.25
2.27
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.