Multiple sequence alignment - TraesCS7A01G211500
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
TraesCS7A01G211500
chr7A
100.000
2122
0
0
1
2122
174275246
174273125
0.000000e+00
3919.0
1
TraesCS7A01G211500
chr7A
100.000
292
0
0
2508
2799
174272739
174272448
8.820000e-150
540.0
2
TraesCS7A01G211500
chr7D
94.531
1536
59
14
592
2121
171373198
171371682
0.000000e+00
2348.0
3
TraesCS7A01G211500
chr7D
92.479
585
13
10
1
575
171373744
171373181
0.000000e+00
808.0
4
TraesCS7A01G211500
chr7D
88.166
169
17
3
2634
2799
164485023
164484855
6.120000e-47
198.0
5
TraesCS7A01G211500
chr7D
91.304
69
6
0
2532
2600
171371303
171371235
8.250000e-16
95.3
6
TraesCS7A01G211500
chr7B
91.827
1248
62
15
592
1826
137881184
137879964
0.000000e+00
1703.0
7
TraesCS7A01G211500
chr7B
93.276
580
16
4
1
575
137881728
137881167
0.000000e+00
833.0
8
TraesCS7A01G211500
chr7B
91.065
291
19
5
1832
2121
137879786
137879502
1.220000e-103
387.0
9
TraesCS7A01G211500
chr4D
88.953
172
15
3
2630
2799
123953057
123952888
2.830000e-50
209.0
10
TraesCS7A01G211500
chr6D
89.697
165
14
3
2636
2799
58220194
58220032
1.020000e-49
207.0
11
TraesCS7A01G211500
chr3D
88.953
172
14
5
2629
2799
21372672
21372839
1.020000e-49
207.0
12
TraesCS7A01G211500
chr2D
88.889
171
15
4
2631
2799
38262272
38262104
1.020000e-49
207.0
13
TraesCS7A01G211500
chr2D
89.697
165
14
3
2637
2799
90367880
90368043
1.020000e-49
207.0
14
TraesCS7A01G211500
chr5D
88.166
169
18
2
2633
2799
463084576
463084744
1.700000e-47
200.0
15
TraesCS7A01G211500
chr3A
88.166
169
17
3
2633
2799
57366833
57366666
6.120000e-47
198.0
16
TraesCS7A01G211500
chr1B
87.861
173
15
6
2631
2799
442065102
442065272
6.120000e-47
198.0
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
TraesCS7A01G211500
chr7A
174272448
174275246
2798
True
2229.500000
3919
100.000000
1
2799
2
chr7A.!!$R1
2798
1
TraesCS7A01G211500
chr7D
171371235
171373744
2509
True
1083.766667
2348
92.771333
1
2600
3
chr7D.!!$R2
2599
2
TraesCS7A01G211500
chr7B
137879502
137881728
2226
True
974.333333
1703
92.056000
1
2121
3
chr7B.!!$R1
2120
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
190
191
0.251354
ATCTCTGCTTGCACGGATGT
59.749
50.0
0.0
0.0
0.0
3.06
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
1885
2105
1.183549
GAACTCGCAACCTCTCCCTA
58.816
55.0
0.0
0.0
0.0
3.53
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
29
30
0.389948
GTGACCCTAGTGGCAACTCG
60.390
60.000
0.00
0.00
37.88
4.18
98
99
7.976135
AACAGATATGAAAGGAGCATATGAC
57.024
36.000
6.97
0.00
38.64
3.06
147
148
6.560003
TTATCTCCTCACAGCTATTTGGAA
57.440
37.500
0.00
0.00
0.00
3.53
186
187
2.789917
GCATCTCTGCTTGCACGG
59.210
61.111
0.00
0.00
45.32
4.94
187
188
1.742880
GCATCTCTGCTTGCACGGA
60.743
57.895
0.00
0.00
45.32
4.69
188
189
1.094073
GCATCTCTGCTTGCACGGAT
61.094
55.000
0.00
0.00
45.32
4.18
189
190
0.656259
CATCTCTGCTTGCACGGATG
59.344
55.000
14.05
14.05
0.00
3.51
190
191
0.251354
ATCTCTGCTTGCACGGATGT
59.749
50.000
0.00
0.00
0.00
3.06
191
192
0.894835
TCTCTGCTTGCACGGATGTA
59.105
50.000
0.00
0.00
0.00
2.29
275
276
0.843984
AACCACCAACTACAGTGCCT
59.156
50.000
0.00
0.00
32.48
4.75
276
277
0.396811
ACCACCAACTACAGTGCCTC
59.603
55.000
0.00
0.00
32.48
4.70
277
278
0.321653
CCACCAACTACAGTGCCTCC
60.322
60.000
0.00
0.00
32.48
4.30
278
279
0.687354
CACCAACTACAGTGCCTCCT
59.313
55.000
0.00
0.00
0.00
3.69
420
435
1.077265
ACCTCCCCACAATGCCAAG
59.923
57.895
0.00
0.00
0.00
3.61
430
445
1.337074
ACAATGCCAAGTTGCCAATCG
60.337
47.619
0.00
0.00
0.00
3.34
459
474
1.271934
CACCCCATCATGAAACGCAAA
59.728
47.619
0.00
0.00
0.00
3.68
460
475
1.545582
ACCCCATCATGAAACGCAAAG
59.454
47.619
0.00
0.00
0.00
2.77
464
479
3.119388
CCCATCATGAAACGCAAAGACAT
60.119
43.478
0.00
0.00
0.00
3.06
487
502
6.947644
TGAAGGACATGTAAATGGATGATG
57.052
37.500
0.00
0.00
0.00
3.07
488
503
5.829391
TGAAGGACATGTAAATGGATGATGG
59.171
40.000
0.00
0.00
0.00
3.51
489
504
5.651612
AGGACATGTAAATGGATGATGGA
57.348
39.130
0.00
0.00
0.00
3.41
490
505
6.210172
AGGACATGTAAATGGATGATGGAT
57.790
37.500
0.00
0.00
0.00
3.41
491
506
6.243900
AGGACATGTAAATGGATGATGGATC
58.756
40.000
0.00
0.00
0.00
3.36
492
507
5.122869
GGACATGTAAATGGATGATGGATCG
59.877
44.000
0.00
0.00
30.87
3.69
493
508
4.456911
ACATGTAAATGGATGATGGATCGC
59.543
41.667
0.00
0.00
30.87
4.58
494
509
4.356405
TGTAAATGGATGATGGATCGCT
57.644
40.909
0.00
0.00
30.87
4.93
495
510
4.717877
TGTAAATGGATGATGGATCGCTT
58.282
39.130
0.00
0.00
30.87
4.68
496
511
4.756642
TGTAAATGGATGATGGATCGCTTC
59.243
41.667
0.00
0.00
30.87
3.86
497
512
3.497103
AATGGATGATGGATCGCTTCA
57.503
42.857
3.42
3.42
30.87
3.02
498
513
2.538512
TGGATGATGGATCGCTTCAG
57.461
50.000
6.15
0.00
30.87
3.02
499
514
1.155042
GGATGATGGATCGCTTCAGC
58.845
55.000
6.73
6.73
37.78
4.26
566
596
0.962356
CGCTGGCTGGAAATGGTTCT
60.962
55.000
0.00
0.00
33.92
3.01
575
605
4.202151
GCTGGAAATGGTTCTTCACTGTTT
60.202
41.667
0.00
0.00
33.92
2.83
576
606
5.682212
GCTGGAAATGGTTCTTCACTGTTTT
60.682
40.000
0.00
0.00
33.92
2.43
577
607
6.293004
TGGAAATGGTTCTTCACTGTTTTT
57.707
33.333
0.00
0.00
33.92
1.94
601
631
3.712091
TTTGCGGGTTAAATTGTTCGT
57.288
38.095
0.00
0.00
0.00
3.85
602
632
2.973419
TGCGGGTTAAATTGTTCGTC
57.027
45.000
0.00
0.00
0.00
4.20
603
633
2.219458
TGCGGGTTAAATTGTTCGTCA
58.781
42.857
0.00
0.00
0.00
4.35
604
634
2.031857
TGCGGGTTAAATTGTTCGTCAC
60.032
45.455
0.00
0.00
0.00
3.67
605
635
2.224784
GCGGGTTAAATTGTTCGTCACT
59.775
45.455
0.00
0.00
0.00
3.41
606
636
3.805823
CGGGTTAAATTGTTCGTCACTG
58.194
45.455
0.00
0.00
0.00
3.66
607
637
3.249080
CGGGTTAAATTGTTCGTCACTGT
59.751
43.478
0.00
0.00
0.00
3.55
608
638
4.260866
CGGGTTAAATTGTTCGTCACTGTT
60.261
41.667
0.00
0.00
0.00
3.16
609
639
5.584442
GGGTTAAATTGTTCGTCACTGTTT
58.416
37.500
0.00
0.00
0.00
2.83
655
692
4.767255
CAGTCGCCCACCTCTGCC
62.767
72.222
0.00
0.00
0.00
4.85
1075
1118
9.619316
CTATACTCCATTATTTCTCTGTTCTCG
57.381
37.037
0.00
0.00
0.00
4.04
1077
1120
4.442706
TCCATTATTTCTCTGTTCTCGCC
58.557
43.478
0.00
0.00
0.00
5.54
1193
1236
1.298264
TGCAAACGCAGCGTCTTTG
60.298
52.632
23.22
22.84
39.99
2.77
1248
1291
1.351076
TCATCTCCTGTTCCAGTGCA
58.649
50.000
0.00
0.00
0.00
4.57
1251
1294
1.071987
CTCCTGTTCCAGTGCAGCA
59.928
57.895
0.00
0.00
0.00
4.41
1253
1296
1.228063
CCTGTTCCAGTGCAGCAGT
60.228
57.895
0.00
0.00
0.00
4.40
1582
1625
4.593864
GATGAGGGACGAGCGGGC
62.594
72.222
0.00
0.00
0.00
6.13
1764
1809
2.488153
GCAAATGGCTTCCTTCGTAGTT
59.512
45.455
0.00
0.00
40.25
2.24
1767
1813
5.528870
CAAATGGCTTCCTTCGTAGTTTTT
58.471
37.500
0.00
0.00
0.00
1.94
1809
1856
2.163818
TCTGTTCGCCGAATCTTTGT
57.836
45.000
1.55
0.00
0.00
2.83
1822
1869
4.201685
CGAATCTTTGTTCCATGTACCGAC
60.202
45.833
0.00
0.00
0.00
4.79
1826
1873
6.045072
TCTTTGTTCCATGTACCGACTAAT
57.955
37.500
0.00
0.00
0.00
1.73
1827
1874
7.172868
TCTTTGTTCCATGTACCGACTAATA
57.827
36.000
0.00
0.00
0.00
0.98
1830
2049
8.795842
TTTGTTCCATGTACCGACTAATATTT
57.204
30.769
0.00
0.00
0.00
1.40
1899
2119
3.081804
ACAAAAATAGGGAGAGGTTGCG
58.918
45.455
0.00
0.00
0.00
4.85
1929
2149
6.311723
CGACCACCACATATTTCAAACTAAC
58.688
40.000
0.00
0.00
0.00
2.34
1930
2150
6.072948
CGACCACCACATATTTCAAACTAACA
60.073
38.462
0.00
0.00
0.00
2.41
1931
2151
7.361713
CGACCACCACATATTTCAAACTAACAT
60.362
37.037
0.00
0.00
0.00
2.71
1932
2152
7.601856
ACCACCACATATTTCAAACTAACATG
58.398
34.615
0.00
0.00
0.00
3.21
1935
2155
9.554724
CACCACATATTTCAAACTAACATGTAC
57.445
33.333
0.00
0.00
0.00
2.90
1948
2168
6.040878
ACTAACATGTACGTAGGAGCATTTC
58.959
40.000
0.00
0.00
0.00
2.17
1990
2210
7.275560
GGCGAAGTTGATACATAAAGCAAAAAT
59.724
33.333
0.00
0.00
0.00
1.82
2107
2328
4.842574
TGCAGTTGTCTATATTGCCTCAA
58.157
39.130
0.00
0.00
33.98
3.02
2121
2342
4.944962
TGCCTCAAAATTGTCGTATCAG
57.055
40.909
0.00
0.00
0.00
2.90
2524
2745
4.830765
TGCACTATGCCGCCGTCC
62.831
66.667
0.00
0.00
44.23
4.79
2525
2746
4.830765
GCACTATGCCGCCGTCCA
62.831
66.667
0.00
0.00
37.42
4.02
2526
2747
2.108976
CACTATGCCGCCGTCCAT
59.891
61.111
0.00
0.00
0.00
3.41
2527
2748
2.108976
ACTATGCCGCCGTCCATG
59.891
61.111
0.00
0.00
0.00
3.66
2528
2749
2.108976
CTATGCCGCCGTCCATGT
59.891
61.111
0.00
0.00
0.00
3.21
2529
2750
1.523711
CTATGCCGCCGTCCATGTT
60.524
57.895
0.00
0.00
0.00
2.71
2530
2751
1.775039
CTATGCCGCCGTCCATGTTG
61.775
60.000
0.00
0.00
0.00
3.33
2539
2760
2.232696
GCCGTCCATGTTGGGTAAAATT
59.767
45.455
0.00
0.00
38.32
1.82
2542
2763
4.262249
CCGTCCATGTTGGGTAAAATTGTT
60.262
41.667
0.00
0.00
38.32
2.83
2545
2766
6.750039
CGTCCATGTTGGGTAAAATTGTTATC
59.250
38.462
0.00
0.00
38.32
1.75
2546
2767
6.750039
GTCCATGTTGGGTAAAATTGTTATCG
59.250
38.462
0.00
0.00
38.32
2.92
2589
2810
4.785301
ACATGCCAGCATCTATAGTTGTT
58.215
39.130
1.19
3.89
33.90
2.83
2597
2818
3.561725
GCATCTATAGTTGTTGGTGCTCC
59.438
47.826
11.53
0.00
0.00
4.70
2600
2821
3.838317
TCTATAGTTGTTGGTGCTCCACT
59.162
43.478
7.09
3.97
44.22
4.00
2601
2822
2.543777
TAGTTGTTGGTGCTCCACTC
57.456
50.000
7.09
4.71
44.22
3.51
2602
2823
0.546122
AGTTGTTGGTGCTCCACTCA
59.454
50.000
7.09
7.34
44.22
3.41
2603
2824
1.143684
AGTTGTTGGTGCTCCACTCAT
59.856
47.619
7.09
0.00
44.22
2.90
2604
2825
1.267806
GTTGTTGGTGCTCCACTCATG
59.732
52.381
7.09
0.00
44.22
3.07
2619
2840
6.364568
CCACTCATGGTAGAATGGATATGA
57.635
41.667
0.00
0.00
41.64
2.15
2620
2841
6.772605
CCACTCATGGTAGAATGGATATGAA
58.227
40.000
0.00
0.00
41.64
2.57
2621
2842
7.400439
CCACTCATGGTAGAATGGATATGAAT
58.600
38.462
0.00
0.00
41.64
2.57
2622
2843
7.336176
CCACTCATGGTAGAATGGATATGAATG
59.664
40.741
0.00
0.00
41.64
2.67
2623
2844
7.336176
CACTCATGGTAGAATGGATATGAATGG
59.664
40.741
0.00
0.00
0.00
3.16
2624
2845
7.017950
ACTCATGGTAGAATGGATATGAATGGT
59.982
37.037
0.00
0.00
0.00
3.55
2625
2846
7.170277
TCATGGTAGAATGGATATGAATGGTG
58.830
38.462
0.00
0.00
0.00
4.17
2626
2847
5.316167
TGGTAGAATGGATATGAATGGTGC
58.684
41.667
0.00
0.00
0.00
5.01
2627
2848
4.702131
GGTAGAATGGATATGAATGGTGCC
59.298
45.833
0.00
0.00
0.00
5.01
2628
2849
4.458256
AGAATGGATATGAATGGTGCCA
57.542
40.909
0.00
0.00
0.00
4.92
2629
2850
4.806892
AGAATGGATATGAATGGTGCCAA
58.193
39.130
0.00
0.00
0.00
4.52
2630
2851
5.399991
AGAATGGATATGAATGGTGCCAAT
58.600
37.500
0.00
0.00
0.00
3.16
2631
2852
5.245301
AGAATGGATATGAATGGTGCCAATG
59.755
40.000
0.00
0.00
0.00
2.82
2632
2853
2.629137
TGGATATGAATGGTGCCAATGC
59.371
45.455
0.00
0.00
38.26
3.56
2633
2854
2.895404
GGATATGAATGGTGCCAATGCT
59.105
45.455
0.00
0.00
38.71
3.79
2634
2855
3.322828
GGATATGAATGGTGCCAATGCTT
59.677
43.478
0.00
0.00
38.71
3.91
2635
2856
4.523943
GGATATGAATGGTGCCAATGCTTA
59.476
41.667
0.00
0.00
38.71
3.09
2636
2857
5.336213
GGATATGAATGGTGCCAATGCTTAG
60.336
44.000
0.00
0.00
38.71
2.18
2637
2858
3.084536
TGAATGGTGCCAATGCTTAGA
57.915
42.857
0.00
0.00
38.71
2.10
2638
2859
3.018856
TGAATGGTGCCAATGCTTAGAG
58.981
45.455
0.00
0.00
38.71
2.43
2639
2860
1.396653
ATGGTGCCAATGCTTAGAGC
58.603
50.000
0.00
0.00
42.82
4.09
2681
2902
2.117423
CCCCCAGGGCGACTTTTT
59.883
61.111
0.00
0.00
35.35
1.94
2695
2916
4.105727
TTTTTCGTGTCGACGCCA
57.894
50.000
22.62
8.06
45.68
5.69
2696
2917
2.381109
TTTTTCGTGTCGACGCCAA
58.619
47.368
22.62
14.24
45.68
4.52
2697
2918
0.725686
TTTTTCGTGTCGACGCCAAA
59.274
45.000
22.62
19.34
45.68
3.28
2698
2919
0.725686
TTTTCGTGTCGACGCCAAAA
59.274
45.000
24.41
24.41
45.68
2.44
2699
2920
0.725686
TTTCGTGTCGACGCCAAAAA
59.274
45.000
22.62
16.67
45.68
1.94
2715
2936
3.340789
AAAAACCCTCAGTCGCGC
58.659
55.556
0.00
0.00
0.00
6.86
2716
2937
2.258726
AAAAACCCTCAGTCGCGCC
61.259
57.895
0.00
0.00
0.00
6.53
2717
2938
4.699522
AAACCCTCAGTCGCGCCC
62.700
66.667
0.00
0.00
0.00
6.13
2720
2941
3.458163
CCCTCAGTCGCGCCCTTA
61.458
66.667
0.00
0.00
0.00
2.69
2721
2942
2.577059
CCTCAGTCGCGCCCTTAA
59.423
61.111
0.00
0.00
0.00
1.85
2722
2943
1.519455
CCTCAGTCGCGCCCTTAAG
60.519
63.158
0.00
0.00
0.00
1.85
2723
2944
1.511305
CTCAGTCGCGCCCTTAAGA
59.489
57.895
0.00
0.00
0.00
2.10
2724
2945
0.802607
CTCAGTCGCGCCCTTAAGAC
60.803
60.000
0.00
1.68
0.00
3.01
2725
2946
2.158959
CAGTCGCGCCCTTAAGACG
61.159
63.158
0.00
8.70
38.53
4.18
2729
2950
4.807039
GCGCCCTTAAGACGCCGA
62.807
66.667
23.99
0.00
46.63
5.54
2730
2951
2.125832
CGCCCTTAAGACGCCGAA
60.126
61.111
3.36
0.00
0.00
4.30
2731
2952
1.738830
CGCCCTTAAGACGCCGAAA
60.739
57.895
3.36
0.00
0.00
3.46
2732
2953
1.087771
CGCCCTTAAGACGCCGAAAT
61.088
55.000
3.36
0.00
0.00
2.17
2733
2954
0.656259
GCCCTTAAGACGCCGAAATC
59.344
55.000
3.36
0.00
0.00
2.17
2734
2955
1.296727
CCCTTAAGACGCCGAAATCC
58.703
55.000
3.36
0.00
0.00
3.01
2735
2956
0.928229
CCTTAAGACGCCGAAATCCG
59.072
55.000
3.36
0.00
38.18
4.18
2736
2957
0.300789
CTTAAGACGCCGAAATCCGC
59.699
55.000
0.00
0.00
36.84
5.54
2737
2958
1.085501
TTAAGACGCCGAAATCCGCC
61.086
55.000
0.00
0.00
36.84
6.13
2755
2976
2.951458
GGCTCGGACCGTTTTTGG
59.049
61.111
14.79
0.15
0.00
3.28
2756
2977
2.622962
GGCTCGGACCGTTTTTGGG
61.623
63.158
14.79
0.00
0.00
4.12
2757
2978
2.951458
CTCGGACCGTTTTTGGGC
59.049
61.111
14.79
0.00
35.71
5.36
2761
2982
3.676605
GACCGTTTTTGGGCCCGG
61.677
66.667
19.37
16.04
45.72
5.73
2764
2985
2.673687
CGTTTTTGGGCCCGGCTA
60.674
61.111
19.37
0.00
0.00
3.93
2765
2986
2.049767
CGTTTTTGGGCCCGGCTAT
61.050
57.895
19.37
0.00
0.00
2.97
2766
2987
1.813859
GTTTTTGGGCCCGGCTATC
59.186
57.895
19.37
1.81
0.00
2.08
2767
2988
1.380650
TTTTTGGGCCCGGCTATCC
60.381
57.895
19.37
2.51
0.00
2.59
2768
2989
2.864770
TTTTTGGGCCCGGCTATCCC
62.865
60.000
19.37
11.11
40.47
3.85
2773
2994
3.942439
GCCCGGCTATCCCAGGAC
61.942
72.222
0.71
0.00
31.45
3.85
2774
2995
3.616721
CCCGGCTATCCCAGGACG
61.617
72.222
0.00
0.00
31.45
4.79
2775
2996
2.520982
CCGGCTATCCCAGGACGA
60.521
66.667
0.00
0.00
31.45
4.20
2776
2997
2.131709
CCGGCTATCCCAGGACGAA
61.132
63.158
0.00
0.00
31.45
3.85
2777
2998
1.067582
CGGCTATCCCAGGACGAAC
59.932
63.158
0.00
0.00
0.00
3.95
2778
2999
1.446366
GGCTATCCCAGGACGAACC
59.554
63.158
0.00
0.00
39.35
3.62
2779
3000
1.335132
GGCTATCCCAGGACGAACCA
61.335
60.000
0.00
0.00
42.04
3.67
2780
3001
0.105039
GCTATCCCAGGACGAACCAG
59.895
60.000
0.00
0.00
42.04
4.00
2781
3002
0.753262
CTATCCCAGGACGAACCAGG
59.247
60.000
7.57
7.57
43.84
4.45
2784
3005
3.636231
CCAGGACGAACCAGGGCA
61.636
66.667
0.00
0.00
41.01
5.36
2785
3006
2.358737
CAGGACGAACCAGGGCAC
60.359
66.667
0.00
0.00
42.04
5.01
2786
3007
2.526873
AGGACGAACCAGGGCACT
60.527
61.111
0.00
0.00
42.04
4.40
2787
3008
2.358737
GGACGAACCAGGGCACTG
60.359
66.667
9.70
9.70
44.51
3.66
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
186
187
6.827641
TGTTTGCGTAAAGAGAATGTACATC
58.172
36.000
9.23
3.13
0.00
3.06
187
188
6.795098
TGTTTGCGTAAAGAGAATGTACAT
57.205
33.333
1.41
1.41
0.00
2.29
188
189
6.606234
TTGTTTGCGTAAAGAGAATGTACA
57.394
33.333
0.00
0.00
0.00
2.90
189
190
9.769093
ATAATTGTTTGCGTAAAGAGAATGTAC
57.231
29.630
0.00
0.00
0.00
2.90
420
435
1.266718
TGCTTCAGAACGATTGGCAAC
59.733
47.619
0.00
0.00
0.00
4.17
430
445
1.747355
CATGATGGGGTGCTTCAGAAC
59.253
52.381
0.00
0.00
0.00
3.01
464
479
5.829391
CCATCATCCATTTACATGTCCTTCA
59.171
40.000
0.00
0.00
0.00
3.02
492
507
3.290619
GTCGATCGACGCTGAAGC
58.709
61.111
30.46
7.41
42.26
3.86
579
609
4.430908
ACGAACAATTTAACCCGCAAAAA
58.569
34.783
0.00
0.00
0.00
1.94
580
610
4.043037
ACGAACAATTTAACCCGCAAAA
57.957
36.364
0.00
0.00
0.00
2.44
581
611
3.066342
TGACGAACAATTTAACCCGCAAA
59.934
39.130
0.00
0.00
0.00
3.68
582
612
2.617308
TGACGAACAATTTAACCCGCAA
59.383
40.909
0.00
0.00
0.00
4.85
583
613
2.031857
GTGACGAACAATTTAACCCGCA
60.032
45.455
0.00
0.00
0.00
5.69
584
614
2.224784
AGTGACGAACAATTTAACCCGC
59.775
45.455
0.00
0.00
0.00
6.13
585
615
3.249080
ACAGTGACGAACAATTTAACCCG
59.751
43.478
0.00
0.00
0.00
5.28
586
616
4.823790
ACAGTGACGAACAATTTAACCC
57.176
40.909
0.00
0.00
0.00
4.11
587
617
5.051973
GCAAACAGTGACGAACAATTTAACC
60.052
40.000
0.00
0.00
0.00
2.85
588
618
5.051973
GGCAAACAGTGACGAACAATTTAAC
60.052
40.000
0.00
0.00
0.00
2.01
589
619
5.038033
GGCAAACAGTGACGAACAATTTAA
58.962
37.500
0.00
0.00
0.00
1.52
590
620
4.096532
TGGCAAACAGTGACGAACAATTTA
59.903
37.500
0.00
0.00
38.59
1.40
591
621
3.119316
TGGCAAACAGTGACGAACAATTT
60.119
39.130
0.00
0.00
38.59
1.82
592
622
2.425312
TGGCAAACAGTGACGAACAATT
59.575
40.909
0.00
0.00
38.59
2.32
593
623
2.020720
TGGCAAACAGTGACGAACAAT
58.979
42.857
0.00
0.00
38.59
2.71
594
624
1.454201
TGGCAAACAGTGACGAACAA
58.546
45.000
0.00
0.00
38.59
2.83
595
625
1.131504
GTTGGCAAACAGTGACGAACA
59.868
47.619
0.00
0.00
38.59
3.18
596
626
1.533129
GGTTGGCAAACAGTGACGAAC
60.533
52.381
11.10
0.00
38.59
3.95
597
627
0.736053
GGTTGGCAAACAGTGACGAA
59.264
50.000
11.10
0.00
38.59
3.85
598
628
0.107410
AGGTTGGCAAACAGTGACGA
60.107
50.000
18.93
0.00
38.59
4.20
599
629
0.307760
GAGGTTGGCAAACAGTGACG
59.692
55.000
18.93
0.00
38.59
4.35
600
630
0.668535
GGAGGTTGGCAAACAGTGAC
59.331
55.000
18.93
3.24
38.10
3.67
601
631
0.817634
CGGAGGTTGGCAAACAGTGA
60.818
55.000
18.93
0.00
38.10
3.41
602
632
0.817634
TCGGAGGTTGGCAAACAGTG
60.818
55.000
18.93
6.18
38.10
3.66
603
633
0.535102
CTCGGAGGTTGGCAAACAGT
60.535
55.000
18.93
0.00
38.10
3.55
604
634
1.856265
GCTCGGAGGTTGGCAAACAG
61.856
60.000
18.93
7.02
38.10
3.16
605
635
1.896660
GCTCGGAGGTTGGCAAACA
60.897
57.895
18.93
0.00
38.10
2.83
606
636
0.321298
TAGCTCGGAGGTTGGCAAAC
60.321
55.000
15.66
7.31
35.40
2.93
607
637
0.036388
CTAGCTCGGAGGTTGGCAAA
60.036
55.000
15.66
0.00
0.00
3.68
608
638
0.902984
TCTAGCTCGGAGGTTGGCAA
60.903
55.000
15.66
0.00
0.00
4.52
609
639
1.304962
TCTAGCTCGGAGGTTGGCA
60.305
57.895
15.66
0.00
0.00
4.92
1077
1120
1.435515
GTAGCTGAGCCAGAGGACG
59.564
63.158
0.00
0.00
32.44
4.79
1251
1294
3.629398
GGCAATTGCATTAGACTGCTACT
59.371
43.478
30.32
0.00
42.75
2.57
1253
1296
2.951642
GGGCAATTGCATTAGACTGCTA
59.048
45.455
30.32
0.00
42.75
3.49
1268
1311
3.426117
CTCGTCGGCGTAGGGCAAT
62.426
63.158
10.18
0.00
46.16
3.56
1582
1625
4.527583
GCCTCCTCTGCAGCTCCG
62.528
72.222
9.47
0.00
0.00
4.63
1775
1821
7.118680
TCGGCGAACAGAAAGAAATTATTAAGT
59.881
33.333
7.35
0.00
0.00
2.24
1877
2096
3.127030
CGCAACCTCTCCCTATTTTTGTC
59.873
47.826
0.00
0.00
0.00
3.18
1885
2105
1.183549
GAACTCGCAACCTCTCCCTA
58.816
55.000
0.00
0.00
0.00
3.53
1899
2119
2.981859
ATATGTGGTGGTCGGAACTC
57.018
50.000
0.00
0.00
0.00
3.01
1948
2168
1.586154
CGCCACCAAAGCCACTTAGG
61.586
60.000
0.00
0.00
41.84
2.69
2064
2285
7.093814
ACTGCATAACATGTTGTGTATGGATTT
60.094
33.333
28.90
11.25
41.14
2.17
2098
2319
5.883661
CTGATACGACAATTTTGAGGCAAT
58.116
37.500
0.00
0.00
0.00
3.56
2099
2320
5.295431
CTGATACGACAATTTTGAGGCAA
57.705
39.130
0.00
0.00
0.00
4.52
2508
2729
4.830765
TGGACGGCGGCATAGTGC
62.831
66.667
17.61
4.82
44.08
4.40
2509
2730
2.108976
ATGGACGGCGGCATAGTG
59.891
61.111
17.61
0.00
0.00
2.74
2510
2731
2.108976
CATGGACGGCGGCATAGT
59.891
61.111
17.61
0.00
0.00
2.12
2511
2732
1.523711
AACATGGACGGCGGCATAG
60.524
57.895
17.61
5.39
0.00
2.23
2512
2733
1.817520
CAACATGGACGGCGGCATA
60.818
57.895
17.61
2.35
0.00
3.14
2513
2734
3.133464
CAACATGGACGGCGGCAT
61.133
61.111
17.61
2.98
0.00
4.40
2516
2737
2.806503
TTACCCAACATGGACGGCGG
62.807
60.000
13.24
0.00
40.96
6.13
2517
2738
0.956410
TTTACCCAACATGGACGGCG
60.956
55.000
4.80
4.80
40.96
6.46
2518
2739
1.249407
TTTTACCCAACATGGACGGC
58.751
50.000
0.00
0.00
40.96
5.68
2519
2740
3.257127
ACAATTTTACCCAACATGGACGG
59.743
43.478
0.00
0.00
40.96
4.79
2520
2741
4.513198
ACAATTTTACCCAACATGGACG
57.487
40.909
0.00
0.00
40.96
4.79
2521
2742
6.750039
CGATAACAATTTTACCCAACATGGAC
59.250
38.462
0.00
0.00
40.96
4.02
2522
2743
6.127591
CCGATAACAATTTTACCCAACATGGA
60.128
38.462
0.00
0.00
40.96
3.41
2523
2744
6.039616
CCGATAACAATTTTACCCAACATGG
58.960
40.000
0.00
0.00
37.25
3.66
2524
2745
6.626302
ACCGATAACAATTTTACCCAACATG
58.374
36.000
0.00
0.00
0.00
3.21
2525
2746
6.661805
AGACCGATAACAATTTTACCCAACAT
59.338
34.615
0.00
0.00
0.00
2.71
2526
2747
6.005198
AGACCGATAACAATTTTACCCAACA
58.995
36.000
0.00
0.00
0.00
3.33
2527
2748
6.403964
GGAGACCGATAACAATTTTACCCAAC
60.404
42.308
0.00
0.00
0.00
3.77
2528
2749
5.648960
GGAGACCGATAACAATTTTACCCAA
59.351
40.000
0.00
0.00
0.00
4.12
2529
2750
5.045432
AGGAGACCGATAACAATTTTACCCA
60.045
40.000
0.00
0.00
0.00
4.51
2530
2751
5.434408
AGGAGACCGATAACAATTTTACCC
58.566
41.667
0.00
0.00
0.00
3.69
2539
2760
3.698040
GGTTGAGTAGGAGACCGATAACA
59.302
47.826
0.00
0.00
0.00
2.41
2542
2763
3.552875
CAGGTTGAGTAGGAGACCGATA
58.447
50.000
0.00
0.00
37.26
2.92
2545
2766
0.173708
GCAGGTTGAGTAGGAGACCG
59.826
60.000
0.00
0.00
37.26
4.79
2546
2767
1.267121
TGCAGGTTGAGTAGGAGACC
58.733
55.000
0.00
0.00
0.00
3.85
2597
2818
7.336176
CCATTCATATCCATTCTACCATGAGTG
59.664
40.741
0.00
0.00
32.84
3.51
2600
2821
7.170277
CACCATTCATATCCATTCTACCATGA
58.830
38.462
0.00
0.00
0.00
3.07
2601
2822
6.127814
GCACCATTCATATCCATTCTACCATG
60.128
42.308
0.00
0.00
0.00
3.66
2602
2823
5.948162
GCACCATTCATATCCATTCTACCAT
59.052
40.000
0.00
0.00
0.00
3.55
2603
2824
5.316167
GCACCATTCATATCCATTCTACCA
58.684
41.667
0.00
0.00
0.00
3.25
2604
2825
4.702131
GGCACCATTCATATCCATTCTACC
59.298
45.833
0.00
0.00
0.00
3.18
2605
2826
5.316167
TGGCACCATTCATATCCATTCTAC
58.684
41.667
0.00
0.00
0.00
2.59
2606
2827
5.581350
TGGCACCATTCATATCCATTCTA
57.419
39.130
0.00
0.00
0.00
2.10
2607
2828
4.458256
TGGCACCATTCATATCCATTCT
57.542
40.909
0.00
0.00
0.00
2.40
2608
2829
5.475719
CATTGGCACCATTCATATCCATTC
58.524
41.667
0.00
0.00
0.00
2.67
2609
2830
4.262721
GCATTGGCACCATTCATATCCATT
60.263
41.667
0.00
0.00
40.72
3.16
2610
2831
3.259876
GCATTGGCACCATTCATATCCAT
59.740
43.478
0.00
0.00
40.72
3.41
2611
2832
2.629137
GCATTGGCACCATTCATATCCA
59.371
45.455
0.00
0.00
40.72
3.41
2612
2833
2.895404
AGCATTGGCACCATTCATATCC
59.105
45.455
0.00
0.00
44.61
2.59
2613
2834
4.595762
AAGCATTGGCACCATTCATATC
57.404
40.909
0.00
0.00
44.61
1.63
2614
2835
5.387788
TCTAAGCATTGGCACCATTCATAT
58.612
37.500
0.00
0.00
44.61
1.78
2615
2836
4.790937
TCTAAGCATTGGCACCATTCATA
58.209
39.130
0.00
0.00
44.61
2.15
2616
2837
3.634504
TCTAAGCATTGGCACCATTCAT
58.365
40.909
0.00
0.00
44.61
2.57
2617
2838
3.018856
CTCTAAGCATTGGCACCATTCA
58.981
45.455
0.00
0.00
44.61
2.57
2618
2839
2.223665
GCTCTAAGCATTGGCACCATTC
60.224
50.000
0.00
0.00
44.61
2.67
2619
2840
1.753073
GCTCTAAGCATTGGCACCATT
59.247
47.619
0.00
0.00
44.61
3.16
2620
2841
1.396653
GCTCTAAGCATTGGCACCAT
58.603
50.000
0.00
0.00
44.61
3.55
2621
2842
2.872408
GCTCTAAGCATTGGCACCA
58.128
52.632
0.00
0.00
44.61
4.17
2631
2852
0.599728
CGGCTGGAGATGCTCTAAGC
60.600
60.000
11.59
11.59
42.82
3.09
2632
2853
0.599728
GCGGCTGGAGATGCTCTAAG
60.600
60.000
0.00
0.00
0.00
2.18
2633
2854
1.443407
GCGGCTGGAGATGCTCTAA
59.557
57.895
0.00
0.00
0.00
2.10
2634
2855
2.849964
CGCGGCTGGAGATGCTCTA
61.850
63.158
0.00
0.00
0.00
2.43
2635
2856
4.218578
CGCGGCTGGAGATGCTCT
62.219
66.667
0.00
0.00
0.00
4.09
2698
2919
2.258726
GGCGCGACTGAGGGTTTTT
61.259
57.895
12.10
0.00
0.00
1.94
2699
2920
2.668550
GGCGCGACTGAGGGTTTT
60.669
61.111
12.10
0.00
0.00
2.43
2700
2921
4.699522
GGGCGCGACTGAGGGTTT
62.700
66.667
13.91
0.00
0.00
3.27
2703
2924
2.907897
CTTAAGGGCGCGACTGAGGG
62.908
65.000
13.91
0.00
0.00
4.30
2704
2925
1.519455
CTTAAGGGCGCGACTGAGG
60.519
63.158
13.91
0.00
0.00
3.86
2705
2926
0.802607
GTCTTAAGGGCGCGACTGAG
60.803
60.000
13.91
9.86
0.00
3.35
2706
2927
1.214589
GTCTTAAGGGCGCGACTGA
59.785
57.895
13.91
0.00
0.00
3.41
2707
2928
2.158959
CGTCTTAAGGGCGCGACTG
61.159
63.158
13.91
0.00
0.00
3.51
2708
2929
2.181021
CGTCTTAAGGGCGCGACT
59.819
61.111
13.91
4.58
0.00
4.18
2709
2930
3.551915
GCGTCTTAAGGGCGCGAC
61.552
66.667
22.26
6.99
41.70
5.19
2714
2935
0.656259
GATTTCGGCGTCTTAAGGGC
59.344
55.000
6.85
6.75
0.00
5.19
2715
2936
1.296727
GGATTTCGGCGTCTTAAGGG
58.703
55.000
6.85
0.00
0.00
3.95
2716
2937
0.928229
CGGATTTCGGCGTCTTAAGG
59.072
55.000
6.85
0.00
34.75
2.69
2717
2938
0.300789
GCGGATTTCGGCGTCTTAAG
59.699
55.000
6.85
0.00
39.69
1.85
2718
2939
2.375981
GCGGATTTCGGCGTCTTAA
58.624
52.632
6.85
0.00
39.69
1.85
2719
2940
4.097828
GCGGATTTCGGCGTCTTA
57.902
55.556
6.85
0.00
39.69
2.10
2738
2959
2.622962
CCCAAAAACGGTCCGAGCC
61.623
63.158
20.51
0.00
0.00
4.70
2739
2960
2.951458
CCCAAAAACGGTCCGAGC
59.049
61.111
20.51
0.00
0.00
5.03
2740
2961
2.622962
GGCCCAAAAACGGTCCGAG
61.623
63.158
20.51
1.98
0.00
4.63
2741
2962
2.595172
GGCCCAAAAACGGTCCGA
60.595
61.111
20.51
0.00
0.00
4.55
2742
2963
3.676605
GGGCCCAAAAACGGTCCG
61.677
66.667
19.95
10.48
34.85
4.79
2743
2964
3.676605
CGGGCCCAAAAACGGTCC
61.677
66.667
24.92
0.00
42.19
4.46
2744
2965
3.676605
CCGGGCCCAAAAACGGTC
61.677
66.667
24.92
0.00
41.34
4.79
2747
2968
2.000215
GATAGCCGGGCCCAAAAACG
62.000
60.000
24.92
6.17
0.00
3.60
2748
2969
1.672854
GGATAGCCGGGCCCAAAAAC
61.673
60.000
24.92
7.96
0.00
2.43
2749
2970
1.380650
GGATAGCCGGGCCCAAAAA
60.381
57.895
24.92
4.16
0.00
1.94
2750
2971
2.277404
GGATAGCCGGGCCCAAAA
59.723
61.111
24.92
3.72
0.00
2.44
2751
2972
3.816090
GGGATAGCCGGGCCCAAA
61.816
66.667
24.92
3.30
41.64
3.28
2756
2977
3.942439
GTCCTGGGATAGCCGGGC
61.942
72.222
12.11
12.11
33.83
6.13
2757
2978
3.616721
CGTCCTGGGATAGCCGGG
61.617
72.222
2.18
0.00
33.83
5.73
2758
2979
2.131709
TTCGTCCTGGGATAGCCGG
61.132
63.158
0.00
0.00
33.83
6.13
2759
2980
1.067582
GTTCGTCCTGGGATAGCCG
59.932
63.158
0.00
0.00
33.83
5.52
2760
2981
1.335132
TGGTTCGTCCTGGGATAGCC
61.335
60.000
0.00
0.00
37.07
3.93
2761
2982
0.105039
CTGGTTCGTCCTGGGATAGC
59.895
60.000
0.00
0.00
37.07
2.97
2768
2989
2.358737
GTGCCCTGGTTCGTCCTG
60.359
66.667
0.00
1.40
37.07
3.86
2769
2990
2.526873
AGTGCCCTGGTTCGTCCT
60.527
61.111
0.00
0.00
37.07
3.85
2770
2991
2.358737
CAGTGCCCTGGTTCGTCC
60.359
66.667
0.00
0.00
34.90
4.79
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.