Multiple sequence alignment - TraesCS7D01G340500
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
TraesCS7D01G340500
chr7D
100.000
2843
0
0
1
2843
436475481
436478323
0.000000e+00
5251.0
1
TraesCS7D01G340500
chr7D
87.172
725
89
4
1
722
421148118
421147395
0.000000e+00
821.0
2
TraesCS7D01G340500
chr7B
93.678
1123
50
7
703
1804
453112678
453113800
0.000000e+00
1661.0
3
TraesCS7D01G340500
chr7B
90.741
270
21
2
2244
2511
453114968
453115235
9.690000e-95
357.0
4
TraesCS7D01G340500
chr7B
86.166
253
17
4
2597
2842
453117474
453117715
1.010000e-64
257.0
5
TraesCS7D01G340500
chr7B
86.826
167
16
4
1984
2147
453114092
453114255
6.260000e-42
182.0
6
TraesCS7D01G340500
chr7B
94.340
53
3
0
2165
2217
518929528
518929580
6.530000e-12
82.4
7
TraesCS7D01G340500
chr7A
88.296
1162
86
17
740
1861
486180730
486179579
0.000000e+00
1347.0
8
TraesCS7D01G340500
chr7A
87.847
288
23
6
2320
2599
486178979
486178696
7.590000e-86
327.0
9
TraesCS7D01G340500
chr7A
83.333
246
21
8
2597
2842
486178656
486178431
2.870000e-50
209.0
10
TraesCS7D01G340500
chr7A
97.619
42
1
0
2253
2294
486179022
486178981
3.930000e-09
73.1
11
TraesCS7D01G340500
chr5D
90.767
704
56
9
3
703
443352264
443352961
0.000000e+00
931.0
12
TraesCS7D01G340500
chr2D
89.400
717
61
6
1
705
601265778
601265065
0.000000e+00
889.0
13
TraesCS7D01G340500
chr2D
81.579
722
91
21
1
703
116650596
116649898
2.470000e-155
558.0
14
TraesCS7D01G340500
chr2D
97.143
35
1
0
2182
2216
376364947
376364913
3.060000e-05
60.2
15
TraesCS7D01G340500
chr3D
87.758
727
59
10
1
703
63396376
63395656
0.000000e+00
822.0
16
TraesCS7D01G340500
chr1B
87.340
703
79
4
1
703
223767804
223768496
0.000000e+00
797.0
17
TraesCS7D01G340500
chr1B
89.286
56
6
0
2162
2217
482703652
482703707
1.410000e-08
71.3
18
TraesCS7D01G340500
chr3B
86.750
717
77
12
1
709
666806731
666806025
0.000000e+00
782.0
19
TraesCS7D01G340500
chr5B
90.317
568
48
7
1
565
628674540
628673977
0.000000e+00
737.0
20
TraesCS7D01G340500
chr5B
89.789
568
51
7
1
565
625094991
625094428
0.000000e+00
721.0
21
TraesCS7D01G340500
chr5B
88.037
535
52
10
77
605
626833504
626832976
8.650000e-175
623.0
22
TraesCS7D01G340500
chr5B
87.664
535
54
10
77
605
623162457
623161929
1.870000e-171
612.0
23
TraesCS7D01G340500
chr5B
91.228
57
4
1
2160
2216
544408155
544408100
3.040000e-10
76.8
24
TraesCS7D01G340500
chr5B
89.474
57
5
1
2160
2216
622082303
622082248
1.410000e-08
71.3
25
TraesCS7D01G340500
chr6B
91.071
56
5
0
2161
2216
102080242
102080187
3.040000e-10
76.8
26
TraesCS7D01G340500
chr6B
92.593
54
3
1
2160
2213
690342203
690342255
3.040000e-10
76.8
27
TraesCS7D01G340500
chr2B
92.453
53
3
1
2165
2217
784485669
784485720
1.090000e-09
75.0
28
TraesCS7D01G340500
chr1D
92.453
53
3
1
2165
2217
234045482
234045533
1.090000e-09
75.0
29
TraesCS7D01G340500
chr6A
92.157
51
4
0
2170
2220
513334071
513334021
3.930000e-09
73.1
30
TraesCS7D01G340500
chr3A
90.741
54
4
1
2160
2213
646736494
646736546
1.410000e-08
71.3
31
TraesCS7D01G340500
chr6D
95.455
44
1
1
2170
2213
79596760
79596802
5.080000e-08
69.4
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
TraesCS7D01G340500
chr7D
436475481
436478323
2842
False
5251.000
5251
100.00000
1
2843
1
chr7D.!!$F1
2842
1
TraesCS7D01G340500
chr7D
421147395
421148118
723
True
821.000
821
87.17200
1
722
1
chr7D.!!$R1
721
2
TraesCS7D01G340500
chr7B
453112678
453117715
5037
False
614.250
1661
89.35275
703
2842
4
chr7B.!!$F2
2139
3
TraesCS7D01G340500
chr7A
486178431
486180730
2299
True
489.025
1347
89.27375
740
2842
4
chr7A.!!$R1
2102
4
TraesCS7D01G340500
chr5D
443352264
443352961
697
False
931.000
931
90.76700
3
703
1
chr5D.!!$F1
700
5
TraesCS7D01G340500
chr2D
601265065
601265778
713
True
889.000
889
89.40000
1
705
1
chr2D.!!$R3
704
6
TraesCS7D01G340500
chr2D
116649898
116650596
698
True
558.000
558
81.57900
1
703
1
chr2D.!!$R1
702
7
TraesCS7D01G340500
chr3D
63395656
63396376
720
True
822.000
822
87.75800
1
703
1
chr3D.!!$R1
702
8
TraesCS7D01G340500
chr1B
223767804
223768496
692
False
797.000
797
87.34000
1
703
1
chr1B.!!$F1
702
9
TraesCS7D01G340500
chr3B
666806025
666806731
706
True
782.000
782
86.75000
1
709
1
chr3B.!!$R1
708
10
TraesCS7D01G340500
chr5B
628673977
628674540
563
True
737.000
737
90.31700
1
565
1
chr5B.!!$R6
564
11
TraesCS7D01G340500
chr5B
625094428
625094991
563
True
721.000
721
89.78900
1
565
1
chr5B.!!$R4
564
12
TraesCS7D01G340500
chr5B
626832976
626833504
528
True
623.000
623
88.03700
77
605
1
chr5B.!!$R5
528
13
TraesCS7D01G340500
chr5B
623161929
623162457
528
True
612.000
612
87.66400
77
605
1
chr5B.!!$R3
528
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
524
575
0.97401
TTTCGACCCGTATCTGCCCT
60.974
55.0
0.0
0.0
0.0
5.19
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2383
3430
0.037232
GCCAACGGTAGAAGCTGACT
60.037
55.0
0.0
0.0
0.0
3.41
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
318
337
2.671963
GGCCCTTGTTCGTCCACC
60.672
66.667
0.00
0.00
0.00
4.61
320
339
1.966451
GCCCTTGTTCGTCCACCTG
60.966
63.158
0.00
0.00
0.00
4.00
461
510
1.813513
CGGCAAGAAATGTGAGGAGT
58.186
50.000
0.00
0.00
0.00
3.85
486
536
2.813908
GGAATTGCGGCGAGACGT
60.814
61.111
12.98
0.00
35.98
4.34
524
575
0.974010
TTTCGACCCGTATCTGCCCT
60.974
55.000
0.00
0.00
0.00
5.19
548
599
5.128171
TGTGAACCCGTAGATATACTGCTTT
59.872
40.000
0.00
0.00
0.00
3.51
553
604
3.323979
CCGTAGATATACTGCTTTGGGGT
59.676
47.826
0.00
0.00
0.00
4.95
574
637
2.936032
GGGAGGGAGTTGTGGGCT
60.936
66.667
0.00
0.00
0.00
5.19
626
689
2.436109
GGGCTCTGTTCTGGCCAA
59.564
61.111
7.01
0.00
46.87
4.52
630
693
1.620323
GGCTCTGTTCTGGCCAAAAAT
59.380
47.619
7.01
0.00
44.69
1.82
655
718
1.440060
CAAGCCCGTATACTCGCCA
59.560
57.895
0.56
0.00
0.00
5.69
665
728
4.438200
CCGTATACTCGCCAAAATTTTGCT
60.438
41.667
22.90
7.73
36.86
3.91
682
745
1.135333
TGCTGGTTCGCGACATATACA
59.865
47.619
9.15
0.00
0.00
2.29
777
840
4.292186
ACAGAGTCAAACATATGCACCT
57.708
40.909
1.58
0.00
0.00
4.00
890
956
9.490379
AATAGACGGAAAAATAATAATCTCGCT
57.510
29.630
0.00
0.00
0.00
4.93
923
998
2.033675
TGACTGAACATTTGTGCTGCAG
59.966
45.455
10.11
10.11
0.00
4.41
968
1045
7.539366
GCTCTAGCTACGAATTAAACAGATAGG
59.461
40.741
0.00
0.00
38.21
2.57
1019
1103
7.348080
TCAGTATGATCTTAGTACCACCAAG
57.652
40.000
0.00
0.00
42.56
3.61
1022
1106
4.471904
TGATCTTAGTACCACCAAGCAG
57.528
45.455
0.00
0.00
0.00
4.24
1034
1118
0.029300
CCAAGCAGGTCACAACAACG
59.971
55.000
0.00
0.00
0.00
4.10
1054
1138
2.013563
GCTTCCAGTGCCGATCATCAA
61.014
52.381
0.00
0.00
0.00
2.57
1059
1143
0.673333
AGTGCCGATCATCAAACGCA
60.673
50.000
0.00
0.00
0.00
5.24
1065
1149
2.652893
GATCATCAAACGCAGCCGCC
62.653
60.000
0.00
0.00
38.22
6.13
1605
1704
3.313874
CCTCCTCAGGCCGACATT
58.686
61.111
0.00
0.00
30.98
2.71
1758
1866
2.965831
TGAGGGTAGGATGTACATGCTC
59.034
50.000
30.31
21.02
40.14
4.26
1790
1902
4.851558
GTCATGGCTGTATTTTTGTTCGAC
59.148
41.667
0.00
0.00
0.00
4.20
1827
1939
8.734386
GTCCATGGTTTCATAGGATTAATGATC
58.266
37.037
12.58
0.00
35.05
2.92
1828
1940
7.607607
TCCATGGTTTCATAGGATTAATGATCG
59.392
37.037
12.58
0.00
33.52
3.69
1829
1941
7.607607
CCATGGTTTCATAGGATTAATGATCGA
59.392
37.037
2.57
0.00
33.52
3.59
1830
1942
9.170734
CATGGTTTCATAGGATTAATGATCGAT
57.829
33.333
0.00
0.00
33.52
3.59
1831
1943
8.777865
TGGTTTCATAGGATTAATGATCGATC
57.222
34.615
18.72
18.72
35.49
3.69
1893
2005
4.860802
TGGATCTCTCTGTCTTCTCTCT
57.139
45.455
0.00
0.00
0.00
3.10
1897
2009
5.163258
GGATCTCTCTGTCTTCTCTCTCTCT
60.163
48.000
0.00
0.00
0.00
3.10
1898
2010
5.344743
TCTCTCTGTCTTCTCTCTCTCTC
57.655
47.826
0.00
0.00
0.00
3.20
1900
2012
6.194967
TCTCTCTGTCTTCTCTCTCTCTCTA
58.805
44.000
0.00
0.00
0.00
2.43
1901
2013
6.096987
TCTCTCTGTCTTCTCTCTCTCTCTAC
59.903
46.154
0.00
0.00
0.00
2.59
1902
2014
5.719563
TCTCTGTCTTCTCTCTCTCTCTACA
59.280
44.000
0.00
0.00
0.00
2.74
1905
2017
6.666113
TCTGTCTTCTCTCTCTCTCTACAGTA
59.334
42.308
0.00
0.00
34.77
2.74
1906
2018
7.344612
TCTGTCTTCTCTCTCTCTCTACAGTAT
59.655
40.741
0.00
0.00
34.77
2.12
1909
2021
9.174166
GTCTTCTCTCTCTCTCTACAGTATTTT
57.826
37.037
0.00
0.00
0.00
1.82
1912
2024
9.961264
TTCTCTCTCTCTCTACAGTATTTTACA
57.039
33.333
0.00
0.00
0.00
2.41
1929
2041
9.921637
GTATTTTACAAATTTCAGGAACATCCA
57.078
29.630
0.00
0.00
39.61
3.41
1932
2044
5.410355
ACAAATTTCAGGAACATCCATGG
57.590
39.130
4.97
4.97
39.61
3.66
1933
2045
5.085920
ACAAATTTCAGGAACATCCATGGA
58.914
37.500
18.88
18.88
39.61
3.41
1934
2046
5.543405
ACAAATTTCAGGAACATCCATGGAA
59.457
36.000
20.67
1.96
39.61
3.53
1936
2048
2.806945
TCAGGAACATCCATGGAACC
57.193
50.000
20.67
18.53
39.61
3.62
1937
2049
1.991813
TCAGGAACATCCATGGAACCA
59.008
47.619
20.67
0.00
39.61
3.67
1938
2050
2.582172
TCAGGAACATCCATGGAACCAT
59.418
45.455
20.67
5.41
39.61
3.55
1939
2051
3.785325
TCAGGAACATCCATGGAACCATA
59.215
43.478
20.67
9.13
39.61
2.74
1940
2052
4.139786
CAGGAACATCCATGGAACCATAG
58.860
47.826
20.67
7.28
39.61
2.23
1941
2053
3.139025
AGGAACATCCATGGAACCATAGG
59.861
47.826
20.67
10.11
39.61
2.57
1942
2054
3.117512
GGAACATCCATGGAACCATAGGT
60.118
47.826
20.67
0.00
36.28
3.08
1943
2055
3.582998
ACATCCATGGAACCATAGGTG
57.417
47.619
20.67
12.30
35.34
4.00
1984
2359
5.275067
ACTAATTTGCACACACCAATGTT
57.725
34.783
0.00
0.00
36.72
2.71
1986
2361
6.112058
ACTAATTTGCACACACCAATGTTTT
58.888
32.000
0.00
0.00
36.72
2.43
1987
2362
7.268586
ACTAATTTGCACACACCAATGTTTTA
58.731
30.769
0.00
0.00
36.72
1.52
1991
2366
6.992063
TTGCACACACCAATGTTTTATTTT
57.008
29.167
0.00
0.00
36.72
1.82
2029
2415
4.918810
AGAAAAACAAGGACGAAGCAAT
57.081
36.364
0.00
0.00
0.00
3.56
2078
2491
4.079558
AGCCACCTCTTTGATGAACCATAT
60.080
41.667
0.00
0.00
0.00
1.78
2095
2508
4.103153
ACCATATGATCTTGATCCAACGGT
59.897
41.667
3.65
6.99
0.00
4.83
2128
2542
1.840635
GCTCCCATCACTAACCTTCCT
59.159
52.381
0.00
0.00
0.00
3.36
2150
2564
7.062322
TCCTATATGCATTTCCACAAGAATGT
58.938
34.615
3.54
0.00
41.61
2.71
2153
2567
2.562298
TGCATTTCCACAAGAATGTCCC
59.438
45.455
0.00
0.00
37.82
4.46
2154
2568
2.562298
GCATTTCCACAAGAATGTCCCA
59.438
45.455
0.00
0.00
37.82
4.37
2155
2569
3.196254
GCATTTCCACAAGAATGTCCCAT
59.804
43.478
0.00
0.00
37.82
4.00
2156
2570
4.402155
GCATTTCCACAAGAATGTCCCATA
59.598
41.667
0.00
0.00
37.82
2.74
2157
2571
5.679638
GCATTTCCACAAGAATGTCCCATAC
60.680
44.000
0.00
0.00
37.82
2.39
2158
2572
4.649267
TTCCACAAGAATGTCCCATACA
57.351
40.909
0.00
0.00
43.86
2.29
2159
2573
3.950397
TCCACAAGAATGTCCCATACAC
58.050
45.455
0.00
0.00
42.09
2.90
2160
2574
2.677836
CCACAAGAATGTCCCATACACG
59.322
50.000
0.00
0.00
42.09
4.49
2164
2578
2.467880
AGAATGTCCCATACACGGTCT
58.532
47.619
0.00
0.00
42.09
3.85
2165
2579
2.838202
AGAATGTCCCATACACGGTCTT
59.162
45.455
0.00
0.00
42.09
3.01
2166
2580
2.981859
ATGTCCCATACACGGTCTTC
57.018
50.000
0.00
0.00
42.09
2.87
2167
2581
0.528924
TGTCCCATACACGGTCTTCG
59.471
55.000
0.00
0.00
45.88
3.79
2177
2591
3.247033
CGGTCTTCGTCCGGTTATC
57.753
57.895
0.00
0.00
43.68
1.75
2178
2592
0.248784
CGGTCTTCGTCCGGTTATCC
60.249
60.000
0.00
0.00
43.68
2.59
2199
2613
9.841295
TTATCCGTTAATTAACTAGGCAATTCT
57.159
29.630
22.57
5.31
34.12
2.40
2210
2624
6.054860
ACTAGGCAATTCTCTTCTGCTTAA
57.945
37.500
0.00
0.00
36.32
1.85
2211
2625
6.657875
ACTAGGCAATTCTCTTCTGCTTAAT
58.342
36.000
0.00
0.00
36.32
1.40
2212
2626
7.115414
ACTAGGCAATTCTCTTCTGCTTAATT
58.885
34.615
0.00
0.00
36.32
1.40
2214
2628
5.948162
AGGCAATTCTCTTCTGCTTAATTGA
59.052
36.000
9.58
0.00
38.99
2.57
2215
2629
6.606395
AGGCAATTCTCTTCTGCTTAATTGAT
59.394
34.615
9.58
0.00
38.99
2.57
2216
2630
6.916932
GGCAATTCTCTTCTGCTTAATTGATC
59.083
38.462
9.58
0.00
38.99
2.92
2217
2631
7.415989
GGCAATTCTCTTCTGCTTAATTGATCA
60.416
37.037
9.58
0.00
38.99
2.92
2218
2632
7.972277
GCAATTCTCTTCTGCTTAATTGATCAA
59.028
33.333
11.26
11.26
38.99
2.57
2222
2636
7.478322
TCTCTTCTGCTTAATTGATCAATTGC
58.522
34.615
33.94
29.44
40.83
3.56
2223
2637
7.121611
TCTCTTCTGCTTAATTGATCAATTGCA
59.878
33.333
33.94
31.53
40.83
4.08
2224
2638
7.778083
TCTTCTGCTTAATTGATCAATTGCAT
58.222
30.769
33.94
17.20
40.83
3.96
2225
2639
7.919091
TCTTCTGCTTAATTGATCAATTGCATC
59.081
33.333
33.94
22.45
40.83
3.91
2226
2640
6.203647
TCTGCTTAATTGATCAATTGCATCG
58.796
36.000
33.94
24.76
40.83
3.84
2227
2641
5.893687
TGCTTAATTGATCAATTGCATCGT
58.106
33.333
33.94
15.61
40.83
3.73
2228
2642
6.331845
TGCTTAATTGATCAATTGCATCGTT
58.668
32.000
33.94
15.59
40.83
3.85
2230
2644
7.009448
TGCTTAATTGATCAATTGCATCGTTTC
59.991
33.333
33.94
16.99
40.83
2.78
2231
2645
7.009448
GCTTAATTGATCAATTGCATCGTTTCA
59.991
33.333
33.94
14.32
40.83
2.69
2233
2647
7.655236
AATTGATCAATTGCATCGTTTCAAA
57.345
28.000
28.57
0.00
39.36
2.69
2236
2650
7.107834
TGATCAATTGCATCGTTTCAAAAAG
57.892
32.000
0.00
0.00
0.00
2.27
2294
3339
4.272100
GCCAGCAGCAAAACCATG
57.728
55.556
0.00
0.00
42.97
3.66
2306
3351
2.627699
CAAAACCATGCCAGTAACAGGT
59.372
45.455
0.00
0.00
0.00
4.00
2313
3358
0.685097
GCCAGTAACAGGTGTGGAGA
59.315
55.000
0.00
0.00
31.04
3.71
2335
3380
3.119990
ACGCACACCAATTAGAATTTCCG
60.120
43.478
0.00
0.00
0.00
4.30
2353
3398
6.721571
TTTCCGTTCAGTCTATTTAGCTTG
57.278
37.500
0.00
0.00
0.00
4.01
2383
3430
1.930133
AGGCATCCACCATGTCCCA
60.930
57.895
0.00
0.00
37.92
4.37
2426
3474
2.157668
CCGACATGAAGGAAAGTTCACG
59.842
50.000
0.00
0.00
39.25
4.35
2477
3525
1.300963
CCTGTCACATCCAGGGGTG
59.699
63.158
0.00
0.00
44.77
4.61
2555
5734
0.029300
TTGACAGCTGTTTTGCGCTC
59.971
50.000
22.65
5.86
38.13
5.03
2564
5743
1.000385
TGTTTTGCGCTCCCAATCAAG
60.000
47.619
9.73
0.00
0.00
3.02
2566
5745
0.881118
TTTGCGCTCCCAATCAAGTC
59.119
50.000
9.73
0.00
0.00
3.01
2569
5748
0.674895
GCGCTCCCAATCAAGTCACT
60.675
55.000
0.00
0.00
0.00
3.41
2650
5891
3.485947
AAATGACACACACACACACAC
57.514
42.857
0.00
0.00
0.00
3.82
2651
5892
2.106477
ATGACACACACACACACACA
57.894
45.000
0.00
0.00
0.00
3.72
2652
5893
1.152510
TGACACACACACACACACAC
58.847
50.000
0.00
0.00
0.00
3.82
2653
5894
1.152510
GACACACACACACACACACA
58.847
50.000
0.00
0.00
0.00
3.72
2654
5895
0.871722
ACACACACACACACACACAC
59.128
50.000
0.00
0.00
0.00
3.82
2655
5896
0.871057
CACACACACACACACACACA
59.129
50.000
0.00
0.00
0.00
3.72
2656
5897
1.136000
CACACACACACACACACACAG
60.136
52.381
0.00
0.00
0.00
3.66
2657
5898
1.270571
ACACACACACACACACACAGA
60.271
47.619
0.00
0.00
0.00
3.41
2658
5899
1.394572
CACACACACACACACACAGAG
59.605
52.381
0.00
0.00
0.00
3.35
2659
5900
0.374758
CACACACACACACACAGAGC
59.625
55.000
0.00
0.00
0.00
4.09
2660
5901
0.036483
ACACACACACACACAGAGCA
60.036
50.000
0.00
0.00
0.00
4.26
2661
5902
0.654160
CACACACACACACAGAGCAG
59.346
55.000
0.00
0.00
0.00
4.24
2662
5903
1.091771
ACACACACACACAGAGCAGC
61.092
55.000
0.00
0.00
0.00
5.25
2663
5904
1.524621
ACACACACACAGAGCAGCC
60.525
57.895
0.00
0.00
0.00
4.85
2664
5905
2.111878
ACACACACAGAGCAGCCC
59.888
61.111
0.00
0.00
0.00
5.19
2665
5906
2.670934
CACACACAGAGCAGCCCC
60.671
66.667
0.00
0.00
0.00
5.80
2666
5907
3.170672
ACACACAGAGCAGCCCCA
61.171
61.111
0.00
0.00
0.00
4.96
2706
5947
1.437986
GAGCCGACGACCTTGCTAT
59.562
57.895
0.00
0.00
33.41
2.97
2707
5948
0.872021
GAGCCGACGACCTTGCTATG
60.872
60.000
0.00
0.00
33.41
2.23
2708
5949
2.526120
GCCGACGACCTTGCTATGC
61.526
63.158
0.00
0.00
0.00
3.14
2709
5950
1.141881
CCGACGACCTTGCTATGCT
59.858
57.895
0.00
0.00
0.00
3.79
2710
5951
0.384309
CCGACGACCTTGCTATGCTA
59.616
55.000
0.00
0.00
0.00
3.49
2732
5973
1.608283
CCAAGGGACCAGAGTCGAAAC
60.608
57.143
0.00
0.00
44.54
2.78
2791
6032
1.732809
GCGGTTGAGAAGAAGCTTACC
59.267
52.381
0.00
0.00
0.00
2.85
2842
6083
0.322816
TCAGCCCTTGCAGAATCACC
60.323
55.000
0.00
0.00
41.13
4.02
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
27
28
4.223964
GGCCGATTTCGACGCAGC
62.224
66.667
0.67
0.00
43.02
5.25
29
30
3.115892
GTGGCCGATTTCGACGCA
61.116
61.111
0.00
0.00
43.02
5.24
446
491
3.244700
CCACTCCACTCCTCACATTTCTT
60.245
47.826
0.00
0.00
0.00
2.52
461
510
2.354729
CCGCAATTCCCCACTCCA
59.645
61.111
0.00
0.00
0.00
3.86
486
536
2.445845
CCTATCCCCTCGCCACCA
60.446
66.667
0.00
0.00
0.00
4.17
494
544
2.926539
GGTCGAAACCCTATCCCCT
58.073
57.895
0.00
0.00
39.93
4.79
524
575
4.212716
AGCAGTATATCTACGGGTTCACA
58.787
43.478
0.00
0.00
31.05
3.58
560
611
4.335647
CGCAGCCCACAACTCCCT
62.336
66.667
0.00
0.00
0.00
4.20
563
614
0.887387
TTTACCGCAGCCCACAACTC
60.887
55.000
0.00
0.00
0.00
3.01
564
615
0.466555
TTTTACCGCAGCCCACAACT
60.467
50.000
0.00
0.00
0.00
3.16
626
689
1.419381
ACGGGCTTGGTCCAAATTTT
58.581
45.000
5.64
0.00
0.00
1.82
630
693
1.910671
AGTATACGGGCTTGGTCCAAA
59.089
47.619
5.64
0.00
0.00
3.28
638
701
0.538118
TTTGGCGAGTATACGGGCTT
59.462
50.000
19.11
0.00
0.00
4.35
655
718
2.124122
GTCGCGAACCAGCAAAATTTT
58.876
42.857
12.06
0.00
36.85
1.82
665
728
1.067974
CCCTGTATATGTCGCGAACCA
59.932
52.381
12.06
6.02
0.00
3.67
682
745
1.190643
GAGCAACTCTAGCAGACCCT
58.809
55.000
0.00
0.00
0.00
4.34
777
840
0.968405
GGCCTTCCTCATGCACAAAA
59.032
50.000
0.00
0.00
0.00
2.44
890
956
4.118093
TGTTCAGTCAAACGAAGACTCA
57.882
40.909
6.27
1.15
44.11
3.41
923
998
6.658188
AGAGCAGGTATAAATAGGACAGAC
57.342
41.667
0.00
0.00
0.00
3.51
1019
1103
0.317020
GAAGCGTTGTTGTGACCTGC
60.317
55.000
0.00
0.00
0.00
4.85
1022
1106
0.307760
CTGGAAGCGTTGTTGTGACC
59.692
55.000
0.00
0.00
0.00
4.02
1024
1108
1.013596
CACTGGAAGCGTTGTTGTGA
58.986
50.000
0.00
0.00
37.60
3.58
1034
1118
0.462581
TGATGATCGGCACTGGAAGC
60.463
55.000
0.00
0.00
37.60
3.86
1065
1149
0.249657
GAAGTAGCAGATGGAGGGCG
60.250
60.000
0.00
0.00
0.00
6.13
1155
1239
1.538876
CAGGTTCACCCCCTGGAGA
60.539
63.158
0.00
0.00
44.77
3.71
1215
1299
2.404789
CAGGCGGCGCTTATGTTG
59.595
61.111
32.30
15.67
0.00
3.33
1407
1491
4.681025
GCAAGAAAAGATTTGTGCGAATGA
59.319
37.500
0.00
0.00
0.00
2.57
1758
1866
1.830279
ACAGCCATGACCACAAGATG
58.170
50.000
0.00
0.00
0.00
2.90
1827
1939
6.128715
CCCAAGTCATTCAGATTAATCGATCG
60.129
42.308
9.36
9.36
0.00
3.69
1828
1940
6.348050
GCCCAAGTCATTCAGATTAATCGATC
60.348
42.308
9.78
0.00
0.00
3.69
1829
1941
5.471456
GCCCAAGTCATTCAGATTAATCGAT
59.529
40.000
9.78
0.00
0.00
3.59
1830
1942
4.816385
GCCCAAGTCATTCAGATTAATCGA
59.184
41.667
9.78
7.68
0.00
3.59
1831
1943
4.576053
TGCCCAAGTCATTCAGATTAATCG
59.424
41.667
9.78
5.54
0.00
3.34
1905
2017
9.439500
CATGGATGTTCCTGAAATTTGTAAAAT
57.561
29.630
0.00
0.00
37.46
1.82
1906
2018
7.877097
CCATGGATGTTCCTGAAATTTGTAAAA
59.123
33.333
5.56
0.00
37.46
1.52
1909
2021
6.252233
TCCATGGATGTTCCTGAAATTTGTA
58.748
36.000
11.44
0.00
37.46
2.41
1910
2022
5.085920
TCCATGGATGTTCCTGAAATTTGT
58.914
37.500
11.44
0.00
37.46
2.83
1912
2024
5.046376
GGTTCCATGGATGTTCCTGAAATTT
60.046
40.000
17.06
0.00
37.46
1.82
1914
2026
4.026052
GGTTCCATGGATGTTCCTGAAAT
58.974
43.478
17.06
0.00
37.46
2.17
1915
2027
3.181424
TGGTTCCATGGATGTTCCTGAAA
60.181
43.478
17.06
0.00
37.46
2.69
1916
2028
2.378208
TGGTTCCATGGATGTTCCTGAA
59.622
45.455
17.06
0.00
37.46
3.02
1917
2029
1.991813
TGGTTCCATGGATGTTCCTGA
59.008
47.619
17.06
0.00
37.46
3.86
1918
2030
2.512692
TGGTTCCATGGATGTTCCTG
57.487
50.000
17.06
0.00
37.46
3.86
1919
2031
3.139025
CCTATGGTTCCATGGATGTTCCT
59.861
47.826
17.06
8.54
37.46
3.36
1920
2032
3.117512
ACCTATGGTTCCATGGATGTTCC
60.118
47.826
17.06
15.59
31.22
3.62
1922
2034
3.902218
CACCTATGGTTCCATGGATGTT
58.098
45.455
17.06
3.78
31.02
2.71
1923
2035
2.423373
GCACCTATGGTTCCATGGATGT
60.423
50.000
17.06
4.65
31.02
3.06
1924
2036
2.233271
GCACCTATGGTTCCATGGATG
58.767
52.381
17.06
9.35
31.02
3.51
1925
2037
1.145738
GGCACCTATGGTTCCATGGAT
59.854
52.381
17.06
2.53
38.83
3.41
1926
2038
0.550914
GGCACCTATGGTTCCATGGA
59.449
55.000
11.44
11.44
38.83
3.41
1927
2039
0.258484
TGGCACCTATGGTTCCATGG
59.742
55.000
4.97
4.97
43.58
3.66
1928
2040
3.901087
TGGCACCTATGGTTCCATG
57.099
52.632
13.86
1.68
43.58
3.66
1932
2044
3.189568
TGCATGGCACCTATGGTTC
57.810
52.632
0.00
0.00
31.02
3.62
1942
2054
0.177373
TTGCTTTTGTGTGCATGGCA
59.823
45.000
0.00
0.00
39.07
4.92
1943
2055
1.003652
GTTTGCTTTTGTGTGCATGGC
60.004
47.619
0.00
0.00
39.07
4.40
1945
2057
5.910637
ATTAGTTTGCTTTTGTGTGCATG
57.089
34.783
0.00
0.00
39.07
4.06
1946
2058
6.717413
CAAATTAGTTTGCTTTTGTGTGCAT
58.283
32.000
0.00
0.00
38.39
3.96
2003
2378
5.099575
GCTTCGTCCTTGTTTTTCTTTTCA
58.900
37.500
0.00
0.00
0.00
2.69
2004
2379
5.099575
TGCTTCGTCCTTGTTTTTCTTTTC
58.900
37.500
0.00
0.00
0.00
2.29
2037
2423
2.879026
GGCTACTGGCAAAGTAATAGCC
59.121
50.000
12.66
12.66
46.12
3.93
2038
2424
3.541632
TGGCTACTGGCAAAGTAATAGC
58.458
45.455
0.00
4.31
46.03
2.97
2078
2491
4.278310
TCTAGACCGTTGGATCAAGATCA
58.722
43.478
11.78
0.00
39.54
2.92
2095
2508
3.181433
TGATGGGAGCGGTCTAATCTAGA
60.181
47.826
21.89
0.00
0.00
2.43
2128
2542
6.265196
GGGACATTCTTGTGGAAATGCATATA
59.735
38.462
0.00
0.00
37.49
0.86
2160
2574
3.656066
GGATAACCGGACGAAGACC
57.344
57.895
9.46
0.00
39.42
3.85
2171
2585
7.790823
TTGCCTAGTTAATTAACGGATAACC
57.209
36.000
20.33
9.84
40.96
2.85
2172
2586
9.874215
GAATTGCCTAGTTAATTAACGGATAAC
57.126
33.333
20.33
11.85
40.96
1.89
2173
2587
9.841295
AGAATTGCCTAGTTAATTAACGGATAA
57.159
29.630
20.33
15.32
40.96
1.75
2174
2588
9.485206
GAGAATTGCCTAGTTAATTAACGGATA
57.515
33.333
20.33
9.83
40.96
2.59
2175
2589
8.211629
AGAGAATTGCCTAGTTAATTAACGGAT
58.788
33.333
20.33
9.30
40.96
4.18
2176
2590
7.562135
AGAGAATTGCCTAGTTAATTAACGGA
58.438
34.615
20.33
13.40
40.96
4.69
2177
2591
7.787725
AGAGAATTGCCTAGTTAATTAACGG
57.212
36.000
19.92
17.06
40.96
4.44
2178
2592
9.099454
AGAAGAGAATTGCCTAGTTAATTAACG
57.901
33.333
19.92
9.40
40.96
3.18
2180
2594
8.893727
GCAGAAGAGAATTGCCTAGTTAATTAA
58.106
33.333
0.00
0.00
31.79
1.40
2188
2602
7.281774
TCAATTAAGCAGAAGAGAATTGCCTAG
59.718
37.037
0.00
0.00
37.40
3.02
2189
2603
7.112122
TCAATTAAGCAGAAGAGAATTGCCTA
58.888
34.615
0.00
0.00
37.40
3.93
2190
2604
5.948162
TCAATTAAGCAGAAGAGAATTGCCT
59.052
36.000
0.00
0.00
37.40
4.75
2199
2613
7.160547
TGCAATTGATCAATTAAGCAGAAGA
57.839
32.000
28.74
14.90
38.84
2.87
2210
2624
7.655236
TTTTGAAACGATGCAATTGATCAAT
57.345
28.000
15.36
15.36
37.14
2.57
2211
2625
7.437565
TCTTTTTGAAACGATGCAATTGATCAA
59.562
29.630
11.26
11.26
36.24
2.57
2212
2626
6.922407
TCTTTTTGAAACGATGCAATTGATCA
59.078
30.769
10.34
0.00
0.00
2.92
2214
2628
7.712264
TTCTTTTTGAAACGATGCAATTGAT
57.288
28.000
10.34
0.00
0.00
2.57
2215
2629
7.531280
TTTCTTTTTGAAACGATGCAATTGA
57.469
28.000
10.34
0.00
39.50
2.57
2216
2630
8.598509
TTTTTCTTTTTGAAACGATGCAATTG
57.401
26.923
0.00
0.00
43.55
2.32
2240
2654
2.812011
GTTGGCAGTACGGAGACATTTT
59.188
45.455
0.00
0.00
0.00
1.82
2241
2655
2.224426
TGTTGGCAGTACGGAGACATTT
60.224
45.455
0.00
0.00
0.00
2.32
2242
2656
1.346395
TGTTGGCAGTACGGAGACATT
59.654
47.619
0.00
0.00
0.00
2.71
2294
3339
0.685097
TCTCCACACCTGTTACTGGC
59.315
55.000
8.22
0.00
0.00
4.85
2306
3351
0.179032
AATTGGTGTGCGTCTCCACA
60.179
50.000
2.70
0.00
42.99
4.17
2313
3358
3.119990
CGGAAATTCTAATTGGTGTGCGT
60.120
43.478
0.00
0.00
0.00
5.24
2335
3380
5.351740
GGGACACAAGCTAAATAGACTGAAC
59.648
44.000
0.00
0.00
0.00
3.18
2383
3430
0.037232
GCCAACGGTAGAAGCTGACT
60.037
55.000
0.00
0.00
0.00
3.41
2477
3525
4.699522
GGACGGGGTGCCACACTC
62.700
72.222
0.00
0.00
34.40
3.51
2489
3537
0.966920
ACTGTAGACCACAAGGACGG
59.033
55.000
0.00
0.00
36.48
4.79
2555
5734
2.341257
CGTCAGAGTGACTTGATTGGG
58.659
52.381
5.57
0.00
44.85
4.12
2564
5743
2.089349
GGAAGCGCGTCAGAGTGAC
61.089
63.158
24.41
1.75
43.65
3.67
2566
5745
2.811317
GGGAAGCGCGTCAGAGTG
60.811
66.667
24.41
0.00
0.00
3.51
2632
5853
1.737236
GTGTGTGTGTGTGTGTGTCAT
59.263
47.619
0.00
0.00
0.00
3.06
2650
5891
2.670934
GTGGGGCTGCTCTGTGTG
60.671
66.667
0.00
0.00
0.00
3.82
2651
5892
3.958860
GGTGGGGCTGCTCTGTGT
61.959
66.667
0.00
0.00
0.00
3.72
2652
5893
4.729918
GGGTGGGGCTGCTCTGTG
62.730
72.222
0.00
0.00
0.00
3.66
2656
5897
4.748144
CTTGGGGTGGGGCTGCTC
62.748
72.222
0.00
0.00
0.00
4.26
2666
5907
1.357272
TTGGTACACAGCCTTGGGGT
61.357
55.000
0.00
0.00
39.29
4.95
2706
5947
0.909610
CTCTGGTCCCTTGGGTAGCA
60.910
60.000
5.51
7.53
0.00
3.49
2707
5948
0.910088
ACTCTGGTCCCTTGGGTAGC
60.910
60.000
5.51
3.44
0.00
3.58
2708
5949
1.196012
GACTCTGGTCCCTTGGGTAG
58.804
60.000
5.51
3.76
36.53
3.18
2709
5950
0.613853
CGACTCTGGTCCCTTGGGTA
60.614
60.000
5.51
0.00
39.15
3.69
2710
5951
1.913762
CGACTCTGGTCCCTTGGGT
60.914
63.158
5.51
0.00
39.15
4.51
2732
5973
1.714899
CCCTATCTTTGCCGCGTTGG
61.715
60.000
4.92
0.00
42.50
3.77
2791
6032
0.718343
GCAAGTAGCTGCTGAGTTCG
59.282
55.000
13.43
0.00
39.34
3.95
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.