Multiple sequence alignment - TraesCS3A01G432200
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
TraesCS3A01G432200
chr3A
100.000
5408
0
0
1
5408
673449647
673444240
0.000000e+00
9987.0
1
TraesCS3A01G432200
chr3A
93.907
755
22
2
1
734
84664162
84664913
0.000000e+00
1118.0
2
TraesCS3A01G432200
chr3B
94.528
4697
194
37
736
5408
712573659
712569002
0.000000e+00
7191.0
3
TraesCS3A01G432200
chr3B
94.324
740
23
10
1
734
452748546
452747820
0.000000e+00
1116.0
4
TraesCS3A01G432200
chr3D
94.121
3776
174
27
736
4491
537918758
537915011
0.000000e+00
5699.0
5
TraesCS3A01G432200
chr3D
89.901
406
35
5
4510
4914
537914867
537914467
8.030000e-143
518.0
6
TraesCS3A01G432200
chr3D
88.387
310
28
6
4916
5224
537914431
537914129
3.080000e-97
366.0
7
TraesCS3A01G432200
chr7A
96.866
734
23
0
1
734
689959764
689960497
0.000000e+00
1229.0
8
TraesCS3A01G432200
chr1A
96.866
734
23
0
1
734
286245639
286244906
0.000000e+00
1229.0
9
TraesCS3A01G432200
chr1A
96.594
734
25
0
1
734
287786275
287785542
0.000000e+00
1218.0
10
TraesCS3A01G432200
chr5A
96.467
736
25
1
1
736
535685504
535686238
0.000000e+00
1214.0
11
TraesCS3A01G432200
chr5A
94.591
758
19
2
1
737
510261272
510260516
0.000000e+00
1153.0
12
TraesCS3A01G432200
chr1B
96.049
734
29
0
1
734
365464483
365465216
0.000000e+00
1195.0
13
TraesCS3A01G432200
chr1B
95.510
735
33
0
1
735
111683793
111684527
0.000000e+00
1175.0
14
TraesCS3A01G432200
chr1B
85.965
57
8
0
3096
3152
474447084
474447140
1.630000e-05
62.1
15
TraesCS3A01G432200
chr2B
95.640
734
32
0
1
734
54336629
54335896
0.000000e+00
1179.0
16
TraesCS3A01G432200
chr4A
94.054
740
25
10
1
734
135352838
135353564
0.000000e+00
1105.0
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
TraesCS3A01G432200
chr3A
673444240
673449647
5407
True
9987.000000
9987
100.000
1
5408
1
chr3A.!!$R1
5407
1
TraesCS3A01G432200
chr3A
84664162
84664913
751
False
1118.000000
1118
93.907
1
734
1
chr3A.!!$F1
733
2
TraesCS3A01G432200
chr3B
712569002
712573659
4657
True
7191.000000
7191
94.528
736
5408
1
chr3B.!!$R2
4672
3
TraesCS3A01G432200
chr3B
452747820
452748546
726
True
1116.000000
1116
94.324
1
734
1
chr3B.!!$R1
733
4
TraesCS3A01G432200
chr3D
537914129
537918758
4629
True
2194.333333
5699
90.803
736
5224
3
chr3D.!!$R1
4488
5
TraesCS3A01G432200
chr7A
689959764
689960497
733
False
1229.000000
1229
96.866
1
734
1
chr7A.!!$F1
733
6
TraesCS3A01G432200
chr1A
286244906
286245639
733
True
1229.000000
1229
96.866
1
734
1
chr1A.!!$R1
733
7
TraesCS3A01G432200
chr1A
287785542
287786275
733
True
1218.000000
1218
96.594
1
734
1
chr1A.!!$R2
733
8
TraesCS3A01G432200
chr5A
535685504
535686238
734
False
1214.000000
1214
96.467
1
736
1
chr5A.!!$F1
735
9
TraesCS3A01G432200
chr5A
510260516
510261272
756
True
1153.000000
1153
94.591
1
737
1
chr5A.!!$R1
736
10
TraesCS3A01G432200
chr1B
365464483
365465216
733
False
1195.000000
1195
96.049
1
734
1
chr1B.!!$F2
733
11
TraesCS3A01G432200
chr1B
111683793
111684527
734
False
1175.000000
1175
95.510
1
735
1
chr1B.!!$F1
734
12
TraesCS3A01G432200
chr2B
54335896
54336629
733
True
1179.000000
1179
95.640
1
734
1
chr2B.!!$R1
733
13
TraesCS3A01G432200
chr4A
135352838
135353564
726
False
1105.000000
1105
94.054
1
734
1
chr4A.!!$F1
733
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
779
832
0.100503
CCCAACGAAATTCCCGATGC
59.899
55.0
7.12
0.0
0.00
3.91
F
1378
1435
0.033991
CCTCGACTTCTCCCTCTCCA
60.034
60.0
0.00
0.0
0.00
3.86
F
1539
1596
0.179108
GCAACGAATCGGCTACCTCT
60.179
55.0
7.80
0.0
0.00
3.69
F
1769
1832
0.248825
CAGGCTCACTTCGATCTCCG
60.249
60.0
0.00
0.0
40.25
4.63
F
1984
2056
0.320374
TTGGCAGAACGTAGACCAGG
59.680
55.0
0.00
0.0
0.00
4.45
F
1991
2063
0.323957
AACGTAGACCAGGGGAAAGC
59.676
55.0
0.00
0.0
0.00
3.51
F
1992
2064
0.544595
ACGTAGACCAGGGGAAAGCT
60.545
55.0
0.00
0.0
0.00
3.74
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2263
2335
0.035056
CAATCCCTTGCCCTTCGAGT
60.035
55.000
0.00
0.0
0.00
4.18
R
2264
2336
0.749454
CCAATCCCTTGCCCTTCGAG
60.749
60.000
0.00
0.0
0.00
4.04
R
3451
3523
1.621672
CCCAGAGGAGGAAGCCACTC
61.622
65.000
0.00
0.0
33.47
3.51
R
4049
4121
1.064017
ACCTTGAACCAACTGGCAAGA
60.064
47.619
14.32
0.0
37.43
3.02
R
4256
4328
1.202879
TCGGCAATGACTGAAACCCTT
60.203
47.619
0.00
0.0
0.00
3.95
R
4320
4392
1.613925
CCTTCAGTCAACCTCGAGTCA
59.386
52.381
12.31
0.0
0.00
3.41
R
4416
4488
3.057456
ACCGTGCAACAAACTAACACAAA
60.057
39.130
0.00
0.0
35.74
2.83
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
0.388294
TCATCTGCTGCCTCATCGAG
59.612
55.000
0.00
0.00
0.00
4.04
169
170
9.499479
CAATCTTTACCTCATTACATAGCTCAT
57.501
33.333
0.00
0.00
0.00
2.90
218
219
3.487372
TGATCTATCCTACACCTCCACG
58.513
50.000
0.00
0.00
0.00
4.94
477
526
1.021390
GGAGGTTGGTCGATGCACAG
61.021
60.000
0.00
0.00
0.00
3.66
486
535
1.811266
CGATGCACAGGGACCGAAG
60.811
63.158
0.00
0.00
0.00
3.79
595
644
4.042187
AGCAAGGAGACTAGTCAAAACCAT
59.958
41.667
24.44
11.77
42.68
3.55
642
694
4.226394
TGGAGGAGAATTGATCCGGTTTTA
59.774
41.667
0.00
0.00
42.02
1.52
645
697
6.152154
GGAGGAGAATTGATCCGGTTTTAAAA
59.848
38.462
0.00
0.00
42.02
1.52
666
718
4.591321
AAGTTTAGGGGCTGATTGATCA
57.409
40.909
0.00
0.00
35.16
2.92
684
736
2.871453
TCAGGTTTTAGACTTTGGGGC
58.129
47.619
0.00
0.00
0.00
5.80
739
791
5.106673
GGAAAACGATACTTTCCTCAAGGTG
60.107
44.000
7.02
0.00
45.66
4.00
751
803
0.111446
TCAAGGTGAATTGGCCGGAA
59.889
50.000
5.05
0.00
0.00
4.30
779
832
0.100503
CCCAACGAAATTCCCGATGC
59.899
55.000
7.12
0.00
0.00
3.91
791
846
1.084370
CCCGATGCGAACCTCTTGTC
61.084
60.000
0.00
0.00
0.00
3.18
817
872
1.699343
GTGACGAACGAGAAAGGAGG
58.301
55.000
0.14
0.00
0.00
4.30
1009
1066
4.489771
CCCCCGACATGGCTCCAC
62.490
72.222
0.00
0.00
35.87
4.02
1012
1069
4.082523
CCGACATGGCTCCACCGT
62.083
66.667
0.00
0.00
43.94
4.83
1080
1137
4.790962
CTGCAGTGCCTGGGCGAT
62.791
66.667
13.72
0.00
45.51
4.58
1378
1435
0.033991
CCTCGACTTCTCCCTCTCCA
60.034
60.000
0.00
0.00
0.00
3.86
1415
1472
3.068691
CTCCGACGAGCCCCTCAA
61.069
66.667
0.00
0.00
0.00
3.02
1444
1501
1.669604
CTCCGTCCTCGAGAATCTCA
58.330
55.000
15.71
0.00
39.71
3.27
1445
1502
1.332375
CTCCGTCCTCGAGAATCTCAC
59.668
57.143
15.71
0.00
39.71
3.51
1448
1505
1.380524
GTCCTCGAGAATCTCACCGA
58.619
55.000
15.71
1.80
0.00
4.69
1473
1530
1.589993
CGCGGCCTACACAGAGATG
60.590
63.158
0.00
0.00
0.00
2.90
1481
1538
1.613317
TACACAGAGATGGCCCACCG
61.613
60.000
0.00
0.00
39.70
4.94
1521
1578
3.435186
GCCTCTTCGTGGCTTGGC
61.435
66.667
0.00
0.00
46.38
4.52
1533
1590
2.690778
GCTTGGCAACGAATCGGCT
61.691
57.895
7.80
0.00
42.51
5.52
1534
1591
1.366111
GCTTGGCAACGAATCGGCTA
61.366
55.000
7.80
0.00
42.51
3.93
1535
1592
0.373716
CTTGGCAACGAATCGGCTAC
59.626
55.000
7.80
0.00
42.51
3.58
1536
1593
1.022451
TTGGCAACGAATCGGCTACC
61.022
55.000
7.80
3.49
42.51
3.18
1537
1594
1.153429
GGCAACGAATCGGCTACCT
60.153
57.895
7.80
0.00
0.00
3.08
1538
1595
1.152383
GGCAACGAATCGGCTACCTC
61.152
60.000
7.80
0.00
0.00
3.85
1539
1596
0.179108
GCAACGAATCGGCTACCTCT
60.179
55.000
7.80
0.00
0.00
3.69
1540
1597
1.841450
CAACGAATCGGCTACCTCTC
58.159
55.000
7.80
0.00
0.00
3.20
1541
1598
0.745468
AACGAATCGGCTACCTCTCC
59.255
55.000
7.80
0.00
0.00
3.71
1542
1599
1.283181
CGAATCGGCTACCTCTCCG
59.717
63.158
0.00
0.00
46.52
4.63
1543
1600
1.007154
GAATCGGCTACCTCTCCGC
60.007
63.158
0.00
0.00
44.91
5.54
1544
1601
2.734756
GAATCGGCTACCTCTCCGCG
62.735
65.000
0.00
0.00
44.91
6.46
1548
1605
3.839432
GCTACCTCTCCGCGGCTT
61.839
66.667
23.51
4.54
0.00
4.35
1549
1606
2.105128
CTACCTCTCCGCGGCTTG
59.895
66.667
23.51
13.37
0.00
4.01
1550
1607
3.432051
CTACCTCTCCGCGGCTTGG
62.432
68.421
23.51
22.77
0.00
3.61
1563
1620
2.007608
CGGCTTGGTAACTTTAGCTCC
58.992
52.381
0.00
0.00
36.74
4.70
1567
1624
0.251073
TGGTAACTTTAGCTCCGCCC
59.749
55.000
0.00
0.00
37.61
6.13
1572
1629
2.285069
TTTAGCTCCGCCCTCCCA
60.285
61.111
0.00
0.00
0.00
4.37
1580
1637
4.135153
CGCCCTCCCAGTCGACAG
62.135
72.222
19.50
10.04
0.00
3.51
1584
1641
2.262915
CTCCCAGTCGACAGCACC
59.737
66.667
19.50
0.00
0.00
5.01
1585
1642
2.203640
TCCCAGTCGACAGCACCT
60.204
61.111
19.50
0.00
0.00
4.00
1596
1653
2.985847
AGCACCTTCTTTGGCCGC
60.986
61.111
0.00
0.00
0.00
6.53
1635
1692
1.275291
CTGCTGGAAAGGTTAGTCGGA
59.725
52.381
0.00
0.00
0.00
4.55
1638
1695
2.280628
CTGGAAAGGTTAGTCGGATGC
58.719
52.381
0.00
0.00
0.00
3.91
1640
1697
2.039216
TGGAAAGGTTAGTCGGATGCAA
59.961
45.455
0.00
0.00
0.00
4.08
1769
1832
0.248825
CAGGCTCACTTCGATCTCCG
60.249
60.000
0.00
0.00
40.25
4.63
1780
1843
1.676678
CGATCTCCGGATGTGGGTGT
61.677
60.000
3.57
0.00
31.46
4.16
1788
1851
1.005037
GATGTGGGTGTGCGTCTCA
60.005
57.895
0.00
0.00
0.00
3.27
1798
1861
0.371645
GTGCGTCTCAAGCTGTATGC
59.628
55.000
0.00
0.00
43.29
3.14
1801
1864
1.004185
GCGTCTCAAGCTGTATGCATG
60.004
52.381
10.16
0.00
45.94
4.06
1803
1866
2.030091
CGTCTCAAGCTGTATGCATGTG
59.970
50.000
10.16
0.04
45.94
3.21
1807
1870
2.946990
TCAAGCTGTATGCATGTGATGG
59.053
45.455
10.16
0.00
45.94
3.51
1825
1888
5.955355
GTGATGGAGCTTACTAGGGAGATAT
59.045
44.000
0.00
0.00
0.00
1.63
1831
1894
4.020662
AGCTTACTAGGGAGATATTGCAGC
60.021
45.833
0.00
0.00
0.00
5.25
1832
1895
4.020662
GCTTACTAGGGAGATATTGCAGCT
60.021
45.833
0.00
0.00
0.00
4.24
1836
1899
0.892814
GGGAGATATTGCAGCTGGCC
60.893
60.000
17.12
0.00
43.89
5.36
1838
1901
1.683943
GAGATATTGCAGCTGGCCAA
58.316
50.000
17.12
12.46
43.89
4.52
1840
1903
2.029623
AGATATTGCAGCTGGCCAAAG
58.970
47.619
17.12
0.00
43.89
2.77
1856
1928
2.103263
CCAAAGAGGGGAAGGACTATCG
59.897
54.545
0.00
0.00
0.00
2.92
1860
1932
0.338814
AGGGGAAGGACTATCGTGGT
59.661
55.000
0.00
0.00
0.00
4.16
1861
1933
0.464452
GGGGAAGGACTATCGTGGTG
59.536
60.000
0.00
0.00
0.00
4.17
1864
1936
2.100418
GGGAAGGACTATCGTGGTGTAC
59.900
54.545
0.00
0.00
0.00
2.90
1873
1945
7.037438
GGACTATCGTGGTGTACTCAATTTTA
58.963
38.462
0.00
0.00
0.00
1.52
1884
1956
9.722056
GGTGTACTCAATTTTAATTATCTGCAG
57.278
33.333
7.63
7.63
0.00
4.41
1886
1958
9.679661
TGTACTCAATTTTAATTATCTGCAGGA
57.320
29.630
15.13
0.57
0.00
3.86
1889
1961
8.897752
ACTCAATTTTAATTATCTGCAGGAGTC
58.102
33.333
15.13
0.00
0.00
3.36
1894
1966
0.461548
TTATCTGCAGGAGTCGCTGG
59.538
55.000
15.13
0.00
0.00
4.85
1895
1967
0.684479
TATCTGCAGGAGTCGCTGGT
60.684
55.000
15.13
0.68
0.00
4.00
1907
1979
2.050077
GCTGGTTTCTGCCGTTGC
60.050
61.111
0.00
0.00
38.26
4.17
1945
2017
3.949754
GCTCATCCTTGATGATGTTTGGA
59.050
43.478
7.19
0.00
46.16
3.53
1950
2022
5.902613
TCCTTGATGATGTTTGGAATGAC
57.097
39.130
0.00
0.00
0.00
3.06
1952
2024
5.774184
TCCTTGATGATGTTTGGAATGACAA
59.226
36.000
0.00
0.00
0.00
3.18
1953
2025
5.865552
CCTTGATGATGTTTGGAATGACAAC
59.134
40.000
0.00
0.00
0.00
3.32
1960
2032
1.890876
TTGGAATGACAACGGGAGTG
58.109
50.000
0.00
0.00
46.69
3.51
1963
2035
1.079503
GAATGACAACGGGAGTGAGC
58.920
55.000
0.00
0.00
46.69
4.26
1977
2049
1.070134
AGTGAGCTTTGGCAGAACGTA
59.930
47.619
0.00
0.00
41.70
3.57
1984
2056
0.320374
TTGGCAGAACGTAGACCAGG
59.680
55.000
0.00
0.00
0.00
4.45
1989
2061
1.621814
CAGAACGTAGACCAGGGGAAA
59.378
52.381
0.00
0.00
0.00
3.13
1991
2063
0.323957
AACGTAGACCAGGGGAAAGC
59.676
55.000
0.00
0.00
0.00
3.51
1992
2064
0.544595
ACGTAGACCAGGGGAAAGCT
60.545
55.000
0.00
0.00
0.00
3.74
1993
2065
0.613777
CGTAGACCAGGGGAAAGCTT
59.386
55.000
0.00
0.00
0.00
3.74
2008
2080
4.572795
GGAAAGCTTTACTATCACCTCTGC
59.427
45.833
14.53
0.00
0.00
4.26
2024
2096
0.809385
CTGCAGAATGGTCAGCAAGG
59.191
55.000
8.42
0.00
44.64
3.61
2037
2109
4.116238
GTCAGCAAGGTAGCAGAATAGTC
58.884
47.826
0.00
0.00
36.85
2.59
2099
2171
3.763557
AAGGATCCCAATGATGTTGGT
57.236
42.857
8.55
0.00
37.88
3.67
2110
2182
2.246469
TGATGTTGGTTGGATTGGGTG
58.754
47.619
0.00
0.00
0.00
4.61
2150
2222
1.498865
CTCAAGAAGCACGCGTTGGT
61.499
55.000
10.22
8.43
37.63
3.67
2158
2230
1.010125
CACGCGTTGGTTTGTGAGG
60.010
57.895
10.22
0.00
34.29
3.86
2165
2237
2.544267
CGTTGGTTTGTGAGGAGAGTTC
59.456
50.000
0.00
0.00
0.00
3.01
2168
2240
2.104792
TGGTTTGTGAGGAGAGTTCTGG
59.895
50.000
0.00
0.00
0.00
3.86
2173
2245
6.410540
GTTTGTGAGGAGAGTTCTGGATATT
58.589
40.000
0.00
0.00
0.00
1.28
2174
2246
5.860941
TGTGAGGAGAGTTCTGGATATTC
57.139
43.478
0.00
0.00
0.00
1.75
2175
2247
5.523588
TGTGAGGAGAGTTCTGGATATTCT
58.476
41.667
0.00
0.00
0.00
2.40
2182
2254
6.097554
GGAGAGTTCTGGATATTCTCAGTTGA
59.902
42.308
2.68
0.00
36.79
3.18
2252
2324
2.354821
CAGCTAAAGTTATTGGCGGGAC
59.645
50.000
0.00
0.00
0.00
4.46
2278
2350
1.221021
GGTACTCGAAGGGCAAGGG
59.779
63.158
0.00
0.00
0.00
3.95
2317
2389
4.716287
TGGAGACAGATATTCATGGTGACA
59.284
41.667
0.00
0.00
40.01
3.58
2403
2475
7.746475
GCATATTGCAGTATATTTCCGAAGAAC
59.254
37.037
0.87
0.00
44.26
3.01
2538
2610
5.296151
TGTTGAGGTCATTCTTTCAGACT
57.704
39.130
0.00
0.00
32.98
3.24
2820
2892
3.930229
AGATAAAGAATGTGCGCACGTTA
59.070
39.130
39.66
27.74
40.35
3.18
2853
2925
6.106673
CGGATGTGATATATCCAAGTTACCC
58.893
44.000
10.25
0.97
43.46
3.69
2964
3036
6.885918
TGCATCTTCAGACTTTTGATATTCCA
59.114
34.615
0.00
0.00
0.00
3.53
3022
3094
1.571460
CAGTTGACCAGCTTGCGAC
59.429
57.895
0.00
0.00
0.00
5.19
3138
3210
1.652947
AGGGGCGAACCTTAGAAGAA
58.347
50.000
0.00
0.00
37.69
2.52
3152
3224
9.844257
AACCTTAGAAGAATTGAAGGATATGAG
57.156
33.333
6.52
0.00
39.17
2.90
3216
3288
2.029649
TCAATGCAAAGAGGAAGCTTGC
60.030
45.455
10.41
10.41
0.00
4.01
3451
3523
2.134789
AGCTAATTGCAGAAGGTGGG
57.865
50.000
0.00
0.00
45.94
4.61
4049
4121
8.525316
TGACTGCAAGAATATCAAATCATTTGT
58.475
29.630
9.98
0.88
38.56
2.83
4213
4285
3.011821
AGTGTCCCTACCTTCTGAGATGA
59.988
47.826
0.00
0.00
0.00
2.92
4256
4328
5.420725
AAACTGAGTATATCACACTGCCA
57.579
39.130
0.00
0.00
33.22
4.92
4320
4392
5.454613
GGAATTTCTTCATTTGGTTGGGTGT
60.455
40.000
0.00
0.00
32.70
4.16
4664
4861
2.182825
GTTCCACACACTAGCGTATCG
58.817
52.381
0.00
0.00
0.00
2.92
4665
4862
1.456296
TCCACACACTAGCGTATCGT
58.544
50.000
0.00
0.00
0.00
3.73
4801
4998
3.700863
ATTAGGGTCCACTAGCTGGTA
57.299
47.619
0.95
0.00
41.52
3.25
4995
5226
1.780919
AGTATGCCCCAGTTTATCCCC
59.219
52.381
0.00
0.00
0.00
4.81
5310
5542
1.283029
CTGGACCATGGTGTTCCTCAT
59.717
52.381
25.52
0.00
34.23
2.90
5324
5556
5.293079
GTGTTCCTCATAGTTCATCTTCTGC
59.707
44.000
0.00
0.00
0.00
4.26
5346
5578
3.467776
CCTCTGCTAGGTTTCTGCC
57.532
57.895
0.00
0.00
40.94
4.85
5347
5579
0.460987
CCTCTGCTAGGTTTCTGCCG
60.461
60.000
0.00
0.00
40.94
5.69
5348
5580
0.532573
CTCTGCTAGGTTTCTGCCGA
59.467
55.000
0.00
0.00
0.00
5.54
5349
5581
1.137872
CTCTGCTAGGTTTCTGCCGAT
59.862
52.381
0.00
0.00
0.00
4.18
5350
5582
2.362397
CTCTGCTAGGTTTCTGCCGATA
59.638
50.000
0.00
0.00
0.00
2.92
5351
5583
2.362397
TCTGCTAGGTTTCTGCCGATAG
59.638
50.000
0.00
0.00
0.00
2.08
5352
5584
2.101582
CTGCTAGGTTTCTGCCGATAGT
59.898
50.000
0.00
0.00
0.00
2.12
5353
5585
2.500098
TGCTAGGTTTCTGCCGATAGTT
59.500
45.455
0.00
0.00
0.00
2.24
5354
5586
3.055385
TGCTAGGTTTCTGCCGATAGTTT
60.055
43.478
0.00
0.00
0.00
2.66
5355
5587
3.309954
GCTAGGTTTCTGCCGATAGTTTG
59.690
47.826
0.00
0.00
0.00
2.93
5356
5588
3.418684
AGGTTTCTGCCGATAGTTTGT
57.581
42.857
0.00
0.00
0.00
2.83
5357
5589
3.074412
AGGTTTCTGCCGATAGTTTGTG
58.926
45.455
0.00
0.00
0.00
3.33
5358
5590
2.812011
GGTTTCTGCCGATAGTTTGTGT
59.188
45.455
0.00
0.00
0.00
3.72
5359
5591
3.364964
GGTTTCTGCCGATAGTTTGTGTG
60.365
47.826
0.00
0.00
0.00
3.82
5360
5592
2.831685
TCTGCCGATAGTTTGTGTGT
57.168
45.000
0.00
0.00
0.00
3.72
5361
5593
2.683968
TCTGCCGATAGTTTGTGTGTC
58.316
47.619
0.00
0.00
0.00
3.67
5400
5632
9.887629
ATATCTGGATTTCATACATGAAGCTAG
57.112
33.333
0.00
8.57
46.34
3.42
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
169
170
6.661805
GGAAGATTGTTTTTATGGGTAGGTCA
59.338
38.462
0.00
0.00
0.00
4.02
204
205
1.763968
CAGATCGTGGAGGTGTAGGA
58.236
55.000
0.00
0.00
0.00
2.94
477
526
0.613777
ATTCAGGTGACTTCGGTCCC
59.386
55.000
0.00
0.00
43.85
4.46
486
535
0.967380
CAGCCCCCAATTCAGGTGAC
60.967
60.000
0.00
0.00
0.00
3.67
616
668
2.551721
CCGGATCAATTCTCCTCCATGG
60.552
54.545
4.97
4.97
37.10
3.66
617
669
2.105477
ACCGGATCAATTCTCCTCCATG
59.895
50.000
9.46
0.00
0.00
3.66
618
670
2.412591
ACCGGATCAATTCTCCTCCAT
58.587
47.619
9.46
0.00
0.00
3.41
622
674
7.232737
ACTTTTTAAAACCGGATCAATTCTCCT
59.767
33.333
9.46
0.00
0.00
3.69
642
694
5.779771
TGATCAATCAGCCCCTAAACTTTTT
59.220
36.000
0.00
0.00
32.11
1.94
645
697
4.530875
CTGATCAATCAGCCCCTAAACTT
58.469
43.478
7.05
0.00
46.63
2.66
666
718
1.422402
TCGCCCCAAAGTCTAAAACCT
59.578
47.619
0.00
0.00
0.00
3.50
684
736
3.123804
CCTGTCTAATGGACCGATTTCG
58.876
50.000
0.00
0.00
43.89
3.46
739
791
1.090052
CGGTCTCTTCCGGCCAATTC
61.090
60.000
2.24
0.00
45.88
2.17
751
803
1.838073
ATTTCGTTGGGCCGGTCTCT
61.838
55.000
5.77
0.00
0.00
3.10
779
832
1.749634
ACGATAGGGACAAGAGGTTCG
59.250
52.381
0.00
0.00
43.77
3.95
815
870
1.244697
TTCGCTGCTTCTCGTCTCCT
61.245
55.000
0.00
0.00
0.00
3.69
816
871
0.388649
TTTCGCTGCTTCTCGTCTCC
60.389
55.000
0.00
0.00
0.00
3.71
817
872
0.711118
GTTTCGCTGCTTCTCGTCTC
59.289
55.000
0.00
0.00
0.00
3.36
1434
1491
1.586564
GGCGTCGGTGAGATTCTCG
60.587
63.158
9.07
0.00
32.35
4.04
1465
1522
4.101448
GCGGTGGGCCATCTCTGT
62.101
66.667
16.16
0.00
34.80
3.41
1513
1570
2.331893
CCGATTCGTTGCCAAGCCA
61.332
57.895
5.20
0.00
0.00
4.75
1521
1578
1.536284
GGAGAGGTAGCCGATTCGTTG
60.536
57.143
5.20
0.00
0.00
4.10
1536
1593
1.810030
GTTACCAAGCCGCGGAGAG
60.810
63.158
33.48
16.97
0.00
3.20
1537
1594
1.823169
AAGTTACCAAGCCGCGGAGA
61.823
55.000
33.48
2.73
0.00
3.71
1538
1595
0.953960
AAAGTTACCAAGCCGCGGAG
60.954
55.000
33.48
17.79
0.00
4.63
1539
1596
0.321021
TAAAGTTACCAAGCCGCGGA
59.679
50.000
33.48
2.66
0.00
5.54
1540
1597
0.725117
CTAAAGTTACCAAGCCGCGG
59.275
55.000
24.05
24.05
0.00
6.46
1541
1598
0.096454
GCTAAAGTTACCAAGCCGCG
59.904
55.000
0.00
0.00
0.00
6.46
1542
1599
1.397343
GAGCTAAAGTTACCAAGCCGC
59.603
52.381
0.00
0.00
35.54
6.53
1543
1600
2.007608
GGAGCTAAAGTTACCAAGCCG
58.992
52.381
0.00
0.00
35.54
5.52
1544
1601
2.007608
CGGAGCTAAAGTTACCAAGCC
58.992
52.381
0.00
0.00
35.54
4.35
1563
1620
4.135153
CTGTCGACTGGGAGGGCG
62.135
72.222
17.92
0.00
0.00
6.13
1567
1624
1.821061
AAGGTGCTGTCGACTGGGAG
61.821
60.000
21.94
10.08
0.00
4.30
1572
1629
1.541233
CCAAAGAAGGTGCTGTCGACT
60.541
52.381
17.92
0.00
0.00
4.18
1579
1636
2.985847
GCGGCCAAAGAAGGTGCT
60.986
61.111
2.24
0.00
31.97
4.40
1580
1637
4.404654
CGCGGCCAAAGAAGGTGC
62.405
66.667
2.24
0.00
0.00
5.01
1611
1668
3.368427
CGACTAACCTTTCCAGCAGATCA
60.368
47.826
0.00
0.00
0.00
2.92
1614
1671
1.275291
CCGACTAACCTTTCCAGCAGA
59.725
52.381
0.00
0.00
0.00
4.26
1618
1675
2.280628
GCATCCGACTAACCTTTCCAG
58.719
52.381
0.00
0.00
0.00
3.86
1635
1692
1.305465
TTGAGCAGGGCCATTGCAT
60.305
52.632
27.09
15.49
43.92
3.96
1638
1695
1.651240
CGAGTTGAGCAGGGCCATTG
61.651
60.000
6.18
3.11
0.00
2.82
1640
1697
2.270205
CGAGTTGAGCAGGGCCAT
59.730
61.111
6.18
0.00
0.00
4.40
1698
1761
3.554692
GTCGTCTTGCCGATGCCG
61.555
66.667
0.00
0.00
39.34
5.69
1769
1832
1.741770
GAGACGCACACCCACATCC
60.742
63.158
0.00
0.00
0.00
3.51
1780
1843
0.037419
TGCATACAGCTTGAGACGCA
60.037
50.000
0.00
0.00
45.94
5.24
1788
1851
3.211865
CTCCATCACATGCATACAGCTT
58.788
45.455
0.00
0.00
45.94
3.74
1798
1861
3.643320
TCCCTAGTAAGCTCCATCACATG
59.357
47.826
0.00
0.00
0.00
3.21
1801
1864
3.567397
TCTCCCTAGTAAGCTCCATCAC
58.433
50.000
0.00
0.00
0.00
3.06
1803
1866
6.629291
GCAATATCTCCCTAGTAAGCTCCATC
60.629
46.154
0.00
0.00
0.00
3.51
1807
1870
5.719173
CTGCAATATCTCCCTAGTAAGCTC
58.281
45.833
0.00
0.00
0.00
4.09
1825
1888
1.904865
CCTCTTTGGCCAGCTGCAA
60.905
57.895
8.66
5.34
43.89
4.08
1831
1894
1.000396
CCTTCCCCTCTTTGGCCAG
60.000
63.158
5.11
0.00
0.00
4.85
1832
1895
1.465188
TCCTTCCCCTCTTTGGCCA
60.465
57.895
0.00
0.00
0.00
5.36
1836
1899
3.460857
CGATAGTCCTTCCCCTCTTTG
57.539
52.381
0.00
0.00
0.00
2.77
1856
1928
9.503427
GCAGATAATTAAAATTGAGTACACCAC
57.497
33.333
0.00
0.00
0.00
4.16
1860
1932
9.679661
TCCTGCAGATAATTAAAATTGAGTACA
57.320
29.630
17.39
0.00
0.00
2.90
1864
1936
8.066595
CGACTCCTGCAGATAATTAAAATTGAG
58.933
37.037
17.39
10.52
0.00
3.02
1873
1945
2.484417
CCAGCGACTCCTGCAGATAATT
60.484
50.000
17.39
0.00
33.85
1.40
1877
1949
1.548357
AACCAGCGACTCCTGCAGAT
61.548
55.000
17.39
0.00
33.85
2.90
1884
1956
2.035442
GGCAGAAACCAGCGACTCC
61.035
63.158
0.00
0.00
0.00
3.85
1886
1958
2.357517
CGGCAGAAACCAGCGACT
60.358
61.111
0.00
0.00
0.00
4.18
1887
1959
2.251642
AACGGCAGAAACCAGCGAC
61.252
57.895
0.00
0.00
0.00
5.19
1889
1961
2.252260
CAACGGCAGAAACCAGCG
59.748
61.111
0.00
0.00
0.00
5.18
1907
1979
1.349026
TGAGCAAGAACCTCTTCCCTG
59.651
52.381
0.00
0.00
33.78
4.45
1945
2017
0.687354
AGCTCACTCCCGTTGTCATT
59.313
50.000
0.00
0.00
0.00
2.57
1950
2022
1.856265
GCCAAAGCTCACTCCCGTTG
61.856
60.000
0.00
0.00
35.50
4.10
1952
2024
2.032681
GCCAAAGCTCACTCCCGT
59.967
61.111
0.00
0.00
35.50
5.28
1953
2025
2.032528
TGCCAAAGCTCACTCCCG
59.967
61.111
0.00
0.00
40.80
5.14
1959
2031
1.343142
TCTACGTTCTGCCAAAGCTCA
59.657
47.619
0.00
0.00
40.80
4.26
1960
2032
1.727335
GTCTACGTTCTGCCAAAGCTC
59.273
52.381
0.00
0.00
40.80
4.09
1963
2035
2.069273
CTGGTCTACGTTCTGCCAAAG
58.931
52.381
0.00
0.00
0.00
2.77
1977
2049
2.349445
AGTAAAGCTTTCCCCTGGTCT
58.651
47.619
16.57
0.38
0.00
3.85
1984
2056
5.119694
CAGAGGTGATAGTAAAGCTTTCCC
58.880
45.833
16.57
7.82
0.00
3.97
1989
2061
4.026744
TCTGCAGAGGTGATAGTAAAGCT
58.973
43.478
13.74
0.00
0.00
3.74
1991
2063
5.757320
CCATTCTGCAGAGGTGATAGTAAAG
59.243
44.000
24.63
8.33
0.00
1.85
1992
2064
5.189736
ACCATTCTGCAGAGGTGATAGTAAA
59.810
40.000
23.10
3.00
32.04
2.01
1993
2065
4.716784
ACCATTCTGCAGAGGTGATAGTAA
59.283
41.667
23.10
3.51
32.04
2.24
2008
2080
2.012673
GCTACCTTGCTGACCATTCTG
58.987
52.381
0.00
0.00
0.00
3.02
2024
2096
5.264712
GTGTAGTCACGACTATTCTGCTAC
58.735
45.833
9.99
0.00
44.73
3.58
2051
2123
1.012086
CATGTCAGCCACCATCTTCG
58.988
55.000
0.00
0.00
0.00
3.79
2099
2171
0.322456
CTCTTCGGCACCCAATCCAA
60.322
55.000
0.00
0.00
0.00
3.53
2110
2182
0.598065
AACAACCAATGCTCTTCGGC
59.402
50.000
0.00
0.00
0.00
5.54
2145
2217
3.561725
CAGAACTCTCCTCACAAACCAAC
59.438
47.826
0.00
0.00
0.00
3.77
2150
2222
6.441924
AGAATATCCAGAACTCTCCTCACAAA
59.558
38.462
0.00
0.00
0.00
2.83
2158
2230
7.106439
TCAACTGAGAATATCCAGAACTCTC
57.894
40.000
0.00
0.39
34.65
3.20
2165
2237
6.477053
TCTCCTTCAACTGAGAATATCCAG
57.523
41.667
0.00
0.00
34.79
3.86
2168
2240
6.709846
CCCAATCTCCTTCAACTGAGAATATC
59.290
42.308
0.00
0.00
40.75
1.63
2173
2245
3.517100
CTCCCAATCTCCTTCAACTGAGA
59.483
47.826
0.00
0.00
41.55
3.27
2174
2246
3.517100
TCTCCCAATCTCCTTCAACTGAG
59.483
47.826
0.00
0.00
0.00
3.35
2175
2247
3.520696
TCTCCCAATCTCCTTCAACTGA
58.479
45.455
0.00
0.00
0.00
3.41
2182
2254
4.017683
AGCAATCTTTCTCCCAATCTCCTT
60.018
41.667
0.00
0.00
0.00
3.36
2223
2295
4.433615
CAATAACTTTAGCTGCGAGAGGA
58.566
43.478
0.00
0.00
0.00
3.71
2252
2324
1.202268
CCCTTCGAGTACCACTAAGCG
60.202
57.143
0.00
0.00
0.00
4.68
2258
2330
0.391263
CCTTGCCCTTCGAGTACCAC
60.391
60.000
0.00
0.00
0.00
4.16
2263
2335
0.035056
CAATCCCTTGCCCTTCGAGT
60.035
55.000
0.00
0.00
0.00
4.18
2264
2336
0.749454
CCAATCCCTTGCCCTTCGAG
60.749
60.000
0.00
0.00
0.00
4.04
2278
2350
5.734720
TGTCTCCAAGATACTGTTCCAATC
58.265
41.667
0.00
0.00
0.00
2.67
2317
2389
2.020720
TGACAAAAGTGTGGCGACAAT
58.979
42.857
2.03
0.00
46.06
2.71
2323
2395
3.923017
ATAGCTTGACAAAAGTGTGGC
57.077
42.857
0.00
0.00
38.41
5.01
2403
2475
4.098501
AGTTTCTTTGGCTCAAACTTCCAG
59.901
41.667
0.00
0.00
37.09
3.86
2418
2490
9.178758
GATATCCACATCCTAACAAGTTTCTTT
57.821
33.333
0.00
0.00
0.00
2.52
2538
2610
3.678529
GCCTTTTGTTTCCTTGCTTGACA
60.679
43.478
0.00
0.00
0.00
3.58
2709
2781
9.877178
GTCCTTAATCTCTTCAGATAGTTTTGA
57.123
33.333
0.00
0.00
38.55
2.69
2713
2785
8.474025
CAGTGTCCTTAATCTCTTCAGATAGTT
58.526
37.037
0.00
0.00
38.55
2.24
2715
2787
8.231692
TCAGTGTCCTTAATCTCTTCAGATAG
57.768
38.462
0.00
0.00
38.55
2.08
2716
2788
8.774546
ATCAGTGTCCTTAATCTCTTCAGATA
57.225
34.615
0.00
0.00
38.55
1.98
2820
2892
8.146053
TGGATATATCACATCCGGTAAAATCT
57.854
34.615
14.60
0.00
44.27
2.40
2853
2925
4.619760
TGAGTTAGTACGTCAATTGCTTCG
59.380
41.667
0.00
8.10
0.00
3.79
2964
3036
1.891150
CCATCAAGCTGGCACTTCTTT
59.109
47.619
0.00
0.00
0.00
2.52
3022
3094
4.627611
ATTTTGACTCGATGCCAAGATG
57.372
40.909
0.00
0.00
0.00
2.90
3138
3210
7.403671
CATGAAGATCCCTCATATCCTTCAAT
58.596
38.462
0.00
0.00
34.06
2.57
3152
3224
2.744352
AAGAAGCCCATGAAGATCCC
57.256
50.000
0.00
0.00
0.00
3.85
3216
3288
3.549070
GCTTATTTGCCAATTGAGCTTCG
59.451
43.478
7.12
0.00
31.99
3.79
3451
3523
1.621672
CCCAGAGGAGGAAGCCACTC
61.622
65.000
0.00
0.00
33.47
3.51
4049
4121
1.064017
ACCTTGAACCAACTGGCAAGA
60.064
47.619
14.32
0.00
37.43
3.02
4256
4328
1.202879
TCGGCAATGACTGAAACCCTT
60.203
47.619
0.00
0.00
0.00
3.95
4320
4392
1.613925
CCTTCAGTCAACCTCGAGTCA
59.386
52.381
12.31
0.00
0.00
3.41
4416
4488
3.057456
ACCGTGCAACAAACTAACACAAA
60.057
39.130
0.00
0.00
35.74
2.83
4426
4498
3.472652
AGAGAACATACCGTGCAACAAA
58.527
40.909
0.00
0.00
35.74
2.83
4664
4861
6.541111
AAAGATTCGAAGTAAACACAGGAC
57.459
37.500
3.35
0.00
0.00
3.85
4665
4862
7.384115
CAGTAAAGATTCGAAGTAAACACAGGA
59.616
37.037
3.35
0.00
0.00
3.86
4744
4941
3.068307
CCCAAGACAGTAATCCTAGTCGG
59.932
52.174
0.00
0.00
36.18
4.79
4801
4998
3.818773
CACGGAGGTAAAACAACAATCCT
59.181
43.478
0.00
0.00
0.00
3.24
4974
5205
2.983898
GGGGATAAACTGGGGCATACTA
59.016
50.000
0.00
0.00
0.00
1.82
4995
5226
2.854777
CAGCTATCGAAGACCAAAGACG
59.145
50.000
0.00
0.00
42.51
4.18
5187
5419
2.181954
TTGCATTGCCAAATGGAACC
57.818
45.000
6.12
0.00
45.73
3.62
5310
5542
4.159321
CAGAGGTGAGCAGAAGATGAACTA
59.841
45.833
0.00
0.00
0.00
2.24
5342
5574
1.390123
CGACACACAAACTATCGGCAG
59.610
52.381
0.00
0.00
0.00
4.85
5345
5577
4.032445
CCATAACGACACACAAACTATCGG
59.968
45.833
0.00
0.00
37.11
4.18
5346
5578
4.860352
TCCATAACGACACACAAACTATCG
59.140
41.667
0.00
0.00
38.71
2.92
5347
5579
5.220416
GCTCCATAACGACACACAAACTATC
60.220
44.000
0.00
0.00
0.00
2.08
5348
5580
4.630069
GCTCCATAACGACACACAAACTAT
59.370
41.667
0.00
0.00
0.00
2.12
5349
5581
3.991773
GCTCCATAACGACACACAAACTA
59.008
43.478
0.00
0.00
0.00
2.24
5350
5582
2.806244
GCTCCATAACGACACACAAACT
59.194
45.455
0.00
0.00
0.00
2.66
5351
5583
2.095919
GGCTCCATAACGACACACAAAC
60.096
50.000
0.00
0.00
0.00
2.93
5352
5584
2.147958
GGCTCCATAACGACACACAAA
58.852
47.619
0.00
0.00
0.00
2.83
5353
5585
1.070914
TGGCTCCATAACGACACACAA
59.929
47.619
0.00
0.00
0.00
3.33
5354
5586
0.682292
TGGCTCCATAACGACACACA
59.318
50.000
0.00
0.00
0.00
3.72
5355
5587
1.803334
TTGGCTCCATAACGACACAC
58.197
50.000
0.00
0.00
0.00
3.82
5356
5588
2.779755
ATTGGCTCCATAACGACACA
57.220
45.000
0.00
0.00
0.00
3.72
5357
5589
4.449068
CAGATATTGGCTCCATAACGACAC
59.551
45.833
0.00
0.00
0.00
3.67
5358
5590
4.503123
CCAGATATTGGCTCCATAACGACA
60.503
45.833
0.00
0.00
40.87
4.35
5359
5591
3.997021
CCAGATATTGGCTCCATAACGAC
59.003
47.826
0.00
0.00
40.87
4.34
5360
5592
4.271696
CCAGATATTGGCTCCATAACGA
57.728
45.455
0.00
0.00
40.87
3.85
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.