Locus 4489

Sequence ID	3L_DroMel_CAF1
Location	12,976,714 – 12,976,858
Length	144
Max. P	0.999254

overview

Window 5

Location	12,976,714 – 12,976,818
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.75
Mean single sequence MFE	-29.88
Consensus MFE	-28.56
Energy contribution	-28.44
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.98
Structure conservation index	0.96
SVM decision value	3.38
SVM RNA-class probability	0.999121
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12976714 104 + 23771897
----------------GUGUUUGAUGGCAUUCGAUUGGCAUUUUCAAUGUAUAUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCG
----------------.((...((((.((......)).))))..))..(((((((((((.((....((((((.(((..(((((......))))))))))))))..)))))))))).))). ( -29.00)
>DroSec_CAF1 94029 104 + 1
----------------GUGUUUGAUGGCAUUCGAUUGGCAUUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCA
----------------.((...((((.((......)).))))..)).((((((((((((.((....((((((.(((..(((((......))))))))))))))..)))))))))).)))) ( -29.20)
>DroSim_CAF1 103728 104 + 1
----------------GUGUUUGAUGGCAUUCGAUUGGCAUUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCA
----------------.((...((((.((......)).))))..)).((((((((((((.((....((((((.(((..(((((......))))))))))))))..)))))))))).)))) ( -29.20)
>DroEre_CAF1 99804 120 + 1
GCUUGUGUUUGUGCUUGUGUUUGAUGGCAUUCGAUUGGCAUUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCA
((..((((..(((((((((...((((.((......)).))))..))(((((.((.....)))))))((((((.(((..(((((......)))))))))))))))))))))..)))).)). ( -33.70)
>DroYak_CAF1 98033 102 + 1
------------------GUUUGAUGGCAUUCGAUUGGCAUUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCA
------------------(...((((.((......)).))))..)..((((((((((((.((....((((((.(((..(((((......))))))))))))))..)))))))))).)))) ( -28.30)
>consensus
________________GUGUUUGAUGGCAUUCGAUUGGCAUUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCA
.................((...((((.((......)).))))..)).((((((((((((.((....((((((.(((..(((((......))))))))))))))..)))))))))).)))) (-28.56 = -28.44 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	12,976,714 – 12,976,818
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.75
Mean single sequence MFE	-19.80
Consensus MFE	-19.16
Energy contribution	-19.16
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.97
SVM decision value	2.13
SVM RNA-class probability	0.988594
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12976714 104 - 23771897
CGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUAUAUACAUUGAAAAUGCCAAUCGAAUGCCAUCAAACAC----------------
.(((((((((.(((...((((((((((((((......))))..)))).))))))..))).....))))))..((((.......))))....)))..........---------------- ( -20.70)
>DroSec_CAF1 94029 104 - 1
UGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAAUGCCAAUCGAAUGCCAUCAAACAC----------------
.(((.......(((...((((((((((((((......))))..)))).))))))..))).............((((.......))))....)))..........---------------- ( -19.10)
>DroSim_CAF1 103728 104 - 1
UGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAAUGCCAAUCGAAUGCCAUCAAACAC----------------
.(((.......(((...((((((((((((((......))))..)))).))))))..))).............((((.......))))....)))..........---------------- ( -19.10)
>DroEre_CAF1 99804 120 - 1
UGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAAUGCCAAUCGAAUGCCAUCAAACACAAGCACAAACACAAGC
...........(((((.((((((((((((((......))))..)))).)))))).............(((.(((((.......)))).).)))...........)))))........... ( -21.00)
>DroYak_CAF1 98033 102 - 1
UGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAAUGCCAAUCGAAUGCCAUCAAAC------------------
.(((.......(((...((((((((((((((......))))..)))).))))))..))).............((((.......))))....)))........------------------ ( -19.10)
>consensus
UGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAAUGCCAAUCGAAUGCCAUCAAACAC________________
.(((.......(((...((((((((((((((......))))..)))).))))))..))).............((((.......))))....))).......................... (-19.16 = -19.16 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	12,976,738 – 12,976,858
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-29.83
Consensus MFE	-29.85
Energy contribution	-29.53
Covariance contribution	-0.32
Combinations/Pair	1.06
Mean z-score	-2.07
Structure conservation index	1.00
SVM decision value	3.22
SVM RNA-class probability	0.998773
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12976738 120 + 23771897
UUUUCAAUGUAUAUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCGCAUAAUUACAUCCGCACAUGCCCACGAUGCCGUCUAAAAA
........((((....((((..((((((((((((...((((((((((..((((.................))))..)))).)))))).))))).))))))))))).)))).......... ( -30.73)
>DroSec_CAF1 94053 120 + 1
UUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCACAUAAUUACAUCCGCACAUGCCCACGAUGCCGUCUAUAAA
...........((((..((((.((((((((((((...((((((((((..((((.................))))..)))).)))))).))))).))))))).......))))..)))).. ( -30.23)
>DroSim_CAF1 103752 120 + 1
UUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCACAUAAUUACAUCCGCACAUGCCCACGAUGCCGUCUAUAAA
...........((((..((((.((((((((((((...((((((((((..((((.................))))..)))).)))))).))))).))))))).......))))..)))).. ( -30.23)
>DroEre_CAF1 99844 120 + 1
UUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCACAUAAUUACAUCCACACAUGCCCACGAUGCCGUCUAUAAA
...........((((..((((.((((((((((((...((((((((((..((((.................))))..)))).)))))).))))).))))))).......))))..)))).. ( -30.23)
>DroYak_CAF1 98055 120 + 1
UUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCACAUAAUUACAUUCACACAUGCCCACGAUGCCGUCUAUAAA
...........((((..((((....(((((((((((.((((((((((..((((.................))))..)))).))))))...))))).....))))))..))))..)))).. ( -27.73)
>consensus
UUUUCAAUGUAUGUAAGUGGCUGCGUGUGGGGUGAAAAGUUAUUGCAUCAUAAUUUCCCCCACUAAGCAUUUAUAUUGCACAUAAUUACAUCCGCACAUGCCCACGAUGCCGUCUAUAAA
........((((....((((..((((((((((((...((((((((((..((((.................))))..)))).)))))).))))).))))))))))).)))).......... (-29.85 = -29.53 +  -0.32)

alignment

secondary structure

dotplot

Window 8

Location	12,976,738 – 12,976,858
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-32.82
Consensus MFE	-32.56
Energy contribution	-32.16
Covariance contribution	-0.40
Combinations/Pair	1.06
Mean z-score	-2.19
Structure conservation index	0.99
SVM decision value	3.46
SVM RNA-class probability	0.999254
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12976738 120 - 23771897
UUUUUAGACGGCAUCGUGGGCAUGUGCGGAUGUAAUUAUGCGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUAUAUACAUUGAAAA
.........(((..(((((((((.((((.(((....))).))))......)))))).((((((((((((((......))))..)))).)))))))))..))).................. ( -34.90)
>DroSec_CAF1 94053 120 - 1
UUUAUAGACGGCAUCGUGGGCAUGUGCGGAUGUAAUUAUGUGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAA
.........(((..(((((((((.((((.(((....))).))))......)))))).((((((((((((((......))))..)))).)))))))))..))).................. ( -33.30)
>DroSim_CAF1 103752 120 - 1
UUUAUAGACGGCAUCGUGGGCAUGUGCGGAUGUAAUUAUGUGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAA
.........(((..(((((((((.((((.(((....))).))))......)))))).((((((((((((((......))))..)))).)))))))))..))).................. ( -33.30)
>DroEre_CAF1 99844 120 - 1
UUUAUAGACGGCAUCGUGGGCAUGUGUGGAUGUAAUUAUGUGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAA
.........(((..(((((((((.((((..((((......)))).)))).)))))).((((((((((((((......))))..)))).)))))))))..))).................. ( -32.00)
>DroYak_CAF1 98055 120 - 1
UUUAUAGACGGCAUCGUGGGCAUGUGUGAAUGUAAUUAUGUGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAA
.........(((..(((((((((.((((..((((......)))).)))).)))))).((((((((((((((......))))..)))).)))))))))..))).................. ( -30.60)
>consensus
UUUAUAGACGGCAUCGUGGGCAUGUGCGGAUGUAAUUAUGUGCAAUAUAAAUGCUUAGUGGGGGAAAUUAUGAUGCAAUAACUUUUCACCCCACACGCAGCCACUUACAUACAUUGAAAA
.........(((..(((((((((.((((.(((....))).))))......)))))).((((((((((((((......))))..)))).)))))))))..))).................. (-32.56 = -32.16 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:43 2006