Locus 4455

Sequence ID 3L_DroMel_CAF1
Location 12,954,149 – 12,954,308
Length 159
Max. P 0.999700
window6934 window6935 window6936

overview

Window 4

Location 12,954,149 – 12,954,268
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.12
Mean single sequence MFE -18.76
Consensus MFE -18.70
Energy contribution -18.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 1.00
SVM decision value 2.22
SVM RNA-class probability 0.990640
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12954149 119 - 23771897
CCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUUUUUUUU-UUUUUAGCUCUCUUUUACAAUGUUACCUUCUUCUUUUG
....(((((.......)))))..(((((((.(...((((((((.........))))))))..).)))))))..........-...................................... ( -18.70)
>DroSec_CAF1 71362 118 - 1
CCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUUUUUUU--UUUUUAGCUCUCUUUUACAAUGUUACCUUCUUCUUUUG
....(((((.......)))))..(((((((.(...((((((((.........))))))))..).))))))).........--...................................... ( -18.70)
>DroSim_CAF1 76192 120 - 1
CCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUUUUUUUUCUUUUUAGCUCUCUUUUACAAUGUUACCUUCUUCUUUUG
....(((((.......)))))..(((((((.(...((((((((.........))))))))..).)))))))................................................. ( -18.70)
>DroEre_CAF1 77436 112 - 1
CCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUU--------UUUUAGCUCUCUUUUACAAUGUUACCUUCUUCUUUUG
....(((((.........((((.(((((((.(...((((((((.........))))))))..).)))))))....--------...))))...........))))).............. ( -18.85)
>DroYak_CAF1 75250 112 - 1
CCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUU--------UUUUAGCUCUCUUUUACAAUGUUACCUUCUUCUUUUG
....(((((.........((((.(((((((.(...((((((((.........))))))))..).)))))))....--------...))))...........))))).............. ( -18.85)
>consensus
CCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUUUUUUU__UUUUUAGCUCUCUUUUACAAUGUUACCUUCUUCUUUUG
....(((((.......)))))..(((((((.(...((((((((.........))))))))..).)))))))................................................. (-18.70 = -18.70 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 12,954,188 – 12,954,308
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.31
Mean single sequence MFE -28.62
Consensus MFE -27.36
Energy contribution -27.76
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.96
SVM decision value 3.91
SVM RNA-class probability 0.999700
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12954188 120 + 23771897
AAAAAAAAAUUACUUAUCUGCGAGCCAAAAUGAUUUAUUGGCCCAAAUGGCAAGCAAAUAGCAUUAAAAGCAUGCUGGGGCCACGACCGAAGGGUUUUCCUUGCAUAAAUUACCCCACCA
..................((((((..............((((((....((((.((..............)).)))).)))))).((((....))))...))))))............... ( -29.04)
>DroSec_CAF1 71400 120 + 1
AAAAAAAAAUUACUUAUCUGCGAGCCAAAAUGAUUUAUUGGCCCAAAUGGCAAGCAAAUAGCAUUAAAAGCAUGCUGGGGCCACGACCGAAUGGUUUUCCUUGCAUAAAUUACCCCACCA
..................((((((..(((((.((((..((((((....((((.((..............)).)))).)))))).....)))).))))).))))))............... ( -26.94)
>DroSim_CAF1 76232 120 + 1
AAAAAAAAAUUACUUAUCUGCGAGCCAAAAUGAUUUAUUGGCCCAAAUGGCAAGCAAAUAGCAUUAAAAGCAUGCUGGGGCCACGACCGAAGGGUUUUCCUUGCAUAAAUUACCCCACCA
..................((((((..............((((((....((((.((..............)).)))).)))))).((((....))))...))))))............... ( -29.04)
>DroEre_CAF1 77473 114 + 1
-----AAAAUUACUUAUCUGCGAGCCAAAAUGAUUUAUUGGCCCAAAUGGCAAGCAAAUAGCAUUAAAAGCAUGCUGGGGCCACGACCGAAGGGU-UUCCUUGCAUAAAUUACCCCACCA
-----.............((((((..............((((((....((((.((..............)).)))).)))))).((((....)))-)..))))))............... ( -29.04)
>DroYak_CAF1 75287 114 + 1
-----AAAAUUACUUAUCUGCGAGCCAAAAUGAUUUAUUGGCCCAAAUGGCAAGCAAAUAGCAUUAAAAGCAUGCUGGGGCCACGACCGAAGGGU-UUCCUUGCAUAAAUUACCCCACAA
-----.............((((((..............((((((....((((.((..............)).)))).)))))).((((....)))-)..))))))............... ( -29.04)
>consensus
AAAAAAAAAUUACUUAUCUGCGAGCCAAAAUGAUUUAUUGGCCCAAAUGGCAAGCAAAUAGCAUUAAAAGCAUGCUGGGGCCACGACCGAAGGGUUUUCCUUGCAUAAAUUACCCCACCA
..................((((((..............((((((....((((.((..............)).)))).)))))).((((....))))...))))))............... (-27.36 = -27.76 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 12,954,188 – 12,954,308
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.31
Mean single sequence MFE -33.26
Consensus MFE -31.86
Energy contribution -32.26
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.96
SVM decision value 2.76
SVM RNA-class probability 0.996845
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12954188 120 - 23771897
UGGUGGGGUAAUUUAUGCAAGGAAAACCCUUCGGUCGUGGCCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUUUUUUU
((.((((((......((.((((.....))))))......)))))).)).........((((((((((..((((..(((.........)))...))))..)))))).)))).......... ( -34.30)
>DroSec_CAF1 71400 120 - 1
UGGUGGGGUAAUUUAUGCAAGGAAAACCAUUCGGUCGUGGCCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUUUUUUU
((.((((((......((...((....))...))......)))))).)).........((((((((((..((((..(((.........)))...))))..)))))).)))).......... ( -30.30)
>DroSim_CAF1 76232 120 - 1
UGGUGGGGUAAUUUAUGCAAGGAAAACCCUUCGGUCGUGGCCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUUUUUUU
((.((((((......((.((((.....))))))......)))))).)).........((((((((((..((((..(((.........)))...))))..)))))).)))).......... ( -34.30)
>DroEre_CAF1 77473 114 - 1
UGGUGGGGUAAUUUAUGCAAGGAA-ACCCUUCGGUCGUGGCCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUU-----
((.((((((......((.((((..-..))))))......)))))).)).........((((((((((..((((..(((.........)))...))))..)))))).)))).....----- ( -34.30)
>DroYak_CAF1 75287 114 - 1
UUGUGGGGUAAUUUAUGCAAGGAA-ACCCUUCGGUCGUGGCCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUU-----
...((((((......((.((((..-..))))))......))))))((((.......))))(((((((..((((..(((.........)))...))))..))))))).........----- ( -33.10)
>consensus
UGGUGGGGUAAUUUAUGCAAGGAAAACCCUUCGGUCGUGGCCCCAGCAUGCUUUUAAUGCUAUUUGCUUGCCAUUUGGGCCAAUAAAUCAUUUUGGCUCGCAGAUAAGUAAUUUUUUUUU
((.((((((......((.((((.....))))))......)))))).)).........((((((((((..((((..(((.........)))...))))..)))))).)))).......... (-31.86 = -32.26 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:32 2006