Locus 3861

Sequence ID 3R_DroMel_CAF1
Location 10,511,833 – 10,512,015
Length 182
Max. P 0.989928
window6182 window6183 window6184

overview

Window 2

Location 10,511,833 – 10,511,948
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 82.65
Mean single sequence MFE -25.84
Consensus MFE -20.44
Energy contribution -20.08
Covariance contribution -0.36
Combinations/Pair 1.12
Mean z-score -1.73
Structure conservation index 0.79
SVM decision value 0.49
SVM RNA-class probability 0.754940
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10511833 115 + 27905053
AAGCAAAUUUGAUCUGGGCUCGAGAAAUUCAUAGUAAAUGUAUGUAGAUACAUUCAUAUGUAUGUAUGUGUACCUGCGAGAUGCUAAACUUGCAUCUUGUAUCCGUUUGGUUUGC
..((((((..(((..(((......................((((((.((((((....)))))).))))))....((((((((((.......))))))))))))))))..)))))) ( -30.00)
>DroSec_CAF1 160442 93 + 1
AAGCAAAUUUGAUCUGGGCUCGAGAAAUUCAUAGUAAAUUUAUGUA----------------------UAUACCUGCAAGAUGAUAAACUUGCAUCUUGUAUCCGUUUGGUUUGC
..((((((..(((..(((..(((((....(((((.....)))))..----------------------......((((((........)))))))))))..))))))..)))))) ( -22.10)
>DroSim_CAF1 58314 91 + 1
AAGCAAAUUUGAUCUGGGCUCGAGAAAUUCAUAGUAAAUGU--GUG----------------------UAUACCUGCAAGAUGAUAAACUUGCAUCUUGUAUCCGUUUGGUUUGC
..((((((..(((..(((..(((((.((.((((.....)))--).)----------------------).....((((((........)))))))))))..))))))..)))))) ( -21.60)
>DroEre_CAF1 58671 107 + 1
AAGCAAAUUUGAUCUGGGCUCGAGAAACUCACAGUAAAUGUAUGUC--------CAUAUGUACGUGUAUGUACCUGCGAGAUGAUAAACUUGCAUCUUGUAUCCGUUGGGUUUGC
..(((((((..((..(((..(((((.....(((....((((((((.--------...))))))))...)))...((((((........)))))))))))..)))))..))))))) ( -29.60)
>DroYak_CAF1 58809 101 + 1
AAGCAAAUUUGAUCUGGGCUCGAGAAACUCACAGUAAAUGUAUCUA--------UAUAUGCAC------AUACCUGCGAGAUGAUAAACUUGCAUCUCGUAUCCGUUUGGUUUGC
..((((((..(((..(((..(((((........(((..(((((...--------...))))).------.))).((((((........)))))))))))..))))))..)))))) ( -25.90)
>consensus
AAGCAAAUUUGAUCUGGGCUCGAGAAAUUCAUAGUAAAUGUAUGUA_________AUAUG_A______UAUACCUGCGAGAUGAUAAACUUGCAUCUUGUAUCCGUUUGGUUUGC
..((((((..(((..(((..(((((.....(((.....))).................................((((((........)))))))))))..))))))..)))))) (-20.44 = -20.08 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,511,868 – 10,511,979
Length 111
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 78.80
Mean single sequence MFE -25.23
Consensus MFE -18.06
Energy contribution -16.86
Covariance contribution -1.20
Combinations/Pair 1.32
Mean z-score -1.43
Structure conservation index 0.72
SVM decision value 0.09
SVM RNA-class probability 0.579536
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10511868 111 + 27905053
AAAUGUAUGUAGAUACAUUCAUAUGUAUGUAUGUGUACCUGCGAGAUGCUAAACUUGCAUCUUGUAUCCGUUUGGUUUGCUCUUAUCUCUGGCCAAU--UGGCUAUGCCAAUG
(((((((((((.((((((....)))))).))))))....((((((((((.......))))))))))..)))))((((.............)))).((--((((...)))))). ( -30.82)
>DroSec_CAF1 160477 91 + 1
AAAUUUAUGUA----------------------UAUACCUGCAAGAUGAUAAACUUGCAUCUUGUAUCCGUUUGGUUUGCUCUUAUCUCUGGCCAAGUAUGGCUAUGCCAUUG
........(((----------------------...((((((((((((.........))))))))).......))).))).........((((((....))))))........ ( -18.31)
>DroSim_CAF1 58349 89 + 1
AAAUGU--GUG----------------------UAUACCUGCAAGAUGAUAAACUUGCAUCUUGUAUCCGUUUGGUUUGCUCUUAUCUCUGGCCAAGUAUGGCUACGUCAUUG
.(((((--(((----------------------((.((((((((((((.........))))))))).......))).)))..........(((((....)))))))).)))). ( -21.41)
>DroEre_CAF1 58706 103 + 1
AAAUGUAUGUC--------CAUAUGUACGUGUAUGUACCUGCGAGAUGAUAAACUUGCAUCUUGUAUCCGUUGGGUUUGCUCUUAUCUCUGGCCAAG--UGGCCAUGCCUGUG
....(((..((--------((...(((((....))))).(((((((((.........))))))))).....))))..))).........(((((...--.)))))........ ( -26.30)
>DroYak_CAF1 58844 97 + 1
AAAUGUAUCUA--------UAUAUGCAC------AUACCUGCGAGAUGAUAAACUUGCAUCUCGUAUCCGUUUGGUUUGCUCUUAUCGCUGGCCAAG--UGGCUGUGCCAGUG
...........--------.....((((------(....(((((((((.........))))))))).(((((((((..((.......))..))))))--))).)))))..... ( -29.30)
>consensus
AAAUGUAUGUA_________AUAUG_A______UAUACCUGCGAGAUGAUAAACUUGCAUCUUGUAUCCGUUUGGUUUGCUCUUAUCUCUGGCCAAG__UGGCUAUGCCAGUG
.......................................(((((((((.........)))))))))......((((.............((((((....)))))).))))... (-18.06 = -16.86 +  -1.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,511,908 – 10,512,015
Length 107
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 91.88
Mean single sequence MFE -32.01
Consensus MFE -27.58
Energy contribution -27.06
Covariance contribution -0.52
Combinations/Pair 1.22
Mean z-score -2.02
Structure conservation index 0.86
SVM decision value 2.19
SVM RNA-class probability 0.989928
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10511908 107 + 27905053
GCGAGAUGCUAAACUUGCAUCUUGUAUCCGUUUGGUUUGCUCUUAUCUCUGGCCAAU--UGGCUAUGCCAAUGGGUUUGCCGAAGGACGCAUAAAUUAACACCCCUUAA
(((((((((.......))))))))).(((.((((((..((((.......(((((...--.))))).......))))..)))))))))...................... ( -34.44)
>DroSec_CAF1 160495 109 + 1
GCAAGAUGAUAAACUUGCAUCUUGUAUCCGUUUGGUUUGCUCUUAUCUCUGGCCAAGUAUGGCUAUGCCAUUGGGUUUGCCGAAGGACGCAUAAAUUAACACCCCUUAA
(((((........)))))....((..(((.((((((..((((.......((((((....)))))).......))))..)))))))))..)).................. ( -31.54)
>DroSim_CAF1 58365 109 + 1
GCAAGAUGAUAAACUUGCAUCUUGUAUCCGUUUGGUUUGCUCUUAUCUCUGGCCAAGUAUGGCUACGUCAUUGGGUUUGCCGAAGGACGCAUAAAUUAACACCCCUUAA
(((((........)))))....((..(((.((((((..((((.......((((((....)))))).......))))..)))))))))..)).................. ( -31.54)
>DroEre_CAF1 58738 107 + 1
GCGAGAUGAUAAACUUGCAUCUUGUAUCCGUUGGGUUUGCUCUUAUCUCUGGCCAAG--UGGCCAUGCCUGUGGGAUAGUCGAAGGACGCAUAAAUUAACACCCCUUAA
((((((((.........))))))))....(((((...(((...(((((((((((...--.))))).......))))))(((....))))))....)))))......... ( -31.81)
>DroYak_CAF1 58870 107 + 1
GCGAGAUGAUAAACUUGCAUCUCGUAUCCGUUUGGUUUGCUCUUAUCGCUGGCCAAG--UGGCUGUGCCAGUGGGAUAAUCGAAGGACGCAUAAAUUAACACCCCUUAA
((((((((.........)))))))).(((.(((((((...(((...(((((((((..--....)).)))))))))).))))))))))...................... ( -30.70)
>consensus
GCGAGAUGAUAAACUUGCAUCUUGUAUCCGUUUGGUUUGCUCUUAUCUCUGGCCAAG__UGGCUAUGCCAGUGGGUUUGCCGAAGGACGCAUAAAUUAACACCCCUUAA
((((((((.........)))))))).(((.((((((..((((.......((((((....)))))).......))))..)))))))))...................... (-27.58 = -27.06 +  -0.52)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:52 2006