Locus 648

Sequence ID 3R_DroMel_CAF1
Location 2,396,959 – 2,397,096
Length 137
Max. P 0.990993
window1025 window1026 window1027 window1028

overview

Window 5

Location 2,396,959 – 2,397,062
Length 103
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 93.45
Mean single sequence MFE -27.84
Consensus MFE -22.24
Energy contribution -21.96
Covariance contribution -0.28
Combinations/Pair 1.12
Mean z-score -1.46
Structure conservation index 0.80
SVM decision value 0.06
SVM RNA-class probability 0.561259
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2396959 103 + 27905053
UCGCGUGCACAUUACUUUGCUCACUUGUGUGCUUAGCCUGCUUACC--GCACUGGCGUCCUGGCCAUGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUAUUUA
..(((.(((((..............)))))((((((..(((.....--)))...(((((.(((.((....)).))))))))..))))))......)))....... ( -25.04)
>DroSec_CAF1 110186 103 + 1
CCGCCUGCACAUUACUUUGCUCAUUUGUGUGCUUAGCCUGCUCAGC--GCACUGGCGUCCUGGCCAUGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUGUUUA
.((((.(((........)))......(((((((.((....)).)))--)))).))))..((((.((....)).))))..((((.((.....)).))))....... ( -27.60)
>DroSim_CAF1 102228 103 + 1
CCGCCUGCACAUUACUUUGCUCAUUUGUGUGCUUAGCCUGCUCAGC--GCACUGGCGUCCUGGCCAUGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUGUUUA
.((((.(((........)))......(((((((.((....)).)))--)))).))))..((((.((....)).))))..((((.((.....)).))))....... ( -27.60)
>DroEre_CAF1 103675 103 + 1
CCGCCUGCACAUUACUUUGCUCAUUUGUGUGCUUAGCCUGCUCAGC--GCACUGGCGUUCUGGCCAGGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUGUUUA
.((((.(((........)))......(((((((.((....)).)))--)))).)))).(((((.(......).))))).((((.((.....)).))))....... ( -27.70)
>DroYak_CAF1 98070 105 + 1
CUGCCUGCAUAUUACUUUGCUCAUUUGUGCGCUUAGCCUGCUCAGUGUGCACUGGCGUUUUGGCCAGGUUUGCACAGAUGCAACUAAGCUUUAUUUGCCUGUUUA
..((..(((((..............)))))((((((..(((((..(((((((((((......)))))...)))))))).))).)))))).......))....... ( -31.24)
>consensus
CCGCCUGCACAUUACUUUGCUCAUUUGUGUGCUUAGCCUGCUCAGC__GCACUGGCGUCCUGGCCAUGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUGUUUA
..((..(((((..............)))))((((((..(((.......)))...((((.((((.((....)).))))))))..)))))).......))....... (-22.24 = -21.96 +  -0.28) 

alignment

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secondary structure

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dotplot

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Window 6

Location 2,396,959 – 2,397,062
Length 103
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 93.45
Mean single sequence MFE -32.72
Consensus MFE -26.08
Energy contribution -26.48
Covariance contribution 0.40
Combinations/Pair 1.07
Mean z-score -2.83
Structure conservation index 0.80
SVM decision value 2.24
SVM RNA-class probability 0.990993
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2396959 103 - 27905053
UAAAUAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACAUGGCCAGGACGCCAGUGC--GGUAAGCAGGCUAAGCACACAAGUGAGCAAAGUAAUGUGCACGCGA
.......((.......((((((((((.(((((.((....)).))))).(((....))--)....))).)))))))......(((.(((......))).))))).. ( -32.20)
>DroSec_CAF1 110186 103 - 1
UAAACAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACAUGGCCAGGACGCCAGUGC--GCUGAGCAGGCUAAGCACACAAAUGAGCAAAGUAAUGUGCAGGCGG
..(((((((.......)))).)))...(((((.((....)).))))).((((.(((.--(((.((....)).))).)))......(((.(....).))).)))). ( -32.30)
>DroSim_CAF1 102228 103 - 1
UAAACAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACAUGGCCAGGACGCCAGUGC--GCUGAGCAGGCUAAGCACACAAAUGAGCAAAGUAAUGUGCAGGCGG
..(((((((.......)))).)))...(((((.((....)).))))).((((.(((.--(((.((....)).))).)))......(((.(....).))).)))). ( -32.30)
>DroEre_CAF1 103675 103 - 1
UAAACAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACCUGGCCAGAACGCCAGUGC--GCUGAGCAGGCUAAGCACACAAAUGAGCAAAGUAAUGUGCAGGCGG
..(((((((.......)))).)))...(((((.((....)).))))).((((.(((.--(((.((....)).))).)))......(((.(....).))).)))). ( -33.40)
>DroYak_CAF1 98070 105 - 1
UAAACAGGCAAAUAAAGCUUAGUUGCAUCUGUGCAAACCUGGCCAAAACGCCAGUGCACACUGAGCAGGCUAAGCGCACAAAUGAGCAAAGUAAUAUGCAGGCAG
.......((.......((((((((((.((((((((...(((((......)))))))))))..))))).)))))))..........(((.(....).)))..)).. ( -33.40)
>consensus
UAAACAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACAUGGCCAGGACGCCAGUGC__GCUGAGCAGGCUAAGCACACAAAUGAGCAAAGUAAUGUGCAGGCGG
.......((.......((((((((...(((((.((....)).)))))..((((((....)))).)).))))))))..........(((.(....).)))..)).. (-26.08 = -26.48 +   0.40) 

alignment

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secondary structure

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dotplot

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Window 7

Location 2,396,997 – 2,397,096
Length 99
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 91.78
Mean single sequence MFE -29.82
Consensus MFE -24.98
Energy contribution -24.94
Covariance contribution -0.04
Combinations/Pair 1.10
Mean z-score -1.30
Structure conservation index 0.84
SVM decision value 0.08
SVM RNA-class probability 0.574376
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2396997 99 + 27905053
UGCUUACC--GCACUGGCGUCCUGGCCAUGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUAUUUACCCCGGUACGGAAAAUAGAGAUCAAGUCAACUGC
(((.....--)))...(((((.(((.((....)).)))))))).(((...((((((((.((....(((....))).)).))))))))....)))....... ( -21.60)
>DroSec_CAF1 110224 99 + 1
UGCUCAGC--GCACUGGCGUCCUGGCCAUGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUGUUUACCACGGCACGGCAAAUAGAGAUCAAGUCAACUGC
....(((.--..(((.(((((.(((.((....)).)))))))).......(((((((((((((((......)))).)))))))))))....)))...))). ( -29.80)
>DroSim_CAF1 102266 99 + 1
UGCUCAGC--GCACUGGCGUCCUGGCCAUGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUGUUUACCCCGGCACGGCAAAUAGAGAUCAAGUCAACUGC
....(((.--..(((.(((((.(((.((....)).)))))))).......(((((((((((((((......)))).)))))))))))....)))...))). ( -29.80)
>DroEre_CAF1 103713 99 + 1
UGCUCAGC--GCACUGGCGUUCUGGCCAGGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUGUUUACCCUGGCAGCGCAAAUAGGGAUCCAGUCAACUGC
....(((.--..((((((((.((((.(......).)))))))).......(((((((((((((((......))))).))))))))))...))))...))). ( -31.70)
>DroYak_CAF1 98108 101 + 1
UGCUCAGUGUGCACUGGCGUUUUGGCCAGGUUUGCACAGAUGCAACUAAGCUUUAUUUGCCUGUUUACCCUGGCACGGCAAAUAGAGAUCAAGUCAAGUGC
(((((..(((((((((((......)))))...)))))))).)))(((...(((((((((((((((......)))).)))))))))))....)))....... ( -36.20)
>consensus
UGCUCAGC__GCACUGGCGUCCUGGCCAUGUUUGCCCAGAUGCAACUAAGCUUUAUUUGCCUGUUUACCCCGGCACGGCAAAUAGAGAUCAAGUCAACUGC
..........(((...((((.((((.((....)).)))))))).(((...(((((((((((((((......)))).)))))))))))....)))....))) (-24.98 = -24.94 +  -0.04) 

alignment

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secondary structure

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dotplot

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Window 8

Location 2,396,997 – 2,397,096
Length 99
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 91.78
Mean single sequence MFE -31.88
Consensus MFE -25.64
Energy contribution -25.76
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -1.50
Structure conservation index 0.80
SVM decision value 0.30
SVM RNA-class probability 0.680429
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2396997 99 - 27905053
GCAGUUGACUUGAUCUCUAUUUUCCGUACCGGGGUAAAUAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACAUGGCCAGGACGCCAGUGC--GGUAAGCA
((((....)).............((((((.((.((((.(((((.......))))).)))).(((((.((....)).)))))...)).))))--))...)). ( -28.50)
>DroSec_CAF1 110224 99 - 1
GCAGUUGACUUGAUCUCUAUUUGCCGUGCCGUGGUAAACAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACAUGGCCAGGACGCCAGUGC--GCUGAGCA
.................((((((((.(((....)))....))))))))..(((((((.((.(((((.((....)).)))))((....))))--))))))). ( -32.70)
>DroSim_CAF1 102266 99 - 1
GCAGUUGACUUGAUCUCUAUUUGCCGUGCCGGGGUAAACAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACAUGGCCAGGACGCCAGUGC--GCUGAGCA
.................((((((((.(((....)))....))))))))..(((((((.((.(((((.((....)).)))))((....))))--))))))). ( -32.70)
>DroEre_CAF1 103713 99 - 1
GCAGUUGACUGGAUCCCUAUUUGCGCUGCCAGGGUAAACAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACCUGGCCAGAACGCCAGUGC--GCUGAGCA
.(((....)))......(((((((.(((..........))))))))))..(((((((.((.(((((.((....)).)))))((....))))--))))))). ( -31.70)
>DroYak_CAF1 98108 101 - 1
GCACUUGACUUGAUCUCUAUUUGCCGUGCCAGGGUAAACAGGCAAAUAAAGCUUAGUUGCAUCUGUGCAAACCUGGCCAAAACGCCAGUGCACACUGAGCA
.................((((((((.(((....)))....))))))))..(((((((.......(((((...(((((......))))))))))))))))). ( -33.81)
>consensus
GCAGUUGACUUGAUCUCUAUUUGCCGUGCCGGGGUAAACAGGCAAAUAAAGCUUAGUUGCAUCUGGGCAAACAUGGCCAGGACGCCAGUGC__GCUGAGCA
.................((((((((.(((....)))....))))))))..((((((((((......))).((.((((......))))))....))))))). (-25.64 = -25.76 +   0.12) 

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 09:48:20 2006