Locus 7652

Sequence ID X_DroMel_CAF1
Location 19,065,109 – 19,065,255
Length 146
Max. P 0.993737
window12562 window12563 window12564

overview

Window 2

Location 19,065,109 – 19,065,219
Length 110
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 83.24
Mean single sequence MFE -35.42
Consensus MFE -26.74
Energy contribution -26.10
Covariance contribution -0.64
Combinations/Pair 1.26
Mean z-score -2.18
Structure conservation index 0.75
SVM decision value 1.18
SVM RNA-class probability 0.926587
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19065109 110 + 22224390
GAUGCUGCGGUCGA--------GUGUGUGUGAAAAGGAAGUUGAGGGGAUUGAUUGGUCAGUAGCUG-UUGGCCAAUUGCCUUGGCUAAUUAUCAAUUUUGGACAACUGACCACCGACC
........((((.(--------((.(((.(((((..(((((..(((....(((((((((((......-))))))))))))))..))).....))..))))).))))))))))....... ( -32.40)
>DroSec_CAF1 16825 101 + 1
-------CGGUCGA--------GUGUGUGUGAAAAGGAAGUUGAGGGGA---AUUGGCCAGUAGCUGGUUGGCCAAUUGUCUUGGCUAAUUAUCAAUUUUGGACAACUGACCACCGACC
-------.((((.(--------((.(((.(((((..(((((..(((.((---.((((((((.......)))))))))).)))..))).....))..))))).))))))))))....... ( -33.80)
>DroSim_CAF1 18808 101 + 1
-------CGGUCGA--------GUGUGUGUGAAAAGGAAGUUGAGGGGA---AUUGGCCAGUAGCUGGUUGGCCAAUUGUCUUGGCUAAUUAUCAAUUUCGGACAACUGACCACCGACC
-------.((((.(--------((.(((.(((((..(((((..(((.((---.((((((((.......)))))))))).)))..))).....))..))))).))))))))))....... ( -36.60)
>DroEre_CAF1 17238 105 + 1
AUUGUUGCGGUUGG----------GUGUGUGGAAAGGAAGUUGAGGGGA---GUUGGCCAGUAGCUGG-UGGCCAAUUGCAUGGGCUAAUUAUCAAUUUUGGACAACUGACCACCGACC
...((((.(((..(----------.(((.(..((..((((((.(..(.(---((((((((.(....).-))))))))).).).)))).....))..))..).))).)..)))..)))). ( -32.70)
>DroYak_CAF1 18364 111 + 1
AAUGUUGCGGUCAGUUGUAUGUUUGUGUGCGAAAAGGAAGUUGAGGGGA---GUUGGCCAGUAGCUGG-UGGCCAAUUGCCUUGGCUAAUUAACAAUUUUGGACAACUGACCAAC----
........((((((((((...((((....)))).....(((..(((.((---.(((((((.(....).-))))))))).)))..)))...............))))))))))...---- ( -41.60)
>consensus
__UG_UGCGGUCGA________GUGUGUGUGAAAAGGAAGUUGAGGGGA___AUUGGCCAGUAGCUGGUUGGCCAAUUGCCUUGGCUAAUUAUCAAUUUUGGACAACUGACCACCGACC
........(((((............(((.(((((..(((((..(((.(....(((((((((.......)))))))))).)))..))).....))..))))).)))..)))))....... (-26.74 = -26.10 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,065,109 – 19,065,219
Length 110
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 83.24
Mean single sequence MFE -27.78
Consensus MFE -20.23
Energy contribution -21.31
Covariance contribution 1.08
Combinations/Pair 1.14
Mean z-score -3.08
Structure conservation index 0.73
SVM decision value 2.42
SVM RNA-class probability 0.993737
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19065109 110 - 22224390
GGUCGGUGGUCAGUUGUCCAAAAUUGAUAAUUAGCCAAGGCAAUUGGCCAA-CAGCUACUGACCAAUCAAUCCCCUCAACUUCCUUUUCACACACAC--------UCGACCGCAGCAUC
((((((((((.(((((((.......))))))).(((((.....)))))...-..)))))))))).................................--------.............. ( -25.50)
>DroSec_CAF1 16825 101 - 1
GGUCGGUGGUCAGUUGUCCAAAAUUGAUAAUUAGCCAAGACAAUUGGCCAACCAGCUACUGGCCAAU---UCCCCUCAACUUCCUUUUCACACACAC--------UCGACCG-------
(((((((((..(((((((.......)))))))..)))....(((((((((.........))))))))---)..........................--------)))))).------- ( -29.70)
>DroSim_CAF1 18808 101 - 1
GGUCGGUGGUCAGUUGUCCGAAAUUGAUAAUUAGCCAAGACAAUUGGCCAACCAGCUACUGGCCAAU---UCCCCUCAACUUCCUUUUCACACACAC--------UCGACCG-------
(((((((((..(((((((.......)))))))..)))....(((((((((.........))))))))---)..........................--------)))))).------- ( -29.70)
>DroEre_CAF1 17238 105 - 1
GGUCGGUGGUCAGUUGUCCAAAAUUGAUAAUUAGCCCAUGCAAUUGGCCA-CCAGCUACUGGCCAAC---UCCCCUCAACUUCCUUUCCACACAC----------CCAACCGCAACAAU
(((.(((((((((((......))))))).....((....))..(((((((-........))))))).---......................)))----------)..)))........ ( -24.50)
>DroYak_CAF1 18364 111 - 1
----GUUGGUCAGUUGUCCAAAAUUGUUAAUUAGCCAAGGCAAUUGGCCA-CCAGCUACUGGCCAAC---UCCCCUCAACUUCCUUUUCGCACACAAACAUACAACUGACCGCAACAUU
----((.((((((((((......((((......((....))..(((((((-........))))))).---.......................))))....))))))))))))...... ( -29.50)
>consensus
GGUCGGUGGUCAGUUGUCCAAAAUUGAUAAUUAGCCAAGGCAAUUGGCCAACCAGCUACUGGCCAAU___UCCCCUCAACUUCCUUUUCACACACAC________UCGACCGCA_CA__
((((((((((((((((((....................)))))))))))).((((...))))...........................................))))))........ (-20.23 = -21.31 +   1.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,065,141 – 19,065,255
Length 114
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 84.22
Mean single sequence MFE -39.28
Consensus MFE -25.75
Energy contribution -28.39
Covariance contribution 2.64
Combinations/Pair 1.07
Mean z-score -2.26
Structure conservation index 0.66
SVM decision value 0.69
SVM RNA-class probability 0.824128
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19065141 114 - 22224390
UUUCUCCAGCUGGGUCGG----GCUGGUCAAUUGGGGCUGGGUCGGUGGUCAGUUGUCCAAAAUUGAUAAUUAGCCAAGGCAAUUGGCCAA-CAGCUACUGACCAAUCAAUCCCCUCAA
.....((((((......)----)))))......((((...((((((((((.(((((((.......))))))).(((((.....)))))...-..)))))))))).......)))).... ( -40.10)
>DroSec_CAF1 16850 112 - 1
UUUCUCCUGGUGGGUCGG----GCUGGUCAAUUGGGGCUGGGUCGGUGGUCAGUUGUCCAAAAUUGAUAAUUAGCCAAGACAAUUGGCCAACCAGCUACUGGCCAAU---UCCCCUCAA
.......(((.(((...(----((..((.......((((((.....((((((((((((....................)))))))))))).))))))))..)))...---.))).))). ( -41.46)
>DroSim_CAF1 18833 112 - 1
UUUCUCCAGGUGGGUCGG----GUUGGUCAAUUGGGGCUGGGUCGGUGGUCAGUUGUCCGAAAUUGAUAAUUAGCCAAGACAAUUGGCCAACCAGCUACUGGCCAAU---UCCCCUCAA
........(((.(((..(----((((((((((((...((.(((..((.(((((((......))))))).))..))).)).)))))))))))))....))).)))...---......... ( -44.00)
>DroEre_CAF1 17268 115 - 1
UUUCUCCAGCUGGGUCGGUCGGGUUGCUCAAUUGGGGCUGGGUCGGUGGUCAGUUGUCCAAAAUUGAUAAUUAGCCCAUGCAAUUGGCCA-CCAGCUACUGGCCAAC---UCCCCUCAA
............(((((((..(((.((.((((((.(..(((((..((.(((((((......))))))).))..)))))).)))))))).)-))....)))))))...---......... ( -39.90)
>DroYak_CAF1 18404 89 - 1
UUUCUCCUGGUGGGUCGG--------------------------GUUGGUCAGUUGUCCAAAAUUGUUAAUUAGCCAAGGCAAUUGGCCA-CCAGCUACUGGCCAAC---UCCCCUCAA
.......(((.(((..((--------------------------((((((((((.((........(((((((.((....)))))))))..-...)).))))))))))---)))))))). ( -30.92)
>consensus
UUUCUCCAGGUGGGUCGG____GCUGGUCAAUUGGGGCUGGGUCGGUGGUCAGUUGUCCAAAAUUGAUAAUUAGCCAAGGCAAUUGGCCAACCAGCUACUGGCCAAU___UCCCCUCAA
..........((((..((......((((((.....((((((.....((((((((((((....................)))))))))))).))))))..))))))......)).)))). (-25.75 = -28.39 +   2.64)

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 12:44:24 2006