Locus 1042

Sequence ID 2L_DroMel_CAF1
Location 2,924,742 – 2,924,896
Length 154
Max. P 0.708558
window1674 window1675 window1676

overview

Window 4

Location 2,924,742 – 2,924,857
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.53
Mean single sequence MFE -21.66
Consensus MFE -16.62
Energy contribution -16.78
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.77
SVM decision value 0.22
SVM RNA-class probability 0.638887
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2924742 115 + 22407834
CUUUCCUUCGUUUC--UCUGCCUCUUGGCUUACAUUUGGCUUGCAAAUUGUUGCUCUCUAUUUAUCGCUUUCUAGCUGAUUUAAUUAAUUUUAUUUCCACUAGUAG---AUACACAAGCA
..............--...(((....))).........((((((((....))))........((((.....((((..((..(((......)))..))..))))..)---)))...)))). ( -17.70)
>DroSec_CAF1 42896 115 + 1
CUUUCCUUCGUUUC--GCUGCCUCUUGGCUUACAUUUGGCUUGCAAAUUGUUGCUCGCUAUUUAUCGCUUUCUAGCUGAUUUAAUUAAUUUUAUUUCCACUAGUAG---AUACACAAGCA
..............--((((((....))).......((((..((((....))))..))))..((((.....((((..((..(((......)))..))..))))..)---)))....))). ( -21.80)
>DroSim_CAF1 43772 117 + 1
CUUUCCUUCGUUUCGCGCUGCCUCUUGGCUUACAUUUGGCUUGCAAAUUGUUGCUCGCUAUUUAUCGCUUUCUAGCUGAUUUAAUUAAUUUUAUUUCCACUAGUAG---AUACACAAGCA
.........((.(((((..(((....))).......((((..((((....))))..)))).....)))...((((..((..(((......)))..))..))))..)---).))....... ( -22.00)
>DroEre_CAF1 43904 118 + 1
CUUUCAUUCGUUUC--GCUGCCUCUUGGCUUACAUUUGGCUUGCAAAUUGUUGCUCGCUAUUUAUCGCUUUCUAGCUGAUUUAAUUUAUUUUAUAUCUACUAGUGGUGUAUAGACAAACA
.........((((.--...(((....))).......((((..((((....))))..))))(((((((((..((((..(((.(((......))).)))..)))).)))).))))).)))). ( -24.90)
>DroYak_CAF1 43949 115 + 1
CUUUCCUUCGUUUC--GCUGCCUCUUGGCUUACAUUUGGCUUGCAAAUUGUUGCUCGCUAUUUAUCGCUUUCUAGCUGAUUUAAUUAAUUUUAUAUCUACUAGUGG---AUACACAAACA
...(((........--((.(((....))).......((((..((((....))))..))))......))...((((..(((.(((......))).)))..)))).))---).......... ( -21.90)
>consensus
CUUUCCUUCGUUUC__GCUGCCUCUUGGCUUACAUUUGGCUUGCAAAUUGUUGCUCGCUAUUUAUCGCUUUCUAGCUGAUUUAAUUAAUUUUAUUUCCACUAGUAG___AUACACAAGCA
.........((((...((.(((....))).......((((..((((....))))..))))......))...((((..((..(((......)))..))..))))............)))). (-16.62 = -16.78 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,924,742 – 2,924,857
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.53
Mean single sequence MFE -22.16
Consensus MFE -18.06
Energy contribution -18.02
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.56
Structure conservation index 0.81
SVM decision value 0.37
SVM RNA-class probability 0.708558
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2924742 115 - 22407834
UGCUUGUGUAU---CUACUAGUGGAAAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGAGAGCAACAAUUUGCAAGCCAAAUGUAAGCCAAGAGGCAGA--GAAACGAAGGAAAG
..(((.(((.(---((((...(((................(((.(((....)))))).........((((....))))...)))...))..(((....)))..)--)).))).))).... ( -18.90)
>DroSec_CAF1 42896 115 - 1
UGCUUGUGUAU---CUACUAGUGGAAAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAAGCCAAAUGUAAGCCAAGAGGCAGC--GAAACGAAGGAAAG
(((((((.(((---(..(((((.((..(((......)))..)).))))).....))))....)))))))....(((((..((.....))..(((....))).))--))).(....).... ( -23.00)
>DroSim_CAF1 43772 117 - 1
UGCUUGUGUAU---CUACUAGUGGAAAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAAGCCAAAUGUAAGCCAAGAGGCAGCGCGAAACGAAGGAAAG
(((((((.(((---(..(((((.((..(((......)))..)).))))).....))))....)))))))....(((((..((.....))..(((....)))...))))).(....).... ( -23.10)
>DroEre_CAF1 43904 118 - 1
UGUUUGUCUAUACACCACUAGUAGAUAUAAAAUAAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAAGCCAAAUGUAAGCCAAGAGGCAGC--GAAACGAAUGAAAG
.((((((..........(((((.(((.(((......))).))).)))))...((........((..((((....))))..)).........(((....))).))--...))))))..... ( -22.50)
>DroYak_CAF1 43949 115 - 1
UGUUUGUGUAU---CCACUAGUAGAUAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAAGCCAAAUGUAAGCCAAGAGGCAGC--GAAACGAAGGAAAG
(((((((.(((---((.(((((.(((.(((......))).))).)))))...).))))....)))))))....(((((..((.....))..(((....))).))--))).(....).... ( -23.30)
>consensus
UGCUUGUGUAU___CUACUAGUGGAAAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAAGCCAAAUGUAAGCCAAGAGGCAGC__GAAACGAAGGAAAG
(((((((.(((......(((((.((..(((......)))..)).)))))......)))....))))))).....(((((.......)))))(((....)))................... (-18.06 = -18.02 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,924,780 – 2,924,896
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.04
Mean single sequence MFE -24.31
Consensus MFE -18.24
Energy contribution -19.44
Covariance contribution 1.20
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.75
SVM decision value 0.20
SVM RNA-class probability 0.630799
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2924780 116 - 22407834
GAAUUCGAUUAAAUAUUAGUUGACGAAGU-AAGGUUUGCUUGCUUGUGUAU---CUACUAGUGGAAAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGAGAGCAACAAUUUGCAA
....(((((((.....)))))))....((-(((..((((((..((((.(((---(..(((((.((..(((......)))..)).))))).....)))).)))).))))))...))))).. ( -21.30)
>DroSec_CAF1 42934 117 - 1
GAAUUCGAUUAAAUAUUAGUUGACGAAGGUAGGUUUUGCUUGCUUGUGUAU---CUACUAGUGGAAAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAA
....(((((((.....))))))).....((((((((((((((((....(((---(..(((((.((..(((......)))..)).))))).....))))...))))))))).))))))).. ( -28.10)
>DroSim_CAF1 43812 117 - 1
GAAUUCGAUUAAAUAUUAGUUGACGAAGGUAGGUUUUGCUUGCUUGUGUAU---CUACUAGUGGAAAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAA
....(((((((.....))))))).....((((((((((((((((....(((---(..(((((.((..(((......)))..)).))))).....))))...))))))))).))))))).. ( -28.10)
>DroEre_CAF1 43942 119 - 1
GAAUUCGAUUUAAUAUUAGAUGACAAAGGUAAG-UUUGCUUGUUUGUCUAUACACCACUAGUAGAUAUAAAAUAAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAA
....................((.((((.....(-((((((.(((((((.........(((((.(((.(((......))).))).))))).....)))))))))))))).....)))))). ( -21.54)
>DroYak_CAF1 43987 116 - 1
GAAUUCGAUUUAAUAUUAGAUGACACAGGUAUG-UUUGCUUGUUUGUGUAU---CCACUAGUAGAUAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAA
.........................(((((.((-((.(((((((....(((---((.(((((.(((.(((......))).))).)))))...).))))...))))))))))))))))... ( -22.50)
>consensus
GAAUUCGAUUAAAUAUUAGUUGACGAAGGUAAG_UUUGCUUGCUUGUGUAU___CUACUAGUGGAAAUAAAAUUAAUUAAAUCAGCUAGAAAGCGAUAAAUAGCGAGCAACAAUUUGCAA
....(((((((.....))))))).....(((((..(((((((((....(((......(((((.((..(((......)))..)).)))))......)))...)))))))))...))))).. (-18.24 = -19.44 +   1.20)

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 09:51:51 2006