Locus 3206

Sequence ID 3L_DroMel_CAF1
Location 9,352,403 – 9,352,530
Length 127
Max. P 0.998176
window4991 window4992 window4993

overview

Window 1

Location 9,352,403 – 9,352,502
Length 99
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 73.58
Mean single sequence MFE -39.27
Consensus MFE -27.77
Energy contribution -30.28
Covariance contribution 2.50
Combinations/Pair 1.17
Mean z-score -2.31
Structure conservation index 0.71
SVM decision value 3.03
SVM RNA-class probability 0.998176
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9352403 99 + 23771897
GCCACUUCCAUGGACUCUGAUUCUGGUUCUGCAACGCCAUUGUUGGCAC------UGGAAGUGGUUCCUGCGGUGGAAGGGGCUUCCACUGCAACAGC---AGCGGCA
((((((((((.(((((........)))))......((((....))))..------))))))))))...(((((((((((...)))))))))))...((---....)). ( -42.90)
>DroAna_CAF1 1738 93 + 1
UCCUCUUCCAUGGGCUCUGG------------CACGCCAUUGUUGGAAGAAGAAGUGGAAGUGCUGGAAGUAGUAGUGGUGGCUUCCACGGCUGCAGC---CUCAACG
..........(((((((..(------------(((.(((((.((......)).)))))..))))..))....(((((.((((...)))).))))).))---).))... ( -33.90)
>DroSim_CAF1 2353 99 + 1
GCCACUUCCAUGGACUCUGGUUCUGGUUCUGCAACGCCAUUGUUGGCAC------UGGAAGUGGUUCCUGCUGUGGAAGGGGCUUCCACUGCAACAGC---AGCAGCG
((((((((((.(((((........)))))......((((....))))..------))))))))))..((((((((((((...))))))).((....))---))))).. ( -40.90)
>DroEre_CAF1 1858 96 + 1
GCCACUUCCAUUGACUCU------GGUUCUGCAACGCCAUUGUUGGCAC------UGGAAGUGGUUCCUGCAGUGGAAGGGGUUUCCACUGCAACAACAGCAGCGGCA
(((((((((((..((..(------(((........))))..))..)...------))))))))))...(((((((((((...)))))))))))......((....)). ( -39.40)
>consensus
GCCACUUCCAUGGACUCUGG____GGUUCUGCAACGCCAUUGUUGGCAC______UGGAAGUGGUUCCUGCAGUGGAAGGGGCUUCCACUGCAACAGC___AGCAGCA
((((((((((.(((((........)))))......((((....))))........))))))))))...(((((((((((...)))))))))))............... (-27.77 = -30.28 +   2.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,352,403 – 9,352,502
Length 99
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 73.58
Mean single sequence MFE -35.77
Consensus MFE -21.42
Energy contribution -22.80
Covariance contribution 1.38
Combinations/Pair 1.17
Mean z-score -2.31
Structure conservation index 0.60
SVM decision value 2.32
SVM RNA-class probability 0.992262
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9352403 99 - 23771897
UGCCGCU---GCUGUUGCAGUGGAAGCCCCUUCCACCGCAGGAACCACUUCCA------GUGCCAACAAUGGCGUUGCAGAACCAGAAUCAGAGUCCAUGGAAGUGGC
..(((((---((....)))))))..(((.((((((..(((((((....)))).------..((((....))))..))).((.......))........)))))).))) ( -35.80)
>DroAna_CAF1 1738 93 - 1
CGUUGAG---GCUGCAGCCGUGGAAGCCACCACUACUACUUCCAGCACUUCCACUUCUUCUUCCAACAAUGGCGUG------------CCAGAGCCCAUGGAAGAGGA
.((((.(---((....)))((((......)))).........)))).........((((((((((.....(((...------------.....)))..)))))))))) ( -30.40)
>DroSim_CAF1 2353 99 - 1
CGCUGCU---GCUGUUGCAGUGGAAGCCCCUUCCACAGCAGGAACCACUUCCA------GUGCCAACAAUGGCGUUGCAGAACCAGAACCAGAGUCCAUGGAAGUGGC
..(((((---((....)).(((((((...))))))))))))...(((((((((------..((((....))))(((....)))...............))))))))). ( -37.60)
>DroEre_CAF1 1858 96 - 1
UGCCGCUGCUGUUGUUGCAGUGGAAACCCCUUCCACUGCAGGAACCACUUCCA------GUGCCAACAAUGGCGUUGCAGAACC------AGAGUCAAUGGAAGUGGC
.((((((((((((((((((((((((.....))))))))).((((....)))).------.....))))))))).........((------(.......))).)))))) ( -39.30)
>consensus
CGCCGCU___GCUGUUGCAGUGGAAGCCCCUUCCACUGCAGGAACCACUUCCA______GUGCCAACAAUGGCGUUGCAGAACC____CCAGAGUCCAUGGAAGUGGC
.((.((....)).))(((.((((((.....)))))).)))....(((((((((........((((....))))(((....)))...............))))))))). (-21.42 = -22.80 +   1.38)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,352,437 – 9,352,530
Length 93
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 92.63
Mean single sequence MFE -32.37
Consensus MFE -28.63
Energy contribution -28.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.88
SVM decision value 0.03
SVM RNA-class probability 0.546305
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9352437 93 - 23771897
CGCCCCCCAUUUCCAAUGAGGCUGCUGCUGCCGCU---GCUGUUGCAGUGGAAGCCCCUUCCACCGCAGGAACCACUUCCAGUGCCAACAAUGGCG
.((..(((((.....))).))..))......((((---..(((((((.((((((....((((......))))...)))))).)).)))))..)))) ( -31.00)
>DroSim_CAF1 2387 93 - 1
CGCCCUCCAUUUCCAAUGAGGCUGCUGCCGCUGCU---GCUGUUGCAGUGGAAGCCCCUUCCACAGCAGGAACCACUUCCAGUGCCAACAAUGGCG
((((......((((.....(((....)))((((((---((....))))((((((...)))))))))).)))).(((.....)))........)))) ( -31.50)
>DroEre_CAF1 1886 96 - 1
CGCCCUCCCUUUCCAAUGAGGCUGCUGCUGCCGCUGCUGUUGUUGCAGUGGAAACCCCUUCCACUGCAGGAACCACUUCCAGUGCCAACAAUGGCG
((((...((((......))))....((.((.(((((..(((.(((((((((((.....))))))))))).)))......))))).)).))..)))) ( -34.60)
>consensus
CGCCCUCCAUUUCCAAUGAGGCUGCUGCUGCCGCU___GCUGUUGCAGUGGAAGCCCCUUCCACAGCAGGAACCACUUCCAGUGCCAACAAUGGCG
((((...............(((.((....)).))).....(((((((.((((((....((((......))))...)))))).)).)))))..)))) (-28.63 = -28.97 +   0.33)

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 10:52:03 2006