Locus 2509

Sequence ID 2L_DroMel_CAF1
Location 6,918,841 – 6,918,938
Length 97
Max. P 0.988141
window4013 window4014

overview

Window 3

Location 6,918,841 – 6,918,938
Length 97
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 75.15
Mean single sequence MFE -21.36
Consensus MFE -9.32
Energy contribution -10.12
Covariance contribution 0.80
Combinations/Pair 1.27
Mean z-score -2.42
Structure conservation index 0.44
SVM decision value 2.11
SVM RNA-class probability 0.988141
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6918841 97 + 22407834
CGUAGGAGGGUGUCUUGCAGCCGCCUGCUACCCUUUUGU---------------UUACCACUUAUUUUAAUUUGUCUAUUUCUAAUCAAAUCAAUCAAACUUUAAUAUCAAU
..((((((((((....((((....)))))))))))))).---------------.......................................................... ( -14.20)
>DroSec_CAF1 3869 95 + 1
CGUAGGAGGGAGGCUUACAGCCGCCUGCUACCCUUUUGU---------------UUACCACUUAUUUAAAUUUGUUUAAUUCGAAUACA--GAAUCAAACUUAAAUAUCAAU
.((((.(((..(((.....))).))).))))........---------------........(((((((....((((.((((.......--)))).)))))))))))..... ( -20.70)
>DroSim_CAF1 3869 110 + 1
CGUAGGAGGGAGGCUUACAGCCGCCUGCUACCCUUUGGUAAAUAAGUGGUAAACAUACCACUUAUUUAAAUUUGUUUAAUUCUAAUACA--GAAUCAAACUUAAAUAUCAGU
.((((.(((..(((.....))).))).))))...(((((((((((((((((....))))))))))).......((((.(((((.....)--)))).)))).....)))))). ( -35.00)
>DroEre_CAF1 3989 94 + 1
CGUAGU-GGGUGGCUUACAGUCGCCAGCUACCCUUUUAU---------------UAACCACUUCUUUCAAUUUGUUUAAUUAUAAUUCA--CAAUCAAACUUAAAUUUGAAU
.(((((-.((((((.....)))))).)))))........---------------...................................--...(((((......))))).. ( -17.00)
>DroYak_CAF1 3944 90 + 1
CAGAGGAAGGUGGC-UACAGCCGCCUUUUACCCUGUUAU---------------UGAGCACUUAUUUCAAUUUGUUUAAUUCAAAAUCA--CG----AACAUAUAUUUAAAU
(((.((((((((((-....))))))))...)))))..((---------------((((((..(......)..)))))))).........--..----............... ( -19.90)
>consensus
CGUAGGAGGGUGGCUUACAGCCGCCUGCUACCCUUUUGU_______________UUACCACUUAUUUAAAUUUGUUUAAUUCUAAUACA__CAAUCAAACUUAAAUAUCAAU
.((((..(((((((.....))))))).))))................................................................................. ( -9.32 = -10.12 +   0.80)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,918,841 – 6,918,938
Length 97
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 75.15
Mean single sequence MFE -23.14
Consensus MFE -8.52
Energy contribution -10.48
Covariance contribution 1.96
Combinations/Pair 1.21
Mean z-score -2.23
Structure conservation index 0.37
SVM decision value 1.55
SVM RNA-class probability 0.963017
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6918841 97 - 22407834
AUUGAUAUUAAAGUUUGAUUGAUUUGAUUAGAAAUAGACAAAUUAAAAUAAGUGGUAA---------------ACAAAAGGGUAGCAGGCGGCUGCAAGACACCCUCCUACG
..................((((((((.(((....))).)))))))).....((((...---------------.....(((((.((((....)))).....))))).)))). ( -17.80)
>DroSec_CAF1 3869 95 - 1
AUUGAUAUUUAAGUUUGAUUC--UGUAUUCGAAUUAAACAAAUUUAAAUAAGUGGUAA---------------ACAAAAGGGUAGCAGGCGGCUGUAAGCCUCCCUCCUACG
.....((((((((((((((((--.......)))))))))....)))))))........---------------........((((.(((.(((.....)))..))).)))). ( -21.60)
>DroSim_CAF1 3869 110 - 1
ACUGAUAUUUAAGUUUGAUUC--UGUAUUAGAAUUAAACAAAUUUAAAUAAGUGGUAUGUUUACCACUUAUUUACCAAAGGGUAGCAGGCGGCUGUAAGCCUCCCUCCUACG
............(((((((((--((...))))))))))).....(((((((((((((....))))))))))))).......((((.(((.(((.....)))..))).)))). ( -37.30)
>DroEre_CAF1 3989 94 - 1
AUUCAAAUUUAAGUUUGAUUG--UGAAUUAUAAUUAAACAAAUUGAAAGAAGUGGUUA---------------AUAAAAGGGUAGCUGGCGACUGUAAGCCACCC-ACUACG
.(((((.(((..(((((((((--((...)))))))))))))))))))....(((((..---------------......((((.(((.((....)).))).))))-))))). ( -21.90)
>DroYak_CAF1 3944 90 - 1
AUUUAAAUAUAUGUU----CG--UGAUUUUGAAUUAAACAAAUUGAAAUAAGUGCUCA---------------AUAACAGGGUAAAAGGCGGCUGUA-GCCACCUUCCUCUG
............(((----((--......))))).......(((((.........)))---------------))..(((((...((((.(((....-))).)))).))))) ( -17.10)
>consensus
AUUGAUAUUUAAGUUUGAUUG__UGAAUUAGAAUUAAACAAAUUGAAAUAAGUGGUAA_______________ACAAAAGGGUAGCAGGCGGCUGUAAGCCACCCUCCUACG
............(((((((((.........)))))))))..........................................((((.(((.(((.....)))..))).)))). ( -8.52 = -10.48 +   1.96)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:33 2006