Locus 3076

Sequence ID X_DroMel_CAF1
Location 8,213,439 – 8,213,603
Length 164
Max. P 0.992325
window5030 window5031

overview

Window 0

Location 8,213,439 – 8,213,529
Length 90
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 84.01
Mean single sequence MFE -39.10
Consensus MFE -27.32
Energy contribution -29.31
Covariance contribution 2.00
Combinations/Pair 1.06
Mean z-score -3.28
Structure conservation index 0.70
SVM decision value 2.32
SVM RNA-class probability 0.992325
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8213439 90 + 22224390
GGAUGCGGACACAUCCACGGAUUUGGAUCCGGAUUCGGAUACGGAUUCAGAUUCGGUGACG------------UCGACGGUGUCGGUGUCGAGCUACGUAUU
(((((......))))).((((((((((((((..........)))))))))))))).((((.------------.((((...))))..))))........... ( -36.50)
>DroSec_CAF1 114824 90 + 1
GGAUGCGGACACAUCCACGGAUUUGGAUCCGGAUUCGGAUGCGGAUUCAGAUUCGGUGACG------------GUGACGGUGUCGGUGUCGAGCUACGUAUU
.(((((.(((((.((..((((((((((((((.((....)).))))))))))))))..))((------------....))))))).)))))............ ( -40.70)
>DroEre_CAF1 104894 102 + 1
GGAUGCGGACACAUCCACGGAUUUGGAUCCGGAUUCGGAUUCGGAUUCAGAUUCGUUGACGGUGUCGUUGUCGGUGUCGGUGUCGGUGUCGAGCUACGUAUU
.(((((.(((((.((.((((((((((((((((((....)))))))))))))))))).))(((..(((....)))..)))))))).)))))............ ( -47.60)
>DroYak_CAF1 105482 90 + 1
GGAUGCGGACACAUCCACGGAUUUGGAUACGUAUUCGGAU------UCCGUUUCGGUGACGGUG------AUGGUGCUGGUGUCGGUGUCGAGCUACGUAUU
.(((((.(((((...(((((((((((((....))))))))------))(((((((....))).)------))))))...))))).)))))............ ( -31.60)
>consensus
GGAUGCGGACACAUCCACGGAUUUGGAUCCGGAUUCGGAU_CGGAUUCAGAUUCGGUGACG____________GUGACGGUGUCGGUGUCGAGCUACGUAUU
.(((((.(((((...((((((((((((((((.((....)).)))))))))))))).)).(((..............)))))))).)))))............ (-27.32 = -29.31 +   2.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,213,500 – 8,213,603
Length 103
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 80.34
Mean single sequence MFE -33.15
Consensus MFE -19.20
Energy contribution -19.26
Covariance contribution 0.06
Combinations/Pair 1.12
Mean z-score -2.32
Structure conservation index 0.58
SVM decision value 0.84
SVM RNA-class probability 0.864949
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8213500 103 - 22224390
AGCAUUUUGUUGGUGG-UGCAACCAACAGCUUGGUGGGUGGGUGCUUCAUCACAAUUCAUUCAGCUUGAAUUCUGAAUACGUAGCUCGACACCGACACCGUCGA-----------
......((((((((..-....)))))))).(((..((((.((((.....(((.((((((.......)))))).)))...((.....)).)))).)).))..)))----------- ( -30.10)
>DroSec_CAF1 114885 96 - 1
AGCAUUUUGUUGGUGGGUGU---UGGUUGCUUGGU-----GGUGCUUCAUCACAAUUCAUUCAGCUUGAAUUCUGAAUACGUAGCUCGACACCGACACCGUCAC-----------
.......((.((((((((((---(((((((...((-----((((...)))))).....((((((........))))))..))))).)))))))..))))).)).----------- ( -32.20)
>DroEre_CAF1 104956 103 - 1
AGCAUUUUGUUGGUGGG-------UG----UUGGUUGGU-GGUGCUUCAUCACAAUUCAUUCAGCUUGAAUUCUGAAUACGUAGCUCGACACCGACACCGACACCGACAACGACA
......(((((((((((-------((----(((((..((-.(.(((...(((.((((((.......)))))).)))......))).).)))))))))))..)))))))))..... ( -37.40)
>DroYak_CAF1 105538 101 - 1
AGCAUUUUGUUGGUGGGUUG---CUG----UUGGUUGGU-GGUGCUUCAUCACAAUUCAUUCAGCUUGAAUUCUGAAUACGUAGCUCGACACCGACACCAGCACCAU------CA
..........((((((..((---(((----...((((((-(..(((...(((.((((((.......)))))).)))......)))....)))))))..)))))))))------)) ( -32.90)
>consensus
AGCAUUUUGUUGGUGGGUG____CUG____UUGGUUGGU_GGUGCUUCAUCACAAUUCAUUCAGCUUGAAUUCUGAAUACGUAGCUCGACACCGACACCGUCAC___________
.......((((((((...............(((((.....(.(((....(((.((((((.......)))))).)))....))).).....)))))))))))))............ (-19.20 = -19.26 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:23 2006