Locus 3415

Sequence ID 2R_DroMel_CAF1
Location 11,553,367 – 11,553,487
Length 120
Max. P 0.945965
window5571 window5572

overview

Window 1

Location 11,553,367 – 11,553,459
Length 92
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 71.81
Mean single sequence MFE -29.27
Consensus MFE -12.48
Energy contribution -13.38
Covariance contribution 0.91
Combinations/Pair 1.27
Mean z-score -2.19
Structure conservation index 0.43
SVM decision value 1.36
SVM RNA-class probability 0.945965
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11553367 92 + 20766785
------------C-CUGUGACUGUGC----CAAGU----GCCUAAUUGUGGAAAUUUCGGGCACU-UUAAGUUCGAUAUUUGGCACGGGCAUUUCAACUUUGAAGAGCCCUACC---
------------.-........((((----(((((----(((.......)).....((((((...-....))))))))))))))))((((.(((((....))))).))))....--- ( -31.40)
>DroSec_CAF1 13637 94 + 1
------------CCCUGUGACUGUGC----CAAGU----GCCUAAUUUUGAAAAUUUCGGGCACUUUCAAGUUCGAUAUUUGGCACGGGCAUUUCAACUUUGAAGUGUCCUACC---
------------..........((((----(((((----(((..(...(....)..)..)))))..((......))...)))))))((((((((((....))))))))))....--- ( -31.90)
>DroSim_CAF1 13667 93 + 1
------------CCAUGUGACUGUGA----CUAGU----GCCUAAUUUUGGAAAUUUCGUGCACU-UCAAGUUCGAUAUUUGGCACGGGCAUUUCAACUUUGAAGUGUCCUACC---
------------.(((......))).----...((----(((.(((.(((((......(....).-.....))))).))).)))))((((((((((....))))))))))....--- ( -25.00)
>DroEre_CAF1 13737 102 + 1
C---ACCCCUGCCCAUGUGACUGUGC----CAGGG----GCCUAAUUGCGGAAAUUUCCAGCACU-UCAAGUUCGAUAUUUGGCACGGGCAAUUCAACUUUGAAGAGCCCUACC---
.---.((((((..(((......))).----)))))----)......((((((....)))......-.(((((.....)))))))).((((..((((....))))..))))....--- ( -28.90)
>DroYak_CAF1 13738 109 + 1
CUGUUCCCAUGGCCAUGUGACUGUGC----CAGGACCCUGCCUAAUUGUGGAAUUUUCGGUCACU-UCAAGUUCGAUAUUUGGCAGGGGCAAUUCAACUUUGAAGAGCCCUACG---
......((.((((((......)).))----))))...(((((.((.(((.((((((..(....).-..)))))).))).)))))))((((..((((....))))..))))....--- ( -32.70)
>DroPer_CAF1 13276 91 + 1
------------C-CUUUUCCUCUGUCAUGCAGGU----GUCUAAUAGCGGAAAUUCUG-GUAUU-UC-------GUAUUUCGUAUUGGAAUUUCAAUUAUGAAGCACCAUGAAGAG
------------.-......((((.((((...(((----((...((((..(((((((..-((((.-..-------.......))))..)))))))..))))...))))))))))))) ( -25.70)
>consensus
____________CCAUGUGACUGUGC____CAAGU____GCCUAAUUGUGGAAAUUUCGGGCACU_UCAAGUUCGAUAUUUGGCACGGGCAUUUCAACUUUGAAGAGCCCUACC___
.......................................(((.........((((.((((((........)))))).)))))))..((((.(((((....))))).))))....... (-12.48 = -13.38 +   0.91)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,553,385 – 11,553,487
Length 102
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 78.64
Mean single sequence MFE -24.02
Consensus MFE -16.42
Energy contribution -17.26
Covariance contribution 0.84
Combinations/Pair 1.09
Mean z-score -1.88
Structure conservation index 0.68
SVM decision value 0.90
SVM RNA-class probability 0.878559
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11553385 102 + 20766785
GCCUAAUUGUGGAAAUUUCGGGCACU-UUAAGUUCGAUAUUUGGCACGGGCAUUUCAACUUUGAAGAGCCCUACCUA-----UCCCGGCCCAGCAGCCACCACCACCC
........((((((((.((((((...-....)))))).))))(((..((((.(((((....))))).))))..((..-----....)).......))).))))..... ( -29.30)
>DroSec_CAF1 13656 89 + 1
GCCUAAUUUUGAAAAUUUCGGGCACUUUCAAGUUCGAUAUUUGGCACGGGCAUUUCAACUUUGAAGUGUCCUACCUA-----UCCCGGCCCA--------------CC
(((.........((((.((((((........)))))).))))((...((((((((((....))))))))))..))..-----....)))...--------------.. ( -25.20)
>DroSim_CAF1 13686 87 + 1
GCCUAAUUUUGGAAAUUUCGUGCACU-UCAAGUUCGAUAUUUGGCACGGGCAUUUCAACUUUGAAGUGUCCUACCUA-----UCCCGACCCA--------------C-
........((((.......((((...-.(((((.....)))))))))((((((((((....))))))))))......-----..))))....--------------.- ( -22.30)
>DroEre_CAF1 13765 90 + 1
GCCUAAUUGCGGAAAUUUCCAGCACU-UCAAGUUCGAUAUUUGGCACGGGCAAUUCAACUUUGAAGAGCCCUACCCCACUUUACCGCCCCC-----------------
........((((((((.((.(((...-....))).)).))))((...((((..((((....))))..))))....))......))))....----------------- ( -20.50)
>DroYak_CAF1 13773 93 + 1
GCCUAAUUGUGGAAUUUUCGGUCACU-UCAAGUUCGAUAUUUGGCAGGGGCAAUUCAACUUUGAAGAGCCCUACGCUACCUUGCCGCACCCA--------------CC
(((.((.(((.((((((..(....).-..)))))).))).))))).(((((..((((....))))..)))))..((......))........--------------.. ( -22.80)
>consensus
GCCUAAUUGUGGAAAUUUCGGGCACU_UCAAGUUCGAUAUUUGGCACGGGCAUUUCAACUUUGAAGAGCCCUACCUA_____UCCCGACCCA______________CC
(((.........((((.((((((........)))))).)))))))..((((.(((((....))))).))))..................................... (-16.42 = -17.26 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:54 2006