Locus 1512

Sequence ID 2R_DroMel_CAF1
Location 5,729,126 – 5,729,290
Length 164
Max. P 0.982467
window2557 window2558 window2559

overview

Window 7

Location 5,729,126 – 5,729,235
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 94.09
Mean single sequence MFE -25.92
Consensus MFE -20.65
Energy contribution -21.15
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.80
SVM decision value 0.60
SVM RNA-class probability 0.794792
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5729126 109 + 20766785
CACGCGGGCGCAAGUAAUCACGAAUGUAGUAUACUCCUAGAUAUAUACCUCGCAUAUAUUCGUGACAAACUCACGCACAAAACGUUAAACUAUGCGAAGAGUUGCAUAG
...(((.((....))..((((((((((((((((..........)))))......)))))))))))........))).............((((((((....)))))))) ( -27.70)
>DroSec_CAF1 19539 106 + 1
CAGGCGGGCGCAAGUAAUCACGAAUGU---AUACUCCUAGAUAUAUACCUCGCAUAUAUUCGUGACAAACUCACGCACAAAACGUUAAACUAUGCGAAGAGUUGCAUAG
..((((.(((..(((..((((((((((---((.(.................).))))))))))))...)))..)))......))))...((((((((....)))))))) ( -27.83)
>DroEre_CAF1 19728 103 + 1
---GCGCUCGCAAGUAAUCACGAAUGU---AUACUCCUAGAUAUAUACCUCGCAUAUAUUCGUGACAAACUCACGCACAAAACGUUAAACUAUGCGAAGAGUUGCAUAG
---(((..(....)...((((((((((---((.(.................).))))))))))))........))).............((((((((....)))))))) ( -23.83)
>DroYak_CAF1 19585 104 + 1
--CACGCGCAGAAGUAAUCACGAAUGU---AUACUCCUAGAUAUAUACCUCGCAUAUAUUCGUGACAAACUCACGCACAAAACGUUAAACUAUGCGAAGAGUUGCAUAG
--...(((..((.((..((((((((((---((.(.................).))))))))))))...)))).))).............((((((((....)))))))) ( -24.33)
>consensus
__CGCGCGCGCAAGUAAUCACGAAUGU___AUACUCCUAGAUAUAUACCUCGCAUAUAUUCGUGACAAACUCACGCACAAAACGUUAAACUAUGCGAAGAGUUGCAUAG
.....(.(((..(((..((((((((((..........((....))..........))))))))))...)))..))).)...........((((((((....)))))))) (-20.65 = -21.15 +   0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,729,126 – 5,729,235
Length 109
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 94.09
Mean single sequence MFE -35.48
Consensus MFE -31.31
Energy contribution -31.88
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -3.58
Structure conservation index 0.88
SVM decision value 1.92
SVM RNA-class probability 0.982467
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5729126 109 - 20766785
CUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAGUUUGUCACGAAUAUAUGCGAGGUAUAUAUCUAGGAGUAUACUACAUUCGUGAUUACUUGCGCCCGCGUG
((((((........))))))....((((...(.(((..(((..(((((((((.(((((.((((....))))....)))))....))))))))).)))..)))).)))). ( -35.70)
>DroSec_CAF1 19539 106 - 1
CUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAGUUUGUCACGAAUAUAUGCGAGGUAUAUAUCUAGGAGUAU---ACAUUCGUGAUUACUUGCGCCCGCCUG
((((((........))))))...........(.(((..(((..(((((((((.(((((.((((....))))....))))---).))))))))).)))..))).)..... ( -36.20)
>DroEre_CAF1 19728 103 - 1
CUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAGUUUGUCACGAAUAUAUGCGAGGUAUAUAUCUAGGAGUAU---ACAUUCGUGAUUACUUGCGAGCGC---
((((((........))))))...........((.((..(((..(((((((((.(((((.((((....))))....))))---).))))))))).)))..)).))..--- ( -34.70)
>DroYak_CAF1 19585 104 - 1
CUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAGUUUGUCACGAAUAUAUGCGAGGUAUAUAUCUAGGAGUAU---ACAUUCGUGAUUACUUCUGCGCGUG--
((((((........))))))...........(((((.((((..(((((((((.(((((.((((....))))....))))---).))))))))).)))).)))))...-- ( -35.30)
>consensus
CUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAGUUUGUCACGAAUAUAUGCGAGGUAUAUAUCUAGGAGUAU___ACAUUCGUGAUUACUUGCGCCCGCG__
((((((........))))))...........(((((..(((..(((((((((..((((.((((....))))....)))).....))))))))).)))..)))))..... (-31.31 = -31.88 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,729,195 – 5,729,290
Length 95
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 73.23
Mean single sequence MFE -18.34
Consensus MFE -13.80
Energy contribution -13.80
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.29
Structure conservation index 0.75
SVM decision value 0.37
SVM RNA-class probability 0.709671
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5729195 95 - 20766785
CAAGCGCCCC-------CCUUCCACCCCACAGUC--CCAAUCCC------C-AACCAGCUGCGUAUCUUAUCUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAG
..........-------.................--........------.-.......((((((.......)))))).(((..(((((((.........))))))).))) ( -13.80)
>DroSec_CAF1 19605 81 - 1
---------C-------CCUUCCUCCCCUCAAU-------UCCC------C-UAACAGCUGCGUAUCUUAUCUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAG
---------.-------..........((((..-------....------.-....((.((((((.......)))))).))...(((((((.........))))))))))) ( -14.00)
>DroEre_CAF1 19791 104 - 1
GG-AGACGCCCCGUCCCCCUCCCUCCGCCCCUUCCACCAUUCCC------CACCACAGCUGCGUAUCUUAUCUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAG
((-.((((...)))).))..........................------((((((((..((((.......((((((........))))))....)))).))))).))).. ( -23.40)
>DroYak_CAF1 19649 108 - 1
AG-GAGCCCCCCGUCCCCUUCCC--CACCUCUUCCGCCGCUCCCUCAUUCCCCCACAGCUGCGUAUCUUAUCUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAG
.(-((((................--.............)))))(((((.....(((((..((((.......((((((........))))))....)))).))))).))))) ( -22.15)
>consensus
_G_G_GCCCC_______CCUCCCUCCCCCCAUUC__CCA_UCCC______C_CAACAGCUGCGUAUCUUAUCUAUGCAACUCUUCGCAUAGUUUAACGUUUUGUGCGUGAG
...........................................................((((((.......)))))).(((..(((((((.........))))))).))) (-13.80 = -13.80 +  -0.00)

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 10:06:33 2006