Locus 2161

Sequence ID 3R_DroMel_CAF1
Location 6,202,572 – 6,202,730
Length 158
Max. P 0.974413
window3517 window3518 window3519

overview

Window 7

Location 6,202,572 – 6,202,664
Length 92
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 75.65
Mean single sequence MFE -20.80
Consensus MFE -12.22
Energy contribution -12.92
Covariance contribution 0.70
Combinations/Pair 1.08
Mean z-score -1.47
Structure conservation index 0.59
SVM decision value 0.18
SVM RNA-class probability 0.621767
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6202572 92 - 27905053
CUAUGUUCCUUCCGAAAUUUGGAGA-----------AGUGUACAGGACCAACGCCAACCUCCUGUGCACUUCCGCUUUGCUGCCUCGCCACUCGUCCUGCUUC
............(((....(((.((-----------(((((((((((............))))))))))))).((......))....))).)))......... ( -24.00)
>DroSec_CAF1 22992 81 - 1
CUAUGUUCCUUACAAAAUUUGGAAA-----------AGUGUACAGGACC------AACCUCCUGUGCACUUCCGCUUUGCUGC-----CACUCGUCCUGCUUC
...(((.....)))......(((..-----------(((((((((((..------....))))))))))))))((...((...-----.....))...))... ( -21.70)
>DroSim_CAF1 23425 92 - 1
CUAUGUUCCUUCCAAAAUUUGGAAA-----------AGUGUACAGGACCAACGCCAACCUCCUGUGCACUUCCGCUUUGCUGCCUCGCCACUCGUCCUGCUUC
.........(((((.....)))))(-----------(((((((((((............))))))))))))..((......)).................... ( -21.20)
>DroEre_CAF1 23590 85 - 1
-------UAUUUAGAAAUUUAGAGA-----------AGUGUACCGGCCCAAUGGCAACCUCCUGUGCACUUCCGCUUUGCUGCCUCGCCACUCGUCCUGCUUC
-------......((......(.((-----------(((((((.((......(....)..)).))))))))))((......)).))................. ( -15.90)
>DroYak_CAF1 20156 86 - 1
------GCCUUUAGAAAUGUAGAGA-----------AGUGUACAGGACCAACGACAACCUCCUGUGCACUUCCGCUUUGCUGCCUCGCCGCUCGUCCUGCUUC
------............((((.((-----------(((((((((((............)))))))))))))......((.((...)).)).....))))... ( -25.30)
>DroAna_CAF1 29551 95 - 1
AAGAAUUGUUUUCAAAACUUACAAAAUACGCAGUUCAGUGUACAG--------CCAUCCUCCCGUGCAUUUCCGCUUUGCUGCCUCGCAACGUGUCCUGCUUC
..(((.....)))................((((...(((((((..--------..........)))))))..(((.((((......)))).)))..))))... ( -16.70)
>consensus
CUAUGUUCCUUUCAAAAUUUAGAAA___________AGUGUACAGGACCAACGCCAACCUCCUGUGCACUUCCGCUUUGCUGCCUCGCCACUCGUCCUGCUUC
....................................(((((((((((............)))))))))))...((......)).................... (-12.22 = -12.92 +   0.70)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,202,601 – 6,202,704
Length 103
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 71.10
Mean single sequence MFE -22.16
Consensus MFE -14.25
Energy contribution -13.88
Covariance contribution -0.38
Combinations/Pair 1.27
Mean z-score -1.64
Structure conservation index 0.64
SVM decision value 1.06
SVM RNA-class probability 0.908608
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6202601 103 - 27905053
AUGCACAUCAAUUCAUUUGAAAUUAGGUUUCGUAAGCUUUCUAUGUUCCUUCCGAAAUUUGGAGA-----------AGUGUACAGGACCAACGCCAACCUCCUGUGCACUUCCG
.......((((.....))))..((((((((((.(((............))).)))))))))).((-----------(((((((((((............))))))))))))).. ( -28.40)
>DroSec_CAF1 23016 97 - 1
AUGCGCAUCAAUCCAUUUGAAAUUAGGCUUCGUAAGCUAUCUAUGUUCCUUACAAAAUUUGGAAA-----------AGUGUACAGGACC------AACCUCCUGUGCACUUCCG
...........((((..(......(((...((((.......))))..)))......)..)))).(-----------(((((((((((..------....))))))))))))... ( -25.60)
>DroSim_CAF1 23454 103 - 1
AUGCGCAUCAAUCCAUUUGAAAUUAGGCUUCGUAAGCUAUCUAUGUUCCUUCCAAAAUUUGGAAA-----------AGUGUACAGGACCAACGCCAACCUCCUGUGCACUUCCG
....(((((((.....)))).....((((.....)))).....)))...(((((.....)))))(-----------(((((((((((............))))))))))))... ( -24.70)
>DroAna_CAF1 29580 103 - 1
---CGAAUCAAAACUUUUUAAAUUGAAGAACAAAUACAAGAAGAAUUGUUUUCAAAACUUACAAAAUACGCAGUUCAGUGUACAG--------CCAUCCUCCCGUGCAUUUCCG
---..........((((.......))))..............(((((((....................)))))))(((((((..--------..........))))))).... (  -9.95)
>consensus
AUGCGCAUCAAUCCAUUUGAAAUUAGGCUUCGUAAGCUAUCUAUGUUCCUUCCAAAAUUUGGAAA___________AGUGUACAGGACC____CCAACCUCCUGUGCACUUCCG
.............................................((((...........))))............(((((((((((............))))))))))).... (-14.25 = -13.88 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,202,635 – 6,202,730
Length 95
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 93.68
Mean single sequence MFE -21.44
Consensus MFE -20.55
Energy contribution -20.44
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.52
Structure conservation index 0.96
SVM decision value 1.73
SVM RNA-class probability 0.974413
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6202635 95 - 27905053
UUCACUUUUCCUUUCAAAACCAAGGAAUGCACAUCAAUUCAUUUGAAAUUAGGUUUCGUAAGCUUUCUAUGUUCCUUCCGAAAUUUGGAGAAGUG
..(((((((((..........(((((((.....((((.....))))...((((...(....)...)))).))))))).........))))))))) ( -21.41)
>DroSec_CAF1 23044 95 - 1
UUAACUUUUCCUUUCAAAACCAAGGAAUGCGCAUCAAUCCAUUUGAAAUUAGGCUUCGUAAGCUAUCUAUGUUCCUUACAAAAUUUGGAAAAGUG
...((((((((..........(((((((.....((((.....)))).....((((.....))))......))))))).........)))))))). ( -20.61)
>DroSim_CAF1 23488 95 - 1
UUCACUUUUCCUUUUAAAACCAAGGAAUGCGCAUCAAUCCAUUUGAAAUUAGGCUUCGUAAGCUAUCUAUGUUCCUUCCAAAAUUUGGAAAAGUG
..(((((((((..........(((((((.....((((.....)))).....((((.....))))......))))))).........))))))))) ( -22.31)
>consensus
UUCACUUUUCCUUUCAAAACCAAGGAAUGCGCAUCAAUCCAUUUGAAAUUAGGCUUCGUAAGCUAUCUAUGUUCCUUCCAAAAUUUGGAAAAGUG
..(((((((((..........(((((((.....((((.....)))).....((((.....))))......))))))).........))))))))) (-20.55 = -20.44 +  -0.11)

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 10:28:48 2006