Locus 4610

Sequence ID 3L_DroMel_CAF1
Location 13,143,608 – 13,143,727
Length 119
Max. P 0.933897
window7234 window7235

overview

Window 4

Location 13,143,608 – 13,143,727
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.95
Mean single sequence MFE -26.40
Consensus MFE -17.09
Energy contribution -17.61
Covariance contribution 0.52
Combinations/Pair 1.23
Mean z-score -2.20
Structure conservation index 0.65
SVM decision value 1.23
SVM RNA-class probability 0.933897
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13143608 119 + 23771897
CAGUGCGAGACAUUAGUGUAAGUGC-AAGGGGAACUUAAAGCAAACUUGUACAAACAAUUCAUUACUAAAAAAAUAUCUGUUAGUUUUAAUACCAUACUUUGCUCUAUGAUACGCACUGU
(((((((..(((....))).((.((-((((((...(((((((.(((..(((.......................)))..))).)))))))..))...)))))).))......))))))). ( -24.50)
>DroSec_CAF1 131304 107 + 1
CAGUGCGAGACAUUAGUGUAAGUGC-AAGGGGUAAUUUAAGCAAAC---------CAUUUCAUUACUGA---AAUAUCUGCUAGUUUACAUACCAUAUUUUGCGCUAUGAUACGCACUGU
(((((((...(((.((((((((...-..((.((((....((((...---------.((((((....)))---)))...))))...))))...))....)))))))))))...))))))). ( -31.10)
>DroSim_CAF1 131205 108 + 1
CAGUGUGAGACAUAAGUGUAAGUGCGAAAGGGAACUUUAAGCAAAU---------CAUUUCAAUAGUGA---AAUAUCUGCUAGUUUAAAUACCAUUUUUUGCGCUAUGAUACGCACUGU
(((((((...((((.(((((((..(....).(((((...((((.((---------.((((((....)))---))))).)))))))))...........)))))))))))...))))))). ( -29.00)
>DroEre_CAF1 128159 113 + 1
CAGUGCGAGACAUUAGUGUAAGUAC-A---GAAACUUUGAGCAAACUUAUUCAAACAGUUCAUUACUCA---GAUAUCUGUUAGCUUAAAUACCAAAUUUUUCGCUAUGAUACGCACUGU
(((((((...(((.(((((((((((-(---((...((((((..((((.........)))).....))))---))..)))))..)))))..............)))))))...))))))). ( -24.93)
>DroYak_CAF1 132656 115 + 1
CAGUGCGAGACAUCAGUGCAAGUAC-AAGGGGAACUUU-AGCAAACUUAUUCAAACAACCCAUUACUUA---AAUAUCUGUUAGCUUAAAUACUUAAUUUUUAGUUAUGAUACGCACUGU
(((((((............(((((.-..(((.......-...................)))..))))).---..((((...(((((.(((........))).))))).))))))))))). ( -22.47)
>consensus
CAGUGCGAGACAUUAGUGUAAGUGC_AAGGGGAACUUUAAGCAAACUU_U_CAAACAAUUCAUUACUGA___AAUAUCUGUUAGUUUAAAUACCAUAUUUUGCGCUAUGAUACGCACUGU
(((((((...(((.((((((((.......((....(((((((.(((.................................))).)))))))..))....)))))))))))...))))))). (-17.09 = -17.61 +   0.52)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,143,608 – 13,143,727
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.95
Mean single sequence MFE -26.65
Consensus MFE -12.16
Energy contribution -12.96
Covariance contribution 0.80
Combinations/Pair 1.19
Mean z-score -2.21
Structure conservation index 0.46
SVM decision value 0.50
SVM RNA-class probability 0.760390
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13143608 119 - 23771897
ACAGUGCGUAUCAUAGAGCAAAGUAUGGUAUUAAAACUAACAGAUAUUUUUUUAGUAAUGAAUUGUUUGUACAAGUUUGCUUUAAGUUCCCCUU-GCACUUACACUAAUGUCUCGCACUG
.(((((((...(((.(((((((.(.((((......))))(((((((....((((....)))).)))))))...).)))))))(((((.(.....-).))))).....)))...))))))) ( -28.00)
>DroSec_CAF1 131304 107 - 1
ACAGUGCGUAUCAUAGCGCAAAAUAUGGUAUGUAAACUAGCAGAUAUU---UCAGUAAUGAAAUG---------GUUUGCUUAAAUUACCCCUU-GCACUUACACUAAUGUCUCGCACUG
.(((((((...(((((.((((.....((((........((((((((((---(((....)))))).---------))))))).....))))..))-)).)).......)))...))))))) ( -31.33)
>DroSim_CAF1 131205 108 - 1
ACAGUGCGUAUCAUAGCGCAAAAAAUGGUAUUUAAACUAGCAGAUAUU---UCACUAUUGAAAUG---------AUUUGCUUAAAGUUCCCUUUCGCACUUACACUUAUGUCUCACACUG
.(((((.(...(((((((....(((.((.((((.....((((((((((---(((....)))))).---------)))))))..)))).)).)))))).........))))...).))))) ( -21.20)
>DroEre_CAF1 128159 113 - 1
ACAGUGCGUAUCAUAGCGAAAAAUUUGGUAUUUAAGCUAACAGAUAUC---UGAGUAAUGAACUGUUUGAAUAAGUUUGCUCAAAGUUUC---U-GUACUUACACUAAUGUCUCGCACUG
.(((((((...((((((...((((.....))))..))))(((((..(.---(((((...(((((.........)))))))))).)...))---)-))...........))...))))))) ( -27.80)
>DroYak_CAF1 132656 115 - 1
ACAGUGCGUAUCAUAACUAAAAAUUAAGUAUUUAAGCUAACAGAUAUU---UAAGUAAUGGGUUGUUUGAAUAAGUUUGCU-AAAGUUCCCCUU-GUACUUGCACUGAUGUCUCGCACUG
.(((((((...(((((((.....((((((((((........)))))))---)))......))))((..(.(((((...((.-...))....)))-)).)..))....)))...))))))) ( -24.90)
>consensus
ACAGUGCGUAUCAUAGCGCAAAAUAUGGUAUUUAAACUAACAGAUAUU___UCAGUAAUGAAAUGUUUG_A_AAGUUUGCUUAAAGUUCCCCUU_GCACUUACACUAAUGUCUCGCACUG
.(((((((...(((...(((((...((((......))))............(((....)))..............)))))...((((.(......).))))......)))...))))))) (-12.16 = -12.96 +   0.80)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:26 2006