Locus 1611

Sequence ID 3R_DroMel_CAF1
Location 4,655,072 – 4,655,192
Length 120
Max. P 0.959560
window2655 window2656

overview

Window 5

Location 4,655,072 – 4,655,162
Length 90
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 80.28
Mean single sequence MFE -26.62
Consensus MFE -19.12
Energy contribution -18.65
Covariance contribution -0.47
Combinations/Pair 1.37
Mean z-score -1.89
Structure conservation index 0.72
SVM decision value 0.85
SVM RNA-class probability 0.866268
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4655072 90 + 27905053
AUUGCU------CCACCAUUCCUUCAUUGUGCAGAUUAUUUUCAAUAGCUGUUGGCUGCUCUGUCUGAUCCGCAGAGCUCUCAGCGGGA------UCACGCU
......------..................((.((......)).....(((((((..(((((((.......)))))))..)))))))..------....)). ( -21.60)
>DroSec_CAF1 4803 90 + 1
CUUGCU------CCACCAUUCCCUCGUUGUGCAGAUUAUUUUCAAUAGCCGUUGGCUGCUCUGUCUGAUCCGCAGAGCUCUCAGCGGGA------UCAUUCU
......------.......((((..(((((...((......)).))))).(((((..(((((((.......)))))))..)))))))))------....... ( -25.20)
>DroSim_CAF1 5019 90 + 1
CUUGUU------CCACCAUUCCCUCGUUGUGCAGAUUAUUUUCAAUAGCCGUUGGCUGCUCUGUCUGAUCAGCAGAGCUCUCAGCGGGA------UCAUUCU
......------.......((((..(((((...((......)).))))).(((((..((((((.((....))))))))..)))))))))------....... ( -25.80)
>DroEre_CAF1 5089 90 + 1
UUUGCU------CCACCAUUCCCUCGUUGUGUAGAUUGUUUUCAAUGGCCGUUGGCAGCUCUGUCUGAUCCGCAGAGCUUUCAGCGGGA------UCAUCCC
......------.......((((((((((.............))))))..(((((.((((((((.......)))))))).)))))))))------....... ( -26.22)
>DroYak_CAF1 5213 90 + 1
CUUGUU------CCACCAUUCCCUCGUUGUGUAGAUUAUUUUCAAUGGCCGUUGGAAGCUCUGUCUGAUCCACAGAGCUCUCAGCGGGA------UCAUUCU
......------.......((((((((((.............))))))..((((..((((((((.......))))))))..))))))))------....... ( -27.22)
>DroAna_CAF1 8441 102 + 1
UUUCAUUGGCCAGCAACAUGGCCUCAUUGUGAUGGUUGUUUUCAAUGGCCGUGACCUGUUCUGUGGCCUCCAUGGAGCUCUCAUCGGGGAUUUCGUCACCCU
.......(((((..((.(..(((((.....)).)))..).))...)))))(((((..(((((((((...)))))))))((((....))))....)))))... ( -33.70)
>consensus
CUUGCU______CCACCAUUCCCUCGUUGUGCAGAUUAUUUUCAAUAGCCGUUGGCUGCUCUGUCUGAUCCGCAGAGCUCUCAGCGGGA______UCAUUCU
............................(((..((......)).....(((((((..(((((((.......)))))))..))))))).........)))... (-19.12 = -18.65 +  -0.47)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,655,102 – 4,655,192
Length 90
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 80.29
Mean single sequence MFE -28.95
Consensus MFE -21.46
Energy contribution -22.18
Covariance contribution 0.72
Combinations/Pair 1.23
Mean z-score -2.93
Structure conservation index 0.74
SVM decision value 1.50
SVM RNA-class probability 0.959560
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4655102 90 + 27905053
UAUUUUCAAUAGCUGUUGGCUGCUCUGUCUGAUCCGCAGAGCUCUCAGCGGGAUCACGCUGAUCCUGAACCUCCUC---CUCUUCGUCA---UCAU
....(((.......(((((..(((((((.......)))))))..)))))((((((.....))))))))).......---..........---.... ( -24.90)
>DroGri_CAF1 5926 93 + 1
GAUUCUCAAUUGUGGUCGGUUGCUCUGCUGGCUCUGCAGAGCUAUCUGCCUCCUGAUCCAGUUCCGGAUCCGCCUGCUGCUCGGCAUCG---UCAU
(((..........(((.(((.(((((((.......))))))).))).)))....(((((......))))).(((........)))...)---)).. ( -30.30)
>DroSec_CAF1 4833 90 + 1
UAUUUUCAAUAGCCGUUGGCUGCUCUGUCUGAUCCGCAGAGCUCUCAGCGGGAUCAUUCUGAUCCUGAACCUCUUC---CUCUUCGUCA---UCAU
....((((.....((((((..(((((((.......)))))))..))))))(((((.....))))))))).......---..........---.... ( -26.60)
>DroSim_CAF1 5049 90 + 1
UAUUUUCAAUAGCCGUUGGCUGCUCUGUCUGAUCAGCAGAGCUCUCAGCGGGAUCAUUCUGAUCCUGAACCUCCUC---AUCUUCGUCA---UCAU
....((((.....((((((..((((((.((....))))))))..))))))(((((.....))))))))).......---..........---.... ( -27.20)
>DroEre_CAF1 5119 90 + 1
UGUUUUCAAUGGCCGUUGGCAGCUCUGUCUGAUCCGCAGAGCUUUCAGCGGGAUCAUCCCGAGCCUGAGCCUGCUC---UUCUUCGUCG---UCAU
........(((((.(((((.((((((((.......)))))))).)))))(((.....)))((((........))))---.........)---)))) ( -30.70)
>DroYak_CAF1 5243 93 + 1
UAUUUUCAAUGGCCGUUGGAAGCUCUGUCUGAUCCACAGAGCUCUCAGCGGGAUCAUUCUGAUCCUGAACCUCCUC---CUCUUGGUCGUCAUCAU
........((((((((((..((((((((.......))))))))..))))((((((.....))))))..........---.....))))))...... ( -34.00)
>consensus
UAUUUUCAAUAGCCGUUGGCUGCUCUGUCUGAUCCGCAGAGCUCUCAGCGGGAUCAUUCUGAUCCUGAACCUCCUC___CUCUUCGUCA___UCAU
....((((.....((((((..(((((((.......)))))))..))))))(((((.....)))))))))........................... (-21.46 = -22.18 +   0.72)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:49 2006