Locus 10182

Sequence ID 3R_DroMel_CAF1
Location 27,310,854 – 27,310,994
Length 140
Max. P 0.978830
window16212 window16213

overview

Window 2

Location 27,310,854 – 27,310,954
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.12
Mean single sequence MFE -36.29
Consensus MFE -31.65
Energy contribution -31.34
Covariance contribution -0.30
Combinations/Pair 1.21
Mean z-score -2.64
Structure conservation index 0.87
SVM decision value 1.82
SVM RNA-class probability 0.978830
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27310854 100 - 27905053
ACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCUGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGCU---------------GCUCAAAUGUGUCCCACAA-----
.(..(((((((..((((((((.....))))).........(((....))))))..)))))))..).....((((((((.(.---------------........)))))))))..----- ( -34.00)
>DroSec_CAF1 15757 100 - 1
ACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGCU---------------GCUCAAAUGUGUCCCACAA-----
.(..(((((((..((((((((.....)))))........(((.....))))))..)))))))..).....((((((((.(.---------------........)))))))))..----- ( -36.60)
>DroSim_CAF1 16213 100 - 1
ACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGCU---------------GCUCAAAUGUGUCCCACAA-----
.(..(((((((..((((((((.....)))))........(((.....))))))..)))))))..).....((((((((.(.---------------........)))))))))..----- ( -36.60)
>DroEre_CAF1 16041 100 - 1
ACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGCU---------------GCUCAAAUGUGUCCCACAA-----
.(..(((((((..((((((((.....)))))........(((.....))))))..)))))))..).....((((((((.(.---------------........)))))))))..----- ( -36.60)
>DroYak_CAF1 12134 100 - 1
ACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGCU---------------GCUCAAAUGUGUCCCACAA-----
.(..(((((((..((((((((.....)))))........(((.....))))))..)))))))..).....((((((((.(.---------------........)))))))))..----- ( -36.60)
>DroAna_CAF1 17695 120 - 1
ACGAAACCCGGCUAGCUUGUCAUAAAUGCGAUUCUGUAACCCAUUUUGCGACUAUUUGGGUUAAGGGCAAGUGGGACAGAUCCACGGAUCACAUUGGCUUGGAUUCGUCCCACAAUUUAG
......((((((......)))...............(((((((.............))))))).)))...(((((((..(((((.((.((.....)))))))))..)))))))....... ( -37.32)
>consensus
ACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGCU_______________GCUCAAAUGUGUCCCACAA_____
.(..(((((((..((((((((.....)))))........(((.....))))))..)))))))..).....(((((((.((........................)))))))))....... (-31.65 = -31.34 +  -0.30)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 3

Location 27,310,874 – 27,310,994
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -39.73
Consensus MFE -35.98
Energy contribution -35.98
Covariance contribution 0.00
Combinations/Pair 1.18
Mean z-score -1.25
Structure conservation index 0.91
SVM decision value 0.48
SVM RNA-class probability 0.752347
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27310874 120 - 27905053
GAGCUGGCCAAAAAGCCUGACUUAUUUGUGGCCGCCAGACACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCUGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGC
..((((.(((....((((.......(((((.........)))))(((((((..((((((((.....))))).........(((....))))))..)))))))..))))...)))..)))) ( -38.50)
>DroSec_CAF1 15777 120 - 1
GAGCUGGCCAAAAAGCCUGACUUAUUUGUGGCCGCCAGACACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGC
..((((.(((....((((.......(((((.........)))))(((((((..((((((((.....)))))........(((.....))))))..)))))))..))))...)))..)))) ( -41.10)
>DroSim_CAF1 16233 120 - 1
GAGCUGGCCAAAAAGCCUGACUUAUUUGUGGCCGCCAGACACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGC
..((((.(((....((((.......(((((.........)))))(((((((..((((((((.....)))))........(((.....))))))..)))))))..))))...)))..)))) ( -41.10)
>DroEre_CAF1 16061 120 - 1
GAGCUGGCCAAAAAGCCUGACUUAUUUGUGGCCGCCAGACACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGC
..((((.(((....((((.......(((((.........)))))(((((((..((((((((.....)))))........(((.....))))))..)))))))..))))...)))..)))) ( -41.10)
>DroYak_CAF1 12154 120 - 1
GAGCUGGCCAAAAAGCCUGACUUAUUUGUGGUCGCCAGACACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGC
..((((.(((....((((.......(((((.((....)))))))(((((((..((((((((.....)))))........(((.....))))))..)))))))..))))...)))..)))) ( -42.50)
>DroAna_CAF1 17735 117 - 1
GAGCUGGUCG---AGCCUGACUUAUUUGUGGCAGCCAGACACGAAACCCGGCUAGCUUGUCAUAAAUGCGAUUCUGUAACCCAUUUUGCGACUAUUUGGGUUAAGGGCAAGUGGGACAGA
..((.(((((---....))))).((((((((((((.((...((.....)).)).)).))))))))))))...(((((..(((((((.((((((.....))))....)))))))))))))) ( -34.10)
>consensus
GAGCUGGCCAAAAAGCCUGACUUAUUUGUGGCCGCCAGACACGAAAUCCAGGGGGCUUGUAAUAAAUGCGAUUCUGUAACCCAUUUCGGGGCUUUCUGGGUUAAGGGCAAGUGGGACAGC
..((((.(((....((((.......(((((.........)))))(((((((..((((((((.....)))))........(((.....))))))..)))))))..))))...)))..)))) (-35.98 = -35.98 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:50:50 2006