Locus 2134

Sequence ID 2L_DroMel_CAF1
Location 5,777,400 – 5,777,527
Length 127
Max. P 0.778811
window3451 window3452

overview

Window 1

Location 5,777,400 – 5,777,495
Length 95
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 71.71
Mean single sequence MFE -20.62
Consensus MFE -6.70
Energy contribution -7.18
Covariance contribution 0.48
Combinations/Pair 1.28
Mean z-score -1.85
Structure conservation index 0.32
SVM decision value 0.55
SVM RNA-class probability 0.778811
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5777400 95 - 22407834
CCCAAGGGGA-GGCAACA----AAAUAUUUGCACAGAGAUGAACUUGUGAAUGCCCUUUGAAAUACUUUUUUUUAAAAAUUAAGCAAUUA-GCAACAUUUU---------------
..(((((((.-(....).----...((((..((.((.......))))..))))))))))).......................((.....-))........--------------- ( -16.50)
>DroSec_CAF1 14505 93 - 1
CACAAGGGGCGGGCAGCA----AAAUAUUUGCACAGAGAUGAACUUGUGAAUGCCCUUUGAAAUACUUU---UCGAAAAUUAAGCAAUUA-GCUACAUUUU---------------
..(((((((((..(((((----(.....))))...(((.....))).))..))))))))).........---..........(((.....-))).......--------------- ( -21.50)
>DroSim_CAF1 15272 93 - 1
CACAAGGGGCGGGCAGCA----AAAUAUUUGCACAGAGAUGAACUUGUGAAUGCCCUUUGAAAUACUUU---UCGAAAAUUAAGCAAUUA-GCUACAUUUU---------------
..(((((((((..(((((----(.....))))...(((.....))).))..))))))))).........---..........(((.....-))).......--------------- ( -21.50)
>DroEre_CAF1 14621 109 - 1
CCCAUGGGG--G-A-CUAUUUUGUUUAUUUUCAGGGAGGUGAACUUGCACAUGCCCUUUGAAAUACUUG---UAAUAAAUUAAACAUUUAUGCAACAUUAAAAAGUAUGUGUAGCA
...((((..--.-.-))))...(((((((((....)))))))))((((((((((..(((((.....(((---((.(((((.....))))))))))..)))))..)))))))))).. ( -25.30)
>DroYak_CAF1 15044 87 - 1
CCCAAAGAG--GGAAGCA-----AAUAUUUGCAGGCAAAUGAACUUGCAAAUGCCCUCUAAAAUACAUU---UAAUACAUUAAACAUUUA-GCAACAA------------------
.....((((--((.....-----..((((((((((........))))))))))))))))..........---..................-.......------------------ ( -18.31)
>consensus
CCCAAGGGG__GGCAGCA____AAAUAUUUGCACAGAGAUGAACUUGUGAAUGCCCUUUGAAAUACUUU___UAAAAAAUUAAGCAAUUA_GCAACAUUUU_______________
..(((((((..(....)........((((((((.((.......)))))))))))))))))........................................................ ( -6.70 =  -7.18 +   0.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,777,424 – 5,777,527
Length 103
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 81.82
Mean single sequence MFE -25.78
Consensus MFE -12.70
Energy contribution -13.18
Covariance contribution 0.48
Combinations/Pair 1.19
Mean z-score -2.30
Structure conservation index 0.49
SVM decision value 0.34
SVM RNA-class probability 0.695987
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5777424 103 - 22407834
GAUUGAACAUCAAAUUCAGAUGUUUUCGCAUUCCCAAGGGGA-GGCAACA----AAAUAUUUGCACAGAGAUGAACUUGUGAAUGCCCUUUGAAAUACUUUUUUUUAA
(...(((((((.......)))))))...).....(((((((.-(....).----...((((..((.((.......))))..)))))))))))................ ( -21.70)
>DroSec_CAF1 14529 101 - 1
GAUUGAACAUCAAAUUCAGAUGUUUUCGCAUUCACAAGGGGCGGGCAGCA----AAAUAUUUGCACAGAGAUGAACUUGUGAAUGCCCUUUGAAAUACUUU---UCGA
((..(((((((.......)))))))))(((((((((((.........(((----(.....)))).((....))..)))))))))))...((((((....))---)))) ( -27.80)
>DroSim_CAF1 15296 101 - 1
GAUUGAACAUCAAAUUCAGAUGUUUUCGCAUUCACAAGGGGCGGGCAGCA----AAAUAUUUGCACAGAGAUGAACUUGUGAAUGCCCUUUGAAAUACUUU---UCGA
((..(((((((.......)))))))))(((((((((((.........(((----(.....)))).((....))..)))))))))))...((((((....))---)))) ( -27.80)
>DroEre_CAF1 14661 101 - 1
GAUUGAACAUCAAAUUCAGAUGUUUUCCCCUUCCCAUGGGG--G-A-CUAUUUUGUUUAUUUUCAGGGAGGUGAACUUGCACAUGCCCUUUGAAAUACUUG---UAAU
....(((((((.......)))))))((((((......))))--)-)-..........((((((.((((..(((......)))...))))..))))))....---.... ( -26.20)
>DroYak_CAF1 15065 98 - 1
GAUUGAACAUCAAAUUCAGAUGUUUUCGCAUUCCCAAAGAG--GGAAGCA-----AAUAUUUGCAGGCAAAUGAACUUGCAAAUGCCCUCUAAAAUACAUU---UAAU
((..(((((((.......)))))))))((.(((((.....)--)))))).-----..((((((((((........))))))))))................---.... ( -25.40)
>consensus
GAUUGAACAUCAAAUUCAGAUGUUUUCGCAUUCCCAAGGGG__GGCAGCA____AAAUAUUUGCACAGAGAUGAACUUGUGAAUGCCCUUUGAAAUACUUU___UAAA
(...(((((((.......)))))))...).....(((((((..(....)........((((((((.((.......)))))))))))))))))................ (-12.70 = -13.18 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:32 2006