Locus 8109

Sequence ID 3L_DroMel_CAF1
Location 21,342,237 – 21,342,349
Length 112
Max. P 0.925861
window13252 window13253

overview

Window 2

Location 21,342,237 – 21,342,349
Length 112
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 87.22
Mean single sequence MFE -24.66
Consensus MFE -19.28
Energy contribution -19.96
Covariance contribution 0.68
Combinations/Pair 1.07
Mean z-score -2.12
Structure conservation index 0.78
SVM decision value 1.17
SVM RNA-class probability 0.925861
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21342237 112 + 23771897
CGGCUUUUUAUGCACUAUUUUUUUUUUUUUUUUUUGAUUUA-----CCGCAACUGCGGUUGCGCCCAUUGUCGCAUAAAUUCAUUCUUAAUUAACAAGAAUGAGGAGCACAUCCCGA
..(((((((((((...........................(-----((((....))))).(((.....))).)))))))(((((((((.......)))))))))))))......... ( -24.40)
>DroSec_CAF1 45129 116 + 1
CUGCUUUCUAGACACUAUUUUUUAUU-UUCUUUUUAAUUUAUGCACUCGCAACUGCGGUUGCGCCCAUUGUCGCAUAAAUUCAUUCUUAAUUAACAAGAAUGAGGAGCACAUCCCGA
.((((((...................-.........((((((((((.((((((....))))))......)).))))))))((((((((.......))))))))))))))........ ( -26.00)
>DroSim_CAF1 46306 116 + 1
CUGCUUUCUAGACACUAUUUUUUCUU-UUCUUUUUAAUUUAUGCCAUCGCAACUGCGGUUGCGCCCAUUGUCGCAUAAAUUUAUUCUUAAUUAACAAGAAUGAGGAGCACAUCCCGA
.((((((...................-.........((((((((.((((((((....))))))......)).))))))))((((((((.......))))))))))))))........ ( -22.70)
>DroEre_CAF1 47253 110 + 1
CCGCUUUCUAGACACUACUUUAUU-------UUUUAAUUUAUGCACUCGCAUUGGCGGUUGCGCCCACUGUCGCAUAAAUUCAUUCUUAAUUAACAAGAAUGAGGAGCACAUCCCGA
..(((((.................-------.....((((((((....(((..((((....))))...))).))))))))((((((((.......)))))))))))))......... ( -24.60)
>DroYak_CAF1 72726 109 + 1
CCGCUUUCUAGACACUAUUUCAUG--------UUUAAUUUAUGCACACGCAUCUGCGGUUGCGCCCAUUGUCGCAUAAAUUCAUUCUUAAUUAACAAGAAUGAGGAGCACAUCCCGA
..(((((.((((((........))--------))))(((((((((((((((........)))).....))).))))))))((((((((.......)))))))))))))......... ( -25.60)
>consensus
CCGCUUUCUAGACACUAUUUUUUUUU_UU_UUUUUAAUUUAUGCACUCGCAACUGCGGUUGCGCCCAUUGUCGCAUAAAUUCAUUCUUAAUUAACAAGAAUGAGGAGCACAUCCCGA
..(((((.............................((((((((...((((((....)))))).........))))))))((((((((.......)))))))))))))......... (-19.28 = -19.96 +   0.68)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,342,237 – 21,342,349
Length 112
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 87.22
Mean single sequence MFE -27.54
Consensus MFE -19.82
Energy contribution -20.86
Covariance contribution 1.04
Combinations/Pair 1.11
Mean z-score -1.84
Structure conservation index 0.72
SVM decision value 0.28
SVM RNA-class probability 0.666977
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21342237 112 - 23771897
UCGGGAUGUGCUCCUCAUUCUUGUUAAUUAAGAAUGAAUUUAUGCGACAAUGGGCGCAACCGCAGUUGCGG-----UAAAUCAAAAAAAAAAAAAAAAAAUAGUGCAUAAAAAGCCG
.(((.(((..((..(((((((((.....))))))))).....((((........))))(((((....))))-----)........................))..)))......))) ( -27.50)
>DroSec_CAF1 45129 116 - 1
UCGGGAUGUGCUCCUCAUUCUUGUUAAUUAAGAAUGAAUUUAUGCGACAAUGGGCGCAACCGCAGUUGCGAGUGCAUAAAUUAAAAAGAA-AAUAAAAAAUAGUGUCUAGAAAGCAG
.....(((..(((.(((((((((.....)))))))))......(((((..(((......)))..))))))))..))).............-.......................... ( -28.40)
>DroSim_CAF1 46306 116 - 1
UCGGGAUGUGCUCCUCAUUCUUGUUAAUUAAGAAUAAAUUUAUGCGACAAUGGGCGCAACCGCAGUUGCGAUGGCAUAAAUUAAAAAGAA-AAGAAAAAAUAGUGUCUAGAAAGCAG
........((((..(((((((((.....))))))).(((((((((.(.......((((((....)))))).).)))))))))........-..................)).)))). ( -23.70)
>DroEre_CAF1 47253 110 - 1
UCGGGAUGUGCUCCUCAUUCUUGUUAAUUAAGAAUGAAUUUAUGCGACAGUGGGCGCAACCGCCAAUGCGAGUGCAUAAAUUAAAA-------AAUAAAGUAGUGUCUAGAAAGCGG
((.(((((((((...((((((((.....))))))))((((((((((...((.((((....))))...))...))))))))))....-------.....)))).))))).))...... ( -30.50)
>DroYak_CAF1 72726 109 - 1
UCGGGAUGUGCUCCUCAUUCUUGUUAAUUAAGAAUGAAUUUAUGCGACAAUGGGCGCAACCGCAGAUGCGUGUGCAUAAAUUAAA--------CAUGAAAUAGUGUCUAGAAAGCGG
......(((((((.(((((((((.....)))))))))....((......))))))))).((((..((((....))))...(((.(--------(((......)))).)))...)))) ( -27.60)
>consensus
UCGGGAUGUGCUCCUCAUUCUUGUUAAUUAAGAAUGAAUUUAUGCGACAAUGGGCGCAACCGCAGUUGCGAGUGCAUAAAUUAAAAA_AA_AAAAAAAAAUAGUGUCUAGAAAGCAG
...(((.....)))(((((((((.....))))))))).....(((.....(((((((...(((....)))(((......)))....................)))))))....))). (-19.82 = -20.86 +   1.04)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:06:30 2006