Locus 5179

Sequence ID 3R_DroMel_CAF1
Location 13,574,632 – 13,574,742
Length 110
Max. P 0.992837
window8459 window8460

overview

Window 9

Location 13,574,632 – 13,574,742
Length 110
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 72.51
Mean single sequence MFE -19.23
Consensus MFE -9.15
Energy contribution -10.15
Covariance contribution 1.00
Combinations/Pair 1.32
Mean z-score -2.17
Structure conservation index 0.48
SVM decision value 0.67
SVM RNA-class probability 0.818729
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13574632 110 + 27905053
------C---UAACCAAAGCCUAUUAAGCACAAUUAUGAGCAACAUAAAUAACUUUUAAUGUUACUCAACGUCAAGUUGCUUGCUUAAUGAACCUCUCAGUCAUAACUUGCAUUUAUAA
------.---........((.((((((((((((((.((((.(((((.((......)).))))).))))......)))))..)))))))))........(((....))).))........ ( -15.80)
>DroSec_CAF1 16346 116 + 1
CAUAUAUUUAUA---AAAACCUAUUAAGCACAAUUAUGAGCAACAAAAAUAACUUUAACUGUUACUCAACGCAAAGUUGCUUGCUUAAUGAACCUCUCAGUCAUAACUGGCAUUUAUAA
.......(((((---((....(((((((((......((((.((((..............)))).))))..(((....))).))))))))).........((((....)))).))))))) ( -20.24)
>DroSim_CAF1 15638 119 + 1
CGUAUAUUCAUAACCAAAACCUAUUAAGCACAAUUAUGAGCAACAUAAAUAACUUUAAAUGUUACUCAACGCAAAGUUGCUUGCUUAAUGAACCUCUCAGUCAUAACUGGCAUUUAUAA
.((..................(((((((((......((((.(((((............))))).))))..(((....))).))))))))).......((((....))))))........ ( -19.60)
>DroEre_CAF1 15003 96 + 1
----------------------UUUAAAAGCCAAACUGAGUGAGAUAAAUAAAUUUAAACUUCAUUCAACAGCAAGCUGCGUGCCUAGUGAAGCUCCUAGGCAUACCAUGCAUUUAUG-
----------------------..((((.((.....((((((((.((((....))))...)))))))).(((....))).((((((((.(.....))))))))).....)).))))..- ( -21.30)
>consensus
______U___UA___AAAACCUAUUAAGCACAAUUAUGAGCAACAUAAAUAACUUUAAAUGUUACUCAACGCAAAGUUGCUUGCUUAAUGAACCUCUCAGUCAUAACUGGCAUUUAUAA
.....................(((((((((......((((.(((((............))))).))))..((......)).)))))))))......(((((....)))))......... ( -9.15 = -10.15 +   1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,574,632 – 13,574,742
Length 110
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 72.51
Mean single sequence MFE -28.45
Consensus MFE -14.29
Energy contribution -14.35
Covariance contribution 0.06
Combinations/Pair 1.25
Mean z-score -2.66
Structure conservation index 0.50
SVM decision value 2.35
SVM RNA-class probability 0.992837
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13574632 110 - 27905053
UUAUAAAUGCAAGUUAUGACUGAGAGGUUCAUUAAGCAAGCAACUUGACGUUGAGUAACAUUAAAAGUUAUUUAUGUUGCUCAUAAUUGUGCUUAAUAGGCUUUGGUUA---G------
................(((((..(((((..(((((((((((........)))(((((((((............))))))))).......))))))))..))))))))))---.------ ( -27.20)
>DroSec_CAF1 16346 116 - 1
UUAUAAAUGCCAGUUAUGACUGAGAGGUUCAUUAAGCAAGCAACUUUGCGUUGAGUAACAGUUAAAGUUAUUUUUGUUGCUCAUAAUUGUGCUUAAUAGGUUUU---UAUAAAUAUAUG
(((((((.(((......((((....)))).((((((((.(((....)))..((((((((((............))))))))))......)))))))).))).))---)))))....... ( -32.10)
>DroSim_CAF1 15638 119 - 1
UUAUAAAUGCCAGUUAUGACUGAGAGGUUCAUUAAGCAAGCAACUUUGCGUUGAGUAACAUUUAAAGUUAUUUAUGUUGCUCAUAAUUGUGCUUAAUAGGUUUUGGUUAUGAAUAUACG
.............(((((((..(((..(..((((((((.(((....)))..((((((((((............))))))))))......))))))))..))))..)))))))....... ( -30.60)
>DroEre_CAF1 15003 96 - 1
-CAUAAAUGCAUGGUAUGCCUAGGAGCUUCACUAGGCACGCAGCUUGCUGUUGAAUGAAGUUUAAAUUUAUUUAUCUCACUCAGUUUGGCUUUUAAA----------------------
-............(..(((((((........)))))))..)((((.((((.((((((((...........))))).)))..))))..))))......---------------------- ( -23.90)
>consensus
UUAUAAAUGCAAGUUAUGACUGAGAGGUUCAUUAAGCAAGCAACUUGGCGUUGAGUAACAUUUAAAGUUAUUUAUGUUGCUCAUAAUUGUGCUUAAUAGGUUUU___UA___A______
........((.....((((((....)).))))...))((((.((.......((((((((((............)))))))))).....))))))......................... (-14.29 = -14.35 +   0.06)

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 11:48:28 2006