Locus 1456

Sequence ID 2L_DroMel_CAF1
Location 3,858,068 – 3,858,199
Length 131
Max. P 0.978707
window2369 window2370 window2371

overview

Window 9

Location 3,858,068 – 3,858,168
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.19
Mean single sequence MFE -34.18
Consensus MFE -30.68
Energy contribution -31.07
Covariance contribution 0.39
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.90
SVM decision value 1.82
SVM RNA-class probability 0.978707
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3858068 100 + 22407834
UCCUCCU--ACU-------------GCCAAUUUAAUGUGUCGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC-----
.......--...-------------(((((((.((((((((.(((((((..((((((.....)))))).))))))).)....))))))).)))))))........(((....)))----- ( -34.40)
>DroSim_CAF1 45779 100 + 1
UCCUCCU--ACU-------------GCCAAUUUAAUGUGUCGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC-----
.......--...-------------(((((((.((((((((.(((((((..((((((.....)))))).))))))).)....))))))).)))))))........(((....)))----- ( -34.40)
>DroEre_CAF1 51657 100 + 1
UCCUCCU--ACU-------------GCCAAUUUAAUGUGUCGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGGC-----
....((.--...-------------(((((((.((((((((.(((((((..((((((.....)))))).))))))).)....))))))).)))))))........(....).)).----- ( -32.40)
>DroWil_CAF1 85561 117 + 1
UCCCUCG--ACUGCAACCAGAGUCCGCCAAUUUAAUGUGUCGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUG-CCAACUGGCCUCGACUUCGGCUCU
......(--(((........)))).(((((((.((((((((.(((((((..((((((.....)))))).))))))).)....))))))).))))(-((....))).........)))... ( -34.60)
>DroYak_CAF1 49167 100 + 1
UCCUCCU--ACU-------------GCCAAUUUAAUGUGUCGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC-----
.......--...-------------(((((((.((((((((.(((((((..((((((.....)))))).))))))).)....))))))).)))))))........(((....)))----- ( -34.40)
>DroAna_CAF1 47313 102 + 1
UCUCCCUGCGCU-------------GCCAAUUUAAUGUGUCGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC-----
......((((((-------------(............(((.(((((((..((((((.....)))))).))))))).))))))))))..((((((.(((.....)))))))))..----- ( -34.90)
>consensus
UCCUCCU__ACU_____________GCCAAUUUAAUGUGUCGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC_____
.........................(((((((.((((((((.(((((((..((((((.....)))))).))))))).)....))))))).)))))))........(((....)))..... (-30.68 = -31.07 +   0.39)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,858,093 – 3,858,199
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.28
Mean single sequence MFE -40.78
Consensus MFE -23.13
Energy contribution -24.44
Covariance contribution 1.31
Combinations/Pair 1.07
Mean z-score -2.56
Structure conservation index 0.57
SVM decision value 0.97
SVM RNA-class probability 0.891683
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3858093 106 + 22407834
CGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC------AGGCAAACGG--UUCGCCAGCAGAGUGCUG-CUG-----
(.(((((((..((((((.....)))))).))))))).)..((((((((((.((((((.((((((((((....)))------).....))))--)).)))))).)))))).)-)))----- ( -47.60)
>DroSec_CAF1 46705 106 + 1
CGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC------AGGCAAACUG--CUGGCCAGCAUAGUGCUG-CUG-----
(.(((((((..((((((.....)))))).))))))).)..(((((((((..((((((((....(((((....)))------))((.....)--)))))))))..))))).)-)))----- ( -45.60)
>DroEre_CAF1 51682 94 + 1
CGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGGC------AGGCAAACUG--CUCGCCAGC------------------
(.(((((((..((((((.....)))))).))))))).)......((...(((((....)))))...))..(((((------..((.....)--)..))))).------------------ ( -34.30)
>DroWil_CAF1 85599 99 + 1
CGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUG-CCAACUGGCCUCGACUUCGGCUCUGCGGCCAACUGGCCUGGCCA--------------------
.((((((((..((((((.....)))))).)))))(((......)))........)-))....((((..(((....).))...((((....)))).)))).-------------------- ( -36.30)
>DroYak_CAF1 49192 112 + 1
CGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC------AGGCAAACUG--UUCGCCAGCAGAGUGCUGGCUGGCAUA
(.(((((((..((((((.....)))))).))))))).).(((((((((((.((((((.((((((((((....)))------).)))....)--)).)))))).))))))..))))).... ( -43.90)
>DroAna_CAF1 47340 105 + 1
CGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC------GAGGCAACUG--CUUGGGGAC-------UGGGCGGAUUG
..(((((((..((((((.....)))))).))))))).((((.((.((..((((((.(((.....)))))))))((------.((((....)--))).))...-------)).)).)))). ( -37.00)
>consensus
CGGCGUGUUUAUCGGCUAAUGAAGUUGACAACACGCGGAUUAGCGCAUUUAGUUGGCCAACUGUUGGCAACUGCC______AGGCAAACUG__CUCGCCAGC_______UG_CUG_____
(.(((((((..((((((.....)))))).))))))).)....(((....(((((.(((.......(((....))).......))).)))))....)))...................... (-23.13 = -24.44 +   1.31)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,858,093 – 3,858,199
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.28
Mean single sequence MFE -33.08
Consensus MFE -20.38
Energy contribution -21.22
Covariance contribution 0.84
Combinations/Pair 1.10
Mean z-score -1.63
Structure conservation index 0.62
SVM decision value 0.14
SVM RNA-class probability 0.604900
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3858093 106 - 22407834
-----CAG-CAGCACUCUGCUGGCGAA--CCGUUUGCCU------GGCAGUUGCCAACAGUUGGCCAACUAAAUGCGCUAAUCCGCGUGUUGUCAACUUCAUUAGCCGAUAAACACGCCG
-----.((-(((....)))))((((..--..(((((..(------(((((((((((.....))).))))).(((((((......))))))).............)))).))))).)))). ( -34.10)
>DroSec_CAF1 46705 106 - 1
-----CAG-CAGCACUAUGCUGGCCAG--CAGUUUGCCU------GGCAGUUGCCAACAGUUGGCCAACUAAAUGCGCUAAUCCGCGUGUUGUCAACUUCAUUAGCCGAUAAACACGCCG
-----.((-(.(((....(.(((((((--(.((.....(------(((....)))))).)))))))).)....)))))).....((((((((((..((.....))..))).))))))).. ( -36.20)
>DroEre_CAF1 51682 94 - 1
------------------GCUGGCGAG--CAGUUUGCCU------GCCAGUUGCCAACAGUUGGCCAACUAAAUGCGCUAAUCCGCGUGUUGUCAACUUCAUUAGCCGAUAAACACGCCG
------------------(((((((.(--(.....)).)------))))))........((((((((......)).))))))..((((((((((..((.....))..))).))))))).. ( -29.20)
>DroWil_CAF1 85599 99 - 1
--------------------UGGCCAGGCCAGUUGGCCGCAGAGCCGAAGUCGAGGCCAGUUGG-CAACUAAAUGCGCUAAUCCGCGUGUUGUCAACUUCAUUAGCCGAUAAACACGCCG
--------------------.(((..((((....))))((.(.(((........))))((((((-((((...(((((......)))))))))))))))......))..........))). ( -36.10)
>DroYak_CAF1 49192 112 - 1
UAUGCCAGCCAGCACUCUGCUGGCGAA--CAGUUUGCCU------GGCAGUUGCCAACAGUUGGCCAACUAAAUGCGCUAAUCCGCGUGUUGUCAACUUCAUUAGCCGAUAAACACGCCG
...((((((((((.....))))))...--.((((.((((------(((....))))......))).))))...)).))......((((((((((..((.....))..))).))))))).. ( -37.10)
>DroAna_CAF1 47340 105 - 1
CAAUCCGCCCA-------GUCCCCAAG--CAGUUGCCUC------GGCAGUUGCCAACAGUUGGCCAACUAAAUGCGCUAAUCCGCGUGUUGUCAACUUCAUUAGCCGAUAAACACGCCG
...........-------........(--(.(((...((------(((((((((((.....))).))))).(((((((......))))))).............)))))..)))..)).. ( -25.80)
>consensus
_____CAG_CA_______GCUGGCGAG__CAGUUUGCCU______GGCAGUUGCCAACAGUUGGCCAACUAAAUGCGCUAAUCCGCGUGUUGUCAACUUCAUUAGCCGAUAAACACGCCG
.....................((((((.....)))))).......(((....)))....((((((((......)).))))))..((((((((((..((.....))..))).))))))).. (-20.38 = -21.22 +   0.84)

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 10:03:07 2006