Locus 439

Sequence ID 2L_DroMel_CAF1
Location 1,305,920 – 1,306,016
Length 96
Max. P 0.755539
window713 window714

overview

Window 3

Location 1,305,920 – 1,306,016
Length 96
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 77.24
Mean single sequence MFE -27.75
Consensus MFE -17.76
Energy contribution -17.43
Covariance contribution -0.33
Combinations/Pair 1.15
Mean z-score -1.48
Structure conservation index 0.64
SVM decision value 0.49
SVM RNA-class probability 0.755539
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1305920 96 + 22407834
AGGCGGUGACUUUUGCGGUG-CCGGGACAAAGGCCAAAAGUGUUUGGCAUGUAACGGAAAUGCGCGGCCAG--GACCACGAAGA-----AGGAAUGGUGGUAAG--------
.((((....)....(((...-(((..(((...((((((....)))))).)))..)))...)))...)))..--.(((((.(...-----.....).)))))...-------- ( -33.00)
>DroVir_CAF1 103556 80 + 1
AGGCGCUGACUUUUGCGGUC-UCGGGACAAAGGCCAAAAGUGUUUGGCAUCUAACGGAAAUGCGCGCCCGG--GGACAGUCCG-----------------------------
.(((((.(...(((.(((((-....)))....((((((....))))))......)).)))..))))))(((--(.....))))----------------------------- ( -25.00)
>DroEre_CAF1 76135 95 + 1
AGGCGGUGACUUUUGCGGUG-CCGGGACAAAGGCCAAAAGUGUUUGGCAUGUAACGGAAAUGCGCGGCCAGGACACCAAGAAGG-----AGGAAUG---GAAAG--------
..(((....)....(((...-(((..(((...((((((....)))))).)))..)))...)))))..(((...(.((.....))-----.)...))---)....-------- ( -28.70)
>DroWil_CAF1 93791 86 + 1
AGGCGGUGACUUUUGCGGUCUUUGGCACAAAGGCCAAAAGUGUUUGGCAUGUAACGGAAAUGCGCGACCAG--CAACCGAAAGG-----ACAA-------------------
....(....)..((((((((((((((......))))))........((((.........))))..)))).)--)))((....))-----....------------------- ( -26.10)
>DroYak_CAF1 67104 92 + 1
AGGCGGUGACUUUUGCGGUG-CCGGGACAAAGGCCAAAAGUGUUUGGCAUGUAACGGAAAUGCGCGGCCAG--CAGCACGAAG------UGGAAUG---GAAAG--------
.((((....)....(((...-(((..(((...((((((....)))))).)))..)))...)))...)))..--...(((...)------)).....---.....-------- ( -27.00)
>DroAna_CAF1 90678 107 + 1
AGGCGGUGACUUUUGUGGUC-CCGGGACAAAGGCCAAAAGUGUUUGGCAUGUAACGGAAAUGCGCGACCAG-AGACCAGAGAGAGAAAAUGGAAUG---GAAAUGGAAAUGG
..(((..((((.....))))-(((..(((...((((((....)))))).)))..))).....)))..(((.-...(((...........)))..))---)............ ( -26.70)
>consensus
AGGCGGUGACUUUUGCGGUC_CCGGGACAAAGGCCAAAAGUGUUUGGCAUGUAACGGAAAUGCGCGGCCAG__CACCAGGAAG______AGGAAUG___GAAAG________
.((((........((((....(((..(((...((((((....)))))).)))..)))...)))))).))........................................... (-17.76 = -17.43 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,305,920 – 1,306,016
Length 96
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 77.24
Mean single sequence MFE -21.55
Consensus MFE -13.12
Energy contribution -13.95
Covariance contribution 0.83
Combinations/Pair 1.05
Mean z-score -1.48
Structure conservation index 0.61
SVM decision value 0.23
SVM RNA-class probability 0.643956
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1305920 96 - 22407834
--------CUUACCACCAUUCCU-----UCUUCGUGGUC--CUGGCCGCGCAUUUCCGUUACAUGCCAAACACUUUUGGCCUUUGUCCCGG-CACCGCAAAAGUCACCGCCU
--------...............-----.....(((((.--...)))))((....(((..(((.((((((....))))))...)))..)))-....)).............. ( -22.80)
>DroVir_CAF1 103556 80 - 1
-----------------------------CGGACUGUCC--CCGGGCGCGCAUUUCCGUUAGAUGCCAAACACUUUUGGCCUUUGUCCCGA-GACCGCAAAAGUCAGCGCCU
-----------------------------(((.......--)))(((((.......((.((((.((((((....)))))).))))...)).-(((.......))).))))). ( -23.30)
>DroEre_CAF1 76135 95 - 1
--------CUUUC---CAUUCCU-----CCUUCUUGGUGUCCUGGCCGCGCAUUUCCGUUACAUGCCAAACACUUUUGGCCUUUGUCCCGG-CACCGCAAAAGUCACCGCCU
--------.....---.......-----.......((((...((((.(((.....(((..(((.((((((....))))))...)))..)))-...)))....)))).)))). ( -22.20)
>DroWil_CAF1 93791 86 - 1
-------------------UUGU-----CCUUUCGGUUG--CUGGUCGCGCAUUUCCGUUACAUGCCAAACACUUUUGGCCUUUGUGCCAAAGACCGCAAAAGUCACCGCCU
-------------------....-----.....((((((--(.(((((.((((.........))))).......((((((......)))))))))))))......))))... ( -20.60)
>DroYak_CAF1 67104 92 - 1
--------CUUUC---CAUUCCA------CUUCGUGCUG--CUGGCCGCGCAUUUCCGUUACAUGCCAAACACUUUUGGCCUUUGUCCCGG-CACCGCAAAAGUCACCGCCU
--------.....---.......------....(((.((--((((..(((......))).(((.((((((....))))))...))).))))-)).))).............. ( -19.90)
>DroAna_CAF1 90678 107 - 1
CCAUUUCCAUUUC---CAUUCCAUUUUCUCUCUCUGGUCU-CUGGUCGCGCAUUUCCGUUACAUGCCAAACACUUUUGGCCUUUGUCCCGG-GACCACAAAAGUCACCGCCU
.............---..................((((((-(.((.((((......))).....((((((....))))))....).)).))-)))))............... ( -20.50)
>consensus
________CUUUC___CAUUCCU______CUUCCUGGUC__CUGGCCGCGCAUUUCCGUUACAUGCCAAACACUUUUGGCCUUUGUCCCGG_CACCGCAAAAGUCACCGCCU
...........................................(((.(((.....(((..(((.((((((....))))))...)))..)))....)))....(....)))). (-13.12 = -13.95 +   0.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:16 2006