Locus 1776

Sequence ID 3L_DroMel_CAF1
Location 5,063,881 – 5,063,995
Length 114
Max. P 0.747668
window2752 window2753

overview

Window 2

Location 5,063,881 – 5,063,995
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.44
Mean single sequence MFE -36.70
Consensus MFE -29.24
Energy contribution -29.88
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -1.63
Structure conservation index 0.80
SVM decision value 0.47
SVM RNA-class probability 0.747668
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5063881 114 + 23771897
CAUUAAUCACACUCAACACUUAGCAGGAGUCUGGGACAGGACUUGAAAUUUCGUCCUAGGUUCACAUUUGGUUUUG------GGAAUGGGCACAAAAUGAGGCCCUCCUGUGGCCAAUGU
((((..((((((((((.(((......((..(((((((.(((........))))))))))..))......))).)))------))...((((.(.......)))))...)))))..)))). ( -34.70)
>DroSec_CAF1 270401 114 + 1
CAUUAAUCACACUCAACACUUAGCAGGAGUCUGGGACAGGACUUGAAAUUUCGUCCUAGGUUCAGUUUUGGUUUUG------GGGAUGGGCGCAAAAUGAGGCCCUCCUGUGGCCAAUGU
((((..((((...(((.(((.(((..((..(((((((.(((........))))))))))..)).)))..))).)))------((((.((((.(.....)..))))))))))))..)))). ( -36.60)
>DroSim_CAF1 291704 114 + 1
CAUUAAUCACACUCAACACUUAGCAGGAGUCUGGGACAGGACUUGAAAUUUCGUCCUAGGUUCAGUUUUGGUUUUG------GGGAGGGGCACAAAAUGAGGCCCUCCUGUGGCCAAUGU
((((..((((...(((.(((.(((..((..(((((((.(((........))))))))))..)).)))..))).)))------(((((((.(.(.....).).)))))))))))..)))). ( -39.50)
>DroEre_CAF1 277265 113 + 1
CAUUAAUCACACUCAACACUUAGCAGGAGUCUGCUACAGGACUUGAAAUUUCGUCCUAGGUUCAGUUUUGGUUUUG-------GGAGGGGUUCGAAAUAAGGCCCUCCUGUGGCCAAUGU
..........(((.(((...((((((....)))))).(((((..........)))))..))).))).(((((..((-------((((((.((.......)).))))))))..)))))... ( -35.40)
>DroYak_CAF1 281053 120 + 1
CAUUAAUCACACUCAACACUUAGCAGGAGUCUGGGACAGGACUUGAAAUUUCGUCCUAGGUUAAGUUUUGGUUUUGGUUGUGGGGAUGGGCACAGAACCAGGCCCUCCUGUGGCCAAUGU
............((((.(((((((......(((((((.(((........))))))))))))))))).))))..(((((..(((((..((((.(.......))))))))))..)))))... ( -37.30)
>consensus
CAUUAAUCACACUCAACACUUAGCAGGAGUCUGGGACAGGACUUGAAAUUUCGUCCUAGGUUCAGUUUUGGUUUUG______GGGAUGGGCACAAAAUGAGGCCCUCCUGUGGCCAAUGU
((((..(((((..(((.(((......((..(((((((.(((........))))))))))..))......))).))).......(((.((((.(.......)))))))))))))..)))). (-29.24 = -29.88 +   0.64)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 5,063,881 – 5,063,995
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.44
Mean single sequence MFE -31.24
Consensus MFE -26.14
Energy contribution -26.58
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.40
Structure conservation index 0.84
SVM decision value 0.35
SVM RNA-class probability 0.698383
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5063881 114 - 23771897
ACAUUGGCCACAGGAGGGCCUCAUUUUGUGCCCAUUCC------CAAAACCAAAUGUGAACCUAGGACGAAAUUUCAAGUCCUGUCCCAGACUCCUGCUAAGUGUUGAGUGUGAUUAAUG
(((((((.....((((((((.......).))))..)))------.....)).))))).....((((((..........))))))...((.((((..((.....)).)))).))....... ( -27.90)
>DroSec_CAF1 270401 114 - 1
ACAUUGGCCACAGGAGGGCCUCAUUUUGCGCCCAUCCC------CAAAACCAAAACUGAACCUAGGACGAAAUUUCAAGUCCUGUCCCAGACUCCUGCUAAGUGUUGAGUGUGAUUAAUG
.(((((..(((.((((((((.......).)))).))).------...........(((....((((((..........))))))...)))((((..((.....)).)))))))..))))) ( -30.00)
>DroSim_CAF1 291704 114 - 1
ACAUUGGCCACAGGAGGGCCUCAUUUUGUGCCCCUCCC------CAAAACCAAAACUGAACCUAGGACGAAAUUUCAAGUCCUGUCCCAGACUCCUGCUAAGUGUUGAGUGUGAUUAAUG
.(((((..(((.((((((.(.(.....).).)))))).------...........(((....((((((..........))))))...)))((((..((.....)).)))))))..))))) ( -30.90)
>DroEre_CAF1 277265 113 - 1
ACAUUGGCCACAGGAGGGCCUUAUUUCGAACCCCUCC-------CAAAACCAAAACUGAACCUAGGACGAAAUUUCAAGUCCUGUAGCAGACUCCUGCUAAGUGUUGAGUGUGAUUAAUG
.(((((..(((.((((((..((.....))..))))))-------..........(((.((((((((((..........))))).((((((....)))))))).))).))))))..))))) ( -35.60)
>DroYak_CAF1 281053 120 - 1
ACAUUGGCCACAGGAGGGCCUGGUUCUGUGCCCAUCCCCACAACCAAAACCAAAACUUAACCUAGGACGAAAUUUCAAGUCCUGUCCCAGACUCCUGCUAAGUGUUGAGUGUGAUUAAUG
.(((((..(((.((((((((.......).)))).))).................((((((((((((((..........)))))....(((....)))...)).))))))))))..))))) ( -31.80)
>consensus
ACAUUGGCCACAGGAGGGCCUCAUUUUGUGCCCAUCCC______CAAAACCAAAACUGAACCUAGGACGAAAUUUCAAGUCCUGUCCCAGACUCCUGCUAAGUGUUGAGUGUGAUUAAUG
.(((((..(((.((((((((.......).)))).)))..................(((....((((((..........))))))...)))((((..((.....)).)))))))..))))) (-26.14 = -26.58 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:06 2006