Locus 1776

Sequence ID 3R_DroMel_CAF1
Location 5,102,845 – 5,103,077
Length 232
Max. P 0.995095
window2916 window2917 window2918

overview

Window 6

Location 5,102,845 – 5,102,965
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -21.76
Consensus MFE -19.44
Energy contribution -19.00
Covariance contribution -0.44
Combinations/Pair 1.11
Mean z-score -1.58
Structure conservation index 0.89
SVM decision value 1.33
SVM RNA-class probability 0.942909
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5102845 120 - 27905053
UCAAUUAAUUACCCAACAUUGACCGCACAAAUGGAACAAAAGUGAGAGAAAAUCAUUAGCCUUGUCCAAAUGGGUUACAAUUAAUUUCUCCGCUUAACGGAAACCCCAUGAUUAGCCCUU
........................((....((((.....(((((.((((((.....((((((.........)))))).......)))))))))))...(....).)))).....)).... ( -20.90)
>DroSec_CAF1 9562 120 - 1
UCAAUUAAUUACCCAACAUUGACCGCACAAAUGGAACAAAAGUGAGAGAAAAUCAUUAGCCCUGUCCAAAUGGGUUACAAUUAAUUUCUCCGCUUAACAGAAACCCCAUGAUUAGCCCUC
....(((((((.(((...(((......))).))).....(((((.((((((.....((((((.........)))))).......))))))))))).............)))))))..... ( -20.70)
>DroSim_CAF1 9796 120 - 1
UCAAUUAAUUACCCAACAUUGACCGCAAAAAUGGAACAAAAGUGAGAGAAAAUCAUUAGCCCUGUCCAAAUGGGUUACAAUUAAUUUCUCCGCUUAACAGAAACCCCAUGAUUAGCCCUC
....(((((((.(((...(((....)))...))).....(((((.((((((.....((((((.........)))))).......))))))))))).............)))))))..... ( -21.40)
>DroEre_CAF1 9863 120 - 1
UCAAUUAAUUAGCCAGCAUUGACCACACAAAUGGUACAAAAGUGAGAGAAAAUCAUUAGCCUUGUCCAAAUGGGUUACAAUUAAUUUCUCCGCUUAACAGAAACCCCAUGAUUAGACCUC
....(((((((.......(((((((......)))).)))(((((.((((((.....((((((.........)))))).......))))))))))).............)))))))..... ( -22.00)
>DroYak_CAF1 10756 120 - 1
UCAAUUAAUUACCCAACAUUGACCACACAAAUGGUACAAAAGUGAGGGAAAAUCAUUAGCCCUGUCUAAAUGGGUUACAAUUAAUUUCUCCGCUUAACAGAAACCCCACGAUUAGCCCUC
..................(((((((......)))).)))....(((((..((((..((((((.........)))))).......(((((.........)))))......))))..))))) ( -23.80)
>consensus
UCAAUUAAUUACCCAACAUUGACCGCACAAAUGGAACAAAAGUGAGAGAAAAUCAUUAGCCCUGUCCAAAUGGGUUACAAUUAAUUUCUCCGCUUAACAGAAACCCCAUGAUUAGCCCUC
....(((((((...........(((......))).....(((((.((((((.....((((((.........)))))).......))))))))))).............)))))))..... (-19.44 = -19.00 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,102,925 – 5,103,044
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.48
Mean single sequence MFE -34.02
Consensus MFE -26.50
Energy contribution -26.50
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -1.75
Structure conservation index 0.78
SVM decision value 0.47
SVM RNA-class probability 0.749094
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5102925 119 - 27905053
UGGCUAACAAUGGGAAAUAUGAGGAAUGAUU-UUGGUAUGCCAUGGCUGCUCCUCGGAGUUCCCUCCUGCAUGGUUGGCUUCAAUUAAUUACCCAACAUUGACCGCACAAAUGGAACAAA
.(((((((...(((((...((((((.(..(.-.(((....)))..)..).))))))...)))))..(.....))))))))............(((...(((......))).)))...... ( -28.10)
>DroSec_CAF1 9642 119 - 1
UGGCCAACAAUGGGAAAUAUGAGGAAUGGUU-UUGGUAUGCCAUGGCUUCUCCUCGGAGUUCCCUGCUGCAUGGUUGCCUUCAAUUAAUUACCCAACAUUGACCGCACAAAUGGAACAAA
.(((((.((..(((((...((((((..(((.-.(((....)))..)))..))))))...)))))...))..)))))((..(((((............)))))..)).............. ( -33.20)
>DroSim_CAF1 9876 119 - 1
UGGCCAACAAUGGGAAAUAUGAGGAAUGGUU-UUGGUAUGCCAUGGCUUCUCCUCGGAGUUCCCUGCUGCAUGGUUGCCUUCAAUUAAUUACCCAACAUUGACCGCAAAAAUGGAACAAA
...........(((((...((((((..(((.-.(((....)))..)))..))))))...)))))((.(.(((..((((..(((((............)))))..))))..))).).)).. ( -35.10)
>DroEre_CAF1 9943 120 - 1
UGGCCAACAAUGGGAAAUAUGAGGAAUGGUCCUUGGUAUGCCAUGGCUUUUCCUCCGAGUUCCCUCUUGCAUGGUUGGCUUCAAUUAAUUAGCCAGCAUUGACCACACAAAUGGUACAAA
..((.......(((((....((((((.((((..(((....))).)))).))))))....)))))....))...(((((((..........))))))).(((((((......)))).))). ( -39.60)
>DroYak_CAF1 10836 120 - 1
UGACCAACAAUGGGAAAUAUGAGGAAUGGUCCUUGGAAUGCCAUGGCUUCUCCUCCGAGUUCCCUCUGGCAUGGUUGACUUCAAUUAAUUACCCAACAUUGACCACACAAAUGGUACAAA
.(((((.((..(((((....(((((..((((..(((....))).))))..)))))....)))))..))...)))))......................(((((((......)))).))). ( -34.10)
>consensus
UGGCCAACAAUGGGAAAUAUGAGGAAUGGUU_UUGGUAUGCCAUGGCUUCUCCUCGGAGUUCCCUCCUGCAUGGUUGCCUUCAAUUAAUUACCCAACAUUGACCGCACAAAUGGAACAAA
.(((((.((..(((((...((((((..((((..(((....))).))))..))))))...)))))...))..)))))....(((((............)))))(((......)))...... (-26.50 = -26.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,102,965 – 5,103,077
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.76
Mean single sequence MFE -40.52
Consensus MFE -26.70
Energy contribution -28.30
Covariance contribution 1.60
Combinations/Pair 1.14
Mean z-score -2.62
Structure conservation index 0.66
SVM decision value 2.54
SVM RNA-class probability 0.995095
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5102965 112 - 27905053
---CCCCAUCUGACCAACCA----ACGUGGCCAUGCCACAUGGCUAACAAUGGGAAAUAUGAGGAAUGAUU-UUGGUAUGCCAUGGCUGCUCCUCGGAGUUCCCUCCUGCAUGGUUGGCU
---..........(((((((----...((((((((...)))))))).....(((((...((((((.(..(.-.(((....)))..)..).))))))...))))).......))))))).. ( -40.80)
>DroSec_CAF1 9682 103 - 1
---CCGCCUCUGACCACCCAUGCCA-------------CAUGGCCAACAAUGGGAAAUAUGAGGAAUGGUU-UUGGUAUGCCAUGGCUUCUCCUCGGAGUUCCCUGCUGCAUGGUUGCCU
---...........((.((((((..-------------((((.....))..(((((...((((((..(((.-.(((....)))..)))..))))))...)))))))..)))))).))... ( -35.30)
>DroSim_CAF1 9916 116 - 1
---CCGCCUCUGACCACCCAUGCCACAUGGCCAUGCCACAUGGCCAACAAUGGGAAAUAUGAGGAAUGGUU-UUGGUAUGCCAUGGCUUCUCCUCGGAGUUCCCUGCUGCAUGGUUGCCU
---...........((.((((((..((((((((((...)))))))).....(((((...((((((..(((.-.(((....)))..)))..))))))...)))))))..)))))).))... ( -48.10)
>DroEre_CAF1 9983 115 - 1
CGUCCUUCUCCAACGU-CCA----ACGGGGCUAUGCCACAUGGCCAACAAUGGGAAAUAUGAGGAAUGGUCCUUGGUAUGCCAUGGCUUUUCCUCCGAGUUCCCUCUUGCAUGGUUGGCU
..............(.-(((----((..(((((((...)))))))..(((.(((((....((((((.((((..(((....))).)))).))))))....)))))..)))....)))))). ( -40.50)
>DroYak_CAF1 10876 100 - 1
C-UCCUGCU-------------------AGCCGUGCCACAUGACCAACAAUGGGAAAUAUGAGGAAUGGUCCUUGGAAUGCCAUGGCUUCUCCUCCGAGUUCCCUCUGGCAUGGUUGACU
.-......(-------------------((((((((((..((.....))..(((((....(((((..((((..(((....))).))))..)))))....)))))..)))))))))))... ( -37.90)
>consensus
___CCGCCUCUGACCA_CCA____AC__GGCCAUGCCACAUGGCCAACAAUGGGAAAUAUGAGGAAUGGUU_UUGGUAUGCCAUGGCUUCUCCUCGGAGUUCCCUCCUGCAUGGUUGCCU
............................((((((((....((.....))..(((((...((((((..((((..(((....))).))))..))))))...)))))....)))))))).... (-26.70 = -28.30 +   1.60)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:05 2006