Locus 5348

Sequence ID 2R_DroMel_CAF1
Location 17,289,367 – 17,289,490
Length 123
Max. P 0.922735
window8544 window8545 window8546

overview

Window 4

Location 17,289,367 – 17,289,457
Length 90
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 94.18
Mean single sequence MFE -20.50
Consensus MFE -18.60
Energy contribution -18.93
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.91
SVM decision value 0.41
SVM RNA-class probability 0.727059
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17289367 90 - 20766785
GUUGGAGCCAAAGGGAAUACUUAUGGGACUAUAAAAUAAGUCCACCACAUGGCCAAUCUGA---AACACUUUAUCCAACGGCACACUUAAGCA
((((((((((...((....(....)(((((........))))).))...)))).....(((---(....)))))))))).((........)). ( -21.20)
>DroSec_CAF1 13731 89 - 1
GUUUGAGCCAAAGGGAAUACUUAUGGGACUAUAA-AUAAGUCCACCACAUGGCCAAUCCGA---AACACUUUAUCCAACGGCGCAAUUAAGCA
(((((((((....(((.........(((((....-...))))).((....)).........---.........)))...)))....)))))). ( -17.40)
>DroSim_CAF1 15439 92 - 1
GUUGGAGCCAAAGGGAAUACUUAUGGGACUAUAA-AUAAGUCCACCACAUGGCCAAUCCGAAGAAACACUUUAUCCAACGGCACAAUUAAGCA
((((((((((...((....(....)(((((....-...))))).))...))))......((((.....)))).)))))).((........)). ( -22.90)
>consensus
GUUGGAGCCAAAGGGAAUACUUAUGGGACUAUAA_AUAAGUCCACCACAUGGCCAAUCCGA___AACACUUUAUCCAACGGCACAAUUAAGCA
((((((((((...((....(....)(((((........))))).))...))))......(......)......)))))).((........)). (-18.60 = -18.93 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,289,389 – 17,289,490
Length 101
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 87.25
Mean single sequence MFE -21.40
Consensus MFE -14.76
Energy contribution -14.82
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.72
Structure conservation index 0.69
SVM decision value 0.19
SVM RNA-class probability 0.628244
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17289389 101 + 20766785
AAGUGUU---UCAGAUUGGCCAUGUGGUGGACUUAUUUUAUAGUCCCAUAAGUAUUCCCUUUGGCUCCAACCAUUUGGUUCAUUUUCAUUAAAAUACUUGUUUG
(((((((---(.((((..((((.((((((((((........)))))...............((....))))))).))))..))))......))))))))..... ( -22.50)
>DroSec_CAF1 13753 100 + 1
AAGUGUU---UCGGAUUGGCCAUGUGGUGGACUUAU-UUAUAGUCCCAUAAGUAUUCCCUUUGGCUCAAACCAUUUGGUUCAUUUUCAUUAAAAUACUUGUUUG
(((((((---(..(.(((((((...((.(((..(((-((((......))))))).))))).)))).)))(((....))).........)..))))))))..... ( -22.90)
>DroSim_CAF1 15461 103 + 1
AAGUGUUUCUUCGGAUUGGCCAUGUGGUGGACUUAU-UUAUAGUCCCAUAAGUAUUCCCUUUGGCUCCAACCAUUUGGUUCAUUUUCAUUAAAAUACUUGUUUG
((((((((....(((...((((...((.(((..(((-((((......))))))).))))).)))))))((((....))))...........))))))))..... ( -23.50)
>DroEre_CAF1 9508 82 + 1
---------------------AUGUGGUGGACUUAU-UUAUAGUCCCAAAGGUAUUCCCUUUGGCUCAAACCAUUUGGUUCAUUUUCAUUAAAAUACUUGUUUG
---------------------..((((((((((...-....)))))((((((.....))))))......))))).............................. ( -16.70)
>consensus
AAGUGUU___UCGGAUUGGCCAUGUGGUGGACUUAU_UUAUAGUCCCAUAAGUAUUCCCUUUGGCUCAAACCAUUUGGUUCAUUUUCAUUAAAAUACUUGUUUG
..........................(.(((((........))))))(((((((((.....(((....((((....)))).....)))....)))))))))... (-14.76 = -14.82 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,289,389 – 17,289,490
Length 101
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 87.25
Mean single sequence MFE -19.85
Consensus MFE -15.54
Energy contribution -16.29
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.78
SVM decision value 1.15
SVM RNA-class probability 0.922735
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17289389 101 - 20766785
CAAACAAGUAUUUUAAUGAAAAUGAACCAAAUGGUUGGAGCCAAAGGGAAUACUUAUGGGACUAUAAAAUAAGUCCACCACAUGGCCAAUCUGA---AACACUU
.....((((.(((((.......(.((((....)))).).((((...((....(....)(((((........))))).))...)))).....)))---)).)))) ( -20.10)
>DroSec_CAF1 13753 100 - 1
CAAACAAGUAUUUUAAUGAAAAUGAACCAAAUGGUUUGAGCCAAAGGGAAUACUUAUGGGACUAUAA-AUAAGUCCACCACAUGGCCAAUCCGA---AACACUU
.....((((.((((.........(((((....)))))(.((((...((....(....)(((((....-...))))).))...))))).....))---)).)))) ( -19.80)
>DroSim_CAF1 15461 103 - 1
CAAACAAGUAUUUUAAUGAAAAUGAACCAAAUGGUUGGAGCCAAAGGGAAUACUUAUGGGACUAUAA-AUAAGUCCACCACAUGGCCAAUCCGAAGAAACACUU
.....((((.((((..........((((....))))(((((((...((....(....)(((((....-...))))).))...))))...)))...)))).)))) ( -21.20)
>DroEre_CAF1 9508 82 - 1
CAAACAAGUAUUUUAAUGAAAAUGAACCAAAUGGUUUGAGCCAAAGGGAAUACCUUUGGGACUAUAA-AUAAGUCCACCACAU---------------------
.......................(((((....)))))....((((((.....))))))(((((....-...))))).......--------------------- ( -18.30)
>consensus
CAAACAAGUAUUUUAAUGAAAAUGAACCAAAUGGUUGGAGCCAAAGGGAAUACUUAUGGGACUAUAA_AUAAGUCCACCACAUGGCCAAUCCGA___AACACUU
.....(((((((((........((((((....))))))........)))))))))...(((((........)))))............................ (-15.54 = -16.29 +   0.75)

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 11:42:46 2006