Locus 148

Sequence ID 3R_DroMel_CAF1
Location 773,642 – 773,790
Length 148
Max. P 0.938475
window240 window241 window242

overview

Window 0

Location 773,642 – 773,750
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.62
Mean single sequence MFE -31.28
Consensus MFE -29.07
Energy contribution -29.57
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.93
SVM decision value 1.29
SVM RNA-class probability 0.938475
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 773642 108 + 27905053
------------UAUUUACGAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUAACAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUAC
------------(((((.((...(((((((.((((....))))..)))))))...............((.(((.((((((.......)))))))))..(((.....))).))))))))). ( -29.90)
>DroSec_CAF1 64430 108 + 1
------------UAUUUACGAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUAACAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGC
------------...........(((((((.((((....))))..)))))))...............((((((.((((((.......))))))))((.(((.....))).))....)))) ( -31.80)
>DroSim_CAF1 34942 108 + 1
------------UAUUUACGAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUAACAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGC
------------...........(((((((.((((....))))..)))))))...............((((((.((((((.......))))))))((.(((.....))).))....)))) ( -31.80)
>DroEre_CAF1 29643 108 + 1
------------CAUUUUCAAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGC
------------...........(((((((.((((....))))..)))))))...............((((((.((((((.......))))))))((.(((.....))).))....)))) ( -31.80)
>DroYak_CAF1 39050 108 + 1
------------UAUUUACCAUUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGC
------------....((((...(((((((.((((....))))..)))))))...............((.(((.((((((.......)))))))))..(((.....))).))...)))). ( -32.30)
>DroAna_CAF1 36548 119 + 1
AGAUUUUAAAUGUA-UUUCUUAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACCCAACCGAGGUGC
..........((((-........(((((((.((((....))))..)))))))..........)))).((((((.((((((.......)))))))).....(((.......)))...)))) ( -30.07)
>consensus
____________UAUUUACGAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUAACAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGC
.......................(((((((.((((....))))..)))))))...............((((((.((((((.......))))))))((.(((.....))).))....)))) (-29.07 = -29.57 +   0.50) 

alignment

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secondary structure

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dotplot

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Window 1

Location 773,642 – 773,750
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.62
Mean single sequence MFE -33.70
Consensus MFE -31.97
Energy contribution -31.55
Covariance contribution -0.42
Combinations/Pair 1.10
Mean z-score -1.15
Structure conservation index 0.95
SVM decision value 0.79
SVM RNA-class probability 0.851952
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 773642 108 - 27905053
GUACCUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGUUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUCGUAAAUA------------
.(((...((((((((((..(.(.(((((((((((....).)))))).))))).)..)))).....))))))((((.(((((....))))))))).......)))....------------ ( -31.60)
>DroSec_CAF1 64430 108 - 1
GCACCUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGUUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUCGUAAAUA------------
((((....((.(((.....))).))(((((((((....).)))))).))))))...............(.(((((.(((((....)))))))))).)...........------------ ( -32.30)
>DroSim_CAF1 34942 108 - 1
GCACCUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGUUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUCGUAAAUA------------
((((....((.(((.....))).))(((((((((....).)))))).))))))...............(.(((((.(((((....)))))))))).)...........------------ ( -32.30)
>DroEre_CAF1 29643 108 - 1
GCACCUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUUGAAAAUG------------
((((....((.(((.....))).))(((((((((....).)))))).)))))).....(((((..(..(.(((((.(((((....)))))))))).)..)..))))).------------ ( -35.70)
>DroYak_CAF1 39050 108 - 1
GCACCUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAAUGGUAAAUA------------
..(((..(((((((.....))).(((((((((((....).)))))).))))................))))((((.(((((....)))))))))......))).....------------ ( -33.50)
>DroAna_CAF1 36548 119 - 1
GCACCUCGGUUGGGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUAAGAAA-UACAUUUAAAAUCU
((((...((((.....)))).....(((((((((....).)))))).))))))(((((.((((((...(.(((((.(((((....)))))))))).).)))))).-)))))......... ( -36.80)
>consensus
GCACCUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUCGUAAAUA____________
((((....((.(((.....))).))(((((((((....).)))))).))))))...............(.(((((.(((((....)))))))))).)....................... (-31.97 = -31.55 +  -0.42) 

alignment

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secondary structure

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dotplot

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Window 2

Location 773,670 – 773,790
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 97.56
Mean single sequence MFE -32.20
Consensus MFE -30.10
Energy contribution -30.77
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -0.93
Structure conservation index 0.93
SVM decision value 0.19
SVM RNA-class probability 0.627082
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 773670 120 + 27905053
GCCAUUCCCGGCUAACAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUACAAUGGCCAAGCCUCACUCCGGAGGAACCGCCUUCGUGAUC
(((((((((((((.................(((.((((((.......)))))))))..(((.....)))))))).))...))))))..........((((((((.....)))))).)).. ( -34.50)
>DroSec_CAF1 64458 120 + 1
GCCAUUCCCGGCUAACAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGCAAUGACCAAGCCUCACUCCGGAGGAACCGCCUUCGUGAUC
.........((((.................(((.((((((.......)))))))))..(((.....)))))))(((((...........)))))..((((((((.....)))))).)).. ( -29.90)
>DroSim_CAF1 34970 120 + 1
GCCAUUCCCGGCUAACAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGCAAUGGCCAAGCCUCACUCCGGAGGAACCGCCUUCGUGAUC
(((((((((((((.................(((.((((((.......)))))))))..(((.....)))))))).))...))))))..........((((((((.....)))))).)).. ( -34.50)
>DroEre_CAF1 29671 120 + 1
GCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGCAAUGGCCAAGCCUCACUCCGGAGGAACCGCCUUCAUGAUC
(((((((((((((.................(((.((((((.......)))))))))..(((.....)))))))).))...)))))).............(((((.....)))))...... ( -32.00)
>DroYak_CAF1 39078 120 + 1
GCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGCAAUGGCCAAGCCUCACUCCGGAGGAACCGCCUUCGUGAUC
(((((((((((((.................(((.((((((.......)))))))))..(((.....)))))))).))...))))))..........((((((((.....)))))).)).. ( -34.50)
>DroAna_CAF1 36587 120 + 1
GCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACCCAACCGAGGUGCAAUGGCCAGGUCUCACUCCGGAGGAACCGCCUUCGUGAUC
(((......)))................((((((((((((.......))))))).((...(((((((((....).)))....))))).((((((......)))..)))))..)))))... ( -27.80)
>consensus
GCCAUUCCCGGCUAACAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAGCCGAGGUGCAAUGGCCAAGCCUCACUCCGGAGGAACCGCCUUCGUGAUC
(((((((((((((.................(((.((((((.......)))))))))..(((.....)))))))).))...))))))..........((((((((.....)))))).)).. (-30.10 = -30.77 +   0.67) 

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 09:34:31 2006