Locus 2965

Sequence ID 3L_DroMel_CAF1
Location 8,484,658 – 8,484,778
Length 120
Max. P 0.994736
window4633 window4634

overview

Window 3

Location 8,484,658 – 8,484,778
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.33
Mean single sequence MFE -38.64
Consensus MFE -29.45
Energy contribution -30.97
Covariance contribution 1.52
Combinations/Pair 1.06
Mean z-score -1.91
Structure conservation index 0.76
SVM decision value 0.59
SVM RNA-class probability 0.791697
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8484658 120 + 23771897
CAAGCUACUGUCCACAACCAUUGGACAGCAGCAGGCUAAGCCGAAGGUCCAGGAGGAGGCAUCUUUGGAAAAUAAGGAUGCGGCUGAAGGUGAAACCUCAACCCAGAAAGACUCACAGGU
...(((.(((((((.......))))))).))).(((...)))......((..(((...(((((((((.....)))))))))((.(((.((.....))))).))........)))...)). ( -38.50)
>DroSec_CAF1 3111 120 + 1
CAAGCUACUGUCCACCACCAUUGGGCAGCAGCAGGCUAAGCCGAAGGUCCGGGAGGAGGCAUCUUUGGAAAAUAAGGAUGCGGCUGAAGGUGAAACCUCAACCCAGGAAGACUCACAGGU
...(((.(((((((.......))))))).))).(((...)))((.(.((((((..((((((((((((.....))))))))).((.....)).....)))..))).)))...)))...... ( -40.90)
>DroSim_CAF1 3095 117 + 1
CAAGCUACUGUCCACCACCAUUGGACAGCAACAGGCUAAGCCGAAGGUCC---AGGAGGCAUCUUUGGAAAAUAAGGAUGCGGCUGAAGGUGAAACCUCAACCCAGGAAGACUCACAGGU
..((((.(((((((.......))))))).....))))..(((..((.(((---.....(((((((((.....)))))))))((.(((.((.....))))).))..)))...))....))) ( -35.10)
>DroEre_CAF1 3346 120 + 1
UAAGCUAAUGUCCACCACCAUUGGACAGCAACAGGCUAAGCCCAAGGUCCAGGAGGAGGCAUCUGUGGAAAAGAACGAUGCGGCUGAGGAUGAAACCUCAACUCAGGAAGCCUCACCGGU
...(((...(((((.......))))))))...(((((.((((.....(((....))).(((((.((........)))))))))))((((......)))).........)))))....... ( -35.10)
>DroYak_CAF1 3137 120 + 1
UAAGCUGCUGUCCACCACCAUUGGACAGCAGCAGGCUAAGCCAAAGGUCCAGGAGGAGGCAUCCUUGGAAAAGAAGGAUGCGGCCGAAGGUGAAACCCCAACUCAGAAAGACUCACAGGU
...(((((((((((.......))))))))))).((((..........(((....))).((((((((.......))))))))))))....((((...................)))).... ( -43.61)
>consensus
CAAGCUACUGUCCACCACCAUUGGACAGCAGCAGGCUAAGCCGAAGGUCCAGGAGGAGGCAUCUUUGGAAAAUAAGGAUGCGGCUGAAGGUGAAACCUCAACCCAGGAAGACUCACAGGU
...(((.(((((((.......))))))).)))..(((.((((.....(((....))).(((((((((.....)))))))))))))....((((...................)))).))) (-29.45 = -30.97 +   1.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,484,658 – 8,484,778
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.33
Mean single sequence MFE -41.06
Consensus MFE -36.54
Energy contribution -36.66
Covariance contribution 0.12
Combinations/Pair 1.15
Mean z-score -2.01
Structure conservation index 0.89
SVM decision value 2.51
SVM RNA-class probability 0.994736
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8484658 120 - 23771897
ACCUGUGAGUCUUUCUGGGUUGAGGUUUCACCUUCAGCCGCAUCCUUAUUUUCCAAAGAUGCCUCCUCCUGGACCUUCGGCUUAGCCUGCUGCUGUCCAAUGGUUGUGGACAGUAGCUUG
.....((((((......((((((((......))))))))(((((.............))))).(((....))).....))))))....(((((((((((.......)))))))))))... ( -41.62)
>DroSec_CAF1 3111 120 - 1
ACCUGUGAGUCUUCCUGGGUUGAGGUUUCACCUUCAGCCGCAUCCUUAUUUUCCAAAGAUGCCUCCUCCCGGACCUUCGGCUUAGCCUGCUGCUGCCCAAUGGUGGUGGACAGUAGCUUG
..(((.(((........((((((((......))))))))(((((.............)))))...))).)))......(((...))).(((((((.(((.......))).)))))))... ( -36.72)
>DroSim_CAF1 3095 117 - 1
ACCUGUGAGUCUUCCUGGGUUGAGGUUUCACCUUCAGCCGCAUCCUUAUUUUCCAAAGAUGCCUCCU---GGACCUUCGGCUUAGCCUGUUGCUGUCCAAUGGUGGUGGACAGUAGCUUG
.((.(.(((........((((((((......))))))))(((((.............))))))))).---))......(((...))).(((((((((((.......)))))))))))... ( -38.92)
>DroEre_CAF1 3346 120 - 1
ACCGGUGAGGCUUCCUGAGUUGAGGUUUCAUCCUCAGCCGCAUCGUUCUUUUCCACAGAUGCCUCCUCCUGGACCUUGGGCUUAGCCUGUUGCUGUCCAAUGGUGGUGGACAUUAGCUUA
.((((.((((......(.(((((((......))))))))(((((.............)))))..)))))))).....((((...))))((((.((((((.......)))))).))))... ( -41.02)
>DroYak_CAF1 3137 120 - 1
ACCUGUGAGUCUUUCUGAGUUGGGGUUUCACCUUCGGCCGCAUCCUUCUUUUCCAAGGAUGCCUCCUCCUGGACCUUUGGCUUAGCCUGCUGCUGUCCAAUGGUGGUGGACAGCAGCUUA
..............((((((..(((.((((.....((..((((((((.......))))))))..))...)))).)))..))))))...(((((((((((.......)))))))))))... ( -47.00)
>consensus
ACCUGUGAGUCUUCCUGGGUUGAGGUUUCACCUUCAGCCGCAUCCUUAUUUUCCAAAGAUGCCUCCUCCUGGACCUUCGGCUUAGCCUGCUGCUGUCCAAUGGUGGUGGACAGUAGCUUG
.....((((((......((((((((......))))))))(((((.............))))).(((....))).....))))))....(((((((((((.......)))))))))))... (-36.54 = -36.66 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:16 2006