Locus 6094

Sequence ID 3R_DroMel_CAF1
Location 15,982,362 – 15,982,452
Length 90
Max. P 0.984355
window9939 window9940

overview

Window 9

Location 15,982,362 – 15,982,452
Length 90
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 85.88
Mean single sequence MFE -20.42
Consensus MFE -14.12
Energy contribution -13.92
Covariance contribution -0.20
Combinations/Pair 1.24
Mean z-score -1.74
Structure conservation index 0.69
SVM decision value 0.06
SVM RNA-class probability 0.564959
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15982362 90 + 27905053
GGUGGCAGUGGGCUGGCUUAUUAGUAAACAGGCCCGAGGUAAAAUAUGCUACGUA--AAGAUAACAGCCGAAUGGCAA---------AAAAAUAAUAUUAG---
.((((((.((((((.(((....))).....))))))..........))))))...--.........(((....)))..---------..............--- ( -21.90)
>DroSim_CAF1 85680 90 + 1
GGUGGCACUGGGCUGGCUUAUUAGUAAACAGGCCCGGGGUAAAAUAUGCUACGUA--AAGAUAGCAGCCGAAUGGCAA---------AAAAAUAAUAUUAG---
..((((.(((((((.(((....))).....))))))).........((((((...--..).)))))))))........---------..............--- ( -24.40)
>DroEre_CAF1 83403 90 + 1
GGUGGCAGUGGGCUGGCUUAUUAGCAAACAGGCCCGGGGUAAAAUAUGCUACGUA--AAGAUAGCAACCGAAUGGCAA---------AAAAAUAAUAUUAG---
(((.((..((((((.(((....))).....))))))..))......((((((...--..).)))))))).........---------..............--- ( -22.10)
>DroYak_CAF1 114357 90 + 1
GGUGGCAGUGGGCUGUCUUAUUAGUAAACAGGCCCGGGGUAAAAUAUGCUACGUA--AAGAUAGCAGCCGAAUGGCAA---------AAAAAUAAUAUUAG---
....((..((((((...(((....)))...))))))..))......((((((...--..).)))))(((....)))..---------..............--- ( -19.80)
>DroAna_CAF1 76406 101 + 1
GAUGGAAAUGGG-UGGCUUAUUAGUAAACAGGCCUUAGGUAAAAUAUGCUUCGGAAAAAGAUAGCAACC--AUUGCGAAAAAAAGAGAAAAAUAAUAAUAGCAA
....(.(((((.-.(((((.((....)).)))))............((((((.......)).)))).))--))).)............................ ( -13.90)
>consensus
GGUGGCAGUGGGCUGGCUUAUUAGUAAACAGGCCCGGGGUAAAAUAUGCUACGUA__AAGAUAGCAGCCGAAUGGCAA_________AAAAAUAAUAUUAG___
..((.((..(((((.(((....))).....)))))..(((......((((((.......).))))))))...)).))........................... (-14.12 = -13.92 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,982,362 – 15,982,452
Length 90
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 85.88
Mean single sequence MFE -18.52
Consensus MFE -14.54
Energy contribution -15.10
Covariance contribution 0.56
Combinations/Pair 1.17
Mean z-score -2.60
Structure conservation index 0.79
SVM decision value 1.97
SVM RNA-class probability 0.984355
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15982362 90 - 27905053
---CUAAUAUUAUUUUU---------UUGCCAUUCGGCUGUUAUCUU--UACGUAGCAUAUUUUACCUCGGGCCUGUUUACUAAUAAGCCAGCCCACUGCCACC
---..............---------.........(((((((((...--...))))))...........((((..(((((....)))))..))))...)))... ( -18.70)
>DroSim_CAF1 85680 90 - 1
---CUAAUAUUAUUUUU---------UUGCCAUUCGGCUGCUAUCUU--UACGUAGCAUAUUUUACCCCGGGCCUGUUUACUAAUAAGCCAGCCCAGUGCCACC
---..............---------.........(((((((((...--...))))))...........((((..(((((....)))))..))))...)))... ( -21.10)
>DroEre_CAF1 83403 90 - 1
---CUAAUAUUAUUUUU---------UUGCCAUUCGGUUGCUAUCUU--UACGUAGCAUAUUUUACCCCGGGCCUGUUUGCUAAUAAGCCAGCCCACUGCCACC
---..............---------.........(((((((((...--...))))))...........((((..(((((....)))))..))))...)))... ( -18.60)
>DroYak_CAF1 114357 90 - 1
---CUAAUAUUAUUUUU---------UUGCCAUUCGGCUGCUAUCUU--UACGUAGCAUAUUUUACCCCGGGCCUGUUUACUAAUAAGACAGCCCACUGCCACC
---..............---------.........(((((((((...--...))))))...........((((.(((((.......)))))))))...)))... ( -21.60)
>DroAna_CAF1 76406 101 - 1
UUGCUAUUAUUAUUUUUCUCUUUUUUUCGCAAU--GGUUGCUAUCUUUUUCCGAAGCAUAUUUUACCUAAGGCCUGUUUACUAAUAAGCCA-CCCAUUUCCAUC
............................(.(((--((.((((.((.......))))))............(((.((((....)))).))).-.))))).).... ( -12.60)
>consensus
___CUAAUAUUAUUUUU_________UUGCCAUUCGGCUGCUAUCUU__UACGUAGCAUAUUUUACCCCGGGCCUGUUUACUAAUAAGCCAGCCCACUGCCACC
...................................(((((((((........))))))...........((((..(((((....)))))..))))...)))... (-14.54 = -15.10 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:33 2006