Locus 1898

Sequence ID 3R_DroMel_CAF1
Location 5,423,538 – 5,423,650
Length 112
Max. P 0.996946
window3124 window3125

overview

Window 4

Location 5,423,538 – 5,423,650
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.25
Mean single sequence MFE -29.05
Consensus MFE -27.24
Energy contribution -27.30
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -2.77
Structure conservation index 0.94
SVM decision value 2.77
SVM RNA-class probability 0.996946
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5423538 112 + 27905053
UUUUUUGGCUUAUAAUU--------UUUUUUCACUAUUUGGGGUUGGCAGCGCUACAAUUUCGGAACUGGAGCUGCUGGCUCCCAAACAAUUUGAGCAUUUGAUUGCUUUAUUUCACUUU
.................--------...........((((((((..(((((.(((............))).)))))..)).))))))......(((((......)))))........... ( -28.40)
>DroSec_CAF1 10181 115 + 1
UUUUUUGGUUUAUGUUUU-----AUUUUUUUCACUAUUUGGGGUUGGCAGCGCUACAAUUUCGGAACUGGGGUUGCUGGCUCCCAAACAAUUUGAGCAUUUGAUUGCUUUAUUUCACUUU
.....(((..((......-----.............((((((((..(((((.(((............))).)))))..)).))))))......(((((......)))))))..))).... ( -27.80)
>DroEre_CAF1 10635 107 + 1
----UUGGUUUAUGUUU---------UUUCUACCUAUUUGGGGUUGGCAGCGCUACAAUUUCGGAACUGGAGCUGCUGGCUCCCAAACAAUUUGAGCAUUUGAUUGCUUUAUUUCACUUU
----..(((........---------.....)))..((((((((..(((((.(((............))).)))))..)).))))))......(((((......)))))........... ( -29.12)
>DroYak_CAF1 10959 116 + 1
----UUGGUUUAUGUUUUUCUUUUUUUUUUUACCUAUUUGGGGUUGGCAGCGCUAGUAUUUCGGAACUGGAACUGCUGGCUCCCAAACAAUUUGAGCAUUUGAUUGCUUUAUUUCACUUU
----.(((..((........................((((((((..((((..(((((........)))))..))))..)).))))))......(((((......)))))))..))).... ( -30.90)
>consensus
____UUGGUUUAUGUUU________UUUUUUAACUAUUUGGGGUUGGCAGCGCUACAAUUUCGGAACUGGAGCUGCUGGCUCCCAAACAAUUUGAGCAUUUGAUUGCUUUAUUUCACUUU
....................................((((((((..(((((.(((............))).)))))..)).))))))......(((((......)))))........... (-27.24 = -27.30 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,423,538 – 5,423,650
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.25
Mean single sequence MFE -23.18
Consensus MFE -19.92
Energy contribution -20.55
Covariance contribution 0.63
Combinations/Pair 1.07
Mean z-score -2.84
Structure conservation index 0.86
SVM decision value 2.29
SVM RNA-class probability 0.991891
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5423538 112 - 27905053
AAAGUGAAAUAAAGCAAUCAAAUGCUCAAAUUGUUUGGGAGCCAGCAGCUCCAGUUCCGAAAUUGUAGCGCUGCCAACCCCAAAUAGUGAAAAAA--------AAUUAUAAGCCAAAAAA
...((((.....((((......))))...((((((((((.(.((((.(((.(((((....))))).))))))).)...)))))))))).......--------..))))........... ( -25.10)
>DroSec_CAF1 10181 115 - 1
AAAGUGAAAUAAAGCAAUCAAAUGCUCAAAUUGUUUGGGAGCCAGCAACCCCAGUUCCGAAAUUGUAGCGCUGCCAACCCCAAAUAGUGAAAAAAAU-----AAAACAUAAACCAAAAAA
...(((......((((......))))...((((((((((.(.((((..(..(((((....)))))..).)))).)...)))))))))).........-----....)))........... ( -20.60)
>DroEre_CAF1 10635 107 - 1
AAAGUGAAAUAAAGCAAUCAAAUGCUCAAAUUGUUUGGGAGCCAGCAGCUCCAGUUCCGAAAUUGUAGCGCUGCCAACCCCAAAUAGGUAGAAA---------AAACAUAAACCAA----
...(((.......(((......)))((...(((((((((.(.((((.(((.(((((....))))).))))))).)...)))))))))...))..---------...))).......---- ( -24.60)
>DroYak_CAF1 10959 116 - 1
AAAGUGAAAUAAAGCAAUCAAAUGCUCAAAUUGUUUGGGAGCCAGCAGUUCCAGUUCCGAAAUACUAGCGCUGCCAACCCCAAAUAGGUAAAAAAAAAAAGAAAAACAUAAACCAA----
...(((......((((......))))....(((((((((.(...(((((.(.(((........))).).)))))...))))))))))...................))).......---- ( -22.40)
>consensus
AAAGUGAAAUAAAGCAAUCAAAUGCUCAAAUUGUUUGGGAGCCAGCAGCUCCAGUUCCGAAAUUGUAGCGCUGCCAACCCCAAAUAGGGAAAAAA________AAACAUAAACCAA____
...(((......((((......))))....(((((((((.(.((((.(((.(((((....))))).))))))).)...)))))))))...................)))........... (-19.92 = -20.55 +   0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:21 2006