Locus 3985

Sequence ID 2R_DroMel_CAF1
Location 13,175,483 – 13,175,587
Length 104
Max. P 0.968420
window6432 window6433

overview

Window 2

Location 13,175,483 – 13,175,587
Length 104
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 78.42
Mean single sequence MFE -38.08
Consensus MFE -25.82
Energy contribution -25.70
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -1.84
Structure conservation index 0.68
SVM decision value 0.84
SVM RNA-class probability 0.862706
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13175483 104 + 20766785
UCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCUCUGCU--A------GCUGGUAGCUGGGAA----
.(((.....))).......(((.(..((((((((((........)))))))).((((((...((.((((.....))))...))....)--)------))))))..).)))..---- ( -36.10)
>DroSec_CAF1 69553 97 + 1
CCCGACUUUAGGCAUUUCGCCGCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCUCU---------------GGGAGCUGGGAU----
(((((((...(((.....))).......((((((((........))))))))..........))))))).....((((.(((...---------------..))).))))..---- ( -35.30)
>DroEre_CAF1 70664 111 + 1
GCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCCCUGGCAUACUGGGUGCUGGGAGCUGGGA-----
((((.....))))....(((((......((((((((........)))))))).(((....)))...)))))...((((.(((((.(((((.....)))))))))).)))).----- ( -47.30)
>DroYak_CAF1 71608 114 + 1
CCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUUCCUGCC--ACUGGGCGCUGGUAGCUGGGAUCCUG
((((.((.(((((....(((((......((((((((........)))))))).(((....)))...)))))..(((((..........--..)))))))))).)).))))...... ( -42.10)
>DroAna_CAF1 68864 80 + 1
CCUGGCUUUCGGCAUUUUGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCCCAGUUAAUUGGUUGGGUGUUGCUGGGU------------------------------------
((..((....(((.....)))....(((((((((((........))))))))((((........)))))))..))..)).------------------------------------ ( -29.60)
>consensus
CCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCCCUG____A______GCUGGGAGCUGGGA_____
..........((((...(((((......((((((((........)))))))).(((....)))...))))).))))........................................ (-25.82 = -25.70 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,175,483 – 13,175,587
Length 104
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 78.42
Mean single sequence MFE -35.04
Consensus MFE -23.68
Energy contribution -24.68
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.68
SVM decision value 1.63
SVM RNA-class probability 0.968420
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13175483 104 - 20766785
----UUCCCAGCUACCAGC------U--AGCAGAGAAAUGGGCAACACCCAACCAAUUAACUGUGGGCCAUUGUGCACAAAAUGGCCCGUGACGGGGCGAAAUGCCGAAAGUCGGA
----.(((((((.....))------)--.((((..((.(((...........))).))..))))((((((((........)))))))).....)))).......(((.....))). ( -32.30)
>DroSec_CAF1 69553 97 - 1
----AUCCCAGCUCCC---------------AGAGAAAUGGGCAACACCCAACCAAUUAACUGUGGGCCAUUGUGCACAAAAUGGCCCGUGACGCGGCGAAAUGCCUAAAGUCGGG
----..((((.(((..---------------.)))...)))).....(((..............((((((((........))))))))..(((..(((.....)))....)))))) ( -32.80)
>DroEre_CAF1 70664 111 - 1
-----UCCCAGCUCCCAGCACCCAGUAUGCCAGGGAAAUGGGCAACACCCAACCAAUUAACUGUGGGCCAUUGUGCACAAAAUGGCCCGUGACGGGGCGAAAUGCCGAAAGUCGGC
-----.....(((((...(((.((((......((....((((.....)))).)).....)))).((((((((........)))))))))))..))))).....((((.....)))) ( -40.40)
>DroYak_CAF1 71608 114 - 1
CAGGAUCCCAGCUACCAGCGCCCAGU--GGCAGGAAAAUGGGCAACACCCAACCAAUUAACUGUGGGCCAUUGUGCACAAAAUGGCCCGUGACGGGGCGAAAUGCCGAAAGUCGGG
......(((.((......(((((.((--.((.((....((((.....)))).))..........((((((((........)))))))))).)).)))))....))(....)..))) ( -42.10)
>DroAna_CAF1 68864 80 - 1
------------------------------------ACCCAGCAACACCCAACCAAUUAACUGGGGGCCAUUGUGCACAAAAUGGCCCGUGACGGGGCAAAAUGCCGAAAGCCAGG
------------------------------------.((..((..(((....(((......)))((((((((........)))))))))))....(((.....)))....))..)) ( -27.60)
>consensus
_____UCCCAGCUACCAGC______U____CAGAGAAAUGGGCAACACCCAACCAAUUAACUGUGGGCCAUUGUGCACAAAAUGGCCCGUGACGGGGCGAAAUGCCGAAAGUCGGG
......................................((((.....)))).((..........((((((((........))))))))..(((..(((.....)))....))))). (-23.68 = -24.68 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:59 2006