Locus 4235

Sequence ID 2L_DroMel_CAF1
Location 12,115,493 – 12,115,691
Length 198
Max. P 0.567758
window6687 window6688

overview

Window 7

Location 12,115,493 – 12,115,613
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.83
Mean single sequence MFE -26.25
Consensus MFE -19.42
Energy contribution -20.50
Covariance contribution 1.08
Combinations/Pair 1.07
Mean z-score -1.88
Structure conservation index 0.74
SVM decision value 0.07
SVM RNA-class probability 0.567758
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12115493 120 - 22407834
AUAUUUUCUUUUCUUUUGGCUAAUAAAUAAGCAAUUUGGUGGCUGCUUCUUUUACUGUCAUCGACUAUUUCUUUAAUUGGUCUGCGCAAGCUGGUAAGCAUUAUUUAAUUAGCAUAGAUU
...........(((....((((((((((((((.....((((((.............))))))(((((..........))))).((....))......)).)))))).))))))..))).. ( -26.82)
>DroSec_CAF1 17592 120 - 1
AUGUUUUCUUUUCUUUUGGCUAAUAAAUAAGCAAUUUGGUGACUGCUUCUUCUACUGUCAUCGACUAUUUCUUUAAUUGGUCUGCGCAAGCUGGUAAGCAUUAUUUAAUUAGCAUAGAUU
...........(((....((((((((((((((.....((((((.............))))))(((((..........))))).((....))......)).)))))).))))))..))).. ( -27.42)
>DroSim_CAF1 17427 120 - 1
AUAUUUUCUUUUCUUUUGGCUAAUAAAUAAGCAAUUUGCUGGCUGCUUCUUCUACUGUCAUCGACUAUUUCUUUAAUUGGUCUGCGCAGGCUGGUAAGCAUUAUUUAAUUAGCAUAGAUU
...........(((....((((((((((((((...((((..(((((..........(....)(((((..........)))))...))).))..)))))).)))))).))))))..))).. ( -26.40)
>DroEre_CAF1 17863 120 - 1
AUAUUUCAUUUUCUUUUGGCUAAUAAAUAAGCAAUUUAGUAGCUGCUUCUUCUGCUGUCAUCGAAUACUUCUUUAAUUGGCCUGCGCAAGCUGGUAAGCAUUAUUUAAUUAGCAUAGAUG
...........(((....((((((((((((((.(((..((..(.((.......)).)..))..))).............(((.((....)).)))..)).)))))).))))))..))).. ( -26.80)
>DroYak_CAF1 17765 120 - 1
AUAUUUUCCCUUCUUUUGGCUAAUAAAUAAGCAAUUUGGUAGCUGCUUCUUCUGCUGUCAUCGACUAUUUCUUUAAUUGGUCUGCGCAAGCCGGUAAGCACUAUAUAAUUUGCAUAGAUG
.((((..((........))..)))).....((((....((((.((((.....(((((.....(((((..........))))).((....))))))))))))))).....))))....... ( -23.80)
>consensus
AUAUUUUCUUUUCUUUUGGCUAAUAAAUAAGCAAUUUGGUGGCUGCUUCUUCUACUGUCAUCGACUAUUUCUUUAAUUGGUCUGCGCAAGCUGGUAAGCAUUAUUUAAUUAGCAUAGAUU
...........(((....((((((((((((((...((((((((.............))))))))................((.((....)).))...)).)))))).))))))..))).. (-19.42 = -20.50 +   1.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,115,573 – 12,115,691
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.29
Mean single sequence MFE -21.04
Consensus MFE -19.96
Energy contribution -19.44
Covariance contribution -0.52
Combinations/Pair 1.15
Mean z-score -1.03
Structure conservation index 0.95
SVM decision value -0.05
SVM RNA-class probability 0.507778
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12115573 118 + 22407834
ACCAAAUUGCUUAUUUAUUAGCCAAAAGAAAAGAAAAUAUCUGGAAACGGCAUGCUAAUGAUGUAAACUAAGCAUUUAACUGUUAAGAUGCCAGCAGCGGCAGGCAAACAU-A-AAAAGU
.......((((((.......(((........(((.....)))(....)))).(((.......)))...))))))......((((....((((.((....)).)))))))).-.-...... ( -20.80)
>DroSec_CAF1 17672 118 + 1
ACCAAAUUGCUUAUUUAUUAGCCAAAAGAAAAGAAAACAUCUGGAAACGGCAUGCUAAUGAUGUAAACUAAGCAUUUAACUGUUAAGAUGCCAGCAGCGGCAGGCAAACAU-A-AAAAGU
.......((((((.......(((........(((.....)))(....)))).(((.......)))...))))))......((((....((((.((....)).)))))))).-.-...... ( -20.80)
>DroSim_CAF1 17507 118 + 1
AGCAAAUUGCUUAUUUAUUAGCCAAAAGAAAAGAAAAUAUCUGGAAACGGCAUGCUAAUGAUGUAAACUAAGCAUUUAACUGUUAAGAUGCCAGCAGCGGCAGGCAAACAU-A-AAAAGU
((((((.((((((.......(((........(((.....)))(....)))).(((.......)))...)))))).))...))))....((((.((....)).)))).....-.-...... ( -21.20)
>DroEre_CAF1 17943 119 + 1
ACUAAAUUGCUUAUUUAUUAGCCAAAAGAAAAUGAAAUAUCUGGAAACGGCAUGCUAAUGAUGUAAACUAAGCAUUUAACUGUUAAGAUGCCAGCAGCGGCAAGCAAACAA-AAAGAAGU
......((((((..((((((((((........))......(((....)))...))))))))......((.((((......)))).))..(((......)))))))))....-........ ( -21.70)
>DroYak_CAF1 17845 120 + 1
ACCAAAUUGCUUAUUUAUUAGCCAAAAGAAGGGAAAAUAUCUGGAAACGGCAUGCUAAUGAUGUAAACUAAGCAUUUAACUGUUAAGAUGCCAGCAGCAGCAAGCAAACGAGAAAGAAGC
......((((((........(((........(((.....)))(....)))).((((..((..(....)...((((((........))))))))..))))..))))))............. ( -20.70)
>consensus
ACCAAAUUGCUUAUUUAUUAGCCAAAAGAAAAGAAAAUAUCUGGAAACGGCAUGCUAAUGAUGUAAACUAAGCAUUUAACUGUUAAGAUGCCAGCAGCGGCAGGCAAACAU_A_AAAAGU
......((((((........(((........(((.....)))(....))))..(((..((.((........((((((........)))))))).))..)))))))))............. (-19.96 = -19.44 +  -0.52)

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 11:13:05 2006