Locus 2090

Sequence ID 3L_DroMel_CAF1
Location 5,749,824 – 5,749,927
Length 103
Max. P 0.947670
window3255 window3256

overview

Window 5

Location 5,749,824 – 5,749,927
Length 103
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 84.22
Mean single sequence MFE -28.52
Consensus MFE -18.26
Energy contribution -19.42
Covariance contribution 1.16
Combinations/Pair 1.18
Mean z-score -2.87
Structure conservation index 0.64
SVM decision value 1.37
SVM RNA-class probability 0.947670
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5749824 103 + 23771897
UCAUUGAAUCGGUAUCCUUGCAUCAAUCGCGUGCUGGCGAUACCGCUUUAAUGACGCCAAUAAUCAGACA----ACAAGGUUACCGCUCUAAUGUUUCAUUUUUAAA
((((((((.(((((((((.((((.......)))).)).))))))).)))))))).((...(((((.....----....)))))..)).................... ( -25.00)
>DroSec_CAF1 8732 103 + 1
GCAUUGGAUCGGUAUCCUUGCACCAAUCGGGUGCUGGGGAUACCGCUUUAAUGGCGCCAAUAAUCAAGCA----ACAAGGUUACCGCUCUAAUGUUUCAUUUUUAAA
((((((((..((((((((((((((.....))))).)))))))))(((.....)))((...(((((.....----....)))))..))))))))))............ ( -34.30)
>DroSim_CAF1 8713 103 + 1
GCAUUGGAUCGGUAUCCUUGCACCAAUCGGGUUCUGGGGAUACCGUUUUAAUGACGCCAAUAAUCAAGCA----ACAAGGUUACCGCUCUAAUGUUUCAUUUUUAAA
((((((((.(((((.(((((..((....))(((.(((..((..((((.....))))...))..)))))).----.))))).))))).))))))))............ ( -28.70)
>DroEre_CAF1 8727 107 + 1
ACACUGCAGCGGCAACCUUGCAUCCAUUGGGCACUAAGGAUACCGCUUUAAUGACGCCAACAAUCAGAAAAAACACAAGGUUACCGCUCUAAUGUUUCAUUUUUAAA
(((.((.(((((.(((((((......(((((((.(((((......))))).)).).))))......(......).))))))).))))).)).)))............ ( -23.90)
>DroYak_CAF1 8733 107 + 1
ACACUGAAGCGGUAACCUUGCAUCCAAUGGAAACAAAGGAUACCGCUUUAAUGACGCCAGUAAUCAGAAAACAAACAAGGUUACCGCUCUAAUGUUUCAUUUUAAAA
(((.((.(((((((((((((.((((..((....))..))))...((.........))..................))))))))))))).)).)))............ ( -30.70)
>consensus
ACAUUGAAUCGGUAUCCUUGCAUCAAUCGGGUACUGGGGAUACCGCUUUAAUGACGCCAAUAAUCAGACA____ACAAGGUUACCGCUCUAAUGUUUCAUUUUUAAA
.(((((((.(((((((((((.(((.....))).).)))))))))).)))))))..((...(((((.............)))))..)).................... (-18.26 = -19.42 +   1.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,749,824 – 5,749,927
Length 103
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 84.22
Mean single sequence MFE -31.88
Consensus MFE -20.32
Energy contribution -19.64
Covariance contribution -0.68
Combinations/Pair 1.28
Mean z-score -2.79
Structure conservation index 0.64
SVM decision value 1.26
SVM RNA-class probability 0.937142
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5749824 103 - 23771897
UUUAAAAAUGAAACAUUAGAGCGGUAACCUUGU----UGUCUGAUUAUUGGCGUCAUUAAAGCGGUAUCGCCAGCACGCGAUUGAUGCAAGGAUACCGAUUCAAUGA
.............((((.((((((((.((((((----.(((.(....((((((..(((.....)))..))))))....))))....)))))).))))).))))))). ( -29.20)
>DroSec_CAF1 8732 103 - 1
UUUAAAAAUGAAACAUUAGAGCGGUAACCUUGU----UGCUUGAUUAUUGGCGCCAUUAAAGCGGUAUCCCCAGCACCCGAUUGGUGCAAGGAUACCGAUCCAAUGC
..................((((..((....)).----.))))...((((((.((.......))(((((((...(((((.....)))))..)))))))...)))))). ( -29.10)
>DroSim_CAF1 8713 103 - 1
UUUAAAAAUGAAACAUUAGAGCGGUAACCUUGU----UGCUUGAUUAUUGGCGUCAUUAAAACGGUAUCCCCAGAACCCGAUUGGUGCAAGGAUACCGAUCCAAUGC
.............((((.((.(((((.(((((.----.(((........)))..((((((..(((..((....))..))).))))))))))).))))).)).)))). ( -25.50)
>DroEre_CAF1 8727 107 - 1
UUUAAAAAUGAAACAUUAGAGCGGUAACCUUGUGUUUUUUCUGAUUGUUGGCGUCAUUAAAGCGGUAUCCUUAGUGCCCAAUGGAUGCAAGGUUGCCGCUGCAGUGU
............(((((..((((((((((((((((((.........(((((.(.((((((..........))))))))))))))))))))))))))))))..))))) ( -36.90)
>DroYak_CAF1 8733 107 - 1
UUUUAAAAUGAAACAUUAGAGCGGUAACCUUGUUUGUUUUCUGAUUACUGGCGUCAUUAAAGCGGUAUCCUUUGUUUCCAUUGGAUGCAAGGUUACCGCUUCAGUGU
............(((((..((((((((((((...((((((.((((.......))))..))))))((((((..((....))..))))))))))))))))))..))))) ( -38.70)
>consensus
UUUAAAAAUGAAACAUUAGAGCGGUAACCUUGU____UGUCUGAUUAUUGGCGUCAUUAAAGCGGUAUCCCCAGCACCCGAUUGAUGCAAGGAUACCGAUCCAAUGC
.............((((.((.(((((.((((....................(((.......)))((((((...(....)...)))))))))).))))).)).)))). (-20.32 = -19.64 +  -0.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:09 2006