Locus 1269

Sequence ID 3L_DroMel_CAF1
Location 3,668,201 – 3,668,293
Length 92
Max. P 0.984740
window1984 window1985

overview

Window 4

Location 3,668,201 – 3,668,293
Length 92
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 79.92
Mean single sequence MFE -27.78
Consensus MFE -20.76
Energy contribution -22.00
Covariance contribution 1.24
Combinations/Pair 1.16
Mean z-score -2.00
Structure conservation index 0.75
SVM decision value 1.19
SVM RNA-class probability 0.928985
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3668201 92 + 23771897
GACGCACGUUGCUCACCCCUCGGGAGGUCAACAUGCAACCAG---------------------CAUCUUGCAACUGGUAACUUGCGAGAAGCUGCUCUUUACCAGCAACAAGC
...(((.((((..(.(((...))).)..)))).)))...(((---------------------(.((((((((........)))))))).))))................... ( -28.00)
>DroSec_CAF1 63334 92 + 1
GACGCACGUUGCUCACCCCUCGGGAGGUCAACAUGCAACCAG---------------------CAACUUGCAACUGGUAACUUGCAACAAGCUGCUCUUUACCAGCAACAAGC
...(((.((((((..(((...))).(((.........)))))---------------------)))).)))..(((((((...(((......)))...)))))))........ ( -27.50)
>DroSim_CAF1 58112 78 + 1
GACGCACGUUGCUCACCCCUCGGGAGGUCAACAUGCAACCAG---------------------CAACUUGCAACUGGUAACUUGCAACAA--------------GCAACAAGC
...(((.((((..(.(((...))).)..)))).))).(((((---------------------..........)))))...((((.....--------------))))..... ( -19.80)
>DroEre_CAF1 57634 113 + 1
GACGCACGUUGCUCACCCCUCGGGAGGUCAACAUGCAACCAGCAACCCGCAACCCGCAACCAGCAACUUGCAACUAGUAACGUGCAACAAGGUGCUCCUUACUAGCAACAAGC
...(((.((((((.......((((..((.....(((.....)))....))..)))).....)))))).)))..(((((((.(.(((......))).).)))))))........ ( -31.70)
>DroYak_CAF1 43992 106 + 1
GACGCACGUUGCUCACCCCUCGGGAGGUCAGCAUGCAACCAGCA-------ACCAGCAGCUUGCAACUUGCAACUGGUAACGUGCAACAAGAUGCUCUUUACUAGCAACAAGC
...((((((((((.(((((...)).))).))).(((.....)))-------(((((....((((.....)))))))))))))))).....(.((((.......)))).).... ( -31.90)
>consensus
GACGCACGUUGCUCACCCCUCGGGAGGUCAACAUGCAACCAG_____________________CAACUUGCAACUGGUAACUUGCAACAAGCUGCUCUUUACCAGCAACAAGC
...(((.((((..(.(((...))).)..)))).)))..............................((((...(((((((...(((......)))...)))))))...)))). (-20.76 = -22.00 +   1.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,668,201 – 3,668,293
Length 92
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 79.92
Mean single sequence MFE -37.98
Consensus MFE -28.20
Energy contribution -30.24
Covariance contribution 2.04
Combinations/Pair 1.04
Mean z-score -2.43
Structure conservation index 0.74
SVM decision value 1.98
SVM RNA-class probability 0.984740
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3668201 92 - 23771897
GCUUGUUGCUGGUAAAGAGCAGCUUCUCGCAAGUUACCAGUUGCAAGAUG---------------------CUGGUUGCAUGUUGACCUCCCGAGGGGUGAGCAACGUGCGUC
.(((((.((((((((...((........))...)))))))).)))))...---------------------......((((((((..(.(((...))).)..))))))))... ( -35.90)
>DroSec_CAF1 63334 92 - 1
GCUUGUUGCUGGUAAAGAGCAGCUUGUUGCAAGUUACCAGUUGCAAGUUG---------------------CUGGUUGCAUGUUGACCUCCCGAGGGGUGAGCAACGUGCGUC
((((((.((((((((...((((....))))...)))))))).))))))..---------------------......((((((((..(.(((...))).)..))))))))... ( -39.40)
>DroSim_CAF1 58112 78 - 1
GCUUGUUGC--------------UUGUUGCAAGUUACCAGUUGCAAGUUG---------------------CUGGUUGCAUGUUGACCUCCCGAGGGGUGAGCAACGUGCGUC
((.((((((--------------((...(((.((.((((((........)---------------------))))).)).)))..(((((....))))))))))))).))... ( -29.80)
>DroEre_CAF1 57634 113 - 1
GCUUGUUGCUAGUAAGGAGCACCUUGUUGCACGUUACUAGUUGCAAGUUGCUGGUUGCGGGUUGCGGGUUGCUGGUUGCAUGUUGACCUCCCGAGGGGUGAGCAACGUGCGUC
((.(((((((.((((..((((.(((((.((.(((.((((((........)))))).))).)).))))).))))..))))......(((((....))))).))))))).))... ( -43.80)
>DroYak_CAF1 43992 106 - 1
GCUUGUUGCUAGUAAAGAGCAUCUUGUUGCACGUUACCAGUUGCAAGUUGCAAGCUGCUGGU-------UGCUGGUUGCAUGCUGACCUCCCGAGGGGUGAGCAACGUGCGUC
((.(((.((((((((..((((.((((((((((.......).))))....))))).))))..)-------))))))).)))((((.(((((....))))).))))....))... ( -41.00)
>consensus
GCUUGUUGCUAGUAAAGAGCAGCUUGUUGCAAGUUACCAGUUGCAAGUUG_____________________CUGGUUGCAUGUUGACCUCCCGAGGGGUGAGCAACGUGCGUC
((((((.((((((((...((........))...)))))))).)))))).............................((((((((..(.(((...))).)..))))))))... (-28.20 = -30.24 +   2.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:29 2006