Locus 7438

Sequence ID 3L_DroMel_CAF1
Location 19,988,755 – 19,988,895
Length 140
Max. P 0.826825
window12084 window12085

overview

Window 4

Location 19,988,755 – 19,988,857
Length 102
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 85.10
Mean single sequence MFE -37.90
Consensus MFE -26.52
Energy contribution -26.60
Covariance contribution 0.08
Combinations/Pair 1.17
Mean z-score -1.64
Structure conservation index 0.70
SVM decision value -0.00
SVM RNA-class probability 0.533343
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19988755 102 + 23771897
GCCAGAACAUGAAAUCCUGU-------CCUGGGACUCAGCCCGGACAAAACAGAUCCCGAUCCCGAGCACUGGGUUGGACUGCAACUGAGCAGUCAACUGGCUCGACUG
(((((............(((-------((.(((......))))))))..........((((((........))))))((((((......))))))..)))))....... ( -35.90)
>DroSec_CAF1 78786 101 + 1
GCCAGAACCUGAAAUCCCGU-------CCUAGGACUCAGCCCGGACAAAACAGAUCCCGAUCCCGAGCUCUGGGUCGG-CUGCAUCUGAGCAGUCAACUGGCUCGACUG
(((((.............(.-------(((((..(((.(..(((............)))...).)))..))))).)((-((((......))))))..)))))....... ( -33.80)
>DroSim_CAF1 37509 101 + 1
GCCAGAACCUGAAAUCCUGU-------CCUGGGACUGAGCCCGGACAAAACAGAUCCCGAUCCCGAGCACUGGGUCGG-CUGCAUCUGAGCAGUCAACUGGCUCGACUG
(((((...(((......(((-------((.(((......))))))))...(((((.(((((((........)))))))-....)))))..)))....)))))....... ( -36.60)
>DroEre_CAF1 29205 99 + 1
GCCAGAACC--AAACCAGGG-------CCCGGGACGCAGCCCGGACAAAACGGAGCCCGAUUCCGAGCACUGGGUCGG-CUGCAUCUGAGCAGUCAGCCGGCCUGACUG
..(((....--...((((.(-------(.(((((((..(((((.......))).)).)).))))).)).))))(((((-(((...((....)).))))))))))).... ( -40.40)
>DroYak_CAF1 30547 106 + 1
GCCAGAACC--AAACCCGGUACUGGGUACUGGGACUCAACCCGGACAAAACCGAUCCAGACUCCGAGCCCUGGGUCGG-CUGCAUCUGAGCAGUCAACGGGCUUGACUG
..(((....--...((((((((...))))))))..((((((((.........(((((((..........)))))))((-((((......))))))..)))).))))))) ( -42.80)
>consensus
GCCAGAACCUGAAAUCCGGU_______CCUGGGACUCAGCCCGGACAAAACAGAUCCCGAUCCCGAGCACUGGGUCGG_CUGCAUCUGAGCAGUCAACUGGCUCGACUG
(((((.......................(((((......)))))........((..(((((((.(....).))))))).((((......))))))..)))))....... (-26.52 = -26.60 +   0.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,988,787 – 19,988,895
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 91.34
Mean single sequence MFE -38.98
Consensus MFE -32.70
Energy contribution -31.26
Covariance contribution -1.44
Combinations/Pair 1.24
Mean z-score -1.54
Structure conservation index 0.84
SVM decision value 0.70
SVM RNA-class probability 0.826825
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19988787 108 + 23771897
CCCGGACAAAACAGAUCCCGAUCCCGAGCACUGGGUUGGACUGCAACUGAGCAGUCAACUGGCUCGACUGGCGUGCAAUUGUCAGCCAUUUGGCUGGCUUUCCCCACU
.((((........(((....))).(((((....(((((.(((((......)))))))))).))))).)))).(((.....(((((((....)))))))......))). ( -39.70)
>DroSec_CAF1 78818 107 + 1
CCCGGACAAAACAGAUCCCGAUCCCGAGCUCUGGGUCGG-CUGCAUCUGAGCAGUCAACUGGCUCGACUGGCGUGCACUUGUCAGCCAUUUGGCUGGCUUUCCCCACU
...(((.....(((((.(((((((.(....).)))))))-....)))))(((((((((.(((((.(((.((......)).)))))))).)))))).))).)))..... ( -39.80)
>DroSim_CAF1 37541 107 + 1
CCCGGACAAAACAGAUCCCGAUCCCGAGCACUGGGUCGG-CUGCAUCUGAGCAGUCAACUGGCUCGACUGGCGUGCACUUGUCAGCCAUUUGGCUGGCUUUCCCCACU
...(((.....(((((.(((((((........)))))))-....)))))(((((((((.(((((.(((.((......)).)))))))).)))))).))).)))..... ( -38.90)
>DroEre_CAF1 29235 105 + 1
CCCGGACAAAACGGAGCCCGAUUCCGAGCACUGGGUCGG-CUGCAUCUGAGCAGUCAGCCGGCCUGACUGCCAUGCACUUGUCAGCUAUUUGGCUGG--UUCCCCACU
.(((.......))).((.((....)).))..((((..((-((((......))))))((((((((.(.(((.((......)).)))).....))))))--)).)))).. ( -36.80)
>DroYak_CAF1 30584 107 + 1
CCCGGACAAAACCGAUCCAGACUCCGAGCCCUGGGUCGG-CUGCAUCUGAGCAGUCAACGGGCUUGACUGGCAUGCACUUGUCAGCUAUUUGGCUGGCUUUCCCCACU
.((((.(((..(((((((((..........)))))))((-((((......))))))...))..))).)))).........(((((((....))))))).......... ( -39.70)
>consensus
CCCGGACAAAACAGAUCCCGAUCCCGAGCACUGGGUCGG_CUGCAUCUGAGCAGUCAACUGGCUCGACUGGCGUGCACUUGUCAGCCAUUUGGCUGGCUUUCCCCACU
...(((.....(((...(((((((.(....).))))))).((((......))))....)))((.((.....)).))....(((((((....)))))))..)))..... (-32.70 = -31.26 +  -1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:04 2006