Locus 4955

Sequence ID 3R_DroMel_CAF1
Location 13,036,130 – 13,036,258
Length 128
Max. P 0.823997
window8108 window8109

overview

Window 8

Location 13,036,130 – 13,036,230
Length 100
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 78.57
Mean single sequence MFE -36.72
Consensus MFE -20.24
Energy contribution -20.37
Covariance contribution 0.13
Combinations/Pair 1.18
Mean z-score -1.90
Structure conservation index 0.55
SVM decision value 0.34
SVM RNA-class probability 0.696983
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13036130 100 + 27905053
GCG-GCCAAACGAAAUGCAUGAGACAGCUUAAGUGAGCUGCGCUGCUGCUACACAAAAGUGUGCGGUGGGCGGUGGGCGGCUGGGC------CAGCAGUUGCGGCAG
.((-(((............((((....)))).((..(((((.(..((((.((((....))))))))..))))))..))))))).((------(.((....))))).. ( -40.60)
>DroSec_CAF1 56197 93 + 1
GCGGGCCAAACGAAAUGCAUGAGACAGCUUAAGUGAGCUGCGCUGCUGCUUCACAAAAGU-------GGGCGGUGGGCGGUUGGGG------CAGCAG-UGCGGCAG
....(((..................(((((....)))))((((((((((((((((....)-------).((.....))...)))))------))))))-)))))).. ( -35.80)
>DroSim_CAF1 48425 92 + 1
GCG-GCCAAACGAAAUGCAUGAGACAGCUUAAGUGAGCUGCGCUGCUGCUUCACAAAAGU-------GGGCGGUGGGCUGCUGGGG------CAGCAG-UGCGGCAG
...-(((..................(((((....)))))(((((((((((((((....))-------.(((((....)))))))))------))))))-)))))).. ( -40.30)
>DroEre_CAF1 56400 88 + 1
GCG-GCCAAACGAAAUGCAUGAGACAGCUUAAGUGAGCUGCGCUGCUGCUCCGCAAAAG--------GGGCAGUGGGCGGAGGGC---------GUUG-GACGGUUG
.((-.((((.((...(((....(.((((((....))))))).(..(((((((......)--------))))))..)))).....)---------))))-).)).... ( -35.30)
>DroAna_CAF1 55691 88 + 1
AAG-GCCAAACGAAAUGCAUGAGACAGCUUAAGUGAGCUGCGC-GCCGCUAC-----CGU-------CGGAGGUG--CGGAUAGGGGCGUCCCAGUAG---UGGCAG
...-((((.((...........(.((((((....)))))))((-(((.((((-----(((-------.......)--))).))).)))))....))..---)))).. ( -31.60)
>consensus
GCG_GCCAAACGAAAUGCAUGAGACAGCUUAAGUGAGCUGCGCUGCUGCUACACAAAAGU_______GGGCGGUGGGCGGAUGGGG______CAGCAG_UGCGGCAG
....(((........(((......((((((....))))))((((((((((..................)))))).))))...............))).....))).. (-20.24 = -20.37 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,036,162 – 13,036,258
Length 96
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 82.98
Mean single sequence MFE -39.08
Consensus MFE -24.36
Energy contribution -25.17
Covariance contribution 0.81
Combinations/Pair 1.22
Mean z-score -2.21
Structure conservation index 0.62
SVM decision value 0.69
SVM RNA-class probability 0.823997
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13036162 96 + 27905053
UGAGCUGCGCUGCUGCUACACAAAAGUGUGCGGUGGGCGGUGGGCGGCUGGGCCAGCAGUUGCGGCAGGGGGCGUGGCAGCGGGCAAAAUGCGGAU----
...(((((.(..((((.((((....))))))))..))))))..(((.....(((.((.((..((.(....).))..)).)).)))....)))....---- ( -41.80)
>DroSec_CAF1 56230 88 + 1
UGAGCUGCGCUGCUGCUUCACAAAAGU-------GGGCGGUGGGCGGUUGGGGCAGCAG-UGCGGCAGGGGGCGUGGCAGCGGGCAAAAUGCGGAU----
...(((((((((((((((((((....)-------).((.....))...)))))))))))-)))))).....((((.((.....))...))))....---- ( -38.70)
>DroSim_CAF1 48457 88 + 1
UGAGCUGCGCUGCUGCUUCACAAAAGU-------GGGCGGUGGGCUGCUGGGGCAGCAG-UGCGGCAGGGGGCGUGGCAGCGGGCAAAAUGCGGAU----
...((((((((((((((((((....))-------.(((((....)))))))))))))))-)))))).....((((.((.....))...))))....---- ( -43.20)
>DroEre_CAF1 56432 88 + 1
UGAGCUGCGCUGCUGCUCCGCAAAAG--------GGGCAGUGGGCGGAGGGC---GUUG-GACGGUUGGGGGCGUGGCAGCGGGCGAAAUGCGGAUGUGG
....((((.(..(((((((......)--------))))))..)))))...((---(((.-..(.((((.........)))).)....)))))........ ( -32.60)
>consensus
UGAGCUGCGCUGCUGCUUCACAAAAGU_______GGGCGGUGGGCGGCUGGGGCAGCAG_UGCGGCAGGGGGCGUGGCAGCGGGCAAAAUGCGGAU____
...(((.((((((((((((((....)).........((.((...((((((...))))))..)).))..)))))..))))))))))............... (-24.36 = -25.17 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:56 2006