Locus 7580

Sequence ID 3L_DroMel_CAF1
Location 20,370,971 – 20,371,069
Length 98
Max. P 0.998927
window12315 window12316

overview

Window 5

Location 20,370,971 – 20,371,069
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 65.54
Mean single sequence MFE -20.26
Consensus MFE -15.40
Energy contribution -15.08
Covariance contribution -0.32
Combinations/Pair 1.29
Mean z-score -2.86
Structure conservation index 0.76
SVM decision value 2.77
SVM RNA-class probability 0.996955
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20370971 98 + 23771897
UAUUCCAAAAGUGUCACAGAAAUAUCUUUCAAUUACAUUGC---UCGAAGAUCGA------AUUUCCUUU-------------CUUAAGAUUGCUGUGACACUUUCAUUUGCCUUUCUUU
.......((((((((((((....(((((.............---(((.....)))------.........-------------...)))))..))))))))))))............... ( -22.41)
>DroSec_CAF1 5000 98 + 1
UAUUCCAAAAGUGUCACAGAAAUAUUUUUAAAUUAUAUUGC---CUGAGGAUCGA------AUUUCCCAU-------------CUUAAGAUUGCUGUGACACUUUCAGUUGCUUUUCUUU
.......((((((((((((.(((((.........)))))..---((.(((((.(.------.....).))-------------))).))....))))))))))))............... ( -20.20)
>DroSim_CAF1 5328 98 + 1
UAUUCCAAAAGUGUCACAGAAAUAUUUUUCAAUUAUAUUGC---CCGAAGAUCGA------AUUUCCCAU-------------CUUAAGAUUGCUGUGACACUUUCACUUGCUUUUCUUU
.......((((((((((((.(((((.........)))))..---...(((((.(.------.....).))-------------))).......))))))))))))............... ( -19.30)
>DroEre_CAF1 4866 85 + 1
UAUUCAAAAAGUGUCACAGAAGUAUCUUUCAAUUAUAUUG----------------------CAACAUUU-------------CUUAAGAUUACUGUGACACUUUUAGUUAGCUUUCUUU
......(((((((((((((....(((((............----------------------........-------------...)))))..))))))))))))).............. ( -19.60)
>DroAna_CAF1 2502 120 + 1
CAUUUUAGGAGUGUCACAAAAAUCACUUUAAAAUAUGCUUUUUUGUAAAGAUUUAAAACUAACAAUACUGUAAAAAGAGACUCGUUGAUUUUUAUGUGACACCUCUCGCAAUAAUUCCUU
......((..(((((((((((((((.((((((...(((......)))....))))))....(((....)))..............)))))))..))))))))..)).............. ( -19.80)
>consensus
UAUUCCAAAAGUGUCACAGAAAUAUCUUUCAAUUAUAUUGC___CCGAAGAUCGA______AUUUCCCUU_____________CUUAAGAUUGCUGUGACACUUUCAGUUGCCUUUCUUU
.......((((((((((((....(((((..........................................................)))))..))))))))))))............... (-15.40 = -15.08 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,370,971 – 20,371,069
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 65.54
Mean single sequence MFE -22.84
Consensus MFE -14.48
Energy contribution -14.16
Covariance contribution -0.32
Combinations/Pair 1.23
Mean z-score -2.98
Structure conservation index 0.63
SVM decision value 3.29
SVM RNA-class probability 0.998927
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20370971 98 - 23771897
AAAGAAAGGCAAAUGAAAGUGUCACAGCAAUCUUAAG-------------AAAGGAAAU------UCGAUCUUCGA---GCAAUGUAAUUGAAAGAUAUUUCUGUGACACUUUUGGAAUA
..............(((((((((((((..(((((...-------------........(------(((.....)))---)((((...)))).)))))....)))))))))))))...... ( -23.10)
>DroSec_CAF1 5000 98 - 1
AAAGAAAAGCAACUGAAAGUGUCACAGCAAUCUUAAG-------------AUGGGAAAU------UCGAUCCUCAG---GCAAUAUAAUUUAAAAAUAUUUCUGUGACACUUUUGGAAUA
............(..((((((((((((..(((....)-------------))((((...------....))))...---......................))))))))))))..).... ( -24.40)
>DroSim_CAF1 5328 98 - 1
AAAGAAAAGCAAGUGAAAGUGUCACAGCAAUCUUAAG-------------AUGGGAAAU------UCGAUCUUCGG---GCAAUAUAAUUGAAAAAUAUUUCUGUGACACUUUUGGAAUA
..............(((((((((((((...(((.(((-------------((.((....------)).))))).))---).......(((....)))....)))))))))))))...... ( -24.60)
>DroEre_CAF1 4866 85 - 1
AAAGAAAGCUAACUAAAAGUGUCACAGUAAUCUUAAG-------------AAAUGUUG----------------------CAAUAUAAUUGAAAGAUACUUCUGUGACACUUUUUGAAUA
............(.(((((((((((((..(((((..(-------------(.((((..----------------------..))))..))..)))))....))))))))))))).).... ( -20.10)
>DroAna_CAF1 2502 120 - 1
AAGGAAUUAUUGCGAGAGGUGUCACAUAAAAAUCAACGAGUCUCUUUUUACAGUAUUGUUAGUUUUAAAUCUUUACAAAAAAGCAUAUUUUAAAGUGAUUUUUGUGACACUCCUAAAAUG
.((((.......(....)((((((((..(((((((..((((..((((((...(((..(............)..))).))))))...)))).....)))))))))))))))))))...... ( -22.00)
>consensus
AAAGAAAAGCAACUGAAAGUGUCACAGCAAUCUUAAG_____________AAGGGAAAU______UCGAUCUUCAG___GCAAUAUAAUUGAAAGAUAUUUCUGUGACACUUUUGGAAUA
..............(((((((((((((..........................................................................)))))))))))))...... (-14.48 = -14.16 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:45 2006