Locus 10301

Sequence ID 3R_DroMel_CAF1
Location 27,619,349 – 27,619,442
Length 93
Max. P 0.853594
window16400 window16401

overview

Window 0

Location 27,619,349 – 27,619,442
Length 93
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 74.34
Mean single sequence MFE -17.60
Consensus MFE -4.82
Energy contribution -5.32
Covariance contribution 0.50
Combinations/Pair 1.25
Mean z-score -1.90
Structure conservation index 0.27
SVM decision value 0.80
SVM RNA-class probability 0.853594
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27619349 93 + 27905053
AAUUAAUUGUAAG-AAUAAAUAACAAAUAUACUUUAUUCAGAGCAAGUGUGCGAUCGUCGCUUAUCACAGCUGGAAAAAC--------GCACACGCACAAG---A-
......((((..(-((((((............)))))))...((..(((((((....(((((......)))..))....)--------)))))))))))).---.- ( -19.50)
>DroVir_CAF1 22081 82 + 1
UGUUUAAUGUAAAUAAUGAAUAAAAACAAUUAUUUAUUGCGAGCA---GUC----------UUAUCACAAGUCC---ACC--------GCACACAAUCAAUGUGAA
........(((((((((...........)))))))))((((.(..---(.(----------((.....))).).---.))--------)))((((.....)))).. ( -11.20)
>DroSec_CAF1 21172 93 + 1
AUUUAAAUGUAAA-AAUAAAUAAAAAGUAUAGUUUAUUCAGAGCAAGUGUGCGAUCGUCGCUUAUCACAGCUGGAAAAAC--------GCACACACACAAG---A-
.......(((...-.................((((.....))))..(((((((....(((((......)))..))....)--------))))))..)))..---.- ( -16.20)
>DroSim_CAF1 21243 93 + 1
AAUUAAAUGUAAG-AAUAAAUAAAAAGUAUAGUUUAUUCAGAGCAAGUGUGCGAUCGUCGCUUAUCACAGCUGGAAAAAC--------GCACACACACAAG---A-
.......(((..(-(((((((..........)))))))).......(((((((....(((((......)))..))....)--------))))))..)))..---.- ( -19.80)
>DroYak_CAF1 21291 101 + 1
AUUUAAAUGCAAG-AGUAAAUAAAAAAUAUAGCUUAUUUAGAGCAAGUGUGCGAUCGUCGCUUAUCACAGCUGGAAACACACGCACACACACCCACACAAG---C-
........((...-.................((((.....))))..(((((((......(((......)))((....))..)))))))............)---)- ( -21.30)
>consensus
AAUUAAAUGUAAG_AAUAAAUAAAAAAUAUAGUUUAUUCAGAGCAAGUGUGCGAUCGUCGCUUAUCACAGCUGGAAAAAC________GCACACACACAAG___A_
.......(((....(((((((..........)))))))....))).(((.(((.....)))....)))...................................... ( -4.82 =  -5.32 +   0.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 27,619,349 – 27,619,442
Length 93
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 74.34
Mean single sequence MFE -20.48
Consensus MFE -5.40
Energy contribution -5.90
Covariance contribution 0.50
Combinations/Pair 1.19
Mean z-score -1.75
Structure conservation index 0.26
SVM decision value 0.36
SVM RNA-class probability 0.705432
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27619349 93 - 27905053
-U---CUUGUGCGUGUGC--------GUUUUUCCAGCUGUGAUAAGCGACGAUCGCACACUUGCUCUGAAUAAAGUAUAUUUGUUAUUUAUU-CUUACAAUUAAUU
-.---.(((((.((((((--------(....((..(((......)))...)).))))))).......(((((((............))))))-).)))))...... ( -21.10)
>DroVir_CAF1 22081 82 - 1
UUCACAUUGAUUGUGUGC--------GGU---GGACUUGUGAUAA----------GAC---UGCUCGCAAUAAAUAAUUGUUUUUAUUCAUUAUUUACAUUAAACA
..((((.....))))(((--------((.---.(.((((...)))----------).)---..).)))).((((((((.(........)))))))))......... ( -13.90)
>DroSec_CAF1 21172 93 - 1
-U---CUUGUGUGUGUGC--------GUUUUUCCAGCUGUGAUAAGCGACGAUCGCACACUUGCUCUGAAUAAACUAUACUUUUUAUUUAUU-UUUACAUUUAAAU
-.---..((((.((((((--------(....((..(((......)))...)).)))))))......((((((((........))))))))..-..))))....... ( -19.20)
>DroSim_CAF1 21243 93 - 1
-U---CUUGUGUGUGUGC--------GUUUUUCCAGCUGUGAUAAGCGACGAUCGCACACUUGCUCUGAAUAAACUAUACUUUUUAUUUAUU-CUUACAUUUAAUU
-.---..((((.((((((--------(....((..(((......)))...)).))))))).......(((((((..(......)..))))))-).))))....... ( -19.70)
>DroYak_CAF1 21291 101 - 1
-G---CUUGUGUGGGUGUGUGUGCGUGUGUUUCCAGCUGUGAUAAGCGACGAUCGCACACUUGCUCUAAAUAAGCUAUAUUUUUUAUUUACU-CUUGCAUUUAAAU
-(---(((((..(((((.(((((((..((((....(((......)))))))..))))))).)))))...)))))).................-............. ( -28.50)
>consensus
_U___CUUGUGUGUGUGC________GUUUUUCCAGCUGUGAUAAGCGACGAUCGCACACUUGCUCUGAAUAAACUAUACUUUUUAUUUAUU_CUUACAUUUAAAU
.....................................(((((...(((.....)))..........((((((((........))))))))....)))))....... ( -5.40 =  -5.90 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:53:36 2006