Locus 5250

Sequence ID 2L_DroMel_CAF1
Location 14,809,524 – 14,809,719
Length 195
Max. P 0.999794
window8358 window8359 window8360

overview

Window 8

Location 14,809,524 – 14,809,623
Length 99
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 95.07
Mean single sequence MFE -32.13
Consensus MFE -28.16
Energy contribution -28.85
Covariance contribution 0.69
Combinations/Pair 1.07
Mean z-score -2.07
Structure conservation index 0.88
SVM decision value 0.90
SVM RNA-class probability 0.876787
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14809524 99 - 22407834
GAGUAGUCAGGUUGUUCUGGCUGU---UGUGAGUGUGGCAGUGCUUGUAUCUGUGUGUUUUGGAUUGCAUGCACGAAUAACAGGACACGGCAGGAAAUGCCA
..((.(((..(((((((..((..(---.......)..)).((((.((((((((.......)))).)))).)))))))))))..)))))((((.....)))). ( -33.60)
>DroSec_CAF1 50943 102 - 1
GAGUAGUCAGGUUGUUCUGGCUGUGAGUGUGAGUGUGGCAGUGCUUGUAUCUGUGUGUUUUGGAUUGCAUGCACGAAUAAUAGGACACGGCAGGAAAUGCCA
..((.(((..(((((((..((..((........))..)).((((.((((((((.......)))).)))).)))))))))))..)))))((((.....)))). ( -31.60)
>DroSim_CAF1 51604 102 - 1
GAGUAGUCAGGUUGUUCUGGCUGUGAGUGUGAGUGUGGCAGUGCUUGUAUCUGUGUGUUUUGGAUUGCAUGCACGAAUAACAGGACACGGCAGGAAAUGCCA
..((.(((..(((((((..((..((........))..)).((((.((((((((.......)))).)))).)))))))))))..)))))((((.....)))). ( -33.10)
>DroYak_CAF1 47727 98 - 1
GAG-UGUCAGUUUGUUCUGGCUGU---UGUGAGUGUGGCAGUGCUUGUAUCUGUGUGUUUUGGAUUGCAUGCACGAAUAGCAGGACACGGCAGGAAAUGGCA
...-(((((.(((((..((.((((---(((..((((((((((.(.................).))))).)))))..)))))))..))..)))))...))))) ( -30.23)
>consensus
GAGUAGUCAGGUUGUUCUGGCUGU___UGUGAGUGUGGCAGUGCUUGUAUCUGUGUGUUUUGGAUUGCAUGCACGAAUAACAGGACACGGCAGGAAAUGCCA
.....(((..(((((((..((..((........))..)).((((.((((((((.......)))).)))).)))))))))))..)))..((((.....)))). (-28.16 = -28.85 +   0.69)

alignment

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secondary structure

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Window 9

Location 14,809,623 – 14,809,719
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 91.15
Mean single sequence MFE -30.08
Consensus MFE -25.48
Energy contribution -26.64
Covariance contribution 1.16
Combinations/Pair 1.14
Mean z-score -4.10
Structure conservation index 0.85
SVM decision value 4.10
SVM RNA-class probability 0.999794
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14809623 96 + 22407834
ACACAAAUACAAGCACAAGCACUCAUUGAGGGGCAAUGCAUUCAAGCGCAAAUUAAGCUUGACAAGCAAAAAUUAAACUGUAUGUAGCUGUGUGGC
(((((..((((.(((...((.(((.....)))))..(((..((((((.........))))))...)))..........))).))))..)))))... ( -25.50)
>DroSec_CAF1 51045 96 + 1
ACACAGAUACGAGCACAAGCACUCAUUGAGGGGCAAUGCAUUCAAGCGCAAAUUAAGCUUGACAAGCAAAAAUUAAACUGUGUGUAUCUGUGUGGC
((((((((((..(((((.((.(((.....)))))..(((..((((((.........))))))...)))..........)))))))))))))))... ( -33.40)
>DroSim_CAF1 51706 96 + 1
ACACAGAUACAAGCACAAGCACUCAUUGAGGGGCAAUGCAUUCAAGCGCAAAUUAAGCUUGACAAGCAAAAAUUAAACUGUGUGUAUCUGUGUGGC
((((((((((..(((((.((.(((.....)))))..(((..((((((.........))))))...)))..........)))))))))))))))... ( -33.40)
>DroYak_CAF1 47825 96 + 1
GCACAGAUACACACACAAGCACUCAUUGAGGGGCAAUGCAUUCAAGCGCAAAUUAAGCUUGACAAGCAAAAAUUAAACUGAGUGUAUCUGUGUGGC
((((((((((((......((.(((.....)))))..(((..((((((.........))))))...))).............))))))))))))... ( -33.90)
>DroAna_CAF1 36914 94 + 1
AUACAAACACAGAGACAAACACCCAUCGAGGGGCAGUGCAUUGAAGCGCAAAUUAAGCUUGACAAGCAAAAAUUAAACUG--UGUAUCUGUGUAGG
......(((((((.((.....(((.....)))(((((((......)).........(((.....))).........))))--))).)))))))... ( -24.20)
>consensus
ACACAGAUACAAGCACAAGCACUCAUUGAGGGGCAAUGCAUUCAAGCGCAAAUUAAGCUUGACAAGCAAAAAUUAAACUGUGUGUAUCUGUGUGGC
(((((((((((.(((...((.(((.....)))))..(((..((((((.........))))))...)))..........))).)))))))))))... (-25.48 = -26.64 +   1.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,809,623 – 14,809,719
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 91.15
Mean single sequence MFE -27.06
Consensus MFE -22.84
Energy contribution -23.60
Covariance contribution 0.76
Combinations/Pair 1.17
Mean z-score -2.83
Structure conservation index 0.84
SVM decision value 3.34
SVM RNA-class probability 0.999038
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14809623 96 - 22407834
GCCACACAGCUACAUACAGUUUAAUUUUUGCUUGUCAAGCUUAAUUUGCGCUUGAAUGCAUUGCCCCUCAAUGAGUGCUUGUGCUUGUAUUUGUGU
...((((((.(((((((((.........(((...((((((.........))))))..)))..((..(((...))).)))))))..)))).)))))) ( -22.30)
>DroSec_CAF1 51045 96 - 1
GCCACACAGAUACACACAGUUUAAUUUUUGCUUGUCAAGCUUAAUUUGCGCUUGAAUGCAUUGCCCCUCAAUGAGUGCUUGUGCUCGUAUCUGUGU
...((((((((((...............(((...((((((.........))))))..)))............(((((....))))))))))))))) ( -29.70)
>DroSim_CAF1 51706 96 - 1
GCCACACAGAUACACACAGUUUAAUUUUUGCUUGUCAAGCUUAAUUUGCGCUUGAAUGCAUUGCCCCUCAAUGAGUGCUUGUGCUUGUAUCUGUGU
...((((((((((((((((.........(((...((((((.........))))))..)))..((..(((...))).)))))))..))))))))))) ( -30.60)
>DroYak_CAF1 47825 96 - 1
GCCACACAGAUACACUCAGUUUAAUUUUUGCUUGUCAAGCUUAAUUUGCGCUUGAAUGCAUUGCCCCUCAAUGAGUGCUUGUGUGUGUAUCUGUGC
....(((((((((((.((..........(((...((((((.........))))))..)))..((..(((...))).))...)).))))))))))). ( -30.70)
>DroAna_CAF1 36914 94 - 1
CCUACACAGAUACA--CAGUUUAAUUUUUGCUUGUCAAGCUUAAUUUGCGCUUCAAUGCACUGCCCCUCGAUGGGUGUUUGUCUCUGUGUUUGUAU
...(((((((.(((--............((((((....((.......))....))).)))..((((......))))...))).)))))))...... ( -22.00)
>consensus
GCCACACAGAUACACACAGUUUAAUUUUUGCUUGUCAAGCUUAAUUUGCGCUUGAAUGCAUUGCCCCUCAAUGAGUGCUUGUGCUUGUAUCUGUGU
...((((((((((((((((.........(((...((((((.........))))))..)))..((..(((...))).)))))))..))))))))))) (-22.84 = -23.60 +   0.76)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:46 2006