Locus 4299

Sequence ID 2R_DroMel_CAF1
Location 14,136,543 – 14,136,644
Length 101
Max. P 0.940876
window6897 window6898

overview

Window 7

Location 14,136,543 – 14,136,644
Length 101
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 78.79
Mean single sequence MFE -32.45
Consensus MFE -20.10
Energy contribution -21.30
Covariance contribution 1.20
Combinations/Pair 1.18
Mean z-score -2.31
Structure conservation index 0.62
SVM decision value 1.31
SVM RNA-class probability 0.940876
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14136543 101 + 20766785
GGAGAGCCGGAGAACUCCGGACUCUCCCACGG------AACUAUAAAACACAUUUUGCGCUUGAUUGUUCAGUACAAAGGCGAUAGUUAGUUGAAUUGGUAAUUGCA---
(((((((((((....))))).)))))).....------..............(((((..((.((....))))..)))))(((((..(((((...)))))..))))).--- ( -29.90)
>DroSec_CAF1 6394 101 + 1
GGAGAGCCGGAGAACUCCGGACUCUCCCACGG------AACUAUAAAAUACAUUUUGUGCUUGCUUGUUUAGUUCAAAGGCGAUAGCUAGUUCAAUUGGUAAUUGCA---
(((((((((((....))))).))))))....(------(((((......(((....((....)).))).))))))....(((((.((((((...)))))).))))).--- ( -33.50)
>DroSim_CAF1 6767 101 + 1
GGAGAGCCGGAGAACUCCGGACUCUCCCACGG------AACUAUAAAACACAUUUUGUGCUUGCUUGUUCAGUGCAAAGGCGAUAGCUAGUUCAAUUGGUAAUUGCA---
(((((((((((....))))).))))))(((.(------(((....((.(((.....))).))....)))).))).....(((((.((((((...)))))).))))).--- ( -37.50)
>DroEre_CAF1 6485 103 + 1
GGAGAGGCGGAGAACUCCGGACUCUCCCACGGACUCACAACUAUAAAAUACAUUUUGUGC----UUGCUCAGUGCAAAGGCAAUAGCUAGUUCAAUUGGUAAUUGCA---
((((((.((((....))))..)))))).........................(((((..(----(.....))..)))))(((((.((((((...)))))).))))).--- ( -31.50)
>DroYak_CAF1 6467 103 + 1
GGAGAGCCGGAGAACUCCGGACUCUCCCACGGGCUAUCAACUAUAAAAUACAUUUUUUGC----UUGUUCAGUGCCAAGGCAAAAGCUAGUUGAAUUGGUAAUUGCU---
(((((((((((....))))).)))))).....(((((((((((.((((......))))((----((......(((....))).)))))))))))..)))).......--- ( -34.00)
>DroAna_CAF1 6678 97 + 1
GGAGUACCGGAGAACCUCGGACUCUCCCGUGGGCC--CUACUAUAAAUGA--UUU---------UCGGUCAGUGGGAAGCCGAUAGUGUGAUCGGUUGGAAGUGGUAACG
.((((.((((......))))))))(((((..((((--.............--...---------..))))..)))))(((((((......)))))))............. ( -28.27)
>consensus
GGAGAGCCGGAGAACUCCGGACUCUCCCACGG______AACUAUAAAAUACAUUUUGUGC____UUGUUCAGUGCAAAGGCGAUAGCUAGUUCAAUUGGUAAUUGCA___
(((((((((((....))))).))))))....................................................(((((.((((((...)))))).))))).... (-20.10 = -21.30 +   1.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,136,543 – 14,136,644
Length 101
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 78.79
Mean single sequence MFE -27.64
Consensus MFE -16.34
Energy contribution -16.76
Covariance contribution 0.42
Combinations/Pair 1.25
Mean z-score -1.72
Structure conservation index 0.59
SVM decision value 0.33
SVM RNA-class probability 0.693010
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14136543 101 - 20766785
---UGCAAUUACCAAUUCAACUAACUAUCGCCUUUGUACUGAACAAUCAAGCGCAAAAUGUGUUUUAUAGUU------CCGUGGGAGAGUCCGGAGUUCUCCGGCUCUCC
---.................................(((.((((.((.((((((.....)))))).)).)))------).)))((((((.(((((....))))))))))) ( -30.10)
>DroSec_CAF1 6394 101 - 1
---UGCAAUUACCAAUUGAACUAGCUAUCGCCUUUGAACUAAACAAGCAAGCACAAAAUGUAUUUUAUAGUU------CCGUGGGAGAGUCCGGAGUUCUCCGGCUCUCC
---........(((...(((((((((...((..(((.......))))).)))((.....))......)))))------)..)))(((((.(((((....)))))))))). ( -27.80)
>DroSim_CAF1 6767 101 - 1
---UGCAAUUACCAAUUGAACUAGCUAUCGCCUUUGCACUGAACAAGCAAGCACAAAAUGUGUUUUAUAGUU------CCGUGGGAGAGUCCGGAGUUCUCCGGCUCUCC
---........(((...(((((((((.((((....))...))...)))((((((.....))))))..)))))------)..)))(((((.(((((....)))))))))). ( -32.10)
>DroEre_CAF1 6485 103 - 1
---UGCAAUUACCAAUUGAACUAGCUAUUGCCUUUGCACUGAGCAA----GCACAAAAUGUAUUUUAUAGUUGUGAGUCCGUGGGAGAGUCCGGAGUUCUCCGCCUCUCC
---........(((...((.((.(((..(((....)))...)))..----.(((((.(((.....)))..)))))))))..)))(((((..((((....)))).))))). ( -24.40)
>DroYak_CAF1 6467 103 - 1
---AGCAAUUACCAAUUCAACUAGCUUUUGCCUUGGCACUGAACAA----GCAAAAAAUGUAUUUUAUAGUUGAUAGCCCGUGGGAGAGUCCGGAGUUCUCCGGCUCUCC
---.............(((((((..((((((.(((........)))----))))))...........))))))).........((((((.(((((....))))))))))) ( -30.42)
>DroAna_CAF1 6678 97 - 1
CGUUACCACUUCCAACCGAUCACACUAUCGGCUUCCCACUGACCGA---------AAA--UCAUUUAUAGUAG--GGCCCACGGGAGAGUCCGAGGUUCUCCGGUACUCC
...((((.(((((..(((((......)))))...(((((((....(---------((.--...))).)))).)--)).....))))).......((....)))))).... ( -21.00)
>consensus
___UGCAAUUACCAAUUGAACUAGCUAUCGCCUUUGCACUGAACAA____GCACAAAAUGUAUUUUAUAGUU______CCGUGGGAGAGUCCGGAGUUCUCCGGCUCUCC
...........(((........((((((.((....)).............(((.....))).....)))))).........)))(((((.(((((....)))))))))). (-16.34 = -16.76 +   0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:29 2006