Locus 4243

Sequence ID 3R_DroMel_CAF1
Location 11,381,520 – 11,381,663
Length 143
Max. P 0.759017
window6881 window6882

overview

Window 1

Location 11,381,520 – 11,381,633
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.82
Mean single sequence MFE -26.53
Consensus MFE -20.27
Energy contribution -20.23
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.48
Structure conservation index 0.76
SVM decision value -0.05
SVM RNA-class probability 0.507970
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11381520 113 - 27905053
CCAGGUCCGAUUCCAUA------ACCAUGUCCAUGUCUAUGGACCCGACCAACUCCCGAACUCCCACUACC-CGGAGCUGAAAUUUAAUGGCCUGGUUUUCCGCUUGGUUAACUCAAUUU
.((((((((..((((((------..(((....)))..))))))..))..((.((((.(............)-.)))).)).........))))))(((..((....))..)))....... ( -27.30)
>DroSec_CAF1 129283 113 - 1
CCAGGUUCGAUUCCAUA------ACCAUGUCCAUGUCUAUGGAGCCGACCAACUCCCGCACUCCCACUCCC-CGGAGCUGAAAUUUAAUGGCCUGGUUUUCCGCUUGGUUAACUCAAUUU
.((((.(((..((((((------..(((....)))..))))))..)))(((.......((((((.......-.)))).))........)))))))(((..((....))..)))....... ( -27.86)
>DroSim_CAF1 120337 113 - 1
GCAGGUUCGAUUCCAUA------ACCAUGUCCAUGUCUAUGGAGCCGACCAACUCCCGAACUCCCACUCCC-CGUAGCUGAAAUUUAAUGGCCUGGUUUUCCGCUUGGUUAACUCAAUUU
...(((.((..((((((------..(((....)))..))))))..)))))....................(-((.(((.((((.(((......))).)))).))))))............ ( -23.60)
>DroEre_CAF1 116769 112 - 1
CCAGGUCCGUUUCCAUAACCAUAACCAUGUCCAUGUCUAUGGACCCGACCAACUCCC--------ACUCCCGCGGAGCUGAAAUUUAAUGGCCUGGUUUUCCGCUUGGUUAACUCAAUUU
.((((((((..((((((..(((..........)))..))))))..))..((.(((((--------......).)))).)).........))))))(((..((....))..)))....... ( -27.60)
>DroYak_CAF1 119375 118 - 1
CCAGGUCCGAUUCCAUAACCAUAACCAUGUCCAUGUCUAUGGACCCGACCAACUCCC--ACUCCCACUCCCGCGGAGCUGAAAUUUAAUGGCCUGGUUUUCCGCUUGGUUAACUCAAUUU
((((((..((..(((...((((......((((((....))))))............(--((((((......).)))).)).......))))..)))..))..))))))............ ( -26.30)
>consensus
CCAGGUCCGAUUCCAUA______ACCAUGUCCAUGUCUAUGGACCCGACCAACUCCCG_ACUCCCACUCCC_CGGAGCUGAAAUUUAAUGGCCUGGUUUUCCGCUUGGUUAACUCAAUUU
.((((((((..((((((........(((....)))..))))))..))..((.((((.................)))).)).........))))))(((..((....))..)))....... (-20.27 = -20.23 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,381,560 – 11,381,663
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.81
Mean single sequence MFE -42.60
Consensus MFE -27.57
Energy contribution -27.93
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -2.03
Structure conservation index 0.65
SVM decision value 0.50
SVM RNA-class probability 0.759017
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11381560 103 + 27905053
CAGCUCCG-GGUAGUGGGAGUUCGGGAGUUGGUCGGGUCCAUAGACAUGGACAUGGU------UAUGGAAUCGGACCUGGAGCAGAGGCAACUCCACUUCAGCCGCUCC----------G
.((((((.-.......))))))..(((((.((((.(((((((((.(((....))).)------))))).))).))))(((((..(((....)))..)))))...)))))----------. ( -42.40)
>DroSec_CAF1 129323 103 + 1
CAGCUCCG-GGGAGUGGGAGUGCGGGAGUUGGUCGGCUCCAUAGACAUGGACAUGGU------UAUGGAAUCGAACCUGGAGCAGAGGCAACUCCACUUCAGCCGCUCC----------G
..(((((.-.......)))))...(((((.(((((..(((((((.(((....))).)------))))))..)))..((((((..(((....)))..)))))))))))))----------. ( -43.10)
>DroSim_CAF1 120377 103 + 1
CAGCUACG-GGGAGUGGGAGUUCGGGAGUUGGUCGGCUCCAUAGACAUGGACAUGGU------UAUGGAAUCGAACCUGCAGCAGAGGCAACUCCACUUCAGCCGCUCC----------G
...(....-)(((((((..(....(((((((.(((..(((((((.(((....))).)------))))))..))).(((.......))))))))))....)..)))))))----------. ( -41.00)
>DroEre_CAF1 116809 112 + 1
CAGCUCCGCGGGAGU--------GGGAGUUGGUCGGGUCCAUAGACAUGGACAUGGUUAUGGUUAUGGAAACGGACCUGGAGUAGAGGGAACUCCACUUCAGCCGCUCCGCUCCGCUCCG
.......((((.(((--------((.(((.(((((..(((((((.(((((......))))).)))))))..)))..(((((((.(((....))).))))))))))))))))))))).... ( -47.30)
>DroYak_CAF1 119415 100 + 1
CAGCUCCGCGGGAGUGGGAGU--GGGAGUUGGUCGGGUCCAUAGACAUGGACAUGGUUAUGGUUAUGGAAUCGGACCUGGAGUAGAGGGAACUCCACUUCA------------------G
..(((((((....)).)))))--.......((((.(((((((((.(((((......))))).)))))).))).))))((((((.(((....))).))))))------------------. ( -39.20)
>consensus
CAGCUCCG_GGGAGUGGGAGU_CGGGAGUUGGUCGGGUCCAUAGACAUGGACAUGGU______UAUGGAAUCGGACCUGGAGCAGAGGCAACUCCACUUCAGCCGCUCC__________G
(((((((.................))))))).(((..((((((..(((....)))........))))))..)))..((((((..(((....)))..)))))).................. (-27.57 = -27.93 +   0.36)

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 11:23:15 2006