Locus 3705

Sequence ID 3L_DroMel_CAF1
Location 10,770,267 – 10,770,402
Length 135
Max. P 0.996245
window5788 window5789

overview

Window 8

Location 10,770,267 – 10,770,362
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 99.58
Mean single sequence MFE -23.90
Consensus MFE -23.90
Energy contribution -23.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 1.00
SVM decision value 2.67
SVM RNA-class probability 0.996245
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10770267 95 - 23771897
CCGCUCUAAGCCAGAAAAUCACAAACAGAAACUGUGACUGAGCGACGGACACUGAACCAGCUGACGUUACAGGUUUUCAAAUCUGGCACAUUAAU
.........((((((...((.......))..((((((((.(((...((........)).))).).))))))).........))))))........ ( -23.90)
>DroSec_CAF1 103930 95 - 1
CCGCUCUAAGCCAGAAAAUCACAAACAGAAACUGUGACUGAGCGACGGACACUGAACCAGCUGACGUUACAGGUUUUCAAAUCUGGCACAUUAAU
.........((((((...((.......))..((((((((.(((...((........)).))).).))))))).........))))))........ ( -23.90)
>DroSim_CAF1 106818 95 - 1
CCGCUCUAAGCCAGAAAAUCACAAACAGAAACUGUGACUGAGCGACGGACACUGAACCAGCUGACGUUACAGGUUUUCAAAUCUGGCACAUUAAU
.........((((((...((.......))..((((((((.(((...((........)).))).).))))))).........))))))........ ( -23.90)
>DroEre_CAF1 108906 95 - 1
CCGCUCUAAGCCAGAAAAUCACAAACAGAAACUGUGACUGAGCGACGGACACUGAACCAGCUGACGUUACAGGUUUUCAAAUCUGGCACAUUAAU
.........((((((...((.......))..((((((((.(((...((........)).))).).))))))).........))))))........ ( -23.90)
>DroYak_CAF1 120156 95 - 1
UCGCUCUAAGCCAGAAAAUCACAAACAGAAACUGUGACUGAGCGACGGACACUGAACCAGCUGACGUUACAGGUUUUCAAAUCUGGCACAUUAAU
.........((((((...((.......))..((((((((.(((...((........)).))).).))))))).........))))))........ ( -23.90)
>consensus
CCGCUCUAAGCCAGAAAAUCACAAACAGAAACUGUGACUGAGCGACGGACACUGAACCAGCUGACGUUACAGGUUUUCAAAUCUGGCACAUUAAU
.........((((((...((.......))..((((((((.(((...((........)).))).).))))))).........))))))........ (-23.90 = -23.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,770,307 – 10,770,402
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 98.95
Mean single sequence MFE -27.20
Consensus MFE -26.64
Energy contribution -26.48
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.77
Structure conservation index 0.98
SVM decision value 1.95
SVM RNA-class probability 0.983780
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10770307 95 + 23771897
UCAGUGUCCGUCGCUCAGUCACAGUUUCUGUUUGUGAUUUUCUGGCUUAGAGCGGCGAAGUUGACGAGUUAACUGAAAGAAACUAAACUGAAAGA
(((((...(((((((((((((.((..((.......))..)).)))))..)))))))).((((((....))))))............))))).... ( -28.70)
>DroSec_CAF1 103970 95 + 1
UCAGUGUCCGUCGCUCAGUCACAGUUUCUGUUUGUGAUUUUCUGGCUUAGAGCGGCCAAGUUGACGAGUUAACUGAAAGAAACUAAACUGAAAGA
(((((....((((((((((((.((..((.......))..)).)))))..)))))))..((((((....))))))............))))).... ( -26.00)
>DroSim_CAF1 106858 95 + 1
UCAGUGUCCGUCGCUCAGUCACAGUUUCUGUUUGUGAUUUUCUGGCUUAGAGCGGCCAAGUUGACGAGUUAACUGAAAGAAACUAAACUGAAAGA
(((((....((((((((((((.((..((.......))..)).)))))..)))))))..((((((....))))))............))))).... ( -26.00)
>DroEre_CAF1 108946 95 + 1
UCAGUGUCCGUCGCUCAGUCACAGUUUCUGUUUGUGAUUUUCUGGCUUAGAGCGGCGAAGUUGACGAGUUAACUGAAAGAAACUAAACUGAAAGA
(((((...(((((((((((((.((..((.......))..)).)))))..)))))))).((((((....))))))............))))).... ( -28.70)
>DroYak_CAF1 120196 95 + 1
UCAGUGUCCGUCGCUCAGUCACAGUUUCUGUUUGUGAUUUUCUGGCUUAGAGCGACCAAGUUGACGAGUUAACUGAAAGAAACUAAACUGAAAGA
(((((....((((((((((((.((..((.......))..)).)))))..)))))))..((((((....))))))............))))).... ( -26.60)
>consensus
UCAGUGUCCGUCGCUCAGUCACAGUUUCUGUUUGUGAUUUUCUGGCUUAGAGCGGCCAAGUUGACGAGUUAACUGAAAGAAACUAAACUGAAAGA
(((((....((((((((((((.((..((.......))..)).)))))..)))))))..((((((....))))))............))))).... (-26.64 = -26.48 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:46 2006