Locus 4566

Sequence ID 3R_DroMel_CAF1
Location 12,069,442 – 12,069,641
Length 199
Max. P 0.963219
window7472 window7473 window7474

overview

Window 2

Location 12,069,442 – 12,069,561
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.39
Mean single sequence MFE -32.02
Consensus MFE -24.03
Energy contribution -23.78
Covariance contribution -0.25
Combinations/Pair 1.16
Mean z-score -1.61
Structure conservation index 0.75
SVM decision value 0.12
SVM RNA-class probability 0.594610
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12069442 119 - 27905053
CAACCACAAAGUCGCCUUAUCAGUUCUAGGGCGAACUGAACUUGUGGCAAGUUCAAGUUACUG-UAAGUCAGUUCGAGGGAUUGAUAUUACUUGGAAUUUGAGCCAGGCACUAAUCUUAC
....(((((((((((((((.......))))))).)))....)))))((..(((((((((...(-((((((((((.....))))))).))))....)))))))))...))........... ( -34.90)
>DroSec_CAF1 6064 104 - 1
CAACCACAAAGUCGCCUUAUCAGUUCUAGGGCGAACUGAACUUGUGGCAAGUUC----------------AGUUUGAGGGAUUGGUAUUACUUGGAAUUUGAGCCAGGCAAUAAUCUUAC
.............(((.((((((((((....(((((((((((((...)))))))----------------)))))).)))))))))).....(((........))))))........... ( -32.60)
>DroSim_CAF1 6496 120 - 1
CAACCACAAAGUCGCCUUAUCAGUUCUAGGGCGAACUGAACUUGUGGCAAGUUCAAGUUACUGAUAAGUCAGUUUGAGGGAUUGGUAUUACUUGGAAUUUGAGCCAGGCAAUAAUCUUAC
....(((((((((((((((.......))))))).)))....)))))((..((((((((((((((....)))))(..((..((....))..))..))))))))))...))........... ( -32.30)
>DroEre_CAF1 7978 118 - 1
CAACCACAAAAUCGCCUUAUCAGUUUUAG-ACAAAUUGAACUUGUGGCAAGUUCAACUUACUGAUA-GUCAGUUUGAGGGAUUGGUACUACUUGGAAUUUGAGCCAUGCGCUUAUCUCAC
......((((...((..(((((((...((-.....(((((((((...))))))))))).)))))))-))...)))).(((((.((..(....(((........))).)..)).))))).. ( -26.20)
>DroYak_CAF1 8101 119 - 1
CAACCACAACAUCGCCUUAUCAGUUCUAG-ACGAACUGAACUUGUGGCAAGUUCAAGUUACUGAUAAGUCAGUUUGAGGGAUUGGUAUUACUUGGAAUGUGAGCCAGGCGCUAAUCUCGC
.............(.(((((((((....(-((....((((((((...)))))))).)))))))))))).).......(((((((((....(((((........))))).))))))))).. ( -34.10)
>consensus
CAACCACAAAGUCGCCUUAUCAGUUCUAGGGCGAACUGAACUUGUGGCAAGUUCAAGUUACUGAUAAGUCAGUUUGAGGGAUUGGUAUUACUUGGAAUUUGAGCCAGGCACUAAUCUUAC
.............(((.((((((((((....(((((((((((((...))))))).....(((....))).)))))).)))))))))).....(((........))))))........... (-24.03 = -23.78 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,069,482 – 12,069,601
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.89
Mean single sequence MFE -36.48
Consensus MFE -27.83
Energy contribution -28.08
Covariance contribution 0.25
Combinations/Pair 1.15
Mean z-score -1.64
Structure conservation index 0.76
SVM decision value 0.23
SVM RNA-class probability 0.645305
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12069482 119 + 27905053
CCCUCGAACUGACUUA-CAGUAACUUGAACUUGCCACAAGUUCAGUUCGCCCUAGAACUGAUAAGGCGACUUUGUGGUUGAGCCUCCGCCAAUUGGGGAAUCUCUCAGGUGGCAUGCCGC
.......((((.....-)))).((((((....(((((((..(((((((......)))))))..((....))))))))).(((..(((.((....)))))..)))))))))((....)).. ( -36.80)
>DroSec_CAF1 6104 104 + 1
CCCUCAAACU----------------GAACUUGCCACAAGUUCAGUUCGCCCUAGAACUGAUAAGGCGACUUUGUGGUUGCGCCUCUGCCAAUUGGGGAAUCUCUCAGGUGGCAUGCCGC
.((.((((((----------------(((((((...))))))))))(((((.((.......)).)))))..))).))..(((.(..(((((.((((((....)))))).))))).).))) ( -36.50)
>DroSim_CAF1 6536 120 + 1
CCCUCAAACUGACUUAUCAGUAACUUGAACUUGCCACAAGUUCAGUUCGCCCUAGAACUGAUAAGGCGACUUUGUGGUUGCGCCUCUGCCAAUUGGGGAAUCUCUCAGGUGGCAUGCCGC
............(((((((((...(((((((((...))))))))).((......)))))))))))((((((....))))))((...(((((.((((((....)))))).))))).))... ( -39.70)
>DroEre_CAF1 8018 118 + 1
CCCUCAAACUGAC-UAUCAGUAAGUUGAACUUGCCACAAGUUCAAUUUGU-CUAAAACUGAUAAGGCGAUUUUGUGGUUGCGCCUCCGCCAAUUGGUGAAUCUCUCAGGUGGCAUACCGU
.............-(((((((((((((((((((...))))))))))))..-.....)))))))..((((((....))))))(((.(((((....)))((.....)).)).)))....... ( -32.81)
>DroYak_CAF1 8141 119 + 1
CCCUCAAACUGACUUAUCAGUAACUUGAACUUGCCACAAGUUCAGUUCGU-CUAGAACUGAUAAGGCGAUGUUGUGGUUGCGCCUCCGCCAAUUGGUGAAUCUCUCAGGUGGCAUGCCGC
........((((.......((((((..((((((((......(((((((..-...)))))))...))))).)))..)))))).....((((....))))......))))((((....)))) ( -36.60)
>consensus
CCCUCAAACUGACUUAUCAGUAACUUGAACUUGCCACAAGUUCAGUUCGCCCUAGAACUGAUAAGGCGACUUUGUGGUUGCGCCUCCGCCAAUUGGGGAAUCUCUCAGGUGGCAUGCCGC
...((((((((......))))...))))..(((((......(((((((......)))))))...)))))....(((((...(((.((.((....)).((.....)).)).)))..))))) (-27.83 = -28.08 +   0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,069,521 – 12,069,641
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.16
Mean single sequence MFE -41.58
Consensus MFE -38.82
Energy contribution -39.10
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -1.49
Structure conservation index 0.93
SVM decision value 1.55
SVM RNA-class probability 0.963219
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12069521 120 + 27905053
UUCAGUUCGCCCUAGAACUGAUAAGGCGACUUUGUGGUUGAGCCUCCGCCAAUUGGGGAAUCUCUCAGGUGGCAUGCCGCACCUGCAGCGUCUCCUUGCGAAAUGCGCGUAGCUUCAACA
.(((((((......))))))).((((.(((.(((((((.(((..(((.((....)))))..)))....((((....))))))).)))).))).))))(((.....)))............ ( -40.50)
>DroSec_CAF1 6128 120 + 1
UUCAGUUCGCCCUAGAACUGAUAAGGCGACUUUGUGGUUGCGCCUCUGCCAAUUGGGGAAUCUCUCAGGUGGCAUGCCGCACCUGCAGCGUCUCCUUGCGAAAUGCGCGUAGCUUCAACA
.(((((((......))))))).((((.(((.(((..(.((((.(..(((((.((((((....)))))).))))).).)))).)..))).))).))))(((.....)))............ ( -45.50)
>DroSim_CAF1 6576 120 + 1
UUCAGUUCGCCCUAGAACUGAUAAGGCGACUUUGUGGUUGCGCCUCUGCCAAUUGGGGAAUCUCUCAGGUGGCAUGCCGCACCUGCAGCGUCUCCUUGCGAAAUGCGCGUAGCUUCAACA
.(((((((......))))))).((((.(((.(((..(.((((.(..(((((.((((((....)))))).))))).).)))).)..))).))).))))(((.....)))............ ( -45.50)
>DroEre_CAF1 8057 119 + 1
UUCAAUUUGU-CUAAAACUGAUAAGGCGAUUUUGUGGUUGCGCCUCCGCCAAUUGGUGAAUCUCUCAGGUGGCAUACCGUACCUGCAGCGUCUCCUUGCGAAAUGCGCGUAGCUUCAACA
.....(((((-(.......))))))((((((((((((..((((...((((....)))).......((((((........))))))..))))..))..))))))).)))............ ( -31.80)
>DroYak_CAF1 8181 119 + 1
UUCAGUUCGU-CUAGAACUGAUAAGGCGAUGUUGUGGUUGCGCCUCCGCCAAUUGGUGAAUCUCUCAGGUGGCAUGCCGCACCUGCAGCGUCUCCUUGCGAAAUGCGCGUAGCUUCAACA
.(((((((..-...))))))).((((.(((((((..(.((((.(...((((.((((.(.....))))).))))..).)))).)..))))))).))))(((.....)))............ ( -44.60)
>consensus
UUCAGUUCGCCCUAGAACUGAUAAGGCGACUUUGUGGUUGCGCCUCCGCCAAUUGGGGAAUCUCUCAGGUGGCAUGCCGCACCUGCAGCGUCUCCUUGCGAAAUGCGCGUAGCUUCAACA
.(((((((......))))))).((((.(((.(((..(.((((.(...((((.((((((....)))))).))))..).)))).)..))).))).))))(((.....)))............ (-38.82 = -39.10 +   0.28)

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 11:32:48 2006