Locus 7286

Sequence ID 2L_DroMel_CAF1
Location 20,409,370 – 20,409,569
Length 199
Max. P 0.990492
window11655 window11656 window11657

overview

Window 5

Location 20,409,370 – 20,409,490
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.75
Mean single sequence MFE -26.18
Consensus MFE -25.85
Energy contribution -25.98
Covariance contribution 0.12
Combinations/Pair 1.06
Mean z-score -2.29
Structure conservation index 0.99
SVM decision value 2.22
SVM RNA-class probability 0.990492
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20409370 120 + 22407834
UAAAUGGAGACAAAGUUUACAUGUUAACAAUAUUAUCGUUUUCGUGUCUACAAUGCUCCAAAAUCAAUAUAUUCGAUCGAAUCAUCCGAAGCAGUCUUAUAUUUCCUUGGAUGAUUUCUU
....(((((.((..((..(((((..(((.........)))..)))))..))..)))))))..................(((((((((((.(.(((.....))).).)))))))))))... ( -27.20)
>DroSec_CAF1 4091 120 + 1
UAAAUGGAGACAAAGUUUACAUGUUAACAAUGCUAUCGUUUUCGUGUCUACAAUGCUCCAAAAUCAAUAUAUCCGAUCGAAUCAUCCGAAGCAUUUUCAUAUUACCUUGGAUGAUUUCUU
....(((((.((..((..(((((..(((.........)))..)))))..))..)))))))..................(((((((((((.................)))))))))))... ( -26.43)
>DroSim_CAF1 5063 120 + 1
UAAAUGGAGACAAAGUUUACAUGUUAAUAAUGCUAUCGUUUUCGUGUCUACAAUGCUCCAAAAUCAAUAUAUCCGAUAGAAUCAUCCGAAGCAGUCUUAUAUUUCCUUGGAUGAUUUCUU
....(((((.((..((..(((((..(((.........)))..)))))..))..)))))))..................(((((((((((.(.(((.....))).).)))))))))))... ( -25.20)
>DroEre_CAF1 4108 120 + 1
UAAAUGGAGACAAAGUUUACAUGUUAGCAGUAUUUUCGUUUUCGUGUCUACAAUGCUCCAAAAUCAAUGUAUCCGAUCCAAUCAUCCGAAGCAGUCUUAUAUUACCUUGGAUGAUUUCUU
....(((((.((..((..(((((..(((.........)))..)))))..))..)))))))...................((((((((((.(.(((.....))).).)))))))))).... ( -25.90)
>consensus
UAAAUGGAGACAAAGUUUACAUGUUAACAAUACUAUCGUUUUCGUGUCUACAAUGCUCCAAAAUCAAUAUAUCCGAUCGAAUCAUCCGAAGCAGUCUUAUAUUACCUUGGAUGAUUUCUU
....(((((.((..((..(((((..(((.........)))..)))))..))..)))))))..................(((((((((((.(.(((.....))).).)))))))))))... (-25.85 = -25.98 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,409,410 – 20,409,530
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.69
Mean single sequence MFE -27.69
Consensus MFE -23.52
Energy contribution -24.52
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.82
Structure conservation index 0.85
SVM decision value 0.79
SVM RNA-class probability 0.851029
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20409410 120 + 22407834
UUCGUGUCUACAAUGCUCCAAAAUCAAUAUAUUCGAUCGAAUCAUCCGAAGCAGUCUUAUAUUUCCUUGGAUGAUUUCUUUGGUGCACAGUGCACAGCUAAUGUAAUCCCAAUGGAGUUA
..............((((((.......(((((((((..(((((((((((.(.(((.....))).).)))))))))))..)))((((.....))))....)))))).......)))))).. ( -28.34)
>DroSec_CAF1 4131 120 + 1
UUCGUGUCUACAAUGCUCCAAAAUCAAUAUAUCCGAUCGAAUCAUCCGAAGCAUUUUCAUAUUACCUUGGAUGAUUUCUUUGGUGCAUAGUGCACAGCUAAUGUAAUCCCAAUGGAGUUA
..............((((((............((((..(((((((((((.................)))))))))))..))))((((((((.....))).))))).......)))))).. ( -28.43)
>DroSim_CAF1 5103 120 + 1
UUCGUGUCUACAAUGCUCCAAAAUCAAUAUAUCCGAUAGAAUCAUCCGAAGCAGUCUUAUAUUUCCUUGGAUGAUUUCUUUGGUGCACAGUGCACAGCUAAUGUAAUCCCAAUGGAGUUA
..............((((((.............(((..(((((((((((.(.(((.....))).).)))))))))))..)))((((.....)))).................)))))).. ( -28.40)
>DroEre_CAF1 4148 118 + 1
UUCGUGUCUACAAUGCUCCAAAAUCAAUGUAUCCGAUCCAAUCAUCCGAAGCAGUCUUAUAUUACCUUGGAUGAUUUCUUUGGUGCACAG--CAAGGCAUAAAUUUUUCUUAUGGAGUUA
..............((((((.......((((.((((...((((((((((.(.(((.....))).).))))))))))...))))))))..(--(...))..............)))))).. ( -25.60)
>consensus
UUCGUGUCUACAAUGCUCCAAAAUCAAUAUAUCCGAUCGAAUCAUCCGAAGCAGUCUUAUAUUACCUUGGAUGAUUUCUUUGGUGCACAGUGCACAGCUAAUGUAAUCCCAAUGGAGUUA
..............((((((.............(((..(((((((((((.(.(((.....))).).)))))))))))..)))((((.....)))).................)))))).. (-23.52 = -24.52 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,409,450 – 20,409,569
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 88.52
Mean single sequence MFE -25.67
Consensus MFE -19.84
Energy contribution -21.65
Covariance contribution 1.81
Combinations/Pair 1.03
Mean z-score -1.86
Structure conservation index 0.77
SVM decision value 0.59
SVM RNA-class probability 0.791881
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20409450 119 - 22407834
AGACACAAAUUGAAGGAAGGUAUACAAAAUAUGCCACUUUAACUCCAUUGGGAUUACAUUAGCUGUGCACUGUGCACCAAAGAAAUCAUCCAAGGAAAUAUAAGACUGCUUCGGAUGAU
.........((((((...((((((.....)))))).)))))).(((....)))...........((((.....)))).......((((((((((.(..........).))).))))))) ( -23.50)
>DroSec_CAF1 4171 119 - 1
AGACACAGAUUAAAGGAAGGUAUAUAAAAUAUGCCACUUUAACUCCAUUGGGAUUACAUUAGCUGUGCACUAUGCACCAAAGAAAUCAUCCAAGGUAAUAUGAAAAUGCUUCGGAUGAU
.(.(((((.((((((...(((((((...))))))).)))))).(((....))).........))))))................(((((((.(((((.........))))).))))))) ( -28.50)
>DroSim_CAF1 5143 119 - 1
AGACACAGAUUAAAGGAAGGUAUAUAAAAUAUGCCACUUUAACUCCAUUGGGAUUACAUUAGCUGUGCACUGUGCACCAAAGAAAUCAUCCAAGGAAAUAUAAGACUGCUUCGGAUGAU
.(.(((((.((((((...(((((((...))))))).)))))).(((....)))................)))))).........((((((((((.(..........).))).))))))) ( -26.10)
>DroEre_CAF1 4188 116 - 1
AGACACAGAUUAAAGGUAAGUAC-UAAUACAUGCCACUUUAACUCCAUAAGAAAAAUUUAUGCCUUG--CUGUGCACCAAAGAAAUCAUCCAAGGUAAUAUAAGACUGCUUCGGAUGAU
.(.(((((......((((.(((.-...))).))))..........((((((.....)))))).....--)))))).........(((((((.(((((.........))))).))))))) ( -24.60)
>consensus
AGACACAGAUUAAAGGAAGGUAUAUAAAAUAUGCCACUUUAACUCCAUUGGGAUUACAUUAGCUGUGCACUGUGCACCAAAGAAAUCAUCCAAGGAAAUAUAAGACUGCUUCGGAUGAU
.(.(((((.((((((...((((((.....)))))).)))))).(((....)))................)))))).........(((((((.(((((.........))))).))))))) (-19.84 = -21.65 +   1.81)

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 12:32:19 2006