Locus 6003

Sequence ID 3L_DroMel_CAF1
Location 16,024,988 – 16,025,128
Length 140
Max. P 0.825499
window9602 window9603 window9604

overview

Window 2

Location 16,024,988 – 16,025,088
Length 100
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 87.90
Mean single sequence MFE -25.10
Consensus MFE -19.75
Energy contribution -20.87
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -2.28
Structure conservation index 0.79
SVM decision value 0.45
SVM RNA-class probability 0.741751
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16024988 100 + 23771897
GGAUUA-UCCACCUAAGGAACGAUUCAUUAGUUGAACAACUUGGCUUUGCUUGAACUUAUGGUAAAGG----UUUUCUUUCCAAAGCUCAUCUGUAUUGUAAUCA
.(((((-(.((.((((.((.....)).)))).)).(((...((((((((...((((((.......)))----)))......)))))).))..)))...)))))). ( -17.30)
>DroSec_CAF1 24714 105 + 1
GGAUUAAUUCACCUAAUGAACGAUUCAUUAGUUGAAAAACUUGGCUUUGCUUGAACUUAUGACAAAGUUUGUUUUUCUUUGCAAAGUUCAUCUGCAAUGUAAUCA
.((((..((((.(((((((.....))))))).)))).......((.((((.(((((((.((.(((((.........))))))))))))))...)))).)))))). ( -28.30)
>DroSim_CAF1 33375 104 + 1
GGAUUAAUUCACCUAAUGAACGAUUCAUUAGUUGAAAAACUUGGUUUUGCUUGAACUUGUGGUGAAGU-UGUUUUUCUUUGCAAAGUUCAUCUGCAAUGUAAUCG
.(((((.((((.(((((((.....))))))).))))..........((((.(((((((...(..(((.-.......)))..).)))))))...))))..))))). ( -29.70)
>consensus
GGAUUAAUUCACCUAAUGAACGAUUCAUUAGUUGAAAAACUUGGCUUUGCUUGAACUUAUGGUAAAGU_UGUUUUUCUUUGCAAAGUUCAUCUGCAAUGUAAUCA
.(((((.((((.(((((((.....))))))).))))...........(((.(((((((...((((((.........)))))).)))))))...)))...))))). (-19.75 = -20.87 +   1.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,024,988 – 16,025,088
Length 100
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 87.90
Mean single sequence MFE -22.20
Consensus MFE -15.46
Energy contribution -15.13
Covariance contribution -0.33
Combinations/Pair 1.12
Mean z-score -2.52
Structure conservation index 0.70
SVM decision value 0.28
SVM RNA-class probability 0.664102
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16024988 100 - 23771897
UGAUUACAAUACAGAUGAGCUUUGGAAAGAAAA----CCUUUACCAUAAGUUCAAGCAAAGCCAAGUUGUUCAACUAAUGAAUCGUUCCUUAGGUGGA-UAAUCC
...............((((((((((((((....----.)))).))).)))))))...........((((((((.((((.((.....)).)))).))))-)))).. ( -20.80)
>DroSec_CAF1 24714 105 - 1
UGAUUACAUUGCAGAUGAACUUUGCAAAGAAAAACAAACUUUGUCAUAAGUUCAAGCAAAGCCAAGUUUUUCAACUAAUGAAUCGUUCAUUAGGUGAAUUAAUCC
.(((((..((((...(((((((.((((((.........))))))...))))))).))))..........((((.(((((((.....))))))).)))).))))). ( -25.30)
>DroSim_CAF1 33375 104 - 1
CGAUUACAUUGCAGAUGAACUUUGCAAAGAAAAACA-ACUUCACCACAAGUUCAAGCAAAACCAAGUUUUUCAACUAAUGAAUCGUUCAUUAGGUGAAUUAAUCC
.(((((..((((...(((((((((..(((.......-.)))...)).))))))).))))..........((((.(((((((.....))))))).)))).))))). ( -20.50)
>consensus
UGAUUACAUUGCAGAUGAACUUUGCAAAGAAAAACA_ACUUUACCAUAAGUUCAAGCAAAGCCAAGUUUUUCAACUAAUGAAUCGUUCAUUAGGUGAAUUAAUCC
.(((((.........(((((((......(((........))).....)))))))...............((((.(((((((.....))))))).)))).))))). (-15.46 = -15.13 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,025,027 – 16,025,128
Length 101
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 74.63
Mean single sequence MFE -20.20
Consensus MFE -10.44
Energy contribution -11.06
Covariance contribution 0.62
Combinations/Pair 1.20
Mean z-score -2.13
Structure conservation index 0.52
SVM decision value 0.70
SVM RNA-class probability 0.825499
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16025027 101 - 23771897
AGCUUUACUAGCGCAGGCUAUUAAAUAUUCAAGUCAUAACUGAUUACAAUACAGAUGAGCUUUGGAAAGAAAA-------------------CCUUUACCAUAAGUUCAAGCAAAGCCAA
.(((.....)))...((((............(((((....)))))..........((((((((((((((....-------------------.)))).))).))))))).....)))).. ( -23.00)
>DroSec_CAF1 24754 103 - 1
GGCUUAACUAGCGCAGGCUAUUAAAUAUUCAAGUC--AACUGAUUACAUUGCAGAUGAACUUUGCAAAGAAAAACA---------------AACUUUGUCAUAAGUUCAAGCAAAGCCAA
.(((.....)))...((((............((((--....))))...((((...(((((((.((((((.......---------------..))))))...))))))).)))))))).. ( -24.10)
>DroSim_CAF1 33415 104 - 1
GGCUUAACUAGCACAGGCUAUUAAAUAUUCAAGUCAUAACCGAUUACAUUGCAGAUGAACUUUGCAAAGAAAAACA----------------ACUUCACCACAAGUUCAAGCAAAACCAA
.(((((((((((....)))........(((.((((......))))...(((((((.....))))))).))).....----------------...........)))).))))........ ( -16.30)
>DroEre_CAF1 27799 115 - 1
AGCUGAACUAGUAC--GCUAUUUCAUAUUCAGGUCAUAACUGAUUAAGUUAGAGAUGAACUUUGGAAUUACAAACAACGCUUACACUAACAAACUUUACUACAAGUUUAAACUAAGC---
.(((......(((.--((.((((((..((((..((.(((((.....)))))))..))))...))))))..........)).)))......((((((......))))))......)))--- ( -17.40)
>consensus
AGCUUAACUAGCACAGGCUAUUAAAUAUUCAAGUCAUAACUGAUUACAUUACAGAUGAACUUUGCAAAGAAAAACA________________ACUUUACCACAAGUUCAAGCAAAGCCAA
.(((.....)))...((((............((((......))))..........((((((((((((((........................)))).))).))))))).....)))).. (-10.44 = -11.06 +   0.62)

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 12:06:32 2006