Locus 1839

Sequence ID 3L_DroMel_CAF1
Location 5,161,166 – 5,161,290
Length 124
Max. P 0.874134
window2870 window2871 window2872

overview

Window 0

Location 5,161,166 – 5,161,265
Length 99
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.47
Mean single sequence MFE -19.92
Consensus MFE -14.95
Energy contribution -14.83
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -1.46
Structure conservation index 0.75
SVM decision value 0.01
SVM RNA-class probability 0.537186
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5161166 99 - 23771897
UGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGGUCAUCACAUUAGUACUCUAAACAAAGAGUAUUACUGAAAA---UGU------------------
.((.((((...)))).))(((((.((((.((((((.....)))))).)))).)).)))....((.(((((((((......))))))))).))....---...------------------ ( -23.00)
>DroSec_CAF1 24507 99 - 1
UGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGAUCAUCACAAUAGUACCUUAAACAAAGAAUAUUACCGAAAA---UGU------------------
(((((((...((.(((((((....(((((((.((....)).)))))))..))))))).))...)))))))..........................---...------------------ ( -16.10)
>DroSim_CAF1 26655 99 - 1
UGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGGUCAUCACAAUAGUACUCUAAACAAAGAAUAUUGCCGAAAA---UGU------------------
(((((((...((.(((((((....(((((((.((....)).)))))))..))))))).))...))))))).............(((((......))---)))------------------ ( -15.70)
>DroYak_CAF1 24935 120 - 1
UGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGGUCAUCACAAUAGUGCUGCAAACAAAGAACAGUAAUGAAAAACAUGUCAAAAACACACAUGAUAU
...(((((((((..((....(((.((((.((((((.....)))))).)))).)))(.((.(((....))).))).......))))))))))).....(((((.........))))).... ( -24.90)
>consensus
UGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGGUCAUCACAAUAGUACUCUAAACAAAGAAUAUUACCGAAAA___UGU__________________
(((((((...((.(((((((....(((((((.((....)).)))))))..))))))).))...))))))).................................................. (-14.95 = -14.83 +  -0.12)

alignment

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secondary structure

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Window 1

Location 5,161,185 – 5,161,290
Length 105
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 84.53
Mean single sequence MFE -28.45
Consensus MFE -20.80
Energy contribution -22.22
Covariance contribution 1.42
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.73
SVM decision value 0.05
SVM RNA-class probability 0.557196
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5161185 105 + 23771897
UUGUUUAGAGUACUAAUGUGAUGACCGCAAUUGUUAAUAUUAAAUACAUUAUCAACGGCGUCGCGAUUACAGUAAUAGCAGCGACGCCGGCAGAAGCAUCCUCCC---
.(((((...((.....((((.....))))..........................(((((((((..(((......)))..)))))))))))..))))).......--- ( -25.00)
>DroSec_CAF1 24526 105 + 1
UUGUUUAAGGUACUAUUGUGAUGAUCGCAAUUGUUAAUAUUAAAUACAUUAUCAACGGCGUCGCGAUUACAGUAAUAGCAGCGACGCCGGCAGAGGCAUCCUCCC---
.(((((((...((.((((((.....)))))).)).....))))))).........(((((((((..(((......)))..)))))))))...((((...))))..--- ( -31.90)
>DroSim_CAF1 26674 105 + 1
UUGUUUAGAGUACUAUUGUGAUGACCGCAAUUGUUAAUAUUAAAUACAUUAUCAACGGCGUCGCGAUUACAGUAAUAGCAGCGACGCCGGCAGAGGCAUCCUCCC---
.(((((((...((.((((((.....)))))).)).....))))))).........(((((((((..(((......)))..)))))))))...((((...))))..--- ( -29.90)
>DroEre_CAF1 24958 99 + 1
------GCAGUACUAUUGAGAUGACCACAAUUGUUAAUAUUAAAUACAUUAUCAACGGCGUCGCGAUUACAGUAAUAGCAGCGACGCCGGCAGAGGCAUCCUCCC---
------...........((((((.((....(((.((((.........)))).)))(((((((((..(((......)))..))))))))).....))))).)))..--- ( -26.30)
>DroYak_CAF1 24975 105 + 1
UUGUUUGCAGCACUAUUGUGAUGACCGCAAUUGUUAAUAUUAAAUACAUUAUCAACGGCGUCGCGAUUACAGUAAUAGCAGCGACGCCGGCAGAAGCAUCCUCCC---
...(((((((((..((((((.....))))))))))....................(((((((((..(((......)))..))))))))))))))...........--- ( -30.30)
>DroAna_CAF1 23546 84 + 1
----------------UGUGAUA--------CGUGUAUAUAAAAUACAUUAUCAGCGGCGUCGCGAUUACAGUAAUAGCAGCGACGCCGGCAGCGGCAUCCUCUUUUC
----------------..(((((--------.((((((.....))))))))))).(((((((((..(((......)))..)))))))))((....))........... ( -27.30)
>consensus
UUGUUUACAGUACUAUUGUGAUGACCGCAAUUGUUAAUAUUAAAUACAUUAUCAACGGCGUCGCGAUUACAGUAAUAGCAGCGACGCCGGCAGAGGCAUCCUCCC___
...........((.((((((.....)))))).)).....................(((((((((..(((......)))..)))))))))((....))........... (-20.80 = -22.22 +   1.42)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,161,185 – 5,161,290
Length 105
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 84.53
Mean single sequence MFE -30.98
Consensus MFE -25.32
Energy contribution -26.27
Covariance contribution 0.95
Combinations/Pair 1.10
Mean z-score -2.43
Structure conservation index 0.82
SVM decision value 0.88
SVM RNA-class probability 0.874134
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5161185 105 - 23771897
---GGGAGGAUGCUUCUGCCGGCGUCGCUGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGGUCAUCACAUUAGUACUCUAAACAA
---.((((((((...((((.(((((((((((.......)))...))))))))(((((((.((....)).)))))))....)))).))))((....)).))))...... ( -33.40)
>DroSec_CAF1 24526 105 - 1
---GGGAGGAUGCCUCUGCCGGCGUCGCUGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGAUCAUCACAAUAGUACCUUAAACAA
---..((((.(((.......(((((((((((.......)))...))))))))(((((((.((....)).))))))).((((.(.....).)))).)))))))...... ( -28.70)
>DroSim_CAF1 26674 105 - 1
---GGGAGGAUGCCUCUGCCGGCGUCGCUGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGGUCAUCACAAUAGUACUCUAAACAA
---.((((((((...((((.(((((((((((.......)))...))))))))(((((((.((....)).)))))))....)))).))))((....)).))))...... ( -33.40)
>DroEre_CAF1 24958 99 - 1
---GGGAGGAUGCCUCUGCCGGCGUCGCUGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGUGGUCAUCUCAAUAGUACUGC------
---..(((.(((((.(....(((((((((((.......)))...))))))))(((((((.((....)).)))))))....).)).))))))...........------ ( -29.80)
>DroYak_CAF1 24975 105 - 1
---GGGAGGAUGCUUCUGCCGGCGUCGCUGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGGUCAUCACAAUAGUGCUGCAAACAA
---((.((((...)))).))(((((((((((.......)))...))))))))(((((((.((....)).)))))))..((((((.(((.......))))))))).... ( -34.60)
>DroAna_CAF1 23546 84 - 1
GAAAAGAGGAUGCCGCUGCCGGCGUCGCUGCUAUUACUGUAAUCGCGACGCCGCUGAUAAUGUAUUUUAUAUACACG--------UAUCACA----------------
........(((((....((.(((((((((((.......)))...))))))))))......(((((.....))))).)--------))))...---------------- ( -26.00)
>consensus
___GGGAGGAUGCCUCUGCCGGCGUCGCUGCUAUUACUGUAAUCGCGACGCCGUUGAUAAUGUAUUUAAUAUUAACAAUUGCGGUCAUCACAAUAGUACUCUAAACAA
........((((...((((((((((((((((.......)))...)))))))))(((.((((((.....)))))).)))..)))).))))................... (-25.32 = -26.27 +   0.95)

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 10:18:03 2006