Locus 6528

Sequence ID 3R_DroMel_CAF1
Location 17,230,179 – 17,230,339
Length 160
Max. P 0.936954
window10619 window10620 window10621

overview

Window 9

Location 17,230,179 – 17,230,299
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.42
Mean single sequence MFE -41.06
Consensus MFE -28.72
Energy contribution -29.52
Covariance contribution 0.80
Combinations/Pair 1.16
Mean z-score -1.64
Structure conservation index 0.70
SVM decision value -0.00
SVM RNA-class probability 0.531576
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17230179 120 - 27905053
CUUCAGAGCCUCGCAGUCCUUCAAGAAGGCUGCGAGCAAUUUUAGAAUAUAGGACGACGGGAGCACCUGGCAGUGAUACAGAUCCACCAUGCAGUGAACCACUCCACGGCACCUGUUCCA
.......((.((((((.((((....))))))))))))..............(((..(((((.((.(.(((.((((.(((..............)))...))))))).))).)))))))). ( -36.54)
>DroSec_CAF1 25627 120 - 1
CUUCAGAGCCUCGCAGUCCUUCAUGAAGGCUGCGAGCAAAUUCAGAAUAUAGGACGACGAGAUCACCCGGCAGUUAUACAGGUCCACCAGGCAGUGGACCACUCCACGGCACUUGUUCCA
.......((.((((((.((((....))))))))))))..............(((..(((((.....((((.(((......(((((((......)))))))))).).)))..)))))))). ( -39.20)
>DroSim_CAF1 26810 120 - 1
CUUCAGAGCCUCGCAGUCCUUCAUGAAGGCUGCGAGCAAAUUCAGAAUAUAGGACGACGGGAUCACCCGGCAGUUAUACAGGUCCACCAGGCAGUGGACCACUCCACGGCACUUGUUCCA
.......(((((((((.((((....))))))))))................(((...((((....))))...........(((((((......)))))))..)))..))).......... ( -42.20)
>DroEre_CAF1 27429 120 - 1
CAUCAGAGCCUCGCACUCCUUUAGGAGGACUGCGAACAUUGUCAGCAUGGAGGACGACGGUAUCACUUGGCAGUUAUACAGGUCCACCAGGAAGUGGACCACACCUCGGCACCUGUCCCA
...(((.((((((((.(((((...))))).)))))..............((((......((((.(((....))).)))).(((((((......)))))))...)))))))..)))..... ( -41.10)
>DroYak_CAF1 34356 120 - 1
CCUCAGAGCCUCGCACUCCUUUAGGAAGACUGCGAGGAGGUUCAGCAGGGAGGACGACGGAAUCACUUGGCAGUUGUACAGGUCCACCAGGAAGUGGACUACUCCCCGGCACUUGGACCA
........(((((((.(((....)))....))))))).((((((((.(((((.(((((..............)))))...(((((((......))))))).)))))..))...)))))). ( -46.24)
>consensus
CUUCAGAGCCUCGCAGUCCUUCAGGAAGGCUGCGAGCAAAUUCAGAAUAUAGGACGACGGGAUCACCUGGCAGUUAUACAGGUCCACCAGGCAGUGGACCACUCCACGGCACUUGUUCCA
.......(((((((((((.........))))))))................(((...((((....))))...........(((((((......)))))))..)))..))).......... (-28.72 = -29.52 +   0.80)

alignment

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secondary structure

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Window 0

Location 17,230,219 – 17,230,339
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.58
Mean single sequence MFE -48.14
Consensus MFE -33.54
Energy contribution -34.22
Covariance contribution 0.68
Combinations/Pair 1.17
Mean z-score -2.42
Structure conservation index 0.70
SVM decision value 1.26
SVM RNA-class probability 0.936954
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17230219 120 + 27905053
UGUAUCACUGCCAGGUGCUCCCGUCGUCCUAUAUUCUAAAAUUGCUCGCAGCCUUCUUGAAGGACUGCGAGGCUCUGAAGGAUCCGGACGAUCUGGUGGGCGUCACACCGCAGAUACGAC
.(((((.(..((((........(((((((...(((((......((((((((((((....)))).)))))).)).....)))))..)))))))))))..)(((......))).)))))... ( -47.20)
>DroSec_CAF1 25667 120 + 1
UGUAUAACUGCCGGGUGAUCUCGUCGUCCUAUAUUCUGAAUUUGCUCGCAGCCUUCAUGAAGGACUGCGAGGCUCUGAAGGAUCCGGACGAUCUGGUGGGCAUCACACCGCAGGUACGAC
.((((..((((.(((((((((((((((((...(((((......((((((((((((....)))).)))))).)).....)))))..))))))).....))).))))).))))))))))... ( -48.50)
>DroSim_CAF1 26850 120 + 1
UGUAUAACUGCCGGGUGAUCCCGUCGUCCUAUAUUCUGAAUUUGCUCGCAGCCUUCAUGAAGGACUGCGAGGCUCUGAAGGAUCCGGACGAUCUGGUGGGCAUCACACCGCAGGUACGAC
.((((..((((.(((((((((((((((((...(((((......((((((((((((....)))).)))))).)).....)))))..))))))).....))).))))).))))))))))... ( -51.50)
>DroEre_CAF1 27469 117 + 1
UGUAUAACUGCCAAGUGAUACCGUCGUCCUCCAUGCUGACAAUGUUCGCAGUCCUCCUAAAGGAGUGCGAGGCUCUGAUGGAUCCGGACGAUGUGGUGGUC---GCUCCGCAGCUGCGUC
.(((...((((..((((((.((((((((((((((.(.((.....((((((.((((.....)))).))))))..)).))))))...)))))))).)...)))---)))..)))).)))... ( -45.60)
>DroYak_CAF1 34396 120 + 1
UGUACAACUGCCAAGUGAUUCCGUCGUCCUCCCUGCUGAACCUCCUCGCAGUCUUCCUAAAGGAGUGCGAGGCUCUGAGGGAUCCGGACGAUGUGGUGGUAGCGGCUCCGCAGACACGUC
(((...((..(((........(((((((((((((.(.((....(((((((.((((.....)))).))))))).)).))))))...)))))))))))..)).(((....)))..))).... ( -47.90)
>consensus
UGUAUAACUGCCAGGUGAUCCCGUCGUCCUAUAUUCUGAAAUUGCUCGCAGCCUUCAUGAAGGACUGCGAGGCUCUGAAGGAUCCGGACGAUCUGGUGGGCAUCACACCGCAGAUACGAC
.((((..((((...(((..((((((((((................((((((((((....)))).))))))((.((.....)).))))))))).....)))...)))...))))))))... (-33.54 = -34.22 +   0.68)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,230,219 – 17,230,339
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.58
Mean single sequence MFE -42.93
Consensus MFE -31.56
Energy contribution -32.36
Covariance contribution 0.80
Combinations/Pair 1.12
Mean z-score -1.51
Structure conservation index 0.74
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17230219 120 - 27905053
GUCGUAUCUGCGGUGUGACGCCCACCAGAUCGUCCGGAUCCUUCAGAGCCUCGCAGUCCUUCAAGAAGGCUGCGAGCAAUUUUAGAAUAUAGGACGACGGGAGCACCUGGCAGUGAUACA
...(((((((((((((....(((....(.((((((..((.((.......(((((((.((((....))))))))))).......)).))...)))))))))).)))))..)))..))))). ( -45.24)
>DroSec_CAF1 25667 120 - 1
GUCGUACCUGCGGUGUGAUGCCCACCAGAUCGUCCGGAUCCUUCAGAGCCUCGCAGUCCUUCAUGAAGGCUGCGAGCAAAUUCAGAAUAUAGGACGACGAGAUCACCCGGCAGUUAUACA
((.(((.((((((.(((((.(......(.((((((.((....))...((.((((((.((((....))))))))))))..............)))))))..)))))))).)))).))))). ( -40.40)
>DroSim_CAF1 26850 120 - 1
GUCGUACCUGCGGUGUGAUGCCCACCAGAUCGUCCGGAUCCUUCAGAGCCUCGCAGUCCUUCAUGAAGGCUGCGAGCAAAUUCAGAAUAUAGGACGACGGGAUCACCCGGCAGUUAUACA
((.(((.((((((.(((((.(((....(.((((((.((....))...((.((((((.((((....))))))))))))..............))))))))))))))))).)))).))))). ( -46.60)
>DroEre_CAF1 27469 117 - 1
GACGCAGCUGCGGAGC---GACCACCACAUCGUCCGGAUCCAUCAGAGCCUCGCACUCCUUUAGGAGGACUGCGAACAUUGUCAGCAUGGAGGACGACGGUAUCACUUGGCAGUUAUACA
.....((((((.(((.---((..(((...((((((...((((((.((...(((((.(((((...))))).)))))...))....).))))))))))).))).)).))).))))))..... ( -41.40)
>DroYak_CAF1 34396 120 - 1
GACGUGUCUGCGGAGCCGCUACCACCACAUCGUCCGGAUCCCUCAGAGCCUCGCACUCCUUUAGGAAGACUGCGAGGAGGUUCAGCAGGGAGGACGACGGAAUCACUUGGCAGUUGUACA
...(((.((((.((((((...........((((((...((((((.((((((((((.(((....)))....)))...))))))).).)))))))))))))).....))).))))...))). ( -41.00)
>consensus
GUCGUACCUGCGGUGUGACGCCCACCAGAUCGUCCGGAUCCUUCAGAGCCUCGCAGUCCUUCAGGAAGGCUGCGAGCAAAUUCAGAAUAUAGGACGACGGGAUCACCUGGCAGUUAUACA
...(((.((((((((.......))))...((((((((.((.....)).))((((((((.........))))))))................))))))((((....))))))))...))). (-31.56 = -32.36 +   0.80)

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 12:23:35 2006