Locus 420

Sequence ID 2L_DroMel_CAF1
Location 1,238,425 – 1,238,581
Length 156
Max. P 0.835609
window680 window681 window682 window683

overview

Window 0

Location 1,238,425 – 1,238,543
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.96
Mean single sequence MFE -40.20
Consensus MFE -36.59
Energy contribution -37.15
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.53
Structure conservation index 0.91
SVM decision value 0.20
SVM RNA-class probability 0.632417
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1238425 118 + 22407834
UGCAUCUGGUCAAAGUUUGCGUGCUGCAAGAGUGUUGCACGCCUCUCGAGGCAAUCAGGCAUGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUCCUUGGCCU
.......((((((.(((((.((((.(((....))).))))((((....))))...)))))..(((((.--...))))).(((((....)))))....................)))))). ( -38.10)
>DroSec_CAF1 15899 118 + 1
UGCAUCUGGCCAAAGUUUGCGUGCUGCAAGAGUGUUGCACGCCUUUCGAGACAAUCAGGCAGGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCU
.......((((((.((((((((((.(((....))).)))))).....((.....)))))).((((((.--...))))))(((((....)))))....................)))))). ( -38.20)
>DroSim_CAF1 12062 118 + 1
UGCAUCUGGCCAAAGUUUGCGUGCUGCAAGAGUGUUGCACGCCUCUCGAGGCAAUCAGGCAGGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCU
.......((((((.(((((.((((.(((....))).))))((((....))))...))))).((((((.--...))))))(((((....)))))....................)))))). ( -42.20)
>DroYak_CAF1 11944 120 + 1
UGCAUCUGGCCAAAGUUUGCGUGCUGCAGGAGUGUUGCACGCCUCUCGAGGCAAUCAGGCUGGGAUCCUGGAAGGUCCUACCGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCU
.......((((((.(....)(((.((.(((((((..((..((((....)))).....((.(((((((......)))))))))))...))))))))))))..............)))))). ( -42.30)
>consensus
UGCAUCUGGCCAAAGUUUGCGUGCUGCAAGAGUGUUGCACGCCUCUCGAGGCAAUCAGGCAGGGAUCC__GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCU
.......((((((.....((((((.(((....))).)))))).....((((......((((((((((......))))).....)))))...))))..................)))))). (-36.59 = -37.15 +   0.56) 

alignment

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secondary structure

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dotplot

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Window 1

Location 1,238,425 – 1,238,543
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.96
Mean single sequence MFE -38.77
Consensus MFE -34.94
Energy contribution -35.50
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.44
Structure conservation index 0.90
SVM decision value -0.02
SVM RNA-class probability 0.523492
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1238425 118 - 22407834
AGGCCAAGGAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCAUGCCUGAUUGCCUCGAGAGGCGUGCAACACUCUUGCAGCACGCAAACUUUGACCAGAUGCA
.((.(((((..................(((((....))))).(((.(...--.).))).(((......((((....))))((((..((....))..)))))))..))))).))....... ( -36.50)
>DroSec_CAF1 15899 118 - 1
AGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCCUGCCUGAUUGUCUCGAAAGGCGUGCAACACUCUUGCAGCACGCAAACUUUGGCCAGAUGCA
.(((((((((((((((...........(((((....))))).(((.(...--.).))).....))))))).)).....((((((..((....))..)))))).....))))))....... ( -39.80)
>DroSim_CAF1 12062 118 - 1
AGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCCUGCCUGAUUGCCUCGAGAGGCGUGCAACACUCUUGCAGCACGCAAACUUUGGCCAGAUGCA
.(((((((................(((((..((((((.....(((.(...--.).)))))))).)....)))))....((((((..((....))..))))))....)))))))....... ( -40.40)
>DroYak_CAF1 11944 120 - 1
AGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCGGUAGGACCUUCCAGGAUCCCAGCCUGAUUGCCUCGAGAGGCGUGCAACACUCCUGCAGCACGCAAACUUUGGCCAGAUGCA
.(((((((................(((((.((....))(((.(((((.....)).)))..)))......)))))....((((((..((....))..))))))....)))))))....... ( -38.40)
>consensus
AGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC__GGAUCCCUGCCUGAUUGCCUCGAGAGGCGUGCAACACUCUUGCAGCACGCAAACUUUGGCCAGAUGCA
.(((((((................(((((..((((((.....(((((.....)).)))))))).)....)))))....((((((..((....))..))))))....)))))))....... (-34.94 = -35.50 +   0.56) 

alignment

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secondary structure

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dotplot

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Window 2

Location 1,238,465 – 1,238,581
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.98
Mean single sequence MFE -42.30
Consensus MFE -27.85
Energy contribution -29.60
Covariance contribution 1.75
Combinations/Pair 1.00
Mean z-score -2.56
Structure conservation index 0.66
SVM decision value 0.73
SVM RNA-class probability 0.835609
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1238465 116 + 22407834
GCCUCUCGAGGCAAUCAGGCAUGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUCCUUGGCCUGGCCAAGGGCUCCUGUUCCUCCUUCGACCUCGCC--UGGC
((((....))))..((((((..((...(--(((((....(((((....))))).................((((((((...))))))))...........)))))).))..)))--))). ( -45.20)
>DroSec_CAF1 15939 113 + 1
GCCUUUCGAGACAAUCAGGCAGGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCUGGCCAAGGCCUGU---UCCUCCUUCGACCUCGCC--UGGC
..............((((((..((...(--(((((....(((((....)))))......................(((((.....)))))...---....)))))).))..)))--))). ( -38.90)
>DroSim_CAF1 12102 113 + 1
GCCUCUCGAGGCAAUCAGGCAGGGAUCC--GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCUGGCCAAGGGCUCC---UGUUCCUUCGACCUCGCC--UGGC
((((....))))..((((((..((...(--(((((..(.((((((..............(((......))).((((((...))))))))))))---.)..)))))).))..)))--))). ( -46.70)
>DroYak_CAF1 11984 111 + 1
GCCUCUCGAGGCAAUCAGGCUGGGAUCCUGGAAGGUCCUACCGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCUGGG------CGGC---UGCUCCUUCGACCUCGUCCUCGGC
(((...((((((.....((.(((((((......)))))))))((.(((((((.(((...(((......)))...)))...)))------))))---.))......).))))).....))) ( -38.40)
>consensus
GCCUCUCGAGGCAAUCAGGCAGGGAUCC__GAAGGUCCUGGAGCUGCCGCUCCUCAUACAUAUAUAAUUAUUCUUGGCCUGGCCAAGGGCUCC___UCCUCCUUCGACCUCGCC__UGGC
(((...((((((...(((((.((((((......))))))(((((....))))).......................)))))((.....))...............).))))).....))) (-27.85 = -29.60 +   1.75) 

alignment

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secondary structure

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dotplot

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Window 3

Location 1,238,465 – 1,238,581
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.98
Mean single sequence MFE -42.40
Consensus MFE -31.67
Energy contribution -31.80
Covariance contribution 0.13
Combinations/Pair 1.08
Mean z-score -1.56
Structure conservation index 0.75
SVM decision value 0.19
SVM RNA-class probability 0.624883
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1238465 116 - 22407834
GCCA--GGCGAGGUCGAAGGAGGAACAGGAGCCCUUGGCCAGGCCAAGGAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCAUGCCUGAUUGCCUCGAGAGGC
..((--((((.(((((((((............(((((((...)))))))..................(((((....)))))....)))))--))..)).))))))...((((....)))) ( -47.10)
>DroSec_CAF1 15939 113 - 1
GCCA--GGCGAGGUCGAAGGAGGA---ACAGGCCUUGGCCAGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCCUGCCUGAUUGUCUCGAAAGGC
..((--((((.(((((((((....---...(((((.....)))))......................(((((....)))))....)))))--))..)).))))))......((....)). ( -41.60)
>DroSim_CAF1 12102 113 - 1
GCCA--GGCGAGGUCGAAGGAACA---GGAGCCCUUGGCCAGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC--GGAUCCCUGCCUGAUUGCCUCGAGAGGC
..((--((((.(((((((((..(.---......((((((...))))))...................(((((....))))).)..)))))--))..)).))))))...((((....)))) ( -44.60)
>DroYak_CAF1 11984 111 - 1
GCCGAGGACGAGGUCGAAGGAGCA---GCCG------CCCAGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCGGUAGGACCUUCCAGGAUCCCAGCCUGAUUGCCUCGAGAGGC
(((.....((((((.(((((..(.---((((------(....(((.....(..(((((....)))))..)..))).))))).)..)))))((((.......))))...))))))...))) ( -36.30)
>consensus
GCCA__GGCGAGGUCGAAGGAGCA___GCAGCCCUUGGCCAGGCCAAGAAUAAUUAUAUAUGUAUGAGGAGCGGCAGCUCCAGGACCUUC__GGAUCCCUGCCUGAUUGCCUCGAGAGGC
(((.....(((((((....))..................(((((.......................(((((....))))).(((((.....)).)))..)))))....)))))...))) (-31.67 = -31.80 +   0.13) 

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 09:35:47 2006