Locus 3080

Sequence ID 3R_DroMel_CAF1
Location 8,123,323 – 8,123,527
Length 204
Max. P 0.999805
window4998 window4999 window5000

overview

Window 8

Location 8,123,323 – 8,123,431
Length 108
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 71.26
Mean single sequence MFE -29.40
Consensus MFE -19.24
Energy contribution -19.48
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -3.27
Structure conservation index 0.65
SVM decision value 4.12
SVM RNA-class probability 0.999805
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8123323 108 + 27905053
AAGCU-GCAAUUGCAUUUGAAUUGGCUGCAUGAGUCCAUAAACUGCAGCCGAUCAAUCGCUGCGCAGCCCAUACCCAAACCCAUACCCAUGCCCAUACCCAUGCCCAUA
..(((-((....((..((((.(((((((((.............)))))))))))))..))...)))))...................((((........))))...... ( -28.52)
>DroVir_CAF1 63720 84 + 1
GCAGC-GCAAUUGCAUUUGAAUUGGCUGCAUGAGUCCAUAAACUGCAGCCGAUCAAUCGCUGCAAUGCCCAAGCCCC------------------------CUCCACCU
(((((-((....))..((((.(((((((((.............)))))))))))))..)))))..............------------------------........ ( -27.32)
>DroSec_CAF1 17012 84 + 1
AAGCU-GCAAUUGCAUUUGAAUUGGCUGCAUGAGUCCAUAAACUGCAGCCGAUCAAUCGCUGCGCAGCCCAUACCCA------------------------UACCCAUG
..(((-((....((..((((.(((((((((.............)))))))))))))..))...))))).........------------------------........ ( -27.42)
>DroSim_CAF1 18266 84 + 1
AAGCU-GCAAUUGCAUUUGAAUUGGCUGCAUGAGUCCAUAAACUGCAGCCGAUCAAUCGCUGCGCAGCCCAUACCCA------------------------UACCCAUC
..(((-((....((..((((.(((((((((.............)))))))))))))..))...))))).........------------------------........ ( -27.42)
>DroAna_CAF1 14451 107 + 1
UUGCUGGCAAUUGCAUUUGAAUUGGCUGCAUGAGUCCAUAAACUGCAGCCGAUCAAUCGCG-UUCUCCCCUGGCUCUGGCU-CUGGCUAUGGCUAUGGCUCUGGCUCCC
..((..(.....((..((((.(((((((((.............)))))))))))))..)).-.....((.(((((.((((.-...)))).))))).))..)..)).... ( -36.32)
>consensus
AAGCU_GCAAUUGCAUUUGAAUUGGCUGCAUGAGUCCAUAAACUGCAGCCGAUCAAUCGCUGCGCAGCCCAUACCCA________________________UACCCAUC
......(((...((..((((.(((((((((.............)))))))))))))..))))).............................................. (-19.24 = -19.48 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,123,323 – 8,123,431
Length 108
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 71.26
Mean single sequence MFE -29.48
Consensus MFE -19.32
Energy contribution -19.32
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.17
Structure conservation index 0.66
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8123323 108 - 27905053
UAUGGGCAUGGGUAUGGGCAUGGGUAUGGGUUUGGGUAUGGGCUGCGCAGCGAUUGAUCGGCUGCAGUUUAUGGACUCAUGCAGCCAAUUCAAAUGCAAUUGC-AGCUU
...((((.(((((...(((....(((((((((....((((((((((((..(((....))))).))))))))))))))))))).))).)))))..(((....))-))))) ( -35.70)
>DroVir_CAF1 63720 84 - 1
AGGUGGAG------------------------GGGGCUUGGGCAUUGCAGCGAUUGAUCGGCUGCAGUUUAUGGACUCAUGCAGCCAAUUCAAAUGCAAUUGC-GCUGC
.(.(.(((------------------------....))).).)...(((((..((((..((((((((((....)))...)))))))...))))..((....))-))))) ( -27.10)
>DroSec_CAF1 17012 84 - 1
CAUGGGUA------------------------UGGGUAUGGGCUGCGCAGCGAUUGAUCGGCUGCAGUUUAUGGACUCAUGCAGCCAAUUCAAAUGCAAUUGC-AGCUU
((((....------------------------....))))(((((((..(((.((((..((((((((((....)))...)))))))...)))).)))...)))-)))). ( -29.10)
>DroSim_CAF1 18266 84 - 1
GAUGGGUA------------------------UGGGUAUGGGCUGCGCAGCGAUUGAUCGGCUGCAGUUUAUGGACUCAUGCAGCCAAUUCAAAUGCAAUUGC-AGCUU
........------------------------.......((((((((..(((.((((..((((((((((....)))...)))))))...)))).)))...)))-))))) ( -29.10)
>DroAna_CAF1 14451 107 - 1
GGGAGCCAGAGCCAUAGCCAUAGCCAG-AGCCAGAGCCAGGGGAGAA-CGCGAUUGAUCGGCUGCAGUUUAUGGACUCAUGCAGCCAAUUCAAAUGCAAUUGCCAGCAA
.((..(..(.((..(.((....)).).-.))).)..)).((.((...-.(((.((((..((((((((((....)))...)))))))...)))).)))..)).))..... ( -26.40)
>consensus
GAUGGGCA________________________UGGGUAUGGGCUGCGCAGCGAUUGAUCGGCUGCAGUUUAUGGACUCAUGCAGCCAAUUCAAAUGCAAUUGC_AGCUU
.................................................(((.((((..((((((((((....)))...)))))))...)))).)))............ (-19.32 = -19.32 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,123,431 – 8,123,527
Length 96
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 85.90
Mean single sequence MFE -27.97
Consensus MFE -22.91
Energy contribution -22.94
Covariance contribution 0.03
Combinations/Pair 1.05
Mean z-score -1.64
Structure conservation index 0.82
SVM decision value 0.00
SVM RNA-class probability 0.533917
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8123431 96 + 27905053
CCCAUGCCCAUACCCAUGGUCUCCAGCUU-------GAAGAUUGUGGGAGACGAGACACGAUCGCGGUAGUAAAAUACCGGGUAUAGACUUACUAGAUCUUCU---
...((((((...((((..((((.(.....-------).))))..)))).(.(((.......))))((((......))))))))))..................--- ( -28.50)
>DroSec_CAF1 17096 96 + 1
CCCAUGCCCAUACCCAUGGUCUCCAGCUC-------GAAGAUUGUGGGAGACGAGACACGAUCGCGGUAGUAAAAUACCGGGUAUAGACUUACUAGACCUUCU---
...((((((...((((..((((.(.....-------).))))..)))).(.(((.......))))((((......))))))))))..................--- ( -28.20)
>DroSim_CAF1 18350 96 + 1
CCCAUGCCCAUACCCAUGGUCUCCAGCUC-------GAAGAUUGUGGGAGACGAGACACGAUCGCGGUAGUAAAAUACCGGGUAUAGACUUACUAGAUCUUCU---
...((((((...((((..((((.(.....-------).))))..)))).(.(((.......))))((((......))))))))))..................--- ( -28.20)
>DroEre_CAF1 16682 85 + 1
-----------ACCCAUGGUCUGCAGCUC-------GAAGAUUGUGGGAGACGAGACACGAUCGCGGUAGUAAAAUACCGGGUAUAGACUUACUAGAUCUUCU---
-----------.((((..((((.......-------..))))..))))...........((((.(((((......)))))((((......)))).))))....--- ( -26.70)
>DroYak_CAF1 16205 85 + 1
-----------ACCCAGGGUCUUCAGCUC-------GAAGAUUGUGGGAGACGAGACACGAUCGCGGUAGUAAAAUACCGGGUAUAGACUUACUAGAUCUUCU---
-----------.((((.(((((((.....-------))))))).))))...........((((.(((((......)))))((((......)))).))))....--- ( -29.30)
>DroPer_CAF1 45260 97 + 1
---------GUCCCCAUCGUUUUCGACUCUUUCUUUGCAGAUUGUGGGAGACGAGACACGAUCGCGGUAGUAAAAUACCGGGUAUAGACUUACUAGAUCUUCUGCU
---------((((((((.((((.(((........))).)))).))))).))).(((...((((.(((((......)))))((((......)))).)))).)))... ( -26.90)
>consensus
_________AUACCCAUGGUCUCCAGCUC_______GAAGAUUGUGGGAGACGAGACACGAUCGCGGUAGUAAAAUACCGGGUAUAGACUUACUAGAUCUUCU___
............((((..((((................))))..))))...........((((.(((((......)))))((((......)))).))))....... (-22.91 = -22.94 +   0.03)

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 10:52:35 2006