Locus 1155

Sequence ID 2L_DroMel_CAF1
Location 3,154,743 – 3,154,869
Length 126
Max. P 0.991171
window1870 window1871 window1872

overview

Window 0

Location 3,154,743 – 3,154,835
Length 92
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 76.82
Mean single sequence MFE -32.60
Consensus MFE -16.92
Energy contribution -16.73
Covariance contribution -0.19
Combinations/Pair 1.32
Mean z-score -2.21
Structure conservation index 0.52
SVM decision value 1.09
SVM RNA-class probability 0.913843
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3154743 92 - 22407834
GGCAGUCAUUGGCAUUGAUUGGCAGUUGAACACGCAACAAUUGUUGCAUGUUUAGGCGUCGGCAGUGACGGUGA-GACGACAACAACUGCA----CA
.(((((..(((.(((((.(((((..(((((((.(((((....))))).)))))))..)))))))))).((....-..)).)))..))))).----.. ( -32.80)
>DroVir_CAF1 13114 92 - 1
GUCAGUCAUUGGCAUUGAUUGGCAGCUGAGCACGCAUCAAUUGUUGCAUG-----GCGCUGGCGCUGACGCUGGCGACGCCUCUUGCUGCAGCAGCA
((((((((.......)))))))).((((((((.(((........)))..(-----((((..(((....)))..))...)))...)))).)))).... ( -37.40)
>DroEre_CAF1 9807 84 - 1
GGCAGUCAUUGGCAUUGAUUGGCAGUUGAACACGCAACAAUUGUUGCAUGUUUAGGCGUCGGCAGUGACGGUGA-GACGACAAC------------A
.....((((((.(((((.(((((..(((((((.(((((....))))).)))))))..)))))))))).))))))-.........------------. ( -28.80)
>DroYak_CAF1 12882 87 - 1
GGCAGUCAUUGGCAUUGAUUGGCAGUUGAACACGCAACAAUUGUUGCAUGUUUAGGCGUCGGCAUUGACGGUGA-GACGACAACAA---------CA
(.((((((.......)))))).).((((((((.(((((....))))).)))).....((((.(((.....))).-..))))..)))---------). ( -27.60)
>DroMoj_CAF1 13538 86 - 1
GUCAGUCAUUGGCAUUGAUUGGCAGCUGAACACGCAACAAUUGUUGCAUG-----GCGCUGGUG------AUGGCGACGCCUCAUGCUGCAGCAGCA
((((((((.......)))))))).((((..((.(((((....))))).))-----((((..(((------(.(((...))))))))).))..)))). ( -32.30)
>DroAna_CAF1 10859 92 - 1
AGCAGCCAUUGGCAUUGAUUGGCGGUUGAUCACGCAACAAUUGUUGCAUGUUCAGGCGUCGGCAGUGGCGGUGG-GACGACAUGAGCAGCG----CA
.((..((((((.(((((.((((((.((((.((.(((((....))))).)).)))).))))))))))).))))))-(.(.......))...)----). ( -36.70)
>consensus
GGCAGUCAUUGGCAUUGAUUGGCAGUUGAACACGCAACAAUUGUUGCAUGUUUAGGCGUCGGCAGUGACGGUGA_GACGACAACAGCUGCA____CA
.....((((((.((.((.(((((.(((...((.(((((....))))).))....)))))))))).)).))))))....................... (-16.92 = -16.73 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,154,773 – 3,154,869
Length 96
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 79.98
Mean single sequence MFE -32.58
Consensus MFE -13.78
Energy contribution -16.06
Covariance contribution 2.28
Combinations/Pair 1.09
Mean z-score -3.13
Structure conservation index 0.42
SVM decision value 2.25
SVM RNA-class probability 0.991171
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3154773 96 + 22407834
CCGACGCCUAAACAUGCAACAAUUGUUGCGUGUUCAACUGCCAAUCAAUGCCAAUG-ACUG-----C----------CGGACCACAGCA---GCAGUGGCAGGAAUCAGGAGCAA
((((..(((.((((((((((....))))))))))...............((((.((-.(((-----(----------.(.....).)))---))).)))))))..)).))..... ( -33.40)
>DroEre_CAF1 9829 96 + 1
CCGACGCCUAAACAUGCAACAAUUGUUGCGUGUUCAACUGCCAAUCAAUGCCAAUG-ACUG-----C----------CGGACCACAGCA---GCAGUGGCAGGAAUCAGGAGCAA
((((..(((.((((((((((....))))))))))...............((((.((-.(((-----(----------.(.....).)))---))).)))))))..)).))..... ( -33.40)
>DroWil_CAF1 18412 110 + 1
UCGACGCCUGUACAUGCAACAAUUGUUGCAUGUUGAACUGCCAAUCAAUGCCAAUGCACUGGGAUGCAGUGCAAUGAAAGACCACAACA---AAGA--UCAACGAUGACGAUCGA
((((((.......(((((((....)))))))(((((.((((........))((.(((((((.....))))))).)).............---.)).--))))).....)).)))) ( -29.50)
>DroYak_CAF1 12907 99 + 1
CCGACGCCUAAACAUGCAACAAUUGUUGCGUGUUCAACUGCCAAUCAAUGCCAAUG-ACUG-----C----------CGGACCACAGCAGCAGCAGUGGCAGGAAUCAGGAGCAA
..(...(((.((((((((((....))))))))))...((((((.....(((...((-.(((-----(----------.(.....).))))))))).)))))).....)))..).. ( -35.00)
>DroAna_CAF1 10889 93 + 1
CCGACGCCUGAACAUGCAACAAUUGUUGCGUGAUCAACCGCCAAUCAAUGCCAAUG-GCUG-----C----------UGGACCACAAAA---GCAG---CAGCAAACAGGGCCAA
..(.((..(((.((((((((....)))))))).)))..)).).......(((....-((((-----(----------((..........---.)))---))))......)))... ( -31.60)
>consensus
CCGACGCCUAAACAUGCAACAAUUGUUGCGUGUUCAACUGCCAAUCAAUGCCAAUG_ACUG_____C__________CGGACCACAGCA___GCAGUGGCAGGAAUCAGGAGCAA
......(((.((((((((((....))))))))))...((((((.....(((.........................................))).)))))).....)))..... (-13.78 = -16.06 +   2.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,154,773 – 3,154,869
Length 96
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 79.98
Mean single sequence MFE -37.14
Consensus MFE -16.90
Energy contribution -16.82
Covariance contribution -0.08
Combinations/Pair 1.17
Mean z-score -2.87
Structure conservation index 0.46
SVM decision value 1.87
SVM RNA-class probability 0.980844
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3154773 96 - 22407834
UUGCUCCUGAUUCCUGCCACUGC---UGCUGUGGUCCG----------G-----CAGU-CAUUGGCAUUGAUUGGCAGUUGAACACGCAACAAUUGUUGCAUGUUUAGGCGUCGG
..(((.(..(((..(((((.(((---(((((.....))----------)-----))).-)).)))))..)))..).)))((((((.(((((....))))).))))))........ ( -36.10)
>DroEre_CAF1 9829 96 - 1
UUGCUCCUGAUUCCUGCCACUGC---UGCUGUGGUCCG----------G-----CAGU-CAUUGGCAUUGAUUGGCAGUUGAACACGCAACAAUUGUUGCAUGUUUAGGCGUCGG
..(((.(..(((..(((((.(((---(((((.....))----------)-----))).-)).)))))..)))..).)))((((((.(((((....))))).))))))........ ( -36.10)
>DroWil_CAF1 18412 110 - 1
UCGAUCGUCAUCGUUGA--UCUU---UGUUGUGGUCUUUCAUUGCACUGCAUCCCAGUGCAUUGGCAUUGAUUGGCAGUUCAACAUGCAACAAUUGUUGCAUGUACAGGCGUCGA
((((.((((...((..(--((..---((((((((....))))(((((((.....)))))))..))))..)))..))......(((((((((....)))))))))...)))))))) ( -43.00)
>DroYak_CAF1 12907 99 - 1
UUGCUCCUGAUUCCUGCCACUGCUGCUGCUGUGGUCCG----------G-----CAGU-CAUUGGCAUUGAUUGGCAGUUGAACACGCAACAAUUGUUGCAUGUUUAGGCGUCGG
.((((..(((((((.(((((.((....)).)))))..)----------)-----.)))-))..)))).....((((..(((((((.(((((....))))).)))))))..)))). ( -36.60)
>DroAna_CAF1 10889 93 - 1
UUGGCCCUGUUUGCUG---CUGC---UUUUGUGGUCCA----------G-----CAGC-CAUUGGCAUUGAUUGGCGGUUGAUCACGCAACAAUUGUUGCAUGUUCAGGCGUCGG
...(((.((.((((((---(..(---....)..)..))----------)-----))).-))..)))......(((((.((((.((.(((((....))))).)).)))).))))). ( -33.90)
>consensus
UUGCUCCUGAUUCCUGCCACUGC___UGCUGUGGUCCG__________G_____CAGU_CAUUGGCAUUGAUUGGCAGUUGAACACGCAACAAUUGUUGCAUGUUUAGGCGUCGG
............................(((..(((........................((((.((.....)).))))((((((.(((((....))))).)))))))))..))) (-16.90 = -16.82 +  -0.08)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:58 2006