Locus 55

Sequence ID 3R_DroMel_CAF1
Location 319,558 – 319,715
Length 157
Max. P 0.808342
window90 window91 window92

overview

Window 0

Location 319,558 – 319,675
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.82
Mean single sequence MFE -44.35
Consensus MFE -28.59
Energy contribution -29.45
Covariance contribution 0.86
Combinations/Pair 1.21
Mean z-score -1.55
Structure conservation index 0.64
SVM decision value 0.14
SVM RNA-class probability 0.601265
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 319558 117 - 27905053
CAGCAAGCCCGGCUCCAGUCGCCUUCUGCGUCGGCAGUUCAGCUUGGAUCGCGACGACCAGCAGGCGAAGGG---AGAGCAGCAGCACCACCAGCACUCCCUGCAGGCAAACACCUACUC
......(((...((((..((((((.(((.((((((.((((.....)))).))..))))))).))))))..))---)).((((..((.......)).....)))).)))............ ( -42.20)
>DroVir_CAF1 4349 114 - 1
UAGCAAGCCCGGCUCUAGUCGCCUGCUGCGCCGUCAGUUCAGUCUGGACCGUGACGACCAGCAGGCCAAGGU---GGAGCAACAGCA---CCAGCUGUCGCUGCAGGCGAACAACUACGC
..(((.((...((((((.(.((((((((.(.(((((((((.....))))..))))).)))))))))...).)---))))).(((((.---...))))).)))))..(((........))) ( -46.80)
>DroGri_CAF1 5053 117 - 1
CAGCAAGCCCGGCUCCAGCCGGCUGCUGCGUCGCCAGUUCAGCUUGGAUCGCGACGAUCAGCAGUCGAAGGUGUCGGAGCAACAGCA---UCAGCUCUCGCUGCAGGCCAACAACUAUGC
..(((.(((((((.((...(((((((((((((((..((((.....)))).))))))..)))))))))..)).))))).))....((.---.((((....))))...)).........))) ( -49.70)
>DroWil_CAF1 9032 117 - 1
UGGCAAACCUGGCUCAAGUCGUCUACUGCGACGUCAAUUCAGUCUGGAUCGUGAUGACCAGCAAUCGAAGGC---AGAGCACCAGCAUCAACAGCAUUCGCUGCAGGUCACCAACUAUGC
(((...(((((((((..(((((.....)))))(((..(((.((((((.((.....))))))..)).))))))---.))))...........((((....)))))))))..)))....... ( -33.20)
>DroMoj_CAF1 491 114 - 1
CAGCAAGCCCGGCUCCAGCCGCCUGCUGCGUCGUCAGUUCAGUCUGGACCGGGACGAUCAGCAGUCCAAAGU---GGAGCAGCAGCA---CCAGCACUCCCUGCAGGCAAGCAAUUAUGC
..((..(((.(((....)))((((((((.((((((.((((.....))))...)))))))))))).....((.---((((..((....---...)).)))))))).)))..))........ ( -41.10)
>DroAna_CAF1 7502 114 - 1
CAGUAAGCCCGGCUCCAGUCGCCUGCUGCGUCGCCAGUUCAGCCUGGACCGCGACGACCAGCAGGCGAAGGG---AGAGCAGCAGCA---CCAGCACUCCCUGCAGGCGUCUAAUUACGC
..((((....(((.((..((((((((((((((((..((((.....)))).))))))..))))))))))((((---((.((.......---...)).))))))...)).)))...)))).. ( -53.10)
>consensus
CAGCAAGCCCGGCUCCAGUCGCCUGCUGCGUCGUCAGUUCAGCCUGGACCGCGACGACCAGCAGGCGAAGGU___AGAGCAGCAGCA___CCAGCACUCCCUGCAGGCAAACAACUACGC
......(((..((((...(((((((((((((((.(.((((.....)))).))))))..))))))))))........)))).............((.......)).)))............ (-28.59 = -29.45 +   0.86)

alignment

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secondary structure

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dotplot

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Window 1

Location 319,598 – 319,715
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.42
Mean single sequence MFE -42.73
Consensus MFE -30.67
Energy contribution -30.81
Covariance contribution 0.14
Combinations/Pair 1.25
Mean z-score -1.16
Structure conservation index 0.72
SVM decision value 0.64
SVM RNA-class probability 0.808342
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 319598 117 + 27905053
GCUCU---CCCUUCGCCUGCUGGUCGUCGCGAUCCAAGCUGAACUGCCGACGCAGAAGGCGACUGGAGCCGGGCUUGCUGUCGAACCGAGAGGCUCCUCCCCCACACCCACUUCCGCUCA
((.((---((..((((((((((((((...))).)).)))....((((....)))).))))))..))))..(((..((..(..((.((....)).))..)...))..)))......))... ( -37.90)
>DroVir_CAF1 4386 100 + 1
GCUCC---ACCUUGGCCUGCUGGUCGUCACGGUCCAGACUGAACUGACGGCGCAGCAGGCGACUAGAGCCGGGCUUGCUAUCAAACUUUGAGGC---------------GCUGCCACU--
((((.---....(.(((((((((((((((((((....))))...))))))).)))))))).)...))))..(((.((((.(((.....))))))---------------)..)))...-- ( -43.60)
>DroPse_CAF1 471 100 + 1
GUUCU---CCCUUCGCCUGCUGGUCGUCGCGAUCGAGACUGAACUGGCGACGCAGCAGGCGACUGGAGCCGGGUUUGCUAUCGAAUUUCGCCG-U--------------ACUGCCGCC--
...((---((..(((((((((((((((((.(.(((....))).)))))))).))))))))))..))))...(((.(((...((.....))..)-)--------------)..)))...-- ( -42.40)
>DroGri_CAF1 5090 103 + 1
GCUCCGACACCUUCGACUGCUGAUCGUCGCGAUCCAAGCUGAACUGGCGACGCAGCAGCCGGCUGGAGCCGGGCUUGCUGUCAAACUUGGAGGU---------------GCUGCCGGC--
...(((.(((((((((((((((..((((((.(((......))..).))))))))))))(((((....)))))..............))))))))---------------)....))).-- ( -41.30)
>DroAna_CAF1 7539 114 + 1
GCUCU---CCCUUCGCCUGCUGGUCGUCGCGGUCCAGGCUGAACUGGCGACGCAGCAGGCGACUGGAGCCGGGCUUACUGUCGUACCGAUUGACUCCUC---CAAUUCCGAUGCCGCUUC
((.((---((..((((((((((((((((.((((....))))....)))))).))))))))))..))))...(((.....((((....(((((.......---))))).)))))))))... ( -48.80)
>DroPer_CAF1 471 100 + 1
GUUCU---CCCUUCGCCUGCUGGUCGUCGCGAUCGAGACUGAACUGGCGACGCAGCAGGCGACUGGAGCCGGGUUUGCUAUCGAAUUUCGCCG-U--------------ACUGCCGCC--
...((---((..(((((((((((((((((.(.(((....))).)))))))).))))))))))..))))...(((.(((...((.....))..)-)--------------)..)))...-- ( -42.40)
>consensus
GCUCU___CCCUUCGCCUGCUGGUCGUCGCGAUCCAGACUGAACUGGCGACGCAGCAGGCGACUGGAGCCGGGCUUGCUAUCGAACUUAGAGGCU______________ACUGCCGCC__
(((((.......(((((((((((((((((.(.((......)).)))))))).))))))))))..)))))..(((......................................)))..... (-30.67 = -30.81 +   0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 319,598 – 319,715
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.42
Mean single sequence MFE -44.47
Consensus MFE -28.12
Energy contribution -28.40
Covariance contribution 0.28
Combinations/Pair 1.21
Mean z-score -1.30
Structure conservation index 0.63
SVM decision value 0.24
SVM RNA-class probability 0.647561
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 319598 117 - 27905053
UGAGCGGAAGUGGGUGUGGGGGAGGAGCCUCUCGGUUCGACAGCAAGCCCGGCUCCAGUCGCCUUCUGCGUCGGCAGUUCAGCUUGGAUCGCGACGACCAGCAGGCGAAGGG---AGAGC
...((....))((((.((..(...(((((....)))))..)..)).))))..((((..((((((.(((.((((((.((((.....)))).))..))))))).))))))..))---))... ( -49.60)
>DroVir_CAF1 4386 100 - 1
--AGUGGCAGC---------------GCCUCAAAGUUUGAUAGCAAGCCCGGCUCUAGUCGCCUGCUGCGCCGUCAGUUCAGUCUGGACCGUGACGACCAGCAGGCCAAGGU---GGAGC
--.(.(((.((---------------...(((.....)))..))..)))).((((((.(.((((((((.(.(((((((((.....))))..))))).)))))))))...).)---))))) ( -39.00)
>DroPse_CAF1 471 100 - 1
--GGCGGCAGU--------------A-CGGCGAAAUUCGAUAGCAAACCCGGCUCCAGUCGCCUGCUGCGUCGCCAGUUCAGUCUCGAUCGCGACGACCAGCAGGCGAAGGG---AGAAC
--((..((.((--------------.-(((......))))).))....))..((((..((((((((((((((((....((......))..))))))..))))))))))..))---))... ( -42.20)
>DroGri_CAF1 5090 103 - 1
--GCCGGCAGC---------------ACCUCCAAGUUUGACAGCAAGCCCGGCUCCAGCCGGCUGCUGCGUCGCCAGUUCAGCUUGGAUCGCGACGAUCAGCAGUCGAAGGUGUCGGAGC
--.(((...((---------------((((.(..(((((....)))))..(((....)))((((((((((((((..((((.....)))).))))))..))))))))).)))))))))... ( -44.20)
>DroAna_CAF1 7539 114 - 1
GAAGCGGCAUCGGAAUUG---GAGGAGUCAAUCGGUACGACAGUAAGCCCGGCUCCAGUCGCCUGCUGCGUCGCCAGUUCAGCCUGGACCGCGACGACCAGCAGGCGAAGGG---AGAGC
...(((((((((..((((---(.....)))))))))((....))..)))...((((..((((((((((((((((..((((.....)))).))))))..))))))))))..))---)).)) ( -49.60)
>DroPer_CAF1 471 100 - 1
--GGCGGCAGU--------------A-CGGCGAAAUUCGAUAGCAAACCCGGCUCCAGUCGCCUGCUGCGUCGCCAGUUCAGUCUCGAUCGCGACGACCAGCAGGCGAAGGG---AGAAC
--((..((.((--------------.-(((......))))).))....))..((((..((((((((((((((((....((......))..))))))..))))))))))..))---))... ( -42.20)
>consensus
__AGCGGCAGC______________AGCCUCGAAGUUCGACAGCAAGCCCGGCUCCAGUCGCCUGCUGCGUCGCCAGUUCAGCCUGGAUCGCGACGACCAGCAGGCGAAGGG___AGAGC
...............................................((((((....)))((((((((((((((..((((.....)))).))))))..))))))))...)))........ (-28.12 = -28.40 +   0.28)

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 09:31:35 2006