Locus 1698

Sequence ID 2R_DroMel_CAF1
Location 6,425,043 – 6,425,180
Length 137
Max. P 0.975687
window2834 window2835 window2836

overview

Window 4

Location 6,425,043 – 6,425,149
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.62
Mean single sequence MFE -30.22
Consensus MFE -19.05
Energy contribution -19.33
Covariance contribution 0.28
Combinations/Pair 1.15
Mean z-score -2.12
Structure conservation index 0.63
SVM decision value 0.69
SVM RNA-class probability 0.824972
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6425043 106 + 20766785
-GUUGCUGGCUUAUAUCAAUAAUUGCCAAAAGCAAAUUGGAAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGCAGUCAA-AAUGGC-GCAACAA-----------CCA
-((((.((((((...(((((..((((.....)))))))))..))))))((((((.(((.....)))(((..((((......)))).)))..-...)))-))).)))-----------).. ( -30.60)
>DroVir_CAF1 46693 118 + 1
-GCCGCUGGCUUAUAUCAAUAAUUGCCAAAAGCAAAUUGGAAAAGUUAUGCGCCAGCAGUUAAUGUGACCAGCGAAAAUAGUCGCAACCCGUAACUGCAGCACCAGCAACAG-CAGCCGC
-((.(((((((.......((((((.((((.......))))...))))))..((..(((((((.((((((...........)))))).....))))))).))...)))..)))-).))... ( -30.70)
>DroPse_CAF1 5381 107 + 1
-GCUGUUGGCUUAUAUCAAUAAUUGCCAAAAGCAAAUUGGAAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGCAGCCAAAAAUGGC-GCAACAG-----------CCG
-(((((((((((...(((((..((((.....)))))))))..))))))((((((.........((((((...........)))))).........)))-)))))))-----------).. ( -33.17)
>DroGri_CAF1 14665 86 + 1
UGGCAGUGGCUUAUAUCAAUAAUUGCCAAAAGCAAAUUGGAAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGCA----------------------------------
.(((.(((((((...(((((..((((.....)))))))))..)))))))..)))((((.....))))....((((......)))).---------------------------------- ( -21.70)
>DroMoj_CAF1 10659 119 + 1
-GCUGCCGGCUUAUAUCAAUAAUUGCCAAAAGCAAAUUGGAAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGUAGCCCAUAACAGCAGCAGCAGCAGCAGUCAGACUA
-(((((.(((((...(((((..((((.....)))))))))..))))).(((..((((.((((.((((((...........)))))).....)))).))))..)))))))).......... ( -32.00)
>DroPer_CAF1 12412 107 + 1
-GCUGUUGGCUUAUAUCAAUAAUUGCCAAAAGCAAAUUGGAAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGCAGCCAAAAAUGGC-GCAACAG-----------CCG
-(((((((((((...(((((..((((.....)))))))))..))))))((((((.........((((((...........)))))).........)))-)))))))-----------).. ( -33.17)
>consensus
_GCUGCUGGCUUAUAUCAAUAAUUGCCAAAAGCAAAUUGGAAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGCAGCCAA_AAUGGC_GCAACAG___________CCA
.(((((.(((.(((((((((..((((.....)))))))))......)))).))).)))))...((((((...........)))))).................................. (-19.05 = -19.33 +   0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,425,043 – 6,425,149
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.62
Mean single sequence MFE -32.12
Consensus MFE -17.38
Energy contribution -18.77
Covariance contribution 1.39
Combinations/Pair 1.15
Mean z-score -2.24
Structure conservation index 0.54
SVM decision value 0.34
SVM RNA-class probability 0.696350
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6425043 106 - 20766785
UGG-----------UUGUUGC-GCCAUU-UUGACUGCGACUAUUUCCGCUGGUCGCAUUAACUGCAGGCGCAUAACUUUUCCAAUUUGCUUUUGGCAAUUAUUGAUAUAAGCCAGCAAC-
.((-----------((((.((-(((...-..(((((((........))).))))(((.....))).)))))))))))........(((((...(((..((((....)))))))))))).- ( -32.30)
>DroVir_CAF1 46693 118 - 1
GCGGCUG-CUGUUGCUGGUGCUGCAGUUACGGGUUGCGACUAUUUUCGCUGGUCACAUUAACUGCUGGCGCAUAACUUUUCCAAUUUGCUUUUGGCAAUUAUUGAUAUAAGCCAGCGGC-
...((((-(((..(((.((((((((((((..(..(((((......)))).)..)....))))))).)))))..........((((((((.....))))..)))).....))))))))))- ( -38.20)
>DroPse_CAF1 5381 107 - 1
CGG-----------CUGUUGC-GCCAUUUUUGGCUGCGACUAUUUCCGCUGGUCGCAUUAACUGCAGGCGCAUAACUUUUCCAAUUUGCUUUUGGCAAUUAUUGAUAUAAGCCAACAGC-
..(-----------(((((((-((((....))))((((((((.......))))))))......)).(((................((((.....))))((((....)))))))))))))- ( -32.70)
>DroGri_CAF1 14665 86 - 1
----------------------------------UGCGACUAUUUCCGCUGGUCGCAUUAACUGCAGGCGCAUAACUUUUCCAAUUUGCUUUUGGCAAUUAUUGAUAUAAGCCACUGCCA
----------------------------------((((((((.......)))))))).........((((((..............)))...((((..((((....))))))))..))). ( -21.24)
>DroMoj_CAF1 10659 119 - 1
UAGUCUGACUGCUGCUGCUGCUGCUGUUAUGGGCUACGACUAUUUCCGCUGGUCGCAUUAACUGCAGGCGCAUAACUUUUCCAAUUUGCUUUUGGCAAUUAUUGAUAUAAGCCGGCAGC-
.............(((((((..(((((((((.(((..(((((.......)))))(((.....))).))).)))))).....((((((((.....))))..)))).....))))))))))- ( -35.60)
>DroPer_CAF1 12412 107 - 1
CGG-----------CUGUUGC-GCCAUUUUUGGCUGCGACUAUUUCCGCUGGUCGCAUUAACUGCAGGCGCAUAACUUUUCCAAUUUGCUUUUGGCAAUUAUUGAUAUAAGCCAACAGC-
..(-----------(((((((-((((....))))((((((((.......))))))))......)).(((................((((.....))))((((....)))))))))))))- ( -32.70)
>consensus
CGG___________CUGUUGC_GCCAUU_UUGGCUGCGACUAUUUCCGCUGGUCGCAUUAACUGCAGGCGCAUAACUUUUCCAAUUUGCUUUUGGCAAUUAUUGAUAUAAGCCAGCAGC_
..................(((.(((.........((((((((.......)))))))).........))))))...............(((.(((((..((((....))))))))).))). (-17.38 = -18.77 +   1.39)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,425,082 – 6,425,180
Length 98
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 72.10
Mean single sequence MFE -26.25
Consensus MFE -15.83
Energy contribution -15.52
Covariance contribution -0.31
Combinations/Pair 1.29
Mean z-score -2.02
Structure conservation index 0.60
SVM decision value 1.75
SVM RNA-class probability 0.975687
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6425082 98 + 20766785
AAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGCAGUCAA-AAUGGC-GCAACAA-----------CCAAACGGAAGUGCCCCAAACGCCCACA--CCCACA
....(((.((((((.(((.....)))(((..((((......)))).)))..-...)))-)))....-----------....((....))......))).......--...... ( -24.40)
>DroVir_CAF1 46732 111 + 1
AAAAGUUAUGCGCCAGCAGUUAAUGUGACCAGCGAAAAUAGUCGCAACCCGUAACUGCAGCACCAGCAACAG-CAGCCGCAGCGGAAGUAUUAUAA-UACAUACAUCCACACA
........((((.(.(((((((.((((((...........)))))).....))))))).((....)).....-..).))))(.(((.((((.....-...)))).))).)... ( -27.20)
>DroSec_CAF1 5519 90 + 1
AAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGCAGUCAA-AAUGGC-GCAACAA-----------CCAAACGGAAGUGCCCCAAACACCCA----------
....(((.((((((.(((.....)))(((..((((......)))).)))..-...)))-)))....-----------....((....))......))).....---------- ( -24.40)
>DroMoj_CAF1 10698 110 + 1
AAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGUAGCCCAUAACAGCAGCAGCAGCAGCAGUCAGACUAAGCGGAAGCACCGCAA-UGCACACA--CAUACA
....((.(((.(..((((((....)).....((((...(((((((.((........)).)).((....)).....))))).((....)).))))..-))))..).--))))). ( -29.00)
>consensus
AAAAGUUAUGCGCCUGCAGUUAAUGCGACCAGCGGAAAUAGUCGCAGCCAA_AACGGC_GCAACAA___________CCAAACGGAAGUACCCCAA_CACACACA__CACACA
........((((((.........((((((...........)))))).........))).)))...................((....))........................ (-15.83 = -15.52 +  -0.31)

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 10:11:02 2006