Locus 7449

Sequence ID 3R_DroMel_CAF1
Location 19,849,620 – 19,849,810
Length 190
Max. P 0.965515
window12045 window12046

overview

Window 5

Location 19,849,620 – 19,849,737
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.82
Mean single sequence MFE -37.62
Consensus MFE -28.77
Energy contribution -29.77
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -2.04
Structure conservation index 0.76
SVM decision value 0.84
SVM RNA-class probability 0.865063
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19849620 117 - 27905053
UUGGCCAUGAAAU---GGCCAUGUUAGGGAGAUUUGUGUGCGGUUCGGUUCCCAGCCGCUGUUUCCAUGCAUUAUAAGCUGUUGACCCAGCAUUUCAUUUUGGCUCUAAACGGGUCCACA
.(((((((...))---)))))(((...((((((......((((((.(....).)))))).))))))..)))......((((......)))).........((((((.....))).))).. ( -36.30)
>DroSec_CAF1 27983 113 - 1
CUGGCCAUGAAAU---GGCCAUGUUAGGGAGAUUUGUGUGCGGUUC----CCAAGCCGUUCUUUCCAUGCAUUAUAAGCUGUUGACCCAGCAUUUCAUUUUGGCUCUAAACGGGCCAACA
.(((((((...))---)))))(((...(((((.....(.(((((..----....))))).))))))..)))......((((......))))........(((((((.....))))))).. ( -35.40)
>DroSim_CAF1 36114 113 - 1
UUGGCCAUGAAAU---GGCCAUGUUAGGGAGAUUUGUGUGCGGUUC----CCAAGCCGCUCUUUCCAUGCAUUAUAAGCUGUUGACCCAGCAUUUCAUUUUGGCUCUAAACGGGCCAACA
.(((((((...))---)))))(((...(((((.....(.(((((..----....))))).))))))..)))......((((......))))........(((((((.....))))))).. ( -37.80)
>DroEre_CAF1 27951 115 - 1
UUGGCCAUGAAAUGGUGGCCAUGUUAGGGAGAUUUGUGUGCGGUUC----CC-AGCCUUUGUUUCCAUGCAUUAUAAGCUGUUGACCCAGCAUUUCAUUUUGGCUUUAACCGGGCCACCA
............((((((((..(((((((.((..((.((((((((.----.(-(((...(((......)))......))))..))))..))))..))..))..)))))))..)))))))) ( -39.40)
>DroYak_CAF1 27894 115 - 1
UUGGCCAUGAAAUGCUGACCAUGUUAGGGAGAUUCGUGUGCGGUUC----CC-AGCCUUUGUUGCCAUGCAUUACAAGCUGUUGACCCAGCAUUUCAUUUUGGCUUUAACCGGGCCACCA
.((((((((((((((((.((......)).............((((.----.(-(((..(((((((...)))..))))))))..)))))))))))))))..(((......))))))))... ( -39.20)
>consensus
UUGGCCAUGAAAU___GGCCAUGUUAGGGAGAUUUGUGUGCGGUUC____CC_AGCCGUUGUUUCCAUGCAUUAUAAGCUGUUGACCCAGCAUUUCAUUUUGGCUCUAAACGGGCCAACA
.(((((..........((((((((...((((((......((((((........)))))).))))))..)))......((((......)))).........))))).......)))))... (-28.77 = -29.77 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,849,700 – 19,849,810
Length 110
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 90.60
Mean single sequence MFE -26.29
Consensus MFE -19.92
Energy contribution -19.60
Covariance contribution -0.32
Combinations/Pair 1.09
Mean z-score -2.68
Structure conservation index 0.76
SVM decision value 1.58
SVM RNA-class probability 0.965515
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19849700 110 + 27905053
CACACAAAUCUCCCUAACAUGGCC---AUUUCAUGGCCAACGGAGGAAAUUAAACCACUCCACCAGGUGGAGCAACUUUCAAUGUUUUCAUUCUCUCGGUGCCCAA-AACCUGC
...................(((((---((...)))))))..((((............))))..(((((((.(((......((((....)))).......)))))..-.))))). ( -26.62)
>DroSec_CAF1 28059 110 + 1
CACACAAAUCUCCCUAACAUGGCC---AUUUCAUGGCCAGCGGAGGAAACCAAACCACUCCACCAGGUGGAGCAACUUUCAAUGUUUUCAUUCUCUCCGUGCCCAA-AACCUGC
...................(((((---((...)))))))(((((((((.........((((((...)))))).(((.......)))....))).))))))......-....... ( -28.10)
>DroSim_CAF1 36190 110 + 1
CACACAAAUCUCCCUAACAUGGCC---AUUUCAUGGCCAACGGAGGAAACCAAACCACUCCACCAGGUGGAGCAACUUUCAAUGUUUUCAUUCUCUCGGUGCCCAA-AACCUGC
...................(((((---((...)))))))..((((............))))..(((((((.(((......((((....)))).......)))))..-.))))). ( -26.62)
>DroEre_CAF1 28026 105 + 1
CACACAAAUCUCCCUAACAUGGCCACCAUUUCAUGGCCAACGGAGGAAA-----CCACUC---CAGGUUGAGCAUCUUUCAAUGUUUUCAUUCUCUCGGUGCCCAA-AACCUGC
........(((((......((((((........))))))..)))))...-----......---((((((..(((((....((((....)))).....)))))....-)))))). ( -27.10)
>DroYak_CAF1 27969 106 + 1
CACACGAAUCUCCCUAACAUGGUCAGCAUUUCAUGGCCAACGGAGGAAA-----CCACUC---CAGGUUGAGCAACUUUCAAUGUUUUCAUUCUCUCGGUGCCUAAAAACCUGC
(((.(((.....(((....((((((........))))))..((((....-----...)))---)))).((((.(((.......))))))).....))))))............. ( -23.00)
>consensus
CACACAAAUCUCCCUAACAUGGCC___AUUUCAUGGCCAACGGAGGAAA__AAACCACUCCACCAGGUGGAGCAACUUUCAAUGUUUUCAUUCUCUCGGUGCCCAA_AACCUGC
........(((((......(((((..........)))))..))))).................(((((.(.(((......((((....)))).......))).)....))))). (-19.92 = -19.60 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:20 2006