Locus 6473

Sequence ID 2R_DroMel_CAF1
Location 20,226,499 – 20,226,633
Length 134
Max. P 0.916817
window10321 window10322

overview

Window 1

Location 20,226,499 – 20,226,593
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.90
Mean single sequence MFE -28.47
Consensus MFE -15.70
Energy contribution -16.51
Covariance contribution 0.81
Combinations/Pair 1.15
Mean z-score -1.75
Structure conservation index 0.55
SVM decision value 0.05
SVM RNA-class probability 0.556394
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20226499 94 - 20766785
CUUUUCCAGGAAGGGUAUCGCUCACCCACACUUUUGCAUG----CAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUGUUCUU---------GGGCUGUUGUUGU-------------
....((((((((((((.......))))......(((((.(----((.(((((..(....)..)))))))).)))))....)))))---------)))..........------------- ( -30.30)
>DroPse_CAF1 19022 93 - 1
CU-GCUAGUGCAGGGUGUCUAUC--GCACACAUUUGUAUG----CAUGCAUUUGAAAUUUUGAGUGCUGCCUGCGACAUGUUCUU---------GGCCUGUUGUUGUUU-----------
..-((....(((((((((.....--))))(((((((((.(----((.(((((..(....)..)))))))).))))).))))....---------..)))))....))..----------- ( -27.00)
>DroEre_CAF1 20554 103 - 1
CUUUUCCAGGAAGGGUAUCGCUCUGCCACACAUUUGCAUG----CAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUGUUCUUGCUGUUCUUGGGCUGUUGUUGU-------------
....((((((((.((((..((...))...(((((((((.(----((.(((((..(....)..)))))))).))))).))))...)))).))))))))..........------------- ( -32.00)
>DroYak_CAF1 18988 94 - 1
CUUUUCCAGGAAGGGUAUCGCUCACCCACACAUUUGCAUG----CAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUGUUCUU---------CUGCUGUUGUUGU-------------
......(((((.((((.......))))..(((((((((.(----((.(((((..(....)..)))))))).))))).))))..))---------)))..........------------- ( -27.00)
>DroAna_CAF1 17419 98 - 1
CUUGUUCCAGAAGGGUAUCCUUCACACACACAUUUAUAUGUGGGCUUGCAUUUGAAAAUUUGAGUGCUGCUUGCGACAUGUUCUU---------GGGCUGUUGUUGU-------------
.........(((((....))))).....(((((....)))))(((..(((((..(....)..))))).))).((((((.(((...---------.)))))))))...------------- ( -26.80)
>DroPer_CAF1 19252 104 - 1
CU-GCUAGUGCAGGGUGUCUAUC--GCACACAUUUGUAUG----CAUGCAUUUGAAAUUUUGAGUGCUGCCUGCGACAUGUUCUU---------GGCCUGUUGUUGUUUCCAUUGCCGUU
((-((....)))).((((.....--))))(((((((((.(----((.(((((..(....)..)))))))).))))).))))....---------(((.((..(....)..))..)))... ( -27.70)
>consensus
CUUGUCCAGGAAGGGUAUCGCUCACCCACACAUUUGCAUG____CAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUGUUCUU_________GGGCUGUUGUUGU_____________
............(((((.(.(((.......((..((((((....))))))..)).......))).).)))))((((((.((((...........))))))))))................ (-15.70 = -16.51 +   0.81)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,226,517 – 20,226,633
Length 116
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 94.05
Mean single sequence MFE -33.87
Consensus MFE -29.88
Energy contribution -30.56
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.51
Structure conservation index 0.88
SVM decision value 1.11
SVM RNA-class probability 0.916817
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20226517 116 - 20766785
AUUGUGCAAUCGAGACUCAAGCUCGAACACUCGUAACAUCCUUUUCCAGGAAGGGUAUCGCUCACCCACACUUUUGCAUGCAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUG
...(((...(((((.(....)))))).)))..((....((((.....)))).((((.......))))))....(((((.(((.(((((..(....)..)))))))).))))).... ( -31.40)
>DroSec_CAF1 19505 116 - 1
AUUGUGCAUUCGAGAAGCAAGCUCGAACACUCGUAACAUCCUCUUCCAGGAAGGGUAUCGCUCACCCACACAUUUGCAUGCAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUG
...(((..((((((.......)))))))))((((....((((.....)))).(((((.((((((......((..((((....))))..))......)))))).))))))))).... ( -33.10)
>DroSim_CAF1 18367 116 - 1
AUUGUGCAUUCGAGAAGCAAGCUCGAACACUCGUAACAUCCUCUUCCUGGAAGGGUAUCGCUCACCCACACAUUUGCAUGCAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUG
...(((..((((((.......)))))))))((((....(((.......))).(((((.((((((......((..((((....))))..))......)))))).))))))))).... ( -32.60)
>DroEre_CAF1 20581 116 - 1
AUCGAGCAUUCGAGAACCGGGCUCGAGCACUCGCAACAUCCUUUUCCAGGAAGGGUAUCGCUCUGCCACACAUUUGCAUGCAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUG
.((((((...((.....)).))))))....((((....((((.....)))).(((((.(((((.......((..((((....))))..)).......))))).))))))))).... ( -36.64)
>DroYak_CAF1 19006 116 - 1
AUUGUGCAUUCGAGAGCCAGGCUCGAGCACUCGUAACAUCCUUUUCCAGGAAGGGUAUCGCUCACCCACACAUUUGCAUGCAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUG
...((((..(((((.......)))))))))((((....((((.....)))).(((((.((((((......((..((((....))))..))......)))))).))))))))).... ( -35.60)
>consensus
AUUGUGCAUUCGAGAACCAAGCUCGAACACUCGUAACAUCCUUUUCCAGGAAGGGUAUCGCUCACCCACACAUUUGCAUGCAUGCAUUUGAAAAUUUGAGUGCUGCCUGCGACAUG
...(((..((((((.......)))))))))((((....((((.....)))).(((((.((((((......((..((((....))))..))......)))))).))))))))).... (-29.88 = -30.56 +   0.68)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:50 2006