Locus 2010

Sequence ID 2R_DroMel_CAF1
Location 7,559,298 – 7,559,391
Length 93
Max. P 0.944051
window3321 window3322

overview

Window 1

Location 7,559,298 – 7,559,391
Length 93
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 77.06
Mean single sequence MFE -28.85
Consensus MFE -17.12
Energy contribution -17.46
Covariance contribution 0.34
Combinations/Pair 1.25
Mean z-score -1.72
Structure conservation index 0.59
SVM decision value 0.62
SVM RNA-class probability 0.801063
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7559298 93 + 20766785
CUGCUGCUUCUCCUCCGCAGGACACGUAGAAGUUACUAUGUGCAGUGCAAUGACAGCA------AACGGGGCAAACUGCCAGCAGCAGAAGCAGCAUCA
.((((((((((.((.((((.(.(((((((......))))))))..)))..........------.....(((.....))).).)).))))))))))... ( -34.30)
>DroSec_CAF1 5777 93 + 1
CUGCUGCUCCUCCUCCGCAGGACCCGUAGAAGUUACUAUGUGUAGUGCAAUGACAGAA------AACGGGGCAAACUGCCAGCAGCAGAAGGAGCAUCA
((((((((........(((..((.(((((......))))).))..)))..........------.....(((.....)))))))))))........... ( -28.40)
>DroSim_CAF1 5913 93 + 1
CUGCUGCUCCUCCUCCGCAGGACCCGUAGAAGUUACUAUGUGCAGUGCAAUGACAGCA------AACGGGGCAAACUGCCAGCAGCAGAAGGAGCAUCA
..(.(((((((.(((((.......(((((......)))))(((.((......)).)))------..)))))....((((.....)))).))))))).). ( -27.40)
>DroEre_CAF1 5761 90 + 1
CUGCUGCUGCUCCUUCGUAGGACCCGC---AGUUACUAUGUGCAGUGCAAUGACAGCA------AACGGGGCAAACUGCCAGCAGCAGAAGGAGCAUCA
(((((((((.((((....))))...((---((((....(((.(..(((.......)))------....).))))))))))))))))))........... ( -32.10)
>DroYak_CAF1 5808 76 + 1
CUGCUGGUCCUCCUCC-----------------UACUAUGUGCAGUGCAAUGACAGCA------AACGGGGCACAUUGCCAGCAGCAGAAGGAGCAUCA
.....(((.(((((.(-----------------(.((.((.(((((((..((......------..))..))))..)))))..)).)).))))).))). ( -21.90)
>DroPer_CAF1 6001 81 + 1
UUGCUGUUGUUCCUGUGUUGGA------------------GGCAGUGCAAUGACAGGACUGCAACAAGGGGCAAGCUGCCAGCAACAGUAGCAAAAGCA
.(((((((((((((.((((...------------------.(((((.(.......).))))))))))))(((.....)))))))))))))((....)). ( -29.00)
>consensus
CUGCUGCUCCUCCUCCGCAGGACCCGU___AGUUACUAUGUGCAGUGCAAUGACAGCA______AACGGGGCAAACUGCCAGCAGCAGAAGGAGCAUCA
((((((((..(((......)))...................(((((((..((..............))..))..))))).))))))))........... (-17.12 = -17.46 +   0.34)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,559,298 – 7,559,391
Length 93
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 77.06
Mean single sequence MFE -32.28
Consensus MFE -17.45
Energy contribution -18.68
Covariance contribution 1.23
Combinations/Pair 1.15
Mean z-score -2.30
Structure conservation index 0.54
SVM decision value 1.34
SVM RNA-class probability 0.944051
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7559298 93 - 20766785
UGAUGCUGCUUCUGCUGCUGGCAGUUUGCCCCGUU------UGCUGUCAUUGCACUGCACAUAGUAACUUCUACGUGUCCUGCGGAGGAGAAGCAGCAG
...((((((((((.((.((((((((..((...)).------.)))))))..(((..((((.(((......))).))))..)))).)).)))))))))). ( -41.10)
>DroSec_CAF1 5777 93 - 1
UGAUGCUCCUUCUGCUGCUGGCAGUUUGCCCCGUU------UUCUGUCAUUGCACUACACAUAGUAACUUCUACGGGUCCUGCGGAGGAGGAGCAGCAG
((.((((((((((.((((.(((.....)))((((.------....((.((((.........)))).))....)))).....)))))))))))))).)). ( -31.90)
>DroSim_CAF1 5913 93 - 1
UGAUGCUCCUUCUGCUGCUGGCAGUUUGCCCCGUU------UGCUGUCAUUGCACUGCACAUAGUAACUUCUACGGGUCCUGCGGAGGAGGAGCAGCAG
((.((((((((((.((((.(((.....)))(((((------((((((...(((...))).))))))).....)))).....)))))))))))))).)). ( -36.50)
>DroEre_CAF1 5761 90 - 1
UGAUGCUCCUUCUGCUGCUGGCAGUUUGCCCCGUU------UGCUGUCAUUGCACUGCACAUAGUAACU---GCGGGUCCUACGAAGGAGCAGCAGCAG
((.((((((((((((.....)))((..(.((((((------((((((...(((...))).)))))))..---))))).)..))))))))))).)).... ( -33.80)
>DroYak_CAF1 5808 76 - 1
UGAUGCUCCUUCUGCUGCUGGCAAUGUGCCCCGUU------UGCUGUCAUUGCACUGCACAUAGUA-----------------GGAGGAGGACCAGCAG
((.(.(((((((((((((..((((((.((......------.))...))))))...))....))))-----------------))))))).).)).... ( -28.10)
>DroPer_CAF1 6001 81 - 1
UGCUUUUGCUACUGUUGCUGGCAGCUUGCCCCUUGUUGCAGUCCUGUCAUUGCACUGCC------------------UCCAACACAGGAACAACAGCAA
((((.(((...((((((..(((((............((((((......)))))))))))------------------..))..))))...))).)))). ( -22.30)
>consensus
UGAUGCUCCUUCUGCUGCUGGCAGUUUGCCCCGUU______UGCUGUCAUUGCACUGCACAUAGUAACU___ACGGGUCCUGCGGAGGAGGAGCAGCAG
((.((((((((((.(((((((((((.................)))))))..))).(((.....))).................).)))))))))).)). (-17.45 = -18.68 +   1.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:43 2006