Locus 215

Sequence ID 2R_DroMel_CAF1
Location 1,543,755 – 1,543,938
Length 183
Max. P 0.689393
window482 window483

overview

Window 2

Location 1,543,755 – 1,543,868
Length 113
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 88.78
Mean single sequence MFE -39.54
Consensus MFE -27.30
Energy contribution -28.66
Covariance contribution 1.36
Combinations/Pair 1.16
Mean z-score -1.95
Structure conservation index 0.69
SVM decision value 0.05
SVM RNA-class probability 0.557384
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1543755 113 + 20766785
CCACACACGUUAGAACAAAAUGCUGGCUCGCCGUGAGUCAGCGAG---GAACUAGUUCGCGGCCGAACCAAAACAUUGAACAGCUGAGUCAGCGCAGCGG-ACAGUUCGCACGGAA-U
((..................(((((((((.....)))))))))..---(((((.((((((.((.....(((....)))....((((...)))))).))))-)))))))....))..-. ( -36.20)
>DroSec_CAF1 4174 116 + 1
CCACUCACGUUAGAACAAAAUGCUGGCUCCCCGUGAGUCAGCGAGCGCGAACUAGUUCGCGGCCGAACCAAAACAUUGAACAGCUGAGUCAGCGCAGCGG-GCAGUUCGCACGGAA-U
((.(((..((....)).....((((((((.....))))))))))).(((((((.((((((.((.....(((....)))....((((...)))))).))))-)))))))))..))..-. ( -42.90)
>DroSim_CAF1 4180 117 + 1
CCACUCACGUUAGAACAAAAUGCUGGCUCCCCGUGAGUCAGCGAGCGCGAACUAGUUCGCGGCCGAACCAAAACAUUGAACAGCUGAGUCAGCGCAGCGCUGCCCGCUGCACGGAA-U
...(((..((....)).....((((((((.....)))))))))))((((((....)))))).(((.................((((...))))((((((.....)))))).)))..-. ( -41.90)
>DroEre_CAF1 5789 114 + 1
CCACUCACGUUAGAACAAAAUGCUAGCUCCCCGUGAGUCAGCGGGGGCGAACUAGUUCGCUGGCGAACCAAAACAUUGAACAGCUGAGUCAGCG--GCGG-GCAGUUCGCACAAGA-A
........(((((.........))))).((((((......))))))(((((((.(((((((((....)).............((((...)))))--))))-)))))))))......-. ( -40.50)
>DroYak_CAF1 6125 117 + 1
CCACUCACGUUAGAACAAAAUGCUAGCUCGCCGUGAGUUAGUGAAGGCGAACUAGUUCGCGGCCGAACCAAAACAUUGAACAGCUGAGUCAGCGCUGCGA-GCAGAUCGCACAAAAUA
.....................((((((((.....))))))))....((((.((.(((((((((.....(((....)))....((((...)))))))))))-)))).))))........ ( -36.20)
>consensus
CCACUCACGUUAGAACAAAAUGCUGGCUCCCCGUGAGUCAGCGAGCGCGAACUAGUUCGCGGCCGAACCAAAACAUUGAACAGCUGAGUCAGCGCAGCGG_GCAGUUCGCACGGAA_U
....................(((((((((.....)))))))))...(((((((.((((((.((.....(((....)))....((((...)))))).)))).)))))))))........ (-27.30 = -28.66 +   1.36) 

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 1,543,832 – 1,543,938
Length 106
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 79.36
Mean single sequence MFE -36.04
Consensus MFE -23.70
Energy contribution -24.62
Covariance contribution 0.92
Combinations/Pair 1.10
Mean z-score -1.71
Structure conservation index 0.66
SVM decision value 0.32
SVM RNA-class probability 0.689393
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1543832 106 + 20766785
CAGCUGAGUCAGCGCAGCGG-ACAGUUCGCACGGAA-UGAGCACCUACCUGUUCGGAUUCGGCGUGGGACAGGAAACUGCCCCAAUUCCCAUG----------ACCAACCAAAGUCAG
..((((((((.(((.(((..-...))))))......-((((((......)))))))))))))).((((.(((....))).)))).......((----------((........)))). ( -38.60)
>DroSec_CAF1 4254 112 + 1
CAGCUGAGUCAGCGCAGCGG-GCAGUUCGCACGGAA-UGAGCAC----CUGUUCGACUUCGGCGUGGGACAGGAAACUGCCCCAAUUCCCAUGAAUCCCCACGACCAACCAAAGCCAG
..((((((((.(((.(((..-...))))))......-.((((..----..))))))))).((((((((.(((....))).....((((....)))).)))))).))......)))... ( -36.40)
>DroSim_CAF1 4260 113 + 1
CAGCUGAGUCAGCGCAGCGCUGCCCGCUGCACGGAA-UGAGCAC----CUGUUCGACUUCGGCGCGGGACAGGAAACUGCCCCAAUUCCCAUGAAUCCCCAUGUCCAACCAAAGCCAG
..((((((((.(.((((((.....)))))).)....-.((((..----..))))))).)))))(((((.(((....))).)))......((((......))))..........))... ( -42.00)
>DroEre_CAF1 5869 97 + 1
CAGCUGAGUCAGCG--GCGG-GCAGUUCGCACAAGA-AGAGCAC----CUGU------UCGGCGUGGGACAGGAGACUGCCCCAAUUCCCACGAAA------GGACAACCAAA-CCAA
..((((...))))(--(.((-((..(((......))-)..)).)----)(((------((..((((((((((....))).......)))))))...------))))).))...-.... ( -33.91)
>DroYak_CAF1 6205 100 + 1
CAGCUGAGUCAGCGCUGCGA-GCAGAUCGCACAAAAUAAAGCAC----CUGU------UCGGCGUGGGACAGGAAACUGCCCCAAUUCCCAUGAAU------GUACAACCAAA-CCAG
..((((((.(((.(((((((-.....)))).........)))..----))))------))))).((((.(((....))).))))((((....))))------...........-.... ( -29.30)
>consensus
CAGCUGAGUCAGCGCAGCGG_GCAGUUCGCACGGAA_UGAGCAC____CUGUUCG__UUCGGCGUGGGACAGGAAACUGCCCCAAUUCCCAUGAAU______GACCAACCAAAGCCAG
..(((((.........((((......))))........(((((......)))))....))))).((((.(((....))).)))).................................. (-23.70 = -24.62 +   0.92) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:39 2006