Locus 4018

Sequence ID 3L_DroMel_CAF1
Location 11,720,064 – 11,720,216
Length 152
Max. P 0.898652
window6258 window6259 window6260

overview

Window 8

Location 11,720,064 – 11,720,155
Length 91
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 88.58
Mean single sequence MFE -40.90
Consensus MFE -31.24
Energy contribution -32.80
Covariance contribution 1.56
Combinations/Pair 1.04
Mean z-score -2.25
Structure conservation index 0.76
SVM decision value 1.00
SVM RNA-class probability 0.898652
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11720064 91 + 23771897
AGAGCUGAACUGGGCGUAAAGUGGGUGGUGGCAAGAGGGCGGGGCGUGGCGUGUUUCCGCCCACCACCUCCUUUGCCACCUGCACAAAUUG
...(((......))).....(((.(.(((((((.(((((.((((.(.((((......))))).)).))))))))))))))).)))...... ( -38.20)
>DroSec_CAF1 32963 91 + 1
AGAGCUGAACUGGGCGUAUUGUGGGUGGUGGCCAGGGGGCGGGGCGUGGCGUGUUGCCGCCCACCACCUCCUUUGCCACCUGCACAAAUUG
...(((......)))...(((((.(.((((((.((((((.((((.(((((.....))))))).)).))))))..))))))).))))).... ( -45.20)
>DroEre_CAF1 29244 87 + 1
AGAGCUGAACUGGGCGUAUAGUGGGUGGUGGAGAGCG---UGGGCGUGGCGUGGGGCCGCCC-CCACCUCCUUUGCCACCUGCACAAAUUG
...(((......))).....(..(((((..(((((.(---((((.(((((.....))))).)-)))))).)))..)))))..)........ ( -44.00)
>DroYak_CAF1 29705 86 + 1
AGAGCUGAGCUGGGCGUAAAGUGGGUGGUGAAAAG-----GGGGCGUGGCAUGGUGCCGCCCACCACCUCCUUUGCCACCUGCACAAAUUG
.....((.((.((..((((((..(((((((....(-----(.((((........)))).)))))))))..))))))..)).)).))..... ( -36.20)
>consensus
AGAGCUGAACUGGGCGUAAAGUGGGUGGUGGAAAG_G___GGGGCGUGGCGUGGUGCCGCCCACCACCUCCUUUGCCACCUGCACAAAUUG
...(((......))).....(..(((((..(..((.(((.((((.(((((.....))))))).)).))).)))..)))))..)........ (-31.24 = -32.80 +   1.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,720,064 – 11,720,155
Length 91
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 88.58
Mean single sequence MFE -35.30
Consensus MFE -26.14
Energy contribution -27.20
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -2.39
Structure conservation index 0.74
SVM decision value 0.98
SVM RNA-class probability 0.893649
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11720064 91 - 23771897
CAAUUUGUGCAGGUGGCAAAGGAGGUGGUGGGCGGAAACACGCCACGCCCCGCCCUCUUGCCACCACCCACUUUACGCCCAGUUCAGCUCU
......(((..(((((((((((.((.((((((((......)))).))))))..))).))))))))...))).....((........))... ( -38.30)
>DroSec_CAF1 32963 91 - 1
CAAUUUGUGCAGGUGGCAAAGGAGGUGGUGGGCGGCAACACGCCACGCCCCGCCCCCUGGCCACCACCCACAAUACGCCCAGUUCAGCUCU
....(((((..((((((..(((.(((((.(((.(((.....))).).))))))).))).))))))...)))))...((........))... ( -38.30)
>DroEre_CAF1 29244 87 - 1
CAAUUUGUGCAGGUGGCAAAGGAGGUGG-GGGCGGCCCCACGCCACGCCCA---CGCUCUCCACCACCCACUAUACGCCCAGUUCAGCUCU
......(((..(((((....((((((((-(.(.(((.....))).).))))---).))))...)))))))).....((........))... ( -31.60)
>DroYak_CAF1 29705 86 - 1
CAAUUUGUGCAGGUGGCAAAGGAGGUGGUGGGCGGCACCAUGCCACGCCCC-----CUUUUCACCACCCACUUUACGCCCAGCUCAGCUCU
....(((.((.((((..((((..(((((((((((((.....)))..)))).-----......))))))..)))).))))..)).))).... ( -33.01)
>consensus
CAAUUUGUGCAGGUGGCAAAGGAGGUGGUGGGCGGCAACACGCCACGCCCC___C_CUUGCCACCACCCACUAUACGCCCAGUUCAGCUCU
....(((.((.((((..((((..(((((((((((((.....)))..))))............))))))..)))).))))..)).))).... (-26.14 = -27.20 +   1.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,720,116 – 11,720,216
Length 100
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 87.95
Mean single sequence MFE -33.00
Consensus MFE -27.06
Energy contribution -27.34
Covariance contribution 0.28
Combinations/Pair 1.19
Mean z-score -1.91
Structure conservation index 0.82
SVM decision value 0.17
SVM RNA-class probability 0.617160
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11720116 100 - 23771897
CCGCCAAAAAUUUCCACUACCGAAAAGGCCACGGAAAAUUACUUACCA-AGUGGCUUGCGGCCAAUUUGUGCAGGUGGCAAAGG-AGGUGGUGGGCGGAAAC
(((((........(((((.((....(((((((((.((.....)).)).-.)))))))((.(((..........))).))...))-.)))))..))))).... ( -35.30)
>DroSec_CAF1 33015 100 - 1
CCGCCAAAAAUUUCCACUACCGAAAAGGCCACGGAAAAUUACUUACCA-AGUGGCUUGCGGCCAAUUUGUGCAGGUGGCAAAGG-AGGUGGUGGGCGGCAAC
(((((........(((((.((....(((((((((.((.....)).)).-.)))))))((.(((..........))).))...))-.)))))..))))).... ( -34.60)
>DroSim_CAF1 27665 101 - 1
CCGCCAAAAAUUUCCACUACCGAAAAGGCCACGGAAAAUUACUUACCA-AGUGGCUUGCGGCCAAUUUGUGCAGGUGGCAAAGGAAGGUGGUGGGCNNNNNN
((((((....(((((.....((...(((((((((.((.....)).)).-.))))))).))((((.(((....)))))))...))))).))))))........ ( -32.40)
>DroEre_CAF1 29293 99 - 1
CCUCCAAAAAUUUCUACUAACGAAAAGGCCACGGAAAAUUACUUACCA-AGUGGCUUGCGGCCAAUUUGUGCAGGUGGCAAAGG-AGGUGG-GGGCGGCCCC
(((((...............((...(((((((((.((.....)).)).-.))))))).))((((.(((....)))))))...))-))).((-((....)))) ( -31.40)
>DroYak_CAF1 29752 100 - 1
CCUCCAAAAAUUUCCACUACCGAAAAGGCCACGGAAAAUUACUUACCA-AGUGGCUUGCGGCCAAUUUGUGCAGGUGGCAAAGG-AGGUGGUGGGCGGCACC
............(((((((((....(((((((((.((.....)).)).-.)))))))((.(((..........))).)).....-.)))))))))....... ( -31.50)
>DroAna_CAF1 25677 95 - 1
----UAAAAAUUUCCACCAACUGUACGGCCGUGGAAAAUUACUCACCAAAGUGGCUUGCGGCCAAUUUG-GCAGGUGGCUUAGA-A-GUGGUGGGUGGGCCG
----......(((((((...((....))..))))))).((((((((((((((.((((((.(......).-)))))).))))...-.-.)))))))))).... ( -32.80)
>consensus
CCGCCAAAAAUUUCCACUACCGAAAAGGCCACGGAAAAUUACUUACCA_AGUGGCUUGCGGCCAAUUUGUGCAGGUGGCAAAGG_AGGUGGUGGGCGGCACC
............(((((((((....(((((((..................)))))))((.(((..........))).)).......)))))))))....... (-27.06 = -27.34 +   0.28)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:32 2006