Locus 117

Sequence ID 2L_DroMel_CAF1
Location 377,862 – 378,136
Length 274
Max. P 0.994870
window176 window177 window178

overview

Window 6

Location 377,862 – 377,982
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.42
Mean single sequence MFE -41.28
Consensus MFE -38.50
Energy contribution -38.58
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.40
Structure conservation index 0.93
SVM decision value 1.06
SVM RNA-class probability 0.907977
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 377862 120 + 22407834
CUUUCCCAUAGGCCGAACCGCCAGAAAGAGGCGGAGUCCGCCUCCCGGCCACCUGCCGCCUCACCUGCGACACCUGCGACGAUCGAUCGACAUGCUCCGAUCGCAUCGCUCCCUCUCGCU
..........(((......))).....(((((((((...(((....)))...)).)))))))....((((.....((((....((((((........))))))..))))......)))). ( -41.50)
>DroSec_CAF1 45494 120 + 1
CCUUCCCAUAGGCCGAACCGCCAGAAAGAGGCGGAGUCCGCCUCCCGGCCACCUGCCGCCUCACCUGCGACACCUGCGACGAUCGAUCGACACGCUCUGAUCGCAUCGCUCCCUCUCGCU
..........(((......))).....(((((((((...(((....)))...)).)))))))....((((.....(((((((((((.((...)).)).)))))..))))......)))). ( -40.20)
>DroSim_CAF1 46137 120 + 1
CCUUCCCAUAGGCCGAACCGCCAGAAAGAGGCGGAGUCCGCCUCCCGGCCACCUGCCGCAUCACGUGCGACACCUGCGACGAUCGAUCGACACGCUCCGAUCGCAUCGCUCCCUCUCGCU
..........(((((...(....)...(((((((...))))))).)))))...((.(((((...))))).))...((((((((((((((........)))))).)))).......)))). ( -41.61)
>DroEre_CAF1 52481 120 + 1
CGUUCCCAUAGGCCGAACCGCCAGAAAGAGGCGGAGUCCGCCUCCCGACCACCUGCCGCCUCACCUGCGACACCUGCGGCGAUCGAUCGACACGCUCCGAUCGCAUCGCUCCCUCUCGCU
..........(((......))).....(((((((.(((........)))......)))))))....((((.....(.((((((((((((........)))))).)))))).)...)))). ( -40.10)
>DroYak_CAF1 46631 120 + 1
CCUUCCCAUAGGCCGAAUCGCCAGAAGGAGGCGGAGUCCGCCGCCCGGCCACCUGCCGCCUCACCUGCGACACCUGCGACGAUCGAUCGACACGCUCCGAUCGCAUCGCUCCCUCUCGCU
(((......))).....((((.((...(((((((((...(((....)))...)).)))))))..)))))).....((((((((((((((........)))))).)))).......)))). ( -43.01)
>consensus
CCUUCCCAUAGGCCGAACCGCCAGAAAGAGGCGGAGUCCGCCUCCCGGCCACCUGCCGCCUCACCUGCGACACCUGCGACGAUCGAUCGACACGCUCCGAUCGCAUCGCUCCCUCUCGCU
..........(((......))).....(((((((((...(((....)))...)).)))))))....((((.....((((....((((((........))))))..))))......)))). (-38.50 = -38.58 +   0.08) 

alignment

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secondary structure

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dotplot

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Window 7

Location 377,902 – 378,022
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.08
Mean single sequence MFE -42.16
Consensus MFE -36.52
Energy contribution -36.80
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -2.14
Structure conservation index 0.87
SVM decision value 2.52
SVM RNA-class probability 0.994870
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 377902 120 + 22407834
CCUCCCGGCCACCUGCCGCCUCACCUGCGACACCUGCGACGAUCGAUCGACAUGCUCCGAUCGCAUCGCUCCCUCUCGCUCUGCGGCACUACGAAACACUAAAAACACUGGGAGGCCAGA
(((((((((.....)))(((.((...((((.....((((....((((((........))))))..))))......))))..)).)))......................))))))..... ( -40.50)
>DroSec_CAF1 45534 120 + 1
CCUCCCGGCCACCUGCCGCCUCACCUGCGACACCUGCGACGAUCGAUCGACACGCUCUGAUCGCAUCGCUCCCUCUCGCUCUGCGGCACUACGAAAGACUAAAAACACUGGGAGGCCAGA
((((((((.....((((((.......((((.....(((((((((((.((...)).)).)))))..))))......))))...))))))...(....)..........))))))))..... ( -41.60)
>DroSim_CAF1 46177 120 + 1
CCUCCCGGCCACCUGCCGCAUCACGUGCGACACCUGCGACGAUCGAUCGACACGCUCCGAUCGCAUCGCUCCCUCUCGCUCUGCAGCACUACGAAACACUAAAAACACUGGGAGGCCAGA
(((((((((.....))).......((((..((...((((((((((((((........)))))).)))).......))))..))..))))....................))))))..... ( -39.41)
>DroEre_CAF1 52521 120 + 1
CCUCCCGACCACCUGCCGCCUCACCUGCGACACCUGCGGCGAUCGAUCGACACGCUCCGAUCGCAUCGCUCCCUCUCGCUCUGCGGCACUAGGAAGCACUGGAAGCACUGGGAGGCCAGA
(((((((......((((((.......((((.....(.((((((((((((........)))))).)))))).)...))))...))))))((((......))))......)))))))..... ( -46.40)
>DroYak_CAF1 46671 120 + 1
CCGCCCGGCCACCUGCCGCCUCACCUGCGACACCUGCGACGAUCGAUCGACACGCUCCGAUCGCAUCGCUCCCUCUCGCUCUGCGGCACUAGGAAGCAGUUAAAACGCUGGGAGGCCAGA
......(((.....)))(((((.((.(((....((((((((((((((((........)))))).)))).))(((...(((....)))...)))..))))......))).))))))).... ( -42.90)
>consensus
CCUCCCGGCCACCUGCCGCCUCACCUGCGACACCUGCGACGAUCGAUCGACACGCUCCGAUCGCAUCGCUCCCUCUCGCUCUGCGGCACUACGAAACACUAAAAACACUGGGAGGCCAGA
(((((((((.....)))(((.((...((((.....((((....((((((........))))))..))))......))))..)).)))......................))))))..... (-36.52 = -36.80 +   0.28) 

alignment

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secondary structure

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dotplot

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Window 8

Location 378,022 – 378,136
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.53
Mean single sequence MFE -31.20
Consensus MFE -27.58
Energy contribution -28.02
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.88
SVM decision value 1.67
SVM RNA-class probability 0.971412
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 378022 114 + 22407834
AAACCACUCUCGCAACAUUGGAAAACAACAACUCCAACCGGUUGUUGU------UUCAGACCCACCAGAGUUUUCACCUGCGCGCCAACUGCUCACCGUGUAGUUUGCUGCCGGCUCUGG
..................(((.(((((((((((......)))))))))------)).....)))((((((......((.(((.((.((((((.......)))))).))))).)))))))) ( -33.30)
>DroSec_CAF1 45654 114 + 1
AAACCACUCUCGCACCAUCGGAAAACAACAACUCCAACCGGUUGUUGU------UUCAGACCCACCAGAGUUUUCACCUGCGCGCCAACUGCUCACCGUGUAGUUUGCUGCCGGCUCUGG
.................((.((((.((((((((......)))))))))------))).))....((((((......((.(((.((.((((((.......)))))).))))).)))))))) ( -33.30)
>DroSim_CAF1 46297 114 + 1
AAACCACUCUCGCAACAUCGGAAAACAACAACUCCAACCGGUUGUUGU------UUCAGACCCACCAGAGUUUUCACCUGCGCGCCAACUGCUCACCGUGUAGUUUGCUGCCGGCUCUGG
.................((.((((.((((((((......)))))))))------))).))....((((((......((.(((.((.((((((.......)))))).))))).)))))))) ( -33.30)
>DroEre_CAF1 52641 114 + 1
AAACCACUCUCGCAACAUCGGAAAACAACAACUCCAACCGGUUGUUGU------CUCAGACCCACCAUACUUUUCACCUGCGCGCCAACUGCUCACCGUGUAGUUUGCUGCCGGCUCUGG
..................((((..(((((((((......)))))))))------......................((.(((.((.((((((.......)))))).))))).)).)))). ( -26.40)
>DroYak_CAF1 46791 120 + 1
AAACCACUCUCGCAACAUCGGAAAACAACAACUCCAACCGGUUGUUGUCGUCGCCUCAGACCCACCAGACUUUUCACCUGCGCGCCAAUUGCUCACCGUGUAGUUUGCUGCCGGCUCUGG
...................((...(((((((((......))))))))).(((......))))).(((((.........((.(((.....))).))(((.((((....))))))).))))) ( -29.70)
>consensus
AAACCACUCUCGCAACAUCGGAAAACAACAACUCCAACCGGUUGUUGU______UUCAGACCCACCAGAGUUUUCACCUGCGCGCCAACUGCUCACCGUGUAGUUUGCUGCCGGCUCUGG
........................(((((((((......)))))))))................((((((......((.(((.((.((((((.......)))))).))))).)))))))) (-27.58 = -28.02 +   0.44) 

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 09:26:21 2006