Locus 6575

Sequence ID X_DroMel_CAF1
Location 16,422,651 – 16,422,851
Length 200
Max. P 0.992395
window10741 window10742 window10743 window10744 window10745

overview

Window 1

Location 16,422,651 – 16,422,771
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -46.12
Consensus MFE -42.70
Energy contribution -43.08
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.93
SVM decision value 0.63
SVM RNA-class probability 0.804993
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16422651 120 - 22224390
CAGUCCCUGGUUGCCCGACCAGCUACUCUCAGCUGGCCACAGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUGGUGCUAAAGCACAUGCCCACGGUGGCCACCUCCAAUUGGC
.(((..((((((....))))))..)))...((.(((((((...((((((......))))))(((((.((.(.....).))((((....)))))))))....))))))).))......... ( -41.50)
>DroSec_CAF1 43362 120 - 1
CAGUCCCUGGUUGCCCGACCAGCUGCUCUCAGCUGGCCACAGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUGGUGCUGAAGCACAUGCCCACGGUGGCCACCUCCAAUUGGC
.(((..((((((....))))))..)))...((.(((((((..(((((((......)))))))((.((((((((.......))))))))))...........))))))).))......... ( -47.40)
>DroSim_CAF1 39638 120 - 1
CAGUCCCUGGUUGCCCGACCAGCUGCUCUCAGCUGGCCACAGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUGGUGCUGAAGCACAUGCCCACGGUGGCCACCUCCAAUUGGC
.(((..((((((....))))))..)))...((.(((((((..(((((((......)))))))((.((((((((.......))))))))))...........))))))).))......... ( -47.40)
>DroYak_CAF1 40793 120 - 1
CCGUCCCUGGUUACCCGACCAGCUGCCCUCAGCUGAUCACGGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUGGUGCUGAAGCACAUGCCCACGGUAGCCACCUCCAACUGGC
.......((((((((.((.((((((....)))))).))..(((((((((......)))))).((.((((((((.......))))))))))....)))...))))))))((.......)). ( -48.20)
>consensus
CAGUCCCUGGUUGCCCGACCAGCUGCUCUCAGCUGGCCACAGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUGGUGCUGAAGCACAUGCCCACGGUGGCCACCUCCAAUUGGC
.......((((((((.(.(((((((....))))))).)....(((((((......)))))))((.((((((((.......))))))))))..........))))))))((.......)). (-42.70 = -43.08 +   0.37)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,422,691 – 16,422,811
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.03
Mean single sequence MFE -45.95
Consensus MFE -43.95
Energy contribution -43.45
Covariance contribution -0.50
Combinations/Pair 1.19
Mean z-score -2.45
Structure conservation index 0.96
SVM decision value 2.33
SVM RNA-class probability 0.992395
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16422691 120 + 22224390
CAUCUUUGCGCUGAAUGCCAUCCAGGAGCAACUGGACGCUGUGGCCAGCUGAGAGUAGCUGGUCGGGCAACCAGGGACUGGAGCCUUGAUUGCCAAGCUCUAAGACACCAACAUUUAAUU
..((((.(.(((....((..(((((......))))).))..((((((((((....))))))))))(((((.(((((.(....)))))).))))).))).).))))............... ( -42.80)
>DroSec_CAF1 43402 119 + 1
CAUCUUUGCGCUGAAUGCCAUCCAGGAGCAACUGGACGCUGUGGCCAGCUGAGAGCAGCUGGUCGGGCAACCAGGGACUGGAGCCUUGAUUGCCCAGCUCUAAGACACC-ACAUUUAAUU
..((((.(.(((....((..(((((......))))).))...(((((((((....)))))))))((((((.(((((.(....)))))).))))))))).).))))....-.......... ( -48.30)
>DroSim_CAF1 39678 119 + 1
CAUCUUUGCGCUGAAUGCCAUCCAGGAGCAACUGGACGCUGUGGCCAGCUGAGAGCAGCUGGUCGGGCAACCAGGGACUGGAGCCUUGAUUGCCCAGCUCUAAGACACC-ACAUUUAAUU
..((((.(.(((....((..(((((......))))).))...(((((((((....)))))))))((((((.(((((.(....)))))).))))))))).).))))....-.......... ( -48.30)
>DroYak_CAF1 40833 118 + 1
CAUCUUUGCGCUGAAUGCCAUCCAGGAGCAACUGGACGCCGUGAUCAGCUGAGGGCAGCUGGUCGGGUAACCAGGGACGGGAGCCCUGAUUGCCUAGAUCUAAAGCACU--CAAUUAAUU
.........((((((((.(.(((((......))))).).)))..)))))((((.((....((((((((((.(((((.(....)))))).)))))).))))....)).))--))....... ( -44.40)
>consensus
CAUCUUUGCGCUGAAUGCCAUCCAGGAGCAACUGGACGCUGUGGCCAGCUGAGAGCAGCUGGUCGGGCAACCAGGGACUGGAGCCUUGAUUGCCCAGCUCUAAGACACC_ACAUUUAAUU
..((((.(.(((....((..(((((......))))).))...(((((((((....)))))))))((((((.(((((.(....)))))).))))))))).).))))............... (-43.95 = -43.45 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,422,691 – 16,422,811
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.03
Mean single sequence MFE -44.20
Consensus MFE -36.78
Energy contribution -37.77
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -2.01
Structure conservation index 0.83
SVM decision value 0.76
SVM RNA-class probability 0.844175
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16422691 120 - 22224390
AAUUAAAUGUUGGUGUCUUAGAGCUUGGCAAUCAAGGCUCCAGUCCCUGGUUGCCCGACCAGCUACUCUCAGCUGGCCACAGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUG
........(((((((((.....(((.((((((((.(((....).)).)))))))).(.((((((......)))))).)..)))((((((......)))))))))).)))))......... ( -41.70)
>DroSec_CAF1 43402 119 - 1
AAUUAAAUGU-GGUGUCUUAGAGCUGGGCAAUCAAGGCUCCAGUCCCUGGUUGCCCGACCAGCUGCUCUCAGCUGGCCACAGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUG
.......(((-((((((.....((((((((((((.(((....).)).)))))))))(.(((((((....))))))).)..)))((((((......)))))))))))....))))...... ( -46.50)
>DroSim_CAF1 39678 119 - 1
AAUUAAAUGU-GGUGUCUUAGAGCUGGGCAAUCAAGGCUCCAGUCCCUGGUUGCCCGACCAGCUGCUCUCAGCUGGCCACAGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUG
.......(((-((((((.....((((((((((((.(((....).)).)))))))))(.(((((((....))))))).)..)))((((((......)))))))))))....))))...... ( -46.50)
>DroYak_CAF1 40833 118 - 1
AAUUAAUUG--AGUGCUUUAGAUCUAGGCAAUCAGGGCUCCCGUCCCUGGUUACCCGACCAGCUGCCCUCAGCUGAUCACGGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUG
......(((--(((((..........((.(((((((((....).)))))))).)).((.((((((....)))))).))....(((((((......))))))))))))))).......... ( -42.10)
>consensus
AAUUAAAUGU_GGUGUCUUAGAGCUGGGCAAUCAAGGCUCCAGUCCCUGGUUGCCCGACCAGCUGCUCUCAGCUGGCCACAGCGUCCAGUUGCUCCUGGAUGGCAUUCAGCGCAAAGAUG
.......(((.((((((.....((((((((((((.(((....).)).)))))))))(.(((((((....))))))).)..)))((((((......))))))))))))....)))...... (-36.78 = -37.77 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,422,731 – 16,422,851
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.07
Mean single sequence MFE -36.64
Consensus MFE -34.58
Energy contribution -33.83
Covariance contribution -0.75
Combinations/Pair 1.22
Mean z-score -2.17
Structure conservation index 0.94
SVM decision value 1.95
SVM RNA-class probability 0.983603
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16422731 120 + 22224390
GUGGCCAGCUGAGAGUAGCUGGUCGGGCAACCAGGGACUGGAGCCUUGAUUGCCAAGCUCUAAGACACCAACAUUUAAUUAUAAGAUGCACGUUGUUGAACAAUUUUUUGAGUAAUAAAC
.((((((((((....))))))))))(((((.(((((.(....)))))).)))))..((((.((((...(((((....(((....)))......)))))......)))).))))....... ( -34.80)
>DroSec_CAF1 43442 119 + 1
GUGGCCAGCUGAGAGCAGCUGGUCGGGCAACCAGGGACUGGAGCCUUGAUUGCCCAGCUCUAAGACACC-ACAUUUAAUUAUAAUAUGCACGUUGUUGAACAAUUUUUUGAGUAAUAAAC
(((((((((((....)))))))..((((((.(((((.(....)))))).))))))............))-))....................((((((..(((....)))..)))))).. ( -38.20)
>DroSim_CAF1 39718 119 + 1
GUGGCCAGCUGAGAGCAGCUGGUCGGGCAACCAGGGACUGGAGCCUUGAUUGCCCAGCUCUAAGACACC-ACAUUUAAUUAUAAUAUGCACGUUGUUGAACAAUUUUUUGAGUAAUAAAC
(((((((((((....)))))))..((((((.(((((.(....)))))).))))))............))-))....................((((((..(((....)))..)))))).. ( -38.20)
>DroYak_CAF1 40873 118 + 1
GUGAUCAGCUGAGGGCAGCUGGUCGGGUAACCAGGGACGGGAGCCCUGAUUGCCUAGAUCUAAAGCACU--CAAUUAAUUAUUAAAUGCACGUUGUUGAACAAUAUUUUUCGUAAUAAAC
(((((((((((....)))))))))((((((.(((((.(....)))))).)))))).........))...--.......((((((.......((((.....))))........)))))).. ( -35.36)
>consensus
GUGGCCAGCUGAGAGCAGCUGGUCGGGCAACCAGGGACUGGAGCCUUGAUUGCCCAGCUCUAAGACACC_ACAUUUAAUUAUAAUAUGCACGUUGUUGAACAAUUUUUUGAGUAAUAAAC
(((((((((((....)))))))))((((((.(((((.(....)))))).)))))).........))..........................((((((..(((....)))..)))))).. (-34.58 = -33.83 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,422,731 – 16,422,851
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.07
Mean single sequence MFE -32.10
Consensus MFE -23.16
Energy contribution -24.73
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -1.80
Structure conservation index 0.72
SVM decision value 0.00
SVM RNA-class probability 0.535773
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16422731 120 - 22224390
GUUUAUUACUCAAAAAAUUGUUCAACAACGUGCAUCUUAUAAUUAAAUGUUGGUGUCUUAGAGCUUGGCAAUCAAGGCUCCAGUCCCUGGUUGCCCGACCAGCUACUCUCAGCUGGCCAC
...................((((.(((....((((.(((....)))))))...)))....))))..((((((((.(((....).)).)))))))).(.((((((......)))))).).. ( -28.10)
>DroSec_CAF1 43442 119 - 1
GUUUAUUACUCAAAAAAUUGUUCAACAACGUGCAUAUUAUAAUUAAAUGU-GGUGUCUUAGAGCUGGGCAAUCAAGGCUCCAGUCCCUGGUUGCCCGACCAGCUGCUCUCAGCUGGCCAC
........(((......(((.....)))....((((((.......)))))-)........)))..(((((((((.(((....).)).)))))))))(.(((((((....))))))).).. ( -34.10)
>DroSim_CAF1 39718 119 - 1
GUUUAUUACUCAAAAAAUUGUUCAACAACGUGCAUAUUAUAAUUAAAUGU-GGUGUCUUAGAGCUGGGCAAUCAAGGCUCCAGUCCCUGGUUGCCCGACCAGCUGCUCUCAGCUGGCCAC
........(((......(((.....)))....((((((.......)))))-)........)))..(((((((((.(((....).)).)))))))))(.(((((((....))))))).).. ( -34.10)
>DroYak_CAF1 40873 118 - 1
GUUUAUUACGAAAAAUAUUGUUCAACAACGUGCAUUUAAUAAUUAAUUG--AGUGCUUUAGAUCUAGGCAAUCAGGGCUCCCGUCCCUGGUUACCCGACCAGCUGCCCUCAGCUGAUCAC
(((....((((......)))).....)))..(((((((((.....))))--)))))..........((.(((((((((....).)))))))).)).((.((((((....)))))).)).. ( -32.10)
>consensus
GUUUAUUACUCAAAAAAUUGUUCAACAACGUGCAUAUUAUAAUUAAAUGU_GGUGUCUUAGAGCUGGGCAAUCAAGGCUCCAGUCCCUGGUUGCCCGACCAGCUGCUCUCAGCUGGCCAC
...................((((........((((...(((......)))..))))....)))).(((((((((.(((....).)).)))))))))(.(((((((....))))))).).. (-23.16 = -24.73 +   1.56)

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 12:17:22 2006