Locus 2863

Sequence ID X_DroMel_CAF1
Location 7,652,841 – 7,653,051
Length 210
Max. P 0.991063
window4693 window4694 window4695 window4696

overview

Window 3

Location 7,652,841 – 7,652,939
Length 98
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 91.70
Mean single sequence MFE -16.62
Consensus MFE -13.26
Energy contribution -13.66
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.80
SVM decision value 0.33
SVM RNA-class probability 0.693618
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7652841 98 + 22224390
UCGC--CACACACUUUUCACCUGCUGCAAGAUUUUCUUCUGCUCUGCUUUUCUCCGUUCUCUUGGCUGGCAAAUUGCCCAGCAACAACAACAGCCUCAAU
..((--................((.(((.((......)))))...))........(((......((((((.....).)))))......))).))...... ( -15.60)
>DroSec_CAF1 69054 98 + 1
CCGA--UGCACACUUUUCACCUGCUGCACGAUUUUCUUCUGCUCUGCUUUUCUCUGUUCUCUUGGCUGGCAAAUUGCCCAGCAACAACAACAGCCUCAAU
..((--.((.............((.(((.((......)))))...)).......((((......((((((.....).)))))......)))))).))... ( -19.20)
>DroSim_CAF1 56951 98 + 1
CCGC--UGCACACUUUUCACCUGCUGCAAGAUUUUCUUCUGCUCUGCUUUUCUCUGUUCUCUUGGCUGGCAAAUUGCCCAGCAACAACAACAGCCUCAAU
..((--((..............((.(((.((......)))))...)).......((((......((((((.....).)))))...)))).))))...... ( -19.00)
>DroEre_CAF1 74863 100 + 1
CCACCCCUCACACUUUCCACCUGCUGCAAGAUUUUCUUAUGCUCUGCUUUUCCCUGUUCUCUUGGCUGGCAAAUUGCCCAGCAACAAAAACAGCCUCAAU
......................((.(((((.....))..)))...))......(((((......((((((.....).)))))......)))))....... ( -16.00)
>DroYak_CAF1 74714 98 + 1
UCAC--CACACACUUUUCACCUGCUGCAAGAUUUUCCUCGGCUCCGCUUUUCUCCGUUCUCCUGGCUGGCAAAUUGCCCAGCAACAAAAACAGCCUCAAU
....--................((((............((....))..................((((((.....).)))))........))))...... ( -13.30)
>consensus
CCGC__CACACACUUUUCACCUGCUGCAAGAUUUUCUUCUGCUCUGCUUUUCUCUGUUCUCUUGGCUGGCAAAUUGCCCAGCAACAACAACAGCCUCAAU
......................(((((((((.........((...))............)))))((((((.....).)))))........))))...... (-13.26 = -13.66 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,652,879 – 7,652,979
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.31
Mean single sequence MFE -31.80
Consensus MFE -22.86
Energy contribution -23.08
Covariance contribution 0.22
Combinations/Pair 1.18
Mean z-score -2.16
Structure conservation index 0.72
SVM decision value 0.13
SVM RNA-class probability 0.598882
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7652879 100 - 22224390
GACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGA-------------------GGCUGUUGUUGUUGCUGGGCAAUUUGCCAGC-CAAGAGAACGGAGAAAAGCAGAGC
..(((.....)))((..((((((((((((.....)))))))))))-------------------).(((((.((...(((((........)))))-...)).)))))......))..... ( -28.90)
>DroSec_CAF1 69092 100 - 1
GACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGA-------------------GGCUGUUGUUGUUGCUGGGCAAUUUGCCAGC-CAAGAGAACAGAGAAAAGCAGAGC
..(((.....)))((..((((((((((((.....)))))))))))-------------------).(((((.((...(((((........)))))-...)).)))))......))..... ( -29.60)
>DroSim_CAF1 56989 100 - 1
GACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGA-------------------GGCUGUUGUUGUUGCUGGGCAAUUUGCCAGC-CAAGAGAACAGAGAAAAGCAGAGC
..(((.....)))((..((((((((((((.....)))))))))))-------------------).(((((.((...(((((........)))))-...)).)))))......))..... ( -29.60)
>DroEre_CAF1 74903 100 - 1
GACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGA-------------------GGCUGUUUUUGUUGCUGGGCAAUUUGCCAGC-CAAGAGAACAGGGAAAAGCAGAGC
..(((.....)))((..((((((((((((.....)))))))))))-------------------).((((((((...(((((........)))))-...))))))))......))..... ( -31.30)
>DroYak_CAF1 74752 100 - 1
GACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGA-------------------GGCUGUUUUUGUUGCUGGGCAAUUUGCCAGC-CAGGAGAACGGAGAAAAGCGGAGC
..(((.....)))((..((((((((((((.....)))))))))))-------------------).((((((((.(.(((((........)))))-.).))))))))......))..... ( -31.30)
>DroPer_CAF1 97553 114 - 1
AGUAGACUGGCUGGCAAUUCAAU-UGCUAACCAGUGGAAAAUUGCUAGCAUUUACACUGCUGUCUGCUGUCUUUGUUGUUGGGCAAUUUGCCAGAAUCAGCGAGCAG---AAAGCACA--
.(((((...((((((((((...(-..((....))..)..)))))))))).)))))..((((.((((((.....(((((...(((.....))).....))))))))))---).))))..-- ( -40.10)
>consensus
GACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGA___________________GGCUGUUGUUGUUGCUGGGCAAUUUGCCAGC_CAAGAGAACAGAGAAAAGCAGAGC
..(((.....)))((...(((((((((((.....))))))))))).....................(((((.((...(((((........)))))....)).)))))......))..... (-22.86 = -23.08 +   0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,652,918 – 7,653,018
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 95.80
Mean single sequence MFE -29.36
Consensus MFE -24.62
Energy contribution -25.26
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.42
Structure conservation index 0.84
SVM decision value 2.25
SVM RNA-class probability 0.991063
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7652918 100 - 22224390
AGUCGUUGUUUUUGCCAGUGUCAAAAGACCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGAGGCUGUUGUUGUUGCU
((((.......(((((.(.(((....))))......((((((...))))))))))).(((((((((((.....)))))))))))))))............ ( -27.90)
>DroSec_CAF1 69131 100 - 1
AGUCGUUGUUUUUGUCAGUGUCAAAAGACCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGAGGCUGUUGUUGUUGCU
.((((.((.((((((((.((((...........)))).)))))))).)).))))..((((((((((((.....))))))))))))((..........)). ( -28.40)
>DroSim_CAF1 57028 100 - 1
AGUCGUUGUUUUUGUCAGUGUCAAAAGACCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGAGGCUGUUGUUGUUGCU
.((((.((.((((((((.((((...........)))).)))))))).)).))))..((((((((((((.....))))))))))))((..........)). ( -28.40)
>DroEre_CAF1 74942 100 - 1
AGUCAGUGUUUUUGUCAGUGUGAAAGGAGCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGAGGCUGUUUUUGUUGCU
.(((((((.((((((((.(((.............))).)))))))).)))))))..((((((((((((.....))))))))))))((..........)). ( -31.72)
>DroYak_CAF1 74791 100 - 1
AGGCGUUGUUUUUGUCAGUGUGAAAAUAGCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGAGGCUGUUUUUGUUGCU
.((((.......))))((((..((((((((...(.(((((((...))))))).)..((((((((((((.....))))))))))))))))))))..).))) ( -30.40)
>consensus
AGUCGUUGUUUUUGUCAGUGUCAAAAGACCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAAAUUGAGGCUGUUGUUGUUGCU
.((((.((.((((((((.((((...........)))).)))))))).)).))))..((((((((((((.....))))))))))))((..........)). (-24.62 = -25.26 +   0.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,652,939 – 7,653,051
Length 112
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 84.78
Mean single sequence MFE -28.04
Consensus MFE -21.80
Energy contribution -22.04
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.24
Structure conservation index 0.78
SVM decision value 1.32
SVM RNA-class probability 0.941973
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7652939 112 - 22224390
AACAUUUA---UCCAGAUUUAAAUGGUAGAGA--UUUUAGUCGUUGUUUUUGCCAGUGUCAAAAGACCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAA
..((((((---........)))))).......--.....(((((((((((((.....(((....))))))))))))))))...(((((((((((......)))....)))))))).. ( -28.30)
>DroSec_CAF1 69152 112 - 1
CAUAUUUA---AACAGACUUAAAUGAUAGAGA--AUUUAGUCGUUGUUUUUGUCAGUGUCAAAAGACCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAA
........---(((.((((.((((........--)))))))))))...(((((((.((((...........)))).)))))))(((((((((((......)))....)))))))).. ( -29.20)
>DroSim_CAF1 57049 112 - 1
CAUAUUUA---AACAGACUUAAACGAUAGAGA--CUUUAGUCGUUGUUUUUGUCAGUGUCAAAAGACCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAA
........---..........((((((...((--(....)))))))))(((((((.((((...........)))).)))))))(((((((((((......)))....)))))))).. ( -28.20)
>DroEre_CAF1 74963 116 - 1
CAUACAUACGACACAGACUGGAAAACUAGAGAG-AUUUAGUCAGUGUUUUUGUCAGUGUGAAAGGAGCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAA
................(((((..(((.(((..(-(.((.(((((((.((((((((.(((.............))).)))))))).))))))))).))..))))))..)))))..... ( -30.52)
>DroYak_CAF1 74812 105 - 1
------------AUAAACUGAAAUCGUUGAGAGUAUUAAGGCGUUGUUUUUGUCAGUGUGAAAAUAGCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAA
------------.....(((....(.((((.....)))).)((((((((((((...(((....))))))))))))))).))).(((((((((((......)))....)))))))).. ( -24.00)
>consensus
CAUAUUUA___AACAGACUUAAAUGAUAGAGA__AUUUAGUCGUUGUUUUUGUCAGUGUCAAAAGACCAAAGAUAGUGACAGAGUCACUGGCAAUUCAAUUUGUUAACCAGUGGCAA
.......................................(((((((((((((...............)))))))))))))...(((((((((((......)))....)))))))).. (-21.80 = -22.04 +   0.24)

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 10:45:20 2006