Locus 103

Sequence ID 2R_DroMel_CAF1
Location 1,348,563 – 1,348,843
Length 280
Max. P 0.933784
window214 window215 window216 window217

overview

Window 4

Location 1,348,563 – 1,348,683
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.00
Mean single sequence MFE -37.98
Consensus MFE -28.18
Energy contribution -29.30
Covariance contribution 1.12
Combinations/Pair 1.14
Mean z-score -1.80
Structure conservation index 0.74
SVM decision value 0.36
SVM RNA-class probability 0.704340
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1348563 120 + 20766785
CGAGUAGUAGUGUGUGCACUCGUUCGCCCGCACGAGUUUUCUUUGCGCUGCUCCUUUGAUAAAUGCGCAUAAUUUCAGUAGGUUUUCCUGGAGUAGUGAGGAAAACUUGUCCGUGUGCGC
(((((.(((.....))))))))..((((((.(((((((((((...(((((((((.((((...............)))).(((....)))))))))))).))))))))))).)).).))). ( -41.96)
>DroSec_CAF1 66867 110 + 1
CGAGUGGUAGUGUGUGCGCUCGUUCGC----------UUUCUUUGCGCUGCUCCUUUGAUAAAUGCGCAUAAUUUCAGUAGGUUUUCCUGGAGUAGCGAGGAAAACUUGUCCGUGUGCGC
.(((..((((((((.(((......)))----------......))))))))..)))........(((((((.......(((((((((((.(.....).)))))))))))....))))))) ( -35.90)
>DroSim_CAF1 45002 110 + 1
CGAGCAGUAGUGUGUGCGCUCGUUCGC----------UUUCUUUGCGCUGCUCCUUUGAUAAAUGCGCAUAAUUUCAGUAGGUUUUCCUGGAGUAGCGAGGAAAACUUGUCCGUGUGCGC
.(((((((((((....)))).....((----------.......)))))))))...........(((((((.......(((((((((((.(.....).)))))))))))....))))))) ( -37.90)
>DroEre_CAF1 47441 115 + 1
-----AGUAGUGUGUGCGCUCGCUCGCCCGCACGAGUUUUCUUUGCGCUGCUCCUUUGAUAAAUGCGCAUAAUUUCAGUAGGUUUUCCUGGAGUAGCGAAGGAAACUUCUCCUUGUGUGC
-----......(((.((....)).))).((((((((..........((((((((.((((...............)))).(((....)))))))))))((((....))))..)))))))). ( -38.16)
>DroYak_CAF1 34974 113 + 1
-----AGUAGUGUGCGCGCUCGUUCGCCCGCAUGAGUUUUCUUUGCGCUGCUCCUUUGAUAAAUGCGCAUAAUUUCAGUAGGUUUUCCUGGAGUAGCGAAGAAAACUUCUUCUUG--UGC
-----......(((((.((......)).)))))(((((((((...(((((((((.((((...............)))).(((....)))))))))))).))))))))).......--... ( -35.96)
>consensus
CGAG_AGUAGUGUGUGCGCUCGUUCGCCCGCA_GAGUUUUCUUUGCGCUGCUCCUUUGAUAAAUGCGCAUAAUUUCAGUAGGUUUUCCUGGAGUAGCGAGGAAAACUUGUCCGUGUGCGC
......(.((((....)))))((.(((......(((((((((...(((((((((.((((...............)))).(((....)))))))))))).)))))))))......))).)) (-28.18 = -29.30 +   1.12)

alignment

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secondary structure

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Window 5

Location 1,348,643 – 1,348,763
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.06
Mean single sequence MFE -31.03
Consensus MFE -22.86
Energy contribution -23.22
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -2.32
Structure conservation index 0.74
SVM decision value 0.95
SVM RNA-class probability 0.887180
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1348643 120 - 20766785
UUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGAGACUAUUGCACACAGCAACAUUCACACACUCGCACUCCAAAGGCGCACACGGACAAGUUUUCCUCACUACUCCAGGAAAACC
......((((((((...........)))))))).(((((....((((.....))))..........)))))..(((............)))...((((((((.........)))))))). ( -31.64)
>DroSec_CAF1 66937 120 - 1
UUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAACGAGACUAUUGCACACAGCAGCACUCACACACUCGCACUCCAGCGGCGCACACGGACAAGUUUUCCUCGCUACUCCAGGAAAACC
.....((((((((((((..........))))))...(((....((((.....))))..)))................))))))...........((((((((.(.....).)))))))). ( -33.40)
>DroSim_CAF1 45072 120 - 1
UUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGAGACUAUUGCACACAGCAGCACUCACACACUCGCACUCCAGCGGCGCACACGGACAAGUUUUCCUCGCUACUCCAGGAAAACC
.....((((((((((((..........)))))).(((((.....(((.....)))(......)...)))))......))))))...........((((((((.(.....).)))))))). ( -37.30)
>DroEre_CAF1 47516 117 - 1
UUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGCGACUAUUGCACACAGAAGCACUUACACACUCACACACUC---GCACACAAGGAGAAGUUUCCUUCGCUACUCCAGGAAAACC
......((((((((...........)))))))).(.((((....(((........))).................))---)).)....((((.(((.......))).))))......... ( -27.30)
>DroYak_CAF1 35049 115 - 1
UUUAACGCUGCGCUGUGAACAAUAAAGCGCAGCAGCGAGACUAUUGCACACAGAAACCCUCACACAUUCACACACUU---GCA--CAAGAAGAAGUUUUCUUCGCUACUCCAGGAAAACC
......((((((((...........)))))))).((((.....))))...........................(((---(..--...(((((.....))))).......))))...... ( -25.50)
>consensus
UUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGAGACUAUUGCACACAGCAGCACUCACACACUCGCACUCCA__GGCGCACACGGACAAGUUUUCCUCGCUACUCCAGGAAAACC
......((((((((...........)))))))).((((.....))))...............................................((((((((.........)))))))). (-22.86 = -23.22 +   0.36)

alignment

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secondary structure

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Window 6

Location 1,348,683 – 1,348,803
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.82
Mean single sequence MFE -28.53
Consensus MFE -22.54
Energy contribution -23.10
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.14
Structure conservation index 0.79
SVM decision value 1.23
SVM RNA-class probability 0.933784
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1348683 120 - 20766785
AAGCUAUCCAAGACAUCCAAGCCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGAGACUAUUGCACACAGCAACAUUCACACACUCGCACUCCAAAG
..........((((((....(((.(....).)))...))))))...((((((((...........)))))))).(((((....((((.....))))..........)))))......... ( -31.14)
>DroSec_CAF1 66977 107 - 1
-------------CAUCCAAGUCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAACGAGACUAUUGCACACAGCAGCACUCACACACUCGCACUCCAGCG
-------------......((((.(((....)))............((((((((...........)))))))).....)))).((((.....))))............(((......))) ( -29.00)
>DroSim_CAF1 45112 107 - 1
-------------CAUCCAAGUCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGAGACUAUUGCACACAGCAGCACUCACACACUCGCACUCCAGCG
-------------...........(((....)))............(((((((((((..........)))))).((((.....)))).....)))))...........(((......))) ( -30.50)
>DroEre_CAF1 47556 107 - 1
----------AGCCAUCCAAGUCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGCGACUAUUGCACACAGAAGCACUUACACACUCACACACUC---
----------.........((((.(((....)))............((((((((...........)))))))).....))))..(((........)))...................--- ( -26.40)
>DroYak_CAF1 35087 102 - 1
---------------UCCAAGCCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGUGAACAAUAAAGCGCAGCAGCGAGACUAUUGCACACAGAAACCCUCACACAUUCACACACUU---
---------------.....(((.(....).)))..(((((.....((((((((...........)))))))).((((.....))))................))))).........--- ( -25.60)
>consensus
_____________CAUCCAAGUCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGAGACUAUUGCACACAGCAGCACUCACACACUCGCACUCCA__G
...................((((.(((....)))............((((((((...........)))))))).....)))).((((.....))))........................ (-22.54 = -23.10 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,348,723 – 1,348,843
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.98
Mean single sequence MFE -27.32
Consensus MFE -23.42
Energy contribution -23.67
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.86
SVM decision value 0.27
SVM RNA-class probability 0.663790
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1348723 120 - 20766785
ACUCAGCCGUUCUAAGCCACCCAAGCCAUCCAAGCUAUCCAAGCUAUCCAAGACAUCCAAGCCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGAGA
.(((.((.(((...(((......(((.......)))......))).....((((((....(((.(....).)))...)))))))))((((((((...........)))))))).))))). ( -31.20)
>DroSec_CAF1 67017 102 - 1
ACUCAGCCCUUCUAAGCCACCCAAGCCAGCCAAGC------------------CAUCCAAGUCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAACGAGA
.(((........(((((.......(((.((...((------------------...........))..)).))).....)))))..((((((((...........))))))))...))). ( -26.40)
>DroSim_CAF1 45152 102 - 1
ACUCAGCCCUUCUAAGCCACCCAAGCCAGCCAAGC------------------CAUCCAAGUCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGAGA
.(((.((.....(((((.......(((.((...((------------------...........))..)).))).....)))))..((((((((...........)))))))).))))). ( -27.40)
>DroEre_CAF1 47593 110 - 1
ACUCAGCCCUUCUAAGCCACCCAAGCCACCCAAGCCACCC----------AGCCAUCCAAGUCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGCGA
.....((.((..(((((................((.....----------.))...........(((....))).....)))))..((((((((...........)))))))))).)).. ( -24.30)
>consensus
ACUCAGCCCUUCUAAGCCACCCAAGCCAGCCAAGC__________________CAUCCAAGUCAGCCAGCCGGCAUAAUGUUUAACGCUGCGCUGCGAACAAUAAAGCGCAGCAGCGAGA
.(((........(((((.......((.......)).............................(((....))).....)))))..((((((((...........))))))))...))). (-23.42 = -23.67 +   0.25)

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 09:27:15 2006