Locus 2795

Sequence ID 3L_DroMel_CAF1
Location 7,958,173 – 7,958,316
Length 143
Max. P 0.994795
window4362 window4363 window4364 window4365

overview

Window 2

Location 7,958,173 – 7,958,276
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.51
Mean single sequence MFE -27.64
Consensus MFE -24.92
Energy contribution -24.80
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -1.79
Structure conservation index 0.90
SVM decision value 1.39
SVM RNA-class probability 0.949605
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7958173 103 + 23771897
----UGCCUUUGUUUUGGCCAGUUACCCGAGUUCCCUUGU-------------UCCCUGGCAACAGGCUCAUUUGGCCAAGAACAAUUUAGAGCCUUUUAAUAGCCUUUAUGUUUUAUUG
----.....(((((((((((((.....((((....)))).-------------..((((....)))).....)))))).)))))))..(((((.((......)).))))).......... ( -26.30)
>DroSec_CAF1 3667 103 + 1
----UGCCUUUGUUUUGGCCAGUUACCCGAGUUCCCUUGU-------------UCCCUGGUAACAGGCUCAUUUGGCCAAGAACAAUUUAGAGCCUUUUAAUGGCCUUUAUGUUUUAUUG
----............(((((((((((((((....)))).-------------.....))))))((((((..(((........)))....)))))).....))))).............. ( -26.90)
>DroSim_CAF1 3668 103 + 1
----UGCCUUUGUUUUGGCCAGUUACCCGAGUUCCCUUGU-------------UCCCUGGUAACAGGCUCAUUUGGCUAAGAACAAUUUAGAGCCUUUUAAUGGCCUUUAUGUUUUAUUG
----............(((((((((((((((....)))).-------------.....))))))((((((..(((........)))....)))))).....))))).............. ( -26.90)
>DroEre_CAF1 3828 114 + 1
CCUUCGCCUUUGUUUUGGCCAGUUACCCGAGUUCCCUUGUCGCCCUGCC-----UCCUGGUAACAGGCUCAUUUGGCCAGGAACAGUUUAGAGCCU-UUAGUGGCCUUUAUGUUUUAUUG
...............(((((((.....((((....))))..(((.((((-----....))))...)))....)))))))((((((....((.(((.-.....)))))...)))))).... ( -30.20)
>DroYak_CAF1 4057 120 + 1
CCUUUGCCUUUGUUUUGGCCAGUUACCCGAGUUCCCUUGCCACCUUGUUCCCUUCCCUGGUAACAGGCUCAUUUGGCCAAGAACAAUUUAGAGCCUUUUAAUGGCCUUUAUGUUUUAUUG
.........(((((((((((((.....((((....))))....((((((.((......)).)))))).....)))))).)))))))..(((((((.......)).))))).......... ( -27.90)
>consensus
____UGCCUUUGUUUUGGCCAGUUACCCGAGUUCCCUUGU_____________UCCCUGGUAACAGGCUCAUUUGGCCAAGAACAAUUUAGAGCCUUUUAAUGGCCUUUAUGUUUUAUUG
...............(((((((.....((((....))))................((((....)))).....)))))))((((((....((.(((.......)))))...)))))).... (-24.92 = -24.80 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,958,173 – 7,958,276
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.51
Mean single sequence MFE -28.38
Consensus MFE -25.44
Energy contribution -25.32
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -2.25
Structure conservation index 0.90
SVM decision value 2.51
SVM RNA-class probability 0.994795
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7958173 103 - 23771897
CAAUAAAACAUAAAGGCUAUUAAAAGGCUCUAAAUUGUUCUUGGCCAAAUGAGCCUGUUGCCAGGGA-------------ACAAGGGAACUCGGGUAACUGGCCAAAACAAAGGCA----
..............(((((.....((((((....(((........)))..))))))((((((.(((.-------------.........))).)))))))))))............---- ( -25.40)
>DroSec_CAF1 3667 103 - 1
CAAUAAAACAUAAAGGCCAUUAAAAGGCUCUAAAUUGUUCUUGGCCAAAUGAGCCUGUUACCAGGGA-------------ACAAGGGAACUCGGGUAACUGGCCAAAACAAAGGCA----
..............(((((.....((((((....(((........)))..))))))((((((.(((.-------------.........))).)))))))))))............---- ( -27.70)
>DroSim_CAF1 3668 103 - 1
CAAUAAAACAUAAAGGCCAUUAAAAGGCUCUAAAUUGUUCUUAGCCAAAUGAGCCUGUUACCAGGGA-------------ACAAGGGAACUCGGGUAACUGGCCAAAACAAAGGCA----
..............(((((.....((((((....(((........)))..))))))((((((.(((.-------------.........))).)))))))))))............---- ( -27.70)
>DroEre_CAF1 3828 114 - 1
CAAUAAAACAUAAAGGCCACUAA-AGGCUCUAAACUGUUCCUGGCCAAAUGAGCCUGUUACCAGGA-----GGCAGGGCGACAAGGGAACUCGGGUAACUGGCCAAAACAAAGGCGAAGG
..............(((((....-..((((......((((((.(((...((..((((....)))).-----..)).))).....))))))..))))...)))))................ ( -30.00)
>DroYak_CAF1 4057 120 - 1
CAAUAAAACAUAAAGGCCAUUAAAAGGCUCUAAAUUGUUCUUGGCCAAAUGAGCCUGUUACCAGGGAAGGGAACAAGGUGGCAAGGGAACUCGGGUAACUGGCCAAAACAAAGGCAAAGG
.............(((((.......))).))...(((((.(((((((..(((((((((((((..(........)..)))))).)))...))))......))))))))))))......... ( -31.10)
>consensus
CAAUAAAACAUAAAGGCCAUUAAAAGGCUCUAAAUUGUUCUUGGCCAAAUGAGCCUGUUACCAGGGA_____________ACAAGGGAACUCGGGUAACUGGCCAAAACAAAGGCA____
..............(((((.....((((((......((.....)).....))))))((((((.(((.......................))).)))))))))))................ (-25.44 = -25.32 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,958,209 – 7,958,316
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.60
Mean single sequence MFE -31.66
Consensus MFE -24.12
Energy contribution -25.00
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -2.90
Structure conservation index 0.76
SVM decision value 2.14
SVM RNA-class probability 0.988969
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7958209 107 + 23771897
-------------UCCCUGGCAACAGGCUCAUUUGGCCAAGAACAAUUUAGAGCCUUUUAAUAGCCUUUAUGUUUUAUUGGUACACACACAUAAUGUGUACAUUGUGGUUACUUUGGAAC
-------------..((((....)))).(((..((((((((((((...(((((.((......)).)))))))))))....(((((((.......)))))))....))))))...)))... ( -27.60)
>DroSec_CAF1 3703 105 + 1
-------------UCCCUGGUAACAGGCUCAUUUGGCCAAGAACAAUUUAGAGCCUUUUAAUGGCCUUUAUGUUUUAUUGGUACAC--ACAUAAUGUGUACAUUGUGGUUACUUUGGAAC
-------------(((..((((((.((((.....)))).((((((....((.(((.......)))))...))))))....((((((--(.....)))))))......))))))..))).. ( -32.20)
>DroSim_CAF1 3704 105 + 1
-------------UCCCUGGUAACAGGCUCAUUUGGCUAAGAACAAUUUAGAGCCUUUUAAUGGCCUUUAUGUUUUAUUGGUACAC--ACAUAAUGUGUACAUUGUGGUUACUUUGGAAC
-------------(((..((((((((((.((((.((((..((.....))..))))....)))))))).............((((((--(.....)))))))......))))))..))).. ( -31.70)
>DroEre_CAF1 3868 109 + 1
CGCCCUGCC-----UCCUGGUAACAGGCUCAUUUGGCCAGGAACAGUUUAGAGCCU-UUAGUGGCCUUUAUGUUUUAUUGGUACA----CAUGAUGUGUGCAUUGUGGCUACAUUG-AAC
.(((.((((-----....))))...)))(((..((((((((((((....((.(((.-.....)))))...))))))....(((((----(.....))))))....))))))...))-).. ( -35.70)
>DroYak_CAF1 4097 115 + 1
CACCUUGUUCCCUUCCCUGGUAACAGGCUCAUUUGGCCAAGAACAAUUUAGAGCCUUUUAAUGGCCUUUAUGUUUUAUUGGUACA----CAUAAUGUGUACAUUGUGGUUACUUUG-AAC
...((((((.((......)).)))))).(((..((((((((((((....((.(((.......)))))...))))))....(((((----(.....))))))....))))))...))-).. ( -31.10)
>consensus
_____________UCCCUGGUAACAGGCUCAUUUGGCCAAGAACAAUUUAGAGCCUUUUAAUGGCCUUUAUGUUUUAUUGGUACAC__ACAUAAUGUGUACAUUGUGGUUACUUUGGAAC
.............(((..((((((((((((..(((........)))....)))))).......(((..((.....))..))).......(((((((....)))))))))))))..))).. (-24.12 = -25.00 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,958,209 – 7,958,316
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.60
Mean single sequence MFE -26.55
Consensus MFE -17.98
Energy contribution -18.74
Covariance contribution 0.76
Combinations/Pair 1.15
Mean z-score -2.16
Structure conservation index 0.68
SVM decision value 0.39
SVM RNA-class probability 0.715988
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7958209 107 - 23771897
GUUCCAAAGUAACCACAAUGUACACAUUAUGUGUGUGUACCAAUAAAACAUAAAGGCUAUUAAAAGGCUCUAAAUUGUUCUUGGCCAAAUGAGCCUGUUGCCAGGGA-------------
..(((...(((((......((((((((.....)))))))).............(((((.......((((.............)))).....))))))))))...)))------------- ( -26.92)
>DroSec_CAF1 3703 105 - 1
GUUCCAAAGUAACCACAAUGUACACAUUAUGU--GUGUACCAAUAAAACAUAAAGGCCAUUAAAAGGCUCUAAAUUGUUCUUGGCCAAAUGAGCCUGUUACCAGGGA-------------
..(((...(((((......((((((((...))--)))))).............((((((((....((((.............)))).)))).)))))))))...)))------------- ( -26.32)
>DroSim_CAF1 3704 105 - 1
GUUCCAAAGUAACCACAAUGUACACAUUAUGU--GUGUACCAAUAAAACAUAAAGGCCAUUAAAAGGCUCUAAAUUGUUCUUAGCCAAAUGAGCCUGUUACCAGGGA-------------
..(((...(((((......((((((((...))--)))))).............((((((((....((((.............)))).)))).)))))))))...)))------------- ( -26.32)
>DroEre_CAF1 3868 109 - 1
GUU-CAAUGUAGCCACAAUGCACACAUCAUG----UGUACCAAUAAAACAUAAAGGCCACUAA-AGGCUCUAAACUGUUCCUGGCCAAAUGAGCCUGUUACCAGGA-----GGCAGGGCG
...-.......(((....((((((.....))----))))..............(((((.....-.))).))...((((((((((.((........))...))))))-----.))))))). ( -27.70)
>DroYak_CAF1 4097 115 - 1
GUU-CAAAGUAACCACAAUGUACACAUUAUG----UGUACCAAUAAAACAUAAAGGCCAUUAAAAGGCUCUAAAUUGUUCUUGGCCAAAUGAGCCUGUUACCAGGGAAGGGAACAAGGUG
...-.......(((.....((((((.....)----))))).............(((((.......))).))...((((((((..((...((..........)).))..))))))))))). ( -25.50)
>consensus
GUUCCAAAGUAACCACAAUGUACACAUUAUGU__GUGUACCAAUAAAACAUAAAGGCCAUUAAAAGGCUCUAAAUUGUUCUUGGCCAAAUGAGCCUGUUACCAGGGA_____________
..(((...(((((......((((((.........)))))).............((((((((....((((.............)))).)))).)))))))))...)))............. (-17.98 = -18.74 +   0.76)

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 10:41:52 2006