Locus 1592

Sequence ID 2L_DroMel_CAF1
Location 4,272,224 – 4,272,345
Length 121
Max. P 0.998815
window2557 window2558 window2559

overview

Window 7

Location 4,272,224 – 4,272,316
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 96.48
Mean single sequence MFE -15.54
Consensus MFE -13.27
Energy contribution -13.91
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -1.37
Structure conservation index 0.85
SVM decision value 0.07
SVM RNA-class probability 0.569800
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4272224 92 + 22407834
CGUAAAUUGACCGCGCUCGGCAUAGUUGCAGAACUAUAUAUUUACCACAAAAUUACACAAAUCAAAUGCAUAAUUCUGCUCUAAUGCCCGGC
..............(((.(((((((..((((((.(((.(((((....................))))).))).)))))).)).))))).))) ( -19.85)
>DroSec_CAF1 26838 90 + 1
CGUAAAUUGACCGCGCUCGGCAUAGUUGCAGAACUAU--AUUUACCACAAAAUUACACAAAUCAAAUGCAUAAUUCUGCUCUAAUGCCCGGG
..........(((.....(((((((..((((((.(((--..............................))).)))))).)).)))))))). ( -16.01)
>DroSim_CAF1 28066 90 + 1
CGUAAAUUGACCGCGCUCGGCAUAGUUGCAGAACUAU--AUUUACCACAAAAUUACACAAAUCAAAUGCAUAAUUCUGCUCUAAUGCCCGGC
..............(((.(((((((..((((((.(((--..............................))).)))))).)).))))).))) ( -17.21)
>DroEre_CAF1 22378 90 + 1
CGUAAAUUGACCUCACUCGGCAUAGUUGCACAACUAU--AUUUACCACAAAAUUACACAAAUCAAAUGCAUAAUUCUGCUCUAAUGCCCAGC
...............((.(((((((((....))))))--............................(((......)))......))).)). ( -11.00)
>DroYak_CAF1 26985 90 + 1
CGUAAAUUGACCGCGCUCGGCAUAGUUGCAGAACUAU--AUUUACCACAAAAUUACACAAAUCAAAUGCAUAAUUCUGCUCUAAUGCCCGAC
..................(((((((..((((((.(((--..............................))).)))))).)).))))).... ( -13.61)
>consensus
CGUAAAUUGACCGCGCUCGGCAUAGUUGCAGAACUAU__AUUUACCACAAAAUUACACAAAUCAAAUGCAUAAUUCUGCUCUAAUGCCCGGC
..............(((.(((((((..((((((.(((..((((....................))))..))).)))))).)).))))).))) (-13.27 = -13.91 +   0.64)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,272,224 – 4,272,316
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 96.48
Mean single sequence MFE -26.16
Consensus MFE -23.68
Energy contribution -23.40
Covariance contribution -0.28
Combinations/Pair 1.11
Mean z-score -2.34
Structure conservation index 0.91
SVM decision value 3.24
SVM RNA-class probability 0.998815
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4272224 92 - 22407834
GCCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAUAUAUAGUUCUGCAACUAUGCCGAGCGCGGUCAAUUUACG
((((.((.(((..(((((((((((((.......)))))))))))))..)))...(((((((....)))))))....)).))))......... ( -27.00)
>DroSec_CAF1 26838 90 - 1
CCCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU--AUAGUUCUGCAACUAUGCCGAGCGCGGUCAAUUUACG
.(((.((......(((((((((((((.......)))))))))))))(((....--((((((....)))))))))..)).))).......... ( -26.10)
>DroSim_CAF1 28066 90 - 1
GCCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU--AUAGUUCUGCAACUAUGCCGAGCGCGGUCAAUUUACG
((((.((......(((((((((((((.......)))))))))))))(((....--((((((....)))))))))..)).))))......... ( -27.30)
>DroEre_CAF1 22378 90 - 1
GCUGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU--AUAGUUGUGCAACUAUGCCGAGUGAGGUCAAUUUACG
(((.(((.(((..(((((((((((((.......)))))))))))))..)))..--((((((....))))))))).))).............. ( -26.60)
>DroYak_CAF1 26985 90 - 1
GUCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU--AUAGUUCUGCAACUAUGCCGAGCGCGGUCAAUUUACG
((((.((......(((((((((((((.......)))))))))))))(((....--((((((....)))))))))..)).))).)........ ( -23.80)
>consensus
GCCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU__AUAGUUCUGCAACUAUGCCGAGCGCGGUCAAUUUACG
.(((.((......(((((((((((((.......)))))))))))))(((......((((((....)))))))))..)).))).......... (-23.68 = -23.40 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,272,244 – 4,272,345
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 96.79
Mean single sequence MFE -23.68
Consensus MFE -22.06
Energy contribution -21.94
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.57
Structure conservation index 0.93
SVM decision value 1.54
SVM RNA-class probability 0.962196
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4272244 101 - 22407834
ACAUUUGAUCUUUUUGUGCUGGUUCAUCGGCCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAUAUAUAGUUCUGCAACUAUG
..(((((.(((...(((.(((((......))))))))..)))(((((((((((((.......)))))))))))))..))))).(((((((....))))))) ( -24.90)
>DroSec_CAF1 26858 99 - 1
ACAUUUGAUCUUUUUGUGCUGGUUCAUCGCCCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU--AUAGUUCUGCAACUAUG
........(((...(((.(.(((.....))).).)))..)))(((((((((((((.......)))))))))))))......(--((((((....))))))) ( -23.30)
>DroSim_CAF1 28086 99 - 1
ACAUUUGAUCUUUUUGUGCUGGUUCAUCGGCCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU--AUAGUUCUGCAACUAUG
........(((...(((.(((((......))))))))..)))(((((((((((((.......)))))))))))))......(--((((((....))))))) ( -24.60)
>DroEre_CAF1 22398 99 - 1
ACAUUUGAUCUUUUUGUGCUGGUUCAUCAGCUGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU--AUAGUUGUGCAACUAUG
...(((((((((.....(((((....))))).))).))))))(((((((((((((.......)))))))))))))......(--((((((....))))))) ( -23.70)
>DroYak_CAF1 27005 99 - 1
ACAUUUGAUCUUUUUGUGCUGGUUCAUUGGUCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU--AUAGUUCUGCAACUAUG
........(((....(((((.(.........).))))).)))(((((((((((((.......)))))))))))))......(--((((((....))))))) ( -21.90)
>consensus
ACAUUUGAUCUUUUUGUGCUGGUUCAUCGGCCGGGCAUUAGAGCAGAAUUAUGCAUUUGAUUUGUGUAAUUUUGUGGUAAAU__AUAGUUCUGCAACUAUG
........(((...(((.(((((......))))))))..)))(((((((((((((.......))))))))))))).........((((((....)))))). (-22.06 = -21.94 +  -0.12)

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 10:06:11 2006