Locus 4094

Sequence ID 2L_DroMel_CAF1
Location 11,783,461 – 11,783,597
Length 136
Max. P 0.816406
window6451 window6452

overview

Window 1

Location 11,783,461 – 11,783,578
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.36
Mean single sequence MFE -33.45
Consensus MFE -24.42
Energy contribution -25.73
Covariance contribution 1.31
Combinations/Pair 1.14
Mean z-score -2.73
Structure conservation index 0.73
SVM decision value 0.09
SVM RNA-class probability 0.576774
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11783461 117 + 22407834
CGGCAACAGCAGAAAGAAAUUACACGCAAGCAACAAGACAACAAAGUUGUCAAUGUCGAUG---UCGAAGUUGUUGGGCAAGCAAAAAAUUUACAUGCUCCGCAUGCUCAGUGGCGUGGC
.(....)...............(((((.((((((..((((((...))))))....(((...---.))).))))))(((((.((..................)).)))))....))))).. ( -31.67)
>DroSec_CAF1 41198 116 + 1
CGGCAACAGCAGAAAGAAAUUACACGCAAGCAACAAGACAACAAAGUUGUCAAUGUCGAUG---UCGACGUUGUUGGGCAAGCAAAAAAUGUACAUGCUCAGCAUA-UCAGUGGCGUGGC
.(....)...............(((((..((.....((((((...))))))(((((((...---.)))))))((((((((.(((.....)))...))))))))...-...)).))))).. ( -35.00)
>DroSim_CAF1 40292 116 + 1
CGGCAACAGCAGAAAGAAAUUACACGCAAGCAACAAGACAACAAAGUUGUCAAUGUCGAUG---UCGACGUUGUUGGGCAAGCAAAAAAUUUACAUGCUCCGCAUA-UCAGUGGCGUGGC
.(....).((.(.((....)).)..((.((((((..((((((...))))))...((((...---.))))))))))..))..))..........(((((..(.....-...)..))))).. ( -32.50)
>DroEre_CAF1 51579 116 + 1
CGGCAACAGCAGAAAGAAAUUACACGCAAGCAACAAGACAACAAAGUUGUCAAUGUCGAUG---UCGACGUUGUUGGGCGAGCAAAGAAUUUACAUGCUCCGCAUA-UCAGGGGCGUGGC
.(....).((.(.((....)).).(((.((((((..((((((...))))))...((((...---.))))))))))..))).))..........((((((((.....-...)))))))).. ( -39.80)
>DroYak_CAF1 43076 116 + 1
GGGCAACAGCAGAAAGAAAUUACACGCAAGCAACAAGACAACAAAGUUGUCAAUGUCGAUG---UCGACGUUGUUGGGCAAACAAAAAAUUUACAUGCUCCUCAUA-UCAGGGGCGUGUU
.(....)..................((.((((((..((((((...))))))...((((...---.))))))))))..)).............((((((((((....-..)))))))))). ( -36.10)
>DroAna_CAF1 42338 97 + 1
CGGCAACAGCAGAAAGAAAUUACAUGCAAACAGCAAGACAACAAAGUUGUCAAUGUCGAUGUUGUUGACGUUGUUUGGCUUGCAACAAAUUUCCACU-----------------------
..(((..(((.(.((....)).)...((((((((..((((((...))))))...((((((...))))))))))))))))))))..............----------------------- ( -25.60)
>consensus
CGGCAACAGCAGAAAGAAAUUACACGCAAGCAACAAGACAACAAAGUUGUCAAUGUCGAUG___UCGACGUUGUUGGGCAAGCAAAAAAUUUACAUGCUCCGCAUA_UCAGUGGCGUGGC
.(....)...............(((((.((((((..((((((...))))))...(((((.....)))))))))))(((((...............))))).............))))).. (-24.42 = -25.73 +   1.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,783,501 – 11,783,597
Length 96
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 80.98
Mean single sequence MFE -30.72
Consensus MFE -18.61
Energy contribution -18.65
Covariance contribution 0.04
Combinations/Pair 1.12
Mean z-score -2.09
Structure conservation index 0.61
SVM decision value 0.67
SVM RNA-class probability 0.816406
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11783501 96 + 22407834
ACAAAGUUGUCAAUGUCGAUGUCGAAGUUGUUGGGCAAGCAAAAAAUUUACAUGCUCCGCAUGCUCAGUGGCGUGGCCUAA---------------AAGGGAUUAAUAAAC------
..........((((.(((....))).))))((((((.((((...........))))...((((((....))))))))))))---------------...............------ ( -20.50)
>DroSec_CAF1 41238 95 + 1
ACAAAGUUGUCAAUGUCGAUGUCGACGUUGUUGGGCAAGCAAAAAAUGUACAUGCUCAGCAUA-UCAGUGGCGUGGCCUAA---------------AGGGGGUUAAUCAAC------
........((((((((((....))))))(((((((((.(((.....)))...)))))))))..-....)))).((((((..---------------...))))))......------ ( -26.70)
>DroSim_CAF1 40332 95 + 1
ACAAAGUUGUCAAUGUCGAUGUCGACGUUGUUGGGCAAGCAAAAAAUUUACAUGCUCCGCAUA-UCAGUGGCGUGGCCUAA---------------AAGGGGUUAAUCAAC------
.....((((.((((((((....))))))))((((((.((((...........))))((((...-...))))....))))))---------------...........))))------ ( -24.80)
>DroEre_CAF1 51619 110 + 1
ACAAAGUUGUCAAUGUCGAUGUCGACGUUGUUGGGCGAGCAAAGAAUUUACAUGCUCCGCAUA-UCAGGGGCGUGGCCUGAUGAAUUCCCCUUUUAAAGGGGCUCAUCAGC------
.....(((..((((((((....))))))))...)))..............((((((((.....-...))))))))..(((((((...(((((.....))))).))))))).------ ( -41.70)
>DroYak_CAF1 43116 116 + 1
ACAAAGUUGUCAAUGUCGAUGUCGACGUUGUUGGGCAAACAAAAAAUUUACAUGCUCCUCAUA-UCAGGGGCGUGUUCUGAAGAAUUUCCCUUUCAAAGGGGCUUAACAACUUUUAA
..((((((((((((((((....)))))))).(((((.............((((((((((....-..))))))))))............((((.....)))))))))))))))))... ( -39.90)
>consensus
ACAAAGUUGUCAAUGUCGAUGUCGACGUUGUUGGGCAAGCAAAAAAUUUACAUGCUCCGCAUA_UCAGUGGCGUGGCCUAA_______________AAGGGGUUAAUCAAC______
.....((((.((((((((....))))))))((((((..............((((((.............))))))))))))..........................))))...... (-18.61 = -18.65 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:12 2006