Locus 1055

Sequence ID 2L_DroMel_CAF1
Location 2,937,598 – 2,937,745
Length 147
Max. P 0.982534
window1700 window1701 window1702

overview

Window 0

Location 2,937,598 – 2,937,716
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.48
Mean single sequence MFE -23.96
Consensus MFE -22.04
Energy contribution -22.44
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.92
SVM decision value 1.78
SVM RNA-class probability 0.977037
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2937598 118 + 22407834
GCACGAAUAUGGAGCCAUAAAAGAGCAUCUACCGCAAAUCGCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAA-AAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAA-
.........(((.(((((.((((........((((....((((.............)))).......))))....(((.-.(((........)))...)))....)))).)))))))).- ( -24.32)
>DroSec_CAF1 52671 118 + 1
ACACGAAUAUGGAGCCAUAAAAGAGCAUGUACCGCAAAUCGCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAA-AAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAA-
.........(((.(((((.((((....(((.((((....((((.............)))).......))))))).(((.-.(((........)))...)))....)))).)))))))).- ( -25.42)
>DroSim_CAF1 54674 118 + 1
ACACGAAUAUGGAGCCAUAAAAGAGCAUGUACCGCAAAUCGCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAA-AAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAA-
.........(((.(((((.((((....(((.((((....((((.............)))).......))))))).(((.-.(((........)))...)))....)))).)))))))).- ( -25.42)
>DroEre_CAF1 54954 119 + 1
ACACGAAUAUGGAGCCAUAAAAAAGCAUGUACCGCAAAUCGCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAAAAAACAAUUUGAAGUUACAUCGACAACUUUAAUGGCCCAA-
.........(((.(((((.........(((.((((....((((.............)))).......)))))))..............(((((((........))))))))))))))).- ( -24.02)
>DroYak_CAF1 54827 120 + 1
ACACGAAUAUGGACCCAUAAAAGAGCAUGUACCGCAAAUCGCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAAAAAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAAA
.........(((..((((.((((....(((.((((....((((.............)))).......))))))).(((...(((........)))...)))....)))).)))).))).. ( -20.62)
>consensus
ACACGAAUAUGGAGCCAUAAAAGAGCAUGUACCGCAAAUCGCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAA_AAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAA_
.........(((.(((((.((((........((((....((((.............)))).......))))....(((...(((........)))...)))....)))).)))))))).. (-22.04 = -22.44 +   0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,937,598 – 2,937,716
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.48
Mean single sequence MFE -32.38
Consensus MFE -31.00
Energy contribution -31.08
Covariance contribution 0.08
Combinations/Pair 1.05
Mean z-score -1.66
Structure conservation index 0.96
SVM decision value 1.92
SVM RNA-class probability 0.982534
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2937598 118 - 22407834
-UUGGGCCAUUAAAGUUGUCGAUGUAACUUUAAAUUGUUU-UUCGUUGCCCGCUUUUAGGCGCUGCUGAGUGAUAUAAGCGAUUUGCGGUAGAUGCUCUUUUAUGGCUCCAUAUUCGUGC
-.((((((((((((((((......)))))))))...((((-.((((....(((((.((..((((....)))).)).)))))....)))).)))).........)))).)))......... ( -30.20)
>DroSec_CAF1 52671 118 - 1
-UUGGGCCAUUAAAGUUGUCGAUGUAACUUUAAAUUGUUU-UUCGUUGCCCGCUUUUAGGCGCUGCUGAGUGAUAUAAGCGAUUUGCGGUACAUGCUCUUUUAUGGCUCCAUAUUCGUGU
-.((((((((.((((..((..(((((.((.((((((((((-.(((..((.((((....))))..))....)))...)))))))))).))))))))).)))).))))).)))......... ( -33.00)
>DroSim_CAF1 54674 118 - 1
-UUGGGCCAUUAAAGUUGUCGAUGUAACUUUAAAUUGUUU-UUCGUUGCCCGCUUUUAGGCGCUGCUGAGUGAUAUAAGCGAUUUGCGGUACAUGCUCUUUUAUGGCUCCAUAUUCGUGU
-.((((((((.((((..((..(((((.((.((((((((((-.(((..((.((((....))))..))....)))...)))))))))).))))))))).)))).))))).)))......... ( -33.00)
>DroEre_CAF1 54954 119 - 1
-UUGGGCCAUUAAAGUUGUCGAUGUAACUUCAAAUUGUUUUUUCGUUGCCCGCUUUUAGGCGCUGCUGAGUGAUAUAAGCGAUUUGCGGUACAUGCUUUUUUAUGGCUCCAUAUUCGUGU
-.((((((((.(((((.....(((((.((.((((((((((..(((..((.((((....))))..))....)))...)))))))))).))))))))))))...))))).)))......... ( -34.20)
>DroYak_CAF1 54827 120 - 1
UUUGGGCCAUUAAAGUUGUCGAUGUAACUUUAAAUUGUUUUUUCGUUGCCCGCUUUUAGGCGCUGCUGAGUGAUAUAAGCGAUUUGCGGUACAUGCUCUUUUAUGGGUCCAUAUUCGUGU
..((((((...((((..((..(((((.((.((((((((((..(((..((.((((....))))..))....)))...)))))))))).))))))))).))))....))))))......... ( -31.50)
>consensus
_UUGGGCCAUUAAAGUUGUCGAUGUAACUUUAAAUUGUUU_UUCGUUGCCCGCUUUUAGGCGCUGCUGAGUGAUAUAAGCGAUUUGCGGUACAUGCUCUUUUAUGGCUCCAUAUUCGUGU
..((((((((.((((..((..(((((.((.((((((((((..(((..((.((((....))))..))....)))...)))))))))).))))))))).)))).))))).)))......... (-31.00 = -31.08 +   0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,937,638 – 2,937,745
Length 107
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 95.92
Mean single sequence MFE -23.22
Consensus MFE -22.68
Energy contribution -23.08
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.98
SVM decision value 1.30
SVM RNA-class probability 0.939241
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2937638 107 + 22407834
GCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAA-AAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAA-AGGGCAA-AAAGAUGGCCAUUACGAUGAGG
..........((((.(..(((......)))(((......-.......((((((((........))))))))..((((..-.))))..-.......))).....).)))). ( -23.30)
>DroSec_CAF1 52711 107 + 1
GCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAA-AAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAA-AGGGCAA-AAAGAUGGCCAUUACGAGGAGC
((((...((.........(((......)))(((......-.......((((((((........))))))))..((((..-.))))..-.......))).....)).)))) ( -23.30)
>DroSim_CAF1 54714 105 + 1
GCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAA-AAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAA-AGGGCAA-AAAGAUGGCCAUUACGAGGA--
..........(((.....(((......)))(((......-.......((((((((........))))))))..((((..-.))))..-.......))).....)))..-- ( -22.30)
>DroEre_CAF1 54994 106 + 1
GCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAAAAAACAAUUUGAAGUUACAUCGACAACUUUAAUGGCCCAA-AGGGCAA-AAAGAUGGCCAUUAGGACGA--
(((..........)))..(((((((....((((...(......)...((((((((........))))))))..))))..-.((.((.-.....)).)).))))).)).-- ( -23.10)
>DroYak_CAF1 54867 108 + 1
GCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAAAAAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAAAAGGGCAAAAAAGAUGGCCAUUAGGAGGA--
..........(((.....(((......)))(((..(((...(((........)))...))).((.((((....((((....))))...)))).))))).....)))..-- ( -24.10)
>consensus
GCUUAUAUCACUCAGCAGCGCCUAAAAGCGGGCAACGAA_AAACAAUUUAAAGUUACAUCGACAACUUUAAUGGCCCAA_AGGGCAA_AAAGAUGGCCAUUACGAGGA__
..........(((.....(((......)))(((..(((...(((........)))...))).((.((((....((((....))))...)))).))))).....))).... (-22.68 = -23.08 +   0.40)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:15 2006