Locus 6319

Sequence ID 2R_DroMel_CAF1
Location 19,808,955 – 19,809,092
Length 137
Max. P 0.999944
window10096 window10097 window10098

overview

Window 6

Location 19,808,955 – 19,809,052
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.03
Mean single sequence MFE -24.83
Consensus MFE -22.10
Energy contribution -22.05
Covariance contribution -0.05
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.89
SVM decision value 0.85
SVM RNA-class probability 0.865137
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19808955 97 + 20766785
GUUCGUUGG-----------------CUCU------CUUUUUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCA
(((.(((((-----------------(...------.......(((((..((((....))))......)))))((((((((((.........)))))))))))))))))))......... ( -23.30)
>DroPse_CAF1 49434 100 + 1
GGCUAUUCC--------------UUUUUUU------UUCUUUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGACCAGCAACCGCAACGCA
.........--------------.......------........(((((...(((..(((((........((.((((((((((.........)))))))))))))))))..)))))))). ( -22.90)
>DroWil_CAF1 101569 84 + 1
------------------------------------CUUUUUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCA
------------------------------------........(((((...(((..(((((........((.((((((((((.........)))))))))))))))))..)))))))). ( -22.40)
>DroMoj_CAF1 113128 98 + 1
----AAUGG-----------------CUUGCCGACGUUU-UUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCA
----..(((-----------------....)))......-....(((((...(((..(((((........((.((((((((((.........)))))))))))))))))..)))))))). ( -24.50)
>DroAna_CAF1 47966 114 + 1
CGUCGUUGGCGUUGUCGUUGUAUUGUUGCU------UUUUUUCCGCGCUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCA
........(((((((.((((((((((.((.------........((((....))))..)).)))))...((..((((((((((.........))))))))))..))))))).))))))). ( -33.00)
>DroPer_CAF1 49050 100 + 1
GGCUAUUCC--------------UUUUUUU------UUCUUUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGACCAGCAACCGCAACGCA
.........--------------.......------........(((((...(((..(((((........((.((((((((((.........)))))))))))))))))..)))))))). ( -22.90)
>consensus
GG__AUUGG_________________UUUU______UUUUUUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCA
............................................(((((...(((..(((((........((.((((((((((.........)))))))))))))))))..)))))))). (-22.10 = -22.05 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,808,972 – 19,809,092
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 97.56
Mean single sequence MFE -35.95
Consensus MFE -34.63
Energy contribution -34.85
Covariance contribution 0.22
Combinations/Pair 1.05
Mean z-score -2.74
Structure conservation index 0.96
SVM decision value 4.74
SVM RNA-class probability 0.999944
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19808972 120 + 20766785
UUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCAAUUUGGCAACACUUGUUGGCCAAUUGGCCAAAAUGUGAAG
....(((((...(((..(((((........((.((((((((((.........)))))))))))))))))..))))))))..........(((...((((((....))))))...)))... ( -36.60)
>DroVir_CAF1 68366 120 + 1
UUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCAAUUUGGCAACACUUGUUGGCCAAUUGGCAAAAACGUGAAA
.(((((((((..(((..(((((........((.((((((((((.........)))))))))))))))))..)))...((...((((((((....))).)))))...))..))))))))). ( -38.30)
>DroPse_CAF1 49454 120 + 1
UUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGACCAGCAACCGCAACGCAAUUUGGCAACACUUGUUGGCCAAUUGGCAAAAAUGUGAAG
.(((((((((..(((..(((((........((.((((((((((.........)))))))))))))))))..)))...((...((((((((....))).)))))...))..))))))))). ( -37.00)
>DroSec_CAF1 51459 120 + 1
UUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCAAUUUGGCAACACUUGUUGGCCAAUUGGCCAAAAUAUGAAG
.((((((((...(((..(((((........((.((((((((((.........)))))))))))))))))..))))))))....((....))....((((((....)))))).....))). ( -34.20)
>DroSim_CAF1 30286 120 + 1
UUUCGCGUUUUAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCAAUUUGGCAACACUUGUUGGCCAAUUGGCCAAAAUGUGAAG
.((((((((((.(((..(((((........((.((((((((((.........)))))))))))))))))..)))...((...((((((((....))).)))))...)).)))))))))). ( -37.10)
>DroAna_CAF1 48000 120 + 1
UUCCGCGCUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCAAUUUGGCAACACUUGUUGGCCAAUUGGCAAAAAUGUGAAG
.......((((((((..(((((........((.((((((((((.........)))))))))))))))))..)))...((...((((((((....))).)))))...)).......))))) ( -32.50)
>consensus
UUUCGCGUUUCAGCGUCUGCUGCAAUUUAUGUGUAUAAAUGACAAAAGUACCGUUAUUUAUGGCCAGCAACCGCAACGCAAUUUGGCAACACUUGUUGGCCAAUUGGCAAAAAUGUGAAG
.(((((((((..(((..(((((........((.((((((((((.........)))))))))))))))))..)))...((...((((((((....))).)))))...))..))))))))). (-34.63 = -34.85 +   0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,808,972 – 19,809,092
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 97.56
Mean single sequence MFE -33.13
Consensus MFE -30.64
Energy contribution -30.37
Covariance contribution -0.28
Combinations/Pair 1.06
Mean z-score -2.06
Structure conservation index 0.92
SVM decision value 2.74
SVM RNA-class probability 0.996730
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19808972 120 - 20766785
CUUCACAUUUUGGCCAAUUGGCCAACAAGUGUUGCCAAAUUGCGUUGCGGUUGCUGGCCAUAAAUAACGGUACUUUUGUCAUUUAUACACAUAAAUUGCAGCAGACGCUGAAACGCGAAA
....(((((((((((....)))))..)))))).......((((((((((.((((((...((((((.((((.....)))).))))))...((.....)))))))).)))...))))))).. ( -34.20)
>DroVir_CAF1 68366 120 - 1
UUUCACGUUUUUGCCAAUUGGCCAACAAGUGUUGCCAAAUUGCGUUGCGGUUGCUGGCCAUAAAUAACGGUACUUUUGUCAUUUAUACACAUAAAUUGCAGCAGACGCUGAAACGCGAAA
.(((.((((((.((((((((((.(((....)))))).))))).(((((((((..((...((((((.((((.....)))).))))))...))..)))))))))....)).)))))).))). ( -35.10)
>DroPse_CAF1 49454 120 - 1
CUUCACAUUUUUGCCAAUUGGCCAACAAGUGUUGCCAAAUUGCGUUGCGGUUGCUGGUCAUAAAUAACGGUACUUUUGUCAUUUAUACACAUAAAUUGCAGCAGACGCUGAAACGCGAAA
.................(((((.(((....)))))))).((((((((((.((((((((.((((((.((((.....)))).)))))))).((.....)))))))).)))...))))))).. ( -31.40)
>DroSec_CAF1 51459 120 - 1
CUUCAUAUUUUGGCCAAUUGGCCAACAAGUGUUGCCAAAUUGCGUUGCGGUUGCUGGCCAUAAAUAACGGUACUUUUGUCAUUUAUACACAUAAAUUGCAGCAGACGCUGAAACGCGAAA
.(((.....((((((....))))))..((((((((......))(((((((((..((...((((((.((((.....)))).))))))...))..))))))))).)))))).......))). ( -33.00)
>DroSim_CAF1 30286 120 - 1
CUUCACAUUUUGGCCAAUUGGCCAACAAGUGUUGCCAAAUUGCGUUGCGGUUGCUGGCCAUAAAUAACGGUACUUUUGUCAUUUAUACACAUAAAUUGCAGCAGACGCUAAAACGCGAAA
....(((((((((((....)))))..)))))).......((((((((((.((((((...((((((.((((.....)))).))))))...((.....)))))))).)))...))))))).. ( -34.20)
>DroAna_CAF1 48000 120 - 1
CUUCACAUUUUUGCCAAUUGGCCAACAAGUGUUGCCAAAUUGCGUUGCGGUUGCUGGCCAUAAAUAACGGUACUUUUGUCAUUUAUACACAUAAAUUGCAGCAGACGCUGAAGCGCGGAA
.............((..(((((.(((....))))))))...((((((((.((((((...((((((.((((.....)))).))))))...((.....)))))))).)))...))))))).. ( -30.90)
>consensus
CUUCACAUUUUGGCCAAUUGGCCAACAAGUGUUGCCAAAUUGCGUUGCGGUUGCUGGCCAUAAAUAACGGUACUUUUGUCAUUUAUACACAUAAAUUGCAGCAGACGCUGAAACGCGAAA
.................(((((.(((....)))))))).((((((((((.((((((...((((((.((((.....)))).))))))...((.....)))))))).)))...))))))).. (-30.64 = -30.37 +  -0.28)

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 12:08:10 2006