Locus 834

Sequence ID 3R_DroMel_CAF1
Location 2,869,882 – 2,870,101
Length 219
Max. P 0.871582
window1321 window1322 window1323

overview

Window 1

Location 2,869,882 – 2,869,985
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.41
Mean single sequence MFE -28.03
Consensus MFE -19.17
Energy contribution -18.80
Covariance contribution -0.37
Combinations/Pair 1.08
Mean z-score -1.59
Structure conservation index 0.68
SVM decision value 0.10
SVM RNA-class probability 0.582758
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2869882 103 - 27905053
ACAGUGCUUAGUUCAAGGAUAACCAAGAC-----------------AAUAAUUGGCAGGUGGAAAUAUGGUCGAAAUCGGUGACCUUGGACCGGCCAUUUACCAAUGGUAAUGACCAUUU
..((((.(..((((((((...(((.....-----------------.......(((..((....))...)))(....))))..))))))))..).))))....((((((....)))))). ( -24.80)
>DroSec_CAF1 822 113 - 1
ACAGC-CUGAGUUCAAGGAUAACCAAAUCGAAAAACAUCG------AACAAUUGGCAGGUGGAAAUAUGGUCGAAAUCUGUGACCUUGGACCGGCCAUUUACCAAUGGUAAUGACCAUUU
...((-(.(.((((((((.........((((......)))------)....(((((..((....))...))))).........))))))))))))........((((((....)))))). ( -28.60)
>DroSim_CAF1 1180 113 - 1
ACAGC-CUGAGUUCAAGGUUAACCAAAUCGAAAAACAUCG------AACAAUUGGCAGGUGGAAAUAUGGUUGAAAUCUGUGACCUUGGACCGGCCAUUUACCAAUGGUAAUGACCAUUU
...((-(.(.(((((((((((.((((.((((......)))------)....))))(((((...(((...)))...))))))))))))))))))))........((((((....)))))). ( -31.50)
>DroEre_CAF1 1724 119 - 1
ACAGC-CUUAGUUCAAGGAUAACCAAAAAUAACAACAUUGAACAGGAACAAUUGGCAGGUGUAAAUAUGGUCAAAAUCGCUGACCUUGGACCGGCCAUUCACCAAUGGUAAUGACCAUUU
....(-((..((((((.....................)))))))))......((((.(((.(((....(((((.......)))))))).))).))))......((((((....)))))). ( -27.20)
>consensus
ACAGC_CUGAGUUCAAGGAUAACCAAAACGAAAAACAUCG______AACAAUUGGCAGGUGGAAAUAUGGUCGAAAUCGGUGACCUUGGACCGGCCAUUUACCAAUGGUAAUGACCAUUU
..........((((((((.................................(((((..((....))...)))))..((...)))))))))).((.((((.(((...))))))).)).... (-19.17 = -18.80 +  -0.37) 

alignment

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secondary structure

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Window 2

Location 2,869,922 – 2,870,025
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.26
Mean single sequence MFE -30.17
Consensus MFE -21.45
Energy contribution -20.95
Covariance contribution -0.50
Combinations/Pair 1.17
Mean z-score -1.79
Structure conservation index 0.71
SVM decision value 0.48
SVM RNA-class probability 0.751558
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2869922 103 - 27905053
UCCAUUGUCAUAGAAAGGGCCAUGGCCCGACUGUCGAAGCACAGUGCUUAGUUCAAGGAUAACCAAGAC-----------------AAUAAUUGGCAGGUGGAAAUAUGGUCGAAAUCGG
((((((((((......((((....))))...((((.((((.....)))).......((....))..)))-----------------).....))))).)))))........((....)). ( -28.00)
>DroSec_CAF1 862 113 - 1
UCCAUUGUUACAGAAAGGGCCAUGGCCCAACUGUCCAGGCACAGC-CUGAGUUCAAGGAUAACCAAAUCGAAAAACAUCG------AACAAUUGGCAGGUGGAAAUAUGGUCGAAAUCUG
..........((((...(((((((..(((.((((((((((...))-))).((((..((....)).....((......)))------)))....))))).)))...)))))))....)))) ( -33.40)
>DroSim_CAF1 1220 113 - 1
UCCAUUGUUACAGAAAGGGCCAUGGCCCAACUGUCGAGGCACAGC-CUGAGUUCAAGGUUAACCAAAUCGAAAAACAUCG------AACAAUUGGCAGGUGGAAAUAUGGUUGAAAUCUG
.((((..((((.....((((....))))..(((((((((...(((-((.......)))))..))...((((......)))------)....)))))))))))....)))).......... ( -32.20)
>DroEre_CAF1 1764 119 - 1
UCCAUUGUCACAGAAAGGACCAUGGUCCAACUGUUGAGGCACAGC-CUUAGUUCAAGGAUAACCAAAAAUAACAACAUUGAACAGGAACAAUUGGCAGGUGUAAAUAUGGUCAAAAUCGC
.((((...(((.....((((....))))..((((..((((...))-)...((((((.....................))))))........)..))))))).....)))).......... ( -27.10)
>consensus
UCCAUUGUCACAGAAAGGGCCAUGGCCCAACUGUCGAGGCACAGC_CUGAGUUCAAGGAUAACCAAAACGAAAAACAUCG______AACAAUUGGCAGGUGGAAAUAUGGUCGAAAUCGG
.((((..((((.....((((....))))..(((((((.(.((........)).)..((....))...........................)))))))))))....)))).......... (-21.45 = -20.95 +  -0.50) 

alignment

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secondary structure

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Window 3

Location 2,869,985 – 2,870,101
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -31.40
Consensus MFE -25.71
Energy contribution -26.27
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -1.90
Structure conservation index 0.82
SVM decision value 0.87
SVM RNA-class probability 0.871582
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2869985 116 + 27905053
GCUUCGACAGUCGGGCCAUGGCCCUUUCUAUGACAAUGGAAUAACUGAUCUGUCAUGGUUAUAAUUUACACAAUGGAAAUAAUAAUCAUCCAUUGCAGGCCGACACU----GGGUUCGGG
((...(((((((((((....)))).((((((....)))))).....)).)))))((((((((.((((.(.....).)))).)))))))).....))...((((....----....)))). ( -32.60)
>DroSec_CAF1 935 114 + 1
GCCUGGACAGUUGGGCCAUGGCCCUUUCUGUAACAAUGGAAUAACUGAUCUGUCAUGGUUAUAAUUUAUACAAUGGAAAUAAUAAUCAUCCAUUGCAGGCCGACAGU----C-UCAC-AU
(((((.((((..((((....))))...))))..(((((((.....(((....)))(((((((.((((.........)))).))))))))))))))))))).......----.-....-.. ( -34.60)
>DroSim_CAF1 1293 116 + 1
GCCUCGACAGUUGGGCCAUGGCCCUUUCUGUAACAAUGGAAUAACUGAUCUGUCAUGGUUAUAAUUUACACAAUGGUAAUAAUAAUCAUCCAUUGCAGGCCGACACU----GGUUACGGU
((((..((((..((((....))))...))))..(((((((.....(((....)))(((((((...((((......))))..)))))))))))))).))))....(((----(....)))) ( -35.20)
>DroEre_CAF1 1843 115 + 1
GCCUCAACAGUUGGACCAUGGUCCUUUCUGUGACAAUGGAAUUACUGAUCUGUCAUGGUUAUAAUUUACACAAGGGAAAUAAUAAUUAUCC-----AGGCUCACAUCCUACGUAUUUACG
((((..((((..((((....))))...)))).......((((((.(((((......)))))))))))......(((.(((....))).)))-----)))).................... ( -23.20)
>consensus
GCCUCGACAGUUGGGCCAUGGCCCUUUCUGUAACAAUGGAAUAACUGAUCUGUCAUGGUUAUAAUUUACACAAUGGAAAUAAUAAUCAUCCAUUGCAGGCCGACACU____GGUUACGGG
((((..((((..((((....))))...))))..(((((((.....(((....)))(((((((.((((.(.....).)))).)))))))))))))).)))).................... (-25.71 = -26.27 +   0.56) 

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 09:53:13 2006