Locus 9528

Sequence ID 3R_DroMel_CAF1
Location 25,179,557 – 25,179,698
Length 141
Max. P 0.933732
window15244 window15245

overview

Window 4

Location 25,179,557 – 25,179,666
Length 109
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 74.19
Mean single sequence MFE -31.28
Consensus MFE -12.81
Energy contribution -16.23
Covariance contribution 3.42
Combinations/Pair 1.17
Mean z-score -2.02
Structure conservation index 0.41
SVM decision value 0.35
SVM RNA-class probability 0.698720
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25179557 109 + 27905053
-GUGGGGGUCCUUG-GGAACCACCCACUUAUCGUUUUCAGUGCGACGAGCGGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCUCCCCUCACUUUU-----UUUUUUUGGC
-(((((((((((((-(....)..((.((..((((.......))))..)).))))))))).......(((((((((....)))))))))...))))))....-----.......... ( -36.20)
>DroSim_CAF1 38234 103 + 1
-G-GGGGGUCCUUG-GGCACCACCCACUUAUCGCUUUCAGUGCGACGAGCGGCAAGGACAUCACUUGAAAAUUGCGUAAGUAGUUUUCGCCCCUCACUUU----------UUUGGC
-(-(((((((((((-(....)..((.((..((((.......))))..)).))))))))).......(((((((((....)))))))))..))))).....----------...... ( -41.50)
>DroEre_CAF1 38739 102 + 1
---GGGGGUGCUUG-GGAACCACCCACUUAUCGCUUUCAGUGCGACGAGAGGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCGCCCCUUACUUUCU----------UGGC
---(((((((((((-((.....))).((..((((.......))))..)))))).............(((((((((....)))))))))))))))........----------.... ( -33.60)
>DroYak_CAF1 40096 115 + 1
CGAGGGGAUCCUUG-GGAACCACCCACUUAUCGCUUUCAGUGCGAGGAGAGGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCGCCCCUCACUUUCUUUCUUUUUUUUGGC
.((((((.((((((-((......)).(((.((((.......)))).)))...))))))........(((((((((....))))))))).))))))..................... ( -37.50)
>DroAna_CAF1 36204 88 + 1
-A-------------GGACCCCUCCACUUAUCGCUUUUAGUUGAACAA--CGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCUCUUCUCAGUU------------UUAGC
-.-------------(((....))).......(((...(..(((....--(....)..........(((((((((....))))))))).....)))..)------------..))) ( -14.70)
>DroPer_CAF1 42827 85 + 1
-GUGGG-----UGGGGUAGCAGCCCACUUAUCGCGUCCAGC-------------AGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCUCU-UUCACUUUU-----------UGGU
-(((((-----((((((....)))).........((((...-------------.))))..)))).(((((((((....)))))))))...-..)))....-----------.... ( -24.20)
>consensus
_G_GGGGGUCCUUG_GGAACCACCCACUUAUCGCUUUCAGUGCGACGAG_GGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCGCCCCUCACUUU___________UUGGC
...((((............((..((.(((.((((.......)))).))).))...)).........(((((((((....))))))))).))))....................... (-12.81 = -16.23 +   3.42)

alignment

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secondary structure

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dotplot

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Window 5

Location 25,179,595 – 25,179,698
Length 103
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 73.72
Mean single sequence MFE -22.28
Consensus MFE -11.52
Energy contribution -11.92
Covariance contribution 0.39
Combinations/Pair 1.22
Mean z-score -2.03
Structure conservation index 0.52
SVM decision value 1.23
SVM RNA-class probability 0.933732
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25179595 103 + 27905053
UGCGACGAGCGGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCUCCCCUCACUUUU--------UUUUUUUGGCCUUGU-CCGCAUUGUUUUAUUCCGUUUCCCUUC-
...((((((((((((((.........(((((((((....)))))))))...((........--------.......))))))).-)))).))))).................- ( -24.46)
>DroSim_CAF1 38271 98 + 1
UGCGACGAGCGGCAAGGACAUCACUUGAAAAUUGCGUAAGUAGUUUUCGCCCCUCACUUU-------------UUUGGCCUUGU-CCGCAUUGUUUUAUUCCGUUUCCCUUU-
...((((((((((((((.........(((((((((....)))))))))...((.......-------------...))))))).-)))).))))).................- ( -28.60)
>DroEre_CAF1 38775 98 + 1
UGCGACGAGAGGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCGCCCCUUACUUUC---U----------UGGCCUUGU-CCGCAUUGUUUUAUUCUGUUUCCCUUU-
(((((((((.(.((((((.......((((((((((....)))))))))).........)))---)----------)).))))))-.))))......................- ( -25.09)
>DroWil_CAF1 117432 102 + 1
CA--------CACAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCUCUUC-AACCAUUUUCCUUCAUGUUUUUGUUGUGUU-UCUUCAUGUUUUGUUGUUAUUUUCGUU-
((--------(((((((((((.....(((((((((....))))))))).....-..............))))))))).))))..-...........................- ( -15.75)
>DroYak_CAF1 40135 108 + 1
UGCGAGGAGAGGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCGCCCCUCACUUUC---UUUCUUUUUUUUGGCCUUGU-CCGCAUUGUUUUAUUCUGUUUCCCUUU-
...((((.((((((.(((((......(((((((((....)))))))))(((..........---............)))..)))-))(.((......)).))))))))))).- ( -23.45)
>DroAna_CAF1 36230 96 + 1
UUGAACAA--CGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCUCUUCUCAGUU---------------UUAGCCUUGUUUUGCUUUGUUUUAUAUUGUUUCCUUUCU
..((((((--.(((((.(((......(((((((((....)))))))))........((.---------------...))..)))))))).))))))................. ( -16.30)
>consensus
UGCGACGAG_GGCAAGGACAUCACUUGAAAAUUGCCUAAGUAGUUUUCGCCCCUCACUUU_____________UUUGGCCUUGU_CCGCAUUGUUUUAUUCUGUUUCCCUUU_
.(((......((((((.......)))(((((((((....))))))))).............................)))......)))........................ (-11.52 = -11.92 +   0.39)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:32 2006