Locus 2611

Sequence ID 3L_DroMel_CAF1
Location 7,228,361 – 7,228,549
Length 188
Max. P 0.859690
window4088 window4089 window4090

overview

Window 8

Location 7,228,361 – 7,228,481
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.95
Mean single sequence MFE -25.62
Consensus MFE -20.68
Energy contribution -20.56
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -1.73
Structure conservation index 0.81
SVM decision value 0.82
SVM RNA-class probability 0.859690
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7228361 120 + 23771897
UAUUUGUUCCCGCAUUUACCAUUUACCAUUUACCUUGGCACUCCGAGAGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCAC
..((((((...((....................(((((....))))).(((.(((.....))).))).........))...))))))........((((((((......)))))).)).. ( -24.10)
>DroSec_CAF1 10072 113 + 1
UGUUUGUUCCCGCAUUUGC-------CAUUUACCUUGGCGCACCGAGAGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGUCUCGAGAACUCACUCGAGAGCAU
.(((((((...((....((-------((.......)))).........(((.(((.....))).))).........))...)))))))........(((((((......))))))).... ( -26.20)
>DroSim_CAF1 9982 120 + 1
UGUUUGUUCCCCCAUUUACCAUUUACCAUUUACCUUGGCGCACCGAGAGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCAU
(((((((..........................(((((....))))).(((.(((.....))).)))..)))))))...................((((((((......)))))).)).. ( -25.40)
>DroEre_CAF1 10089 113 + 1
UGCUUGUUCCCGCAUUUAC-------CAUUCACCUUGCCGCACCGCGUGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGCCUCGAGAACUCGCUCGAGAGCAU
(((........))).....-------..(((((...((......))(((((.(((.....))).)))))....................))))).((((((((......)))))).)).. ( -27.60)
>DroYak_CAF1 11035 120 + 1
UGCUUGUUCCCGCAUUUACCAUCUACCAUUUACCUUGCCACAUCGAGUGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCAU
((((.......((.(((((.................(((((.....)))))........((((.((..........)).))))......))))).))((((((......)))))))))). ( -24.80)
>consensus
UGUUUGUUCCCGCAUUUACCAU_UACCAUUUACCUUGGCGCACCGAGAGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCAU
............................(((((((((......)))).(((.(((.....))).)))......................))))).((((((((......)))))).)).. (-20.68 = -20.56 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,228,401 – 7,228,515
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.29
Mean single sequence MFE -24.37
Consensus MFE -18.93
Energy contribution -19.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.78
SVM decision value 0.73
SVM RNA-class probability 0.836397
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7228401 114 + 23771897
CUCCGAGAGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCACCGUUAGUUUCAUAUAUAUAUUUAUAUAUGUACUA------
...((...(((.(((.....))).)))............................((((((((......)))))).))..)).((((..((((((((....)))))))).))))------ ( -24.50)
>DroEre_CAF1 10122 110 + 1
CACCGCGUGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGCCUCGAGAACUCGCUCGAGAGCAUCGUUAGUUUCAUGCACAAAGAUAU----AUUCUA------
....(((((((.(((.....))).)))))....................((((((((((((((......)))))).))..(....)))))))))....(((...----..))).------ ( -25.30)
>DroYak_CAF1 11075 116 + 1
CAUCGAGUGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCAUCGUUAGUUGCAAGCACAAAAAUAU----AUAAUAUAAUAU
......(((((.(((.....))).)))))....................(((...((((((((......)))))).))...((.....))...)))........----............ ( -23.30)
>consensus
CACCGAGUGGCCUUAACAUUUAACGCCACAUAAACAGCCUUAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCAUCGUUAGUUUCAUGCACAAAAAUAU____AUACUA______
......(((((.(((.....))).)))))..........................((((((((......)))))).)).......................................... (-18.93 = -19.27 +   0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,228,441 – 7,228,549
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 75.51
Mean single sequence MFE -22.57
Consensus MFE -13.44
Energy contribution -13.00
Covariance contribution -0.44
Combinations/Pair 1.17
Mean z-score -1.65
Structure conservation index 0.60
SVM decision value 0.15
SVM RNA-class probability 0.609561
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7228441 108 + 23771897
UAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCACCGUUAGUUUCAUAUAUAUAUUUAUAUAUGUACUA-------UAUAUGCAUGUUA-----CUUAUAAGGAGGCAACCAUAU
.........(((...((((((((......)))....(((....((((..((((((((....)))))))).))))-------....)))......-----........)))))...))).. ( -25.30)
>DroEre_CAF1 10162 101 + 1
UAAUAAACCGUGAAAGCCUCGAGAACUCGCUCGAGAGCAUCGUUAGUUUCAUGCACAAAGAUAU----AUUCUA-------UAUACCAAUUUUU-----CUUAUAAGGGGGC-ACC--AU
.........((((((((((((((......)))))).))..(....)))))))((....(((...----..))).-------....((..((...-----.....))..))))-...--.. ( -17.60)
>DroYak_CAF1 11115 115 + 1
UAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCAUCGUUAGUUGCAAGCACAAAAAUAU----AUAAUAUAAUAUGUAUAUGCAUUUUACAUAUGUUAUAAGGGGUU-ACCACAU
.....(((((((...((((((((......)))))).))...((.....))...))).......(----(((((...(((((((.........)))))))))))))...))))-....... ( -24.80)
>consensus
UAAUAAACCGUGAAAGCCUCGAGAACUCACUCGAGAGCAUCGUUAGUUUCAUGCACAAAAAUAU____AUACUA_______UAUAUGCAUUUUA_____CUUAUAAGGGGGC_ACCA_AU
.......((......((((((((......)))))).)).......((.....))....................................................))............ (-13.44 = -13.00 +  -0.44)

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 10:37:28 2006