Locus 2005

Sequence ID 3L_DroMel_CAF1
Location 5,509,005 – 5,509,126
Length 121
Max. P 0.651825
window3138 window3139

overview

Window 8

Location 5,509,005 – 5,509,104
Length 99
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 76.14
Mean single sequence MFE -23.98
Consensus MFE -10.07
Energy contribution -11.35
Covariance contribution 1.28
Combinations/Pair 1.26
Mean z-score -2.11
Structure conservation index 0.42
SVM decision value 0.25
SVM RNA-class probability 0.651825
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5509005 99 - 23771897
UACUAUCCCGGCUCGGGAUAUGGAUCUACCACCUACUACCCAAACCAGGGGAGCUACGGUUCCUCCGGCUACUACCCAACUCAAGGCUAU---------AACUAUUAU
...(((((((...)))))))(((.....))).............((.(((((((....))))))).))......................---------......... ( -24.40)
>DroSec_CAF1 71136 99 - 1
UACUAUCCCGGCUCGGGAUAUGGAUCUACCACCUACUAUCCCAACCAGGGGAGCUACGGUUCCUCCGGCUACUACCCAACUCAAGGCUAU---------AACUAUUAU
.........((((.((((((.((........))...))))))..((.(((((((....))))))).))................))))..---------......... ( -27.80)
>DroSim_CAF1 72614 99 - 1
UACUAUCCCGGGUCGGGAUAUGGAUCUACCACCUACUAUCCCAACCAGGGGAGCUACGGUUCCGCCGGCUACUACCCAACUCAAGGCUAU---------AACUAUUAU
.......((.(((.((((((.((........))...)))))).))).))(((((....)))))(((..................)))...---------......... ( -28.87)
>DroEre_CAF1 69013 99 - 1
UAUUAUCCAGGCUCGGGAUAUGGCUCUACCACCUACUACCCCAACCAGGGGGGCUAUGGUUCCUCCAGCUACUACCCCACCCAAGGCUAU---------AACUAUUAU
.........((...(((...(((((.....(((.....((((......)))).....)))......)))))...)))...))........---------......... ( -21.90)
>DroYak_CAF1 60084 93 - 1
UAUUACCCAGGUUCUGGAUACGGAUCUACCGCCUACUAUCCCAACCAGGGCGGCUAUGGUUCC------UACUAUCCAACCCAGGGCUAU---------AACUACUAU
(((..(((.(((..((((((.(((.(((((((((.............))))))...))).)))------...)))))))))..)))..))---------)........ ( -27.02)
>DroAna_CAF1 31153 97 - 1
-----UCCCAG------CUAUGGCUCUUCCAACUACUAUCCUAACACCGGGUAUUAUGGAUCCUCAAAUGUCUAUUCCAGCCAAGGAUAUGUCCCCAACAAUUACUAC
-----......------...(((((...........(((((.......)))))..((((((........))))))...))))).(((....))).............. ( -13.90)
>consensus
UACUAUCCCGGCUCGGGAUAUGGAUCUACCACCUACUAUCCCAACCAGGGGAGCUACGGUUCCUCCGGCUACUACCCAACCCAAGGCUAU_________AACUAUUAU
...((((((.....))))))(((.....)))(((.....((......))(((((....)))))....................)))...................... (-10.07 = -11.35 +   1.28)

alignment

Postscript

secondary structure

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dotplot

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Window 9

Location 5,509,026 – 5,509,126
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 88.90
Mean single sequence MFE -31.12
Consensus MFE -21.46
Energy contribution -21.66
Covariance contribution 0.20
Combinations/Pair 1.12
Mean z-score -2.13
Structure conservation index 0.69
SVM decision value 0.19
SVM RNA-class probability 0.627739
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5509026 100 - 23771897
GAACUACUACGGCUCAUCGGGAUACUAUCCCGGCUCGGGAUAUGGAUCUACCACCUACUACCCAAACCAGGGGAGCUACGGUUCCUCCGGCUACUACCCA
..........((......(((....(((((((...)))))))(((.....))).......)))...((.(((((((....))))))).)).......)). ( -31.40)
>DroSec_CAF1 71157 100 - 1
GAACUACUACGGCUCAUCGGGAUACUAUCCCGGCUCGGGAUAUGGAUCUACCACCUACUAUCCCAACCAGGGGAGCUACGGUUCCUCCGGCUACUACCCA
..........((......((((((.(((((((...)))))))(((.....))).....))))))..((.(((((((....))))))).)).......)). ( -34.70)
>DroSim_CAF1 72635 100 - 1
GAACUACUACGGCUCAUCGGGAUACUAUCCCGGGUCGGGAUAUGGAUCUACCACCUACUAUCCCAACCAGGGGAGCUACGGUUCCGCCGGCUACUACCCA
.........((((....((((((...))))))(((.((((((.((........))...)))))).)))...(((((....)))))))))........... ( -37.90)
>DroEre_CAF1 69034 100 - 1
CAACUACUACGGCUCAUCGGGAUAUUAUCCAGGCUCGGGAUAUGGCUCUACCACCUACUACCCCAACCAGGGGGGCUAUGGUUCCUCCAGCUACUACCCC
..........((((.....((((...)))).)))).(((...(((((.....(((.....((((......)))).....)))......)))))...))). ( -24.30)
>DroYak_CAF1 60105 94 - 1
GAACUACUACGGCUCAUCGGGCUAUUACCCAGGUUCUGGAUACGGAUCUACCGCCUACUAUCCCAACCAGGGCGGCUAUGGUUCC------UACUAUCCA
(((((.(....)......(((......))).))))).(((((.(((.(((((((((.............))))))...))).)))------...))))). ( -27.32)
>consensus
GAACUACUACGGCUCAUCGGGAUACUAUCCCGGCUCGGGAUAUGGAUCUACCACCUACUAUCCCAACCAGGGGAGCUACGGUUCCUCCGGCUACUACCCA
(((((.....(((((...(((....(((((((...)))))))(((.....)))))).....(((.....))))))))..)))))................ (-21.46 = -21.66 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:17 2006