Locus 4311

Sequence ID 3L_DroMel_CAF1
Location 12,679,112 – 12,679,260
Length 148
Max. P 0.697482
window6668 window6669

overview

Window 8

Location 12,679,112 – 12,679,220
Length 108
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 74.32
Mean single sequence MFE -29.48
Consensus MFE -16.79
Energy contribution -16.73
Covariance contribution -0.05
Combinations/Pair 1.22
Mean z-score -1.41
Structure conservation index 0.57
SVM decision value -0.02
SVM RNA-class probability 0.521947
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12679112 108 + 23771897
AACCAAACAACUAAUCAGAGUGUUAUCUUUUGGGGUU-UUU-------UUUCUUUUCAACAGGCUGGCAUCGAUCUGAAGGAGAACCUGGUGGCCGGAGCAUCGCCCUGGCCAUAU
.(((..........((((((((((((((.(((..(..-...-------.....)..))).))).))))))...)))))(((....))))))((((((.((...)).)))))).... ( -30.60)
>DroVir_CAF1 51942 93 + 1
AUGCCAAA-GUUAAU-AG---AUUAUGCUU-----UU-AU------UCGAUUG------CAGGCCGGCAUUGAUUUAAAGGAGAACCUGGUGGCCGGAGCUGCACCAUGGCCGUAU
..((((.(-((((((-((---(.......)-----))-))------).))))(------(((.(((((..........(((....)))....)))))..))))....))))..... ( -24.44)
>DroSec_CAF1 42961 115 + 1
AACCAAACAACUAAUCAGAGCGUUAUCUUUCGGGUUU-UUUUCUUUCUUUUUUUUUCAACAGGCUGGCAUCGAUCUGAAGGAGAACCUUGUGGCCGGAGCAUCGCCCUGGCCAUAU
.................(((.(((.(((((((((((.-.(.((..(((.((......)).)))..)).)..))))))))))).))))))((((((((.((...)).)))))))).. ( -30.40)
>DroSim_CAF1 41768 116 + 1
AACCAAACAACUAAUCAGAGCGUUAUCUUUCGGGUUUUUUUUCUUUCUUUUUUUUUCAACAGGCUGGCAUCGAUCUGAAGGAGAACCUGGUGGCCGGAGCAUCGCCCUGGCCAUAU
................(((......)))..(((((((((((((..((........................))...)))))))))))))((((((((.((...)).)))))))).. ( -28.76)
>DroEre_CAF1 43584 87 + 1
AAUCAAAAUUCUAAU-----------CUUUGGGUUUU-UUUU-----------------CAGGCUGGCAUCGAUCUGAAGGAGAACCUGGUGGCCGGAGCAUCGCCCUGGCCAUAU
...............-----------....(((((((-((((-----------------(((..((....))..)))))))))))))).((((((((.((...)).)))))))).. ( -33.50)
>DroYak_CAF1 44617 104 + 1
AAUCAAAAAUCUAAU-----------CUUUUGGGUUU-UUUUGUUUGUUUUCGUUCCAACAGGCUGGCAUCGAUCUGAAGGAGAACCUGGUGGCCGGAGCAUCGCCCUGGCCAUAU
....((((((((((.-----------...))))))))-)).............((((..(((..((....))..)))..))))......((((((((.((...)).)))))))).. ( -29.20)
>consensus
AACCAAAAAACUAAU_AG___GUUAUCUUUCGGGUUU_UUUU_____UUUUUUUUUCAACAGGCUGGCAUCGAUCUGAAGGAGAACCUGGUGGCCGGAGCAUCGCCCUGGCCAUAU
...........................................................(((..((....))..))).(((....))).((((((((.((...)).)))))))).. (-16.79 = -16.73 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,679,148 – 12,679,260
Length 112
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 78.37
Mean single sequence MFE -36.85
Consensus MFE -26.14
Energy contribution -26.58
Covariance contribution 0.45
Combinations/Pair 1.18
Mean z-score -1.23
Structure conservation index 0.71
SVM decision value 0.34
SVM RNA-class probability 0.697482
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12679148 112 + 23771897
UUUU-------UUUCUUUUCAACAGGCUGGCAUCGAUCUGAAGGAGAACCUGGUGGCCGGAGCAUCGCCCUGGCCAUAUCCAUCCAUGUAUCAUCCAUACGACGCGGCCUUCGCCGGCU
....-------.............(((((((...........(((.......((((((((.((...)).)))))))).....))).((..((........))..))......))))))) ( -33.60)
>DroPse_CAF1 35270 112 + 1
-UUUUCUGUCAUCUUU------CAGGCUGGAAUCGAUCUGAAGGAGAACCUUGUUGCCGGCGCAUCCCCGUGGCCAUAUCCGUCGAUGUAUCAUCCGUAUGAUGCCGCGUUUGCCGGCU
-......((..(((((------(((..((....))..))))))))..))......(((((((......((((((.(((((....)))))(((((....)))))))))))..))))))). ( -38.10)
>DroGri_CAF1 25390 107 + 1
UUU------UUGAUUG------CAGGCUGGCAUCGACUUGAAGGAGAAUUUGGUGGCUGGAGCUGCUCCAUGGCCGUAUCCAUCAAUGUAUCAUCCGUAUGACGCAGCGUUUGCCGGCU
...------.......------..((((((((.((..((((.(((.....((((.(.(((((...)))))).))))..))).))))((..((((....))))..)).))..)))))))) ( -35.00)
>DroEre_CAF1 43609 102 + 1
UUUUU-----------------CAGGCUGGCAUCGAUCUGAAGGAGAACCUGGUGGCCGGAGCAUCGCCCUGGCCAUAUCCCUCCAUGUAUCAUCCGUACGACGCGGCCUUCGCCGGCU
.....-----------------..(((((((...........((((......((((((((.((...)).))))))))....)))).........((((.....)))).....))))))) ( -37.30)
>DroMoj_CAF1 52478 105 + 1
--U------UCCAUUG------CAGGCUGGCAUCGAUCUGAAGGAGAAUCUAGUGGCCGGCGGAGCACCCUGGCCAUAUCCAUCGAUGUAUCAUCCGUAUGACGCAGCCUUUGCCGGUU
--.------.((...(------(((((((((((((((.....(((.......((((((((.((....)))))))))).))))))))))).((((....))))..)))))..))).)).. ( -37.10)
>DroAna_CAF1 43686 104 + 1
C------------UCGUUU---CAGGCCGGCAUCGAUUUGAAGGAGAACCUGGUGGCCGGAGCAACACCCUGGCCAUAUCCCUCGAUGUAUCAUCCGUAUGAUGCGGCCUUCGCCGGCU
.------------......---..((((((((((((.....(((....))).((((((((.(.....).)))))))).....)))))(((((((....))))))).......))))))) ( -40.00)
>consensus
UUU__________UUG______CAGGCUGGCAUCGAUCUGAAGGAGAACCUGGUGGCCGGAGCAUCACCCUGGCCAUAUCCAUCGAUGUAUCAUCCGUAUGACGCGGCCUUCGCCGGCU
........................(((((((........((.(((.......((((((((.(.....).)))))))).))).))..(((.((((....)))).)))......))))))) (-26.14 = -26.58 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:14 2006