Locus 3010

Sequence ID 2L_DroMel_CAF1
Location 8,604,331 – 8,604,478
Length 147
Max. P 0.959188
window4788 window4789

overview

Window 8

Location 8,604,331 – 8,604,440
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.74
Mean single sequence MFE -22.12
Consensus MFE -12.90
Energy contribution -13.10
Covariance contribution 0.20
Combinations/Pair 1.21
Mean z-score -1.74
Structure conservation index 0.58
SVM decision value 0.47
SVM RNA-class probability 0.748428
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8604331 109 - 22407834
CUCC----CCCUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACA--CACAACCCGCCCCA-----UACCCCGUCGUCCUGGCCCUUCUACUCGUCCUUCCACUAACAAGAA
....----...(((((.((((((((((((((...))))))))........)))--))).....(((...-----.((......))...))).......................))))). ( -20.90)
>DroSec_CAF1 32753 96 - 1
CUCC----CCCUUUUGAGUCUGUUGACCAACAAUGUUGGUCACAACAUGUACA--CACAG----C-CCA-----UGUCCUG--------GCCCUUCUACUCGUCCUUCCACUAACAAGAA
....----.......((((.(((.(((((((...))))))))))(((((..(.--....)----.-.))-----)))....--------........))))................... ( -17.30)
>DroSim_CAF1 38438 102 - 1
CUCC----CCCUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACA--CACAGCUCGC-CCA-----UACCCCGUC------GUCCUUCUACUCGUCCUUCCACUAACAAGAA
....----...(((((.((((((((((((((...))))))))........)))--))).......-...-----......(.(------(..........)).)..........))))). ( -18.00)
>DroEre_CAF1 34498 104 - 1
CUCC----CACUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACACACACAG----C-CCA-------GCCCCUCGUCCUGCUCGUCCUGCUCGUCCUUCCACUAACAAGAA
....----...(((((.((((((((((((((...))))))))........)))))).(((----.-.((-------((..........))).)..)))................))))). ( -22.00)
>DroYak_CAF1 35075 102 - 1
CUUC----CCCUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACA--CACAG----C-CCA-------UCCCGUCGUCCUGGUCCUCCUGCUCGUCCUUCCACUAACAAGAA
....----...(((((.((((((((((((((...))))))))........)))--)))..----.-...-------....(.((..(.((....)).)..)).)..........))))). ( -21.60)
>DroAna_CAF1 33907 108 - 1
UUCCGCCACCCCAUCGAGUGUGUUGACCGACAAUGUUGGUCACAACAUGCACACACACAGUCCGGUCCAGGGGUCACCCCG-----------AUUCCGGCAGUUGUUCC-CUAACAAGAU
....(((..........((((((((((((((...))))))))......)))))).........((....((((...)))).-----------...)))))..(((((..-..)))))... ( -32.90)
>consensus
CUCC____CCCUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACA__CACAG____C_CCA_____UACCCCGUC______GUCCUUCUACUCGUCCUUCCACUAACAAGAA
..............(((((((((.(((((((...))))))))))...(((......))).....................................)))))).................. (-12.90 = -13.10 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 8,604,371 – 8,604,478
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.20
Mean single sequence MFE -30.73
Consensus MFE -18.39
Energy contribution -18.45
Covariance contribution 0.06
Combinations/Pair 1.15
Mean z-score -2.24
Structure conservation index 0.60
SVM decision value 1.50
SVM RNA-class probability 0.959188
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8604371 107 - 22407834
AGUGGCAGCGGGCAAAGCCGCCCCAACCCU--UCGUCCACCUCC----CCCUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACA--CACAACCCGCCCCA-----UACCCC
.((((..((((((......)))).......--............----.........((((((((((((((...))))))))........)))--))).....)).)))-----)..... ( -29.60)
>DroSec_CAF1 32785 104 - 1
AGUGGCAGCGGGCACAGUCGCCCCAACCCACAACGCCCACCUCC----CCCUUUUGAGUCUGUUGACCAACAAUGUUGGUCACAACAUGUACA--CACAG----C-CCA-----UGUCCU
.((((....((((......))))....)))).........(((.----.......)))..(((.(((((((...))))))))))(((((..(.--....)----.-.))-----)))... ( -27.60)
>DroSim_CAF1 38472 108 - 1
AGUGGCAGCGGGCACAGUCGCCCCAACCCACCACGCCCACCUCC----CCCUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACA--CACAGCUCGC-CCA-----UACCCC
.(.((((((((((......)))).....................----.........((((((((((((((...))))))))........)))--))).))).))-)).-----...... ( -32.90)
>DroEre_CAF1 34538 101 - 1
AGUGGCAGCGGGCAAAGCCAUCCCAAGC---AGCACCCACCUCC----CACUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACACACACAG----C-CCA-------GCCC
...(((...((((...((........))---.............----......((.((((((((((((((...))))))))........)))))).)))----)-)).-------))). ( -29.60)
>DroYak_CAF1 35115 92 - 1
AGUGGCAGUGGGCAAAGCCAUCCCAA----------CCACCUUC----CCCUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACA--CACAG----C-CCA-------UCCC
.(.(((.((((...............----------))))....----.........((((((((((((((...))))))))........)))--))).)----)-)).-------.... ( -25.96)
>DroAna_CAF1 33935 115 - 1
AGUGGCAGUGGGCAAAGCACUU---GCCUU--UGGUCCCCUUCCGCCACCCCAUCGAGUGUGUUGACCGACAAUGUUGGUCACAACAUGCACACACACAGUCCGGUCCAGGGGUCACCCC
.((((.((.(((((((((....---).)))--))..))))).)))).(((((((((.((((((((((((((...))))))))..........))))))....))))...)))))...... ( -38.70)
>consensus
AGUGGCAGCGGGCAAAGCCGCCCCAACCC___ACGCCCACCUCC____CCCUUUUGAGUGUGUUGACCAACAAUGUUGGUCACAACAUGUACA__CACAG____C_CCA_____UACCCC
.(((.....((((.....................)))).................(.(..(((((((((((...))))))))..)))..).)...)))...................... (-18.39 = -18.45 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:04 2006