Locus 3072

Sequence ID	2L_DroMel_CAF1
Location	8,763,443 – 8,763,579
Length	136
Max. P	0.976934

overview

Window 6

Location	8,763,443 – 8,763,544
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	84.93
Mean single sequence MFE	-29.66
Consensus MFE	-24.66
Energy contribution	-24.97
Covariance contribution	0.31
Combinations/Pair	1.16
Mean z-score	-1.59
Structure conservation index	0.83
SVM decision value	0.09
SVM RNA-class probability	0.579972
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8763443 101 + 22407834
GUUUCCCUGUAUUUGAAGUGCCAAAAAGCACACUUUGGAUGCU------------UUUUUUGUC-------GCCGCCGUUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCA
........(((((..(((((..........)))))..))))).------------.........-------...((((...(((((((.....((((....)))).)))))))..)))). ( -29.00)
>DroSec_CAF1 67720 101 + 1
GUUUCCCUGUAUUUGAAGUGCCAAAAAGCACACUUUGGAUGCU------------UUUUUUGUC-------GCCGCCGCUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCA
........(((((..(((((..........)))))..))))).------------.....((((-------(.(((((((((.(((((......)))))...)))))).)))...))))) ( -31.80)
>DroSim_CAF1 70335 101 + 1
GUUUCCCUGUAUUUGAAGUGCCAAAAAGCACACUUUGGAUGCU------------UUUUUUGUC-------GCCGCCGCUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCA
........(((((..(((((..........)))))..))))).------------.....((((-------(.(((((((((.(((((......)))))...)))))).)))...))))) ( -31.80)
>DroEre_CAF1 71676 99 + 1
AGUUCCCUGUAUUUGAAGUGCCAAAAAGCACACUUUGGAUGCC-------AU---UUUUUU-----------GCGCCGCUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCA
..........(((..(((((..........)))))..)))(((-------(.---......-----------((((((((((.(((((......)))))...)))))).))))..)))). ( -33.40)
>DroYak_CAF1 70700 105 + 1
AGUUCCCUGUAUUUGAAGUGCCAAAAAGCACACUUUGGAUGCU-------AU---UUUUUUGUU-----GUGGCGCCGUUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCA
........(((((..(((((..........)))))..))))).-------..---.....((((-----(.(((((((((((.(((((......)))))...)))))).))))).))))) ( -31.00)
>DroAna_CAF1 69252 119 + 1
AGUUGCCUGUAUUUGAAGUGCCAAAAAGCACACUUUGACUUGUUCUUUUUAUUUAUUUUUUGUUUUUGUGUUCCGCUG-UUGUAGUCGUAUUAUUGGGUUGUCGAGUGCGCGCUUUAGUG
............(((((((((.....(((((((...(((......................)))...))))...))).-..(((.(((.(((....)))...))).)))))))))))).. ( -20.95)
>consensus
AGUUCCCUGUAUUUGAAGUGCCAAAAAGCACACUUUGGAUGCU____________UUUUUUGUC_______GCCGCCGCUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCA
........(((((..(((((..........)))))..)))))................................((((...(((((((.....((((....)))).)))))))..)))). (-24.66 = -24.97 +   0.31)

alignment

secondary structure

dotplot

Window 7

Location	8,763,483 – 8,763,579
Length	96
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	93.26
Mean single sequence MFE	-31.06
Consensus MFE	-25.02
Energy contribution	-25.26
Covariance contribution	0.24
Combinations/Pair	1.07
Mean z-score	-2.31
Structure conservation index	0.81
SVM decision value	1.78
SVM RNA-class probability	0.976934
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8763483 96 + 22407834
GCU--UUUUUUGUC--GCCGCCGUUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCAAGGAUUUAUGCUCGAUGGCG---AUAUUUGUUUAGCCG
(((--.....((((--(((((((...(((((((.....((((....)))).)))))))..))))...((.......))...))))---))).......))).. ( -29.20)
>DroSec_CAF1 67760 96 + 1
GCU--UUUUUUGUC--GCCGCCGCUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCAAGGAUUUAUGCUCGAUGGCG---AUAUUUGUUUAGCCG
(((--.....((((--(((((((((((.(((((......)))))...)))))).))...((((((........))).))).))))---))).......))).. ( -32.00)
>DroSim_CAF1 70375 96 + 1
GCU--UUUUUUGUC--GCCGCCGCUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCAAGGAUUUAUGCUCGAUGGCG---AUAUUUGUUUAGCCG
(((--.....((((--(((((((((((.(((((......)))))...)))))).))...((((((........))).))).))))---))).......))).. ( -32.00)
>DroEre_CAF1 71716 94 + 1
GCCAUUUUUUU------GCGCCGCUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCAAGGAUUUAUGCUCGAUGGCG---AUAUUUGUUUAGCCG
((((((.....------((((((((((.(((((......)))))...)))))).))))...((((........)))).)))))).---............... ( -31.00)
>DroYak_CAF1 70740 103 + 1
GCUAUUUUUUUGUUGUGGCGCCGUUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCAAGGAUUUAUGCUCGAUGGCGAUGAUAUUUGUUUAGCCG
((((..(((((((((.(((((((((((.(((((......)))))...)))))).))))).)))))))))..)).)).....(((...(((....)))..))). ( -31.10)
>consensus
GCU__UUUUUUGUC__GCCGCCGCUUGUGCUCGUAUUAUUGAGUUGUCGAGUGAGCGCUUUGGCAAGGAUUUAUGCUCGAUGGCG___AUAUUUGUUUAGCCG
((....((((((((....(((((((((.(((((......)))))...)))))).)))....)))))))).....)).....(((...............))). (-25.02 = -25.26 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	8,763,483 – 8,763,579
Length	96
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	93.26
Mean single sequence MFE	-17.56
Consensus MFE	-14.41
Energy contribution	-14.41
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.82
SVM decision value	0.08
SVM RNA-class probability	0.575813
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8763483 96 - 22407834
CGGCUAAACAAAUAU---CGCCAUCGAGCAUAAAUCCUUGCCAAAGCGCUCACUCGACAACUCAAUAAUACGAGCACAAACGGCGGC--GACAAAAAA--AGC
..............(---((((..((.(((........)))....(.((((....................)))).)...))..)))--)).......--... ( -18.25)
>DroSec_CAF1 67760 96 - 1
CGGCUAAACAAAUAU---CGCCAUCGAGCAUAAAUCCUUGCCAAAGCGCUCACUCGACAACUCAAUAAUACGAGCACAAGCGGCGGC--GACAAAAAA--AGC
..............(---((((...(.(((........))))....((((..((((..............))))....))))..)))--)).......--... ( -18.54)
>DroSim_CAF1 70375 96 - 1
CGGCUAAACAAAUAU---CGCCAUCGAGCAUAAAUCCUUGCCAAAGCGCUCACUCGACAACUCAAUAAUACGAGCACAAGCGGCGGC--GACAAAAAA--AGC
..............(---((((...(.(((........))))....((((..((((..............))))....))))..)))--)).......--... ( -18.54)
>DroEre_CAF1 71716 94 - 1
CGGCUAAACAAAUAU---CGCCAUCGAGCAUAAAUCCUUGCCAAAGCGCUCACUCGACAACUCAAUAAUACGAGCACAAGCGGCGC------AAAAAAAUGGC
...............---.(((((.(.(((........))))...((((.(.((.(....(((........)))..).)).)))))------......))))) ( -17.40)
>DroYak_CAF1 70740 103 - 1
CGGCUAAACAAAUAUCAUCGCCAUCGAGCAUAAAUCCUUGCCAAAGCGCUCACUCGACAACUCAAUAAUACGAGCACAAACGGCGCCACAACAAAAAAAUAGC
.(((((......)).....(((...(.(((........))))...(.((((....................)))).)....))))))................ ( -15.05)
>consensus
CGGCUAAACAAAUAU___CGCCAUCGAGCAUAAAUCCUUGCCAAAGCGCUCACUCGACAACUCAAUAAUACGAGCACAAGCGGCGGC__GACAAAAAA__AGC
..................((((...(.(((........))))...(.((((....................)))).)....)))).................. (-14.41 = -14.41 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:39 2006