Locus 6858

Sequence ID	3R_DroMel_CAF1
Location	18,142,122 – 18,142,268
Length	146
Max. P	0.999867

overview

Window 8

Location	18,142,122 – 18,142,233
Length	111
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	87.34
Mean single sequence MFE	-29.22
Consensus MFE	-23.22
Energy contribution	-24.90
Covariance contribution	1.68
Combinations/Pair	1.07
Mean z-score	-2.59
Structure conservation index	0.79
SVM decision value	2.07
SVM RNA-class probability	0.987130
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18142122 111 + 27905053
CGCAUUCAUGUAAUGCACAUGCAAACAUUUGUGCUGAAAUGCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAGAUACUAC---UACUACAACUACAGCUGCAGAUGUAG--
.((((..((((..(((....))).))))..)))).............((((((((((((.(((.((((((...........))).---.)))...)))))))))))))))....-- ( -31.60)
>DroSec_CAF1 170769 114 + 1
CGCAUUCAUGUAAUGCACAUGCAAACAUUUGUGCUGAAAUGCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAGAUACUACUACUACUACAACUACAGCUGCAGAUGUAG--
.((((..((((..(((....))).))))..)))).............((((((((((((..(((.....)))....((......))............))))))))))))....-- ( -31.40)
>DroSim_CAF1 175690 114 + 1
CGCAUUCAUGUAAUGCACAUGCAAACAUUUGUGCUGAAAUGCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAGAUACUACUACUACUACAACUACAGCUGCAGAUGUAG--
.((((..((((..(((....))).))))..)))).............((((((((((((..(((.....)))....((......))............))))))))))))....-- ( -31.40)
>DroEre_CAF1 182392 105 + 1
CGCAUUCAUGUAAUGCACAUGCAAACAUUUGUGCUGAAAUGCAACUUGUCUGCAGCUGUCAGUCAGUUAGAUACACAGAUACUACUACUACU---------GCUGCAGAUGUAC--
.((((..((((..(((....))).))))..)))).............(((((((((.((.(((.(((...((......))...)))))))).---------)))))))))....-- ( -29.20)
>DroAna_CAF1 165482 108 + 1
CGCAUUCAAGUAAUGCACAUGCAAACAUUUGUGCUGAAAUGCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAAAUACAC--------ACACAGACAAUCGCACAAGCGCCC
.(((((.....)))))..............(((((....(((...(((((((.(((((.....))))).(.....)........--------...)))))))..)))..))))).. ( -22.50)
>consensus
CGCAUUCAUGUAAUGCACAUGCAAACAUUUGUGCUGAAAUGCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAGAUACUACUACUACUACAACUACAGCUGCAGAUGUAG__
.(((((((......(((((..........))))))).))))).....((((((((((((..(((.....)))....((......))............))))))))))))...... (-23.22 = -24.90 +   1.68)

alignment

secondary structure

dotplot

Window 9

Location	18,142,122 – 18,142,233
Length	111
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	87.34
Mean single sequence MFE	-32.34
Consensus MFE	-23.77
Energy contribution	-24.65
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-1.81
Structure conservation index	0.74
SVM decision value	0.33
SVM RNA-class probability	0.693323
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18142122 111 - 27905053
--CUACAUCUGCAGCUGUAGUUGUAGUA---GUAGUAUCUGUGUGUCUAACUGACUGACAGCUGCAGACAAGUUGCAUUUCAGCACAAAUGUUUGCAUGUGCAUUACAUGAAUGCG
--((((..(((((((....)))))))..---))))...((((..(((.....)))..)))).((((((((...(((......)))....))))))))...(((((.....))))). ( -33.70)
>DroSec_CAF1 170769 114 - 1
--CUACAUCUGCAGCUGUAGUUGUAGUAGUAGUAGUAUCUGUGUGUCUAACUGACUGACAGCUGCAGACAAGUUGCAUUUCAGCACAAAUGUUUGCAUGUGCAUUACAUGAAUGCG
--((((..(((((((....)))))))..))))..((((..(((((((.....)))((...((((((((((...(((......)))....)))))))).)).))..))))..)))). ( -34.20)
>DroSim_CAF1 175690 114 - 1
--CUACAUCUGCAGCUGUAGUUGUAGUAGUAGUAGUAUCUGUGUGUCUAACUGACUGACAGCUGCAGACAAGUUGCAUUUCAGCACAAAUGUUUGCAUGUGCAUUACAUGAAUGCG
--((((..(((((((....)))))))..))))..((((..(((((((.....)))((...((((((((((...(((......)))....)))))))).)).))..))))..)))). ( -34.20)
>DroEre_CAF1 182392 105 - 1
--GUACAUCUGCAGC---------AGUAGUAGUAGUAUCUGUGUAUCUAACUGACUGACAGCUGCAGACAAGUUGCAUUUCAGCACAAAUGUUUGCAUGUGCAUUACAUGAAUGCG
--.....((((((((---------..((((((((((((....))).)).))).))))...))))))))......(((((.(((((((..((....)))))))......))))))). ( -27.90)
>DroAna_CAF1 165482 108 - 1
GGGCGCUUGUGCGAUUGUCUGUGU--------GUGUAUUUGUGUGUCUAACUGACUGACAGCUGCAGACAAGUUGCAUUUCAGCACAAAUGUUUGCAUGUGCAUUACUUGAAUGCG
(((((.((((((((.(((...(((--------.((((.((((..(((.....)))..)))).)))).)))....)))..)).)))))).)))))((((...((.....)).)))). ( -31.70)
>consensus
__CUACAUCUGCAGCUGUAGUUGUAGUAGUAGUAGUAUCUGUGUGUCUAACUGACUGACAGCUGCAGACAAGUUGCAUUUCAGCACAAAUGUUUGCAUGUGCAUUACAUGAAUGCG
.......(((((((((((..........................(((.....)))..)))))))))))......(((((.(((((((..((....)))))))......))))))). (-23.77 = -24.65 +   0.88)

alignment

secondary structure

dotplot

Window 0

Location	18,142,162 – 18,142,268
Length	106
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	72.79
Mean single sequence MFE	-21.64
Consensus MFE	-13.52
Energy contribution	-15.20
Covariance contribution	1.68
Combinations/Pair	1.12
Mean z-score	-3.38
Structure conservation index	0.62
SVM decision value	4.31
SVM RNA-class probability	0.999867
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18142162 106 + 27905053
GCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAGAUACUAC---UACUACAACUACAGCUGCAGAUGUAG---UACAUAACCACCCGCACACCCACACACCCACACAC
...((((((((((((((((.(((.((((((...........))).---.)))...)))))))))))))))).))---).................................. ( -23.50)
>DroSec_CAF1 170809 93 + 1
GCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAGAUACUACUACUACUACAACUACAGCUGCAGAUGUAG---UACAUAACCAC----------------CCACACAC
...((((((((((((((((..(((.....)))....((......))............))))))))))))).))---)..........----------------........ ( -23.30)
>DroSim_CAF1 175730 93 + 1
GCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAGAUACUACUACUACUACAACUACAGCUGCAGAUGUAG---UACAUAACCAC----------------CCACACAC
...((((((((((((((((..(((.....)))....((......))............))))))))))))).))---)..........----------------........ ( -23.30)
>DroEre_CAF1 182432 98 + 1
GCAACUUGUCUGCAGCUGUCAGUCAGUUAGAUACACAGAUACUACUACUACU---------GCUGCAGAUGUAC---UACAUACCC--CCAUACAUCCACACACCCACACAC
.......(((((((((.((.(((.(((...((......))...)))))))).---------)))))))))....---.........--........................ ( -19.50)
>DroAna_CAF1 165522 88 + 1
GCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAAAUACAC--------ACACAGACAAUCGCACAAGCGCCCUGGCAGACUCAC----------------AGAUACAC
......((((((.(((((((((((.....)))............--------...........(((....)))...)))))).))..)----------------)))))... ( -18.60)
>consensus
GCAACUUGUCUGCAGCUGUCAGUCAGUUAGACACACAGAUACUACUACUACUACAACUACAGCUGCAGAUGUAG___UACAUAACCAC________________CCACACAC
.......((((((((((((..(((.....)))....((......))............)))))))))))).......................................... (-13.52 = -15.20 +   1.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:41 2006