Locus 7920

Sequence ID	X_DroMel_CAF1
Location	19,714,937 – 19,715,061
Length	124
Max. P	0.987120

overview

Window 6

Location	19,714,937 – 19,715,028
Length	91
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	71.06
Mean single sequence MFE	-25.10
Consensus MFE	-10.94
Energy contribution	-12.03
Covariance contribution	1.09
Combinations/Pair	1.35
Mean z-score	-1.80
Structure conservation index	0.44
SVM decision value	0.38
SVM RNA-class probability	0.714226
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19714937 91 + 22224390
CAAAAGCGUUUAGCGGCAGUCAGAUUAUACUUGCGUUUAUGCUAAUGC----------U----------UUUAUGCUGCUCUGAUGACGAAUCAAUGUCAUCAAGGGUGGU
.(((((((((.((((...((.((......)).)).....)))))))))----------)----------)))..((..(((((((((((......))))))).))))..)) ( -30.20)
>DroSec_CAF1 11151 88 + 1
CAAAAGCGUUUAGCGGCAGUCAGAUUAUACUUGCGUUUAUGCUAAUGC----------U----------UUUAUGCUGCUCUGAUGACGAAUCAAUGUCAUCAAGGG---U
.(((((((((.((((...((.((......)).)).....)))))))))----------)----------))).....((((((((((((......))))))).))))---) ( -25.80)
>DroEre_CAF1 8075 88 + 1
CCAAAGCGUUUAGCGGCAGUCAGAUUAUACUUGCGUUUAUGCUAAUGC----------U----------UUUAUGCUGCCCUGAUGACGAAUCAAUGUCAUCAAGGU---A
..((((((((.((((...((.((......)).)).....)))))))))----------)----------)).....((((.((((((((......)))))))).)))---) ( -25.50)
>DroWil_CAF1 11913 78 + 1
UA-AAGCGUUUUGCUGGAAAAGGAUUAUGUUUACACUUACAUUUGUGC----------U----------UAUUUAACGCAUUGACAGCCAAU----GGCAACG--------
..-....(((.(((((((.(((.((.((((........))))..)).)----------)----------).))))..)))..))).(((...----)))....-------- ( -12.30)
>DroYak_CAF1 7959 88 + 1
CAAAAGCGUUUAGCGGCAGUCAGAUUAUACUUGCGUUUAUGCUAAUGC----------U----------UUUAUGCUGCUCUGAUGACAAAUCAAUGUCAUCAAGGG---U
.(((((((((.((((...((.((......)).)).....)))))))))----------)----------))).....((((((((((((......))))))).))))---) ( -27.00)
>DroAna_CAF1 13196 104 + 1
CAAAAGCGUUUAGCGGCAGCCAGAUUAUGUUUGCGUUUAUGCUGAUGGCUGCUGCUGCUUCUCUUCCUCUUCUUGCUGCACU---GACGAGCCAAGGUCGUUAAGGG----
...((((....(((((((((((...((((........))))....)))))))))))))))(((((.....(((((..((...---.....))))))).....)))))---- ( -29.80)
>consensus
CAAAAGCGUUUAGCGGCAGUCAGAUUAUACUUGCGUUUAUGCUAAUGC__________U__________UUUAUGCUGCUCUGAUGACGAAUCAAUGUCAUCAAGGG___U
............((((((((........))..(((((......))))).........................))))))..(((((((........)))))))........ (-10.94 = -12.03 +   1.09)

alignment

secondary structure

dotplot

Window 7

Location	19,714,968 – 19,715,061
Length	93
Sequences	4
Columns	94
Reading direction	forward
Mean pairwise identity	81.64
Mean single sequence MFE	-28.73
Consensus MFE	-19.99
Energy contribution	-19.43
Covariance contribution	-0.56
Combinations/Pair	1.19
Mean z-score	-2.65
Structure conservation index	0.70
SVM decision value	2.07
SVM RNA-class probability	0.987120
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19714968 93 + 22224390
UGCGUUUAUGCUAAUGCUUUUAUGCUGCUCUGAUGACGAAUCAAUGUCAUCAAGGGUGGUGUGCAAUUGAGAGUGU-GGGAGUGGGGCGGACAA
..(((((...((.((((((((((((..(((((((((((......))))))).))))..))))......))))))))-.))....)))))..... ( -28.10)
>DroSec_CAF1 11182 91 + 1
UGCGUUUAUGCUAAUGCUUUUAUGCUGCUCUGAUGACGAAUCAAUGUCAUCAAGGG---UGCGCAAAUGAGAGUGGCAGUGGUGGGGUGGGCAA
...((((((.(((.((((....((((((((((((((((......))))))).))))---)).))).((....))))))....))).)))))).. ( -28.50)
>DroEre_CAF1 8106 76 + 1
UGCGUUUAUGCUAAUGCUUUUAUGCUGCCCUGAUGACGAAUCAAUGUCAUCAAGGU---AGUG---------------GGAGUGGGGUAGGCAA
...((((((.((...((((((..((((((.((((((((......)))))))).)))---))))---------------))))))).)))))).. ( -28.70)
>DroYak_CAF1 7990 88 + 1
UGCGUUUAUGCUAAUGCUUUUAUGCUGCUCUGAUGACAAAUCAAUGUCAUCAAGGG---UGUGCAAGUGGCAUU---CGUAGUGGGGUGGACAA
...((((((.((((((((....((((((((((((((((......))))))).))))---)).)))...))))).---.....))).)))))).. ( -29.60)
>consensus
UGCGUUUAUGCUAAUGCUUUUAUGCUGCUCUGAUGACGAAUCAAUGUCAUCAAGGG___UGUGCAA_UGAGAGU____GGAGUGGGGUGGACAA
...((((((.(((..((......))..((.((((((((......)))))))).))...........................))).)))))).. (-19.99 = -19.43 +  -0.56)

alignment

secondary structure

dotplot

Window 8

Location	19,714,968 – 19,715,061
Length	93
Sequences	4
Columns	94
Reading direction	reverse
Mean pairwise identity	81.64
Mean single sequence MFE	-16.93
Consensus MFE	-12.12
Energy contribution	-11.88
Covariance contribution	-0.25
Combinations/Pair	1.08
Mean z-score	-2.05
Structure conservation index	0.72
SVM decision value	1.01
SVM RNA-class probability	0.900506
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19714968 93 - 22224390
UUGUCCGCCCCACUCCC-ACACUCUCAAUUGCACACCACCCUUGAUGACAUUGAUUCGUCAUCAGAGCAGCAUAAAAGCAUUAGCAUAAACGCA
.................-...........(((.........((((((((........))))))))....((......))....)))........ ( -13.70)
>DroSec_CAF1 11182 91 - 1
UUGCCCACCCCACCACUGCCACUCUCAUUUGCGCA---CCCUUGAUGACAUUGAUUCGUCAUCAGAGCAGCAUAAAAGCAUUAGCAUAAACGCA
.(((.(..........(((((........)).)))---....(((((((........)))))))).)))((......))....((......)). ( -16.30)
>DroEre_CAF1 8106 76 - 1
UUGCCUACCCCACUCC---------------CACU---ACCUUGAUGACAUUGAUUCGUCAUCAGGGCAGCAUAAAAGCAUUAGCAUAAACGCA
.(((............---------------..((---.((((((((((........)))))))))).)).......((....))......))) ( -19.00)
>DroYak_CAF1 7990 88 - 1
UUGUCCACCCCACUACG---AAUGCCACUUGCACA---CCCUUGAUGACAUUGAUUUGUCAUCAGAGCAGCAUAAAAGCAUUAGCAUAAACGCA
.................---(((((....(((...---.(.(((((((((......))))))))).)..))).....))))).((......)). ( -18.70)
>consensus
UUGCCCACCCCACUAC____ACUCUCA_UUGCACA___CCCUUGAUGACAUUGAUUCGUCAUCAGAGCAGCAUAAAAGCAUUAGCAUAAACGCA
.(((.....................................((((((((........))))))))....((......))....)))........ (-12.12 = -11.88 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:52 2006