Locus 4766

Sequence ID	2L_DroMel_CAF1
Location	13,582,792 – 13,582,941
Length	149
Max. P	0.868224

overview

Window 5

Location	13,582,792 – 13,582,901
Length	109
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.96
Mean single sequence MFE	-39.42
Consensus MFE	-28.54
Energy contribution	-28.85
Covariance contribution	0.31
Combinations/Pair	1.07
Mean z-score	-2.77
Structure conservation index	0.72
SVM decision value	0.86
SVM RNA-class probability	0.868224
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13582792 109 - 22407834
AUAUUGUUGAAGGGAAGUGUUGCAA--GAUACACGCAAUCAGGAGGGCCACAGACUUUGGUGGUCUCUCAAAAUGUGUAGCACACACAAGGGGGCGUCUUUUGCGGCACUG---------
...............((((((((((--((...((((..((..(((((((((........)))))).)))....(((((.....))))).))..)))).)))))))))))).--------- ( -39.50)
>DroSec_CAF1 15764 109 - 1
AUAUUGUUGAAGGGAAGUGUUGCAA--GAUACACGCAAUCAGGAGGGCCACAGACUUUGGUGGUCUCUCCAAAAGUGUAGCACACACAAGGGGGCGUCUUUUGUGGCACUG---------
...............(((((..(((--((...((((..((.((((((((((........)))))).))))....((((.....))))..))..)))).)))))..))))).--------- ( -40.80)
>DroEre_CAF1 16141 109 - 1
AUAUUGUUGAAGGGAAGUGUUGCGA--GAUACACGCAAUCAGGAGGGCCACAGACUUCUGUGGUAUCUCAAAAUGUGUAGCAUACACAAGGGGGCGUCUUUUGUGGCACUG---------
...............(((((..(((--((...((((..((..(((((((((((....))))))).))))....((((((...)))))).))..)))).)))))..))))).--------- ( -40.30)
>DroYak_CAF1 13030 119 - 1
AUAUUGUUGAAGAGAAGUGUUGCGAGAGAUACACGCAAUCAGGAGGG-CACAGACUUCGGUGGUCUCUCAAAAUGUGUAGCAUACACAAGGGGUCGUCUUUUGUGGCACUGCAGAGCACU
....((((...(...(((((..((((((((((.(.(......(((((-.((..((....)).)))))))....((((((...)))))).).))).))))))))..))))).)..)))).. ( -37.10)
>consensus
AUAUUGUUGAAGGGAAGUGUUGCAA__GAUACACGCAAUCAGGAGGGCCACAGACUUCGGUGGUCUCUCAAAAUGUGUAGCACACACAAGGGGGCGUCUUUUGUGGCACUG_________
...............((((((((((.......((((..((..(((((((((........)))))).))).....((((.....))))..))..))))...)))))))))).......... (-28.54 = -28.85 +   0.31)

alignment

secondary structure

dotplot

Window 6

Location	13,582,823 – 13,582,941
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.26
Mean single sequence MFE	-34.33
Consensus MFE	-28.05
Energy contribution	-28.17
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-2.02
Structure conservation index	0.82
SVM decision value	0.44
SVM RNA-class probability	0.739254
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13582823 118 - 22407834
AAUGCCUGACAAGGUACACAUGUCGAACAACAUCGUGAAAAUAUUGUUGAAGGGAAGUGUUGCAA--GAUACACGCAAUCAGGAGGGCCACAGACUUUGGUGGUCUCUCAAAAUGUGUAG
..(.(((((((.(.....).))))...(((((..((....))..))))).))).).(((((....--)))))(((((.....(((((((((........)))))).)))....))))).. ( -33.50)
>DroSec_CAF1 15795 118 - 1
AAUGCCUGACAAGGUACAUAUGUCGAACAACAUCGUGGAAAUAUUGUUGAAGGGAAGUGUUGCAA--GAUACACGCAAUCAGGAGGGCCACAGACUUUGGUGGUCUCUCCAAAAGUGUAG
...((((....))))((((.((.((..(((((..((....))..))))).......(((((....--))))).))))....((((((((((........)))))).))))....)))).. ( -33.30)
>DroEre_CAF1 16172 118 - 1
AAUGCCUGACAAGGUACACAUGUCGAACAACAUCGUGGAAAUAUUGUUGAAGGGAAGUGUUGCGA--GAUACACGCAAUCAGGAGGGCCACAGACUUCUGUGGUAUCUCAAAAUGUGUAG
...((((....))))((((((......(((((..((....))..)))))..((((...((((((.--......)))))).......(((((((....))))))).))))...)))))).. ( -36.50)
>DroYak_CAF1 13070 119 - 1
AAUGCCUGACAAGGUACACAUGUCGAACAACAUUGUGGAAAUAUUGUUGAAGAGAAGUGUUGCGAGAGAUACACGCAAUCAGGAGGG-CACAGACUUCGGUGGUCUCUCAAAAUGUGUAG
...((((....))))((((((......(((((.(((....))).)))))..((...((((..(....)..))))....))..(((((-.((..((....)).)))))))...)))))).. ( -34.00)
>consensus
AAUGCCUGACAAGGUACACAUGUCGAACAACAUCGUGGAAAUAUUGUUGAAGGGAAGUGUUGCAA__GAUACACGCAAUCAGGAGGGCCACAGACUUCGGUGGUCUCUCAAAAUGUGUAG
..(((((....)))))(((.(.((...(((((..((....))..)))))..)).).)))..........(((((........(((((((((........)))))).))).....))))). (-28.05 = -28.17 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:50 2006