Locus 1525

Sequence ID	2R_DroMel_CAF1
Location	5,777,498 – 5,777,592
Length	94
Max. P	0.999673

overview

Window 7

Location	5,777,498 – 5,777,592
Length	94
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	93.42
Mean single sequence MFE	-25.54
Consensus MFE	-22.36
Energy contribution	-23.00
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.79
Structure conservation index	0.88
SVM decision value	3.87
SVM RNA-class probability	0.999673
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5777498 94 + 20766785
GCAAUUAUACAUAAACAUGUGUCCGAAUAAAAGGAAGGCGCUUUCUGUGUGCUG--------GCAUGCUGCUAUGUAUAAUUGAUAUAUUUUCAUUCUCAAU
.((((((((((((.((((((.(((........))).(((((.......))))).--------))))).)..))))))))))))................... ( -25.60)
>DroSec_CAF1 67790 94 + 1
GCAAUUAUACAUAAACAUGUGUCCGAAUAAAAGGAAGGCGCUUUGUGUGCGCUG--------GCAUGCUGCUAUGUAUAAUUGAUAUAUUUUCAUUCUCAAU
.((((((((((((.((((((.(((........))).(((((.......))))).--------))))).)..))))))))))))................... ( -27.50)
>DroSim_CAF1 68934 94 + 1
GCAAUUAUACAUAAACAUGUGUCCGAAUAAAAGGAAGGCGCUUUGUGUGUGCUG--------GCAUGCUGCUAUGUAUAAUUGAUAUAUUUUCAUUCUCAAU
.((((((((((((.((((((.(((........))).(((((.......))))).--------))))).)..))))))))))))................... ( -25.60)
>DroEre_CAF1 70879 91 + 1
GCAAUUAUACAUAAACAUGUGUCCGAAUAAAAGGAAGGCGCUUUGUGUGUG-----------CCAUGCUUCUAUGUAUAAUUGAUAUAUUUUCAUUCUCAAU
.((((((((((((........(((........))).(((((.......)))-----------)).......))))))))))))................... ( -23.90)
>DroYak_CAF1 68427 102 + 1
GCAAUUAUACAUAAACAUGUGUCCGAAUAAAAGGAAGGCGCUUUGUGUGUGCUGCCACGCUGCCAUGCUUCUAUGUAUAAUUGAUAUAUUUUCAUUCUCAAU
.((((((((((((.....((((((........))).(((((.......)))))..)))((......))...))))))))))))................... ( -25.10)
>consensus
GCAAUUAUACAUAAACAUGUGUCCGAAUAAAAGGAAGGCGCUUUGUGUGUGCUG________GCAUGCUGCUAUGUAUAAUUGAUAUAUUUUCAUUCUCAAU
.((((((((((((..(((((.(((........))).(((((.......))))).........)))))....))))))))))))................... (-22.36 = -23.00 +   0.64)

alignment

secondary structure

dotplot

Window 8

Location	5,777,498 – 5,777,592
Length	94
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	93.42
Mean single sequence MFE	-21.28
Consensus MFE	-18.04
Energy contribution	-18.24
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.85
SVM decision value	2.60
SVM RNA-class probability	0.995674
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5777498 94 - 20766785
AUUGAGAAUGAAAAUAUAUCAAUUAUACAUAGCAGCAUGC--------CAGCACACAGAAAGCGCCUUCCUUUUAUUCGGACACAUGUUUAUGUAUAAUUGC
...................(((((((((((((..(((((.--------..((.........))....(((........)))..)))))))))))))))))). ( -18.90)
>DroSec_CAF1 67790 94 - 1
AUUGAGAAUGAAAAUAUAUCAAUUAUACAUAGCAGCAUGC--------CAGCGCACACAAAGCGCCUUCCUUUUAUUCGGACACAUGUUUAUGUAUAAUUGC
...................(((((((((((((..(((((.--------..((((.......))))..(((........)))..)))))))))))))))))). ( -24.30)
>DroSim_CAF1 68934 94 - 1
AUUGAGAAUGAAAAUAUAUCAAUUAUACAUAGCAGCAUGC--------CAGCACACACAAAGCGCCUUCCUUUUAUUCGGACACAUGUUUAUGUAUAAUUGC
...................(((((((((((((..(((((.--------..((.........))....(((........)))..)))))))))))))))))). ( -18.90)
>DroEre_CAF1 70879 91 - 1
AUUGAGAAUGAAAAUAUAUCAAUUAUACAUAGAAGCAUGG-----------CACACACAAAGCGCCUUCCUUUUAUUCGGACACAUGUUUAUGUAUAAUUGC
...................(((((((((((((..((((((-----------(.(.......).))).(((........)))...))))))))))))))))). ( -19.90)
>DroYak_CAF1 68427 102 - 1
AUUGAGAAUGAAAAUAUAUCAAUUAUACAUAGAAGCAUGGCAGCGUGGCAGCACACACAAAGCGCCUUCCUUUUAUUCGGACACAUGUUUAUGUAUAAUUGC
...................(((((((((((((..(((((.......(((.((.........))))).(((........)))..)))))))))))))))))). ( -24.40)
>consensus
AUUGAGAAUGAAAAUAUAUCAAUUAUACAUAGCAGCAUGC________CAGCACACACAAAGCGCCUUCCUUUUAUUCGGACACAUGUUUAUGUAUAAUUGC
...................(((((((((((((..(((((...........((.........))....(((........)))..)))))))))))))))))). (-18.04 = -18.24 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:51 2006