Locus 3996

Sequence ID	X_DroMel_CAF1
Location	10,583,083 – 10,583,215
Length	132
Max. P	0.908735

overview

Window 0

Location	10,583,083 – 10,583,176
Length	93
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	96.73
Mean single sequence MFE	-24.64
Consensus MFE	-21.52
Energy contribution	-22.12
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.87
SVM decision value	1.06
SVM RNA-class probability	0.908735
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10583083 93 + 22224390
GAGUUUUCAGUUUAUUCUAAUAAUUCAGUGGGUGGAAAAACG-----CUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCCAGCAGCAACGCUGAAAAAC
..((.((((((...((((....((((((((..(....)..))-----))).)))....)))).....)))))).))..((((......))))...... ( -22.20)
>DroSec_CAF1 22930 98 + 1
GAGUUUUCAGUUUAUUCUAAUAAUUCAGUGGGUGGAAAAACGCCAGGCUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCCAGCAGCAACGCUGAAAAAC
..((.((((((...((((....(((((((.((((......))))..)))).)))....)))).....)))))).))..((((......))))...... ( -25.00)
>DroSim_CAF1 24737 98 + 1
GAGUUUUCAGUUUAUUCUAAUAAUUCAGUGGGUGGAAAAACGCCAGGCUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCCAGCAGCAACGCUGAAAAAC
..((.((((((...((((....(((((((.((((......))))..)))).)))....)))).....)))))).))..((((......))))...... ( -25.00)
>DroEre_CAF1 22796 98 + 1
GAAUUUUCAGUUUAUUCUAAUAAUUCAGUGGGUGGAAAAACGCCAAGCUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCUAGCAGCAACGCUGAAAAAC
.......................(((((((((((......))))..(((((((((((..((.......))..)).)))).)))))..))))))).... ( -26.60)
>DroYak_CAF1 24855 98 + 1
GAGUUUUCAGUUUAUUCUAAUAAUUCAGUGGGUGGAAAAACGCCAAGCUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCCAGCAGCAACGCUGAAAAAC
.......................(((((((((((......))))..((((((....).((...((((...))))...)).)))))..))))))).... ( -24.40)
>consensus
GAGUUUUCAGUUUAUUCUAAUAAUUCAGUGGGUGGAAAAACGCCAAGCUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCCAGCAGCAACGCUGAAAAAC
...((((((((...((((....(((((((.((((......))))..)))).)))....))))......(((..(((....))).))).)))))))).. (-21.52 = -22.12 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	10,583,101 – 10,583,215
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.91
Mean single sequence MFE	-29.45
Consensus MFE	-22.48
Energy contribution	-22.85
Covariance contribution	0.37
Combinations/Pair	1.07
Mean z-score	-1.82
Structure conservation index	0.76
SVM decision value	0.18
SVM RNA-class probability	0.620212
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10583101 114 + 22224390
AAUAAUUCAGUGGGUGGAAAAACG-----CUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCCAGCAGCAACGCUGAAAAACGCUGAUGAACAAGCAGCAGAAGACCAAGAGCAAGA-GCAA
.....(((((((.((......))(-----(((((....).((...((((...))))...)).)))))..)))))))....((((.........))))............((....-)).. ( -24.20)
>DroSec_CAF1 22948 120 + 1
AAUAAUUCAGUGGGUGGAAAAACGCCAGGCUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCCAGCAGCAACGCUGAAAAACGCUGAUGAACAAGCAGCAGAAGAGCAAGAGCACGAGGCAC
.....(((((((((((......))))..((((((....).((...((((...))))...)).)))))..)))))))....(((........))).((....(.((....)).)...)).. ( -31.20)
>DroSim_CAF1 24755 118 + 1
AAUAAUUCAGUGGGUGGAAAAACGCCAGGCUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCCAGCAGCAACGCUGAAAAACGCUGAUGAACCAGCAGCAGAAGAGCAAGAGCACGAGGC--
.....(((((((((((......))))..((((((....).((...((((...))))...)).)))))..)))))))....((((......)))).((....(.((....)).)...))-- ( -31.90)
>DroEre_CAF1 22814 113 + 1
AAUAAUUCAGUGGGUGGAAAAACGCCAAGCUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCUAGCAGCAACGCUGAAAAACGCUGAUGAACAGGC---AGAAGAGCAAGAGCAAGA-G---
.....(((((((((((......))))..(((((((((((..((.......))..)).)))).)))))..)))))))....(((........)))---......((....))....-.--- ( -30.50)
>consensus
AAUAAUUCAGUGGGUGGAAAAACGCCAGGCUGCAGUGAUGGGAAAAUUUAUUGAAUGCGCCAGCAGCAACGCUGAAAAACGCUGAUGAACAAGCAGCAGAAGAGCAAGAGCAAGA_GC__
.....(((((((((((......))))..(((((.....((((...((((...)))).).))))))))..)))))))....(((........))).......................... (-22.48 = -22.85 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:51 2006