Locus 4280

Sequence ID	3R_DroMel_CAF1
Location	11,405,561 – 11,405,713
Length	152
Max. P	0.897322

overview

Window 7

Location	11,405,561 – 11,405,673
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.80
Mean single sequence MFE	-30.19
Consensus MFE	-23.69
Energy contribution	-24.73
Covariance contribution	1.04
Combinations/Pair	1.03
Mean z-score	-1.96
Structure conservation index	0.78
SVM decision value	0.98
SVM RNA-class probability	0.893798
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11405561 112 + 27905053
UUGUUGUUUAAUUUUCUCGUUAGCACCGUGCUCUUUAAUGGACUCACGGCUC--------AAGGGGUAGAUUGGCCUUUAGCUGGUUAUCCAGCGCUAUAAAUCAAUAAUUAAAUAUUUU
....(((((((((.......((((.(((((.(((.....)))..)))))...--------.((((((......)))))).(((((....))))))))).........))))))))).... ( -29.49)
>DroSec_CAF1 153219 112 + 1
UUCUUGUUUAAUUUUCUCGUUAGCACCGUGCUCUUUAAUGGACUCACGGCUC--------AAGGGGUAGAUUGGCCUCUAGCUGGUUAUCCAGCGCUAUAAAUCAAUAAUUAAAUAUUUU
....(((((((((.......((((.(((((.(((.....)))..)))))...--------.((((((......)))))).(((((....))))))))).........))))))))).... ( -31.99)
>DroSim_CAF1 144696 112 + 1
UUCUUGUUUAAUUUUCUCGUUAGCACCGUGCUCUUUAAUGGACUCACGGCUC--------AAGGGGUAGAUUGGCCUUUAGCUGGUUAUCCAGCGCUAUAAAUCAAUAAUUAAAUAUUUU
....(((((((((.......((((.(((((.(((.....)))..)))))...--------.((((((......)))))).(((((....))))))))).........))))))))).... ( -29.49)
>DroEre_CAF1 141074 112 + 1
UUGCUGUUUAAUUUCCUCGUUAGCAGCGAGCUCUUUAAUGGACUCACGGCUG--------AAGGGGUAGGUUGGCCUUUGGCUGGUUGUGCAGCGCUAUAAAUCAAUAAUUAAAUAUUUC
..(((((.(((((.((((.(((((.(.(((.(((.....)))))).).))))--------).))))......((((...))))))))).))))).......................... ( -29.50)
>DroYak_CAF1 144657 120 + 1
UGGUUGUUUAAUUUUCUCGUUAACACCGAGCUCUUUAAUGGACUCCGGGCCGAGGGACUCAAGGGGUAGAUUGGCCUUUAGCUGGUUAUCCAGCGCUAUAAAUCAAUAAUUAAAUAUUUU
....(((((((((......(((.....(((.(((.....)))))).(((((((...(((.....)))...)))))))...(((((....)))))....)))......))))))))).... ( -30.50)
>consensus
UUGUUGUUUAAUUUUCUCGUUAGCACCGUGCUCUUUAAUGGACUCACGGCUC________AAGGGGUAGAUUGGCCUUUAGCUGGUUAUCCAGCGCUAUAAAUCAAUAAUUAAAUAUUUU
....(((((((((.......((((.(((((.(((.....)))..)))))............((((((......)))))).(((((....))))))))).........))))))))).... (-23.69 = -24.73 +   1.04)

alignment

secondary structure

dotplot

Window 8

Location	11,405,601 – 11,405,713
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-27.32
Consensus MFE	-25.20
Energy contribution	-25.64
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.35
Structure conservation index	0.92
SVM decision value	1.00
SVM RNA-class probability	0.897322
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11405601 112 - 27905053
AGGAUUUUCACACGUUCCAGUGAAUCGACCACCGUCGACCAAAAUAUUUAAUUAUUGAUUUAUAGCGCUGGAUAACCAGCUAAAGGCCAAUCUACCCCUU--------GAGCCGUGAGUC
.((...(((((........)))))(((((....)))))))................(((((((...(((((....)))))....((((((........))--------).)))))))))) ( -28.70)
>DroSec_CAF1 153259 112 - 1
AGGAUUUUCACACGUUCCAGUGAAUCGACCACCGUCGACCAAAAUAUUUAAUUAUUGAUUUAUAGCGCUGGAUAACCAGCUAGAGGCCAAUCUACCCCUU--------GAGCCGUGAGUC
.((...(((((........)))))(((((....)))))))................(((((((...(((((....)))))....((((((........))--------).)))))))))) ( -28.70)
>DroSim_CAF1 144736 112 - 1
AGGAUUUUCACACGUUCCAGUGAAUCGACCACCGUCGACCAAAAUAUUUAAUUAUUGAUUUAUAGCGCUGGAUAACCAGCUAAAGGCCAAUCUACCCCUU--------GAGCCGUGAGUC
.((...(((((........)))))(((((....)))))))................(((((((...(((((....)))))....((((((........))--------).)))))))))) ( -28.70)
>DroEre_CAF1 141114 112 - 1
AGGAUUUUCACACGUUCCAGUGAAUCGACCACCGUCGACCGAAAUAUUUAAUUAUUGAUUUAUAGCGCUGCACAACCAGCCAAAGGCCAACCUACCCCUU--------CAGCCGUGAGUC
.((...(((((........)))))(((((....)))))))................((((((..((((((......))))...(((....))).......--------..))..)))))) ( -24.30)
>DroYak_CAF1 144697 120 - 1
AGGAUUUUCACACGUUCCAGUGAAUCGACCACCGUCGACCAAAAUAUUUAAUUAUUGAUUUAUAGCGCUGGAUAACCAGCUAAAGGCCAAUCUACCCCUUGAGUCCCUCGGCCCGGAGUC
.((...(((((........)))))(((((....)))))))................(((((.....(((((....)))))....((((..((........))(.....)))))..))))) ( -26.20)
>consensus
AGGAUUUUCACACGUUCCAGUGAAUCGACCACCGUCGACCAAAAUAUUUAAUUAUUGAUUUAUAGCGCUGGAUAACCAGCUAAAGGCCAAUCUACCCCUU________GAGCCGUGAGUC
.((...(((((........)))))(((((....)))))))................(((((((.(((((((....)))))..((((..........))))..........)).))))))) (-25.20 = -25.64 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:29 2006