Locus 9347

Sequence ID	3R_DroMel_CAF1
Location	24,841,051 – 24,841,163
Length	112
Max. P	0.801546

overview

Window 8

Location	24,841,051 – 24,841,163
Length	112
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	82.66
Mean single sequence MFE	-28.42
Consensus MFE	-17.19
Energy contribution	-17.55
Covariance contribution	0.36
Combinations/Pair	1.24
Mean z-score	-2.32
Structure conservation index	0.60
SVM decision value	0.19
SVM RNA-class probability	0.624058
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24841051 112 + 27905053
UAA--GAUGACUUGCCAAAA--GUCUGGCAAAAAUAUUCCACUCCGCAAAUCAGGUCUCAAUUGGAAUAAUUCAAUUAAUAUUGAGUCAUGAAGUUGUCAUUGA-GUGCAGUUGCGG
...--......((((((...--...))))))............((((((.((((....(((((...((.(((((((....))))))).))..)))))...))))-......)))))) ( -25.70)
>DroSec_CAF1 56834 114 + 1
UAACCGAUGACUUGCCAAAA--GUCUGGCAAAAAUAUUCCACUCCGCAAAUCAGGUCUCAAUUGGAAUAAUUCAAUUAAUAUUGAGUCAUGAAGUUGUCAUUGA-GUGCAGUUGCGG
...(((.((((((((((...--...))))))........(((((.((((.(((.(.((((((...(((......)))...)))))).).)))..))))....))-)))..))))))) ( -28.30)
>DroSim_CAF1 60355 114 + 1
UAUCCGAUGACUUGCCAAAA--GUCUGGCAAAAAUAUUCCACUCCGCAAAUCAGGUCUCAAUUGGAAUAAUUCAAUUAAUAUUGAGUCAUGAAGUUGUCAUUGA-GUGCAGUUGCGG
...(((.((((((((((...--...))))))........(((((.((((.(((.(.((((((...(((......)))...)))))).).)))..))))....))-)))..))))))) ( -27.90)
>DroEre_CAF1 54958 111 + 1
UAG--AAUGACUUGCCAAAA--GUCUGGCAA-AAUAUUCCACUCCGCAAAUCAAGCCUCAAUUGGAAUAAUUCAAUUAAUAAUGAGUUAUGAAGUUGUCAUCGG-CUGCAUUUGCGG
..(--((((..((((((...--...))))))-..)))))....((((((((..((((.(((((...((((((((........))))))))..))))).....))-))..)))))))) ( -35.70)
>DroYak_CAF1 53073 112 + 1
UAA--GAUGACUUGCCAAAA--GUCUGGCAAAAAUAUUCCACUUCGCAAAUCAAAUCUCAAUUGGAAUAAUUCAAUUAAUAUUGAGCUAUGAAGUUGUCAUCAA-GUGCAUUUGCGC
...--((((((((((((...--...)))))).........((((((....((((.....(((((((....)))))))....))))....)))))).))))))..-((((....)))) ( -29.60)
>DroAna_CAF1 51468 107 + 1
AGA--GAUGACUUGCCAAAAAAACUUUGCCGGAAUAUUCCACUCAAGAAAUCAAGCGUCGAUUGCAGUAAUUCAAUUAGUUUUGAGGUGGAA---UGUCAUCGGAAAACAGU-----
...--(((((((((.((((.....)))).)))...(((((((((((((......(((.....))).(.....)......)))))).))))))---)))))))..........----- ( -23.30)
>consensus
UAA__GAUGACUUGCCAAAA__GUCUGGCAAAAAUAUUCCACUCCGCAAAUCAAGUCUCAAUUGGAAUAAUUCAAUUAAUAUUGAGUCAUGAAGUUGUCAUCGA_GUGCAGUUGCGG
.....((((((((((((........))))))...................(((.(.((((((...(((......)))...)))))).).)))....))))))............... (-17.19 = -17.55 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	24,841,051 – 24,841,163
Length	112
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	82.66
Mean single sequence MFE	-28.38
Consensus MFE	-19.83
Energy contribution	-20.88
Covariance contribution	1.06
Combinations/Pair	1.16
Mean z-score	-2.43
Structure conservation index	0.70
SVM decision value	0.62
SVM RNA-class probability	0.801546
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24841051 112 - 27905053
CCGCAACUGCAC-UCAAUGACAACUUCAUGACUCAAUAUUAAUUGAAUUAUUCCAAUUGAGACCUGAUUUGCGGAGUGGAAUAUUUUUGCCAGAC--UUUUGGCAAGUCAUC--UUA
..((....))..-...(((((.(((((..((.(((...(((((((........)))))))....))).))..))))).........(((((((..--..)))))))))))).--... ( -25.30)
>DroSec_CAF1 56834 114 - 1
CCGCAACUGCAC-UCAAUGACAACUUCAUGACUCAAUAUUAAUUGAAUUAUUCCAAUUGAGACCUGAUUUGCGGAGUGGAAUAUUUUUGCCAGAC--UUUUGGCAAGUCAUCGGUUA
((((....))..-...(((((.(((((..((.(((...(((((((........)))))))....))).))..))))).........(((((((..--..)))))))))))).))... ( -26.60)
>DroSim_CAF1 60355 114 - 1
CCGCAACUGCAC-UCAAUGACAACUUCAUGACUCAAUAUUAAUUGAAUUAUUCCAAUUGAGACCUGAUUUGCGGAGUGGAAUAUUUUUGCCAGAC--UUUUGGCAAGUCAUCGGAUA
((((....))..-...(((((.(((((..((.(((...(((((((........)))))))....))).))..))))).........(((((((..--..)))))))))))).))... ( -27.10)
>DroEre_CAF1 54958 111 - 1
CCGCAAAUGCAG-CCGAUGACAACUUCAUAACUCAUUAUUAAUUGAAUUAUUCCAAUUGAGGCUUGAUUUGCGGAGUGGAAUAUU-UUGCCAGAC--UUUUGGCAAGUCAUU--CUA
((((((((..((-(((((((............))))).(((((((........)))))))))))..))))))))..((((((..(-(((((((..--..))))))))..)))--))) ( -36.50)
>DroYak_CAF1 53073 112 - 1
GCGCAAAUGCAC-UUGAUGACAACUUCAUAGCUCAAUAUUAAUUGAAUUAUUCCAAUUGAGAUUUGAUUUGCGAAGUGGAAUAUUUUUGCCAGAC--UUUUGGCAAGUCAUC--UUA
..((....))..-..((((((.(((((.(((.((((..(((((((........)))))))...)))).))).))))).........(((((((..--..)))))))))))))--... ( -31.50)
>DroAna_CAF1 51468 107 - 1
-----ACUGUUUUCCGAUGACA---UUCCACCUCAAAACUAAUUGAAUUACUGCAAUCGACGCUUGAUUUCUUGAGUGGAAUAUUCCGGCAAAGUUUUUUUGGCAAGUCAUC--UCU
-----..........(((((((---((((((.((((........((((((..((.......)).)))))).))))))))))).....(.(((((...))))).)..))))))--... ( -23.30)
>consensus
CCGCAACUGCAC_UCAAUGACAACUUCAUAACUCAAUAUUAAUUGAAUUAUUCCAAUUGAGACCUGAUUUGCGGAGUGGAAUAUUUUUGCCAGAC__UUUUGGCAAGUCAUC__UUA
................(((((.(((((.(((.(((...(((((((........)))))))....))).))).))))).........((((((((....)))))))))))))...... (-19.83 = -20.88 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:32:20 2006