Locus 2107

Sequence ID	3R_DroMel_CAF1
Location	6,009,805 – 6,009,962
Length	157
Max. P	0.920272

overview

Window 4

Location	6,009,805 – 6,009,897
Length	92
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	83.62
Mean single sequence MFE	-26.05
Consensus MFE	-18.27
Energy contribution	-18.63
Covariance contribution	0.36
Combinations/Pair	1.30
Mean z-score	-1.74
Structure conservation index	0.70
SVM decision value	-0.03
SVM RNA-class probability	0.520484
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6009805 92 - 27905053
ACCAAUACACUUGGCAAAUAA-CCGAGCCACUG---AGUUGGCGCAAUUUAACGCCGCGUCGAUCCAGCAGUGCGAAUUAUUUCGCUCAAUGCUGG-------
.........(((((.......-)))))......---.((((((((...........))))))))((((((..(((((....)))))....))))))------- ( -28.70)
>DroPse_CAF1 20604 99 - 1
----AUAUAGUUUGUAUACAAUUCCAGCCACUCGGAGGCUGACGCAAUUUAACGCCGCGUUGCUUUUGCCGUGCAAAUUAUUUCGCCCAAUGCUAAUGCCUCU
----..(((((((((((.......(((((.......)))))..((((..(((((...)))))...)))).)))))))))))..........((....)).... ( -22.70)
>DroSec_CAF1 21736 92 - 1
ACCAAUACACUUGGCAAAUAA-CCGAGCCACUG---AGUUGGCGCAAUUUAACGCCGCGUUGAUCCAGCAGUGCGAAUUAUUUUGCUCAAUGCUGA-------
..(((..(.(((((.......-)))))......---....((((........)))))..)))...(((((..(((((....)))))....))))).------- ( -24.50)
>DroSim_CAF1 21748 92 - 1
ACCAAUACACUUGGCAAAUAA-CCGAGCCACUG---AGUUGGCGCAAUUUAACGCCGCGUUGAUCCAGCAGUGCGAAUUAUUUUGCUCAAUGCUGA-------
..(((..(.(((((.......-)))))......---....((((........)))))..)))...(((((..(((((....)))))....))))).------- ( -24.50)
>DroEre_CAF1 22015 92 - 1
ACCAAUACACUUGGCAAAUAA-CCGAGCCACUG---AGUUGGCGCAAUUUAACGCAGCGCUGAUCCAGCAGUGCGAAUUAUUUUGCUCAAUGCUAG-------
...........(((((.....-....((((...---...))))((((..(((..(.((((((......)))))))..)))..))))....))))).------- ( -25.60)
>DroYak_CAF1 23555 92 - 1
ACCAAUUCAGUUGGCAAAUAA-CUGAGCCACUG---AGUUGGCGCAAUUUAACGCGGCGCUGAUCCAGCAGUGCGAAUUAUUUUACUCAAUGCUGG-------
.((((((((((.(((......-....)))))))---))))))(((........)))((((((......))))))......................------- ( -30.30)
>consensus
ACCAAUACACUUGGCAAAUAA_CCGAGCCACUG___AGUUGGCGCAAUUUAACGCCGCGUUGAUCCAGCAGUGCGAAUUAUUUUGCUCAAUGCUGA_______
...........((((...........)))).......((((((((...........))))))))((((((..(((((....)))))....))))))....... (-18.27 = -18.63 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	6,009,864 – 6,009,962
Length	98
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	69.60
Mean single sequence MFE	-27.69
Consensus MFE	-12.05
Energy contribution	-13.67
Covariance contribution	1.62
Combinations/Pair	1.22
Mean z-score	-1.99
Structure conservation index	0.44
SVM decision value	1.13
SVM RNA-class probability	0.920272
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6009864 98 + 27905053
UCAGUGGCUCGGUUAUUUGCCAAGUGUAUUGGUAUUGCUCUGAUCCAACAGAGCUAGUGGCUCGGCA-----GUGAUGCCAGCAAUAUCAA---AAAACACUA---AUG----
....((((..........))))(((((.(((((((((((...........((((.....))))((((-----....)))))))))))))))---...))))).---...---- ( -35.70)
>DroSec_CAF1 21795 98 + 1
UCAGUGGCUCGGUUAUUUGCCAAGUGUAUUGGUAUUACUCCGGUCUCACAGAGCUUGUGGCUCGGCA-----GUGAUGCCAGCAAUAUCAA---AAAUCAGUA---AUC----
...((((..(((.....((((((.....)))))).....)))..).))).((((.....))))((((-----....))))...........---.........---...---- ( -29.20)
>DroSim_CAF1 21807 98 + 1
UCAGUGGCUCGGUUAUUUGCCAAGUGUAUUGGUAUUACUCCGGUCACACAGAGCUAGUGGCUCGGCA-----GUGAUGCCAGCAAUAUCAA---AAAACAGUA---AUC----
.((.(((((((((.....)))..(((((((((.......))))).)))).)))))).))(((.((((-----....)))))))........---.........---...---- ( -34.60)
>DroEre_CAF1 22074 100 + 1
UCAGUGGCUCGGUUAUUUGCCAAGUGUAUUGGUAU--CUAUUGUCCCACAGAGCUGGUAGCUCGCCA-----GUGAUACCAGCGAUAUCAA---AAAAGAAUA---AAAUAUG
...((((..((((....((((((.....)))))).--..))))..))))...(((((((..(((...-----.))))))))))........---.........---....... ( -27.40)
>DroYak_CAF1 23614 106 + 1
UCAGUGGCUCAGUUAUUUGCCAACUGAAUUGGUAUUGCUAUAAUCCCACAGAGCUGCUAGCUUGAUAGUGUAGUGAUGCCAGCAAUAUCAA---AAACAA-AA---ACCCUUU
((((((((..........))).))))).(((((((..(((((........((((.....)))).....)))))..))))))).........---......-..---....... ( -29.62)
>DroAna_CAF1 19584 85 + 1
GCAGU-------------GCCAGCCGGAUUGGUU------UGAUCUCACAGCUUAAUAGACAUAAUA-----GUGAUUCCAUCAAUCUACAGAGAAAACACGAUAAAUU----
.((((-------------.((....))))))(((------(..((((...(((....)).)......-----((((((.....)))).)).))))))))..........---- (  -9.60)
>consensus
UCAGUGGCUCGGUUAUUUGCCAAGUGUAUUGGUAUU_CUCUGAUCCCACAGAGCUAGUGGCUCGGCA_____GUGAUGCCAGCAAUAUCAA___AAAACACUA___AUC____
....((((..........))))......((((((((((............((((.....)))).........))))))))))............................... (-12.05 = -13.67 +   1.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:35 2006