Locus 3708

Sequence ID	3R_DroMel_CAF1
Location	10,084,149 – 10,084,291
Length	142
Max. P	0.731041

overview

Window 1

Location	10,084,149 – 10,084,258
Length	109
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	82.31
Mean single sequence MFE	-36.42
Consensus MFE	-22.99
Energy contribution	-25.89
Covariance contribution	2.89
Combinations/Pair	1.26
Mean z-score	-2.34
Structure conservation index	0.63
SVM decision value	0.42
SVM RNA-class probability	0.731041
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10084149 109 - 27905053
GA-AGGCGAUUGU--GGGGGAAUUGGGGGAUUGUGGGCAGGAAUGCCCUGCCUGCGGUUAUUCAAAUAGUUUUUCCAUCAAAUUAUCAACCGAAACUGUU-GAGGUUGCCUUG
.(-((((((((((--((..((((((.(((((((..((((((.....))))))..)))))..))...))))))..)))).......(((((.......)))-))))))))))). ( -44.80)
>DroPse_CAF1 144176 89 - 1
----GGUGGUU---------CCUUGGA-------GGGGAGAGAUG----GCCUGCGGUUAUUCAAAUAGUUUUUCCAUCAAAUCAUCAGCAAAAACUGUUUGGGGUUGUCUUG
----.....((---------(((....-------)))))((((..----((((.........((((((((((((.(............).))))))))))))))))..)))). ( -23.00)
>DroSec_CAF1 142928 110 - 1
GAAAGGCGAUUGU--GGGGGCAUUGGGGGAUUGUGGGCAGGAAUGCCCUGCCUGCGGUUAUUCAAAUAGUUUUUCCAUCAAAUUAUCAACCGAAACUGUU-GAGGUUGCCUUG
..(((((((((((--((..(.((((.(((((((..((((((.....))))))..)))))..))...)))).)..)))).......(((((.......)))-))))))))))). ( -40.80)
>DroSim_CAF1 144847 110 - 1
GAAAGGCGAUUGU--GGGGGCAUUGGGGGAUUGUGGGCAGGAAUGCCCUGCCUGCGGUUAUUCAAAUAGUUUUUCCAUCAAAUUAUCAACCGAAACUGUU-GAGGUUGCCUUG
..(((((((((((--((..(.((((.(((((((..((((((.....))))))..)))))..))...)))).)..)))).......(((((.......)))-))))))))))). ( -40.80)
>DroEre_CAF1 155198 108 - 1
GCAGGG--AAUGA--AUGGGCGUUGGAGGACUGCGGGCAGGAAUGCCCUGGCUGCGGUUAUUCAAAUAGUUUUUCCAUCAAAUUAUCAACCGAAACUGUU-GAGGCUGCCUUG
((((((--((.((--((.....(((((.((((((((.((((.....)))).)))))))).)))))...)))))))).........(((((.......)))-))..)))).... ( -38.10)
>DroYak_CAF1 150166 110 - 1
GAAGGG--UAUGGGCAUUGGCGUUGGCGAAUUGUGGGCAGGAAUGCCCUGGCUGCGGUUAUUCAAAUAGUUUUUCCAUCAAAUUAUCAACCGAAACUGUU-GAGGUUGCCUUG
.(((((--.(((((....(((.((((..(((((..(.((((.....)))).)..)))))..))))...)))..)))))).......(((((.........-..))))))))). ( -31.00)
>consensus
GAAAGGCGAUUGU__GGGGGCAUUGGGGGAUUGUGGGCAGGAAUGCCCUGCCUGCGGUUAUUCAAAUAGUUUUUCCAUCAAAUUAUCAACCGAAACUGUU_GAGGUUGCCUUG
..(((((((((...........(((((.(((((((((((((.....))))))))))))).)))))((((((((..................))))))))....))))))))). (-22.99 = -25.89 +   2.89)

alignment

secondary structure

dotplot

Window 2

Location	10,084,185 – 10,084,291
Length	106
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	85.95
Mean single sequence MFE	-36.80
Consensus MFE	-26.66
Energy contribution	-27.22
Covariance contribution	0.56
Combinations/Pair	1.20
Mean z-score	-1.69
Structure conservation index	0.72
SVM decision value	0.14
SVM RNA-class probability	0.603583
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10084185 106 - 27905053
AAUGC---CACCAUGGACACCAUGCAAAUCGCAAAGGA-AGGCGAUUGU--GGGGGAAUUGGGGGAUUGUGGGCAGGAAUGCCCUGCCUGCGGUUAUUCAAAUAGUUUUUCC
....(---((((((((...)))))..((((((......-..))))))))--))((((((((((.(((((..((((((.....))))))..))))).)))))......))))) ( -39.40)
>DroSec_CAF1 142964 106 - 1
AAUGC---CAU-GUGGCCACCAUGCAAAUCGCAGAGGAAAGGCGAUUGU--GGGGGCAUUGGGGGAUUGUGGGCAGGAAUGCCCUGCCUGCGGUUAUUCAAAUAGUUUUUCC
..(.(---((.-(((.((.((((...((((((.........))))))))--)))).)))))).)(((((..((((((.....))))))..)))))................. ( -39.70)
>DroSim_CAF1 144883 106 - 1
AAUGC---CAU-GUGGCCACCAUGCAAAUCGCAGAGGAAAGGCGAUUGU--GGGGGCAUUGGGGGAUUGUGGGCAGGAAUGCCCUGCCUGCGGUUAUUCAAAUAGUUUUUCC
..(.(---((.-(((.((.((((...((((((.........))))))))--)))).)))))).)(((((..((((((.....))))))..)))))................. ( -39.70)
>DroEre_CAF1 155234 107 - 1
AAUGCCACCAU-GUGGCCACCAUGAAAAUCGCAGAGGCAGGG--AAUGA--AUGGGCGUUGGAGGACUGCGGGCAGGAAUGCCCUGGCUGCGGUUAUUCAAAUAGUUUUUCC
...(((((...-)))))..((((.....((((....)).)).--.....--))))((.(((((.((((((((.((((.....)))).)))))))).)))))...))...... ( -36.20)
>DroYak_CAF1 150202 106 - 1
AAUGC---CAU-GUGGCUACCAUGAAAAGCGGAGAGGAAGGG--UAUGGGCAUUGGCGUUGGCGAAUUGUGGGCAGGAAUGCCCUGGCUGCGGUUAUUCAAAUAGUUUUUCC
(((((---((.-...((..(((((.....(......).....--)))))))..)))))))((..(((((..(.((((.....)))).)..)))))..))............. ( -29.00)
>consensus
AAUGC___CAU_GUGGCCACCAUGCAAAUCGCAGAGGAAAGGCGAUUGU__GGGGGCAUUGGGGGAUUGUGGGCAGGAAUGCCCUGCCUGCGGUUAUUCAAAUAGUUUUUCC
..(((.......((((...)))).......)))..((((((((...((........))(((((.(((((((((((((.....))))))))))))).)))))...)))))))) (-26.66 = -27.22 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:59 2006