Locus 5621

Sequence ID	3R_DroMel_CAF1
Location	14,815,014 – 14,815,117
Length	103
Max. P	0.981669

overview

Window 8

Location	14,815,014 – 14,815,117
Length	103
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	85.08
Mean single sequence MFE	-34.86
Consensus MFE	-22.46
Energy contribution	-23.70
Covariance contribution	1.24
Combinations/Pair	1.04
Mean z-score	-2.96
Structure conservation index	0.64
SVM decision value	1.29
SVM RNA-class probability	0.938508
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14815014 103 + 27905053
GUUGCC----UGCUGCUGCUGCUGCUGAUGGAUUCCUAUGCAACCGCAGCAACUCCAGCUCCAAGAGCAACUGCA---------GCAACAUCAGCAACAGCGACAACCGCAGCAAG
.((((.----(((((.((.((((((.(.((((......(((....))).....))))((((...))))..).)))---------))).)).)))))...(((.....))).)))). ( -37.10)
>DroSec_CAF1 7629 97 + 1
GUUGCC----UGCUG------CUGCUGAUGGAUUCCUAUGCAACCGCAGCAACUCCAGCUCCAAGAGCAACUGCA---------GCAACAUCAGCAACUGCGACAACCGCAGCAAG
(((((.----(((((------((((.(.((.((....)).)).).))))))......((((...))))....)))---------)))))........(((((.....))))).... ( -33.00)
>DroSim_CAF1 7659 97 + 1
GUUGCC----UGCUG------UUGCUGAUGGAUUCCUAUGCAACCGCAGCAACUCCAGCUCCAAGAGCAACUGCA---------GCAACAUCAGCAACAGCGACAACCGCAGCAAG
(((((.----.((((------(((((((((........(((....)))(((......((((...))))...))).---------....)))))))))))))(.....))))))... ( -36.60)
>DroEre_CAF1 9373 88 + 1
GUUGCC----UGCUG------UUGCUGAUGGAUUCCUAUGCAACCGCAGCAACUCCAGCUCCGAGAGCAACUGCAGC------------------AGCAACGACAACCGCAGCAAG
(((((.----(((((------((((.(.((((......(((....))).....))))((((...))))..).)))))------------------))))..(.....))))))... ( -30.50)
>DroYak_CAF1 8379 110 + 1
GUUGCCUGCCUGCUG------CUGCUGAUGGAUUCCUAUGCAACCGCAGCAACUCCAGCUCCAAGAGCAACGGCAGCCACUGCAGCAAUAUCAGCAAUAGCGACAACCGCAGCAAG
(((((.(((.(((.(------((((((.((((......(((....))).....))))((((...))))..)))))))....))))))......((....)).......)))))... ( -37.10)
>consensus
GUUGCC____UGCUG______CUGCUGAUGGAUUCCUAUGCAACCGCAGCAACUCCAGCUCCAAGAGCAACUGCA_________GCAACAUCAGCAACAGCGACAACCGCAGCAAG
(((((.....(((((.......((((((((((......(((....))).....))))((((...))))......................)))))).)))))......)))))... (-22.46 = -23.70 +   1.24)

alignment

secondary structure

dotplot

Window 9

Location	14,815,014 – 14,815,117
Length	103
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	85.08
Mean single sequence MFE	-45.90
Consensus MFE	-28.18
Energy contribution	-30.06
Covariance contribution	1.88
Combinations/Pair	1.03
Mean z-score	-3.88
Structure conservation index	0.61
SVM decision value	1.89
SVM RNA-class probability	0.981669
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14815014 103 - 27905053
CUUGCUGCGGUUGUCGCUGUUGCUGAUGUUGC---------UGCAGUUGCUCUUGGAGCUGGAGUUGCUGCGGUUGCAUAGGAAUCCAUCAGCAGCAGCAGCAGCA----GGCAAC
.(((((...(((((.((((((((((((((.((---------((((((.(((((.......))))).)))))))).))...((...)))))))))))))).))))).----))))). ( -54.20)
>DroSec_CAF1 7629 97 - 1
CUUGCUGCGGUUGUCGCAGUUGCUGAUGUUGC---------UGCAGUUGCUCUUGGAGCUGGAGUUGCUGCGGUUGCAUAGGAAUCCAUCAGCAG------CAGCA----GGCAAC
(((((((((.....))).(((((((((((.((---------((((((.(((((.......))))).)))))))).))...((...))))))))))------)))))----)).... ( -44.20)
>DroSim_CAF1 7659 97 - 1
CUUGCUGCGGUUGUCGCUGUUGCUGAUGUUGC---------UGCAGUUGCUCUUGGAGCUGGAGUUGCUGCGGUUGCAUAGGAAUCCAUCAGCAA------CAGCA----GGCAAC
.........((((((((((((((((((((.((---------((((((.(((((.......))))).)))))))).))...((...))))))))))------)))).----)))))) ( -48.00)
>DroEre_CAF1 9373 88 - 1
CUUGCUGCGGUUGUCGUUGCU------------------GCUGCAGUUGCUCUCGGAGCUGGAGUUGCUGCGGUUGCAUAGGAAUCCAUCAGCAA------CAGCA----GGCAAC
(((((((..((((....(((.------------------((((((((.((((.((....)))))).)))))))).)))..((...))..))))..------)))))----)).... ( -36.80)
>DroYak_CAF1 8379 110 - 1
CUUGCUGCGGUUGUCGCUAUUGCUGAUAUUGCUGCAGUGGCUGCCGUUGCUCUUGGAGCUGGAGUUGCUGCGGUUGCAUAGGAAUCCAUCAGCAG------CAGCAGGCAGGCAAC
(((((((((((....)))..(((((((...(((((((..(((.(((..((((...))))))))))..)))))))......((...))))))))))------)))))))........ ( -46.30)
>consensus
CUUGCUGCGGUUGUCGCUGUUGCUGAUGUUGC_________UGCAGUUGCUCUUGGAGCUGGAGUUGCUGCGGUUGCAUAGGAAUCCAUCAGCAG______CAGCA____GGCAAC
.(((((...((((......(((((((((..............(((((.(((((.......))))).)))))((((.(...).)))))))))))))......)))).....))))). (-28.18 = -30.06 +   1.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:36 2006