Locus 5842

Sequence ID	3L_DroMel_CAF1
Location	15,763,894 – 15,764,068
Length	174
Max. P	0.922456

overview

Window 3

Location	15,763,894 – 15,764,013
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.66
Mean single sequence MFE	-34.17
Consensus MFE	-25.70
Energy contribution	-28.68
Covariance contribution	2.98
Combinations/Pair	1.04
Mean z-score	-2.48
Structure conservation index	0.75
SVM decision value	1.15
SVM RNA-class probability	0.922456
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15763894 119 + 23771897
GGAUAUUCUU-UUCCCACAGUAGAAAGGAUAAUAAAAUGCCUACGGGCAAACAAAAAUAAACAAGAUACGUACGCCCGCUUGGAUGCAUCCUCAAAGGAUGGAUCCUUGAGGCAAGUCGA
.(((..((((-(((........)))))))........(((((.(((((..((.................))..)))))(..((((.(((((.....))))).))))..)))))).))).. ( -35.93)
>DroSec_CAF1 15466 120 + 1
GGAUAUUCUUUUUCCCACAGUAGAAAGGAUAAUAAAAUGCCUACGGGCAAACAAAAAUAAACAAGAUGCGUACGCCCGGUUGGAUGCAUCCUCAAAGGAUGGAUCCUUGAGGGAAGUCGA
...((((((((((........))))))))))......((((....))))...................((....(((....((((.(((((.....))))).))))....)))....)). ( -36.20)
>DroSim_CAF1 16465 120 + 1
GGAUAUUCUUUUUCCCACAGUAGAAAGGAUAAUAAAAUGCCUACGGGCAAACAAAAAUAAACAAGAUGCGUACGCCCGGUUGGAUGCAUCCUCAAAGGAUGGAUCCUUGAGGGAAGUCGA
...((((((((((........))))))))))......((((....))))...................((....(((....((((.(((((.....))))).))))....)))....)). ( -36.20)
>DroEre_CAF1 15603 119 + 1
GGAUAUUCUU-UUCCCACAGUAGAAAGGAUAAUAAAAUGCCUGCGGGCAAACAAAAAUAAACAAGAUGCGUACGACCGGUUGGGUGCAUCCUCAAAGGAUGGAUCCUUGAGGGAGGACGA
......((((-(((........)))))))........((((....))))...................(((.(..((....((((.(((((.....))))).))))....))..).))). ( -32.10)
>DroAna_CAF1 10635 119 + 1
GGUUAUUCAUUUUCCCACACAAGAAAGGAUAAUAAAAUGCCUCGGGGCAAACAAAAAUAAACAACAUGCGUACGCCCGACUGGCUGCAUCCUUUAAGGAUGGAUCCUUGACGG-GGCCAA
.(((((((.((((........)))).))))))).....((((((((((..((.................))..))))....((.(.(((((.....))))).).))....)))-)))... ( -30.43)
>consensus
GGAUAUUCUUUUUCCCACAGUAGAAAGGAUAAUAAAAUGCCUACGGGCAAACAAAAAUAAACAAGAUGCGUACGCCCGGUUGGAUGCAUCCUCAAAGGAUGGAUCCUUGAGGGAAGUCGA
...((((((((((........))))))))))......((((....))))...................((....(((....((((.(((((.....))))).))))....)))....)). (-25.70 = -28.68 +   2.98)

alignment

secondary structure

dotplot

Window 4

Location	15,763,894 – 15,764,013
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.66
Mean single sequence MFE	-32.36
Consensus MFE	-23.60
Energy contribution	-24.68
Covariance contribution	1.08
Combinations/Pair	1.10
Mean z-score	-1.97
Structure conservation index	0.73
SVM decision value	0.18
SVM RNA-class probability	0.623384
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15763894 119 - 23771897
UCGACUUGCCUCAAGGAUCCAUCCUUUGAGGAUGCAUCCAAGCGGGCGUACGUAUCUUGUUUAUUUUUGUUUGCCCGUAGGCAUUUUAUUAUCCUUUCUACUGUGGGAA-AAGAAUAUCC
..((..(((((...((((.(((((.....))))).))))..(((((((.(((...............))).))))))))))))..))....((.(((((......))))-).))...... ( -35.36)
>DroSec_CAF1 15466 120 - 1
UCGACUUCCCUCAAGGAUCCAUCCUUUGAGGAUGCAUCCAACCGGGCGUACGCAUCUUGUUUAUUUUUGUUUGCCCGUAGGCAUUUUAUUAUCCUUUCUACUGUGGGAAAAAGAAUAUCC
((...(((((.((.((((.(((((.....))))).))))....(((((...(((.............))).)))))(((((...............))))))).)))))...))...... ( -32.18)
>DroSim_CAF1 16465 120 - 1
UCGACUUCCCUCAAGGAUCCAUCCUUUGAGGAUGCAUCCAACCGGGCGUACGCAUCUUGUUUAUUUUUGUUUGCCCGUAGGCAUUUUAUUAUCCUUUCUACUGUGGGAAAAAGAAUAUCC
((...(((((.((.((((.(((((.....))))).))))....(((((...(((.............))).)))))(((((...............))))))).)))))...))...... ( -32.18)
>DroEre_CAF1 15603 119 - 1
UCGUCCUCCCUCAAGGAUCCAUCCUUUGAGGAUGCACCCAACCGGUCGUACGCAUCUUGUUUAUUUUUGUUUGCCCGCAGGCAUUUUAUUAUCCUUUCUACUGUGGGAA-AAGAAUAUCC
.........((((((((....))).)))))((((((((.....))).....))))).....(((((((.....(((((((....................)))))))..-)))))))... ( -28.35)
>DroAna_CAF1 10635 119 - 1
UUGGCC-CCGUCAAGGAUCCAUCCUUAAAGGAUGCAGCCAGUCGGGCGUACGCAUGUUGUUUAUUUUUGUUUGCCCCGAGGCAUUUUAUUAUCCUUUCUUGUGUGGGAAAAUGAAUAACC
....((-(((.((((((..(((((.....)))))..(((..(((((.(((.(((.............))).))))))))))).............)))))))).)))............. ( -33.72)
>consensus
UCGACUUCCCUCAAGGAUCCAUCCUUUGAGGAUGCAUCCAACCGGGCGUACGCAUCUUGUUUAUUUUUGUUUGCCCGUAGGCAUUUUAUUAUCCUUUCUACUGUGGGAAAAAGAAUAUCC
((...(((((.((.((((.(((((.....))))).))))....(((((.(((...............))).)))))(((((...............))))))).)))))...))...... (-23.60 = -24.68 +   1.08)

alignment

secondary structure

dotplot

Window 5

Location	15,763,973 – 15,764,068
Length	95
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.48
Mean single sequence MFE	-29.82
Consensus MFE	-22.90
Energy contribution	-22.78
Covariance contribution	-0.12
Combinations/Pair	1.16
Mean z-score	-1.61
Structure conservation index	0.77
SVM decision value	0.22
SVM RNA-class probability	0.638026
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15763973 95 + 23771897
UGGAUGCAUCCUCAAAGGAUGGAUCCUUGAGGCAAGUCGAGGUGAAGGUUUAGAC-------------------------UUAGAUUGUGGCAUUGAUUUCAUUUUCAGCUGUCUAUCAA
.((((.(((((.....))))).))))...(((((.((((..((..((((....))-------------------------))..))..)))).((((........)))).)))))..... ( -25.40)
>DroSec_CAF1 15546 95 + 1
UGGAUGCAUCCUCAAAGGAUGGAUCCUUGAGGGAAGUCGAGGUGAAGGCUUGGAC-------------------------UUAGAUUGUGGCAUUGAUUUCAUUUUCAGCUGUCUAUCAA
.((((.(((((.....))))).)))).......(((((.((((....)))).)))-------------------------)).(((...((((((((........)))).)))).))).. ( -30.80)
>DroSim_CAF1 16545 95 + 1
UGGAUGCAUCCUCAAAGGAUGGAUCCUUGAGGGAAGUCGAGGUGAAGGCUUGGAC-------------------------UUAGAUUGUGGCAUUGAUUUCAUUUUCAGCUGUCUAUCAA
.((((.(((((.....))))).)))).......(((((.((((....)))).)))-------------------------)).(((...((((((((........)))).)))).))).. ( -30.80)
>DroEre_CAF1 15682 95 + 1
UGGGUGCAUCCUCAAAGGAUGGAUCCUUGAGGGAGGACGAGCUGCAGGUUUAGAC-------------------------UUAGAUUGUGGCAUUGAUUUCAUUUUCAGCUGUCUAUCAA
.((((.(((((.....))))).)))).....((.(((((.((..(((.((((...-------------------------.)))))))..)).((((........)))).))))).)).. ( -27.10)
>DroAna_CAF1 10715 119 + 1
UGGCUGCAUCCUUUAAGGAUGGAUCCUUGACGG-GGCCAAGGGAAAGGCUUAGAGACAAGCUCGGUGAUGCAGUGAUUGUUGGGAUUGUGGCAUUGAUUUCAUUUUCAGCUGUCUAUCAA
..(((((((((((((((((....)))))))..(-((((........))))).(((.....))))).))))))))(((.((((..(..((((........)))))..)))).)))...... ( -35.00)
>consensus
UGGAUGCAUCCUCAAAGGAUGGAUCCUUGAGGGAAGUCGAGGUGAAGGCUUAGAC_________________________UUAGAUUGUGGCAUUGAUUUCAUUUUCAGCUGUCUAUCAA
.((((.(((((.....))))).)))).......(((((........)))))................................(((...((((((((........)))).)))).))).. (-22.90 = -22.78 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:49 2006