Locus 8073

Sequence ID	X_DroMel_CAF1
Location	20,102,474 – 20,102,591
Length	117
Max. P	0.970616

overview

Window 1

Location	20,102,474 – 20,102,591
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	79.52
Mean single sequence MFE	-45.45
Consensus MFE	-26.21
Energy contribution	-30.15
Covariance contribution	3.94
Combinations/Pair	1.09
Mean z-score	-2.66
Structure conservation index	0.58
SVM decision value	1.66
SVM RNA-class probability	0.970616
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20102474 117 + 22224390
ACUUUAAGCCGCGGC---CAGUGCGGCGGAGAAGAGCAUCUGUGAUGCGCCAAUGCUUGAUUUAUUGCACCCUGGCAACCCUUAUCCGCCGCCCAUUGGCCCAUUGGCCACGCCCACUUA
.......((((.(((---((((((((((((.(((.(((((...)))))((((.(((..........)))...))))....))).))))))))..)))))))...))))............ ( -48.10)
>DroSec_CAF1 12550 117 + 1
UCUUUAAGCCGCGGC---CAGUGCGGCGGUGAAGAGCAUCUGUGAUGCGCCAAUGCUUGAUUUAUUGCACCCUGGCAACCCUUAUCCGCCGCCCAUUGGCCCGUUGGCCACGCCCACUUA
.......((((((((---(((((.(((((((....(((((...)))))((((.(((..........)))...))))..........))))))))))))).))).))))............ ( -48.10)
>DroEre_CAF1 9548 114 + 1
GCUUUAAGCCGCGGC---CAGUGAGGCGGAGAGGAGCAUCUGUGAUGCGCCAAUGCUUGAUUUAUUGCACCCUGGCAGCCCUUAUCCGCCGCCCAUUGGCCC---GGCCACGCCCACUUA
.......((((.(((---(((((.((((((((((.(((((...)))))((((.(((..........)))...))))...)))).))))))...)))))))))---)))............ ( -52.20)
>DroAna_CAF1 7569 101 + 1
UCCUUAAGCUCUGGCCGACAGGGGGAGGGAGAAGAGCAUCUGGGAUGCGCCAAUGCUUGAUUUAUUGGACCCG---------CUCCCGCUCCCCA----------GGACACGCCUACAAA
((((......(((.....)))(((((((((........)))((((.(((((((((.......))))))...))---------))))).)))))))----------)))............ ( -33.40)
>consensus
UCUUUAAGCCGCGGC___CAGUGCGGCGGAGAAGAGCAUCUGUGAUGCGCCAAUGCUUGAUUUAUUGCACCCUGGCAACCCUUAUCCGCCGCCCAUUGGCCC___GGCCACGCCCACUUA
............(((.....(.((((((((.(((.(((((...)))))((((.(((..........)))...))))....))).)))))))).)..(((((....))))).)))...... (-26.21 = -30.15 +   3.94)

alignment

secondary structure

dotplot

Window 2

Location	20,102,474 – 20,102,591
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	79.52
Mean single sequence MFE	-47.23
Consensus MFE	-29.85
Energy contribution	-33.48
Covariance contribution	3.62
Combinations/Pair	1.14
Mean z-score	-2.16
Structure conservation index	0.63
SVM decision value	1.09
SVM RNA-class probability	0.912896
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20102474 117 - 22224390
UAAGUGGGCGUGGCCAAUGGGCCAAUGGGCGGCGGAUAAGGGUUGCCAGGGUGCAAUAAAUCAAGCAUUGGCGCAUCACAGAUGCUCUUCUCCGCCGCACUG---GCCGCGGCUUAAAGU
.....((.((((((((.((.(((....)))((((((.((((...((((..((((..........))))))))(((((...))))))))).)))))).)).))---)))))).))...... ( -52.70)
>DroSec_CAF1 12550 117 - 1
UAAGUGGGCGUGGCCAACGGGCCAAUGGGCGGCGGAUAAGGGUUGCCAGGGUGCAAUAAAUCAAGCAUUGGCGCAUCACAGAUGCUCUUCACCGCCGCACUG---GCCGCGGCUUAAAGA
.....((.((((((((.....((...))(((((((..((((...((((..((((..........))))))))(((((...)))))))))..)))))))..))---)))))).))...... ( -48.50)
>DroEre_CAF1 9548 114 - 1
UAAGUGGGCGUGGCC---GGGCCAAUGGGCGGCGGAUAAGGGCUGCCAGGGUGCAAUAAAUCAAGCAUUGGCGCAUCACAGAUGCUCCUCUCCGCCUCACUG---GCCGCGGCUUAAAGC
.....((.(((((((---(((((....)))((((((..((((..((((..((((..........))))))))(((((...))))))))).))))))...)))---)))))).))...... ( -53.30)
>DroAna_CAF1 7569 101 - 1
UUUGUAGGCGUGUCC----------UGGGGAGCGGGAG---------CGGGUCCAAUAAAUCAAGCAUUGGCGCAUCCCAGAUGCUCUUCUCCCUCCCCCUGUCGGCCAGAGCUUAAGGA
....(((((.((.((----------.((((.(.(((((---------.(((.(((((.........))))))(((((...))))).)).))))).)))))....)).))..))))).... ( -34.40)
>consensus
UAAGUGGGCGUGGCC___GGGCCAAUGGGCGGCGGAUAAGGGUUGCCAGGGUGCAAUAAAUCAAGCAUUGGCGCAUCACAGAUGCUCUUCUCCGCCGCACUG___GCCGCGGCUUAAAGA
(((((.(((.(((((....)))))..((((((((((.((((((......(((((..(((........)))..)))))......)))))).)))))))).))....)))...))))).... (-29.85 = -33.48 +   3.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:48 2006