Locus 4537

Sequence ID	3R_DroMel_CAF1
Location	12,037,912 – 12,038,098
Length	186
Max. P	0.999897

overview

Window 6

Location	12,037,912 – 12,038,006
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	97.45
Mean single sequence MFE	-29.76
Consensus MFE	-28.36
Energy contribution	-28.56
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.21
Structure conservation index	0.95
SVM decision value	0.34
SVM RNA-class probability	0.696239
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12037912 94 + 27905053
UAUGUGCCCCACUUAGGUUCGCCUCAAUGGGGCCUAGCCCCUUCGACUGGCUGUUGUUGUUUUCGUUGGUGUUGAACCAAUGCCAAGUCAACUG
.....((((((.(.(((....))).).)))))).(((((.........)))))..(((((((.(((((((.....)))))))..))).)))).. ( -29.90)
>DroSec_CAF1 9213 94 + 1
UAUGUGCCCCACUUAGGUUCGCCUCAAUGGGGCCUAGCCCCUUCGACUGGCUGUUGUUGUUUUCGUUGGUGUUGAACCAAUGCCAAGUCAACUG
.....((((((.(.(((....))).).)))))).(((((.........)))))..(((((((.(((((((.....)))))))..))).)))).. ( -29.90)
>DroSim_CAF1 9250 94 + 1
UAUGUGCCCCACUUAGGUUCGCCUCAAUGGGGCCUAGCCCCUUCGACUGGCUGUUGUUGUUUUCGUUGGUGUUGAACCAAUGCCAAGUCAACUG
.....((((((.(.(((....))).).)))))).(((((.........)))))..(((((((.(((((((.....)))))))..))).)))).. ( -29.90)
>DroEre_CAF1 8476 94 + 1
UGUGUGCCCCACUUAGGUUCGCCUCAAUGGGGCCUAGCCCCAUCGACUGACUGUUGUUGUUUUCGUUGGUGCUGAACCAAUGCCAAGUCAACUG
.((..((((((.(.(((....))).).))))))...))......(((((((....))).....(((((((.....)))))))...))))..... ( -27.90)
>DroYak_CAF1 8789 94 + 1
UGUGUGCCCCACUUAGGUUCGCCUCAAUGGGGCCUAGCCCCAUCGACUGGCUGUGGUUGUUUUCGUUGGUGUUGAACCAAUGCCAAGUCAACUG
.....((((((.(.(((....))).).)))))).(((((.........))))).((((((((.(((((((.....)))))))..))).))))). ( -31.20)
>consensus
UAUGUGCCCCACUUAGGUUCGCCUCAAUGGGGCCUAGCCCCUUCGACUGGCUGUUGUUGUUUUCGUUGGUGUUGAACCAAUGCCAAGUCAACUG
.....((((((.(.(((....))).).)))))).(((((.........)))))..(((((((.(((((((.....)))))))..))).)))).. (-28.36 = -28.56 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	12,037,912 – 12,038,006
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	97.45
Mean single sequence MFE	-32.16
Consensus MFE	-31.68
Energy contribution	-31.52
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.59
Structure conservation index	0.99
SVM decision value	4.44
SVM RNA-class probability	0.999897
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12037912 94 - 27905053
CAGUUGACUUGGCAUUGGUUCAACACCAACGAAAACAACAACAGCCAGUCGAAGGGGCUAGGCCCCAUUGAGGCGAACCUAAGUGGGGCACAUA
(..((((((.(((.(((((.....))))).(....).......)))))))))..)......((((((((.(((....))).))))))))..... ( -32.30)
>DroSec_CAF1 9213 94 - 1
CAGUUGACUUGGCAUUGGUUCAACACCAACGAAAACAACAACAGCCAGUCGAAGGGGCUAGGCCCCAUUGAGGCGAACCUAAGUGGGGCACAUA
(..((((((.(((.(((((.....))))).(....).......)))))))))..)......((((((((.(((....))).))))))))..... ( -32.30)
>DroSim_CAF1 9250 94 - 1
CAGUUGACUUGGCAUUGGUUCAACACCAACGAAAACAACAACAGCCAGUCGAAGGGGCUAGGCCCCAUUGAGGCGAACCUAAGUGGGGCACAUA
(..((((((.(((.(((((.....))))).(....).......)))))))))..)......((((((((.(((....))).))))))))..... ( -32.30)
>DroEre_CAF1 8476 94 - 1
CAGUUGACUUGGCAUUGGUUCAGCACCAACGAAAACAACAACAGUCAGUCGAUGGGGCUAGGCCCCAUUGAGGCGAACCUAAGUGGGGCACACA
..(((((((.(((.(((((.....))))).(....).......))))))))))........((((((((.(((....))).))))))))..... ( -30.00)
>DroYak_CAF1 8789 94 - 1
CAGUUGACUUGGCAUUGGUUCAACACCAACGAAAACAACCACAGCCAGUCGAUGGGGCUAGGCCCCAUUGAGGCGAACCUAAGUGGGGCACACA
..(((((((.(((..(((((................)))))..))))))))))........((((((((.(((....))).))))))))..... ( -33.89)
>consensus
CAGUUGACUUGGCAUUGGUUCAACACCAACGAAAACAACAACAGCCAGUCGAAGGGGCUAGGCCCCAUUGAGGCGAACCUAAGUGGGGCACAUA
(..((((((.(((.(((((.....))))).(....).......)))))))))..)......((((((((.(((....))).))))))))..... (-31.68 = -31.52 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	12,038,006 – 12,038,098
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	96.63
Mean single sequence MFE	-29.08
Consensus MFE	-25.52
Energy contribution	-27.12
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.88
SVM decision value	0.31
SVM RNA-class probability	0.683902
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12038006 92 + 27905053
CGUGUAGUACUGCCAUGAGAUAUUUUUUUGGGACGUUCCCAGAGUUCAGGCUCGGUACGGUACGGUUUGGUUCGUCACUCGGCAAGCAAACA
((((..((((((((.((((......(((((((.....))))))))))))))..)))))..))))(((((.((.(((....))))).))))). ( -31.30)
>DroSec_CAF1 9307 92 + 1
CGUGUAGUACUGCCAUGAGAUAUUUUUUUGGGACGUUCCCAGAGUUCAGGCUCGGUACGGUACGGUUUGGUUCGUCACUCGGCAAGCAAACA
((((..((((((((.((((......(((((((.....))))))))))))))..)))))..))))(((((.((.(((....))))).))))). ( -31.30)
>DroSim_CAF1 9344 92 + 1
CGUGUAGUACUGCCAUGAGAUAUUUUUUUGGGACGUUCCCAGAGUUCAGGCUCGGUACGGUACGGUUUGGUUCGUCACUCGGCAAGCAAACA
((((..((((((((.((((......(((((((.....))))))))))))))..)))))..))))(((((.((.(((....))))).))))). ( -31.30)
>DroEre_CAF1 8570 85 + 1
CGUGUAGUACUGCCAUGAGAUAUUU-UUUGGGACGUUCCCAGAGUUCAGGCUCGGUACGG------UUGGUUCGUCACUCGGCAAGCAAACA
......((((((((.((((.....(-((((((.....))))))))))))))..))))).(------((.(((.(((....))).))).))). ( -24.80)
>DroYak_CAF1 8883 92 + 1
CGUGUAGUACUGCCAUGAGAUAUUUUUUUGGGACGUUCCCAGAGUUCAGGCUCGGUACGGUAAGGUUUGGUUCGUCACUCGGCAAGCAAACA
......((((((((.((((......(((((((.....))))))))))))))..)))))......(((((.((.(((....))))).))))). ( -26.70)
>consensus
CGUGUAGUACUGCCAUGAGAUAUUUUUUUGGGACGUUCCCAGAGUUCAGGCUCGGUACGGUACGGUUUGGUUCGUCACUCGGCAAGCAAACA
((((..((((((((.((((......(((((((.....))))))))))))))..)))))..))))(((((.((.(((....))))).))))). (-25.52 = -27.12 +   1.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:44 2006