Locus 4462

Sequence ID	X_DroMel_CAF1
Location	11,811,105 – 11,811,196
Length	91
Max. P	0.946047

overview

Window 2

Location	11,811,105 – 11,811,196
Length	91
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	89.07
Mean single sequence MFE	-21.28
Consensus MFE	-16.28
Energy contribution	-16.44
Covariance contribution	0.16
Combinations/Pair	1.05
Mean z-score	-2.35
Structure conservation index	0.76
SVM decision value	1.36
SVM RNA-class probability	0.946047
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11811105 91 + 22224390
GACAUGAUUGUCGCAGACAUUGAAAGCUCCUCCACGACAAUCAUGUGCCACAA-ACAAUCAUUCUAGUCAAA-AAGAGUACGUUUCAAACGAA
.((((((((((((..((.............))..)))))))))))).......-......(((((.......-.))))).(((.....))).. ( -19.22)
>DroSec_CAF1 14865 89 + 1
GACAUGAUUGUCGCAGACAUGGAUAGCUCCACCGCGACAAUCAUGUGCC-CAA-ACAACCAUUCUAGUCAAA-AAGAGUACGUUUCAAACGA-
.(((((((((((((.(...((((....))))).)))))))))))))...-...-......(((((.......-.))))).(((.....))).- ( -26.20)
>DroSim_CAF1 16738 91 + 1
GACAUGAUUGUCGCAGACAUGGAUAGCUCCGCCACGACAAUCAUGUGCCACAA-ACAACCAUUCUAGUCAAA-AAGAGUACGUUUCAAACGAA
.((((((((((((..(....(((....))).)..)))))))))))).......-......(((((.......-.))))).(((.....))).. ( -21.60)
>DroEre_CAF1 14698 88 + 1
GACAUGGUUGCCGCCGAUACGGAGUGCUC---CACGACAACCAUGUGCCACAA-ACAACCAUUCUAGUCAAA-AAGAGUACGUUUCAAACGAA
.((((((((((((......))).(((...---)))..))))))))).......-......(((((.......-.))))).(((.....))).. ( -18.90)
>DroYak_CAF1 11904 88 + 1
GACAUGAUUGUCGCAGCU--GGAAAGCUC---CACGACAACCAUGUGCCACAAAACAACCAUUCUAGUCAAAAAAGAGUACGUUUCAAACGAA
.(((((.((((((.((((--....)))).---..)))))).)))))..............(((((.........))))).(((.....))).. ( -20.50)
>consensus
GACAUGAUUGUCGCAGACAUGGAAAGCUCC_CCACGACAAUCAUGUGCCACAA_ACAACCAUUCUAGUCAAA_AAGAGUACGUUUCAAACGAA
.((((((((((((.....................))))))))))))..............(((((.........))))).(((.....))).. (-16.28 = -16.44 +   0.16)

alignment

secondary structure

dotplot

Window 3

Location	11,811,105 – 11,811,196
Length	91
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	89.07
Mean single sequence MFE	-29.24
Consensus MFE	-20.30
Energy contribution	-20.02
Covariance contribution	-0.28
Combinations/Pair	1.22
Mean z-score	-2.77
Structure conservation index	0.69
SVM decision value	0.83
SVM RNA-class probability	0.861564
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11811105 91 - 22224390
UUCGUUUGAAACGUACUCUU-UUUGACUAGAAUGAUUGU-UUGUGGCACAUGAUUGUCGUGGAGGAGCUUUCAAUGUCUGCGACAAUCAUGUC
...(((..(((((...(((.-.......))).....)))-))..)))((((((((((((..((.(.........).))..)))))))))))). ( -25.30)
>DroSec_CAF1 14865 89 - 1
-UCGUUUGAAACGUACUCUU-UUUGACUAGAAUGGUUGU-UUG-GGCACAUGAUUGUCGCGGUGGAGCUAUCCAUGUCUGCGACAAUCAUGUC
-..(((..((....(((.((-((.....)))).)))..)-)..-)))(((((((((((((((((((....))))...))))))))))))))). ( -34.20)
>DroSim_CAF1 16738 91 - 1
UUCGUUUGAAACGUACUCUU-UUUGACUAGAAUGGUUGU-UUGUGGCACAUGAUUGUCGUGGCGGAGCUAUCCAUGUCUGCGACAAUCAUGUC
...(((..(((((.(((.((-((.....)))).))))))-))..)))(((((((((((((((((((....)))..))).))))))))))))). ( -29.60)
>DroEre_CAF1 14698 88 - 1
UUCGUUUGAAACGUACUCUU-UUUGACUAGAAUGGUUGU-UUGUGGCACAUGGUUGUCGUG---GAGCACUCCGUAUCGGCGGCAACCAUGUC
...(((..(((((.(((.((-((.....)))).))))))-))..)))(((((((((((((.---((((.....)).)).))))))))))))). ( -29.60)
>DroYak_CAF1 11904 88 - 1
UUCGUUUGAAACGUACUCUUUUUUGACUAGAAUGGUUGUUUUGUGGCACAUGGUUGUCGUG---GAGCUUUCC--AGCUGCGACAAUCAUGUC
...((((((((((.(((.((((......)))).)))))))))).)))(((((((((((((.---.((((....--))))))))))))))))). ( -27.50)
>consensus
UUCGUUUGAAACGUACUCUU_UUUGACUAGAAUGGUUGU_UUGUGGCACAUGAUUGUCGUGG_GGAGCUAUCCAUGUCUGCGACAAUCAUGUC
.((((((....((..........))....))))))............(((((((((((((((...............))))))))))))))). (-20.30 = -20.02 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:40 2006