Locus 27

Sequence ID	3R_DroMel_CAF1
Location	231,934 – 232,089
Length	155
Max. P	0.876311

overview

Window 4

Location	231,934 – 232,051
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.89
Mean single sequence MFE	-45.92
Consensus MFE	-30.58
Energy contribution	-31.42
Covariance contribution	0.84
Combinations/Pair	1.32
Mean z-score	-2.00
Structure conservation index	0.67
SVM decision value	0.89
SVM RNA-class probability	0.876311
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 231934 117 + 27905053
GGGUGGUGCACGCAUCGAAGCUGUCGACACCACCACAGUAUAGUAUGACUUUGCGCUUGGCGCAGCCAAUGAACGGUCGCGGCGGACUUCCGCCGACAGC---GCAAUGUUUGGAGUUCA
.((((((((((((......)).)).).)))))))............(((.(((((((.(..((.(((.......))).))(((((....)))))..))))---)))).)))......... ( -43.70)
>DroPse_CAF1 1808 117 + 1
GAGCGCUGCACGUAUCGAGUCUGUGGACACCACCACAGUAUAGUAUGACCAAGCGCUUAGCGCAGCCACCAAACGGCUGCGGCGGAUGUCCGCCUGCAGU---GCCACGCAUGGAGUUCA
((((.((((.(((((.....((((((......))))))....))))).....(((((..((((((((.......))))))(((((....))))).)))))---))...))).)..)))). ( -49.20)
>DroWil_CAF1 2637 120 + 1
GGGCGCUGCACGCAUCGAGUCGGUGGACACCACCACUGUAUAGUACGACCAAGAGCUUGGUGCAGCCAACAAAAUGUUUAGGCGGAUGUCCGCCAGCAGUAGCAUCGCGUUUGGAGUUCA
(((((((((((((.((..((((((((...)))))(((....)))..)))...))))...))))))).....((((((...(((((....))))).((....))...))))))...)))). ( -43.10)
>DroMoj_CAF1 1753 117 + 1
UGGCGCUUCACGUAUUGAGUCUGUGGACACAACCACAGUAUAGUAUGACCAAUUCGGUAGCGCUGCCACAAAAAGGCCACGGCGGAUGUCCGCCGCCAGC---GCCACAUGUGGAGUUCA
.((((((...(((((((...((((((......))))))..)))))))(((.....))))))))).(((((....((((.((((((....))))))...).---)))...)))))...... ( -47.30)
>DroAna_CAF1 1815 117 + 1
GGGUGGUGCUCGUAUCGAAUCUGUGGACACCACCACAGUAUAGUAUGACCCAGCAGUCAGCUCAGCCACAAAAUGGUUGCGGCGGAUGUCCGCCGGCAGC---AUAACGUUUGGAGUUCA
((((.(((((.(((......((((((......)))))))))))))).))))(((.....))).(((..((((...((((((((((....))))).)))))---......))))..))).. ( -43.00)
>DroPer_CAF1 1808 117 + 1
GAGCGCUGCACGUAUCGAGUCUGUGGACACCACCACAGUAUAGUAUGACCAAGCGCUUAGCGCAGCCACCAAACGGCUGCGGCGGAUGUCCGCCUGCAGU---GCCACGCAUGGAGUUCA
((((.((((.(((((.....((((((......))))))....))))).....(((((..((((((((.......))))))(((((....))))).)))))---))...))).)..)))). ( -49.20)
>consensus
GGGCGCUGCACGUAUCGAGUCUGUGGACACCACCACAGUAUAGUAUGACCAAGCGCUUAGCGCAGCCACCAAACGGCUGCGGCGGAUGUCCGCCGGCAGC___GCCACGUUUGGAGUUCA
((((......(((((.....((((((......))))))....))))).(((.(((....((((((((.......))))))(((((....))))).........))..))).))).)))). (-30.58 = -31.42 +   0.84)

alignment

secondary structure

dotplot

Window 5

Location	231,974 – 232,089
Length	115
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	80.58
Mean single sequence MFE	-34.06
Consensus MFE	-20.39
Energy contribution	-20.87
Covariance contribution	0.48
Combinations/Pair	1.41
Mean z-score	-1.60
Structure conservation index	0.60
SVM decision value	-0.05
SVM RNA-class probability	0.507508
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 231974 115 - 27905053
U-CCCGAUUUUUUCUAAACAAAAUGUUACUUUUUUUCGUUGAACUCCAAACAUUGCGCUGUCGGCGGAAGUCCGCCGCGACCGUUCAUUGGCUGCGCCAAGCGCAAAGUCAUACUA
.-...((((((..........((((((.....(((.....))).....))))))(((((...(((((....)))))(((.(((.....))).)))....)))))))))))...... ( -30.40)
>DroVir_CAF1 1806 115 - 1
U-UUCUGUUGCGUCUAAACAAAAUGUUACUCUUUUUCGUUGAACUCCACACGUGGCGCUGGCGGCGGACAUCCGCCUUGGCCGUUUUGUGGCAGAACUACCAACAUGAUCAUACUA
.-.(((((((..(((..((((((((....................(((....))).((..(.(((((....))))))..))))))))))...))).....))))).))........ ( -30.00)
>DroPse_CAF1 1848 115 - 1
U-CUCGGCUUUUUCUAAACAAAAUGUUACUUUUUUUCGUUGAACUCCAUGCGUGGCACUGCAGGCGGACAUCCGCCGCAGCCGUUUGGUGGCUGCGCUAAGCGCUUGGUCAUACUA
.-.(((((........(((.....)))..........)))))...(((.(((((((......(((((....)))))(((((((.....))))))))))..)))).)))........ ( -37.37)
>DroMoj_CAF1 1793 115 - 1
U-UUGUGUUGUGUCUAAACAAAAUGUUACUCUUUUUCGUUGAACUCCACAUGUGGCGCUGGCGGCGGACAUCCGCCGUGGCCUUUUUGUGGCAGCGCUACCGAAUUGGUCAUACUA
.-.....((((......))))...((....((..(((((.(....).))..((((((((.(((((((....))))))).(((.......))))))))))).)))..))....)).. ( -37.30)
>DroAna_CAF1 1855 116 - 1
UUUUAGACUUUCUCUAAACAAAAUGUUACUCUUUUUCGAUGAACUCCAAACGUUAUGCUGCCGGCGGACAUCCGCCGCAACCAUUUUGUGGCUGAGCUGACUGCUGGGUCAUACUA
..(((((.....)))))((((((((............(...(((.......)))...)(((.(((((....))))))))..))))))))((((.(((.....))).))))...... ( -31.90)
>DroPer_CAF1 1848 115 - 1
U-CUCGGCUUUUUCUAAACAAAAUGUUACUUUUUUUCGUUGAACUCCAUGCGUGGCACUGCAGGCGGACAUCCGCCGCAGCCGUUUGGUGGCUGCGCUAAGCGCUUGGUCAUACUA
.-.(((((........(((.....)))..........)))))...(((.(((((((......(((((....)))))(((((((.....))))))))))..)))).)))........ ( -37.37)
>consensus
U_CUCGGCUUUUUCUAAACAAAAUGUUACUCUUUUUCGUUGAACUCCAAACGUGGCGCUGCCGGCGGACAUCCGCCGCAGCCGUUUUGUGGCUGCGCUAACCGCUUGGUCAUACUA
...................................................(((((......(((((....)))))(((((((.....)))))))............))))).... (-20.39 = -20.87 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:40 2006