Locus 6450

Sequence ID 2L_DroMel_CAF1
Location 18,127,486 – 18,127,625
Length 139
Max. P 0.970471
window10303 window10304

overview

Window 3

Location 18,127,486 – 18,127,591
Length 105
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 77.34
Mean single sequence MFE -35.73
Consensus MFE -27.01
Energy contribution -27.35
Covariance contribution 0.34
Combinations/Pair 1.09
Mean z-score -2.09
Structure conservation index 0.76
SVM decision value 1.66
SVM RNA-class probability 0.970471
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18127486 105 - 22407834
CGUAUCUCCAAGUCCAGUUUGCAAUGGCUACUAGUAAACAAAUGGCUGCCGCUGUGGAUUGGCCAGGGACCCGAUUGCAAGGUAAAAAAC-AUUU---UCUCUUCUU---UU------
((..((.((..(.((((((..((.((((..(((.........)))..)))).))..)))))))..))))..)).....(((..((((...-.)))---)..)))...---..------ ( -25.30)
>DroVir_CAF1 20027 102 - 1
CGCAUCUCCAAGUCCAGUUUGCAGUGGCUGCUGGUCAACAAGUGGCUGCCGCUGUGGAUUGGCCAGGGACCCGAGUGCAAGGUGAG-CCUUAAAU---AAU-------AUUAA-----
.((((.(((..(.((((((..(((((((.((((.(.....).)))).)))))))..)))))).)..))).....))))((((....-))))....---...-------.....----- ( -39.10)
>DroPse_CAF1 20011 100 - 1
CGCAUAUCCAAGUCCAGUUUGCAGUGGCUGCUCGUGAACAAAUGGCUGCCACUGUGGAUUGGCCAGGGACCCGAUUGCAAGGUAGG-AUUCA-----------ACUU---UAAAC---
.(((..(((..(.((((((..(((((((.((.(((......))))).)))))))..)))))).)..)))......)))(((((...-.....-----------))))---)....--- ( -37.80)
>DroGri_CAF1 18955 114 - 1
CGCAUCUCCAAGUCCAGUUUGCAGUGGCUCCUGGUGAACAAGUGGCUGCCACUGUGGAUUGGCCAGGGACCCGAGUGCAAGGUGAG-CAGCAGUU---AUUCAUCUGUAUUAAUCGAU
......(((..(.((((((..(((((((.((..(....)....))..)))))))..)))))).)..)))..((((((((.((((((-........---.)))))))))))...))).. ( -40.30)
>DroYak_CAF1 31925 108 - 1
CGGAUCUCCAAGUCCAGUUUGCAAUGGCUGCUAGUAAACAAAUGGCUGCCACUGUGGAUUGGCCAGGGACCCGAUUGCAAGGUAGA-AUCCCUUCGUUAUUUUUAUC---UU------
(((.((.((..(.((((((..((.((((.((((.........)))).)))).))..)))))))..)))).))).....((((((((-(............)))))))---))------ ( -36.10)
>DroPer_CAF1 20039 100 - 1
CGCAUAUCCAAGUCCAGUUUGCAGUGGCAUCUCGUGAACAAAUGGCUGCCACUGUGGAUUGGCCAGGGACCCGAUUGCAAGGUAGG-AUUCA-----------ACUU---UAAAC---
.(((..(((..(.((((((..((((((((.(.(((......)))).))))))))..)))))).)..)))......)))(((((...-.....-----------))))---)....--- ( -35.80)
>consensus
CGCAUCUCCAAGUCCAGUUUGCAGUGGCUGCUAGUGAACAAAUGGCUGCCACUGUGGAUUGGCCAGGGACCCGAUUGCAAGGUAAG_AUUCA_UU___A_U__UCUU___UAA_____
......(((..(.((((((..(((((((..(((.(.....).)))..)))))))..)))))).)..))).((........)).................................... (-27.01 = -27.35 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 18,127,511 – 18,127,625
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.02
Mean single sequence MFE -40.30
Consensus MFE -25.62
Energy contribution -26.15
Covariance contribution 0.53
Combinations/Pair 1.23
Mean z-score -1.61
Structure conservation index 0.64
SVM decision value 0.28
SVM RNA-class probability 0.667095
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18127511 114 - 22407834
A---UCUGGAGAUACCAAUGGCAAU---GGGACUUUGAAUCGUAUCUCCAAGUCCAGUUUGCAAUGGCUACUAGUAAACAAAUGGCUGCCGCUGUGGAUUGGCCAGGGACCCGAUUGCAA
.---..(((.....)))...(((((---(((((........))...(((..(.((((((..((.((((..(((.........)))..)))).))..)))))).)..)))))).))))).. ( -34.70)
>DroVir_CAF1 20049 114 - 1
CUCCUCCUCGGAUGCC---GGCAAU---GGCACCUUGAAUCGCAUCUCCAAGUCCAGUUUGCAGUGGCUGCUGGUCAACAAGUGGCUGCCGCUGUGGAUUGGCCAGGGACCCGAGUGCAA
......(((((.((((---(....)---))))(((((....((........))((((((..(((((((.((((.(.....).)))).)))))))..)))))).)))))..)))))..... ( -46.20)
>DroGri_CAF1 18989 117 - 1
UUCCUCGUCGGAUGGC---AGCAACAAUGGCACCUUGAAUCGCAUCUCCAAGUCCAGUUUGCAGUGGCUCCUGGUGAACAAGUGGCUGCCACUGUGGAUUGGCCAGGGACCCGAGUGCAA
...((((..((.((.(---(.......)).))))............(((..(.((((((..(((((((.((..(....)....))..)))))))..)))))).)..)))..))))..... ( -40.10)
>DroMoj_CAF1 22510 111 - 1
C---UCUUCGGAUUCC---GGCAAC---AAUACCUUGAACCGCAUAUCCAAGUCCAGUCUUCAGUGGCUGCUGGUCAACAAGUGGCUGCCUCUGUGGAUUGGCCAGGGACCCGAAUGCAA
.---..(((((.((((---(((...---.....((((...........))))..((((((.(((.(((.((((.(.....).)))).))).))).))))))))).)))).)))))..... ( -37.60)
>DroAna_CAF1 17802 108 - 1
G---UCGGGAGAUGCCA------AU---GGAACCUUGAACCGCAUCUCCAAGUCGAGCUUGCAGUGGCUGUUGGUGAACAAAUGGUUGCCAUUGUGGAUUGGCCAGGGUCCUGACUGCAA
(---(((((((((((((------(.---(....))))....)))))(((..(((((..(..(((((((..(((.....)))......)))))))..).)))))..))))))))))..... ( -38.10)
>DroPer_CAF1 20059 114 - 1
U---UCGGGAGAUGCCAAUGGGAAU---AACACUCUGAAUCGCAUAUCCAAGUCCAGUUUGCAGUGGCAUCUCGUGAACAAAUGGCUGCCACUGUGGAUUGGCCAGGGACCCGAUUGCAA
.---(((((..((((...(.(((..---.....))).)...)))).(((..(.((((((..((((((((.(.(((......)))).))))))))..)))))).)..))))))))...... ( -45.10)
>consensus
C___UCGGCAGAUGCC___GGCAAU___GGCACCUUGAAUCGCAUCUCCAAGUCCAGUUUGCAGUGGCUGCUGGUGAACAAAUGGCUGCCACUGUGGAUUGGCCAGGGACCCGAGUGCAA
.........................................((((((((..(.((((((..(((((((..(((.(.....).)))..)))))))..)))))).)..)))...)).))).. (-25.62 = -26.15 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:34 2006