Locus 4934

Sequence ID	3R_DroMel_CAF1
Location	12,979,093 – 12,979,202
Length	109
Max. P	0.999006

overview

Window 5

Location	12,979,093 – 12,979,202
Length	109
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	70.75
Mean single sequence MFE	-33.30
Consensus MFE	-15.65
Energy contribution	-18.27
Covariance contribution	2.62
Combinations/Pair	1.25
Mean z-score	-3.04
Structure conservation index	0.47
SVM decision value	3.22
SVM RNA-class probability	0.998766
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12979093 109 + 27905053
UACGUCCUAAGCUAACUCUUCGGUUCGAUCGUUUGCUGCGC--CAGCUUAUUGCCUCGAUCGCAAUCAGCUAGCUGCCAAGCUGGCCAUCAAGU-------GCUGGCGCAGCAAACGA
..((.((.(((......))).))..)).(((((((((((((--((((..(((((.......)))))..(((((((....)))))))........-------))))))))))))))))) ( -51.30)
>DroSec_CAF1 2706 108 + 1
UACGUCCUAAGCUAACUCUUCUGUUCGAUCGUUUGCUGCGCGUCAGCUUAUUGCCUCGAUCGCAAUCAGCUAGUUA---AGCUGGCCAUCAAGU-------GCUGGCGCAGCAAACGA
..((..(.(((......)))..)..)).(((((((((((((..((((..(((((.......)))))..(((((...---..)))))........-------))))))))))))))))) ( -38.10)
>DroSim_CAF1 4045 106 + 1
UACGUCCUAAGCUAACUCUUCUGUUCGAUCGUUUGCUGCGC--CAGCUUAUUGCCUCGAUCGCAAUCAGCUANNNN---NNNNNNNNNNNNNNN-------NNNNNNNNNNNNNNNNN
.........(((((((......)))((((((...((.((..--..)).....))..)))))).....)))).....---...............-------................. ( -13.90)
>DroEre_CAF1 2697 113 + 1
UACGUCCUAAGCUAACUCUUCUGUUCGAUCGUUUGCUGUGC--CAGCUUAUUACCUCGACCGCAAUCAGCUAGUUA---AACUGGCCAUCAAGCACAAACAACUGGCGCAGCAAACAA
..((..(.(((......)))..)..))...(((((((((((--(((...........((......)).(((((...---..)))))................)))))))))))))).. ( -32.50)
>DroYak_CAF1 3431 113 + 1
UACGUCCUAAACUAUUUCUUCUGUUCGAUCGUUUGCUGUGC--CAGCUUAUUACCUCGAUCGCAAUCAGCUGGUUA---AACUGGCCAUCGAACUCAAACAACUGGCGCAGCAAACAA
..............................(((((((((((--(((.........(((((.((.....)).((((.---....)))))))))..........)))))))))))))).. ( -33.41)
>DroAna_CAF1 2992 105 + 1
UAUGUUCUAAGCUAAAUCUUGAAUUCGAUCGUUUGCUGCGC--CAGCUGUUGCACUCGGAUGCGAUUGGAUUAAUA---AUCUGGCU--------UGAGCGGCUAGCGAAGCAAACAA
...((((.(((......)))))))......(((((((.(((--.(((((((.((.((((((...((((...)))).---))))))..--------))))))))).))).))))))).. ( -30.60)
>consensus
UACGUCCUAAGCUAACUCUUCUGUUCGAUCGUUUGCUGCGC__CAGCUUAUUGCCUCGAUCGCAAUCAGCUAGUUA___AACUGGCCAUCAAG________GCUGGCGCAGCAAACAA
..............................(((((((((((....((..............)).....(((((((....)))))))...................))))))))))).. (-15.65 = -18.27 +   2.62)

alignment

secondary structure

dotplot

Window 6

Location	12,979,093 – 12,979,202
Length	109
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	70.75
Mean single sequence MFE	-37.28
Consensus MFE	-16.05
Energy contribution	-21.36
Covariance contribution	5.31
Combinations/Pair	1.28
Mean z-score	-3.19
Structure conservation index	0.43
SVM decision value	3.32
SVM RNA-class probability	0.999006
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12979093 109 - 27905053
UCGUUUGCUGCGCCAGC-------ACUUGAUGGCCAGCUUGGCAGCUAGCUGAUUGCGAUCGAGGCAAUAAGCUG--GCGCAGCAAACGAUCGAACCGAAGAGUUAGCUUAGGACGUA
(((((((((((((((((-------.((((((.(((((((........)))))...)).)))))).......))))--))))))))))))).....((.(((......))).))..... ( -51.60)
>DroSec_CAF1 2706 108 - 1
UCGUUUGCUGCGCCAGC-------ACUUGAUGGCCAGCU---UAACUAGCUGAUUGCGAUCGAGGCAAUAAGCUGACGCGCAGCAAACGAUCGAACAGAAGAGUUAGCUUAGGACGUA
(((((((((((((((((-------.((((((.(((((((---.....)))))...)).)))))).......))))..)))))))))))))..........(((....)))........ ( -43.30)
>DroSim_CAF1 4045 106 - 1
NNNNNNNNNNNNNNNNN-------NNNNNNNNNNNNNNN---NNNNUAGCUGAUUGCGAUCGAGGCAAUAAGCUG--GCGCAGCAAACGAUCGAACAGAAGAGUUAGCUUAGGACGUA
.................-------...............---....(((((.(((((.......))))).)))))--(((((((.(((..((.....))...))).)))...).))). ( -16.40)
>DroEre_CAF1 2697 113 - 1
UUGUUUGCUGCGCCAGUUGUUUGUGCUUGAUGGCCAGUU---UAACUAGCUGAUUGCGGUCGAGGUAAUAAGCUG--GCACAGCAAACGAUCGAACAGAAGAGUUAGCUUAGGACGUA
((((((((((.(((((((.....((((((((.(((((((---.....)))))...)).))).)))))...)))))--)).))))))))))..........(((....)))........ ( -40.90)
>DroYak_CAF1 3431 113 - 1
UUGUUUGCUGCGCCAGUUGUUUGAGUUCGAUGGCCAGUU---UAACCAGCUGAUUGCGAUCGAGGUAAUAAGCUG--GCACAGCAAACGAUCGAACAGAAGAAAUAGUUUAGGACGUA
((((((((((.(((((((.....(.((((((.(((((((---.....)))))...)).)))))).)....)))))--)).))))))))))............................ ( -41.10)
>DroAna_CAF1 2992 105 - 1
UUGUUUGCUUCGCUAGCCGCUCA--------AGCCAGAU---UAUUAAUCCAAUCGCAUCCGAGUGCAACAGCUG--GCGCAGCAAACGAUCGAAUUCAAGAUUUAGCUUAGAACAUA
(((((((((.((((((((((((.--------.....(((---(........))))......))))).....))))--))).))))))))).....((((((......))).))).... ( -30.40)
>consensus
UUGUUUGCUGCGCCAGC________CUUGAUGGCCAGCU___UAACUAGCUGAUUGCGAUCGAGGCAAUAAGCUG__GCGCAGCAAACGAUCGAACAGAAGAGUUAGCUUAGGACGUA
((((((((((.((((((........((((((.(((((((........)))))...)).)))))).......))))..)).))))))))))............................ (-16.05 = -21.36 +   5.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:26 2006