Locus 4638

Sequence ID	2R_DroMel_CAF1
Location	15,165,836 – 15,165,960
Length	124
Max. P	0.993969

overview

Window 5

Location	15,165,836 – 15,165,927
Length	91
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	80.97
Mean single sequence MFE	-32.27
Consensus MFE	-18.98
Energy contribution	-19.73
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-3.36
Structure conservation index	0.59
SVM decision value	2.44
SVM RNA-class probability	0.993969
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15165836 91 + 20766785
AUA---CAUACAUAUCAAGUGACACAGGUGCUUGAAAUGGUGGGCUUAAAGGCUCAUUUAAGCCCUCUUUGUGUGUG-----UCAUUGGGCCAACUCAC
..(---((((((((((((((.((....))))))))...((.(((((((((......))))))))).)).))))))))-----)...((((....)))). ( -30.10)
>DroSec_CAF1 4262 94 + 1
GCA---CAUACAUAUCAAGUGACACAGGUGCUUGAAAUGGUGGGCUUAAAGGCUCAUUUAAGCCCUCUCCGUGUGUGUGCGCUCUUUGGGCCAACUA--
(((---(((((((.((((((.((....))))))))...((.(((((((((......)))))))))...))))))))))))(((.....)))......-- ( -39.50)
>DroEre_CAF1 6053 88 + 1
AUACUAUGUACAUAUCAUGUGACACAGGUGCUGGAAAUGGUGGGCUUAAAGGCUCAUUUAAGCCCUCAGUGUAUGUGUGCG---------CCAACUA--
..................(((.((((.((((......(((.(((((((((......))))))))))))..)))).))))))---------)......-- ( -26.50)
>DroYak_CAF1 4232 90 + 1
AU-------ACAUAUCAUGUGACACAGGUGCUUGAAAUGGAGGGCUUAAAGGCUCAUUUAAGCCCUCUUUGCAUGUGUGCGCUCAUUGGGCCAACUA--
..-------.....(((.(((.((((.((((.......((((((((((((......))))))))))))..)))).)))))))....)))........-- ( -33.00)
>consensus
AUA___CAUACAUAUCAAGUGACACAGGUGCUUGAAAUGGUGGGCUUAAAGGCUCAUUUAAGCCCUCUUUGUAUGUGUGCG_UCAUUGGGCCAACUA__
..........(((.((((((.((....)))))))).)))(.(((((((((......))))))))).)................................ (-18.98 = -19.73 +   0.75)

alignment

secondary structure

dotplot

Window 6

Location	15,165,852 – 15,165,960
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.70
Mean single sequence MFE	-40.32
Consensus MFE	-27.80
Energy contribution	-28.04
Covariance contribution	0.24
Combinations/Pair	1.20
Mean z-score	-2.45
Structure conservation index	0.69
SVM decision value	1.39
SVM RNA-class probability	0.949175
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15165852 108 + 20766785
UGACACAGGUGCUUGAAAUGGUGGGCUUAAAGGCUCAUUUAAGCCCUCUUUGUGUGUG-----UCAUUGGGCCAACUCACUAGGUGGCUGCGCGAA------UAGU-UGCACUUGAUGUA
..((((((((((.......((.(((((((((......))))))))).))(((((((.(-----((((..((........))..)))))))))))).------....-.))))))).))). ( -38.40)
>DroSec_CAF1 4278 110 + 1
UGACACAGGUGCUUGAAAUGGUGGGCUUAAAGGCUCAUUUAAGCCCUCUCCGUGUGUGUGCGCUCUUUGGGCCAACUA----------UUCGCGAAGCCACCUAGCGGGCACUUGAUGUA
..(((((((((((((...(((((((((((((......)))))))))....((((....((.(((.....)))))....----------..))))..)))).....)))))))))).))). ( -42.20)
>DroSim_CAF1 5888 110 + 1
UGACACAGGUGCUUGAAAUGGUGGGCUUAAAGGCUCAUUUAAGCCCUCUCCGUGUGUGUGCGCUCAUUGGGCCAACUA----------UUCGCGAAGCCACCUAGCGGGCACUUGAUGUA
..(((((((((((((...(((((((((((((......)))))))))....((((....((.(((.....)))))....----------..))))..)))).....)))))))))).))). ( -42.20)
>DroEre_CAF1 6072 101 + 1
UGACACAGGUGCUGGAAAUGGUGGGCUUAAAGGCUCAUUUAAGCCCUCAGUGUAUGUGUGCG---------CCAACUA----------UUCGUGCAGCCACCUAGCGGGCGCUUGAUGUA
..(((((((((((.(...(((((((((((((......)))))))))....((((((.((...---------...))..----------..)))))))))).....).)))))))).))). ( -37.60)
>DroYak_CAF1 4244 110 + 1
UGACACAGGUGCUUGAAAUGGAGGGCUUAAAGGCUCAUUUAAGCCCUCUUUGCAUGUGUGCGCUCAUUGGGCCAACUA----------UUCGUGCAGCCACCUAGCGGCCACUUGAUGUA
.(.((((.((((.......((((((((((((......))))))))))))..)))).)))))(((((...((((..(((----------...(((....))).))).))))...))).)). ( -41.20)
>consensus
UGACACAGGUGCUUGAAAUGGUGGGCUUAAAGGCUCAUUUAAGCCCUCUCUGUGUGUGUGCGCUCAUUGGGCCAACUA__________UUCGCGAAGCCACCUAGCGGGCACUUGAUGUA
..((((((((((......(((((((((((((......)))))))))....(((......)))........))))...............((((...........))))))))))).))). (-27.80 = -28.04 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:24 2006