Locus 3568

Sequence ID	X_DroMel_CAF1
Location	9,583,956 – 9,584,046
Length	90
Max. P	0.992322

overview

Window 8

Location	9,583,956 – 9,584,046
Length	90
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	85.24
Mean single sequence MFE	-33.46
Consensus MFE	-26.06
Energy contribution	-26.50
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-2.87
Structure conservation index	0.78
SVM decision value	2.32
SVM RNA-class probability	0.992322
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9583956 90 + 22224390
U-----------UCGAGGCACAUAUUUUUGUCUGAGUGUAGCGCAGCAACAUUAUGCUUAAGCGCUGCAAGCGCUUCGUGCUUAAAAGCGCGCGACACACA
.-----------((.(((((........)))))))((((..(((((((......))))...(((((..((((((...))))))...))))))))..)))). ( -32.50)
>DroSec_CAF1 42813 88 + 1
U-----------UUGUGGCACG--UUUUUUUCUGAGUGUAGCGCAGCAACAUUAUGCUUAAGCGCUGCAAGCGGUUCGUGCUUAAAAGCGCGCGACACACA
.-----------.(((.((...--.......(((..((((((((((((......))))...))))))))..)))...(((((....))))))).))).... ( -32.80)
>DroSim_CAF1 29317 88 + 1
U-----------UUGUGGCACG--UUUUUGUCUGAGUGUAGCGCAGCAACAUUAUGCUUAAGCGCUGCAAGCGGUUCGUGCUUAAAAGCGCGCGACACACA
.-----------.(((.((.((--((((((.(((..((((((((((((......))))...))))))))..)))........)))))))).)).))).... ( -33.50)
>DroEre_CAF1 47646 99 + 1
UCAAAUGCCACAUUGAGGCACGG-CUUUUUUCCGAGUGUAGAGCAGCAACAUUAUGCUUAAGCGCUGCAAGCGGUUCGUGCUUAAAAGCGCGCGACACAC-
.....((((.......))))(((-.......))).((((...((((((......))))...(((((..(((((.....)))))...))))))).))))..- ( -30.10)
>DroYak_CAF1 45081 99 + 1
UCAAAUGCCUCAUUUGAGGGCGU-UUUUUUUCUGAGUGUCGCGCAGCAACAUUAUGCUUAAGCGCUGCAAGCGGUUCGUGCUUAAAAGCGCGCGACACAC-
..(((((((((....)).)))))-)).........(((((((((.(((......)))((((((((.((.....))..))))))))....)))))))))..- ( -38.40)
>consensus
U___________UUGAGGCACG__UUUUUUUCUGAGUGUAGCGCAGCAACAUUAUGCUUAAGCGCUGCAAGCGGUUCGUGCUUAAAAGCGCGCGACACACA
...............................(((..((((((((((((......))))...))))))))..))).((((((........))))))...... (-26.06 = -26.50 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	9,583,956 – 9,584,046
Length	90
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	85.24
Mean single sequence MFE	-29.56
Consensus MFE	-25.20
Energy contribution	-25.60
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.85
SVM decision value	1.50
SVM RNA-class probability	0.959128
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9583956 90 - 22224390
UGUGUGUCGCGCGCUUUUAAGCACGAAGCGCUUGCAGCGCUUAAGCAUAAUGUUGCUGCGCUACACUCAGACAAAAAUAUGUGCCUCGA-----------A
((.((((.(((((((....)))...((((((.....)))))).((((......)))))))).)))).))....................-----------. ( -28.90)
>DroSec_CAF1 42813 88 - 1
UGUGUGUCGCGCGCUUUUAAGCACGAACCGCUUGCAGCGCUUAAGCAUAAUGUUGCUGCGCUACACUCAGAAAAAAA--CGUGCCACAA-----------A
.(((((.((((((((..(((((.......))))).)))))...((((......))))))).)))))...........--..........-----------. ( -26.40)
>DroSim_CAF1 29317 88 - 1
UGUGUGUCGCGCGCUUUUAAGCACGAACCGCUUGCAGCGCUUAAGCAUAAUGUUGCUGCGCUACACUCAGACAAAAA--CGUGCCACAA-----------A
.(((((.((((((((..(((((.......))))).)))))...((((......))))))).)))))...........--..........-----------. ( -26.40)
>DroEre_CAF1 47646 99 - 1
-GUGUGUCGCGCGCUUUUAAGCACGAACCGCUUGCAGCGCUUAAGCAUAAUGUUGCUGCUCUACACUCGGAAAAAAG-CCGUGCCUCAAUGUGGCAUUUGA
-(((((..(((((((..(((((.......))))).)))))...((((......))))))..))))).(((.......-)))((((.......))))..... ( -30.30)
>DroYak_CAF1 45081 99 - 1
-GUGUGUCGCGCGCUUUUAAGCACGAACCGCUUGCAGCGCUUAAGCAUAAUGUUGCUGCGCGACACUCAGAAAAAAA-ACGCCCUCAAAUGAGGCAUUUGA
-(.((((((((((((..(((((.......))))).))).....((((......))))))))))))).).........-..(((.((....)))))...... ( -35.80)
>consensus
UGUGUGUCGCGCGCUUUUAAGCACGAACCGCUUGCAGCGCUUAAGCAUAAUGUUGCUGCGCUACACUCAGAAAAAAA__CGUGCCACAA___________A
.(((((.((((((((..(((((.......))))).)))))...((((......))))))).)))))................................... (-25.20 = -25.60 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:37 2006