Locus 15538

Sequence ID	dm3.chrX
Location	19,452,097 – 19,452,164
Length	67
Max. P	0.991093

overview

Window 9

Location	19,452,097 – 19,452,164
Length	67
Sequences	5
Columns	74
Reading direction	forward
Mean pairwise identity	72.64
Shannon entropy	0.46427
G+C content	0.54258
Mean single sequence MFE	-25.26
Consensus MFE	-15.58
Energy contribution	-17.14
Covariance contribution	1.56
Combinations/Pair	1.23
Mean z-score	-2.30
Structure conservation index	0.62
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.46
SVM RNA-class probability	0.991093
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19452097 67 + 22422827
UUCCUUCUAAGUGGGUCGCUUGUA-GUGCGGCCCAUUGUCCAAGGACACGUGUCAUGUGGAAGCUGGA------
.(((..((.((((((((((.....-..)))))))))).((((..(((....)))...))))))..)))------ ( -28.50, z-score =  -3.33, R)
>droSec1.super_8 1734328 73 + 3762037
CUCCUUCUAAGUGGGUCGCUUGUA-GUGCGGCCCAUUGUCCAAGGACACGUGUCAUGUGGAAGCUGGAGAUGAA
((((..((.((((((((((.....-..)))))))))).((((..(((....)))...))))))..))))..... ( -32.00, z-score =  -3.92, R)
>droYak2.chrX 9884359 67 - 21770863
CUCCUUCUAAGUGGGUCGCUUGUA-GUGCGGCCCAUUGUCCAAGGACACGUGUCAUGUGGCAGCUGGA------
.(((..((.((((((((((.....-..))))))))))(.(((..(((....)))...))))))..)))------ ( -26.80, z-score =  -2.19, R)
>droEre2.scaffold_4690 9688422 67 + 18748788
CUCCCUCUAAGUGGGUCGCUUGUA-GUGCGGUCCAUUGUCCAAGGACACGUGCCAUGUGGAAGCCGGA------
.(((..((.(((((..(((.....-..)))..))))).((((.((.(....)))...))))))..)))------ ( -20.90, z-score =  -0.25, R)
>droGri2.scaffold_15081 2229333 63 - 4274704
GGUGCCAUACAUAUAUAGCUAGCACGCACUUCCUAACGCCUACAGA-----GUCGUGUGCCAGCUAAA------
...............(((((.((((((((((..((.....))..))-----)).)))))).)))))..------ ( -18.10, z-score =  -1.80, R)
>consensus
CUCCUUCUAAGUGGGUCGCUUGUA_GUGCGGCCCAUUGUCCAAGGACACGUGUCAUGUGGAAGCUGGA______
.(((..((.((((((((((........)))))))))).((((..(((....)))...))))))..)))...... (-15.58 = -17.14 +   1.56)

alignment

secondary structure

dotplot

Window 0

Location	19,452,097 – 19,452,164
Length	67
Sequences	5
Columns	74
Reading direction	reverse
Mean pairwise identity	72.64
Shannon entropy	0.46427
G+C content	0.54258
Mean single sequence MFE	-18.90
Consensus MFE	-12.10
Energy contribution	-11.90
Covariance contribution	-0.20
Combinations/Pair	1.43
Mean z-score	-1.13
Structure conservation index	0.64
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.46
SVM RNA-class probability	0.702556
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19452097 67 - 22422827
------UCCAGCUUCCACAUGACACGUGUCCUUGGACAAUGGGCCGCAC-UACAAGCGACCCACUUAGAAGGAA
------(((....((((...(((....)))..))))...((((.(((..-.....))).)))).......))). ( -19.10, z-score =  -1.81, R)
>droSec1.super_8 1734328 73 - 3762037
UUCAUCUCCAGCUUCCACAUGACACGUGUCCUUGGACAAUGGGCCGCAC-UACAAGCGACCCACUUAGAAGGAG
.....((((....((((...(((....)))..))))...((((.(((..-.....))).)))).......)))) ( -21.00, z-score =  -2.20, R)
>droYak2.chrX 9884359 67 + 21770863
------UCCAGCUGCCACAUGACACGUGUCCUUGGACAAUGGGCCGCAC-UACAAGCGACCCACUUAGAAGGAG
------(((..((((((...(((....)))..)))....((((.(((..-.....))).))))..)))..))). ( -18.80, z-score =  -1.24, R)
>droEre2.scaffold_4690 9688422 67 - 18748788
------UCCGGCUUCCACAUGGCACGUGUCCUUGGACAAUGGACCGCAC-UACAAGCGACCCACUUAGAGGGAG
------((((...((((...(((....)))..))))...)))).(((..-.....))).(((.......))).. ( -16.40, z-score =   0.20, R)
>droGri2.scaffold_15081 2229333 63 + 4274704
------UUUAGCUGGCACACGAC-----UCUGUAGGCGUUAGGAAGUGCGUGCUAGCUAUAUAUGUAUGGCACC
------..((((((((((.((..-----(((..........)))..)).))))))))))............... ( -19.20, z-score =  -0.58, R)
>consensus
______UCCAGCUUCCACAUGACACGUGUCCUUGGACAAUGGGCCGCAC_UACAAGCGACCCACUUAGAAGGAG
......(((.................((((....)))).((((.(((........))).)))).......))). (-12.10 = -11.90 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:01:23 2011