Locus 15253

Sequence ID	dm3.chrX
Location	18,133,677 – 18,133,781
Length	104
Max. P	0.995337

overview

Window 2

Location	18,133,677 – 18,133,781
Length	104
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	80.49
Shannon entropy	0.31457
G+C content	0.48328
Mean single sequence MFE	-25.55
Consensus MFE	-19.30
Energy contribution	-19.04
Covariance contribution	-0.25
Combinations/Pair	1.25
Mean z-score	-2.27
Structure conservation index	0.76
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.89
SVM RNA-class probability	0.973372
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18133677 104 + 22422827
AAGCCUACAGCCUUCCACCCAGACAGUCCGACUAUUACUAGCCAAUAGCCAAUUGCCAGAUUGGCCAAGCCGCUCAAUAGGUUAAUUAAACGAUCACGGACUGC
.......................(((((((.(((((...(((.....(((((((....)))))))......))).)))))(((.....))).....))))))). ( -24.90, z-score =  -2.24, R)
>droYak2.chrX 16763413 85 + 21770863
-------------------CAGACAGUGCGACUAUGACUGGCAAAUGGCCGAUUGGCAAAUUGGCCAAGCCGCUUAAUAGGUUAGUUAAACGAUCUCGAACUGC
-------------------....((((.(((((((...((((...(((((((((....))))))))).))))....))))(((.....)))....))).)))). ( -26.80, z-score =  -2.39, R)
>droSec1.super_8 446030 101 + 3762037
AAG---GCAGCCUUCCGGCCAGACAGUCCGACUAUGACUAGCCAAUAGCCAAUUGACAGAUUGACCAAACCGAUCAAUAGGUUAAUUAAACGAUUACGGACUGC
..(---((.........)))...(((((((.((((.........))))..(((((((..(((((.(.....).)))))..))))))).........))))))). ( -25.60, z-score =  -2.76, R)
>droSim1.chrX 13998723 101 + 17042790
AAG---GCAGCCUUCCGGCCAGACAGUCCGACUAUGACUAGCCAAUAGCCGAUUGACAGAUUGACCAAACCGCUCAAUAGGUUAAUGAAACGAUUACGGACUGC
..(---((.........)))...(((((((....((.(((.....))).))((((((..(((((.(.....).)))))..))))))..........))))))). ( -24.90, z-score =  -1.69, R)
>consensus
AAG___GCAGCCUUCCGGCCAGACAGUCCGACUAUGACUAGCCAAUAGCCAAUUGACAGAUUGACCAAACCGCUCAAUAGGUUAAUUAAACGAUCACGGACUGC
.......................(((((((.((((.........))))..(((((...((((((((.............))))))))...))))).))))))). (-19.30 = -19.04 +  -0.25)

alignment

secondary structure

dotplot

Window 3

Location	18,133,677 – 18,133,781
Length	104
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	80.49
Shannon entropy	0.31457
G+C content	0.48328
Mean single sequence MFE	-33.15
Consensus MFE	-27.74
Energy contribution	-29.30
Covariance contribution	1.56
Combinations/Pair	1.18
Mean z-score	-2.72
Structure conservation index	0.84
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.79
SVM RNA-class probability	0.995337
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18133677 104 - 22422827
GCAGUCCGUGAUCGUUUAAUUAACCUAUUGAGCGGCUUGGCCAAUCUGGCAAUUGGCUAUUGGCUAGUAAUAGUCGGACUGUCUGGGUGGAAGGCUGUAGGCUU
(((((((....(((((((((......)))))))))..((((((((......))))))))..(((((....)))))))))))).........((((.....)))) ( -35.40, z-score =  -1.57, R)
>droYak2.chrX 16763413 85 - 21770863
GCAGUUCGAGAUCGUUUAACUAACCUAUUAAGCGGCUUGGCCAAUUUGCCAAUCGGCCAUUUGCCAGUCAUAGUCGCACUGUCUG-------------------
(((((.(((....((((((........))))))(((.(((((.(((....))).)))))...)))........))).)))))...------------------- ( -25.00, z-score =  -2.45, R)
>droSec1.super_8 446030 101 - 3762037
GCAGUCCGUAAUCGUUUAAUUAACCUAUUGAUCGGUUUGGUCAAUCUGUCAAUUGGCUAUUGGCUAGUCAUAGUCGGACUGUCUGGCCGGAAGGCUGC---CUU
((((((((.(((((.(((((......))))).)))))((((((((..(((....))).))))))))........))))))))..((((....))))..---... ( -36.00, z-score =  -3.70, R)
>droSim1.chrX 13998723 101 - 17042790
GCAGUCCGUAAUCGUUUCAUUAACCUAUUGAGCGGUUUGGUCAAUCUGUCAAUCGGCUAUUGGCUAGUCAUAGUCGGACUGUCUGGCCGGAAGGCUGC---CUU
((((((((.((((((((.((......)).))))))))((((((((..(((....))).))))))))........))))))))..((((....))))..---... ( -36.20, z-score =  -3.14, R)
>consensus
GCAGUCCGUAAUCGUUUAAUUAACCUAUUGAGCGGCUUGGCCAAUCUGUCAAUCGGCUAUUGGCUAGUCAUAGUCGGACUGUCUGGCCGGAAGGCUGC___CUU
((((((((.(((((((((((......)))))))))))((((((((..(((....))).))))))))........))))))))..((((....))))........ (-27.74 = -29.30 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:55:50 2011