Locus 13819

Sequence ID dm3.chrX
Location 9,375,357 – 9,375,448
Length 91
Max. P 0.990916
window19012 window19013

overview

Window 2

Location 9,375,357 – 9,375,448
Length 91
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 74.77
Shannon entropy 0.40824
G+C content 0.36726
Mean single sequence MFE -18.15
Consensus MFE -13.06
Energy contribution -13.25
Covariance contribution 0.19
Combinations/Pair 1.17
Mean z-score -1.08
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.641716
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9375357 91 + 22422827
GUUUGAGGAGAGUCUCGGAAUCGUUUCGAUUCGACAAACAAACUUGUCGAGGGGUAAAAUUUUUUUUUUGUUUUUGGCUUUUUCGCCAAUU
....((((((((((((.((((((...))))))(((((......)))))))).......)))))))))......(((((......))))).. ( -20.11, z-score =  -0.22, R)
>droEre2.scaffold_4690 13010004 74 - 18748788
-UUU--UAGGAGUCUC--AAUCGUUUUGAUUCGACAAAC----UUGUCGGUUGGUAUUAUUUGUACUGC-UUUUUGGCUCGUUU-------
-...--...(((((((--((.....)))).((((((...----.))))))..(((((.....)))))..-.....)))))....------- ( -15.70, z-score =  -1.77, R)
>droSec1.super_15 142555 85 + 1954846
GUU---GGAGAGUCUCCGAAUCGUUUCGAUUCGACAAACAAACUUGUCGAGAGGUA---UUAUUUUUUUAUUUUUGGCUUUUUCGCCAUUU
...---((((...))))((((((...))))))(((((......)))))((((((..---....)))))).....((((......))))... ( -19.60, z-score =  -1.44, R)
>droSim1.chrX 7472425 82 + 17042790
GUU---GGAGAGUCUCCGAAUCGUUUCGAUUCGACAAACAAACUUGUCGAGAGGUA---UUAUUUUUUU---UUUAGCUUUUUCGCCAUUU
(((---((((((((((.((((((...))))))(((((......)))))))))....---.......)))---))))))............. ( -17.20, z-score =  -0.90, R)
>consensus
GUU___GGAGAGUCUCCGAAUCGUUUCGAUUCGACAAACAAACUUGUCGAGAGGUA___UUAUUUUUUU_UUUUUGGCUUUUUCGCCAUUU
.......(((((((...((((((...))))))(((((......)))))...........................)))))))......... (-13.06 = -13.25 +   0.19) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,375,357 – 9,375,448
Length 91
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 74.77
Shannon entropy 0.40824
G+C content 0.36726
Mean single sequence MFE -16.98
Consensus MFE -10.45
Energy contribution -12.32
Covariance contribution 1.88
Combinations/Pair 1.06
Mean z-score -2.59
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.45
SVM RNA-class probability 0.990916
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9375357 91 - 22422827
AAUUGGCGAAAAAGCCAAAAACAAAAAAAAAAUUUUACCCCUCGACAAGUUUGUUUGUCGAAUCGAAACGAUUCCGAGACUCUCCUCAAAC
..(((((......)))))......................(((((((((....))))))((((((...)))))).)))............. ( -20.00, z-score =  -3.05, R)
>droEre2.scaffold_4690 13010004 74 + 18748788
-------AAACGAGCCAAAAA-GCAGUACAAAUAAUACCAACCGACAA----GUUUGUCGAAUCAAAACGAUU--GAGACUCCUA--AAA-
-------....(((.(.....-....................(((((.----...)))))((((.....))))--..).)))...--...- (  -8.60, z-score =  -1.29, R)
>droSec1.super_15 142555 85 - 1954846
AAAUGGCGAAAAAGCCAAAAAUAAAAAAAUAA---UACCUCUCGACAAGUUUGUUUGUCGAAUCGAAACGAUUCGGAGACUCUCC---AAC
...((((......))))...............---....((((((((((....))))))((((((...)))))).))))......---... ( -20.80, z-score =  -3.45, R)
>droSim1.chrX 7472425 82 - 17042790
AAAUGGCGAAAAAGCUAAA---AAAAAAAUAA---UACCUCUCGACAAGUUUGUUUGUCGAAUCGAAACGAUUCGGAGACUCUCC---AAC
...((((......))))..---..........---....((((((((((....))))))((((((...)))))).))))......---... ( -18.50, z-score =  -2.56, R)
>consensus
AAAUGGCGAAAAAGCCAAAAA_AAAAAAAAAA___UACCUCUCGACAAGUUUGUUUGUCGAAUCGAAACGAUUCGGAGACUCUCC___AAC
...((((......)))).......................(((((((((....))))))(((((.....))))).)))............. (-10.45 = -12.32 +   1.88) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:28:24 2011