Locus 390

Sequence ID dm3.chr2L
Location 2,693,989 – 2,694,093
Length 104
Max. P 0.981526
window532 window533

overview

Window 2

Location 2,693,989 – 2,694,093
Length 104
Sequences 7
Columns 111
Reading direction forward
Mean pairwise identity 75.33
Shannon entropy 0.46273
G+C content 0.44176
Mean single sequence MFE -25.30
Consensus MFE -14.89
Energy contribution -14.93
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.53
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.89
SVM RNA-class probability 0.844725
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2693989 104 + 23011544
-GUGUGUGUGUGUGGUAA-GUUAAUAUUUGCUGCAUAAAUUCCAGUGCGUCGGAAUUUACUGCGCUUCGUU-----UUGCUCUUCUCGUUUUUGCCGCUCCUGGGAUGGUC
-.......((((..((((-((....))))))..)))).(((((((.(((.(((((......(.((......-----..)).).......))))).)))..))))))).... ( -27.92, z-score =  -1.99, R)
>droSim1.chr2L 2653955 110 + 22036055
GGUGUGUGUGUGUGGUAA-GUUAAUAUUUGCUGCAUAAAUUCCAGUGCGUCGGAAUUUACUGCGCUUCGUUUCGUUUCGCUCCUCUCGUUUUUGCCGCUCCUGGGAGGGCC
((.(((..((((..((((-((....))))))..)))).........(((.(((......))))))............))).))..........(((.(((....)))))). ( -30.40, z-score =  -0.95, R)
>droSec1.super_5 860818 109 + 5866729
GGUGUAUGUGUGUGGUAA-GUUAAUAUUUGCUGCAUAAAUUCCACUGCGUCGGAAUUUACUGCGCUUCGUUUCGUUUCGCUCCUCUCGUUUUUGCUGCUCCUGG-AGGGCC
((((((.(((((..((((-((....))))))..)))(((((((........)))))))))))))))............((.(((((.((.......))....))-))))). ( -28.40, z-score =  -1.10, R)
>droAna3.scaffold_12984 140900 100 + 754457
--UGUAUGUGUGCGGUAA-GUUAAUAUUUGCUGCAUAAAUUCCAGUGCGUUGGAAUUUACUGCGCUUCGUUUCGC----UCUUUUCGGCUUUCCUCGUCCUUUGGCU----
--.....(((((((((((-((....))))))))).((((((((((....))))))))))..))))........((----(.....(((......)))......))).---- ( -24.80, z-score =  -1.48, R)
>dp4.chr4_group4 2022691 96 + 6586962
UAUCUGUGUGUGCGGUAA-GUUAAUAUUUGCUGCAUAAAUUCCAGUGCGUUGGAAUUUACUGCGCUCCGUUUCGU----UCCUUUUGGCUUUUGUCGUCGU----------
.....(((((((((((((-((....)))))))))))(((((((((....)))))))))...))))..........----.......(((....))).....---------- ( -25.30, z-score =  -2.43, R)
>droPer1.super_10 1027919 96 + 3432795
UAUCUGUGUGUGCGGUAA-GUUAAUAUUUGCUGCAUAAAUUCCAGUGCGUUGGAAUUUACUGCGCUCCGUUUCGU----UCCUUUUGGCUUUUGUCGUCGU----------
.....(((((((((((((-((....)))))))))))(((((((((....)))))))))...))))..........----.......(((....))).....---------- ( -25.30, z-score =  -2.43, R)
>droWil1.scaffold_180772 1415528 89 + 8906247
UGUUUGUGUGUGUGGAAAAGUUAAUAUUUGCUGCAUAAAUUCCAGGACUUUGGAAUUUUCUGCGCUUGUUCUCGU-----CGUUUUUGUUUUUG-----------------
...........(..((((.(..((((...((.(((.(((((((((....)))))))))..))))).))))..)..-----..))))..).....----------------- ( -15.00, z-score =  -0.35, R)
>consensus
UGUGUGUGUGUGUGGUAA_GUUAAUAUUUGCUGCAUAAAUUCCAGUGCGUUGGAAUUUACUGCGCUUCGUUUCGU____CCCUUUUCGUUUUUGCCGCCCCU_G_______
.......(((((((((((.........))))))).((((((((........))))))))..)))).............................................. (-14.89 = -14.93 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 2,693,989 – 2,694,093
Length 104
Sequences 7
Columns 111
Reading direction reverse
Mean pairwise identity 75.33
Shannon entropy 0.46273
G+C content 0.44176
Mean single sequence MFE -18.51
Consensus MFE -14.13
Energy contribution -14.03
Covariance contribution -0.10
Combinations/Pair 1.07
Mean z-score -1.73
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.08
SVM RNA-class probability 0.981526
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2693989 104 - 23011544
GACCAUCCCAGGAGCGGCAAAAACGAGAAGAGCAA-----AACGAAGCGCAGUAAAUUCCGACGCACUGGAAUUUAUGCAGCAAAUAUUAAC-UUACCACACACACACAC-
(.((.((....))..)))......(..(((.((..-----......))(((.(((((((((......))))))))))))............)-))..)............- ( -17.40, z-score =  -1.45, R)
>droSim1.chr2L 2653955 110 - 22036055
GGCCCUCCCAGGAGCGGCAAAAACGAGAGGAGCGAAACGAAACGAAGCGCAGUAAAUUCCGACGCACUGGAAUUUAUGCAGCAAAUAUUAAC-UUACCACACACACACACC
.((((((....))).)))..........((..((........))..(((((.(((((((((......)))))))))))).))..........-...))............. ( -25.10, z-score =  -2.14, R)
>droSec1.super_5 860818 109 - 5866729
GGCCCU-CCAGGAGCAGCAAAAACGAGAGGAGCGAAACGAAACGAAGCGCAGUAAAUUCCGACGCAGUGGAAUUUAUGCAGCAAAUAUUAAC-UUACCACACACAUACACC
.(((((-(..(............)..)))).)).............(((((.(((((((((......)))))))))))).))..........-.................. ( -21.70, z-score =  -1.38, R)
>droAna3.scaffold_12984 140900 100 - 754457
----AGCCAAAGGACGAGGAAAGCCGAAAAGA----GCGAAACGAAGCGCAGUAAAUUCCAACGCACUGGAAUUUAUGCAGCAAAUAUUAAC-UUACCGCACACAUACA--
----.......((..(((....(((.....).----))........(((((.(((((((((......)))))))))))).)).........)-)).))...........-- ( -18.90, z-score =  -1.26, R)
>dp4.chr4_group4 2022691 96 - 6586962
----------ACGACGACAAAAGCCAAAAGGA----ACGAAACGGAGCGCAGUAAAUUCCAACGCACUGGAAUUUAUGCAGCAAAUAUUAAC-UUACCGCACACACAGAUA
----------.((.((.......((....)).----......))..(((((.(((((((((......)))))))))))).))..........-....))............ ( -16.44, z-score =  -1.50, R)
>droPer1.super_10 1027919 96 - 3432795
----------ACGACGACAAAAGCCAAAAGGA----ACGAAACGGAGCGCAGUAAAUUCCAACGCACUGGAAUUUAUGCAGCAAAUAUUAAC-UUACCGCACACACAGAUA
----------.((.((.......((....)).----......))..(((((.(((((((((......)))))))))))).))..........-....))............ ( -16.44, z-score =  -1.50, R)
>droWil1.scaffold_180772 1415528 89 - 8906247
-----------------CAAAAACAAAAACG-----ACGAGAACAAGCGCAGAAAAUUCCAAAGUCCUGGAAUUUAUGCAGCAAAUAUUAACUUUUCCACACACACAAACA
-----------------..............-----..........(((((..((((((((......)))))))).))).))............................. ( -13.60, z-score =  -2.92, R)
>consensus
_______C_AAGAACGACAAAAACCAAAAGGA____ACGAAACGAAGCGCAGUAAAUUCCAACGCACUGGAAUUUAUGCAGCAAAUAUUAAC_UUACCACACACACACACA
..............................................(((((.(((((((((......)))))))))))).))............................. (-14.13 = -14.03 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:12:03 2011