Locus 6885

Sequence ID dm3.chr3L
Location 10,486,897 – 10,487,024
Length 127
Max. P 0.898808
window9478 window9479

overview

Window 8

Location 10,486,897 – 10,486,995
Length 98
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 75.03
Shannon entropy 0.47911
G+C content 0.36544
Mean single sequence MFE -17.62
Consensus MFE -10.09
Energy contribution -10.48
Covariance contribution 0.39
Combinations/Pair 1.14
Mean z-score -1.65
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.14
SVM RNA-class probability 0.898808
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10486897 98 - 24543557
AACUGCUGUCCACUGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAA-AAAUGCGAGACGCACAUAAAAACGAAAUAAAUAUACAUAUACAAG----
...(((.(((....(((((.((((.......)))).)))))..((((......-....))))))))))...............................---- ( -17.70, z-score =  -1.72, R)
>droSim1.chr3L 9884014 96 - 22553184
AACUGCUGUCCACUGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAA-AAAUGCGAGACGCACAUAAAAAUGAAAUAAAUAUACAUACAAG------
...(((.(((....(((((.((((.......)))).)))))..((((......-....)))))))))).............................------ ( -17.70, z-score =  -1.79, R)
>droSec1.super_0 2697449 96 - 21120651
AACUGCUGUCCACUGGAUAAUGGCGAAAAUGGUUAAUAUCCGUUCGCUUGGAA-AAAUGCGAGACGCACAUAAAAAUGAAAUAAAUAUACAUACAAG------
...(((.(((....(((((.((((.......)))).)))))..((((......-....)))))))))).............................------ ( -17.20, z-score =  -1.02, R)
>droYak2.chr3L 10478635 97 - 24197627
AACUGCUGUCCACAGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAA-AAAAGCGAGCCAUACAUAAAAAUGUAAUAUAUAUACAUACAACC-----
..............(((((.((((.......)))).)))))((((((((....-..))))))))..(((((....)))))..................----- ( -22.10, z-score =  -3.03, R)
>droEre2.scaffold_4784 10479887 99 - 25762168
AACUGCUGUCCACUGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAAGAAAGGCGAGC----CAUAAAAAUGAAAUAAAUAUACUCGUACAUACAAU
......(((.(...(((((.((((.......)))).)))))((((((((.......))))))))----........................).)))...... ( -19.70, z-score =  -1.52, R)
>dp4.chrXR_group6 8893295 77 - 13314419
AGGAGCAGCAGCAAGGAUAAUGAUGAAAAUGGUUAAUAUCCGAACG-----AAAAGAGAGGAAACCCA-AGAAACAUUUCGUG--------------------
.(((((....)).....((((.((....)).))))...)))..(((-----(((.....((....)).-.......)))))).-------------------- ( -11.32, z-score =  -0.82, R)
>consensus
AACUGCUGUCCACUGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAA_AAAUGCGAGACGCACAUAAAAAUGAAAUAAAUAUACAUACAAA______
..............(((((.((((.......)))).))))).(((((...........)))))........................................ (-10.09 = -10.48 +   0.39)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,486,930 – 10,487,024
Length 94
Sequences 8
Columns 111
Reading direction reverse
Mean pairwise identity 63.48
Shannon entropy 0.66150
G+C content 0.45100
Mean single sequence MFE -24.36
Consensus MFE -6.96
Energy contribution -6.53
Covariance contribution -0.44
Combinations/Pair 1.44
Mean z-score -1.73
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.553634
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10486930 94 - 24543557
------------AAAUGUCCAACGGUCACGUGUGAAGCAGUA-ACUG---CUGUCCACUGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAA-AAAUGCGAGACG
------------.....(((((((..(..(((.(((((((..-.)))---)).))))).(((((.((((.......)))).))))))..)).))))).-............ ( -25.00, z-score =  -1.57, R)
>droSim1.chr3L 9884045 94 - 22553184
------------AAAUGUCCAACGGUCACGUGUGAAGCAGUA-ACUG---CUGUCCACUGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAA-AAAUGCGAGACG
------------.....(((((((..(..(((.(((((((..-.)))---)).))))).(((((.((((.......)))).))))))..)).))))).-............ ( -25.00, z-score =  -1.57, R)
>droSec1.super_0 2697480 94 - 21120651
------------AAAUGUACAAAGGUCACGUGUGAAGCAGUA-ACUG---CUGUCCACUGGAUAAUGGCGAAAAUGGUUAAUAUCCGUUCGCUUGGAA-AAAUGCGAGACG
------------............(((..(((.(((((((..-.)))---)).))))).(((((.((((.......)))).)))))..((((......-....))))))). ( -24.00, z-score =  -1.31, R)
>droYak2.chr3L 10478667 94 - 24197627
------------AAAUGUCCAACGGACACGUGUGAAGCAGUA-ACUG---CUGUCCACAGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAA-AAAAGCGAGCCA
------------...(((((...))))).(((.(((((((..-.)))---)).))))).(((((.((((.......)))).)))))((((((((....-..)))))))).. ( -33.80, z-score =  -4.47, R)
>droEre2.scaffold_4784 10479920 95 - 25762168
------------AAAUGUCCAACGGUCACGUGUUAAGCAGUA-ACUG---CUGUCCACUGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAAGAAAGGCGAGCCA
------------...((.((...)).)).(((...(((((..-.)))---))...))).(((((.((((.......)))).)))))((((((((.......)))))))).. ( -27.80, z-score =  -1.90, R)
>dp4.chrXR_group6 8893317 87 - 13314419
AAAUGGCAUCAGGCACGUGUAAGGGCAACAGCAGG-----------AGCAGCAGCAA--GGAUAAUGAUGAAAAUGGUUAAUAUCCGAACGAAAAGAGAG-----------
.....((.....((.(.(((...(....).))).)-----------.))....))..--(((((.((((.......)))).)))))..............----------- ( -15.30, z-score =  -0.87, R)
>droPer1.super_35 119163 98 + 973955
AAAUGGCAUCAGGCACGUGUAAGGGCAACAGCAGGAGCUGUAUAGCAGCAGCAGCAA--GGAUAAUGAUGAAAAUGGUUAAUAUCCGAACGAAAAGAGAG-----------
.....((.((..((...(((....)))...))..))(((((......))))).))..--(((((.((((.......)))).)))))..............----------- ( -21.00, z-score =  -1.33, R)
>droWil1.scaffold_181017 9987 81 + 939937
------------GUGUGUGCCAGGGCCAGGCACGUAGU-GUA-AGUGGCACUGGCCACUGGAUAAUGAUGAAAACGGUUAAUACUUAUAUGAACG----------------
------------..((((.((((((((((((((.....-...-.)).)).)))))).)))).((((..(....)..))))))))...........---------------- ( -23.00, z-score =  -0.79, R)
>consensus
____________AAAUGUCCAACGGUCACGUGUGAAGCAGUA_ACUG___CUGUCCACUGGAUAAUGACGAAAAUGGUUAAUAUCCGUUCGCUUGGAA_AAA_GCGAG_C_
...........................................................(((((.((((.......)))).)))))......................... ( -6.96 =  -6.53 +  -0.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:16:23 2011