Locus 2264

Sequence ID dm3.chr2L
Location 17,377,236 – 17,377,353
Length 117
Max. P 0.979653
window3118 window3119 window3120

overview

Window 8

Location 17,377,236 – 17,377,326
Length 90
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 72.05
Shannon entropy 0.53610
G+C content 0.47010
Mean single sequence MFE -18.04
Consensus MFE -10.01
Energy contribution -9.98
Covariance contribution -0.02
Combinations/Pair 1.38
Mean z-score -1.91
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979653
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17377236 90 - 23011544
GCAAUUGCUUGAAUCCCCAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUUACAUCAUCAAAUUGC---UCCAUUGCCAU
((((((...(((........-......((.((((((((........)))))))).))...........)))...))))))---........... ( -19.51, z-score =  -3.35, R)
>droSim1.chr2L 17079512 93 - 22036055
GCAAUUGUUUGAAUGCCCAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUUACAUCAUCAAAUUGCUCCUCCAUUGCCAU
((((((...(((.((.....-......((.((((((((........)))))))).)).........)))))...)))))).............. ( -20.35, z-score =  -3.07, R)
>droSec1.super_7 1015297 93 - 3727775
GCAAUUGUUUGAAUGCCCAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCGGCUCCACUUACAUCAUCAAAUUGCUCCUCCAUUGCCAU
((((((...(((.((.....-.....((..((((((((........)))))))).)).........)))))...)))))).............. ( -20.91, z-score =  -2.56, R)
>droYak2.chr2R 17412838 87 + 21139217
GCAAUUGUUUGAAUAUCUAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUAACUUCA--AAUUG----UUCCACGGCUGU
(.(((.(((((((.......-......((.((((((((........)))))))).))..........))))--))).)----)).)........ ( -16.90, z-score =  -1.23, R)
>droEre2.scaffold_4845 15713012 89 + 22589142
GUAAUGGCUUGGAUCUCCAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUUACAUCAUCAAAUG----UUCCACGGCUGU
...((((((((((.......-......((.((((((((........)))))))).))........((((......)))----))))).)))))) ( -22.20, z-score =  -1.73, R)
>droPer1.super_1 4934900 88 - 10282868
-----GGAUUGUGCACUAAUAUACUUCCCAUAGAUGCCAUAUCCGUCUCUCUUGUAGUCCCCUUCUCAUCCACGG-UGUUUUUCUCAUUUCCCU
-----((((((.((((((............))).))))).))))......................(((.....)-))................ (  -8.40, z-score =   0.50, R)
>consensus
GCAAUUGUUUGAAUACCCAU_UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUUACAUCAUCAAAUGGC__UUCCAUUGCCAU
..............................((((((((........))))))))........................................ (-10.01 =  -9.98 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,377,253 – 17,377,353
Length 100
Sequences 7
Columns 132
Reading direction forward
Mean pairwise identity 56.95
Shannon entropy 0.72677
G+C content 0.39488
Mean single sequence MFE -23.45
Consensus MFE -8.23
Energy contribution -9.23
Covariance contribution 1.00
Combinations/Pair 1.56
Mean z-score -1.10
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.07
SVM RNA-class probability 0.531246
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17377253 100 + 23011544
UGAUGAUGUAAGUGGAGCAGGGAACGUCUCGGUUAUGACGCUCCUUGGAGGUA-AUGGGG-----AUUCAAGCAAUUGCAUUUGCAUAAAUUCCUCUAGAAAACUG--------------------------
..........((((((((.(....)(((........))))))))(((((((..-(((.((-----((.(((....))).)))).))).....)))))))...))).-------------------------- ( -27.90, z-score =  -1.47, R)
>droSim1.chr2L 17079532 99 + 22036055
UGAUGAUGUAAGUGGAGCAGGGAACGUCUCGGUUAUGACGCUCCUUGGAGGUA-AUGGGC-----AUUCAAACAAUUGCAUUUGCAUAAAUUCCUUUUAAAAAAU---------------------------
.....(((((((((.((((((((.((((........)))).))))))(((((.-....))-----.)))......)).)))))))))..................--------------------------- ( -24.40, z-score =  -1.20, R)
>droSec1.super_7 1015317 98 + 3727775
UGAUGAUGUAAGUGGAGCCGGGAACGUCUCGGUUAUGACGCUCCUUGGAGGUA-AUGGGC-----AUUCAAACAAUUGCAUUUGCAUAAAUUCCUCU-AAAAAAU---------------------------
..........((((.(((((((.....)))))))....))))..(((((((.(-((..((-----(..(((....)))....)))....))))))))-)).....--------------------------- ( -24.50, z-score =  -0.91, R)
>droYak2.chr2R 17412855 97 - 21139217
---UGAAGUUAGUGGAGCAGGGAACGUCUCGGUUAUGACGCUCCUUGGAGGUA-AUAGAU-----AUUCAAACAAUUGCAUUUACAUAAAUUCCUCUAGAAAACUA--------------------------
---.....((((.((((((((((.((((........)))).))))))...(((-((....-----.........)))))...........)))).)))).......-------------------------- ( -22.02, z-score =  -1.08, R)
>droEre2.scaffold_4845 15713029 99 - 22589142
-GAUGAUGUAAGUGGAGCAGGGAACGUCUCGGUUAUGACGCUCCUUGGAGGUA-AUGGAG-----AUCCAAGCCAUUACAUUUACAUAAAUUCCUCUGAAAAACUG--------------------------
-....(((((((((...((((((.((((........)))).))))))..(((.-.(((..-----..))).)))....)))))))))...................-------------------------- ( -29.50, z-score =  -2.36, R)
>droPer1.super_1 4934925 102 + 10282868
------UGAGAAGGGGACUACAAGAGAGACGGAUAUGGCAUCUAUGGGAAGUAUAUUAGUGCACAAUCCAAAGGGAUAAUAUUCUGUAAAUCCUUAUCUCCGAUUGCA------------------------
------.((((..((((.(((.........((((.((((((..(((.......)))..)))).))))))....(((......))))))..))))..))))........------------------------ ( -22.10, z-score =  -0.06, R)
>dp4.chr4_group3 3457389 85 + 11692001
-----------------------------------------------GAAGUAUAUUAGUGCACAAUCCAAAGGGAUAAUAUUCUGUAAAUCCUUAUCUCCGAUUGCAGAUUUUUUUAUAGAUAAUAUAGCA
-----------------------------------------------....(((((((.......((((....)))).....((((((((.....((((........))))...)))))))))))))))... ( -13.70, z-score =  -0.60, R)
>consensus
_GAUGAUGUAAGUGGAGCAGGGAACGUCUCGGUUAUGACGCUCCUUGGAGGUA_AUGGGU_____AUUCAAACAAUUGCAUUUGCAUAAAUUCCUCUAAAAAACUG__________________________
.............((((((((((.((((........)))).))))))........................((((......)))).....))))...................................... ( -8.23 =  -9.23 +   1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,377,253 – 17,377,353
Length 100
Sequences 7
Columns 132
Reading direction reverse
Mean pairwise identity 56.95
Shannon entropy 0.72677
G+C content 0.39488
Mean single sequence MFE -19.57
Consensus MFE -8.98
Energy contribution -8.51
Covariance contribution -0.46
Combinations/Pair 1.50
Mean z-score -1.26
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.66
SVM RNA-class probability 0.958807
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17377253 100 - 23011544
--------------------------CAGUUUUCUAGAGGAAUUUAUGCAAAUGCAAUUGCUUGAAU-----CCCCAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUUACAUCAUCA
--------------------------(((.......(.((.(((((.((((......)))).)))))-----.)))..-.........((((((((........)))))))))))................. ( -21.70, z-score =  -2.02, R)
>droSim1.chr2L 17079532 99 - 22036055
---------------------------AUUUUUUAAAAGGAAUUUAUGCAAAUGCAAUUGUUUGAAU-----GCCCAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUUACAUCAUCA
---------------------------...........((((((((.((((......)))).)))))-----......-......((.((((((((........)))))))).)).)))............. ( -20.30, z-score =  -2.01, R)
>droSec1.super_7 1015317 98 - 3727775
---------------------------AUUUUUU-AGAGGAAUUUAUGCAAAUGCAAUUGUUUGAAU-----GCCCAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCGGCUCCACUUACAUCAUCA
---------------------------.......-...((((((((.((((......)))).)))))-----(((...-.........((((((((........)))))))).))))))............. ( -20.72, z-score =  -1.33, R)
>droYak2.chr2R 17412855 97 + 21139217
--------------------------UAGUUUUCUAGAGGAAUUUAUGUAAAUGCAAUUGUUUGAAU-----AUCUAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUAACUUCA---
--------------------------((((......(((((((..((((....((....))....))-----))..))-).))))((.((((((((........)))))))).))....))))......--- ( -21.60, z-score =  -2.15, R)
>droEre2.scaffold_4845 15713029 99 + 22589142
--------------------------CAGUUUUUCAGAGGAAUUUAUGUAAAUGUAAUGGCUUGGAU-----CUCCAU-UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUUACAUCAUC-
--------------------------............(((............(((((((.......-----..))))-)))...((.((((((((........)))))))).)).)))............- ( -22.60, z-score =  -1.15, R)
>droPer1.super_1 4934925 102 - 10282868
------------------------UGCAAUCGGAGAUAAGGAUUUACAGAAUAUUAUCCCUUUGGAUUGUGCACUAAUAUACUUCCCAUAGAUGCCAUAUCCGUCUCUCUUGUAGUCCCCUUCUCA------
------------------------(((((..((((((..((((............))))....((((((.((((((............))).))))).)))))))))).)))))............------ ( -19.70, z-score =  -0.59, R)
>dp4.chr4_group3 3457389 85 - 11692001
UGCUAUAUUAUCUAUAAAAAAAUCUGCAAUCGGAGAUAAGGAUUUACAGAAUAUUAUCCCUUUGGAUUGUGCACUAAUAUACUUC-----------------------------------------------
(((((((.....)))).........((((((((.(((((..((((...)))).)))))))....)))))))))............----------------------------------------------- ( -10.40, z-score =   0.41, R)
>consensus
__________________________CAGUUUUUGAGAGGAAUUUAUGCAAAUGCAAUUGUUUGAAU_____ACCCAU_UACCUCCAAGGAGCGUCAUAACCGAGACGUUCCCUGCUCCACUUACAUCAUC_
......................................((((((((.((..........)).))))).....................((((((((........))))))))....)))............. ( -8.98 =  -8.51 +  -0.46)

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 21:47:57 2011