Locus 11721

Sequence ID dm3.chr3R
Location 23,324,101 – 23,324,228
Length 127
Max. P 0.932018
window16101 window16102 window16103

overview

Window 1

Location 23,324,101 – 23,324,193
Length 92
Sequences 7
Columns 106
Reading direction reverse
Mean pairwise identity 66.70
Shannon entropy 0.64153
G+C content 0.50194
Mean single sequence MFE -29.06
Consensus MFE -12.51
Energy contribution -12.01
Covariance contribution -0.50
Combinations/Pair 1.67
Mean z-score -1.06
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.619548
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23324101 92 - 27905053
--AGAAGCUGGCUCAGUUUUCGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUAUUUUUCGGUCAGAGGUUGG-GCCCGGAUACG
--.....((((..(((((((((((((((-----------(((.(....))))))))))))))).))))(((((....((((.....)))).)))-))))))..... ( -33.70, z-score =  -1.58, R)
>droSim1.chr3R 23061616 92 - 27517382
--AGAAGCUGGCUCAGUUUUAGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUAUUUUUCGGUCAGAGGUUGG-GCACGGAUACG
--.(((((((...))))))).(((((((-----------(((.(....)))))))))))...(((((((((((....((((.....)))).)))-)).))).))). ( -30.60, z-score =  -1.31, R)
>droSec1.super_13 2067407 92 - 2104621
--AGAAGCUGGCUCAGUUUUAGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUAUUUUUCGGUCAGAGGUUGG-GCACGGAUACG
--.(((((((...))))))).(((((((-----------(((.(....)))))))))))...(((((((((((....((((.....)))).)))-)).))).))). ( -30.60, z-score =  -1.31, R)
>droYak2.chr3R 5673010 94 + 28832112
-UAGAAACUGGCUCAGUUGUAGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUAUUUUUCGGUCAGAGGUUGGUUCCCGGAUACG
-..((((.(((..((((....(((((((-----------(((.(....))))))))))).....))))..)))....)))).(((.(.((......))).)))... ( -26.50, z-score =   0.03, R)
>droEre2.scaffold_4820 5763231 92 + 10470090
--AGCAGCUGGCUCAGUUUUAGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUAUUUUUUGGUCAGAAGUUGG-GCCAGGCUACG
--(((..((((((((..((..(((((((-----------(((.(....)))))))))))......((((.(((.......)))))))))..)))-))))))))... ( -35.50, z-score =  -2.24, R)
>droAna3.scaffold_13340 4344468 97 + 23697760
--GGAAGCCGGCUUCUCUCUCCCUCUGUCAUUUUGACCAAUAUGCAUGUGGUGUUGGCC-AAGUGCUGGUCCAUAAUUUUUGGUCCGAGGCCCGGGCCAC------
--((...((((((((...........(((.....)))......((((.((((....)))-).)))).((.(((.......))).)))))).)))).))..------ ( -30.50, z-score =  -0.39, R)
>droWil1.scaffold_181089 3566432 92 - 12369635
AAAUUCGUUGGCCAAGUUGAAAGUCUAUUACACCUGUUACUUUCCGACUAAUGUCAGCUGGAUAAUUUCAUUAUGCAUUUGACUUGUAAAAG--------------
..((((((((((..((((((((((.....((....)).))))).)))))...)))))).))))..........((((.......))))....-------------- ( -16.00, z-score =  -0.61, R)
>consensus
__AGAAGCUGGCUCAGUUUUAGGCCGAU___________AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUAUUUUUCGGUCAGAGGUUGG_GCCCGGAUACG
.....((((((((........))))............................((((((((((..............)))))))))).)))).............. (-12.51 = -12.01 +  -0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 23,324,131 – 23,324,228
Length 97
Sequences 7
Columns 114
Reading direction forward
Mean pairwise identity 70.51
Shannon entropy 0.56266
G+C content 0.48373
Mean single sequence MFE -25.91
Consensus MFE -14.95
Energy contribution -15.61
Covariance contribution 0.67
Combinations/Pair 1.53
Mean z-score -0.93
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.63
SVM RNA-class probability 0.766727
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23324131 97 + 27905053
UAUGGACCAGCACUUCGGCCAACACCGCAUGCAAAU-----------AUCGGCCGAAAACUGAGCCAGCUUCU--GGAGGAGAAUUAAAAACUGAGAU----GUUGGCCGAGUC
.............(((((((((((.(.((.......-----------...(((((.....)).)))..((((.--...))))..........)).).)----)))))))))).. ( -26.40, z-score =  -1.02, R)
>droSim1.chr3R 23061646 97 + 27517382
UAUGGACCAGCACUUCGGCCAACACCGCAUGCAAAU-----------AUCGGCCUAAAACUGAGCCAGCUUCU--GGAGGCGAAUUAAAAACUGAGAU----GUUGGCCGAGUC
.............(((((((((((.(.((.......-----------...((((.......).))).((((..--..))))...........)).).)----)))))))))).. ( -27.50, z-score =  -1.20, R)
>droSec1.super_13 2067437 97 + 2104621
UAUGGACCAGCACUUCGGCCAACACCGCAUGCAAAU-----------AUCGGCCUAAAACUGAGCCAGCUUCU--GGAGGAGAAUUAAAAACUGAGAU----GUUGGCCGAUUC
..............((((((((((.(.((.......-----------...((((.......).)))..((((.--...))))..........)).).)----)))))))))... ( -25.70, z-score =  -1.25, R)
>droYak2.chr3R 5673041 99 - 28832112
UAUGGACCAGCACUUCGGCCAACACCGCAUGCAAAU-----------AUCGGCCUACAACUGAGCCAGUUUCUACGGAGGAGAAUUAAAAACUGAGAU----GUUGGCCAAGUC
...........((((.((((((((.(.((.......-----------...((((.......).)))..((((....))))............)).).)----))))))))))). ( -24.40, z-score =  -0.73, R)
>droEre2.scaffold_4820 5763261 97 - 10470090
UAUGGACCAGCACUUCGGCCAACACCGCAUGCAAAU-----------AUCGGCCUAAAACUGAGCCAGCUGCU--GGAGGAGAAUUAAAAACUGAGAU----GUUGGCCGAGUC
.............((((((((((((((((.((....-----------.((((.......))))....))))).--))((............))....)----)))))))))).. ( -26.30, z-score =  -0.87, R)
>droAna3.scaffold_13340 4344493 107 - 23697760
UAUGGACCAGCACUU-GGCCAACACCACAUGCAUAUUGGUCAAAAUGACAGAGGGAGAGAGAAGCCGGCUUCC--GAGGAUGAAUUAGAAACUGCGAU----GUUGGUCGAGAC
............(((-((((((((.(.(((.(......(((.....)))...(((((...(....)..)))))--..).))).....(......)).)----)))))))))).. ( -26.60, z-score =  -0.73, R)
>droWil1.scaffold_181089 3566462 101 + 12369635
-------------UCCAGCUGACAUUAGUCGGAAAGUAACAGGUGUAAUAGACUUUCAACUUGGCCAACGAAUUUGGUUAAACUUGAGUAGUUGGGGUUGAGGUUGGUUGUAUU
-------------..((((..((.(((..(.((((((.((....)).....)))))).......(((((..(((..(......)..))).))))))..))).))..)))).... ( -24.50, z-score =  -0.70, R)
>consensus
UAUGGACCAGCACUUCGGCCAACACCGCAUGCAAAU___________AUCGGCCUAAAACUGAGCCAGCUUCU__GGAGGAGAAUUAAAAACUGAGAU____GUUGGCCGAGUC
.............((((((((((...........................(((..........)))..((((....))))......................)))))))))).. (-14.95 = -15.61 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 23,324,131 – 23,324,228
Length 97
Sequences 7
Columns 114
Reading direction reverse
Mean pairwise identity 70.51
Shannon entropy 0.56266
G+C content 0.48373
Mean single sequence MFE -28.19
Consensus MFE -15.27
Energy contribution -15.73
Covariance contribution 0.46
Combinations/Pair 1.50
Mean z-score -1.46
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.932018
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23324131 97 - 27905053
GACUCGGCCAAC----AUCUCAGUUUUUAAUUCUCCUCC--AGAAGCUGGCUCAGUUUUCGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUA
.(((((((((((----(((.((((....(((..((..((--..((((((...))))))..))..)).-----------))).)).)).))))))))))).)))........... ( -31.70, z-score =  -1.99, R)
>droSim1.chr3R 23061646 97 - 27517382
GACUCGGCCAAC----AUCUCAGUUUUUAAUUCGCCUCC--AGAAGCUGGCUCAGUUUUAGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUA
.(((((((((((----(((.((((.....(((.((((..--.(((((((...))))))))))).)))-----------....)).)).))))))))))).)))........... ( -35.10, z-score =  -2.69, R)
>droSec1.super_13 2067437 97 - 2104621
GAAUCGGCCAAC----AUCUCAGUUUUUAAUUCUCCUCC--AGAAGCUGGCUCAGUUUUAGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUA
...(((((((((----(((.((((....(((..((..((--.(((((((...))))))).))..)).-----------))).)).)).)))))))))))).............. ( -31.00, z-score =  -1.88, R)
>droYak2.chr3R 5673041 99 + 28832112
GACUUGGCCAAC----AUCUCAGUUUUUAAUUCUCCUCCGUAGAAACUGGCUCAGUUGUAGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUA
.(((((((((((----(((.(((((((((...........)))))))))((.....((((((.....-----------.)))))).)))))))))))).))))........... ( -30.90, z-score =  -1.67, R)
>droEre2.scaffold_4820 5763261 97 + 10470090
GACUCGGCCAAC----AUCUCAGUUUUUAAUUCUCCUCC--AGCAGCUGGCUCAGUUUUAGGCCGAU-----------AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUA
.(((((((((((----(((..((.........)).....--.((((((((((........)))))..-----------....)).)))))))))))))).)))........... ( -29.10, z-score =  -0.99, R)
>droAna3.scaffold_13340 4344493 107 + 23697760
GUCUCGACCAAC----AUCGCAGUUUCUAAUUCAUCCUC--GGAAGCCGGCUUCUCUCUCCCUCUGUCAUUUUGACCAAUAUGCAUGUGGUGUUGGCC-AAGUGCUGGUCCAUA
.....(((((((----((((((((...............--(((((....)))))..........(((.....)))......)).)))))))))(((.-....))))))).... ( -23.60, z-score =  -0.17, R)
>droWil1.scaffold_181089 3566462 101 - 12369635
AAUACAACCAACCUCAACCCCAACUACUCAAGUUUAACCAAAUUCGUUGGCCAAGUUGAAAGUCUAUUACACCUGUUACUUUCCGACUAAUGUCAGCUGGA-------------
.......(((...........((((.....))))...........((((((..((((((((((.....((....)).))))).)))))...))))))))).------------- ( -15.90, z-score =  -0.80, R)
>consensus
GACUCGGCCAAC____AUCUCAGUUUUUAAUUCUCCUCC__AGAAGCUGGCUCAGUUUUAGGCCGAU___________AUUUGCAUGCGGUGUUGGCCGAAGUGCUGGUCCAUA
...(((((((((.......(((((((((.............)))))))))...........((((......................))))))))))))).............. (-15.27 = -15.73 +   0.46)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:48:17 2011