Locus 4667

Sequence ID dm3.chr2R
Location 14,947,485 – 14,947,608
Length 123
Max. P 0.808831
window6406 window6407 window6408 window6409

overview

Window 6

Location 14,947,485 – 14,947,585
Length 100
Sequences 7
Columns 119
Reading direction forward
Mean pairwise identity 59.98
Shannon entropy 0.73623
G+C content 0.52586
Mean single sequence MFE -26.81
Consensus MFE -11.28
Energy contribution -11.94
Covariance contribution 0.66
Combinations/Pair 1.50
Mean z-score -0.99
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.76
SVM RNA-class probability 0.808831
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14947485 100 + 21146708
------GCUCCACA-ACCACCACCGCAUUAUCAUCAUCACUUGCUGCUGUGGCAUCCACAUCCUCGCCUCCGGAUGCCGGAAAAUUUCAGCUAGUGGAGGAUCUGCU------------
------.((((((.-....((((.(((.((...........)).))).))))..(((.(((((........)))))..)))............))))))........------------ ( -27.60, z-score =  -1.28, R)
>droSim1.chr2R 13647028 100 + 19596830
------GCUCCACA-ACCACCACCGCAUUAUCAUCAUCACUUGCUGCUGUGGCAUCCACAUCCUCGCCUCCGGAUGCCGGAAAAUUCCAGCUAGUGGAGGAUCUGCU------------
------.((((((.-.........(((..............))).(((..(((((((..............)))))))(((....))))))..))))))........------------ ( -29.08, z-score =  -1.71, R)
>droSec1.super_1 12453988 97 + 14215200
------GCUACACA-ACCACCACCGCAUUAUCAUC---ACUUGCUGCUGUGGCAUCCACAUCCUCGCCUCUGGAUGCCGGAAAAUUCCAGCUAGUGGAGGAUCUGCU------------
------........-.((.((((.(((........---...))).(((..((((((((............))))))))(((....))))))..)))).)).......------------ ( -27.90, z-score =  -1.47, R)
>droYak2.chr2R 6903172 100 - 21139217
------GCUCCACA-ACCACCACCGCAUUAUCAUCCUCACUUGCAGCUGUGGCAUCCACAUCCUCGCCUCCGGAUGCCGGAAAAUUCCAGCUGGUCGAGGAUCUAAU------------
------........-.................((((((((...(((((..(((((((..............)))))))(((....)))))))))).)))))).....------------ ( -28.44, z-score =  -2.22, R)
>droEre2.scaffold_4845 9144651 100 + 22589142
------GCUCCACG-ACCACCACCACAUUAUCAUCCUCACUUGCUGCUGUGGCAUCCACAUCCCCGCCGCCGGAUGCCGGAAAAUUCCAGCUGGUGGAGGAUCUAAU------------
------.......(-(((.((((((......((........))..(((..(((((((..............)))))))(((....)))))))))))).)).))....------------ ( -28.74, z-score =  -1.14, R)
>droWil1.scaffold_180697 2593263 117 + 4168966
--GAAGACUGCAAAUGGAACCACCACUGAGAAGGCUGAAUUAAUUCCAUCUGUUACUGCUUCAUCGAUGCCAUUUGCUGGGGCUUUUGGAAAGGUGGAGCUGAUUUUGGAUGAUGGACU
--.......((...(((.....)))((....)))).........((((((.(((...((((((((....(((...((....))...)))...))))))))........))))))))).. ( -26.90, z-score =   0.50, R)
>droGri2.scaffold_15245 18050029 83 + 18325388
GUCAAGACUACGGACAAAACUG---------AAACUGACGUUGCCACAGCCACAAAUGCUGCAGCAGAUGCAGUUGCUGAGA------AAAAGCUGCA---------------------
((((......(((......)))---------....)))).((((..((((.......))))..)))).(((((((.......------...)))))))--------------------- ( -19.00, z-score =   0.40, R)
>consensus
______GCUCCACA_ACCACCACCGCAUUAUCAUCAUCACUUGCUGCUGUGGCAUCCACAUCCUCGCCUCCGGAUGCCGGAAAAUUCCAGCUGGUGGAGGAUCUGCU____________
................((.((((...........................(((((((..............)))))))(((....))).....)))).))................... (-11.28 = -11.94 +   0.66)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,947,485 – 14,947,585
Length 100
Sequences 7
Columns 119
Reading direction reverse
Mean pairwise identity 59.98
Shannon entropy 0.73623
G+C content 0.52586
Mean single sequence MFE -31.19
Consensus MFE -14.66
Energy contribution -16.05
Covariance contribution 1.40
Combinations/Pair 1.48
Mean z-score -0.72
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.802415
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14947485 100 - 21146708
------------AGCAGAUCCUCCACUAGCUGAAAUUUUCCGGCAUCCGGAGGCGAGGAUGUGGAUGCCACAGCAGCAAGUGAUGAUGAUAAUGCGGUGGUGGU-UGUGGAGC------
------------........((((((.((((.......((((.(((((........))))))))).(((((.(((.((........))....))).))))))))-))))))).------ ( -34.30, z-score =  -1.09, R)
>droSim1.chr2R 13647028 100 - 19596830
------------AGCAGAUCCUCCACUAGCUGGAAUUUUCCGGCAUCCGGAGGCGAGGAUGUGGAUGCCACAGCAGCAAGUGAUGAUGAUAAUGCGGUGGUGGU-UGUGGAGC------
------------........((((((.((((.......((((.(((((........))))))))).(((((.(((.((........))....))).))))))))-))))))).------ ( -34.30, z-score =  -0.85, R)
>droSec1.super_1 12453988 97 - 14215200
------------AGCAGAUCCUCCACUAGCUGGAAUUUUCCGGCAUCCAGAGGCGAGGAUGUGGAUGCCACAGCAGCAAGU---GAUGAUAAUGCGGUGGUGGU-UGUGUAGC------
------------.(((.(.((.(((((.((((((....)))((((((((.(........).))))))))..))).(((...---........)))))))).)).-).)))...------ ( -35.80, z-score =  -1.82, R)
>droYak2.chr2R 6903172 100 + 21139217
------------AUUAGAUCCUCGACCAGCUGGAAUUUUCCGGCAUCCGGAGGCGAGGAUGUGGAUGCCACAGCUGCAAGUGAGGAUGAUAAUGCGGUGGUGGU-UGUGGAGC------
------------.(((.(((((((.((.((((((....))))))....))...))))))).)))...(((((((..(......(.((....)).)....)..))-)))))...------ ( -37.00, z-score =  -1.93, R)
>droEre2.scaffold_4845 9144651 100 - 22589142
------------AUUAGAUCCUCCACCAGCUGGAAUUUUCCGGCAUCCGGCGGCGGGGAUGUGGAUGCCACAGCAGCAAGUGAGGAUGAUAAUGUGGUGGUGGU-CGUGGAGC------
------------....((.((.((((((((((((....))))))((((.((.((...(.(((((...))))).).))..))..)))).......)))))).)))-).......------ ( -36.70, z-score =  -0.98, R)
>droWil1.scaffold_180697 2593263 117 - 4168966
AGUCCAUCAUCCAAAAUCAGCUCCACCUUUCCAAAAGCCCCAGCAAAUGGCAUCGAUGAAGCAGUAACAGAUGGAAUUAAUUCAGCCUUCUCAGUGGUGGUUCCAUUUGCAGUCUUC--
......(((((........(((.............))).(((.....)))....)))))........(((((((((((......(((........))))))))))))))........-- ( -20.02, z-score =   0.76, R)
>droGri2.scaffold_15245 18050029 83 - 18325388
---------------------UGCAGCUUUU------UCUCAGCAACUGCAUCUGCUGCAGCAUUUGUGGCUGUGGCAACGUCAGUUU---------CAGUUUUGUCCGUAGUCUUGAC
---------------------(((((.....------.........)))))((.(((((.(((.(((..((((((....)).))))..---------)))...)))..)))))...)). ( -20.24, z-score =   0.84, R)
>consensus
____________AGCAGAUCCUCCACCAGCUGGAAUUUUCCGGCAUCCGGAGGCGAGGAUGUGGAUGCCACAGCAGCAAGUGAAGAUGAUAAUGCGGUGGUGGU_UGUGGAGC______
....................((((((..............(.((((((........)))))).)..(((((.((.(((..............))).)).)))))..))))))....... (-14.66 = -16.05 +   1.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,947,511 – 14,947,608
Length 97
Sequences 7
Columns 120
Reading direction forward
Mean pairwise identity 62.65
Shannon entropy 0.67013
G+C content 0.56121
Mean single sequence MFE -34.26
Consensus MFE -14.27
Energy contribution -14.63
Covariance contribution 0.36
Combinations/Pair 1.72
Mean z-score -1.00
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.622805
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14947511 97 + 21146708
-----UCAUCACUUGCUGCUGUGGCAUCCACAUCCUCGCCUCCGGAUGCCGGAAAAUUUCAGCUAGU---GGAGGAUCUGCUGGGACUGCGCCGUCCCAAGAGGC---------------
-----((..((((.((((.(.((((((((..............)))))))).)......)))).)))---)..)).(((..((((((......))))))..))).--------------- ( -33.04, z-score =  -0.22, R)
>droSim1.chr2R 13647054 97 + 19596830
-----UCAUCACUUGCUGCUGUGGCAUCCACAUCCUCGCCUCCGGAUGCCGGAAAAUUCCAGCUAGU---GGAGGAUCUGCUGGGACUGCGCCGUCCCAAGAGGC---------------
-----..............(((((...))))).((((.((((((...((.(((....))).))...)---)))))......((((((......)))))).)))).--------------- ( -34.70, z-score =  -0.60, R)
>droSec1.super_1 12454011 97 + 14215200
-----UCAUCACUUGCUGCUGUGGCAUCCACAUCCUCGCCUCUGGAUGCCGGAAAAUUCCAGCUAGU---GGAGGAUCUGCUGGGACUGCGCCGUCCCAAGAGGC---------------
-----((..((((.(((.....((((((((............))))))))(((....)))))).)))---)..)).(((..((((((......))))))..))).--------------- ( -35.50, z-score =  -0.87, R)
>droYak2.chr2R 6903198 97 - 21139217
-----UCCUCACUUGCAGCUGUGGCAUCCACAUCCUCGCCUCCGGAUGCCGGAAAAUUCCAGCUGGU---CGAGGAUCUAAUGGGACUGCGCCGUCCCAAGAGGC---------------
-----.((((.(((((((((..(((((((..............)))))))(((....))))))))..---)))).......((((((......)))))).)))).--------------- ( -39.24, z-score =  -2.30, R)
>droEre2.scaffold_4845 9144677 97 + 22589142
-----UCCUCACUUGCUGCUGUGGCAUCCACAUCCCCGCCGCCGGAUGCCGGAAAAUUCCAGCUGGU---GGAGGAUCUAAUGGGACUGCGACGUCCCAAGAGGC---------------
-----((((((((.(((.....(((((((..............)))))))(((....)))))).)))---.)))))(((..((((((......))))))..))).--------------- ( -39.04, z-score =  -1.84, R)
>droWil1.scaffold_180697 2593303 115 + 4168966
-----AUUCCAUCUGUUACUGCUUCAUCGAUGCCAUUUGCUGGGGCUUUUGGAAAGGUGGAGCUGAUUUUGGAUGAUGGACUACCAAUGGAACUAACCAAAUUGCAUCAUGGCAAACGUC
-----..((((...((((..((((((((....(((...((....))...)))...))))))))))))..)))).((((.........(((......)))..((((......)))).)))) ( -29.80, z-score =  -0.49, R)
>droGri2.scaffold_15245 18050048 89 + 18325388
CUGAAACUGACGUUGCCACAGCCACAAAUGCUGCAGCAGAUGCAGUUGCUGAGAAAAAGCUGCAGCUGCUGGAUGAUUUUCAGCCCAGU-------------------------------
((((((....((((....((((.......))))((((((.(((((((..........))))))).))))))))))..))))))......------------------------------- ( -28.50, z-score =  -0.66, R)
>consensus
_____UCAUCACUUGCUGCUGUGGCAUCCACAUCCUCGCCUCCGGAUGCCGGAAAAUUCCAGCUGGU___GGAGGAUCUACUGGGACUGCGCCGUCCCAAGAGGC_______________
..........(((.((((.((((.....))))........(((((...)))))......)))).))).........(((..((((((......))))))..)))................ (-14.27 = -14.63 +   0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,947,511 – 14,947,608
Length 97
Sequences 7
Columns 120
Reading direction reverse
Mean pairwise identity 62.65
Shannon entropy 0.67013
G+C content 0.56121
Mean single sequence MFE -34.86
Consensus MFE -16.47
Energy contribution -18.13
Covariance contribution 1.66
Combinations/Pair 1.37
Mean z-score -0.87
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.734679
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14947511 97 - 21146708
---------------GCCUCUUGGGACGGCGCAGUCCCAGCAGAUCCUCC---ACUAGCUGAAAUUUUCCGGCAUCCGGAGGCGAGGAUGUGGAUGCCACAGCAGCAAGUGAUGA-----
---------------..((.(((((((......))))))).))......(---(((.((((.........((((((((.(........).))))))))....)))).))))....----- ( -35.52, z-score =  -0.71, R)
>droSim1.chr2R 13647054 97 - 19596830
---------------GCCUCUUGGGACGGCGCAGUCCCAGCAGAUCCUCC---ACUAGCUGGAAUUUUCCGGCAUCCGGAGGCGAGGAUGUGGAUGCCACAGCAGCAAGUGAUGA-----
---------------.(((((((((((......))))))).....(((((---....((((((....))))))....))))).)))).(((((...)))))..............----- ( -38.00, z-score =  -1.06, R)
>droSec1.super_1 12454011 97 - 14215200
---------------GCCUCUUGGGACGGCGCAGUCCCAGCAGAUCCUCC---ACUAGCUGGAAUUUUCCGGCAUCCAGAGGCGAGGAUGUGGAUGCCACAGCAGCAAGUGAUGA-----
---------------..((.(((((((......))))))).))......(---(((.((((((....)))((((((((.(........).)))))))).....))).))))....----- ( -38.30, z-score =  -1.44, R)
>droYak2.chr2R 6903198 97 + 21139217
---------------GCCUCUUGGGACGGCGCAGUCCCAUUAGAUCCUCG---ACCAGCUGGAAUUUUCCGGCAUCCGGAGGCGAGGAUGUGGAUGCCACAGCUGCAAGUGAGGA-----
---------------..((..((((((......))))))..)).((((((---..((((((((....)))((((((((.(........).))))))))..)))))....))))))----- ( -43.60, z-score =  -2.60, R)
>droEre2.scaffold_4845 9144677 97 - 22589142
---------------GCCUCUUGGGACGUCGCAGUCCCAUUAGAUCCUCC---ACCAGCUGGAAUUUUCCGGCAUCCGGCGGCGGGGAUGUGGAUGCCACAGCAGCAAGUGAGGA-----
---------------..((..((((((......))))))..)).(((((.---((..((((((....)))((((((((.((.......)))))))))).....)))..)))))))----- ( -39.10, z-score =  -1.06, R)
>droWil1.scaffold_180697 2593303 115 - 4168966
GACGUUUGCCAUGAUGCAAUUUGGUUAGUUCCAUUGGUAGUCCAUCAUCCAAAAUCAGCUCCACCUUUCCAAAAGCCCCAGCAAAUGGCAUCGAUGAAGCAGUAACAGAUGGAAU-----
(((..((((......))))....))).((((((((..((.(.(.(((((........(((.............))).(((.....)))....))))).).).))...))))))))----- ( -18.82, z-score =   1.73, R)
>droGri2.scaffold_15245 18050048 89 - 18325388
-------------------------------ACUGGGCUGAAAAUCAUCCAGCAGCUGCAGCUUUUUCUCAGCAACUGCAUCUGCUGCAGCAUUUGUGGCUGUGGCAACGUCAGUUUCAG
-------------------------------.(((((.((.....)))))))..((((((((.......(((...))).....))))))))...((..((((((....)).))))..)). ( -30.70, z-score =  -0.98, R)
>consensus
_______________GCCUCUUGGGACGGCGCAGUCCCAGCAGAUCCUCC___ACCAGCUGGAAUUUUCCGGCAUCCGGAGGCGAGGAUGUGGAUGCCACAGCAGCAAGUGAUGA_____
.....................((((((......))))))..................((((......(((.((((((........))))))))).....))))................. (-16.47 = -18.13 +   1.66)

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 22:33:43 2011