Locus 4269

Sequence ID dm3.chr2R
Location 11,787,658 – 11,787,775
Length 117
Max. P 0.974265
window5849 window5850 window5851

overview

Window 9

Location 11,787,658 – 11,787,759
Length 101
Sequences 7
Columns 115
Reading direction forward
Mean pairwise identity 67.90
Shannon entropy 0.57618
G+C content 0.53008
Mean single sequence MFE -35.54
Consensus MFE -15.56
Energy contribution -15.26
Covariance contribution -0.30
Combinations/Pair 1.35
Mean z-score -1.40
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.709994
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11787658 101 + 21146708
---UGUUGGUGCUGA-CUGGUGACCCCAUUUGUGGGGUGACCCUGC---------CAUGUGGUGACACCUUAACAGU-UAGCCAAGUGGCCAGACUAUUUCCCUCCACGAGAUGA
---..((((((((((-(((((.((((((....)))))).)).....---------...(((....))).....))))-))))......)))))..((((((.......)))))). ( -34.80, z-score =  -1.43, R)
>droSim1.chrU 12444360 101 + 15797150
---UGUUGGUGCUGG-CUGGUGACCCCAUUUGUGGGGUGACCCCGC---------CAUGUGGUGACACCUUAACAGU-UAGCCAAGUGGCCAGACGUUUUCCCUCCACGAGAUGA
---..((((((((((-(.(((.((((((....)))))).)))..))---------)..(((....)))......)))-..)))))((((...((.....))...))))....... ( -36.70, z-score =  -1.21, R)
>droSec1.super_1 9283535 100 + 14215200
---UGUUGGUGCUGG-CUGGUGACCCCAUUUGUGGGGUGACCCCGC---------CAUGUGGUGACACCUUAACAGU-UAGCCAAGUGGCCAGAC-UUUUCCCUCCACGAGAUGA
---..((((((((((-(.(((.((((((....)))))).)))..))---------)..(((....)))......)))-..)))))((((...((.-...))...))))....... ( -36.70, z-score =  -1.36, R)
>droYak2.chr2R 3944288 97 - 21139217
------UGUUGGUG--CUGGUGACCCCAUUUAUGGGGUGACCCUGC---------CAUGUGGAGACACCUUUACAGU-UAGCCAAAUGGCCAGACUUUCUCCCACCAUGAGAUGA
------...(((((--..(((.((((((....)))))).)))((((---------(((.(((.(((.........))-)..))).)))).))).........)))))........ ( -33.30, z-score =  -1.80, R)
>droEre2.scaffold_4845 8518659 91 - 22589142
------------UG--UUGGUGACCCCAUUUGUGGGGUGACCCUGC---------CAUGUGGAGACACCUUUACUGU-UAGCCAAAUGGCCAGACUUUCUCCCCCCAUGAGAUGA
------------..--..(((.((((((....)))))).)))((((---------(((.(((.((((.......)))-)..))).)))).)))....((((.......))))... ( -30.90, z-score =  -2.32, R)
>dp4.chr3 17847152 113 + 19779522
CGCUGGAAUUCCUACAUUUGUGACCCCAUUUGAGGGGUGACCCCACACAUACUUUGGUGGUGUGGUGACCCCACUCUGCUGUUGAUUUCUGGGG-UAAAUCAUCC-AAGAGAUGA
.(..((....))..)....((.(((((......))))).)).((((((.(((....)))))))))..((((((.....(....).....)))))-)...(((((.-....))))) ( -35.90, z-score =  -0.56, R)
>droPer1.super_73 63954 115 - 267513
CGCUGGAGUUCCUACAUUUGUGACCCCAUUUGAGGGGUGACCCCACACAUACUUUUGUGGAGUGGUGACCCCACUCUGCUGUUGAUUUCGGGGGGUAAAUCAUCCCAAGAGAUGA
.((.(((((.....((..((......))..)).(((((.((((..((((......))))..).))).)))))))))))).....(((((..(((((.....)))))..))))).. ( -40.50, z-score =  -1.12, R)
>consensus
___UGUUGGUGCUG__CUGGUGACCCCAUUUGUGGGGUGACCCCGC_________CAUGUGGUGACACCUUAACAGU_UAGCCAAGUGGCCAGACUUUUUCCCCCCACGAGAUGA
..................(((.(((((......))))).))).................(((..(.((.......)).)..))).((((...((.....))...))))....... (-15.56 = -15.26 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,787,658 – 11,787,759
Length 101
Sequences 7
Columns 115
Reading direction reverse
Mean pairwise identity 67.90
Shannon entropy 0.57618
G+C content 0.53008
Mean single sequence MFE -36.62
Consensus MFE -15.92
Energy contribution -17.74
Covariance contribution 1.82
Combinations/Pair 1.11
Mean z-score -1.51
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.755715
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11787658 101 - 21146708
UCAUCUCGUGGAGGGAAAUAGUCUGGCCACUUGGCUA-ACUGUUAAGGUGUCACCACAUG---------GCAGGGUCACCCCACAAAUGGGGUCACCAG-UCAGCACCAACA---
...((((.....))))((((((.(((((....)))))-))))))..(((((.......((---------((..(((.((((((....)))))).))).)-))))))))....--- ( -37.81, z-score =  -2.02, R)
>droSim1.chrU 12444360 101 - 15797150
UCAUCUCGUGGAGGGAAAACGUCUGGCCACUUGGCUA-ACUGUUAAGGUGUCACCACAUG---------GCGGGGUCACCCCACAAAUGGGGUCACCAG-CCAGCACCAACA---
...((((.....)))).((((..(((((....)))))-..))))..(((((.......((---------((..(((.((((((....)))))).))).)-))))))))....--- ( -39.21, z-score =  -1.85, R)
>droSec1.super_1 9283535 100 - 14215200
UCAUCUCGUGGAGGGAAAA-GUCUGGCCACUUGGCUA-ACUGUUAAGGUGUCACCACAUG---------GCGGGGUCACCCCACAAAUGGGGUCACCAG-CCAGCACCAACA---
...((((.....))))..(-((.(((((....)))))-))).....(((((.......((---------((..(((.((((((....)))))).))).)-))))))))....--- ( -38.41, z-score =  -1.64, R)
>droYak2.chr2R 3944288 97 + 21139217
UCAUCUCAUGGUGGGAGAAAGUCUGGCCAUUUGGCUA-ACUGUAAAGGUGUCUCCACAUG---------GCAGGGUCACCCCAUAAAUGGGGUCACCAG--CACCAACA------
........((((((((((.(((.(((((....)))))-))).........))))).....---------....(((.((((((....)))))).)))..--)))))...------ ( -36.20, z-score =  -1.86, R)
>droEre2.scaffold_4845 8518659 91 + 22589142
UCAUCUCAUGGGGGGAGAAAGUCUGGCCAUUUGGCUA-ACAGUAAAGGUGUCUCCACAUG---------GCAGGGUCACCCCACAAAUGGGGUCACCAA--CA------------
.....(((((.(((((.(....((((((....)))..-.)))......).))))).))))---------)...(((.((((((....)))))).)))..--..------------ ( -31.90, z-score =  -1.26, R)
>dp4.chr3 17847152 113 - 19779522
UCAUCUCUU-GGAUGAUUUA-CCCCAGAAAUCAACAGCAGAGUGGGGUCACCACACCACCAAAGUAUGUGUGGGGUCACCCCUCAAAUGGGGUCACAAAUGUAGGAAUUCCAGCG
(((((....-.)))))...(-(((((....((.......)).))))))..((((((.((....))..)))))).((.(((((......))))).))....((.((....)).)). ( -34.80, z-score =  -0.80, R)
>droPer1.super_73 63954 115 + 267513
UCAUCUCUUGGGAUGAUUUACCCCCCGAAAUCAACAGCAGAGUGGGGUCACCACUCCACAAAAGUAUGUGUGGGGUCACCCCUCAAAUGGGGUCACAAAUGUAGGAACUCCAGCG
((((((....))))))......(((((............((((((.....))))))((((......)))))))))..(((((......))))).......((.((....)).)). ( -38.00, z-score =  -1.12, R)
>consensus
UCAUCUCGUGGAGGGAAAAAGUCUGGCCACUUGGCUA_ACUGUUAAGGUGUCACCACAUG_________GCGGGGUCACCCCACAAAUGGGGUCACCAG__CAGCAACAACA___
...((((.....))))....((.(((((....))))).)).................................(((.(((((......))))).))).................. (-15.92 = -17.74 +   1.82)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,787,670 – 11,787,775
Length 105
Sequences 7
Columns 115
Reading direction forward
Mean pairwise identity 72.48
Shannon entropy 0.49740
G+C content 0.52834
Mean single sequence MFE -38.46
Consensus MFE -19.82
Energy contribution -20.10
Covariance contribution 0.28
Combinations/Pair 1.36
Mean z-score -2.16
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.90
SVM RNA-class probability 0.974265
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11787670 105 + 21146708
CUGGUGACCCCAUUUGUGGGGUGACCCUGC---------CAUGUGGUGACACCUUAACAGU-UAGCCAAGUGGCCAGACUAUUUCCCUCCACGAGAUGACCCCAUCCUAAGUGGU
..(((.((((((....)))))).)))((((---------(((.(((((((.........))-)).))).)))).)))...........((((..((((....))))....)))). ( -37.50, z-score =  -2.16, R)
>droSim1.chrU 12444372 105 + 15797150
CUGGUGACCCCAUUUGUGGGGUGACCCCGC---------CAUGUGGUGACACCUUAACAGU-UAGCCAAGUGGCCAGACGUUUUCCCUCCACGAGAUGACCCCAUCCUAAGUGGU
..(((.((((((....)))))).)))..((---------(((.(((((((.........))-)).))).)))))..............((((..((((....))))....)))). ( -36.80, z-score =  -1.87, R)
>droSec1.super_1 9283547 104 + 14215200
CUGGUGACCCCAUUUGUGGGGUGACCCCGC---------CAUGUGGUGACACCUUAACAGU-UAGCCAAGUGGCCAGAC-UUUUCCCUCCACGAGAUGACCCCAUCCUAAGUGGU
..(((.((((((....)))))).)))..((---------(((.(((((((.........))-)).))).))))).....-........((((..((((....))))....)))). ( -36.80, z-score =  -2.05, R)
>droYak2.chr2R 3944296 105 - 21139217
CUGGUGACCCCAUUUAUGGGGUGACCCUGC---------CAUGUGGAGACACCUUUACAGU-UAGCCAAAUGGCCAGACUUUCUCCCACCAUGAGAUGACCCCAUCCUAAGUGGU
..(((.((((((....)))))).)))((((---------(((.(((.(((.........))-)..))).)))).)))........((((...(.((((....)))))...)))). ( -35.40, z-score =  -2.07, R)
>droEre2.scaffold_4845 8518662 104 - 22589142
-UGGUGACCCCAUUUGUGGGGUGACCCUGC---------CAUGUGGAGACACCUUUACUGU-UAGCCAAAUGGCCAGACUUUCUCCCCCCAUGAGAUGACCCCAUCCUAAGUGGU
-.(((.((((((....)))))).)))((((---------(((.(((.((((.......)))-)..))).)))).)))...........((((..((((....))))....)))). ( -35.40, z-score =  -2.12, R)
>dp4.chr3 17847168 113 + 19779522
UUUGUGACCCCAUUUGAGGGGUGACCCCACACAUACUUUGGUGGUGUGGUGACCCCACUCUGCUGUUGAUUUCUGGGG-UAAAUCAUCC-AAGAGAUGAUCGCAAUUCGAAUGGU
.........(((((((((((((.(((.(((.(((......)))))).))).)))))....(((.(((.((((((.(((-(.....))))-.))))))))).)))..)))))))). ( -43.20, z-score =  -2.52, R)
>droPer1.super_73 63970 115 - 267513
UUUGUGACCCCAUUUGAGGGGUGACCCCACACAUACUUUUGUGGAGUGGUGACCCCACUCUGCUGUUGAUUUCGGGGGGUAAAUCAUCCCAAGAGAUGAUCUCAAUUCGAAUGGU
.........(((((((((((((((((((............(..((((((.....))))))..)............))))....)))))))..(((.....)))...)))))))). ( -44.15, z-score =  -2.30, R)
>consensus
CUGGUGACCCCAUUUGUGGGGUGACCCCGC_________CAUGUGGUGACACCUUAACAGU_UAGCCAAGUGGCCAGACUUUUUCCCCCCACGAGAUGACCCCAUCCUAAGUGGU
..(((.(((((......))))).))).............(((.(((..(.((.......)).)..))).)))................((((..((((....))))....)))). (-19.82 = -20.10 +   0.28)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:25:55 2011