Locus 14987

Sequence ID dm3.chrX
Location 16,828,538 – 16,828,676
Length 138
Max. P 0.977246
window20651 window20652 window20653

overview

Window 1

Location 16,828,538 – 16,828,641
Length 103
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 78.30
Shannon entropy 0.37087
G+C content 0.39472
Mean single sequence MFE -23.34
Consensus MFE -15.80
Energy contribution -16.56
Covariance contribution 0.76
Combinations/Pair 1.13
Mean z-score -2.30
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.97
SVM RNA-class probability 0.977246
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16828538 103 + 22422827
CUCGCGCUUCCUUAAUAAAAAUCCACUCCAAAGAUGGUCAUAAAGAAUUGCGAAAAGUCAGCGGCAAUCUUAUCGGAUCG----UAAAGAUUGAAAAGAUUGCCACG---
.(((((.(((.(((........(((((....)).)))...))).))).))))).......(.(((((((((.(((.(((.----....)))))).))))))))).).--- ( -26.30, z-score =  -2.68, R)
>droSim1.chrX 13019150 99 + 17042790
----AACUUCCUGUAUAAAAUUCCAUGCCAGAGAUGGUCAUAAAGAAUUGCGAAAAGUCAGCGGCAAUCUUAUCGGAUCA----UAAAGACUGAAAAGAUUGCCACG---
----.((((..((((....((((.((((((....))).)))...))))))))..))))..(.(((((((((.((((.((.----....)))))).))))))))).).--- ( -27.30, z-score =  -3.33, R)
>droSec1.super_17 662613 99 + 1527944
----AACUUCCUGUAUAAAAUUCCAUGCCAGAGAUGGUCAUAAAGAAUUGCGAAAAGUCAGCGGCAAUCUUAUCGGAUCA----UAAAGACUGAAAAGAUUGCCACG---
----.((((..((((....((((.((((((....))).)))...))))))))..))))..(.(((((((((.((((.((.----....)))))).))))))))).).--- ( -27.30, z-score =  -3.33, R)
>droYak2.chrX 15439183 98 + 21770863
--------CACUCUCGAAAUGGUCAUAACUGAG----UCAUAAACAAUUGCGAAAAGUCACCAGCAAUCUAAUCAGAUCGAUCGUAAAGACUGAAAAGAUUGCCAACUCG
--------......(((..((((....(((...----((.(((....))).))..))).))))(((((((..((((.((.........))))))..)))))))....))) ( -18.30, z-score =  -1.15, R)
>droEre2.scaffold_4690 7183190 100 + 18748788
----CACUUCCUUUAUAAAAAUCCACUCCAGAGAUGGUCAUAAAGAAUUUCGAAAAGUCACCGGCAAUCUUAUCGGCUCA----UAAAGACUGCAAAGAUUGCUUAAG--
----......((((((......(((((....)).)))..)))))).................(((((((((..(((.((.----....)))))..)))))))))....-- ( -17.50, z-score =  -1.00, R)
>consensus
____AACUUCCUGUAUAAAAAUCCAUGCCAGAGAUGGUCAUAAAGAAUUGCGAAAAGUCAGCGGCAAUCUUAUCGGAUCA____UAAAGACUGAAAAGAUUGCCACG___
................................(((..((.(((....))).))...)))...(((((((((.((((.((.........)))))).)))))))))...... (-15.80 = -16.56 +   0.76)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,828,538 – 16,828,641
Length 103
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 78.30
Shannon entropy 0.37087
G+C content 0.39472
Mean single sequence MFE -27.88
Consensus MFE -16.42
Energy contribution -18.50
Covariance contribution 2.08
Combinations/Pair 1.20
Mean z-score -2.47
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.76
SVM RNA-class probability 0.965726
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16828538 103 - 22422827
---CGUGGCAAUCUUUUCAAUCUUUA----CGAUCCGAUAAGAUUGCCGCUGACUUUUCGCAAUUCUUUAUGACCAUCUUUGGAGUGGAUUUUUAUUAAGGAAGCGCGAG
---.(((((((((((.((.(((....----.)))..)).))))))))))).......((((..((((((((((..((((.......))))..))).)))))))..)))). ( -32.70, z-score =  -3.65, R)
>droSim1.chrX 13019150 99 - 17042790
---CGUGGCAAUCUUUUCAGUCUUUA----UGAUCCGAUAAGAUUGCCGCUGACUUUUCGCAAUUCUUUAUGACCAUCUCUGGCAUGGAAUUUUAUACAGGAAGUU----
---.(((((((((((.((.(((....----.)))..)).))))))))))).((((((..(.((((((..(((.(((....)))))))))))).....)..))))))---- ( -29.90, z-score =  -3.48, R)
>droSec1.super_17 662613 99 - 1527944
---CGUGGCAAUCUUUUCAGUCUUUA----UGAUCCGAUAAGAUUGCCGCUGACUUUUCGCAAUUCUUUAUGACCAUCUCUGGCAUGGAAUUUUAUACAGGAAGUU----
---.(((((((((((.((.(((....----.)))..)).))))))))))).((((((..(.((((((..(((.(((....)))))))))))).....)..))))))---- ( -29.90, z-score =  -3.48, R)
>droYak2.chrX 15439183 98 - 21770863
CGAGUUGGCAAUCUUUUCAGUCUUUACGAUCGAUCUGAUUAGAUUGCUGGUGACUUUUCGCAAUUGUUUAUGA----CUCAGUUAUGACCAUUUCGAGAGUG--------
....(..(((((((..((((((.........)).))))..)))))))..)..(((((.((.((.((.((((((----(...))))))).)).))))))))).-------- ( -26.70, z-score =  -1.77, R)
>droEre2.scaffold_4690 7183190 100 - 18748788
--CUUAAGCAAUCUUUGCAGUCUUUA----UGAGCCGAUAAGAUUGCCGGUGACUUUUCGAAAUUCUUUAUGACCAUCUCUGGAGUGGAUUUUUAUAAAGGAAGUG----
--.....((((((((.((..((....----.))))....)))))))).(....).........(((((((((((((.((....)))))....))))))))))....---- ( -20.20, z-score =   0.04, R)
>consensus
___CGUGGCAAUCUUUUCAGUCUUUA____UGAUCCGAUAAGAUUGCCGCUGACUUUUCGCAAUUCUUUAUGACCAUCUCUGGAAUGGAAUUUUAUAAAGGAAGUG____
....(((((((((((.((.(((.........)))..)).))))))))))).............((((((((((((((.......))))....))))))))))........ (-16.42 = -18.50 +   2.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,828,574 – 16,828,676
Length 102
Sequences 7
Columns 113
Reading direction forward
Mean pairwise identity 65.99
Shannon entropy 0.64399
G+C content 0.33420
Mean single sequence MFE -20.34
Consensus MFE -6.91
Energy contribution -7.94
Covariance contribution 1.03
Combinations/Pair 1.64
Mean z-score -1.50
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.563840
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16828574 102 + 22422827
GUCAUAAAGAAUUGCGAAAAGUCAGCGGC-AAUCUUAUCGGAUCG----UAA--AGAUUGAAAAGAUUGCCA---CGGCUCUUAAAUUAAUAAAGUAUUAGCUUUUGAUUUU-
((((.((((...(((.((.((((.(.(((-((((((.(((.(((.----...--.)))))).))))))))).---))))).))...........)))....))))))))...- ( -24.40, z-score =  -2.10, R)
>droSim1.chrX 13019182 102 + 17042790
GUCAUAAAGAAUUGCGAAAAGUCAGCGGC-AAUCUUAUCGGAUCA----UAA--AGACUGAAAAGAUUGCCA---CGGCUCUUAAAUUAAUAAAGUAUUAGCUUUUGAUUUU-
((((.((((...(((.((.((((.(.(((-((((((.((((.((.----...--.)))))).))))))))).---))))).))...........)))....))))))))...- ( -25.60, z-score =  -2.75, R)
>droSec1.super_17 662645 102 + 1527944
GUCAUAAAGAAUUGCGAAAAGUCAGCGGC-AAUCUUAUCGGAUCA----UAA--AGACUGAAAAGAUUGCCA---CGGCUCUUAAAUUAAUAAAGUAUUAGCUUUUGAUUUU-
((((.((((...(((.((.((((.(.(((-((((((.((((.((.----...--.)))))).))))))))).---))))).))...........)))....))))))))...- ( -25.60, z-score =  -2.75, R)
>droYak2.chrX 15439207 109 + 21770863
GUCAUAAACAAUUGCGAAAAGUCACCAGC-AAUCUAAUCAGAUCGAUCGUAA--AGACUGAAAAGAUUGCCAACUCGACUCUUAAAUUAAUAAAGUAUUAGCUUUUGAUUUA-
........(((..((....((((....((-(((((..((((.((........--.))))))..)))))))......)))).......(((((...)))))))..))).....- ( -19.60, z-score =  -1.65, R)
>droEre2.scaffold_4690 7183222 103 + 18748788
GUCAUAAAGAAUUUCGAAAAGUCACCGGC-AAUCUUAUCGGCUCA----UAA--AGACUGCAAAGAUUGCUUA--AGGCUCUUAAAUUAAUAAACUAUUAGCUUUUGAUUUU-
.................(((((((..(((-((((((..(((.((.----...--.)))))..))))))))).(--(((((..((...........))..)))))))))))))- ( -19.00, z-score =  -1.06, R)
>droAna3.scaffold_13334 968404 96 - 1562580
-------------GUCCAAUUCCAGAAGCUAAUCUUAUCGUAUCGGCACUAAUAAGCCCAUAAAAACUGGCU----ACCAAAAAUAUUAAUUCCGAAUUAGUAUUUGAUUUUA
-------------.........((((.((((((.........((((...(((((((((..........))))----........)))))...)))))))))).))))...... ( -13.20, z-score =  -0.95, R)
>droVir3.scaffold_13049 12711650 88 + 25233164
-------------GCCAUAAAGUGCUACAAAAGCUGGGUAGAUCA---------AGGCGAUAUUAAUUAAAAA--ACUUAAGCAGGUAGCUUAGCCAUCAGCUUUCGAUUUU-
-------------..............(.((((((((((..(((.---------....)))............--...(((((.....))))))))..))))))).).....- ( -15.00, z-score =   0.74, R)
>consensus
GUCAUAAAGAAUUGCGAAAAGUCAGCGGC_AAUCUUAUCGGAUCA____UAA__AGACUGAAAAGAUUGCCA___CGGCUCUUAAAUUAAUAAAGUAUUAGCUUUUGAUUUU_
.................(((((((..(((.((((((.((((.((...........)))))).))))))(((.....))).....................)))..))))))). ( -6.91 =  -7.94 +   1.03)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:50:53 2011