Locus 15856

Sequence ID dm3.chrX
Location 21,664,635 – 21,664,827
Length 192
Max. P 0.995007
window21849 window21850 window21851 window21852

overview

Window 9

Location 21,664,635 – 21,664,749
Length 114
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 56.09
Shannon entropy 0.61723
G+C content 0.45684
Mean single sequence MFE -32.47
Consensus MFE -16.99
Energy contribution -15.57
Covariance contribution -1.42
Combinations/Pair 1.54
Mean z-score -0.77
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.651493
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 21664635 114 + 22422827
----CAGUGGGGAGCCGGUUGGCCGUCUUGUUUCUAUGAUGAAAUAGGAUGAUUACGUUGGAAGG-AGACUGUCCUUCAAUACCGCUGGCCUAGAGACUCAGCCGGUAUAUUUUGUAAU
----.........(((((((((((((((((((((......))))))))))......((..(((((-(.....))))))...))....))))..(.....))))))))............ ( -35.70, z-score =  -1.38, R)
>droWil1.scaffold_181075 769677 103 - 1141854
------------CGGUGGUGGG--AUCCAACUUAUGGGUAGAUUUAUGUUGAUUAGGA-GGAGAUACGAUUAAGUAUCUGAAUCACCGUCCUUGUGGAUCAG-CAAUAUAUUAGAAAUU
------------...(((((..--(((((.....))))).......((((((((((((-((((((((......))))))......)).))))....))))))-))...)))))...... ( -22.50, z-score =  -0.02, R)
>droVir3.scaffold_13050 3111345 118 - 3426691
CCAAUAGUGCGUAGCCGGUUGGCCGCACUGCUCCUAUGUUGAGAUAGGGAGAUUAGGGUGGAAGGGAAACUGUCCUUCGAUACCGCUGGCC-AUAGACUCAGUCGGUAUAUUGGUUAAU
(((((((((((..(((....))))))))).(((((.(((....))))))))....(((.(((.((....)).)))))).((((((((((..-......)))).)))))))))))..... ( -39.20, z-score =  -0.91, R)
>consensus
_____AGUG_G_AGCCGGUUGGCCGUCCUGCUUCUAUGUUGAAAUAGGAUGAUUAGGAUGGAAGG_AGACUGUCCUUCAAUACCGCUGGCCUAGAGACUCAG_CGGUAUAUUAGAUAAU
.............((((((.((.(((((((.((((((......))))))....)))))))(((((........)))))....))))))))............................. (-16.99 = -15.57 +  -1.42)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,664,635 – 21,664,749
Length 114
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 56.09
Shannon entropy 0.61723
G+C content 0.45684
Mean single sequence MFE -27.33
Consensus MFE -13.58
Energy contribution -12.37
Covariance contribution -1.21
Combinations/Pair 1.44
Mean z-score -2.13
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.76
SVM RNA-class probability 0.995007
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 21664635 114 - 22422827
AUUACAAAAUAUACCGGCUGAGUCUCUAGGCCAGCGGUAUUGAAGGACAGUCU-CCUUCCAACGUAAUCAUCCUAUUUCAUCAUAGAAACAAGACGGCCAACCGGCUCCCCACUG----
(((((.....((((((.(((.(((....)))))))))))).((((((.....)-)))))....)))))....((((......)))).........((((....))))........---- ( -27.70, z-score =  -1.86, R)
>droWil1.scaffold_181075 769677 103 + 1141854
AAUUUCUAAUAUAUUG-CUGAUCCACAAGGACGGUGAUUCAGAUACUUAAUCGUAUCUCC-UCCUAAUCAACAUAAAUCUACCCAUAAGUUGGAU--CCCACCACCG------------
....((((((..((..-(((.(((....))))))..))..((((((......))))))..-...........................)))))).--..........------------ ( -17.30, z-score =  -1.46, R)
>droVir3.scaffold_13050 3111345 118 + 3426691
AUUAACCAAUAUACCGACUGAGUCUAU-GGCCAGCGGUAUCGAAGGACAGUUUCCCUUCCACCCUAAUCUCCCUAUCUCAACAUAGGAGCAGUGCGGCCAACCGGCUACGCACUAUUGG
.....(((((((((((.(((.((....-.))))))))))).(((((........)))))............(((((......)))))...(((((((((....)))..))))))))))) ( -37.00, z-score =  -3.06, R)
>consensus
AUUAACAAAUAUACCG_CUGAGUCUCUAGGCCAGCGGUAUAGAAGGACAGUCU_CCUUCCAACCUAAUCAACCUAUAUCAACAUAGAAGCAGGACGGCCAACCGGCU_C_CACU_____
...........(((((.(((.(((....)))))))))))..(((((........)))))............................................................ (-13.58 = -12.37 +  -1.21)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,664,671 – 21,664,787
Length 116
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 62.25
Shannon entropy 0.53446
G+C content 0.40173
Mean single sequence MFE -21.57
Consensus MFE -16.40
Energy contribution -15.30
Covariance contribution -1.10
Combinations/Pair 1.40
Mean z-score -1.36
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.978824
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 21664671 116 - 22422827
UA-UAACGAAACUCCGGCACUUAGCCGUUAAACCUUUUU-AUUACAAAAUAUACCGGCUGAGUCUCUAGGCCAGCGGUAUUGAAGGACAGUCU-CCUUCCAACGUAAUCAUCCUAUUUC
..-....((((...((((.....))))............-(((((.....((((((.(((.(((....)))))))))))).((((((.....)-)))))....))))).......)))) ( -28.80, z-score =  -2.80, R)
>droWil1.scaffold_181075 769703 111 + 1141854
------CAUAACUCCGACACUUGGCCGUAACACAAAUUAUAAUUUCUAAUAUAUUG-CUGAUCCACAAGGACGGUGAUUCAGAUACUUAAUCGUAUCUCC-UCCUAAUCAACAUAAAUC
------.........((.....((............................((..-(((.(((....))))))..))..((((((......))))))))-......)).......... ( -13.80, z-score =  -0.16, R)
>droVir3.scaffold_13050 3111385 116 + 3426691
UAUUCAUGAAACUUCGGUACUUAGCCGUUAAAUC-UUUA-AUUAACCAAUAUACCGACUGAGUCUAU-GGCCAGCGGUAUCGAAGGACAGUUUCCCUUCCACCCUAAUCUCCCUAUCUC
.......((((((.((((.....)))).......-....-.....((...((((((.(((.((....-.)))))))))))....))..))))))......................... ( -22.10, z-score =  -1.12, R)
>consensus
UA_U_ACGAAACUCCGGCACUUAGCCGUUAAACC_UUUA_AUUAACAAAUAUACCG_CUGAGUCUCUAGGCCAGCGGUAUAGAAGGACAGUCU_CCUUCCAACCUAAUCAACCUAUAUC
..............((((.....))))........................(((((.(((.(((....)))))))))))..(((((........))))).................... (-16.40 = -15.30 +  -1.10)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,664,710 – 21,664,827
Length 117
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 60.85
Shannon entropy 0.54852
G+C content 0.36219
Mean single sequence MFE -19.95
Consensus MFE -13.65
Energy contribution -13.67
Covariance contribution 0.01
Combinations/Pair 1.37
Mean z-score -0.91
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.883391
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 21664710 117 - 22422827
GUUCUGAUUUUAUAUUCAAUUAAUAAAGAGCACAAGCUCAUA-UAACGAAACUCCGGCACUUAGCCGUUAAACCUUUUU-AUUACAAAAUAUACCGGCUGAGUCUCUAGGCCAGCGGUA
....(((........)))..(((((((((((....))))...-...........((((.....)))).........)))-)))).......(((((.(((.(((....))))))))))) ( -26.90, z-score =  -2.47, R)
>droWil1.scaffold_181075 769742 103 + 1141854
----GUUUUGUAUAACCAAUUAAACAAUAAAG-----------ACGCAUAACUCCGACACUUGGCCGUAACACAAAUUAUAAUUUCUAAUAUAUUG-CUGAUCCACAAGGACGGUGAUU
----(((((....................)))-----------))........((((...))))............................((..-(((.(((....))))))..)). (  -9.45, z-score =   1.57, R)
>droVir3.scaffold_13050 3111425 116 + 3426691
GUUCAUAUUUGAUAUUCAAUAAAUCAAGAGCACCAGCUCCUAUUCAUGAAACUUCGGUACUUAGCCGUUAAAUC-UUUA-AUUAACCAAUAUACCGACUGAGUCUAU-GGCCAGCGGUA
.(((((..(((((.........)))))((((....))))......)))))....((((.....)))).......-....-...........(((((.(((.((....-.)))))))))) ( -23.50, z-score =  -1.84, R)
>consensus
GUUCAUAUUUUAUAUUCAAUUAAUCAAGAGCAC_AGCUC_UA_UCACGAAACUCCGGCACUUAGCCGUUAAACC_UUUA_AUUAACAAAUAUACCG_CUGAGUCUCUAGGCCAGCGGUA
...........................((((....))))...............((((.....))))........................(((((.(((.(((....))))))))))) (-13.65 = -13.67 +   0.01)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:07:11 2011