Locus 5760

Sequence ID dm3.chr3L
Location 932,242 – 932,434
Length 192
Max. P 0.995438
window7920 window7921 window7922

overview

Window 0

Location 932,242 – 932,357
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 53.06
Shannon entropy 0.67257
G+C content 0.42680
Mean single sequence MFE -31.43
Consensus MFE -10.73
Energy contribution -10.74
Covariance contribution 0.01
Combinations/Pair 1.36
Mean z-score -1.59
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.56
SVM RNA-class probability 0.744757
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 932242 115 + 24543557
-----AGUCGACUAAUAAGUAAACUUAGGACCACCCUAAUUCCUUAGGGUCACCCUAGUAGAUCUUUAGAUACACCCUAAUACUAAAUAUGCGAAUUCAGCAUGUACGCCUUUAGGGGUC
-----.(((.((((.((((....))))((...(((((((....)))))))...)))))).)))...........((((((......((((((.......))))))......))))))... ( -29.60, z-score =  -1.82, R)
>droEre2.scaffold_4784 2474268 120 - 25762168
AGCUAACACUGUUAAUGGGUAAAAUUAAGUCGAUAUAAGUCCGGGGUUGUUACCCUAACAUUACACUAAUGUUACCCUAACAUUUUAUAUGCAGAUUCAGCAUAAGCGCCUCUAGGGGCC
.(((.....(((((..((((((.((((.((.(((....))).(((((....)))))........)))))).))))))))))).....(((((.......))))))))((((....)))). ( -31.60, z-score =  -1.51, R)
>droAna3.scaffold_12948 55913 106 + 692136
AGUUAACACUUCUGAGGGGUAACAAACAGUCGGUAGAAAUCUUGGGUGAUU--------------CUUGGAUCACCCUAGUCUUUAUAAUGUCGACUCAGCAUACCCGCCUUUGGGGGCC
................(((((......(((((..(.(((.((.((((((((--------------....)))))))).))..)))....)..))))).....)))))((((....)))). ( -33.10, z-score =  -1.44, R)
>consensus
AG_UAACACUACUAAUGGGUAAAAUUAAGUCGAUACAAAUCCCGGGUGGUUACCCUA__A___C_CUAGAAUCACCCUAAUAUUUAAUAUGCAGAUUCAGCAUAAACGCCUUUAGGGGCC
..........................................................................((((((.......(((((.......))))).......))))))... (-10.73 = -10.74 +   0.01)

alignment

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secondary structure

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dotplot

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Window 1

Location 932,277 – 932,396
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 52.51
Shannon entropy 0.69196
G+C content 0.47983
Mean single sequence MFE -36.03
Consensus MFE -16.91
Energy contribution -17.04
Covariance contribution 0.13
Combinations/Pair 1.41
Mean z-score -1.96
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.80
SVM RNA-class probability 0.995438
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 932277 119 + 24543557
UCCUUAGGGUCACCCUAGUAGAUCUUUAGAUACACCCUAAUACUAAAUAUGCGAAUUCAGCAUGUACGCCUUUAGGGGUCGCACUCGACUCCCAUUGGU-UAUCGAGUAUGAACUACAUA
....(((((...)))))((((.............((((((......((((((.......))))))......)))))).(((.((((((..((....)).-..)))))).))).))))... ( -34.20, z-score =  -2.62, R)
>droEre2.scaffold_4784 2474308 119 - 25762168
CCGGGGUUGUUACCCUAACAUUACACUAAUGUUACCCUAACAUUUUAUAUGCAGAUUCAGCAUAAGCGCCUCUAGGGGCCGUGCCUGGUUCUGAUAGGUCUCCCCAGUAUGGGGAGAUA-
..(((((....)))))(((((((...)))))))..((((.(((.....)))((((..((((((..((.((....)).)).))).)))..)))).))))(((((((.....)))))))..- ( -42.00, z-score =  -2.11, R)
>droAna3.scaffold_12948 55953 94 + 692136
-------------CUUGGGUGAUUCUUGGAU-CACCCUAGUCUUUAUAAUGUCGACUCAGCAUACCCGCCUUUGGGGGCCGUGCCUGGAUCCCACUGGU-UUCCG-GUAU----------
-------------...((((((((....)))-))))).((((...........))))....(((((.(((..((((..(((....)))..))))..)))-....)-))))---------- ( -31.90, z-score =  -1.16, R)
>consensus
_C______GU_ACCCUAGCAGAUCAUUAGAU_CACCCUAAUAUUUAAUAUGCAGAUUCAGCAUAAACGCCUUUAGGGGCCGUGCCUGGAUCCCAUUGGU_UACCGAGUAUG_________
..................................((((((.......(((((.......))))).......)))))).((((((.(((..((....))....))).))))))........ (-16.91 = -17.04 +   0.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 932,317 – 932,434
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 52.59
Shannon entropy 0.65035
G+C content 0.49331
Mean single sequence MFE -35.47
Consensus MFE -13.56
Energy contribution -12.90
Covariance contribution -0.66
Combinations/Pair 1.40
Mean z-score -2.28
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.20
SVM RNA-class probability 0.985375
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 932317 117 + 24543557
UACUAAAUAUGCGAAUUCAGCAUGUACGCCUUUAGGGGUCGCACUCGACUCCCAUUGGU-UAUCGAGUAUGAACUACAUACUUACAUAUUGCAGAAUUUGCUAGUGUCAGCA--CUUGGC
..((((....((((((((.((((((..(((..(.(((((((....))))))).)..)))-....(((((((.....))))))))))...))).))))))))..(((....))--))))). ( -35.30, z-score =  -2.87, R)
>droEre2.scaffold_4784 2474348 110 - 25762168
CAUUUUAUAUGCAGAUUCAGCAUAAGCGCCUCUAGGGGCCGUGCCUGGUUCUGAUAGGUCUCCCCAGUAUGGGG---------AGAUAU-GCUGUUUCUGCUUGUGUCAGCAGUCUUGCC
.....((((.(((((..(((((((...((((...(((((((....)))))))...))))((((((.....))))---------)).)))-))))..))))).))))...((......)). ( -44.80, z-score =  -3.19, R)
>droAna3.scaffold_12948 55979 92 + 692136
UCUUUAUAAUGUCGACUCAGCAUACCCGCCUUUGGGGGCCGUGCCUGGAUCCCACUGGU--UUCCGGUAUCUUGC--------GAUCGU--CAGCAUUUCCCAC----------------
.......(((((.(((...(((((((.(((..((((..(((....)))..))))..)))--....))))...)))--------....))--).)))))......---------------- ( -26.30, z-score =  -0.79, R)
>consensus
UAUUUAAUAUGCAGAUUCAGCAUAAACGCCUUUAGGGGCCGUGCCUGGAUCCCAUUGGU_UAUCCAGUAUGAAG_________AAAUAU_GCAGAAUUUGCUAGUGUCAGCA__CUUG_C
.......(((((.......)))))...(((....(((((((....)))))))....)))............................................................. (-13.56 = -12.90 +  -0.66)

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 22:54:39 2011