Locus 6381

Sequence ID dm3.chr3L
Location 6,131,863 – 6,132,034
Length 171
Max. P 0.931172
window8779 window8780 window8781

overview

Window 9

Location 6,131,863 – 6,131,922
Length 59
Sequences 8
Columns 59
Reading direction forward
Mean pairwise identity 95.28
Shannon entropy 0.08736
G+C content 0.34534
Mean single sequence MFE -9.92
Consensus MFE -9.06
Energy contribution -8.63
Covariance contribution -0.42
Combinations/Pair 1.13
Mean z-score -2.09
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.36
SVM RNA-class probability 0.931172
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6131863 59 + 24543557
AGGUAUCUUCCAAAUUUCAUUAGCAUCGCAUGAAAUUUAAAUCAACGCCUGAAAUUAAC
((((.......(((((((((..((...)))))))))))........))))......... (  -7.96, z-score =  -1.49, R)
>droSim1.chr3L 5632857 59 + 22553184
AGGUGUCUUCCAAAUUUCAUUAGCAUCGCAUGAAAUUUAAAUCAACGCCUGAAAUUAAC
((((((.....(((((((((..((...)))))))))))......))))))......... ( -11.90, z-score =  -2.77, R)
>droSec1.super_2 6076614 59 + 7591821
AGGUGUCUUCCAAAUUUCAUUAGCAUCGCAUGAAAUUUAAAUCAACGCCUGAAAUUAAC
((((((.....(((((((((..((...)))))))))))......))))))......... ( -11.90, z-score =  -2.77, R)
>droYak2.chr3L 6715810 59 + 24197627
AGGCAUCUUCCAAAUUUCAUUAGCAUCGCAUGAAAUUUAAAUCAACGCCUGAAAUUAAC
((((.......(((((((((..((...)))))))))))........))))......... (  -9.56, z-score =  -1.97, R)
>droEre2.scaffold_4784 8828339 59 + 25762168
AGGCAUCUUCCAAAUUUCAUUAGCAUCGCAUGAAAUUUAAAUCAACGCCUGAAAUUAAC
((((.......(((((((((..((...)))))))))))........))))......... (  -9.56, z-score =  -1.97, R)
>droAna3.scaffold_13337 2490586 59 - 23293914
AGGCAUCUUCCAAAUUUCAUUAGCAUCGCAUGAAAUUUAAAUCAACGCCAGAAAUUAAC
.(((.......(((((((((..((...)))))))))))........))).......... (  -9.16, z-score =  -2.27, R)
>dp4.chrXR_group6 3776451 59 - 13314419
UGGCAUCUUCCAAAUUUCAUUAGCACCGCAUGAAAUUUAAAUCAGCGCCAGAAAUUAAC
((((.......(((((((((..((...)))))))))))........))))......... (  -9.66, z-score =  -1.71, R)
>droPer1.super_35 186814 59 + 973955
UGGCAUCUUCCAAAUUUCAUUAGCACCGCAUGAAAUUUAAAUCAGCGCCAGAAAUUAAC
((((.......(((((((((..((...)))))))))))........))))......... (  -9.66, z-score =  -1.71, R)
>consensus
AGGCAUCUUCCAAAUUUCAUUAGCAUCGCAUGAAAUUUAAAUCAACGCCUGAAAUUAAC
((((.......(((((((((..((...)))))))))))........))))......... ( -9.06 =  -8.63 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,131,863 – 6,131,922
Length 59
Sequences 8
Columns 59
Reading direction reverse
Mean pairwise identity 95.28
Shannon entropy 0.08736
G+C content 0.34534
Mean single sequence MFE -15.75
Consensus MFE -12.07
Energy contribution -11.95
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -2.77
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.22
SVM RNA-class probability 0.911144
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6131863 59 - 24543557
GUUAAUUUCAGGCGUUGAUUUAAAUUUCAUGCGAUGCUAAUGAAAUUUGGAAGAUACCU
.........(((..((..((((((((((((.........)))))))))))).))..))) ( -12.60, z-score =  -1.89, R)
>droSim1.chr3L 5632857 59 - 22553184
GUUAAUUUCAGGCGUUGAUUUAAAUUUCAUGCGAUGCUAAUGAAAUUUGGAAGACACCU
.........(((.(((..((((((((((((.........)))))))))))).))).))) ( -14.70, z-score =  -2.70, R)
>droSec1.super_2 6076614 59 - 7591821
GUUAAUUUCAGGCGUUGAUUUAAAUUUCAUGCGAUGCUAAUGAAAUUUGGAAGACACCU
.........(((.(((..((((((((((((.........)))))))))))).))).))) ( -14.70, z-score =  -2.70, R)
>droYak2.chr3L 6715810 59 - 24197627
GUUAAUUUCAGGCGUUGAUUUAAAUUUCAUGCGAUGCUAAUGAAAUUUGGAAGAUGCCU
.........(((((((..((((((((((((.........)))))))))))).))))))) ( -18.30, z-score =  -3.70, R)
>droEre2.scaffold_4784 8828339 59 - 25762168
GUUAAUUUCAGGCGUUGAUUUAAAUUUCAUGCGAUGCUAAUGAAAUUUGGAAGAUGCCU
.........(((((((..((((((((((((.........)))))))))))).))))))) ( -18.30, z-score =  -3.70, R)
>droAna3.scaffold_13337 2490586 59 + 23293914
GUUAAUUUCUGGCGUUGAUUUAAAUUUCAUGCGAUGCUAAUGAAAUUUGGAAGAUGCCU
..........((((((..((((((((((((.........)))))))))))).)))))). ( -17.60, z-score =  -3.78, R)
>dp4.chrXR_group6 3776451 59 + 13314419
GUUAAUUUCUGGCGCUGAUUUAAAUUUCAUGCGGUGCUAAUGAAAUUUGGAAGAUGCCA
..........((((((..((((((((((((.........)))))))))))))).)))). ( -14.90, z-score =  -1.83, R)
>droPer1.super_35 186814 59 - 973955
GUUAAUUUCUGGCGCUGAUUUAAAUUUCAUGCGGUGCUAAUGAAAUUUGGAAGAUGCCA
..........((((((..((((((((((((.........)))))))))))))).)))). ( -14.90, z-score =  -1.83, R)
>consensus
GUUAAUUUCAGGCGUUGAUUUAAAUUUCAUGCGAUGCUAAUGAAAUUUGGAAGAUGCCU
.........(((.(((..((((((((((((.........)))))))))))).))).))) (-12.07 = -11.95 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,131,922 – 6,132,034
Length 112
Sequences 8
Columns 113
Reading direction reverse
Mean pairwise identity 93.84
Shannon entropy 0.11309
G+C content 0.36301
Mean single sequence MFE -29.94
Consensus MFE -21.42
Energy contribution -21.86
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.46
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.706652
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6131922 112 - 24543557
CAGCCAAACAUGUUUGGGUUUUUGUUGUCUUUGUAAUUAAUACAUAAUUAAAGUGGCGCAUAUUGAAAAAUGUGCGAGGGAUCUGGCCACAAAUGAAAACGAAGUUU-UGAAG
...(((((....)))))(((((..((.......((((((.....))))))..((((((((((((....)))))))((....))..))))).))..))))).......-..... ( -29.80, z-score =  -2.51, R)
>droSim1.chr3L 5632916 112 - 22553184
CAGCCAAACAUGUUUGGGUUUUUGUUGUCUUUGUAAUUAAUACAUAAUUAAAGUGGCGCAUAUUGAAAAAUGUGCGAGGGAUCUGGCCACAAAUGAAAACGAAGUUU-UGAAG
...(((((....)))))(((((..((.......((((((.....))))))..((((((((((((....)))))))((....))..))))).))..))))).......-..... ( -29.80, z-score =  -2.51, R)
>droSec1.super_2 6076673 112 - 7591821
CAGCCAAACAUGUUUGGGUUUCUGUUGUCUUUGUAAUUAAUACAUAAUUAAAGUGGCGCAUAUUGAAAAAUGUGCGAGGGAUCUGGCCACAAAUGAAAACGAAGUUU-UGAAG
...(((((....)))))..(((......((((((..(((((.....))))).((((((((((((....)))))))((....))..)))))........))))))...-.))). ( -28.40, z-score =  -1.97, R)
>droYak2.chr3L 6715869 112 - 24197627
CAGCCAAACAUGUUUGGGUUUUUGUUGUCUUUGUAAUUAAUACAUAAUUAAAGUGGCGCAUAUUGAAAAAUGUGCGAGGGAUCUGGCCACAAAUGAAAACGAAGUUU-UGAAG
...(((((....)))))(((((..((.......((((((.....))))))..((((((((((((....)))))))((....))..))))).))..))))).......-..... ( -29.80, z-score =  -2.51, R)
>droEre2.scaffold_4784 8828398 112 - 25762168
CAGCCAAACAUGUUUGGGUUUUUGUUGUCUUUGUAAUUAAUACAUAAUUAAAGUGGCGCAUAUUGAAAAAUGUGCGAGGGAUCUGGCCACAAAUGAAAACGAAGUUU-UGAAG
...(((((....)))))(((((..((.......((((((.....))))))..((((((((((((....)))))))((....))..))))).))..))))).......-..... ( -29.80, z-score =  -2.51, R)
>droAna3.scaffold_13337 2490645 112 + 23293914
CGUUGAAACUUGUUUGGGUUUUUGUUGUCGUUGUAAUUAAUACAUAAUUAAAGUGGCGCAUAUUGAAAUAUGUGCGAGCGAUCUGGCCACGAAUGAAAACGAAGUUU-UGAAG
............((..((.(((((((.(((((.((((((.....))))))..(((((((((((......))))))((....))..))))).))))).))))))).))-..)). ( -27.30, z-score =  -1.48, R)
>dp4.chrXR_group6 3776510 113 + 13314419
CGUUGAAACUUGUUUGGGUUUUUGUUUUCUUUGUAAUUAAUACAUAAUUAAAGCCGCGCAUAUGGAAAUAUGUGCGAGCGAUCUGGCCACGAAUGAAAACGAAGUUUCUGAAG
............((..((.(((((((((((((((..(((((.....))))).(((((((((((....))))))))).)).........))))).))))))))))..))..)). ( -32.30, z-score =  -3.09, R)
>droPer1.super_35 186873 113 - 973955
CGUUGAAACUUGUUUGGGUUUUUGUUUUCUUUGUAAUUAAUACAUAAUUAAAGCCGCGCAUAUGGAAAUAUGUGCGAGCGAUCUGGCCACGAAUGAAAACGAAGUUUCUGAAG
............((..((.(((((((((((((((..(((((.....))))).(((((((((((....))))))))).)).........))))).))))))))))..))..)). ( -32.30, z-score =  -3.09, R)
>consensus
CAGCCAAACAUGUUUGGGUUUUUGUUGUCUUUGUAAUUAAUACAUAAUUAAAGUGGCGCAUAUUGAAAAAUGUGCGAGGGAUCUGGCCACAAAUGAAAACGAAGUUU_UGAAG
.................(((((((((.......((((((.....))))))..((((((((((((....)))))))((....))..))))).)))))))))............. (-21.42 = -21.86 +   0.44)

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 23:06:39 2011