Locus 12010

Sequence ID dm3.chr3R
Location 25,099,135 – 25,099,261
Length 126
Max. P 0.971502
window16508 window16509 window16510

overview

Window 8

Location 25,099,135 – 25,099,232
Length 97
Sequences 7
Columns 97
Reading direction forward
Mean pairwise identity 78.65
Shannon entropy 0.40504
G+C content 0.50299
Mean single sequence MFE -25.01
Consensus MFE -16.97
Energy contribution -16.79
Covariance contribution -0.18
Combinations/Pair 1.14
Mean z-score -2.06
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.85
SVM RNA-class probability 0.971502
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25099135 97 + 27905053
ACCCAAAAGCAGAAGGCUAAACCCGUGGCAAGUACAAAUUGCCGUUACCGGCGAAUGCAGCCAAGCAAAAGGCUGCAAUCCUACAGGGGAAAACAUG
.(((...(((.....)))......((((..........((((((....)))))).(((((((........)))))))...)))).)))......... ( -31.60, z-score =  -2.34, R)
>droSim1.chr3R 24772967 97 + 27517382
ACCCAAAAGCAGAAGGCUAAACCCGUGGCAAGUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGCAAAAGGCUGCAAUCCUACAGGGGAAACCAUG
.(((....((....((......))..(((((.......))))).......))((.(((((((........))))))).)).....)))......... ( -29.60, z-score =  -1.93, R)
>droSec1.super_4 3959940 97 + 6179234
ACCCAAAAGCAGAAGGCUAAACCCGUGGCAAGUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGCAAAAGGCUGCAAUACUACAGGGGAAGCCAUG
..............((((...(((..(((((.......)))))............(((((((........)))))))........)))..))))... ( -32.20, z-score =  -2.43, R)
>droEre2.scaffold_4820 7543448 95 - 10470090
ACCCAAAAGCAGAGAGCGAAACCCGUGGCAAGUACAAAUUGCCGUUACCCGCGGAUGCAGCCAAGCAAAAGGCUGCAAUCCCACUGGGAAG--CAUG
.((((...((.....(((.....)))(((((.......))))).......))((((((((((........)))))).))))...))))...--.... ( -33.10, z-score =  -2.91, R)
>droAna3.scaffold_12911 4788047 96 + 5364042
UCCUAAAGGUAGAAACCCAAAGCCAAAACAACUACAAAUUGCCGUUACCCGCGAAUGCAACCAAGCAAAAGGCUGCAAUCCU-CAAGGAAAACAUUG
((((..(((...........((((..............((((........)))).(((......)))...)))).....)))-..))))........ ( -16.59, z-score =  -1.02, R)
>dp4.chr2 1938108 90 + 30794189
GCAUAAACCCAAGUCCCAAAUCCCACAAGAGCUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGC----GGCUGCAAUCCC---AAGAAAAACAUG
((..................((......))((........))........))((.(((((((....----))))))).))..---............ ( -16.00, z-score =  -1.89, R)
>droPer1.super_7 2102199 90 + 4445127
GCAUAAACCCAAGUCCCAAAUCCCACAAGAGCUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGC----GGCUGCAAUCCC---AAGAAAAACAUG
((..................((......))((........))........))((.(((((((....----))))))).))..---............ ( -16.00, z-score =  -1.89, R)
>consensus
ACCCAAAAGCAGAAGGCUAAACCCGUGGCAAGUACAAAUUGCCGUUACCCGCGAAUGCAGCCAAGCAAAAGGCUGCAAUCCUACAGGGAAAAACAUG
.(((..................................((((........)))).(((((((........)))))))........)))......... (-16.97 = -16.79 +  -0.18)

alignment

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secondary structure

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dotplot

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Window 9

Location 25,099,135 – 25,099,232
Length 97
Sequences 7
Columns 97
Reading direction reverse
Mean pairwise identity 78.65
Shannon entropy 0.40504
G+C content 0.50299
Mean single sequence MFE -30.99
Consensus MFE -19.38
Energy contribution -18.81
Covariance contribution -0.57
Combinations/Pair 1.43
Mean z-score -1.35
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.602807
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25099135 97 - 27905053
CAUGUUUUCCCCUGUAGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCCGGUAACGGCAAUUUGUACUUGCCACGGGUUUAGCCUUCUGCUUUUGGGU
.........(((.((((((.(((((((........))))))).))(((.((...(((((.......))))))).)))........))))....))). ( -33.40, z-score =  -1.79, R)
>droSim1.chr3R 24772967 97 - 27517382
CAUGGUUUCCCCUGUAGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCACGGGUUUAGCCUUCUGCUUUUGGGU
.........(((.....((.(((((((........))))))).))(((((....(((((.......)))))..(((.....))))))))....))). ( -33.40, z-score =  -1.16, R)
>droSec1.super_4 3959940 97 - 6179234
CAUGGCUUCCCCUGUAGUAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCACGGGUUUAGCCUUCUGCUUUUGGGU
...((((.((((((..(...(((((((........))))))).)..))).....(((((.......)))))..)))...)))).............. ( -33.90, z-score =  -1.29, R)
>droEre2.scaffold_4820 7543448 95 + 10470090
CAUG--CUUCCCAGUGGGAUUGCAGCCUUUUGCUUGGCUGCAUCCGCGGGUAACGGCAAUUUGUACUUGCCACGGGUUUCGCUCUCUGCUUUUGGGU
....--...(((((..((((.((((((........))))))))))(((((....(((((.......)))))..(((.....))))))))..))))). ( -36.50, z-score =  -2.02, R)
>droAna3.scaffold_12911 4788047 96 - 5364042
CAAUGUUUUCCUUG-AGGAUUGCAGCCUUUUGCUUGGUUGCAUUCGCGGGUAACGGCAAUUUGUAGUUGUUUUGGCUUUGGGUUUCUACCUUUAGGA
........((((.(-(((..(((((((........)))))))...((.((.((((((........)))))))).))............)))).)))) ( -27.50, z-score =  -1.36, R)
>dp4.chr2 1938108 90 - 30794189
CAUGUUUUUCUU---GGGAUUGCAGCC----GCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUAGCUCUUGUGGGAUUUGGGACUUGGGUUUAUGC
..(((..(((((---(.((.(((((((----....))))))).)).)))).))..)))......(((((..((..........))..)))))..... ( -26.10, z-score =  -0.92, R)
>droPer1.super_7 2102199 90 - 4445127
CAUGUUUUUCUU---GGGAUUGCAGCC----GCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUAGCUCUUGUGGGAUUUGGGACUUGGGUUUAUGC
..(((..(((((---(.((.(((((((----....))))))).)).)))).))..)))......(((((..((..........))..)))))..... ( -26.10, z-score =  -0.92, R)
>consensus
CAUGGUUUUCCCUGUAGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCACGGGUUUAGCCUUCUGCUUUUGGGU
.........(((....((((.((((((........))))))))))((.(....).))...........((...(((.....)))...))....))). (-19.38 = -18.81 +  -0.57)

alignment

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secondary structure

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dotplot

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Window 0

Location 25,099,159 – 25,099,261
Length 102
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 85.02
Shannon entropy 0.27970
G+C content 0.50937
Mean single sequence MFE -31.22
Consensus MFE -21.96
Energy contribution -22.43
Covariance contribution 0.47
Combinations/Pair 1.20
Mean z-score -1.93
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.781759
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25099159 102 - 27905053
GCCCAACUCUUUGCUUUGCCAGCUUUUUCCAUGUUUUCCCCUGUAGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCCGGUAACGGCAAUUUGUACUUGCCAC
((...((...((((((((((.((.............(((......))).(((((((........)))))))...)).))))).)))))...))....))... ( -29.30, z-score =  -1.90, R)
>droSim1.chr3R 24772991 102 - 27517382
GCCCAGCUCUUUGCCUUGCCAGCUUUUUCCAUGGUUUCCCCUGUAGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCAC
((...((...((((((((((.((......((.((....)).))...((.(((((((........))))))).)))).))))).)))))...))....))... ( -33.90, z-score =  -1.57, R)
>droSec1.super_4 3959964 102 - 6179234
GCCCAACUCUUUGCCUUGCCAGCUUUUUCCAUGGCUUCCCCUGUAGUAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCAC
((...((...(((((..((((..........))))....((((..(...(((((((........))))))).)..))))....)))))...))....))... ( -32.20, z-score =  -1.89, R)
>droYak2.chr3R 7440748 95 + 28832112
GCCCAACUCUUUG-----GCAGCUUUUUCCAUG--UUUCCCUGUGGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCAC
(((.........)-----))............(--((..((((((((..(((((((........))))))))))))))).)))(((((.......))))).. ( -32.90, z-score =  -2.11, R)
>droEre2.scaffold_4820 7543472 95 + 10470090
GCCCAACUCUUUG-----CCAGCUUUUUCCAUG--CUUCCCAGUGGGAUUGCAGCCUUUUGCUUGGCUGCAUCCGCGGGUAACGGCAAUUUGUACUUGCCAC
((...((...(((-----(((((.........)--)).(((.(((((..(((((((........)))))))))))))))....)))))...))....))... ( -33.40, z-score =  -2.13, R)
>droPer1.super_7 2102223 88 - 4445127
--GUAACUCUUUC-----UUAGCUUUUUCCAUG--UUUUUCU-UGGGAUUGCAGCC----GCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUAGCUCUUGU
--...........-----..((((.......((--(..((((-((.((.(((((((----....))))))).)).)))).))..)))......))))..... ( -25.62, z-score =  -1.97, R)
>consensus
GCCCAACUCUUUG_____CCAGCUUUUUCCAUG__UUCCCCUGUAGGAUUGCAGCCUUUUGCUUGGCUGCAUUCGCGGGUAACGGCAAUUUGUACUUGCCAC
.......................................(((((.((((.((((((........)))))))))))))))....(((((.......))))).. (-21.96 = -22.43 +   0.47)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:59 2011