Locus 7637

Sequence ID dm3.chr3L
Location 16,147,901 – 16,148,034
Length 133
Max. P 0.969409
window10511 window10512 window10513 window10514

overview

Window 1

Location 16,147,901 – 16,148,005
Length 104
Sequences 7
Columns 112
Reading direction forward
Mean pairwise identity 72.61
Shannon entropy 0.52448
G+C content 0.48010
Mean single sequence MFE -32.54
Consensus MFE -16.01
Energy contribution -16.54
Covariance contribution 0.53
Combinations/Pair 1.25
Mean z-score -2.00
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956477
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16147901 104 + 24543557
---CUGUCUGCGCUCCAGUUUCUUCGGCUCGGAUGAUUUUCCAGCUGAGAAUGAUAUAUGGC-----AGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCA
---(((.((((........((((.(((((.(((......)))))))))))).........))-----)).)))...(((((((..((((((.....))))))..))))))). ( -35.63, z-score =  -2.76, R)
>droSim1.chr3L 15481138 107 + 22553184
CUGCUGUCUGCGCUCCAGUUUCUUCGGCUCGGAUGAUUUUCCAGCUCGGAAUGAUAUAUGGC-----AGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCA
..((((.((((.(....(((..(((((((.(((......)))))).))))..)))....)))-----)).))))..(((((((..((((((.....))))))..))))))). ( -38.70, z-score =  -3.20, R)
>droSec1.super_0 8247471 104 + 21120651
---CUGUCUGCGCUCCAGUUUCUUCGGCUCGGAUGAUUUUCCAGCUCGGAAUGAUAUAUGAC-----AGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCA
---(((((.........(((((...((((.(((......))))))).))))).......)))-----)).......(((((((..((((((.....))))))..))))))). ( -31.99, z-score =  -2.05, R)
>droYak2.chr3L 2172365 104 - 24197627
---CUGUCAGCGCUCCAGUUUCUUCGGCUCGGAUGAUUUUCCAGGCCAGAAUGAUAUAUGGC-----AGUGAGCUGGGCGUAUACGUAAUACCAUCGAUUACUCAUACGCCA
---....((((((((((...((((((((..(((......)))..))).))).))....))).-----)))..))))(((((((..(((((.......)))))..))))))). ( -37.30, z-score =  -3.02, R)
>droEre2.scaffold_4784 18395253 104 + 25762168
---CUGUCUGCGCUCCAGUUUCUUCGGCUCGGAUGAUUUUCCAGCUCAGAAUGAUAUAUGGC-----AGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCA
---(((.((((........((((..((((.(((......))))))).)))).........))-----)).)))...(((((((..((((((.....))))))..))))))). ( -32.23, z-score =  -2.04, R)
>droVir3.scaffold_13049 1119505 90 + 25233164
--------CGUGCUC-AGCU--UUUGGCUUGGCCCGUGCUCAAUGGCUGUUCGUUUCGCUGG-----AAUU-GCGCUGCGUAUACGUAAUAU-----AUUACUCAUACGCAG
--------.((((.(-((((--.(((((.........)).))).)))))((((......)))-----)...-))))(((((((..((((...-----.))))..))))))). ( -25.10, z-score =  -0.21, R)
>droGri2.scaffold_15110 2258626 104 + 24565398
----UGCCAAAGUUU-UGCUGUUUGUUGUCAAGCUGUUUUCUGUGUGUGCUCGCCACAUGACGUCAAAGUCAUCGUUGCGUAUACGUAAUGGAU---AUUACUCAUACGCAG
----...........-.((.(((((....))))).))...(((((((((..(((.(((((((......))))).)).))).....(((((....---))))).))))))))) ( -26.80, z-score =  -0.68, R)
>consensus
___CUGUCUGCGCUCCAGUUUCUUCGGCUCGGAUGAUUUUCCAGCUCAGAAUGAUAUAUGGC_____AGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCA
.....(((((.(((...........))).)))))..........................................(((((((..(((((.......)))))..))))))). (-16.01 = -16.54 +   0.53)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,147,901 – 16,148,005
Length 104
Sequences 7
Columns 112
Reading direction reverse
Mean pairwise identity 72.61
Shannon entropy 0.52448
G+C content 0.48010
Mean single sequence MFE -29.98
Consensus MFE -15.83
Energy contribution -16.04
Covariance contribution 0.21
Combinations/Pair 1.26
Mean z-score -1.93
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.81
SVM RNA-class probability 0.969409
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16147901 104 - 24543557
UGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACU-----GCCAUAUAUCAUUCUCAGCUGGAAAAUCAUCCGAGCCGAAGAAACUGGAGCGCAGACAG---
.((((((((.((((((.....)))))).)))))))).......((-----((.........(((((.((((((......))).))).).))))........))))....--- ( -31.23, z-score =  -2.09, R)
>droSim1.chr3L 15481138 107 - 22553184
UGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACU-----GCCAUAUAUCAUUCCGAGCUGGAAAAUCAUCCGAGCCGAAGAAACUGGAGCGCAGACAGCAG
.((((((((.((((((.....)))))).))))))))..(((..((-----((.........(((((.((((((......))).)))))..)))........))))..))).. ( -33.73, z-score =  -2.44, R)
>droSec1.super_0 8247471 104 - 21120651
UGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACU-----GUCAUAUAUCAUUCCGAGCUGGAAAAUCAUCCGAGCCGAAGAAACUGGAGCGCAGACAG---
.((((((((.((((((.....)))))).)))))))).......((-----(((.....((.(((((.((((((......))).)))))..)))....)).....)))))--- ( -31.80, z-score =  -2.25, R)
>droYak2.chr3L 2172365 104 + 24197627
UGGCGUAUGAGUAAUCGAUGGUAUUACGUAUACGCCCAGCUCACU-----GCCAUAUAUCAUUCUGGCCUGGAAAAUCAUCCGAGCCGAAGAAACUGGAGCGCUGACAG---
.((((((((.((((((....).))))).))))))))((((...((-----.(((....((.(((.(((.((((......)))).))))))))...))))).))))....--- ( -33.00, z-score =  -2.20, R)
>droEre2.scaffold_4784 18395253 104 - 25762168
UGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACU-----GCCAUAUAUCAUUCUGAGCUGGAAAAUCAUCCGAGCCGAAGAAACUGGAGCGCAGACAG---
.((((((((.((((((.....)))))).)))))))).......((-----((.........((((..((((((......))).)))...))))........))))....--- ( -31.13, z-score =  -2.06, R)
>droVir3.scaffold_13049 1119505 90 - 25233164
CUGCGUAUGAGUAAU-----AUAUUACGUAUACGCAGCGC-AAUU-----CCAGCGAAACGAACAGCCAUUGAGCACGGGCCAAGCCAAA--AGCU-GAGCACG--------
(((((((((.((((.-----...)))).)))))))))(((-....-----...)))....(..((((..(((.((.........))))).--.)))-)..)...-------- ( -25.30, z-score =  -1.73, R)
>droGri2.scaffold_15110 2258626 104 - 24565398
CUGCGUAUGAGUAAU---AUCCAUUACGUAUACGCAACGAUGACUUUGACGUCAUGUGGCGAGCACACACAGAAAACAGCUUGACAACAAACAGCA-AAACUUUGGCA----
.((((((((.(((((---....))))).))))))))...(((((......)))))((..(((((..............)))))...)).....((.-........)).---- ( -23.64, z-score =  -0.75, R)
>consensus
UGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACU_____GCCAUAUAUCAUUCUGAGCUGGAAAAUCAUCCGAGCCGAAGAAACUGGAGCGCAGACAG___
.((((((((.(((((.......))))).))))))))..(((............................((((......))))..(((.......))))))........... (-15.83 = -16.04 +   0.21)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,147,931 – 16,148,034
Length 103
Sequences 7
Columns 108
Reading direction forward
Mean pairwise identity 73.78
Shannon entropy 0.50476
G+C content 0.47512
Mean single sequence MFE -31.26
Consensus MFE -18.37
Energy contribution -17.94
Covariance contribution -0.42
Combinations/Pair 1.27
Mean z-score -1.48
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.21
SVM RNA-class probability 0.909573
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16147931 103 + 24543557
UGAUUUUCCAGCUGAGAAUGAUAU-----AUGGCAGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCACGGGUCACAGAGCCGUGGAAUUGCGUUGU
.......((((((((...((....-----....)).))))))))((((((..((((((.....))))))..)))).((((((.((...)).))))))....))..... ( -33.70, z-score =  -1.95, R)
>droSim1.chr3L 15481171 103 + 22553184
UGAUUUUCCAGCUCGGAAUGAUAU-----AUGGCAGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCACGGGUCACAGCGCCGGCGAAUUGCGUUGU
.....((((.....))))......-----...((((((.((..(((((((..((((((.....))))))..))))))).(((((....)).))))).))))))..... ( -32.40, z-score =  -0.86, R)
>droSec1.super_0 8247501 103 + 21120651
UGAUUUUCCAGCUCGGAAUGAUAU-----AUGACAGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCACGGGUCACAGCGCCGGCGAAUUGCGUUGU
..........(((((.........-----....(((....)))(((((((..((((((.....))))))..))))))).))))).(((((((.........))))))) ( -32.10, z-score =  -1.21, R)
>droYak2.chr3L 2172395 103 - 24197627
UGAUUUUCCAGGCCAGAAUGAUAU-----AUGGCAGUGAGCUGGGCGUAUACGUAAUACCAUCGAUUACUCAUACGCCACGGGUCACAGCGCCGGGGAAUUGCGUUGU
.((((..((..((((.........-----.)))).((((.((((((((((..(((((.......)))))..))))))).))).))))......))..))))....... ( -37.40, z-score =  -2.42, R)
>droEre2.scaffold_4784 18395283 103 + 25762168
UGAUUUUCCAGCUCAGAAUGAUAU-----AUGGCAGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCACGGGUCACAGCGCCAAGGAAUUGCGUUGU
.(((((..(((((.....((....-----....))...)))))(((((((..((((((.....))))))..)))))))..)))))(((((((.((....))))))))) ( -31.50, z-score =  -1.71, R)
>droVir3.scaffold_13049 1119527 91 + 25233164
CCGUGCUCAAUGGCUGUUCGUUUC-----GCUGGAAUUG-CGCUGCGUAUACGUAAU---AU--AUUACUCAUACGCAGACA---ACAAUGC---GAAAUUGCGUUUU
((((.....))))..((..(((((-----((.....(((-..((((((((..((((.---..--.))))..)))))))).))---)....))---))))).))..... ( -24.80, z-score =  -0.83, R)
>droGri2.scaffold_15110 2258654 100 + 24565398
CUGUUUUCUGUGUGUGCUCGCCACAUGACGUCAAAGUCAUCGUUGCGUAUACGUAAUGG-AU--AUUACUCAUACGCAGCAAU--AAAAUGC---GAAAUUGCGUCUC
.........(((((.(....))))))((((.(((..((.....(((((((..(((((..-..--)))))..)))))))(((..--....)))---))..))))))).. ( -26.90, z-score =  -1.40, R)
>consensus
UGAUUUUCCAGCUCAGAAUGAUAU_____AUGGCAGUUAGCUGGGCGUAUACGUAAUCCCAUCGAUUACUCAUACGCCACGGGUCACAGCGCCGGGGAAUUGCGUUGU
.................................(((....)))(((((((..(((((.......)))))..))))))).......(((((((.........))))))) (-18.37 = -17.94 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,147,931 – 16,148,034
Length 103
Sequences 7
Columns 108
Reading direction reverse
Mean pairwise identity 73.78
Shannon entropy 0.50476
G+C content 0.47512
Mean single sequence MFE -29.26
Consensus MFE -15.53
Energy contribution -15.53
Covariance contribution 0.00
Combinations/Pair 1.17
Mean z-score -1.46
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.797228
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16147931 103 - 24543557
ACAACGCAAUUCCACGGCUCUGUGACCCGUGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACUGCCAU-----AUAUCAUUCUCAGCUGGAAAAUCA
............(((((.((...)).)))))(((((((.((((((.....)))))).)))))))((((((.........-----...........))))))....... ( -29.65, z-score =  -1.72, R)
>droSim1.chr3L 15481171 103 - 22553184
ACAACGCAAUUCGCCGGCGCUGUGACCCGUGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACUGCCAU-----AUAUCAUUCCGAGCUGGAAAAUCA
........(((..(((((...((((...(.((((((((.((((((.....)))))).))))))))).((.....))...-----...)))).....)))))..))).. ( -31.00, z-score =  -1.02, R)
>droSec1.super_0 8247501 103 - 21120651
ACAACGCAAUUCGCCGGCGCUGUGACCCGUGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACUGUCAU-----AUAUCAUUCCGAGCUGGAAAAUCA
........(((..(((((..((((((..(.((((((((.((((((.....)))))).)))))))))((....)))))))-----)..((.....)))))))..))).. ( -30.60, z-score =  -0.92, R)
>droYak2.chr3L 2172395 103 + 24197627
ACAACGCAAUUCCCCGGCGCUGUGACCCGUGGCGUAUGAGUAAUCGAUGGUAUUACGUAUACGCCCAGCUCACUGCCAU-----AUAUCAUUCUGGCCUGGAAAAUCA
.........((((..(((((.((((.(.(.((((((((.((((((....).))))).))))))))).).)))).))((.-----(......).))))).))))..... ( -29.00, z-score =  -0.82, R)
>droEre2.scaffold_4784 18395283 103 - 25762168
ACAACGCAAUUCCUUGGCGCUGUGACCCGUGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACUGCCAU-----AUAUCAUUCUGAGCUGGAAAAUCA
.........((((..(((.(.((((...(.((((((((.((((((.....)))))).))))))))).((.....))...-----...))))...).)))))))..... ( -28.90, z-score =  -1.04, R)
>droVir3.scaffold_13049 1119527 91 - 25233164
AAAACGCAAUUUC---GCAUUGU---UGUCUGCGUAUGAGUAAU--AU---AUUACGUAUACGCAGCG-CAAUUCCAGC-----GAAACGAACAGCCAUUGAGCACGG
.....((..((((---((...((---((((((((((((.((((.--..---.)))).))))))))).)-))))....))-----))))(((.......))).)).... ( -27.20, z-score =  -2.26, R)
>droGri2.scaffold_15110 2258654 100 - 24565398
GAGACGCAAUUUC---GCAUUUU--AUUGCUGCGUAUGAGUAAU--AU-CCAUUACGUAUACGCAACGAUGACUUUGACGUCAUGUGGCGAGCACACACAGAAAACAG
..(((((((..((---(((....--..)))((((((((.(((((--..-..))))).)))))))).....))..))).)))).((((.......)))).......... ( -28.50, z-score =  -2.48, R)
>consensus
ACAACGCAAUUCCCCGGCGCUGUGACCCGUGGCGUAUGAGUAAUCGAUGGGAUUACGUAUACGCCCAGCUAACUGCCAU_____AUAUCAUUCUGAGCUGGAAAAUCA
...............(((...((.......((((((((.(((((.......))))).))))))))......)).)))............................... (-15.53 = -15.53 +   0.00)

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 23:30:40 2011