Locus 7017

Sequence ID dm3.chr3L
Location 11,527,204 – 11,527,331
Length 127
Max. P 0.982184
window9658 window9659

overview

Window 8

Location 11,527,204 – 11,527,313
Length 109
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 60.88
Shannon entropy 0.74699
G+C content 0.34770
Mean single sequence MFE -25.60
Consensus MFE -6.42
Energy contribution -8.47
Covariance contribution 2.05
Combinations/Pair 1.32
Mean z-score -2.68
Structure conservation index 0.25
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.10
SVM RNA-class probability 0.982184
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11527204 109 + 24543557
CUUUAAAAAACUUAAUUGCUUAGAAUGAACUGCAUGAGUUAGCCUUCAAGCGUUCAUUUGAGCCAUUGAAAAUGAAUAAGUUCA--UUUUGGUUCAUUUUUAAAACUGAUC
.((((((((.............((((((((.((.((((......)))).))))))))))((((((....(((((((....))))--))))))))).))))))))....... ( -26.70, z-score =  -2.91, R)
>droEre2.scaffold_4784 11527602 86 + 25762168
GGGCAAAACACAUAACUGCUU-----------------------UCGAAGCGUUCAUUUUAGCCUUCGGAAAUGAAUAGGUUCA--UUUUGGUUCAUUUUUAAAAGUGAUC
........(((..........-----------------------.(((((.(((......))))))))(((((((((..(....--..)..))))))))).....)))... ( -15.60, z-score =  -0.48, R)
>droYak2.chr3L 11561212 98 + 24197627
GGCCAAAACACUUGAUUGCUUAGAAUGAACG-----------UGUCACAGCGUUCAUUUUAGCCUCUGAAAAUGAACAAGUUCA--UUUGGCUUCAUUUUCAAAAGUGAUC
(((((((..(((((...(((.((((((((((-----------(......)))))))))))))).((.......)).)))))...--)))))))((((((....)))))).. ( -29.80, z-score =  -3.61, R)
>droSec1.super_0 3726801 102 + 21120651
-GUUAUAACACUUGAUUGCUUAGAAUGAACU-CAUGAA-----CUCAAAGCGUUCCUUUGAGCCAUUGAAAAUGAAUGAUUUCA--UUUUGGUUCAUUUUUAAAAGUGAUC
-............(((..(((((((((((((-((....-----(((((((.....)))))))....))((((((((....))))--))))))))))))))...)))..))) ( -26.90, z-score =  -3.40, R)
>droSim1.chr3L 10909919 99 + 22553184
----AUAACACUUGAAUGCUUAGAAUGAACU-CAUGAA-----UUCAAAGCGUUCCUUUGAGCCAUUGAAAAUGAAUGAGUUCA--UUUUGGUUCAUUUUUAAAAGUGAUC
----....((((((((((.((((((((((((-(((...-----(((((.(.((((....))))).))))).....)))))))))--))))))..)))))....)))))... ( -29.20, z-score =  -4.13, R)
>droMoj3.scaffold_6680 18367160 86 + 24764193
-----------------GCUUUGAUUCAGAUUCAGGUUGACUGAAUGCAGCGCUCAGCUGCAAAUUCAAAGUUCACAGAGCAAAGCUUUCAAUUGGGUUUCAU--------
-----------------((((((......((((((.....))))))(((((.....)))))..............)))))).((((((......))))))...-------- ( -25.40, z-score =  -1.57, R)
>consensus
_G__AAAACACUUGAUUGCUUAGAAUGAACU_CAUGA______CUCAAAGCGUUCAUUUGAGCCAUUGAAAAUGAAUAAGUUCA__UUUUGGUUCAUUUUUAAAAGUGAUC
........(((((....((((.((....................)).))))..............((((((((((((.((........)).)))))))))))))))))... ( -6.42 =  -8.47 +   2.05)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,527,225 – 11,527,331
Length 106
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 76.83
Shannon entropy 0.39483
G+C content 0.32597
Mean single sequence MFE -24.76
Consensus MFE -11.28
Energy contribution -13.72
Covariance contribution 2.44
Combinations/Pair 1.18
Mean z-score -2.55
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.903238
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11527225 106 + 24543557
AGAAUGAACUGCAUGAGUUAGCCUUCAAGCGUUCAUUUGAGCCAUUGAAAAUGAAUAAGUUCAUUUUGGUUCAUUUUUAAAACUGAUCACUA---UGAUCAAGAAUUUG
.((((((((.((.((((......)))).))))))))))((((((....(((((((....)))))))))))))...........(((((....---.)))))........ ( -28.20, z-score =  -2.92, R)
>droEre2.scaffold_4784 11527623 86 + 25762168
-----------------------UCGAAGCGUUCAUUUUAGCCUUCGGAAAUGAAUAGGUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACCAGACUGAUGAACAAUUUG
-----------------------((((((.(((......)))))))))..........((((((((((((((((((....))))))..)))))...)))))))...... ( -20.80, z-score =  -2.00, R)
>droYak2.chr3L 11561233 98 + 24197627
AGAAUGAACG-----UG------UCACAGCGUUCAUUUUAGCCUCUGAAAAUGAACAAGUUCAUUUGGCUUCAUUUUCAAAAGUGAUCACAAGACUGAUCCACAAUUUG
((((((((((-----(.------.....)))))))))))......(((((((((.((((....))))...)))))))))...(((((((......)))).)))...... ( -26.40, z-score =  -2.74, R)
>droSec1.super_0 3726821 99 + 21120651
AGAAUGAACU-CAUGAA-----CUCAAAGCGUUCCUUUGAGCCAUUGAAAAUGAAUGAUUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACUA----GAUUAAUAAUUUG
((((((((((-((....-----(((((((.....)))))))....))((((((((....))))))))))))))))))......(((((....----)))))........ ( -22.50, z-score =  -2.27, R)
>droSim1.chr3L 10909936 100 + 22553184
AGAAUGAACU-CAUGAA-----UUCAAAGCGUUCCUUUGAGCCAUUGAAAAUGAAUGAGUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACUA---UGAUCAAUAAUUUG
((((((((((-(((...-----(((((.(.((((....))))).))))).....)))))))))))))................(((((....---.)))))........ ( -25.90, z-score =  -2.80, R)
>consensus
AGAAUGAACU_CAUGAA______UCAAAGCGUUCAUUUGAGCCAUUGAAAAUGAAUAAGUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACUA___UGAUCAACAAUUUG
((((((((((.............((((.(.((((....))))).))))(((((((....))))))).)))))))))).....(((((((......))))).))...... (-11.28 = -13.72 +   2.44)

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 23:18:52 2011