Locus 2958

Sequence ID dm3.chr2R
Location 230,660 – 230,840
Length 180
Max. P 0.899603
window4060 window4061

overview

Window 0

Location 230,660 – 230,772
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 66.72
Shannon entropy 0.60210
G+C content 0.56734
Mean single sequence MFE -42.64
Consensus MFE -16.82
Energy contribution -16.34
Covariance contribution -0.48
Combinations/Pair 1.48
Mean z-score -1.88
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.899603
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 230660 112 + 21146708
ACCCAAGCAGUUCUCACUGAGUAAAAGUGAAGAAUUGCAAGCCA---UAUCCCGUGGCCUGCACGCGCGGUCAGGAAAAUGCUGGUUGUGCACUCCAGGGGCAACGGCCAGGAGC-----
..((..((((((((((((.......)))).))))))))..(((.---...(((.(((..(((((((.(((.((......)))))).))))))..))).)))....)))..))...----- ( -44.40, z-score =  -2.26, R)
>droSec1.super_79 15328 117 + 133581
ACACAAGCAGUUCUCACGGAGUCAGACUGCCGAAUUGCAAGCUG---UAUCCGGUGGCCUGCACGCGCAGCGAGGAUAUUGCUGAUCGCGCAUUCCAAGGGCAAUUGCCCGGAGUCCGCC
......((((..(.(.((((..(((..(((......)))..)))---..))))).)..)))).....((((((.....))))))...(((.(((((..((((....))))))))).))). ( -45.70, z-score =  -1.60, R)
>droSim1.chrU 7081155 107 + 15797150
ACACAAGCAGUUCUCAUGGAGU---------GAAUC-CAGGCCA---UAUCCAGUGGUCUGCACGCGCACUAAGCAAACUGCUGAUCGCGUAUUCCAGGUGCAAUUGCCCGGAGCCCGCA
.....(((((((..(.(((.((---------(....-(((((((---(.....))))))))....))).))).)..)))))))....(((..((((.((.((....))))))))..))). ( -40.50, z-score =  -2.55, R)
>droEre2.scaffold_4784 24528627 120 + 25762168
GCACAAGCGGUUCUUACGGAAAGAUACCGCUGAAUUGCAGGCCACCAUAUCGGAUGGCUUACACGCGCAUCGGAAGAACUGCUGAUCGCGCAUUCCAAGGGCAAUUGCCCGGAGCCCGGU
(((..((((((((((.....)))).))))))....)))((((((((.....)).))))))....(((((((((........))))).)))).((((..((((....))))))))...... ( -46.50, z-score =  -2.44, R)
>droAna3.scaffold_13230 550919 113 - 3602488
GCGAAUGCAGAAUUUAGGAAAAG----UGCCAAAUUGCACACCG---GAUCCGGUGGCCCGCACGCGUAACGAAAGAGGUGCUGACUACGCAUUCCAAGGGCAACUGUCCGCGGACCAGC
((...(((........((((..(----(((......((.(((((---....)))))))..))))((((..(....).(((....))))))).))))..((((....))))))).....)) ( -36.10, z-score =  -0.57, R)
>consensus
ACACAAGCAGUUCUCACGGAGUGA_A_UGCCGAAUUGCAAGCCA___UAUCCGGUGGCCUGCACGCGCAGCGAGAAAACUGCUGAUCGCGCAUUCCAAGGGCAAUUGCCCGGAGCCCGCC
......(((((((..................)))))))..((((..........))))......((((...................)))).((((..((((....))))))))...... (-16.82 = -16.34 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 1

Location 230,737 – 230,840
Length 103
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 65.34
Shannon entropy 0.55997
G+C content 0.61911
Mean single sequence MFE -48.26
Consensus MFE -14.57
Energy contribution -17.32
Covariance contribution 2.75
Combinations/Pair 1.29
Mean z-score -2.30
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.56
SVM RNA-class probability 0.742791
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 230737 103 + 21146708
GCUGGUUGUGCACUCCAGGGGCAACGGCCAGGAGC--------AGCA---GCGGAGCGAGUGAUCG-----GACCGGACGAAGAACUGCUGACCUG-GCUCUUUGGCGGCAGCACUACAG
.(((...((((.(.((((((.....(((((((..(--------((((---((((..(((....)))-----..))).........)))))).))))-))))))))).)...))))..))) ( -42.20, z-score =  -0.98, R)
>droSec1.super_79 15405 114 + 133581
GCUGAUCGCGCAUUCCAAGGGCAAUUGCCCGGAGUCCGCCCGAAACACUCGCGGAGCGAGUGAUCG-----G-CCGGAUACAGGAGUGCUGACUUAAGCGCUCUGCCGAAAACGCUGCAA
((((((((((.(((((..((((....))))))))).))).......((((((...)))))))))))-----)-)(((.....((((((((......)))))))).)))............ ( -51.50, z-score =  -3.26, R)
>droSim1.chrU 7081222 113 + 15797150
GCUGAUCGCGUAUUCCAGGUGCAAUUGCCCGGAGCCCGCACGGAGCACUCGCGGAGCGAGUGAUCG-----G-CCUGACGCAGAAGUGCUGACCUG-GCCUUCUGCCAGCAGUUCUGCUG
((((((((((..((((.((.((....))))))))..))).......((((((...)))))))))))-----)-).....(((((((.(((.....)-)))))))))(((((....))))) ( -52.30, z-score =  -2.40, R)
>droAna3.scaffold_13230 550992 118 - 3602488
GCUGACUACGCAUUCCAAGGGCAACUGUCCGCGGACCAGCCCGGACACUUGCGCAACAAGUGAUCGUUGCUGGCCGGAUACGGAA-UGCUGAAACU-GCAACUGGGUAACUGCGCCGCAG
((.......(((((((..((((....)))).(((.(((((.(((.((((((.....)))))).)))..)))))))).....))))-))).......-))..((((((......))).))) ( -47.04, z-score =  -2.55, R)
>consensus
GCUGAUCGCGCAUUCCAAGGGCAACUGCCCGGAGCCCGCCCGGAACACUCGCGGAGCGAGUGAUCG_____G_CCGGACACAGAAGUGCUGACCUG_GCACUCUGCCAACAGCGCUGCAG
((((.........(((..((((....))))...............((((((.....)))))).............)))....(((((((........)))))))..)))).......... (-14.57 = -17.32 +   2.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:01:00 2011