Locus 12599

Sequence ID dm3.chrX
Location 1,116,196 – 1,116,295
Length 99
Max. P 0.684117
window17328 window17329

overview

Window 8

Location 1,116,196 – 1,116,295
Length 99
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 83.78
Shannon entropy 0.27909
G+C content 0.44736
Mean single sequence MFE -24.86
Consensus MFE -16.90
Energy contribution -17.54
Covariance contribution 0.64
Combinations/Pair 1.14
Mean z-score -1.72
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.547660
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1116196 99 + 22422827
CGACUAACAAGGUCUCAACUAGAAGCGUAAAUC---AAAGGAUAUGUAGUCGAUCGUCUAUUGAUCGACUACGAGGAACCCGCUGCCCAUAUUCAUGCUUUU
.((((.....))))......((((((((.....---...(((((((((((((((((.....)))))))))))..((..........)))))))))))))))) ( -28.20, z-score =  -2.74, R)
>droEre2.scaffold_4644 1101480 96 + 2521924
CGACUAACAAGGCCUCAACUAGAAGCGUAAAUGUAAAAGGGAUAUGCAGUCGAUCGUCUGUUGAUCGACAAUAAGCAACCCGCUGCCCAGAUUUUA------
...........((.((.....)).))............(((.......((((((((.....))))))))....(((.....))).)))........------ ( -21.10, z-score =  -0.62, R)
>droYak2.chrX 1030915 90 + 21770863
CGACUAACAAGGCGUCAACUAGAAGCGUAA-UAUAAAAAGGAUAUGCAGUCGAUCGUCUAUUGAUCGACAAUGAGGAACCCGCUGCCCAGA-----------
..........((((.(........(((((.-...........))))).((((((((.....))))))))............).))))....----------- ( -20.10, z-score =  -0.84, R)
>droSec1.super_10 950402 99 + 3036183
CGACUAACAAGGUCUCAACUAGAAGCGUAAAUC---AAAGGGUAUGUAGUCGAUCGUCUAUUGAUCGACUACGAGGAACCCGCUGCCCAUAGUCAUGCUAUU
.(((((.....(..((.....))..).......---...(((((((((((((((((.....)))))))))))).((...))..))))).)))))........ ( -31.70, z-score =  -3.25, R)
>droSim1.chrX_random 899771 99 + 5698898
CGACUAACAAGGUCUCAACUAGAAGCGUAAAUC---AAAGGGUAUAUAGUCGACCGUCUAUUGAUCGACUACGAGGAACCCGCUGCCCAUAUUCAUGCUAUU
.((((.....)))).........(((((.(((.---...(((((..(((((((.((.....)).)))))))((.(....))).)))))..))).)))))... ( -23.20, z-score =  -1.13, R)
>consensus
CGACUAACAAGGUCUCAACUAGAAGCGUAAAUC___AAAGGAUAUGUAGUCGAUCGUCUAUUGAUCGACUACGAGGAACCCGCUGCCCAUAUUCAUGCU_UU
..........(((.((.....))((((.................((((((((((((.....)))))))))))).(....))))))))............... (-16.90 = -17.54 +   0.64)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 1,116,196 – 1,116,295
Length 99
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 83.78
Shannon entropy 0.27909
G+C content 0.44736
Mean single sequence MFE -26.50
Consensus MFE -20.38
Energy contribution -20.50
Covariance contribution 0.12
Combinations/Pair 1.20
Mean z-score -1.53
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.684117
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1116196 99 - 22422827
AAAAGCAUGAAUAUGGGCAGCGGGUUCCUCGUAGUCGAUCAAUAGACGAUCGACUACAUAUCCUUU---GAUUUACGCUUCUAGUUGAGACCUUGUUAGUCG
..((((.(((((..(((....(((...)))((((((((((.......))))))))))....)))..---.))))).))))........(((.......))). ( -26.50, z-score =  -1.36, R)
>droEre2.scaffold_4644 1101480 96 - 2521924
------UAAAAUCUGGGCAGCGGGUUGCUUAUUGUCGAUCAACAGACGAUCGACUGCAUAUCCCUUUUACAUUUACGCUUCUAGUUGAGGCCUUGUUAGUCG
------.........(((((((((.(((.....(((((((.......))))))).)))...)))............(((((.....)))))...))).))). ( -27.70, z-score =  -2.15, R)
>droYak2.chrX 1030915 90 - 21770863
-----------UCUGGGCAGCGGGUUCCUCAUUGUCGAUCAAUAGACGAUCGACUGCAUAUCCUUUUUAUA-UUACGCUUCUAGUUGACGCCUUGUUAGUCG
-----------.(((((.(((((....).....(((((((.......))))))).................-...)))))))))..(((.........))). ( -20.30, z-score =  -0.35, R)
>droSec1.super_10 950402 99 - 3036183
AAUAGCAUGACUAUGGGCAGCGGGUUCCUCGUAGUCGAUCAAUAGACGAUCGACUACAUACCCUUU---GAUUUACGCUUCUAGUUGAGACCUUGUUAGUCG
........(((((.((.((((((((.....((((((((((.......))))))))))..))))...---((........))..))))...))....))))). ( -32.20, z-score =  -2.99, R)
>droSim1.chrX_random 899771 99 - 5698898
AAUAGCAUGAAUAUGGGCAGCGGGUUCCUCGUAGUCGAUCAAUAGACGGUCGACUAUAUACCCUUU---GAUUUACGCUUCUAGUUGAGACCUUGUUAGUCG
.........((((.((.((((((((.....((((((((((.......))))))))))..))))...---((........))..))))...)).))))..... ( -25.80, z-score =  -0.81, R)
>consensus
AA_AGCAUGAAUAUGGGCAGCGGGUUCCUCGUAGUCGAUCAAUAGACGAUCGACUACAUAUCCUUU___GAUUUACGCUUCUAGUUGAGACCUUGUUAGUCG
...............((((((((((..(((((((((((((.......))))))))))...................((.....)).)))))).)))).))). (-20.38 = -20.50 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:05:22 2011