Locus 9254

Sequence ID dm3.chr3R
Location 5,252,314 – 5,252,437
Length 123
Max. P 0.939984
window12683 window12684 window12685

overview

Window 3

Location 5,252,314 – 5,252,412
Length 98
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 77.33
Shannon entropy 0.38530
G+C content 0.62208
Mean single sequence MFE -40.10
Consensus MFE -26.28
Energy contribution -27.32
Covariance contribution 1.04
Combinations/Pair 1.18
Mean z-score -1.76
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.878286
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5252314 98 - 27905053
-------CCGGAACCCAGAGUCACUGGAGUCACUGGGCAUUUUUGUUACGCCCCCGCUCUCAACCGUAGGGAUAAGUAGGGGGUGUGGCACUCGGAUGGGGCGGG
-------(((...((((((.((....)).)).(((((......((((((((((((...((...((....))...))..))))))))))))))))).)))).))). ( -40.40, z-score =  -1.17, R)
>droSim1.chr3R 11441529 89 + 27517382
--------------CCGUA--CUCCGGAGUCACUGGGCAUUUUUGUAACGCCCCCGCUCUCAACAGUGAGGAUAAGUAGGGGGCGUGGCACUCGGAUGGGGCGGG
--------------((((.--((((((.(((((...(((....)))...(((((((((((((....))))....))).))))))))))).).)))).)..)))). ( -37.70, z-score =  -1.78, R)
>droSec1.super_0 4477233 84 + 21120651
---------------------CACUGGAGUCACUGGGCAUUUUUGUAACGCCCCCGCUCUCAACAGUGAGGAUAAGUAGGGGGCGUGGCACUCGGAUGGGGCGGG
---------------------..((.(..((((((((......(((.(((((((((((((((....))))....))).)))))))).)))))))).)))..).)) ( -31.30, z-score =  -1.08, R)
>droYak2.chr3R 9299535 94 - 28832112
-------CCGGUCUCCGGACU--CCGGAGUCACUGGGCUUUUUUGUUACGCCCAGGCUCUCAACGGUAAGGAUAAGUAGGGGGCGUGGCACUCGGAUGGUGGG--
-------(((((((((((...--))))))..)))))(((.(((((((((((((..(((.....(.....)....)))...))))))))))...))).)))...-- ( -34.50, z-score =  -0.37, R)
>droEre2.scaffold_4770 1395248 102 + 17746568
CGGGGCUCGGGACUCCGGACUCACUGGAGUCACUGGGC-UUUUUGUUACGCCCCCGCUCUCAGCGGAAAGCGUAGGCAGGGGGCGUGGCACUCGGAUGGUGGG--
((((((((((((((((((.....)))))))).))))))-....(((((((((((((((..(.((.....)))..))).)))))))))))))))).........-- ( -56.60, z-score =  -4.41, R)
>consensus
_______C_GG___CCGGA_UCACUGGAGUCACUGGGCAUUUUUGUUACGCCCCCGCUCUCAACAGUAAGGAUAAGUAGGGGGCGUGGCACUCGGAUGGGGCGGG
..............((((.....))))..((((((((......(((((((((((((((.....(.....)....))).))))))))))))))))).)))...... (-26.28 = -27.32 +   1.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,252,342 – 5,252,437
Length 95
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 77.51
Shannon entropy 0.38151
G+C content 0.53257
Mean single sequence MFE -34.58
Consensus MFE -16.06
Energy contribution -16.26
Covariance contribution 0.20
Combinations/Pair 1.11
Mean z-score -2.76
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.44
SVM RNA-class probability 0.939984
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5252342 95 + 27905053
ACUUAUCCCUACGGUUGAGAGCGGGGGCGUAACAAAAAUGCCCAGUGACUCCAGUGACUCUGGGUUCC-------GGAUUCCGGAAUCCAGACAGUUAUCAA
.((((.((....)).)))).((..((((((.......)))))).)).......(((((((((((((((-------((...))))))))))))..)))))... ( -35.50, z-score =  -2.47, R)
>droSim1.chr3R 11441557 86 - 27517382
ACUUAUCCUCACUGUUGAGAGCGGGGGCGUUACAAAAAUGCCCAGUGACUCCGGAGUAC----------------GGAUUCCGGAAUCCGGACAGUUAUCAA
..........((((((..((((..(((((((.....))))))).))...((((((((..----------------..)))))))).))..))))))...... ( -29.30, z-score =  -1.84, R)
>droSec1.super_0 4477261 81 - 21120651
ACUUAUCCUCACUGUUGAGAGCGGGGGCGUUACAAAAAUGCCCAGUGACUCCAGUGAA---------------------UCCGGAAUCCGGACAGUUAUCAA
........((((((..(((.((..(((((((.....))))))).))..))))))))).---------------------(((((...))))).......... ( -27.90, z-score =  -2.54, R)
>droYak2.chr3R 9299561 93 + 28832112
ACUUAUCCUUACCGUUGAGAGCCUGGGCGUAACAAAAAAGCCCAGUGACUCCGGAGUCC--GGAGACC-------GGAGUCCGGUAUCCGGACAGUUAUCAA
...........(((....((((((((((...........)))))).).)))))).((((--(((.(((-------((...))))).)))))))......... ( -38.80, z-score =  -3.93, R)
>droEre2.scaffold_4770 1395274 101 - 17746568
GCCUACGCUUUCCGCUGAGAGCGGGGGCGUAACAAAAA-GCCCAGUGACUCCAGUGAGUCCGGAGUCCCGAGCCCCGAGUCCGGAAUCCGGACAGUUAUCAA
(((..(((((((....)))))))..)))(((((.....-...((.((....)).)).(((((((...(((..(.....)..)))..))))))).)))))... ( -41.40, z-score =  -3.05, R)
>consensus
ACUUAUCCUUACCGUUGAGAGCGGGGGCGUAACAAAAAUGCCCAGUGACUCCAGUGAAC__GG___CC_______GGAGUCCGGAAUCCGGACAGUUAUCAA
..............(((.((((..((((((.......))))))...).)))))).........................(((((...))))).......... (-16.06 = -16.26 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,252,342 – 5,252,437
Length 95
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 77.51
Shannon entropy 0.38151
G+C content 0.53257
Mean single sequence MFE -33.02
Consensus MFE -18.89
Energy contribution -18.73
Covariance contribution -0.16
Combinations/Pair 1.18
Mean z-score -1.93
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.793989
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5252342 95 - 27905053
UUGAUAACUGUCUGGAUUCCGGAAUCC-------GGAACCCAGAGUCACUGGAGUCACUGGGCAUUUUUGUUACGCCCCCGCUCUCAACCGUAGGGAUAAGU
.((((.....(((((.((((((...))-------)))).))))))))).((((((....((((...........))))..)))).)).((....))...... ( -27.60, z-score =  -0.28, R)
>droSim1.chr3R 11441557 86 + 27517382
UUGAUAACUGUCCGGAUUCCGGAAUCC----------------GUACUCCGGAGUCACUGGGCAUUUUUGUAACGCCCCCGCUCUCAACAGUGAGGAUAAGU
........(((((.(((((((((....----------------....)))))))))...((((.((.....)).)))).((((......)))).)))))... ( -28.10, z-score =  -1.87, R)
>droSec1.super_0 4477261 81 + 21120651
UUGAUAACUGUCCGGAUUCCGGA---------------------UUCACUGGAGUCACUGGGCAUUUUUGUAACGCCCCCGCUCUCAACAGUGAGGAUAAGU
........(((((.((((((((.---------------------....))))))))...((((.((.....)).)))).((((......)))).)))))... ( -24.10, z-score =  -1.19, R)
>droYak2.chr3R 9299561 93 - 28832112
UUGAUAACUGUCCGGAUACCGGACUCC-------GGUCUCC--GGACUCCGGAGUCACUGGGCUUUUUUGUUACGCCCAGGCUCUCAACGGUAAGGAUAAGU
........(((((...(((((((((((-------((((...--.))..)))))))).((((((...........))))))........))))).)))))... ( -38.50, z-score =  -3.06, R)
>droEre2.scaffold_4770 1395274 101 + 17746568
UUGAUAACUGUCCGGAUUCCGGACUCGGGGCUCGGGACUCCGGACUCACUGGAGUCACUGGGC-UUUUUGUUACGCCCCCGCUCUCAGCGGAAAGCGUAGGC
.........((((((...))))))..(((((((((((((((((.....)))))))).))))))-)))...((((((..((((.....))))...)))))).. ( -46.80, z-score =  -3.24, R)
>consensus
UUGAUAACUGUCCGGAUUCCGGAAUCC_______GG___CC__AGUCACUGGAGUCACUGGGCAUUUUUGUUACGCCCCCGCUCUCAACAGUAAGGAUAAGU
........(((((.((((((((..........................))))))))...((((...........))))................)))))... (-18.89 = -18.73 +  -0.16)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:00:49 2011