Locus 5274

Sequence ID dm3.chr2R
Location 19,121,568 – 19,121,684
Length 116
Max. P 0.985884
window7226 window7227

overview

Window 6

Location 19,121,568 – 19,121,675
Length 107
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 91.43
Shannon entropy 0.14437
G+C content 0.40505
Mean single sequence MFE -26.54
Consensus MFE -23.58
Energy contribution -23.90
Covariance contribution 0.32
Combinations/Pair 1.11
Mean z-score -2.20
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.62
SVM RNA-class probability 0.955743
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19121568 107 - 21146708
AAAAAAAAAAAGGUGUGAACUUGU--GGGUUUUCAGUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGAUGGCAUUAGUUAUGGGAACCAAAUCAUCGGAUGAA
............((((((((((.(--((((((.....)))))))..)))))))))).....(((..((..(((((.......)))))..)).))).............. ( -23.70, z-score =  -1.60, R)
>droEre2.scaffold_4845 20490436 98 - 22589142
--------AAAGGUGUGAACUUGU--GGGCAUUCAGUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGUUGGCAUUAGUUAUGGGAA-CAAGCCAUCGGCUGAA
--------....((((((((((.(--((((.........)))))..))))))))))........(((........))).((((((((((...-....)))).)))))). ( -27.30, z-score =  -1.56, R)
>droYak2.chr2R 19086453 101 - 21139217
-------AAAAGGUGUGAACUUGUGGGGGUUUUCAGUGAGCUUUAAGAGUUCACGCAAAAAUGGGCUUAAAUGUUGGCAUUAGUUAUGGGAA-CAAGCCAUCGGAUGAA
-------.....((((((((((...(((((((.....)))))))..)))))))))).......(((((.((((....))))......(....-)))))).......... ( -28.50, z-score =  -2.44, R)
>droSec1.super_9 2415176 98 - 3197100
--------AAAGGUGUGAACUUGU--GGGUUUUCAGUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGGUGGCAUUAGUUAUGGGAA-CAAGUCAUCGGAUGAA
--------....((((((((((.(--((((((.....)))))))..)))))))))).......(((((...(.(((((....))))).)...-.))))).......... ( -26.20, z-score =  -2.55, R)
>droSim1.chr2R 17703606 98 - 19596830
--------AAAAGUGUGAACUUGU--GGGUUUUCAGUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGGUGGCAUUAGUUAUGGGGA-CAAGUCAUCGGAUGAA
--------....((((((((((.(--((((((.....)))))))..)))))))))).......(((((.....(((((....)))))(....-)))))).......... ( -27.00, z-score =  -2.85, R)
>consensus
________AAAGGUGUGAACUUGU__GGGUUUUCAGUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGGUGGCAUUAGUUAUGGGAA_CAAGUCAUCGGAUGAA
............((((((((((....((((((.....))))))...)))))))))).......(((((...(.(((((....))))).).....))))).......... (-23.58 = -23.90 +   0.32)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 19,121,577 – 19,121,684
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.48
Shannon entropy 0.47756
G+C content 0.41476
Mean single sequence MFE -29.00
Consensus MFE -16.59
Energy contribution -17.35
Covariance contribution 0.76
Combinations/Pair 1.24
Mean z-score -2.25
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.22
SVM RNA-class probability 0.985884
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19121577 107 - 21146708
GGCCCAAAAAAAAAAAAAAAGGUGUGAACUUGU--GGGUUUUCA--GUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGAUGGCAUUAGUUAUGGGAACCAAAUCA---------
((((((...............((((((((((.(--((((((...--..)))))))..))))))))))........(((........)))........))))..))......--------- ( -28.10, z-score =  -2.36, R)
>droEre2.scaffold_4845 20490445 98 - 22589142
GGCCC--------AAAAAAAGGUGUGAACUUGU--GGGCAUUCA--GUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGUUGGCAUUAGUUAUGGGAA-CAAGCCA---------
(((((--------(.......((((((((((.(--((((.....--....)))))..)))))))))).....)))))).......((((.((.(((.....))-)))))))--------- ( -30.60, z-score =  -2.32, R)
>droYak2.chr2R 19086462 101 - 21139217
GGCCC-------AAAAAAAAGGUGUGAACUUGUGGGGGUUUUCA--GUGAGCUUUAAGAGUUCACGCAAAAAUGGGCUUAAAUGUUGGCAUUAGUUAUGGGAA-CAAGCCA---------
(((((-------(........((((((((((...(((((((...--..)))))))..)))))))))).....)))))).......((((.((.(((.....))-)))))))--------- ( -32.32, z-score =  -2.65, R)
>droSec1.super_9 2415185 98 - 3197100
GGCCC--------AAAAAAAGGUGUGAACUUGU--GGGUUUUCA--GUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGGUGGCAUUAGUUAUGGGAA-CAAGUCA---------
(((((--------(.......((((((((((.(--((((((...--..)))))))..)))))))))).....))))))....(.(((((....))))).)...-.......--------- ( -29.90, z-score =  -2.80, R)
>droSim1.chr2R 17703615 98 - 19596830
GGCCC--------AAGAAAAAGUGUGAACUUGU--GGGUUUUCA--GUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGGUGGCAUUAGUUAUGGGGA-CAAGUCA---------
(((((--------(.......((((((((((.(--((((((...--..)))))))..)))))))))).....))))))......(((((....)))))(....-)......--------- ( -29.90, z-score =  -2.69, R)
>droVir3.scaffold_12875 3105430 104 - 20611582
------------ACCUUAAAUCAGAGCUCUUGUCGUUGUUUCCAUUGUGAGCACGCGACAACAACAUGAAACU----UAAGGUGUGAGCGCAAUUCAAGGUAAUAAAUUUGAAGAAGCCC
------------(((((((.(((......((((((((((((.......))))).))))))).....)))...)----))))))....((....((((((........))))))...)).. ( -23.20, z-score =  -0.68, R)
>consensus
GGCCC________AAAAAAAGGUGUGAACUUGU__GGGUUUUCA__GUGAGCUUAAAGAGUUCACGCAAAAAUGGGCUUAAAUGUUGGCAUUAGUUAUGGGAA_CAAGUCA_________
(((((................((((((((((....((((((.......))))))...))))))))))......)))))..((((....))))............................ (-16.59 = -17.35 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:45:05 2011