Locus 1714

Sequence ID dm3.chr2L
Location 13,190,013 – 13,190,149
Length 136
Max. P 0.971827
window2338 window2339 window2340

overview

Window 8

Location 13,190,013 – 13,190,110
Length 97
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 86.80
Shannon entropy 0.22636
G+C content 0.41081
Mean single sequence MFE -25.66
Consensus MFE -19.36
Energy contribution -20.28
Covariance contribution 0.92
Combinations/Pair 1.28
Mean z-score -2.67
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.86
SVM RNA-class probability 0.971827
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13190013 97 - 23011544
CAUUGCGUGCGAAUGGAAAUCUGUCGUUGGAGAAGUGGGAACUUGUCCACAUCCAGACAGACACUAUUAUAAUGCAUUAUU---AAAAGAAGAAUACUAC
...(((((...(((((...((((((..((((...(((((......))))).))))))))))..)))))...))))).....---................ ( -26.90, z-score =  -3.16, R)
>droSim1.chr2L 12984590 94 - 22036055
CAUUGCGUGCGAAUGGAAAUCUGUCGUUGGAGAAGUGGAAACUCGUCCACAUCCAGACAGACACUAUUAUAAUGCAUUAUU---AAAAGAAUGCUAC---
...(((((...(((((...((((((..((((...(((((......))))).))))))))))..)))))...))))).....---.............--- ( -27.80, z-score =  -3.45, R)
>droSec1.super_16 1344686 93 - 1878335
CAUUGCGUGCGAAUGGAAAUCUGUCGUUGGAGAAGUGGAAACUCGUCCACAUCCAGACAGACAUU-UUAUAAUGCAUUAUU---AAAAGAAUGCUAC---
...(((((..(((((....((((((..((((...(((((......))))).))))))))))))))-)....))))).....---.............--- ( -24.90, z-score =  -2.42, R)
>droYak2.chr2L 9613589 96 - 22324452
CAUUGCGUGCGAAUGGAAAUCUGGCGUUGGGGAAGAGGCAACUCCUUCACAUCCAGACAGACACCAUCAUAAUGCAUUAUUU-AAGAAGAAUACUAC---
...(((((....((((...((((...(((((((((((....)).))))...))))).))))..))))....)))))......-..............--- ( -24.10, z-score =  -1.88, R)
>droEre2.scaffold_4929 14390780 97 + 26641161
CAUUGCGUGCGAAUGAAAAACUGGCGUUGGAGAAGAGGAAACUCCUCCACAUCCAGACAGACAUGGUAGUGAUGCAUUAUUUAAAGAAGAAUACUAC---
(((..(.(((..(((.....((((...(((((..(((....))))))))...)))).....))).))))..))).......................--- ( -24.60, z-score =  -2.44, R)
>consensus
CAUUGCGUGCGAAUGGAAAUCUGUCGUUGGAGAAGUGGAAACUCGUCCACAUCCAGACAGACACUAUUAUAAUGCAUUAUU___AAAAGAAUACUAC___
...(((((...(((((...((((((..((((...(((((......))))).))))))))))..)))))...)))))........................ (-19.36 = -20.28 +   0.92)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,190,050 – 13,190,149
Length 99
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 72.91
Shannon entropy 0.52356
G+C content 0.42567
Mean single sequence MFE -24.50
Consensus MFE -10.13
Energy contribution -12.63
Covariance contribution 2.50
Combinations/Pair 1.14
Mean z-score -1.72
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.636517
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13190050 99 + 23011544
CUGUCUGGAUGUGGACAAGUUCCCACUUCUCCAACGACAGAUU-UCCAUUCGCACGCAAUGAAGAU-UAAGAACUUUAAGGCAUGCAAGGAACUAAAAAGU
(((((((((.((((........))))...))))..)))))..(-(((.((.(((.((..(((((..-......)))))..)).)))))))))......... ( -27.10, z-score =  -2.41, R)
>droMoj3.scaffold_6500 12519242 82 + 32352404
-------------------UCUUUUGAAUAGAGACAACAUCUUGCUUAUCGAUAUGAAAUCAAAUUGUAACAAUUUCAAGGCUCACCAGGAACCCACCAGG
-------------------...........(((........(((.(((.((((.((....)).))))))))))........))).((.((......)).)) (  -8.19, z-score =   1.18, R)
>droSim1.chr2L 12984624 98 + 22036055
CUGUCUGGAUGUGGACGAGUUUCCACUUCUCCAACGACAGAUU-UCCAUUCGCACGCAAUGAAGAU-UAAGAACUUUAAGGCAUGCAAGAAACUAAAAAG-
(((((((((.(((((......)))))...))))..)))))...-.......(((.((..(((((..-......)))))..)).)))..............- ( -26.10, z-score =  -2.57, R)
>droSec1.super_16 1344719 99 + 1878335
CUGUCUGGAUGUGGACGAGUUUCCACUUCUCCAACGACAGAUU-UCCAUUCGCACGCAAUGAAGAU-UAAGAACUUUAAGGCAUGCAAGGAACUAAAAAGU
(((((((((.(((((......)))))...))))..)))))..(-(((.((.(((.((..(((((..-......)))))..)).)))))))))......... ( -28.40, z-score =  -2.63, R)
>droYak2.chr2L 9613625 99 + 22324452
CUGUCUGGAUGUGAAGGAGUUGCCUCUUCCCCAACGCCAGAUU-UCCAUUCGCACGCAAUGAAGAU-UAAGAACUUUAGGGCAUGCUGGGAACUACAAUAU
..((((((...((..((((......))))..))...))))))(-((((...(((.((..(((((..-......)))))..)).)))))))).......... ( -26.50, z-score =  -0.96, R)
>droEre2.scaffold_4929 14390817 99 - 26641161
CUGUCUGGAUGUGGAGGAGUUUCCUCUUCUCCAACGCCAGUUU-UUCAUUCGCACGCAAUGAAGAU-UAAGAACUUUAAGGCAUGCAACGUACUACUACGU
....((((...((((((((......))))))))...))))...-.......(((.((..(((((..-......)))))..)).))).(((((....))))) ( -30.70, z-score =  -2.92, R)
>consensus
CUGUCUGGAUGUGGACGAGUUUCCACUUCUCCAACGACAGAUU_UCCAUUCGCACGCAAUGAAGAU_UAAGAACUUUAAGGCAUGCAAGGAACUAAAAAGU
..(((((....((((.(((......))).))))....))))).........(((.((..(((((.........)))))..)).)))............... (-10.13 = -12.63 +   2.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,190,050 – 13,190,149
Length 99
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 72.91
Shannon entropy 0.52356
G+C content 0.42567
Mean single sequence MFE -26.57
Consensus MFE -9.90
Energy contribution -11.10
Covariance contribution 1.20
Combinations/Pair 1.39
Mean z-score -1.97
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.668239
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13190050 99 - 23011544
ACUUUUUAGUUCCUUGCAUGCCUUAAAGUUCUUA-AUCUUCAUUGCGUGCGAAUGGA-AAUCUGUCGUUGGAGAAGUGGGAACUUGUCCACAUCCAGACAG
.........((((((((((((..(.(((......-..))).)..))))))))..)))-)..(((((..((((...(((((......))))).))))))))) ( -29.50, z-score =  -2.60, R)
>droMoj3.scaffold_6500 12519242 82 - 32352404
CCUGGUGGGUUCCUGGUGAGCCUUGAAAUUGUUACAAUUUGAUUUCAUAUCGAUAAGCAAGAUGUUGUCUCUAUUCAAAAGA-------------------
...(((((((((.....))))).((((((((........))))))))))))(((((........))))).............------------------- ( -12.80, z-score =   1.10, R)
>droSim1.chr2L 12984624 98 - 22036055
-CUUUUUAGUUUCUUGCAUGCCUUAAAGUUCUUA-AUCUUCAUUGCGUGCGAAUGGA-AAUCUGUCGUUGGAGAAGUGGAAACUCGUCCACAUCCAGACAG
-.......(((((((((((((..(.(((......-..))).)..)))))))...)))-)))(((((..((((...(((((......))))).))))))))) ( -28.70, z-score =  -2.83, R)
>droSec1.super_16 1344719 99 - 1878335
ACUUUUUAGUUCCUUGCAUGCCUUAAAGUUCUUA-AUCUUCAUUGCGUGCGAAUGGA-AAUCUGUCGUUGGAGAAGUGGAAACUCGUCCACAUCCAGACAG
.........((((((((((((..(.(((......-..))).)..))))))))..)))-)..(((((..((((...(((((......))))).))))))))) ( -30.40, z-score =  -3.28, R)
>droYak2.chr2L 9613625 99 - 22324452
AUAUUGUAGUUCCCAGCAUGCCCUAAAGUUCUUA-AUCUUCAUUGCGUGCGAAUGGA-AAUCUGGCGUUGGGGAAGAGGCAACUCCUUCACAUCCAGACAG
.........((((..((((((....(((......-..)))....))))))....)))-).(((((...((.(((.(((....))).))).)).)))))... ( -27.50, z-score =  -1.28, R)
>droEre2.scaffold_4929 14390817 99 + 26641161
ACGUAGUAGUACGUUGCAUGCCUUAAAGUUCUUA-AUCUUCAUUGCGUGCGAAUGAA-AAACUGGCGUUGGAGAAGAGGAAACUCCUCCACAUCCAGACAG
.((((....))))((((((((..(.(((......-..))).)..)))))))).....-...((((...(((((..(((....))))))))...)))).... ( -30.50, z-score =  -2.92, R)
>consensus
ACUUUUUAGUUCCUUGCAUGCCUUAAAGUUCUUA_AUCUUCAUUGCGUGCGAAUGGA_AAUCUGUCGUUGGAGAAGAGGAAACUCGUCCACAUCCAGACAG
.............((((((((..(.(((.........))).)..)))))))).........(((...(((((.....(((......)))...))))).))) ( -9.90 = -11.10 +   1.20)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:37:11 2011