Locus 5866

Sequence ID dm3.chr3L
Location 1,913,604 – 1,913,706
Length 102
Max. P 0.971249
window8068 window8069

overview

Window 8

Location 1,913,604 – 1,913,706
Length 102
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 79.04
Shannon entropy 0.36514
G+C content 0.36426
Mean single sequence MFE -23.54
Consensus MFE -13.74
Energy contribution -15.18
Covariance contribution 1.44
Combinations/Pair 1.14
Mean z-score -2.57
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.82
SVM RNA-class probability 0.969437
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1913604 102 + 24543557
AAUAACAUUUACUUAACAGUAUCUACAGGUAGCCAACAGAAACU---AGUUUCUCUGCU--UAACAUAGCAAGGCCCGACACAUAAUCAGAUACUGUUAAGGUUGAG
...........(((((((((((((...((..(((...(((((..---..))))).((((--......)))).)))))((.......)))))))))))))))...... ( -28.90, z-score =  -4.37, R)
>droEre2.scaffold_4784 1902339 107 + 25762168
AAUAACAUUUAUUUGACAGUAUCUACAAGUUUCCAGCAGAAACUGCAAUUAUUGUUGCUGCUAACAUAGCACUGCUCGCCACAUAAUCAGAUACUGUUAAAGCUGAG
...........(((((((((((((....((..(.(((((.....(((((....)))))(((((...)))))))))).)..))......)))))))))))))...... ( -28.90, z-score =  -3.24, R)
>droYak2.chr3L 1867550 85 + 24197627
AAUACAUCUUUCUUGAAUGUAUCUACAACUUUCCAACAGAAACU---AGUUUCUCUGCU-------UA------------ACAUAAUCAGAUACUGUUAAAGUUGAG
.(((((((......).))))))...(((((((..((((((((..---..))))((((.(-------((------------...))).))))...))))))))))).. ( -14.00, z-score =  -1.40, R)
>droSec1.super_2 1939310 101 + 7591821
AAUAACAUUUAGU-AACAGUAUCUACAGGUAGCCAACAGAAGCU---AGUUUCUCGGCA--UAACAUAGCACUGCUCGCCACAUAAUCAGAUACUGUUAAGGUUGAG
..((((......(-((((((((((....((.((...(((..(((---((((........--.))).)))).)))...)).))......)))))))))))..)))).. ( -23.50, z-score =  -1.89, R)
>droSim1.chr3L 1468981 102 + 22553184
AAUAACAUUUAGUUAACAGUAUCUACAGGUAGCCAACAGAAACU---AGUUUCUCGGCA--UAACAUAGCACUGCUCGCCACAUAAUCAGAUACUGUUAAGGUUGAG
............((((((((((((.......(((...(((((..---..))))).))).--.......((.......)).........))))))))))))....... ( -22.40, z-score =  -1.96, R)
>consensus
AAUAACAUUUACUUAACAGUAUCUACAGGUAGCCAACAGAAACU___AGUUUCUCUGCU__UAACAUAGCACUGCUCGCCACAUAAUCAGAUACUGUUAAGGUUGAG
............((((((((((((.............((((((.....))))))..(((........)))..................))))))))))))....... (-13.74 = -15.18 +   1.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,913,604 – 1,913,706
Length 102
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 79.04
Shannon entropy 0.36514
G+C content 0.36426
Mean single sequence MFE -29.10
Consensus MFE -14.47
Energy contribution -17.54
Covariance contribution 3.07
Combinations/Pair 1.14
Mean z-score -2.90
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.85
SVM RNA-class probability 0.971249
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1913604 102 - 24543557
CUCAACCUUAACAGUAUCUGAUUAUGUGUCGGGCCUUGCUAUGUUA--AGCAGAGAAACU---AGUUUCUGUUGGCUACCUGUAGAUACUGUUAAGUAAAUGUUAUU
......((((((((((((((((.....))).(((((((((......--)))))(((((..---..)))))...))))......)))))))))))))........... ( -30.60, z-score =  -3.22, R)
>droEre2.scaffold_4784 1902339 107 - 25762168
CUCAGCUUUAACAGUAUCUGAUUAUGUGGCGAGCAGUGCUAUGUUAGCAGCAACAAUAAUUGCAGUUUCUGCUGGAAACUUGUAGAUACUGUCAAAUAAAUGUUAUU
...(((((((((((((((((.....((..(.((((((((((...)))))((((......)))).....))))).)..))...))))))))))....)))).)))... ( -30.20, z-score =  -1.77, R)
>droYak2.chr3L 1867550 85 - 24197627
CUCAACUUUAACAGUAUCUGAUUAUGU------------UA-------AGCAGAGAAACU---AGUUUCUGUUGGAAAGUUGUAGAUACAUUCAAGAAAGAUGUAUU
(((((((((..(((...))).......------------..-------((((((((....---..))))))))..))))))).))(((((((.......))))))). ( -17.40, z-score =  -0.98, R)
>droSec1.super_2 1939310 101 - 7591821
CUCAACCUUAACAGUAUCUGAUUAUGUGGCGAGCAGUGCUAUGUUA--UGCCGAGAAACU---AGCUUCUGUUGGCUACCUGUAGAUACUGUU-ACUAAAUGUUAUU
........((((((((((((.....(((((.(((((.((((.(((.--........))))---)))..))))).)))))...)))))))))))-)............ ( -34.10, z-score =  -4.32, R)
>droSim1.chr3L 1468981 102 - 22553184
CUCAACCUUAACAGUAUCUGAUUAUGUGGCGAGCAGUGCUAUGUUA--UGCCGAGAAACU---AGUUUCUGUUGGCUACCUGUAGAUACUGUUAACUAAAUGUUAUU
.......(((((((((((((.....(((((.(((((.((((.(((.--........))))---)))..))))).)))))...)))))))))))))............ ( -33.20, z-score =  -4.21, R)
>consensus
CUCAACCUUAACAGUAUCUGAUUAUGUGGCGAGCAGUGCUAUGUUA__AGCAGAGAAACU___AGUUUCUGUUGGCUACCUGUAGAUACUGUUAACUAAAUGUUAUU
......((((((((((((((.....((((((.....))))))......((((((((.........)))))))).........))))))))))))))........... (-14.47 = -17.54 +   3.07)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:56:43 2011