Locus 11612

Sequence ID dm3.chr3R
Location 22,422,481 – 22,422,590
Length 109
Max. P 0.993006
window15954 window15955 window15956

overview

Window 4

Location 22,422,481 – 22,422,575
Length 94
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 74.40
Shannon entropy 0.46995
G+C content 0.53684
Mean single sequence MFE -33.90
Consensus MFE -21.45
Energy contribution -24.12
Covariance contribution 2.67
Combinations/Pair 1.13
Mean z-score -2.32
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.58
SVM RNA-class probability 0.993006
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 22422481 94 + 27905053
GUAGCGAGAGUGUUUCAACGAAAAGUUUCUCUCUCCCUU-------ACCGCCGCUGGUGCUCCAAGGACCAAGGAC-------UAAGGAGCCCGGCGGCGUUCAAAUU
((((.(((((.(....(((.....))).).))))).).)-------))(((((((((.(((((..((.(....).)-------)..))))))))))))))........ ( -37.70, z-score =  -3.30, R)
>droSim1.chr3R 22250798 94 + 27517382
GUAGCGAGAGUGUUUCAACGAAAAGUUUCUCUCUCCCUU-------ACCGCCGCUGGUGCUCCAAGGACCAAGGAC-------UAAGGAGCCCGGCGGCGUUCAAAUU
((((.(((((.(....(((.....))).).))))).).)-------))(((((((((.(((((..((.(....).)-------)..))))))))))))))........ ( -37.70, z-score =  -3.30, R)
>droSec1.super_13 1197481 94 + 2104621
GUAGCGAGAGUGUUUCAACGAAAAGUUUCUCUCUCCCUU-------ACCGCUGCUUGUGCUCCAAGGACCAAGGAC-------UAAGGAGCCCGGCGGCGUUCAAAUU
((((.(((((.(....(((.....))).).))))).).)-------))(((((((.(.(((((..((.(....).)-------)..)))))).)))))))........ ( -29.70, z-score =  -1.24, R)
>droYak2.chr3R 4754209 101 - 28832112
GUAGCGAGAGUGUUUCAACGAAAAGUUUCUCUUUCUCUCCCCAACCGCCGCCGCUGGUGCUCCAAGGACCAAGGAC-------UAAGGAGCCCGGCGGCGUUCAAAUU
.....(((((......(((.....))).......))))).........(((((((((.(((((..((.(....).)-------)..))))))))))))))........ ( -36.42, z-score =  -2.25, R)
>droEre2.scaffold_4820 4836716 101 - 10470090
GUAGCGAGAGUGUUUCAACGAAAAGUUUCUCUCUCCCUU-------ACCGCCGCUGGUGCUCCAAGGACCAAGGACCCAGGACUAAGGAGCCCGGCGGCGUUCAAAUU
((((.(((((.(....(((.....))).).))))).).)-------))(((((((((.(((((..((.((.........)).))..))))))))))))))........ ( -38.80, z-score =  -2.68, R)
>droWil1.scaffold_181130 9881714 87 - 16660200
------CUUGUGUUCCUAGGUGAACUUUCGCUCCCUG---------------GCCAAGAAGCCAAAUGCCGUCGACUACGUUGUAGACGACGACGAGAUGAGCAAAUU
------.....((((......))))....((((..((---------------((......))))..((.(((((.((((...)))).))))).))....))))..... ( -23.10, z-score =  -1.17, R)
>consensus
GUAGCGAGAGUGUUUCAACGAAAAGUUUCUCUCUCCCUU_______ACCGCCGCUGGUGCUCCAAGGACCAAGGAC_______UAAGGAGCCCGGCGGCGUUCAAAUU
.....(((((.(....(((.....))).).))))).............(((((((((.(((((.......................))))))))))))))........ (-21.45 = -24.12 +   2.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,422,481 – 22,422,575
Length 94
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 74.40
Shannon entropy 0.46995
G+C content 0.53684
Mean single sequence MFE -35.55
Consensus MFE -19.53
Energy contribution -22.18
Covariance contribution 2.65
Combinations/Pair 1.12
Mean z-score -2.22
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.97
SVM RNA-class probability 0.977196
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 22422481 94 - 27905053
AAUUUGAACGCCGCCGGGCUCCUUA-------GUCCUUGGUCCUUGGAGCACCAGCGGCGGU-------AAGGGAGAGAGAAACUUUUCGUUGAAACACUCUCGCUAC
........((((((.(((((((...-------(.(....).)...))))).)).))))))..-------.((.(((((.(((....)))((....)).))))).)).. ( -36.10, z-score =  -2.26, R)
>droSim1.chr3R 22250798 94 - 27517382
AAUUUGAACGCCGCCGGGCUCCUUA-------GUCCUUGGUCCUUGGAGCACCAGCGGCGGU-------AAGGGAGAGAGAAACUUUUCGUUGAAACACUCUCGCUAC
........((((((.(((((((...-------(.(....).)...))))).)).))))))..-------.((.(((((.(((....)))((....)).))))).)).. ( -36.10, z-score =  -2.26, R)
>droSec1.super_13 1197481 94 - 2104621
AAUUUGAACGCCGCCGGGCUCCUUA-------GUCCUUGGUCCUUGGAGCACAAGCAGCGGU-------AAGGGAGAGAGAAACUUUUCGUUGAAACACUCUCGCUAC
........(((.((..((((((...-------(.(....).)...))))).)..)).)))..-------.((.(((((.(((....)))((....)).))))).)).. ( -26.90, z-score =   0.04, R)
>droYak2.chr3R 4754209 101 + 28832112
AAUUUGAACGCCGCCGGGCUCCUUA-------GUCCUUGGUCCUUGGAGCACCAGCGGCGGCGGUUGGGGAGAGAAAGAGAAACUUUUCGUUGAAACACUCUCGCUAC
........((((((((((((((...-------(.(....).)...))))).))...)))))))..(((.(((((...((((....))))((....)).))))).))). ( -38.30, z-score =  -1.54, R)
>droEre2.scaffold_4820 4836716 101 + 10470090
AAUUUGAACGCCGCCGGGCUCCUUAGUCCUGGGUCCUUGGUCCUUGGAGCACCAGCGGCGGU-------AAGGGAGAGAGAAACUUUUCGUUGAAACACUCUCGCUAC
........((((((.(((((((..((..(..(....)..)..)).))))).)).))))))..-------.((.(((((.(((....)))((....)).))))).)).. ( -39.50, z-score =  -1.94, R)
>droWil1.scaffold_181130 9881714 87 + 16660200
AAUUUGCUCAUCUCGUCGUCGUCUACAACGUAGUCGACGGCAUUUGGCUUCUUGGC---------------CAGGGAGCGAAAGUUCACCUAGGAACACAAG------
..(((((((.....(((((((.((((...)))).))))))).(((((((....)))---------------))))))))))).((((......)))).....------ ( -36.40, z-score =  -5.37, R)
>consensus
AAUUUGAACGCCGCCGGGCUCCUUA_______GUCCUUGGUCCUUGGAGCACCAGCGGCGGU_______AAGGGAGAGAGAAACUUUUCGUUGAAACACUCUCGCUAC
........((((((.(((((((.......................))))).)).))))))..........((.(((((.(.(((.....)))....).))))).)).. (-19.53 = -22.18 +   2.65)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,422,491 – 22,422,590
Length 99
Sequences 7
Columns 113
Reading direction forward
Mean pairwise identity 74.50
Shannon entropy 0.50003
G+C content 0.46831
Mean single sequence MFE -28.29
Consensus MFE -11.59
Energy contribution -13.87
Covariance contribution 2.28
Combinations/Pair 1.14
Mean z-score -2.42
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.940343
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 22422491 99 + 27905053
UGUUUCAACGAAAAGUUUCUCUCUCCCUU-------ACCGCCGCUGGUGCUCCAAGGACCAAGGAC-------UAAGGAGCCCGGCGGCGUUCAAAUUGAAAAACAUAAAUCA
..((((((.(((....)))..........-------..(((((((((.(((((..((.(....).)-------)..))))))))))))))......))))))........... ( -32.80, z-score =  -3.22, R)
>droSim1.chr3R 22250808 99 + 27517382
UGUUUCAACGAAAAGUUUCUCUCUCCCUU-------ACCGCCGCUGGUGCUCCAAGGACCAAGGAC-------UAAGGAGCCCGGCGGCGUUCAAAUUGAAAAACAUAAAUCA
..((((((.(((....)))..........-------..(((((((((.(((((..((.(....).)-------)..))))))))))))))......))))))........... ( -32.80, z-score =  -3.22, R)
>droSec1.super_13 1197491 99 + 2104621
UGUUUCAACGAAAAGUUUCUCUCUCCCUU-------ACCGCUGCUUGUGCUCCAAGGACCAAGGAC-------UAAGGAGCCCGGCGGCGUUCAAAUUGAAAAACAUAAAUCA
..((((((.(((....)))..........-------..(((((((.(.(((((..((.(....).)-------)..)))))).)))))))......))))))........... ( -24.80, z-score =  -1.11, R)
>droYak2.chr3R 4754219 106 - 28832112
UGUUUCAACGAAAAGUUUCUCUUUCUCUCCCCAACCGCCGCCGCUGGUGCUCCAAGGACCAAGGAC-------UAAGGAGCCCGGCGGCGUUCAAAUUGAAAAACAUAAAUCA
..((((((.((((((.....)))).))...........(((((((((.(((((..((.(....).)-------)..))))))))))))))......))))))........... ( -34.10, z-score =  -2.90, R)
>droEre2.scaffold_4820 4836726 106 - 10470090
UGUUUCAACGAAAAGUUUCUCUCUCCCUU-------ACCGCCGCUGGUGCUCCAAGGACCAAGGACCCAGGACUAAGGAGCCCGGCGGCGUUCAAAUUGAAAAACAUAAAUCA
..((((((.(((....)))..........-------..(((((((((.(((((..((.((.........)).))..))))))))))))))......))))))........... ( -33.90, z-score =  -2.48, R)
>droAna3.scaffold_13340 6779446 78 - 23697760
UGUUUCAACGAAAAGUUUCUCU-UCUUUU--------CCGUUGCUCCU--UUUAACG------------------------CCGCCGGCGUUCAAAUUGAAAAACAUAAAUCA
(((((((((((((((.......-.)))))--------.))))).((..--(((((((------------------------((...)))))).)))..)).)))))....... ( -16.50, z-score =  -2.77, R)
>droWil1.scaffold_181130 9881718 98 - 16660200
UGUUCCUAGGUGAACUUUCGCU--CCCUG-------------GCCAAGAAGCCAAAUGCCGUCGACUACGUUGUAGACGACGACGAGAUGAGCAAAUUGAAAAACAUAAAUCA
.((((......))))....(((--(..((-------------((......))))..((.(((((.((((...)))).))))).))....)))).................... ( -23.10, z-score =  -1.27, R)
>consensus
UGUUUCAACGAAAAGUUUCUCUCUCCCUU_______ACCGCCGCUGGUGCUCCAAGGACCAAGGAC_______UAAGGAGCCCGGCGGCGUUCAAAUUGAAAAACAUAAAUCA
..((((((.((........)).................(((((((.(.(((((.......................)))))).)))))))......))))))........... (-11.59 = -13.87 +   2.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:46:13 2011