Locus 12404

Sequence ID dm3.chr4
Location 724,813 – 725,007
Length 194
Max. P 0.993718
window17042 window17043 window17044

overview

Window 2

Location 724,813 – 724,931
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 65.09
Shannon entropy 0.64112
G+C content 0.52440
Mean single sequence MFE -37.55
Consensus MFE -16.38
Energy contribution -18.25
Covariance contribution 1.87
Combinations/Pair 1.35
Mean z-score -1.49
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.915447
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 724813 118 + 1351857
CUGGGGGGGGGGGGGGUGUGGCACUGGGCGACUUCUCGAAAGGCGGUGAAAGCGGCAGGCGCUGCACCGUUUACACACAGUUUCUUGCUGGAAGG--AACAACAUCCAGUUCCAGACCAG
((((.(((((..(..(((((((.....))...........((((((((..((((.....)))).)))))))).)))))..)..)))((((((.(.--.....).)))))).))...)))) ( -43.60, z-score =  -0.81, R)
>droAna3.scaffold_13099 2631239 94 - 3324263
-----------------------UCUAACAAAUAACCCUAA---GAAAAAAGUAAUAGGUAUUCCUAUCUAAAAAAAAACCUACAUACAUAAAUGUUGAUCGCAUGUGUUUAUAUUUUGG
-----------------------..............((((---((........(((((....)))))................(((.(((.((((.....)))).))).))).)))))) (  -7.90, z-score =   0.54, R)
>droEre2.scaffold_4512 746406 111 - 1286254
-------CUGGAAGAGUGUGAUGCCGGGCGCCUUUUCGGGAGGCGGUGAGAGCGGCAGCCGCUGCACCGUUUACAAGCAGCAUCUUACUGGAAGG--AAUAGCAUUCAGUUCCAGACCAA
-------(((((((((((((((((...(((((((.....)))))((((..(((((...))))).))))........)).)))))...((....))--....))))))..))))))..... ( -42.30, z-score =  -1.54, R)
>droYak2.chr4 783105 111 + 1374474
-------AUGGAGGAGUGUGAGGCCGGGCGCCUUCUGGAGACGCGGUGAGCGCGGCAACCGCUGCACCGUUUAUAAACAGCAUCUCACGGGAAGG--AACAACAUUCAGUUCCAGAACAG
-------.((((.((((((..(((.....)))(((((((((.((((((((((.(....))))).))))(((....))).)).)))).)))))...--....))))))...))))...... ( -41.50, z-score =  -2.02, R)
>droSec1.super_30 441762 111 + 664411
-------CUGGAGGAGUGUGGCACUGGGCGCCUUCUCGGAAGGCGGUAAAAGCGGUAGCUACUGCACCGUUUACACACAGCUUCUUGCUGGAAGG--AACAACAUCCAGUUCCAGACCAG
-------(((((((((((((........(((((((...)))))))((((..(((((.((....))))))))))).)))).))))..((((((.(.--.....).)))))))))))..... ( -44.40, z-score =  -2.57, R)
>droSim1.chr4 551742 111 + 949497
-------CUGGAGGAGUGUGGCACUGGGCGCCUUCUCGGAAGGCGGUGAAAGCGGUAGCUACUGCACCGUUUACACACAGCUUCUUGCUGGAAGG--AACAACAUCCAGUUCCAGACCAG
-------......(.((.(((.(((((((((((((...)))))))(((.(((((((.((....))))))))).))).((((.....)))).....--.......)))))).))).))).. ( -45.60, z-score =  -2.55, R)
>consensus
_______CUGGAGGAGUGUGGCACCGGGCGCCUUCUCGGAAGGCGGUGAAAGCGGCAGCCACUGCACCGUUUACAAACAGCUUCUUACUGGAAGG__AACAACAUCCAGUUCCAGACCAG
..........((((((.(((........)))))))))...(((((((....(((((....))))))))))))..........(((.((((((.(........).))))))...))).... (-16.38 = -18.25 +   1.87)

alignment

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secondary structure

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dotplot

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Window 3

Location 724,853 – 724,967
Length 114
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 68.62
Shannon entropy 0.59160
G+C content 0.46432
Mean single sequence MFE -30.88
Consensus MFE -12.65
Energy contribution -13.43
Covariance contribution 0.78
Combinations/Pair 1.32
Mean z-score -1.62
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.806570
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 724853 114 + 1351857
AGGCGGUGAAAGCGGCAGGCGCUGCACCGUUUACACACAGUUUCUUGCUGGAAGG--AACAACAUCCAGUUCCAGACCAGCACUUUCAUGU---CUGUUCAGGACCAAACCAUUCCAUU
((((((((..((((.....)))).))))))))(((.(((......((((((..((--(((........)))))...))))))......)))---.)))...(((.........)))... ( -35.50, z-score =  -1.90, R)
>droAna3.scaffold_13099 2631259 105 - 3324263
------AAAAAGUAAUAGGUAUUCCUAUCUAAAAAAAAACCUACAUACAUAAAUGUUGAUCGCAUGUGUUUAUAUUUUGGCAUUGCUUUAC------UUC--CAUCUACCAUUCUCAAU
------...((((((((((....)))).............(.((((......)))).)...(((.(((((........)))))))).))))------)).--................. ( -11.90, z-score =  -0.33, R)
>droEre2.scaffold_4512 746439 117 - 1286254
AGGCGGUGAGAGCGGCAGCCGCUGCACCGUUUACAAGCAGCAUCUUACUGGAAGG--AAUAGCAUUCAGUUCCAGACCAAAUUUUCCAUGUAGACUGUUCAGAACGGAACCAUACUAGU
....(((....(((((....))))).((((((...(((((..(((.(((((((((--(((........)))))..........))))).))))))))))..)))))).)))........ ( -32.20, z-score =  -1.02, R)
>droYak2.chr4 783138 117 + 1374474
ACGCGGUGAGCGCGGCAACCGCUGCACCGUUUAUAAACAGCAUCUCACGGGAAGG--AACAACAUUCAGUUCCAGAACAGGAGUUCCUUGUAGACAGUUCAGGACGGAACCAUACCACU
..((((((((((.(....))))).))))))............(((.(((((..((--(((........))))).((((....))))))))))))..((((......))))......... ( -34.50, z-score =  -1.84, R)
>droSec1.super_30 441795 117 + 664411
AGGCGGUAAAAGCGGUAGCUACUGCACCGUUUACACACAGCUUCUUGCUGGAAGG--AACAACAUCCAGUUCCAGACCAGCAGUUUCAUGUAGACAGUUCAGGACGAAACCAUUCCAGU
.((.(((...(((....))).(((.((.(((((((...((((....(((((..((--(((........)))))...)))))))))...))))))).)).)))......)))...))... ( -33.90, z-score =  -2.08, R)
>droSim1.chr4 551775 117 + 949497
AGGCGGUGAAAGCGGUAGCUACUGCACCGUUUACACACAGCUUCUUGCUGGAAGG--AACAACAUCCAGUUCCAGACCAGCAGUUUCAUGUAGACAGUUCAGGACGAAACCAUUCCAGU
((((.(((.(((((((.((....))))))))).)))...))))..((((((..((--(((........)))))...))))))(((((.((....))(((...))))))))......... ( -37.30, z-score =  -2.57, R)
>consensus
AGGCGGUGAAAGCGGCAGCCACUGCACCGUUUACAAACAGCUUCUUACUGGAAGG__AACAACAUCCAGUUCCAGACCAGCAGUUCCAUGUAGACAGUUCAGGACGAAACCAUUCCAGU
(((((((....(((((....))))))))))))..........(((.((((((.(........).))))))...)))........................................... (-12.65 = -13.43 +   0.78)

alignment

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secondary structure

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dotplot

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Window 4

Location 724,893 – 725,007
Length 114
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 83.59
Shannon entropy 0.29308
G+C content 0.47130
Mean single sequence MFE -39.00
Consensus MFE -27.18
Energy contribution -32.06
Covariance contribution 4.88
Combinations/Pair 1.14
Mean z-score -3.07
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.64
SVM RNA-class probability 0.993718
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 724893 114 - 1351857
AAUAAAGGAAGAACCAACUCUAGACGGACCAGCAGCACAUAAUGGAAUGGUUUGGUCCUGAACAG---ACAUGAAAGUGCUGGUCUGGAACUGGAUGUUGUUCCUUCCAGCAAGAAA
......(((((...(((((((((.((((((((((...(((......)))(((((........)))---)).......))))))))))...))))).))))...)))))......... ( -39.90, z-score =  -3.52, R)
>droEre2.scaffold_4512 746479 117 + 1286254
AAUAAAGGACGGCCCAACACCAGCCGCACCAGCAGCACAUACUAGUAUGGUUCCGUUCUGAACAGUCUACAUGGAAAAUUUGGUCUGGAACUGAAUGCUAUUCCUUCCAGUAAGAUG
......(((.((..........((.((....)).))......(((((((((((((..(..((...(((....)))...))..)..)))))))..))))))..)).)))......... ( -27.30, z-score =  -0.24, R)
>droYak2.chr4 783178 112 - 1374474
AAUAAAGG-----CCAAAUGCAAACGCUCCAGCAGCACAUAGUGGUAUGGUUCCGUCCUGAACUGUCUACAAGGAACUCCUGUUCUGGAACUGAAUGUUGUUCCUUCCCGUGAGAUG
....((((-----.(((..((....))(((((.(((.....((((.(((((((......))))))))))).(((....)))))))))))........)))..))))..(....)... ( -25.80, z-score =   0.01, R)
>droSec1.super_30 441835 117 - 664411
AAUAAAGGAAGGACCGACUCCAGACGGACCAGCAGCACAUACUGGAAUGGUUUCGUCCUGAACUGUCUACAUGAAACUGCUGGUCUGGAACUGGAUGUUGUUCCUUCCAGCAAGAAG
......(((((((.(((((((((.(((((((((((..(((..((((.((((((......)))))))))).)))...)))))))))))...))))).)))).)))))))......... ( -51.00, z-score =  -5.81, R)
>droSim1.chr4 551815 117 - 949497
AAUAAAGGAAGGACCGACUCCAGACGGACCAGCAGCACAUACUGGAAUGGUUUCGUCCUGAACUGUCUACAUGAAACUGCUGGUCUGGAACUGGAUGUUGUUCCUUCCAGCAAGAAG
......(((((((.(((((((((.(((((((((((..(((..((((.((((((......)))))))))).)))...)))))))))))...))))).)))).)))))))......... ( -51.00, z-score =  -5.81, R)
>consensus
AAUAAAGGAAGGACCAACUCCAGACGGACCAGCAGCACAUACUGGAAUGGUUUCGUCCUGAACUGUCUACAUGAAACUGCUGGUCUGGAACUGGAUGUUGUUCCUUCCAGCAAGAAG
......(((((((.(((((((((.(((((((((((.......(((.(((((((......)))))))))).......)))))))))))...))))).)))).)))))))......... (-27.18 = -32.06 +   4.88)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:01:27 2011