Locus 5069

Sequence ID dm3.chr2R
Location 17,510,346 – 17,510,449
Length 103
Max. P 0.981059
window6958 window6959

overview

Window 8

Location 17,510,346 – 17,510,449
Length 103
Sequences 10
Columns 109
Reading direction forward
Mean pairwise identity 63.55
Shannon entropy 0.76988
G+C content 0.60985
Mean single sequence MFE -40.64
Consensus MFE -16.96
Energy contribution -16.38
Covariance contribution -0.58
Combinations/Pair 1.75
Mean z-score -1.36
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.73
SVM RNA-class probability 0.964115
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17510346 103 + 21146708
UUCUCGGCGCUAGGCUUGCGCCUAUUCCAAACUUCGAGCCACCGUCCACGCUACAGGCGGACUUCAGUUCAAAGUCCCCCAAACUGGGGGUUAAACUGGCGUC------
.....((((((((((....)))).......((((.((((....((((..((.....))))))....)))).))))(((((.....))))).......))))))------ ( -34.60, z-score =  -1.59, R)
>droSim1.chr2R 16158709 103 + 19596830
UUCUCGGCGCUAGGCUUGCACCUAUUCCAAACUUUGAGCCGCCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCCAAACUGGGGGUUAAACUGGCGUC------
.....((((((((.................(((((((((.(..((((..((.....))))))..).)))))))))(((((.....))))).....))))))))------ ( -39.30, z-score =  -2.41, R)
>droSec1.super_9 836381 103 + 3197100
UUCUCGGCGCUAGGCUUGCACCUAUUCCAAACUUUGAGCCACCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCCAAACUGGGGGUUAAACUGGCGUC------
.....((((((((.................(((((((((....((((..((.....))))))....)))))))))(((((.....))))).....))))))))------ ( -38.60, z-score =  -2.64, R)
>droYak2.chr2R 9477623 103 - 21139217
UUCUCGGCGCUAGGCUUGCGCCUAUUCCAAACUUGGAGCCGCCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCAAGGCUGGGGGUUAGGCUUGCGUC------
.....(((((.(((((((.((((...(((..(((((.(((((.((....)).)).)))((((((.......)))))))))))..)))))))))))))))))))------ ( -43.20, z-score =  -1.52, R)
>droEre2.scaffold_4845 11659244 103 + 22589142
UUCUCGGCGCUAGGCUUGCGCCUAUUCCAAACUUGGAGCCGCCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCCAGGCUGGGGGUUAAGCUGGCGUC------
.....((((((((.(((((.((((.((((....))))(((((.((....)).)).((.((((((.......)))))).)).))))))).).))))))))))))------ ( -41.60, z-score =  -0.86, R)
>droAna3.scaffold_13266 8996739 103 + 19884421
UCCUCGGGGCCAGACUAGCACCCAACCCGAACUUGGAGCCCCCGUCCACGCUGCAGGCGGACCUCAGCUCCGACUCACCCAGGCUGGGAGUCAGACUGGACUC------
.....(((((..(.....)..((((.......)))).))))).(((((.((((.(((....)))))))((.(((((.((......))))))).)).)))))..------ ( -35.40, z-score =   0.54, R)
>dp4.chr3 4986161 109 + 19779522
UGCGCGGCGCCAAAGUGGCGCCCAGGCCGAACUUUGAGCUGCUGUCCACGCUGCAGGCGGACUUCAGCUCGGCGGCGCUGCGCUGCGGGGAGUCACUAAGGCUCAUUUC
.((((((((((((((((((......)))..)))))((((((..((((..((.....))))))..))))))...))))))))))......(((((.....)))))..... ( -54.30, z-score =  -1.47, R)
>droPer1.super_2 5185302 109 + 9036312
UGCGCGGCGCCAAAGUGGCGCCCAGGCCGAACUUUGAGCUGCUGUCCACGCUGCAGGCGGACUUCAGCUCGGCGGCGCUGCGCUGCGGGGAGUCACUAAGGCUCAUUUC
.((((((((((((((((((......)))..)))))((((((..((((..((.....))))))..))))))...))))))))))......(((((.....)))))..... ( -54.30, z-score =  -1.47, R)
>droWil1.scaffold_181141 1004565 106 - 5303230
UACGUGGCGCCAAGUUGGCUCCCAAACCAAAUUUGGAGCUGCUAUCCACACUGGAUGCCGAUUUUAACUCCGCCGCACUCCGCUGGGGCGAGUCACUA---CUCAGCUC
...((((((...((((((((((.((......)).))))))((.((((.....)))))).......)))).)))))).....((((((...........---)))))).. ( -35.00, z-score =  -1.67, R)
>anoGam1.chr2L 42465745 86 + 48795086
--------------CUGGUGGUGAUAGU-AGUGAUGGUUUGCCGCC---GUCCGAUACUGGUAUCGCUUCGGCGUCGUUGGCACGGAAACGGAAGACACCCGUC-----
--------------..(((((((.((((-(..((((((.....)))---)))...))))).))))))).(((.((.(((..(.((....)))..))))))))..----- ( -30.10, z-score =  -0.54, R)
>consensus
UUCUCGGCGCUAGGCUUGCGCCUAUUCCAAACUUUGAGCCGCCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCCAGACUGGGGGUUAAACUGGCGUC______
.....((.((.......)).))....((...((((((((....((((..((.....))))))....))))))))...((((...))))))................... (-16.96 = -16.38 +  -0.58)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 17,510,346 – 17,510,449
Length 103
Sequences 10
Columns 109
Reading direction reverse
Mean pairwise identity 63.55
Shannon entropy 0.76988
G+C content 0.60985
Mean single sequence MFE -42.17
Consensus MFE -17.74
Energy contribution -17.59
Covariance contribution -0.15
Combinations/Pair 1.65
Mean z-score -1.53
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.06
SVM RNA-class probability 0.981059
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17510346 103 - 21146708
------GACGCCAGUUUAACCCCCAGUUUGGGGGACUUUGAACUGAAGUCCGCCUGUAGCGUGGACGGUGGCUCGAAGUUUGGAAUAGGCGCAAGCCUAGCGCCGAGAA
------..((((((((((((((((.....)))))...)))))))...(((((((....).))))))))))........(((((..(((((....)))))...))))).. ( -46.30, z-score =  -3.65, R)
>droSim1.chr2R 16158709 103 - 19596830
------GACGCCAGUUUAACCCCCAGUUUGGGGGACUUUGAACUGAAGUCCGCCUGCAGCGUGGACGGCGGCUCAAAGUUUGGAAUAGGUGCAAGCCUAGCGCCGAGAA
------....((((.....(((((.....)))))(((((((.(((..(((((((....).))))))..))).)))))))))))....(((((.......)))))..... ( -43.00, z-score =  -2.48, R)
>droSec1.super_9 836381 103 - 3197100
------GACGCCAGUUUAACCCCCAGUUUGGGGGACUUUGAACUGAAGUCCGCCUGCAGCGUGGACGGUGGCUCAAAGUUUGGAAUAGGUGCAAGCCUAGCGCCGAGAA
------....((((.....(((((.....)))))(((((((.(((..(((((((....).))))))..))).)))))))))))....(((((.......)))))..... ( -41.00, z-score =  -2.14, R)
>droYak2.chr2R 9477623 103 + 21139217
------GACGCAAGCCUAACCCCCAGCCUUGGGGACUUUGAACUGAAGUCCGCCUGCAGCGUGGACGGCGGCUCCAAGUUUGGAAUAGGCGCAAGCCUAGCGCCGAGAA
------.......(((....((((......)))).............(((((((....).)))))))))(((((((....)))).(((((....)))))..)))..... ( -41.30, z-score =  -1.53, R)
>droEre2.scaffold_4845 11659244 103 - 22589142
------GACGCCAGCUUAACCCCCAGCCUGGGGGACUUUGAACUGAAGUCCGCCUGCAGCGUGGACGGCGGCUCCAAGUUUGGAAUAGGCGCAAGCCUAGCGCCGAGAA
------...(((.......(((((.....))))).............(((((((....).)))))))))(((((((....)))).(((((....)))))..)))..... ( -45.20, z-score =  -2.20, R)
>droAna3.scaffold_13266 8996739 103 - 19884421
------GAGUCCAGUCUGACUCCCAGCCUGGGUGAGUCGGAGCUGAGGUCCGCCUGCAGCGUGGACGGGGGCUCCAAGUUCGGGUUGGGUGCUAGUCUGGCCCCGAGGA
------(.(.((((.(((.(.(((((((((..(.....((((((...(((((((....).))))))...))))))..)..))))))))).).))).)))).).)..... ( -47.90, z-score =  -0.59, R)
>dp4.chr3 4986161 109 - 19779522
GAAAUGAGCCUUAGUGACUCCCCGCAGCGCAGCGCCGCCGAGCUGAAGUCCGCCUGCAGCGUGGACAGCAGCUCAAAGUUCGGCCUGGGCGCCACUUUGGCGCCGCGCA
.............(((......))).((((((.((((..((((((..(((((((....).))))))..))))))......)))))).((((((.....)))))))))). ( -50.10, z-score =  -1.38, R)
>droPer1.super_2 5185302 109 - 9036312
GAAAUGAGCCUUAGUGACUCCCCGCAGCGCAGCGCCGCCGAGCUGAAGUCCGCCUGCAGCGUGGACAGCAGCUCAAAGUUCGGCCUGGGCGCCACUUUGGCGCCGCGCA
.............(((......))).((((((.((((..((((((..(((((((....).))))))..))))))......)))))).((((((.....)))))))))). ( -50.10, z-score =  -1.38, R)
>droWil1.scaffold_181141 1004565 106 + 5303230
GAGCUGAG---UAGUGACUCGCCCCAGCGGAGUGCGGCGGAGUUAAAAUCGGCAUCCAGUGUGGAUAGCAGCUCCAAAUUUGGUUUGGGAGCCAACUUGGCGCCACGUA
..(((((.---...(((((((((.((......)).))).))))))...))))).......((((........(((((((...))))))).(((.....))).))))... ( -35.10, z-score =   0.06, R)
>anoGam1.chr2L 42465745 86 - 48795086
-----GACGGGUGUCUUCCGUUUCCGUGCCAACGACGCCGAAGCGAUACCAGUAUCGGAC---GGCGGCAAACCAUCACU-ACUAUCACCACCAG--------------
-----((((((.....))))))..(((....))).(((((...(((((....)))))..)---)))).............-..............-------------- ( -21.70, z-score =  -0.02, R)
>consensus
______GACGCCAGUUUAACCCCCAGUCUGGGGGACUCUGAACUGAAGUCCGCCUGCAGCGUGGACGGCGGCUCAAAGUUUGGAAUAGGCGCAAGCCUAGCGCCGAGAA
.....................((((...))))....((((((((...((((((.......))))))..........))))))))...(((((.......)))))..... (-17.74 = -17.59 +  -0.15)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:41:16 2011