Locus 15223

Sequence ID dm3.chrX
Location 18,031,142 – 18,031,261
Length 119
Max. P 0.862894
window20968 window20969 window20970

overview

Window 8

Location 18,031,142 – 18,031,239
Length 97
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 79.03
Shannon entropy 0.36305
G+C content 0.54534
Mean single sequence MFE -32.96
Consensus MFE -19.42
Energy contribution -20.06
Covariance contribution 0.64
Combinations/Pair 1.24
Mean z-score -1.85
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.725527
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18031142 97 + 22422827
CCUGCACGGUCGCAGCGCAGUCAUACUGG-UUCGGUAUUUUUAAGAAGAACGGUCACACUGGCCCGUGCGCUUAACAGGGCCGAACUGCUGAUUUAAC
............((((.(((.....)))(-((((((....(((((....((((((.....)).))))...)))))....))))))).))))....... ( -28.60, z-score =  -0.25, R)
>droSim1.chrX_random 148578 88 + 5698898
--------CCUGCUG-GCAGUCAUACUAG-GACGGUAUUUUUCAGCAGUACGGCCACACUAGCCCGUGCGCUUAACAGGGCCGAACUGCUGAUUUAAC
--------(((.(((-(........))))-.).))......((((((((.(((((.....(((......)))......))))).))))))))...... ( -30.90, z-score =  -2.24, R)
>droSec1.super_8 340857 88 + 3762037
--------CCUGCUG-GCAGUCAUACUAG-GACGGUAUUUUUCAGCAGUACGGCCACACUAGCCCGUGCGCUUAACAGGGCCGAACUGCUGAUUUAAC
--------(((.(((-(........))))-.).))......((((((((.(((((.....(((......)))......))))).))))))))...... ( -30.90, z-score =  -2.24, R)
>droYak2.chrX 16654160 98 + 21770863
CCUGCUGAGUCGUGUCGCGGUCAUACUGGCGGCGGUAUUUUUCAGCAGGACGGCCACACUGAUAUGCACGCUUAACAGGGGCAAACUGCUGAUUUAAC
(((((((((..((..(((.(((.....))).)))..))..)))))))))...(((...(((.((.(....).)).))).)))................ ( -36.50, z-score =  -2.60, R)
>droEre2.scaffold_4690 8359199 98 + 18748788
CCUUUUGGGCCGUGGCGCGGUCAUACUGGCGGCGGUAUUAUUCAGCAGGACGGCCACACUGGCCUGCACGCUUAACAGGGGCUAACUGCUGAUUUAAC
((....))(((((.((.(((.....))))).))))).....(((((((...((((.....)))).....((((.....))))...)))))))...... ( -37.90, z-score =  -1.96, R)
>consensus
CCU_____GCCGCGGCGCAGUCAUACUGG_GACGGUAUUUUUCAGCAGGACGGCCACACUGGCCCGUGCGCUUAACAGGGCCGAACUGCUGAUUUAAC
.........((((...))))..((((((....))))))...(((((((..(((((.....(((......)))......)))))..)))))))...... (-19.42 = -20.06 +   0.64)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,031,171 – 18,031,261
Length 90
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 84.84
Shannon entropy 0.25409
G+C content 0.46182
Mean single sequence MFE -26.95
Consensus MFE -17.65
Energy contribution -18.49
Covariance contribution 0.84
Combinations/Pair 1.14
Mean z-score -2.39
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.862894
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18031171 90 + 22422827
UUCGGUAUUUUUAAGAAGAACGGUCACACUGGCCCGUGCGCUUAACAGGGCCGAACUGCUGAUUUAACAGCGAA---------CAACACUAUGUUAAAU
((((((....(((((....((((((.....)).))))...)))))....)))))).(((((......)))))((---------((......)))).... ( -23.00, z-score =  -1.51, R)
>droSim1.chrX_random 148598 90 + 5698898
GACGGUAUUUUUCAGCAGUACGGCCACACUAGCCCGUGCGCUUAACAGGGCCGAACUGCUGAUUUAACAGCGAA---------CAACACUAUGUUAAAU
...........((((((((.(((((.....(((......)))......))))).))))))))(((((((.....---------........))))))). ( -30.02, z-score =  -3.63, R)
>droSec1.super_8 340877 90 + 3762037
GACGGUAUUUUUCAGCAGUACGGCCACACUAGCCCGUGCGCUUAACAGGGCCGAACUGCUGAUUUAACAGCGAA---------CAACACUAUGUUAAAU
...........((((((((.(((((.....(((......)))......))))).))))))))(((((((.....---------........))))))). ( -30.02, z-score =  -3.63, R)
>droYak2.chrX 16654190 99 + 21770863
GGCGGUAUUUUUCAGCAGGACGGCCACACUGAUAUGCACGCUUAACAGGGGCAAACUGCUGAUUUAACAGCGAAAAGCCAGAAUAACACUAUGUUAAAU
(((.((.....(((((((....(((...(((.((.(....).)).))).)))...)))))))....))........)))....((((.....))))... ( -25.00, z-score =  -1.78, R)
>droEre2.scaffold_4690 8359229 99 + 18748788
GGCGGUAUUAUUCAGCAGGACGGCCACACUGGCCUGCACGCUUAACAGGGGCUAACUGCUGAUUUAACAGCGAAAAGCCAAAAUAACACUAUGUUAAAU
(((.((.(((.(((((((...((((.....)))).....((((.....))))...)))))))..)))..)).....)))....((((.....))))... ( -26.70, z-score =  -1.39, R)
>consensus
GACGGUAUUUUUCAGCAGGACGGCCACACUGGCCCGUGCGCUUAACAGGGCCGAACUGCUGAUUUAACAGCGAA_________CAACACUAUGUUAAAU
...........(((((((..(((((.....(((......)))......)))))..)))))))(((((((......................))))))). (-17.65 = -18.49 +   0.84)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,031,171 – 18,031,261
Length 90
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 84.84
Shannon entropy 0.25409
G+C content 0.46182
Mean single sequence MFE -27.60
Consensus MFE -18.76
Energy contribution -19.36
Covariance contribution 0.60
Combinations/Pair 1.11
Mean z-score -1.97
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.667127
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18031171 90 - 22422827
AUUUAACAUAGUGUUG---------UUCGCUGUUAAAUCAGCAGUUCGGCCCUGUUAAGCGCACGGGCCAGUGUGACCGUUCUUCUUAAAAAUACCGAA
......((((.(....---------...((((......)))).....((((((((.....))).)))))).))))........................ ( -20.80, z-score =  -0.53, R)
>droSim1.chrX_random 148598 90 - 5698898
AUUUAACAUAGUGUUG---------UUCGCUGUUAAAUCAGCAGUUCGGCCCUGUUAAGCGCACGGGCUAGUGUGGCCGUACUGCUGAAAAAUACCGUC
.(((((((..(((...---------..))))))))))((((((((.(((((((....)).((((......))))))))).))))))))........... ( -32.40, z-score =  -3.19, R)
>droSec1.super_8 340877 90 - 3762037
AUUUAACAUAGUGUUG---------UUCGCUGUUAAAUCAGCAGUUCGGCCCUGUUAAGCGCACGGGCUAGUGUGGCCGUACUGCUGAAAAAUACCGUC
.(((((((..(((...---------..))))))))))((((((((.(((((((....)).((((......))))))))).))))))))........... ( -32.40, z-score =  -3.19, R)
>droYak2.chrX 16654190 99 - 21770863
AUUUAACAUAGUGUUAUUCUGGCUUUUCGCUGUUAAAUCAGCAGUUUGCCCCUGUUAAGCGUGCAUAUCAGUGUGGCCGUCCUGCUGAAAAAUACCGCC
.(((((((..(((..(........)..))))))))))(((((((..((((((((.((.(....).)).))).).)).))..)))))))........... ( -23.00, z-score =  -0.93, R)
>droEre2.scaffold_4690 8359229 99 - 18748788
AUUUAACAUAGUGUUAUUUUGGCUUUUCGCUGUUAAAUCAGCAGUUAGCCCCUGUUAAGCGUGCAGGCCAGUGUGGCCGUCCUGCUGAAUAAUACCGCC
..........(((((((((.((((..(.((((......)))).)..)))).......((((....((((.....))))....))))))))))))).... ( -29.40, z-score =  -2.00, R)
>consensus
AUUUAACAUAGUGUUG_________UUCGCUGUUAAAUCAGCAGUUCGGCCCUGUUAAGCGCACGGGCCAGUGUGGCCGUACUGCUGAAAAAUACCGCC
.(((((((..(((..............))))))))))(((((((..(((((((....)).((((......)))))))))..)))))))........... (-18.76 = -19.36 +   0.60)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:55:15 2011