Locus 14955

Sequence ID dm3.chrX
Location 16,568,501 – 16,568,605
Length 104
Max. P 0.999548
window20606 window20607 window20608

overview

Window 6

Location 16,568,501 – 16,568,595
Length 94
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 68.87
Shannon entropy 0.56305
G+C content 0.48791
Mean single sequence MFE -35.26
Consensus MFE -20.26
Energy contribution -23.66
Covariance contribution 3.40
Combinations/Pair 1.21
Mean z-score -3.01
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.00
SVM RNA-class probability 0.999548
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16568501 94 + 22422827
UCUCCCACAAAUUGACAAUCCAAAGUGGCUACCAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGACUCUUCCGCUUUGGAUCCAUCAGUGGGGGU---
.(((((((....(((..(((((((((((...((((.(((((((.....)))))))))))((....))..)))))))))))...)))))))))).--- ( -41.40, z-score =  -4.24, R)
>droAna3.scaffold_13334 970066 91 + 1562580
UUUCUAAAAACCUAGUACUUUCCA------ACCAGGGCUGAAAGUCCUCCUACUGGUUCUAACUUCCAAGUGACUCAUAGCUAUUUUUGGGCCUGGG
........................------.(((((.(..(((((....(((..((((...(((....)))))))..)))..)))))..).))))). ( -19.90, z-score =   0.09, R)
>droEre2.scaffold_4690 6926839 92 + 18748788
UCCCCCACAAGUUGACAAUCCAAAGUGAGUUCUAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGAUUCUUCCGCUUUGGAGCCAUCAGCGGGU-----
...(((....(((((...((((((((.........((((((((.....))))))))..(((((...)))))))))))))....)))))))).----- ( -34.20, z-score =  -3.03, R)
>droSec1.super_17 391158 97 + 1527944
UCUCCCACAAAUUGGCAAUCCAAAGUGGCUACCAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGACUCUUCCGCUUUGGAUCCAUCUGUGGAGUGUGU
....(((((...(((..(((((((((((...((((.(((((((.....)))))))))))((....))..))))))))))))))..)))))....... ( -39.70, z-score =  -4.13, R)
>droSim1.chrX 12736629 97 + 17042790
UCUCCCACAAAUUGGCAAUCCAAAGUGGCUACCAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGACUCUUCCGCUUUGGAUCCAUCAGUGGAGUGGGU
...(((((..(((((..(((((((((((...((((.(((((((.....)))))))))))((....))..)))))))))))...)))))...))))). ( -41.10, z-score =  -3.74, R)
>consensus
UCUCCCACAAAUUGGCAAUCCAAAGUGGCUACCAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGACUCUUCCGCUUUGGAUCCAUCAGUGGGGUG_G_
...(((((....(((..((((((((((....((((.(((((((.....)))))))))))((((...)))))))))))))))))...)))))...... (-20.26 = -23.66 +   3.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,568,501 – 16,568,595
Length 94
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 68.87
Shannon entropy 0.56305
G+C content 0.48791
Mean single sequence MFE -31.57
Consensus MFE -20.74
Energy contribution -21.98
Covariance contribution 1.24
Combinations/Pair 1.32
Mean z-score -1.65
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.40
SVM RNA-class probability 0.989996
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16568501 94 - 22422827
---ACCCCCACUGAUGGAUCCAAAGCGGAAGAGUCUUCCCAUCCGGAACGGAAAAUUCCGGAAUGGUAGCCACUUUGGAUUGUCAAUUUGUGGGAGA
---...((((((((..(.(((((((.((..........((((((((((.......)))))).))))...)).))))))))..)))....)))))... ( -35.12, z-score =  -2.25, R)
>droAna3.scaffold_13334 970066 91 - 1562580
CCCAGGCCCAAAAAUAGCUAUGAGUCACUUGGAAGUUAGAACCAGUAGGAGGACUUUCAGCCCUGGU------UGGAAAGUACUAGGUUUUUAGAAA
................(((..(((((.(((((.........)))..))...)))))..)))((((((------........)))))).......... ( -17.30, z-score =   1.61, R)
>droEre2.scaffold_4690 6926839 92 - 18748788
-----ACCCGCUGAUGGCUCCAAAGCGGAAGAAUCUUCCCAUCCGGAACGGAAAAUUCCGGAAUAGAACUCACUUUGGAUUGUCAACUUGUGGGGGA
-----.((((((((..(.(((((((.(((((...)))))..(((((((.......)))))))..........))))))))..)))....)))))... ( -34.40, z-score =  -2.61, R)
>droSec1.super_17 391158 97 - 1527944
ACACACUCCACAGAUGGAUCCAAAGCGGAAGAGUCUUCCCAUCCGGAACGGAAAAUUCCGGAAUGGUAGCCACUUUGGAUUGCCAAUUUGUGGGAGA
.....((((((((((((((((((((.((..........((((((((((.......)))))).))))...)).))))))))..)).)))))).)))). ( -36.72, z-score =  -3.08, R)
>droSim1.chrX 12736629 97 - 17042790
ACCCACUCCACUGAUGGAUCCAAAGCGGAAGAGUCUUCCCAUCCGGAACGGAAAAUUCCGGAAUGGUAGCCACUUUGGAUUGCCAAUUUGUGGGAGA
.(((((((((....))))(((((((.((..........((((((((((.......)))))).))))...)).)))))))..........)))))... ( -34.32, z-score =  -1.92, R)
>consensus
_C_AACCCCACUGAUGGAUCCAAAGCGGAAGAGUCUUCCCAUCCGGAACGGAAAAUUCCGGAAUGGUAGCCACUUUGGAUUGCCAAUUUGUGGGAGA
......(((((...(((((((((((.(((((...)))))..(((((((.......)))))))..........))))))))..)))....)))))... (-20.74 = -21.98 +   1.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,568,501 – 16,568,605
Length 104
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 71.73
Shannon entropy 0.51886
G+C content 0.47823
Mean single sequence MFE -36.48
Consensus MFE -16.88
Energy contribution -19.47
Covariance contribution 2.59
Combinations/Pair 1.25
Mean z-score -2.46
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.16
SVM RNA-class probability 0.984273
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16568501 104 + 22422827
-------UCUCCCACAAAUUGACAAUCC-AAAGUGGCUACCAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGACUCUUCCGCUUUGGAUCCAUCAGUGGGG---GUGAAUCAUCGA
-------.(((((((....(((..((((-(((((((...((((.(((((((.....)))))))))))((....))..)))))))))))...)))))))))---)........... ( -41.40, z-score =  -3.28, R)
>droAna3.scaffold_13334 970066 101 + 1562580
-------UUUCUAAAAACCUAGUACUUU-------CCAACCAGGGCUGAAAGUCCUCCUACUGGUUCUAACUUCCAAGUGACUCAUAGCUAUUUUUGGGCCUGGGAACUUAUCAA
-------..........(((((.....(-------((((....(((((..((((((.....(((.........))))).))))..)))))....))))).))))).......... ( -20.70, z-score =   0.27, R)
>droEre2.scaffold_4690 6926839 102 + 18748788
-------UCCCCCACAAGUUGACAAUCC-AAAGUGAGUUCUAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGAUUCUUCCGCUUUGGAGCCAUCAGCGG-----GUGAAUCAUCGG
-------.....(((..(((((...(((-(((((.........((((((((.....))))))))..(((((...)))))))))))))....)))))..-----)))......... ( -36.70, z-score =  -2.66, R)
>droYak2.chrX 10675522 110 + 21770863
UUUGUUCUCUCCCGCAAAUUGGCAAUCCCAAAGUGGCUUCUAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGAUUCUUCCGCUUUGCCUCCAUCAGUGG-----GUGAAUCAUCGA
...((((...(((((....(((......(((((((((((((..((((((((.....))))))))..)))))......))))))))...)))...))))-----).))))...... ( -37.00, z-score =  -2.59, R)
>droSec1.super_17 391158 107 + 1527944
-------UCUCCCACAAAUUGGCAAUCC-AAAGUGGCUACCAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGACUCUUCCGCUUUGGAUCCAUCUGUGGAGUGUGUGAAUCAUCGA
-------....(((((...(((..((((-(((((((...((((.(((((((.....)))))))))))((....))..))))))))))))))..)))))................. ( -39.70, z-score =  -3.08, R)
>droSim1.chrX 12736629 107 + 17042790
-------UCUCCCACAAAUUGGCAAUCC-AAAGUGGCUACCAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGACUCUUCCGCUUUGGAUCCAUCAGUGGAGUGGGUGAAUCAUCGA
-------((.(((((..(((((..((((-(((((((...((((.(((((((.....)))))))))))((....))..)))))))))))...)))))...))))).))........ ( -43.40, z-score =  -3.42, R)
>consensus
_______UCUCCCACAAAUUGGCAAUCC_AAAGUGGCUACCAUUCCGGAAUUUUCCGUUCCGGAUGGGAAGACUCUUCCGCUUUGGAUCCAUCAGUGG_G___GUGAAUCAUCGA
...........((((....(((..((((.((((((....((((.(((((((.....)))))))))))((((...)))))))))))))))))...))))................. (-16.88 = -19.47 +   2.59)

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 01:50:16 2011