Locus 14854

Sequence ID dm3.chrX
Location 15,876,759 – 15,876,934
Length 175
Max. P 0.953091
window20456 window20457 window20458 window20459

overview

Window 6

Location 15,876,759 – 15,876,868
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.36
Shannon entropy 0.09399
G+C content 0.47315
Mean single sequence MFE -34.36
Consensus MFE -29.45
Energy contribution -29.45
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.872601
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15876759 109 + 22422827
CAGUUUGACCUAAAAAUGAAAAUACAAAUACCUACUGAGUCAUCGCUAUACC----ACUC--AGUAUGUGCGUGUGUCCAUGUCGGAGC-----AUGCUCCGAACGUGGGUUGCUGGCCA
((((..((((...........(((((..(((.((((((((............----))))--)))).)))..))))).((((((((((.-----...))))).))))))))))))).... ( -37.10, z-score =  -3.41, R)
>droEre2.scaffold_4690 7575303 115 - 18748788
CAGUUUGACCUAAAAAUGAAAAUACAAAUACCUACUGAGUCAUCGCUAUACCGAAUACUCGUAGUAUGUGCGUGUGUCCAUGUCGGAGC-----AUGCUCCGAACGCGGGUUGCUGGCCA
((((..(((((....(((...(((((..(((.((((((((..(((......)))..))))..)))).)))..))))).))).((((((.-----...))))))....))))))))).... ( -32.70, z-score =  -1.51, R)
>droYak2.chrX 10065550 120 + 21770863
CAGUUUGACCUAAAAAUGAAAAUACAAAUACCUACUGAGUCAUCGCUAUACCCAAUACUCGUAGUAUGUGCGUGUGUCCAUGUCGGAGCGGAGCAUGCUCCGAACGCGGGUUGCUGGCCA
((((..(((((....(((...(((((..(((.((((((((................))))..)))).)))..))))).))).((((((((.....))))))))....))))))))).... ( -31.99, z-score =  -0.38, R)
>droSec1.super_183 1701 109 + 33538
CAGUUUGACCUAAAAAUGAAAAUACAAAUACCUACUGAGUCAUCGCUAUACC----ACUC--AGUAUGUGUGUGUGUCCAUGUCGGAGC-----AUGCUCCGAACGCGGGUUGCUGGCCA
((((..(((((....(((...(((((.((((.((((((((............----))))--)))).)))).))))).))).((((((.-----...))))))....))))))))).... ( -35.50, z-score =  -2.91, R)
>droSim1.chrX 12288367 109 + 17042790
CAGUUUGACCUAAAAAUGAAAAUACAAAUACCUACUGAGUCAUCGCUAUACC----ACUC--AGUAUGUGCGUGUGUCCAUGUCGGAGC-----AUGCUCCGAACGCGGGUUGCUGGCCA
((((..(((((....(((...(((((..(((.((((((((............----))))--)))).)))..))))).))).((((((.-----...))))))....))))))))).... ( -34.50, z-score =  -2.50, R)
>consensus
CAGUUUGACCUAAAAAUGAAAAUACAAAUACCUACUGAGUCAUCGCUAUACC____ACUC__AGUAUGUGCGUGUGUCCAUGUCGGAGC_____AUGCUCCGAACGCGGGUUGCUGGCCA
((((..(((((....(((...(((((..(((.((((((((................))))..)))).)))..))))).))).(((((((.......)))))))....))))))))).... (-29.45 = -29.45 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,876,759 – 15,876,868
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.36
Shannon entropy 0.09399
G+C content 0.47315
Mean single sequence MFE -34.12
Consensus MFE -29.30
Energy contribution -28.98
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -2.19
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.888824
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15876759 109 - 22422827
UGGCCAGCAACCCACGUUCGGAGCAU-----GCUCCGACAUGGACACACGCACAUACU--GAGU----GGUAUAGCGAUGACUCAGUAGGUAUUUGUAUUUUCAUUUUUAGGUCAAACUG
(((((......(((.((.(((((...-----.))))))).)))(((.(..(...((((--((((----.((......)).)))))))).)..).))).............)))))..... ( -35.20, z-score =  -2.89, R)
>droEre2.scaffold_4690 7575303 115 + 18748788
UGGCCAGCAACCCGCGUUCGGAGCAU-----GCUCCGACAUGGACACACGCACAUACUACGAGUAUUCGGUAUAGCGAUGACUCAGUAGGUAUUUGUAUUUUCAUUUUUAGGUCAAACUG
(((((......(((.((.(((((...-----.))))))).)))......(((.(((((((((((..(((......)))..)))).))).)))).))).............)))))..... ( -33.30, z-score =  -2.08, R)
>droYak2.chrX 10065550 120 - 21770863
UGGCCAGCAACCCGCGUUCGGAGCAUGCUCCGCUCCGACAUGGACACACGCACAUACUACGAGUAUUGGGUAUAGCGAUGACUCAGUAGGUAUUUGUAUUUUCAUUUUUAGGUCAAACUG
(((((......(((.((.((((((.......)))))))).)))......(((.(((((((((((((((.......)))).)))).))).)))).))).............)))))..... ( -33.90, z-score =  -1.24, R)
>droSec1.super_183 1701 109 - 33538
UGGCCAGCAACCCGCGUUCGGAGCAU-----GCUCCGACAUGGACACACACACAUACU--GAGU----GGUAUAGCGAUGACUCAGUAGGUAUUUGUAUUUUCAUUUUUAGGUCAAACUG
(((((......(((.((.(((((...-----.))))))).)))..(((.(.((.((((--((((----.((......)).)))))))).)).).))).............)))))..... ( -33.70, z-score =  -2.42, R)
>droSim1.chrX 12288367 109 - 17042790
UGGCCAGCAACCCGCGUUCGGAGCAU-----GCUCCGACAUGGACACACGCACAUACU--GAGU----GGUAUAGCGAUGACUCAGUAGGUAUUUGUAUUUUCAUUUUUAGGUCAAACUG
(((((......(((.((.(((((...-----.))))))).)))(((.(..(...((((--((((----.((......)).)))))))).)..).))).............)))))..... ( -34.50, z-score =  -2.32, R)
>consensus
UGGCCAGCAACCCGCGUUCGGAGCAU_____GCUCCGACAUGGACACACGCACAUACU__GAGU____GGUAUAGCGAUGACUCAGUAGGUAUUUGUAUUUUCAUUUUUAGGUCAAACUG
(((((......(((.((.((((((.......)))))))).)))......(((.(((((..((((....(......)....))))....))))).))).............)))))..... (-29.30 = -28.98 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,876,799 – 15,876,908
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.32
Shannon entropy 0.11204
G+C content 0.52461
Mean single sequence MFE -45.90
Consensus MFE -36.88
Energy contribution -36.76
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.67
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.45
SVM RNA-class probability 0.938903
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15876799 109 + 22422827
CAUCGCUAUACC----ACUC--AGUAUGUGCGUGUGUCCAUGUCGGA-----GCAUGCUCCGAACGUGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGCGAGUUUGCGU
..(((((((((.----....--.)))))((((.((((((((((((((-----(....))))).))))..(((((..((((......))))..))))).))))))))))))))........ ( -45.80, z-score =  -3.05, R)
>droEre2.scaffold_4690 7575343 115 - 18748788
CAUCGCUAUACCGAAUACUCGUAGUAUGUGCGUGUGUCCAUGUCGGA-----GCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGCGAGUUUGCGU
..((((((((((((....)))..)))))((((.((((((...(((((-----(....))))))......(((((..((((......))))..))))).))))))))))))))........ ( -45.90, z-score =  -2.55, R)
>droYak2.chrX 10065590 120 + 21770863
CAUCGCUAUACCCAAUACUCGUAGUAUGUGCGUGUGUCCAUGUCGGAGCGGAGCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUGGCAGCGAGUUUGCGU
....((((((.((.((((.((((.....)))).))))((.((((((((((.....))))))).))).))(((((..((((......))))..))))).)).)))))).(((....))).. ( -49.60, z-score =  -2.44, R)
>droSec1.super_183 1741 109 + 33538
CAUCGCUAUACC----ACUC--AGUAUGUGUGUGUGUCCAUGUCGGA-----GCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGCGAGUUUGUGU
..((((((((((----((..--.....))).))))((((...(((((-----(....))))))......(((((..((((......))))..))))).)))).....)))))........ ( -43.20, z-score =  -2.49, R)
>droSim1.chrX 12288407 109 + 17042790
CAUCGCUAUACC----ACUC--AGUAUGUGCGUGUGUCCAUGUCGGA-----GCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGUGAGUUUGCGU
...(((...(((----((((--(((((.(.(((((.......(((((-----(....))))))))))).(((((..((((......))))..))))).).)))))).)))).))..))). ( -45.01, z-score =  -2.82, R)
>consensus
CAUCGCUAUACC____ACUC__AGUAUGUGCGUGUGUCCAUGUCGGA_____GCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGCGAGUUUGCGU
..(((((((((............)))))((((.((((((...(((((...........)))))......(((((..((((......))))..))))).))))))))))))))........ (-36.88 = -36.76 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,876,833 – 15,876,934
Length 101
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.26
Shannon entropy 0.22434
G+C content 0.59296
Mean single sequence MFE -44.50
Consensus MFE -39.82
Energy contribution -39.70
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.93
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.59
SVM RNA-class probability 0.953091
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15876833 101 + 22422827
-----UGUCGGAGCAUGCUCCGAACGUGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGCGAGUUUGCGUGUCCGCGCAGCCCGACGACUCCCAGG--------------
-----..((((((....)))))).((((((((((..(((((((....)))))))....((((((.((((.....))))))))))..))))))).))).........-------------- ( -44.40, z-score =  -2.57, R)
>droEre2.scaffold_4690 7575383 115 - 18748788
-----UGUCGGAGCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGCGAGUUUGCGUGUCCGCGCAGCACGACGACUCCCAAAUCCCAGGUCCCAAG
-----..((((((....))))))....(((((((..((((......))))..))))).((((.(((..(.(((((..(((((.......)))))..)))))))))))))......))... ( -43.40, z-score =  -1.46, R)
>droYak2.chrX 10065630 120 + 21770863
UGUCGGAGCGGAGCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUGGCAGCGAGUUUGCGUGUCCGCGCAGCCCGACGACUCCCAAAUCCCAAAUCCCAGG
.(((((.((((((....))))....(((.(((((..((((......))))..))))).(((((((.(((.....)))))))))).))).)))))))........................ ( -50.00, z-score =  -2.15, R)
>droSec1.super_183 1775 101 + 33538
-----UGUCGGAGCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGCGAGUUUGUGUGUCCGCGCAGCGCGACGACUCCCAGG--------------
-----.((((..((.(((.(((....)))(((((..((((......))))..))))).((((((.((((.....))))))))))..)))..))..)))).......-------------- ( -40.60, z-score =  -1.22, R)
>droSim1.chrX 12288441 101 + 17042790
-----UGUCGGAGCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGUGAGUUUGCGUGUCCGCGCAGCGCGACGACUCCCAGG--------------
-----.((((..((.(((.(((....)))(((((..((((......))))..))))).((((((.((((.....))))))))))..)))..))..)))).......-------------- ( -44.10, z-score =  -2.26, R)
>consensus
_____UGUCGGAGCAUGCUCCGAACGCGGGUUGCUGGCCAAUUAUCUGGUUGGCAACAGGAUAUUGCAGCGAGUUUGCGUGUCCGCGCAGCCCGACGACUCCCAGG______________
.......((((((....))))))..(((.(((((..((((......))))..))))).((((((.((((.....)))))))))).)))................................ (-39.82 = -39.70 +  -0.12)

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 01:48:11 2011