Locus 2793

Sequence ID dm3.chr2L
Location 22,411,986 – 22,412,129
Length 143
Max. P 0.999762
window3843 window3844

overview

Window 3

Location 22,411,986 – 22,412,129
Length 143
Sequences 5
Columns 172
Reading direction forward
Mean pairwise identity 72.16
Shannon entropy 0.50547
G+C content 0.53388
Mean single sequence MFE -56.20
Consensus MFE -33.70
Energy contribution -35.70
Covariance contribution 2.00
Combinations/Pair 1.15
Mean z-score -1.82
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.90
SVM RNA-class probability 0.974106
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22411986 143 + 23011544
--------------UUCUUGGCUUCAGAAU--------------ACCCGGGCUUGAA-CUUCGGCCGGCGGUAGUGCUCUACUGACUGUGGUCUCGGAGCUCUACUCACUCCACCACCGCCGGCGGCAAUGGCACAGCAUCCUGGGGUAACCUUGAACUUCGUCUGAUUUGA
--------------.........(((((..--------------.((((((..((..-.....(((((((((((.(((((...(((....)))..))))).))............))))))))).((....))....)).))))))((........))....)))))..... ( -46.50, z-score =  -0.19, R)
>droSim1.chrU 12456498 161 - 15797150
--------UUUUGCUUUUUGGCUUCAGAAUACCACA--UACCAUACCUGGGUUUGAA-CUCCGGCCGGCGGUAGUGCUCUACUGACUAGGGUGUCGGAGCUCUACUCACUCCACUACCGCCGGCGGCAAUGGCAUAGCAUCCUGGGAUAAGCUUGAAUUUCGUCUGAUUUGA
--------....(((....))).(((((........--..((((.(((((((....)-).)))(((((((((((((......(((.((((((......)))))).)))...)))))))))))))))..))))((.((((((....)))..))))).......)))))..... ( -53.00, z-score =  -1.60, R)
>droSec1.super_162 22550 170 + 37850
--UUUUGCUUUUUGUUUUUGGCUUCAGAAUACCACACAUACCAAACCUGGGUUUGAAACUCCGGCCGGCGGUAGUGCUCUACUGACUGGGGUGUCGGAGCUCUACUCACUCCACUACCGCCGGCGGCAAUGGCAUAGCAUCCUGGGAUAAACUUGAAUUUCGUCUGAUUUGA
--....(((...(((..(((.(((((((...(((.............))).))))))......(((((((((((((......(((.((((((......)))))).)))...)))))))))))))).)))..))).)))(((....)))....(..((((......))))..) ( -54.12, z-score =  -1.72, R)
>droYak2.chrU 23210840 165 - 28119190
UUUAGAACUUUUACCACCGGGAUUAAGUCCCGGUUCCAUACUAUACCUGGGCUUGAA-CUCCGGCCGGCGUCAGUUCUCU-CCGACAAGGAUGUCGAAGCUG-----ACUCCACUACCGCCGGCGGCAAUGGGACAGCAUCCUAGGUUAAACUUGAACUUUGUCUGCUCUGA
.(((((.......(((.((((.((((((((.(((..........))).)))))))).-).)))(((((((..(((((.((-.(((((....))))).))..)-----)....)))..))))))).....)))....(((..(.(((((.......))))).)..)))))))) ( -53.00, z-score =  -1.32, R)
>droEre2.scaffold_4929 12731544 166 - 26641161
---CUUAGGUUCGGAACC-GACGUCGGUUCUGGUUCUGUCCCACGUA-GGGCUUGAA-CUCCGGCCGGCGGUAGCACUCUCCUAACUGGGGAGACCGAGCUCUACUCACUCCACUACCGCCGGCCCCGAUGGGACAGCAUCCUAGGUUUAACUUGAACUACGUCUGCUUUGA
---((((((.((((((((-(....)))))))))..((((((((((..-(((......-.)))((((((((((((..((((((.....))))))...(((.....)))......)))))))))))).)).))))))))...)))))).......................... ( -74.40, z-score =  -4.28, R)
>consensus
________UUUUGCUUCUUGGCUUCAGAAUACCACA__UACCAUACCUGGGCUUGAA_CUCCGGCCGGCGGUAGUGCUCUACUGACUGGGGUGUCGGAGCUCUACUCACUCCACUACCGCCGGCGGCAAUGGCACAGCAUCCUGGGAUAAACUUGAACUUCGUCUGAUUUGA
.............................................((((((..((.....(((((((((((((((((((((.....))))))...((((.........)))))))))))))))).....))).....)).)))))).......................... (-33.70 = -35.70 +   2.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,411,986 – 22,412,129
Length 143
Sequences 5
Columns 172
Reading direction reverse
Mean pairwise identity 72.16
Shannon entropy 0.50547
G+C content 0.53388
Mean single sequence MFE -62.34
Consensus MFE -35.02
Energy contribution -37.22
Covariance contribution 2.20
Combinations/Pair 1.30
Mean z-score -3.72
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.33
SVM RNA-class probability 0.999762
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22411986 143 - 23011544
UCAAAUCAGACGAAGUUCAAGGUUACCCCAGGAUGCUGUGCCAUUGCCGCCGGCGGUGGUGGAGUGAGUAGAGCUCCGAGACCACAGUCAGUAGAGCACUACCGCCGGCCGAAG-UUCAAGCCCGGGU--------------AUUCUGAAGCCAAGAA--------------
.....(((((.(((.(((..(((....((((....))).).....)))(((((((((((((((((.......)))))..(((....)))........)))))))))))).))).-)))..((....))--------------..))))).........-------------- ( -51.00, z-score =  -2.05, R)
>droSim1.chrU 12456498 161 + 15797150
UCAAAUCAGACGAAAUUCAAGCUUAUCCCAGGAUGCUAUGCCAUUGCCGCCGGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCUAGUCAGUAGAGCACUACCGCCGGCCGGAG-UUCAAACCCAGGUAUGGUA--UGUGGUAUUCUGAAGCCAAAAAGCAAAA--------
....................((((....((((((((((((((((.((((((((((((((((((((.......)))))(((......)))........)))))))))))).((.(-(....)))).)))))))).--.)))))))))))))))............-------- ( -62.50, z-score =  -4.83, R)
>droSec1.super_162 22550 170 - 37850
UCAAAUCAGACGAAAUUCAAGUUUAUCCCAGGAUGCUAUGCCAUUGCCGCCGGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCCAGUCAGUAGAGCACUACCGCCGGCCGGAGUUUCAAACCCAGGUUUGGUAUGUGUGGUAUUCUGAAGCCAAAAACAAAAAGCAAAA--
.......((((.........))))....(((((((((((((.....(((((((((((((((((((.......)))))(((......)))........))))))))))).)))....((((((....))))))...)))))))))))))......................-- ( -59.50, z-score =  -3.86, R)
>droYak2.chrU 23210840 165 + 28119190
UCAGAGCAGACAAAGUUCAAGUUUAACCUAGGAUGCUGUCCCAUUGCCGCCGGCGGUAGUGGAGU-----CAGCUUCGACAUCCUUGUCGG-AGAGAACUGACGCCGGCCGGAG-UUCAAGCCCAGGUAUAGUAUGGAACCGGGACUUAAUCCCGGUGGUAAAAGUUCUAAA
..(((((.((((..((((.((......)).))))..))))(((((((((....))))))))).((-----(((((((((((....))))))-))....)))))((((.((((..-((.((((((.(((..........)))))).)))))..))))))))....)))))... ( -64.60, z-score =  -3.52, R)
>droEre2.scaffold_4929 12731544 166 + 26641161
UCAAAGCAGACGUAGUUCAAGUUAAACCUAGGAUGCUGUCCCAUCGGGGCCGGCGGUAGUGGAGUGAGUAGAGCUCGGUCUCCCCAGUUAGGAGAGUGCUACCGCCGGCCGGAG-UUCAAGCCC-UACGUGGGACAGAACCAGAACCGACGUC-GGUUCCGAACCUAAG---
..............((((............((...((((((((.((.(((((((((((((.((((.......))))(.(((((.......))))).))))))))))))))((.(-(....))))-..))))))))))..)).((((((....)-))))).)))).....--- ( -74.10, z-score =  -4.35, R)
>consensus
UCAAAUCAGACGAAGUUCAAGUUUAACCCAGGAUGCUGUGCCAUUGCCGCCGGCGGUAGUGGAGUGAGUAGAGCUCCGACACCCCAGUCAGUAGAGCACUACCGCCGGCCGGAG_UUCAAGCCCAGGUAUGGUA__GAACCUAUUCUGAAGCCAAGAACCAAAA________
.....((((.....((((............))))...((((((.(((((((((((((((((((((.......)))))(((......)))........)))))))))))).((..........)).))))))))))..........))))....................... (-35.02 = -37.22 +   2.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:58:03 2011