Locus 8484

Sequence ID dm3.chr3L
Location 23,557,000 – 23,557,192
Length 192
Max. P 0.999334
window11651 window11652 window11653

overview

Window 1

Location 23,557,000 – 23,557,111
Length 111
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 65.59
Shannon entropy 0.63985
G+C content 0.45874
Mean single sequence MFE -36.53
Consensus MFE -19.03
Energy contribution -18.92
Covariance contribution -0.11
Combinations/Pair 1.45
Mean z-score -2.61
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.80
SVM RNA-class probability 0.999334
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23557000 111 + 24543557
----AAAGUGCUGGCGCGGCAGUUCU-GGUUUCUUUUGCGGGAACUGUCGCAAUUUACAUCCCGUCUAAAUGCGGUGUCAGCA-UUGCGACAAAGUAGCACCGAGUUAGACUCGUGU
----..((((((((((((((((((((-.((.......)).)))))))))))..........((((......)))).)))))))-))...........((((.(((.....))))))) ( -45.00, z-score =  -3.67, R)
>droEre2.scaffold_4845 1256725 113 + 22589142
CAAUAAAGUGUUGAUGCGGCAGUUCU-AGUUUUGCUUAUGAGAACUGUCGCAACUGACAUCCUGUCAAAGUGCUUGGUCGGCAUUUGCAACAUAGUAGCACAUUCCAUUGUUUA---
.......((((((.((((((((((((-.((.......)).))))))))))))..((((.....))))(((((((.....))))))).........)))))).............--- ( -33.50, z-score =  -1.79, R)
>droYak2.chrU 1961451 111 + 28119190
CAAGAAAACGCUAGUGCGGCAGUUCUCAUUUCUGUUUAUAAGAACUGUCGCAAUGGACAUUCUGUCAAAGUGCUGUGUUGGCACUUGCAACAUUGUAAUAUAUUCCAUUGC------
.........((....))(((((((((.((........)).)))))))))((((((((..........(((((((.....)))))))(((....))).......))))))))------ ( -33.50, z-score =  -2.70, R)
>droSim1.chrU 2955080 100 + 15797150
----GAAAUGCUGCUGCGGCAGUUCU-AGGUUUGUUUACCAGAACUGUCGCAAUCGACAUCCUGUCCAC-UGCUACGUCAGCA-UUGCAACAGUGUUGGAGUUAGUG----------
----..........((((((((((((-.(((......)))))))))))))))...(((.....)))(((-((..((..(((((-(((...))))))))..)))))))---------- ( -38.30, z-score =  -3.30, R)
>droSec1.super_174 7093 100 - 34763
----GAAGUGCUGCUGCGGCAGUUCU-AGUUUUGUUUACCAGAACUGUCGCAAUCAACAUCCUGUCCAC-UGCUGCGUCAGCA-UUGCAACAGUGUUGGAGUUAGUG----------
----.....(((((((((((((((((-.((.......)).)))))))))))..((((((..((((.((.-(((((...)))))-.))..)))))))))))).)))).---------- ( -36.00, z-score =  -2.33, R)
>droVir3.scaffold_12728 224981 103 + 808307
UUACAAAUUGCCGUUGCAGCAGUUCA-AGUGUCUUGCAUGAGAACUGUCGCAACCAACAU------AAAGUGCUAGAACAGCA-UUGCACCAUAGUGUCACAAUGCUGUGC------
............(((((.(((((((.-.(((.....)))..))))))).)))))......------...........((((((-((((((....)))...)))))))))..------ ( -32.90, z-score =  -1.88, R)
>consensus
____AAAGUGCUGCUGCGGCAGUUCU_AGUUUUGUUUACGAGAACUGUCGCAAUCGACAUCCUGUCAAAGUGCUGCGUCAGCA_UUGCAACAUAGUAGCACAUAGCA_UGC______
.........(((((((((((((((((..............)))))))))))......(((.........)))....))))))................................... (-19.03 = -18.92 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 23,557,000 – 23,557,111
Length 111
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 65.59
Shannon entropy 0.63985
G+C content 0.45874
Mean single sequence MFE -34.16
Consensus MFE -15.36
Energy contribution -14.92
Covariance contribution -0.44
Combinations/Pair 1.33
Mean z-score -2.74
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.52
SVM RNA-class probability 0.998865
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23557000 111 - 24543557
ACACGAGUCUAACUCGGUGCUACUUUGUCGCAA-UGCUGACACCGCAUUUAGACGGGAUGUAAAUUGCGACAGUUCCCGCAAAAGAAACC-AGAACUGCCGCGCCAGCACUUU----
...((((.....))))(((((..((((((..((-(((.......)))))..)))))).........(((.((((((..............-.)))))).)))...)))))...---- ( -31.16, z-score =  -1.29, R)
>droEre2.scaffold_4845 1256725 113 - 22589142
---UAAACAAUGGAAUGUGCUACUAUGUUGCAAAUGCCGACCAAGCACUUUGACAGGAUGUCAGUUGCGACAGUUCUCAUAAGCAAAACU-AGAACUGCCGCAUCAACACUUUAUUG
---....(((((((.((((((..(((.((((((((((.......))).)))).))).)))..)))((((.(((((((.............-))))))).))))...))).))))))) ( -27.22, z-score =  -1.23, R)
>droYak2.chrU 1961451 111 - 28119190
------GCAAUGGAAUAUAUUACAAUGUUGCAAGUGCCAACACAGCACUUUGACAGAAUGUCCAUUGCGACAGUUCUUAUAAACAGAAAUGAGAACUGCCGCACUAGCGUUUUCUUG
------((((((((...((((....(((((.((((((.......))))))))))).))))))))))))..((((((((((........)))))))))).(((....)))........ ( -35.50, z-score =  -4.31, R)
>droSim1.chrU 2955080 100 - 15797150
----------CACUAACUCCAACACUGUUGCAA-UGCUGACGUAGCA-GUGGACAGGAUGUCGAUUGCGACAGUUCUGGUAAACAAACCU-AGAACUGCCGCAGCAGCAUUUC----
----------............(((((((((..-.......))))))-)))....((((((.(.(((((.((((((((((......))).-))))))).)))))).)))))).---- ( -35.80, z-score =  -3.29, R)
>droSec1.super_174 7093 100 + 34763
----------CACUAACUCCAACACUGUUGCAA-UGCUGACGCAGCA-GUGGACAGGAUGUUGAUUGCGACAGUUCUGGUAAACAAAACU-AGAACUGCCGCAGCAGCACUUC----
----------.......(((..(((((((((..-.......))))))-)))....)))(((((.(((((.((((((((((.......)))-))))))).))))))))))....---- ( -42.30, z-score =  -5.13, R)
>droVir3.scaffold_12728 224981 103 - 808307
------GCACAGCAUUGUGACACUAUGGUGCAA-UGCUGUUCUAGCACUUU------AUGUUGGUUGCGACAGUUCUCAUGCAAGACACU-UGAACUGCUGCAACGGCAAUUUGUAA
------((((((((((((..(.....)..))))-))))))..(((((....------.)))))((((((.((((((...((.....))..-.)))))).)))))).))......... ( -33.00, z-score =  -1.19, R)
>consensus
______GCA_AACAAUGUGCUACAAUGUUGCAA_UGCUGACACAGCACUUUGACAGGAUGUCGAUUGCGACAGUUCUCAUAAACAAAACU_AGAACUGCCGCACCAGCACUUU____
.........................(((((....(((.......)))..................((((.((((((................)))))).)))).)))))........ (-15.36 = -14.92 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 23,557,081 – 23,557,192
Length 111
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 63.21
Shannon entropy 0.65332
G+C content 0.49717
Mean single sequence MFE -33.64
Consensus MFE -11.92
Energy contribution -12.88
Covariance contribution 0.96
Combinations/Pair 1.22
Mean z-score -1.49
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.645509
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23557081 111 + 24543557
CGACAAAGUAGCACCGAGUUAGACUCGUGUAAGCAAUAAACU---UCUUGGCGGCUUGGCGGGGGGUACCGAAUUGUAUAUAUCCUGUAUGGUGGAUUCGGUAACUCAUGCACA
.......((.(((..(((((...(((((.(((((..(((...---..)))...))))))))))....((((((((...(((((...)))))...))))))))))))).))))). ( -29.50, z-score =   0.02, R)
>droEre2.scaffold_4845 1256811 114 + 22589142
CAACAUAGUAGCACAUUCCAUUGUUUAUGUGAGCAAUGAACUCUGUCUCGGCGGCUUGGCGGGUGGUACCGAAUCGUAUAUACUCUGUAAUGCGGUAUCGGUAACUCACGCGUA
.........(((......((((((((....)))))))).....(((....))))))..(((.(((((((((((((((((.(((...)))))))))).))))).)).))).))). ( -32.60, z-score =  -0.53, R)
>droSim1.chrU 2955160 103 + 15797150
----------CAACAGUGUUGGAGUUAGUGGAGCGAUGAACUGCUCCUAGGUGGCUUGGUGGGUGGUACCGAAUUGUGUAUACUCUGUAUAGGCGAUUCGGUAACUCCUCCCC-
----------((((...))))((((((.(((((((......))))))..).))))))((..((.(.(((((((((((.(((((...))))).))))))))))).).))..)).- ( -41.20, z-score =  -3.36, R)
>droSec1.super_174 7173 101 - 34763
----------CAACAGUGUUGGAGUUAGUGGGGCGAUGAACUGCUCCUAGGUGGCUUGGCGGGUGGUACCGAAUUGUAUAUACUCUGUAUAGGCGAUUCGGUAACUCGUGC---
----------((((...))))((((((.(((((((......))))))..).)))))).((((((..(((((((((((.(((((...))))).)))))))))))))))))..--- ( -37.50, z-score =  -2.83, R)
>droVir3.scaffold_12728 225060 95 + 808307
--------CACCAUAGUGUCA----CAAUGCUGUGCUG--CCGCCGCC--GUUUCUUGGCGGGGUGUACCGAAUCAUUUAUACCCUAUAUGGUAUAUUCAGUAACUCGCGC---
--------((.((((((((..----..)))))))).))--.(((((((--(.....)))))((((.(((.(((.....((((((......))))))))).)))))))))).--- ( -27.40, z-score =  -0.74, R)
>consensus
_________ACCACAGUGUUAGAGUUAGUGGAGCGAUGAACUGCUCCUAGGUGGCUUGGCGGGUGGUACCGAAUUGUAUAUACUCUGUAUAGGCGAUUCGGUAACUCAUGC___
..........................................................(((.(...(((((((((...(((((...)))))...)))))))))...).)))... (-11.92 = -12.88 +   0.96)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:46:28 2011