Locus 8962

Sequence ID	dm3.chr3R
Location	3,006,335 – 3,006,447
Length	112
Max. P	0.983272

overview

Window 3

Location	3,006,335 – 3,006,447
Length	112
Sequences	7
Columns	113
Reading direction	forward
Mean pairwise identity	68.22
Shannon entropy	0.64277
G+C content	0.57371
Mean single sequence MFE	-30.59
Consensus MFE	-11.67
Energy contribution	-14.31
Covariance contribution	2.64
Combinations/Pair	1.33
Mean z-score	-2.14
Structure conservation index	0.38
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.88
SVM RNA-class probability	0.973032
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3006335 112 + 27905053
ACAACCUGGGACCACAAGUUAGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGACCACCACCACCUCCGCCCCACCAGCAACACCAAUCCCUGACACC-
.......((((...............((((((...((((((...))))))....))))))..(((((....)))))......((.......))........)))).......- ( -28.50, z-score =  -2.59, R)
>droSim1.chr3R 3048670 103 + 27517382
ACAAUCUGGGACCACAAGUUAGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGACCGCC---------GCCCAACCAGCAACACCAGUCACUGACACC-
.....((((.................((((((...((((((...))))))....))))))..(((((....))---------)))...))))........(((...)))...- ( -27.40, z-score =  -1.51, R)
>droSec1.super_6 3098555 110 + 4358794
ACAACCUGGGACCGCAAGUUAGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGACCACCACCACCGCCGCCCCACCAGCAACACCAGUCACUGACA---
......((((.(.((...........((((((...((((((...))))))....))))))..(((((....)))))...)).).)))).(((..((....))..)))...--- ( -33.60, z-score =  -2.93, R)
>droYak2.chr3R_random 773275 109 + 3277457
ACAACUUGGGACCACAAGUUCGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGACCACCACCG---CCGCCCCAUCAGCAGCACCAGUCUCUAACACC-
.......(((((..............((((((...((((((...))))))....))))))..(((((....)))))(---(.((.......)).))....))))).......- ( -31.40, z-score =  -2.68, R)
>droEre2.scaffold_4770 3268700 109 + 17746568
ACAACCUGGGACCGCAAGUUAGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGCGGAUCACCACCG---CCGCCUCAUCAGCAACACCAGUCCCAGCAUCC-
.....((((((((....)...((...((((((...((((((...))))))....))))))..(((((.......)))---))......))..........))))))).....- ( -37.00, z-score =  -4.46, R)
>droAna3.scaffold_13340 2779710 89 + 23697760
ACAAUUUACCCUCGCAAGUGAGAAUCGAGCAGAUAUUGCAACACCUGCAGCAAAGUGUUCCAGGAGGACCUAC------------CCACCAGCAGCAGCAA------------
..........((((....)))).(((.....))).((((....((((.(((.....))).)))).((......------------))....))))......------------ ( -16.10, z-score =   0.29, R)
>anoGam1.chr2R 23269641 101 + 62725911
---------ACUCGCAAGAUCCGAACCAGCUGGCG--GCACCGCCCG-GGCAUGGUCUACUGCACGGCCAGAACGUGCCACCGUACCAGCCACAGCUUCCGGCGCCGCCCGCC
---------..((....)).........((.((((--((.(((..(.-(((.(((((....(((((.......)))))....).)))))))...)....))).)))))).)). ( -40.10, z-score =  -1.07, R)
>consensus
ACAACCUGGGACCGCAAGUUAGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGACCACCACCG___CCGCCCCACCAGCAACACCAGUCACUGACACC_
.....((((.................((((((...((((((...))))))....))))))..(((((.............)))))............))))............ (-11.67 = -14.31 +   2.64)

alignment

secondary structure

dotplot

Window 4

Location	3,006,335 – 3,006,447
Length	112
Sequences	7
Columns	113
Reading direction	reverse
Mean pairwise identity	68.22
Shannon entropy	0.64277
G+C content	0.57371
Mean single sequence MFE	-43.61
Consensus MFE	-18.43
Energy contribution	-20.08
Covariance contribution	1.64
Combinations/Pair	1.56
Mean z-score	-2.05
Structure conservation index	0.42
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.13
SVM RNA-class probability	0.983272
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3006335 112 - 27905053
-GGUGUCAGGGAUUGGUGUUGCUGGUGGGGCGGAGGUGGUGGUGGUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCUAACUUGUGGUCCCAGGUUGU
-....((((.(((....))).))))((((((.((((((((((....)))))..((((((..((((((((...)))))))).)))))).......)))).).))))))...... ( -44.40, z-score =  -2.23, R)
>droSim1.chr3R 3048670 103 - 27517382
-GGUGUCAGUGACUGGUGUUGCUGGUUGGGC---------GGCGGUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCUAACUUGUGGUCCCAGAUUGU
-....((((..((....))..))))((((((---------.((((....))..((((((..((((((((...)))))))).))))))...........)).).)))))..... ( -38.60, z-score =  -1.40, R)
>droSec1.super_6 3098555 110 - 4358794
---UGUCAGUGACUGGUGUUGCUGGUGGGGCGGCGGUGGUGGUGGUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCUAACUUGCGGUCCCAGGUUGU
---..((((..((....))..))))((((((.((((((((((....)))))..((((((..((((((((...)))))))).)))))).......)).))).))))))...... ( -51.30, z-score =  -3.63, R)
>droYak2.chr3R_random 773275 109 - 3277457
-GGUGUUAGAGACUGGUGCUGCUGAUGGGGCGG---CGGUGGUGGUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCGAACUUGUGGUCCCAAGUUGU
-((..((((...))))..)).....((((((.(---((((((....)))))..((((((..((((((((...)))))))).))))))...........)).))))))...... ( -44.90, z-score =  -2.46, R)
>droEre2.scaffold_4770 3268700 109 - 17746568
-GGAUGCUGGGACUGGUGUUGCUGAUGAGGCGG---CGGUGGUGAUCCGCCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCUAACUUGCGGUCCCAGGUUGU
-.....(((((((((..((((((.....)))))---)(((((....)))))..((((((..((((((((...)))))))).))))))............)))))))))..... ( -50.60, z-score =  -3.87, R)
>droAna3.scaffold_13340 2779710 89 - 23697760
------------UUGCUGCUGCUGGUGG------------GUAGGUCCUCCUGGAACACUUUGCUGCAGGUGUUGCAAUAUCUGCUCGAUUCUCACUUGCGAGGGUAAAUUGU
------------(((((..(((.(((((------------(..(.(((....))).)...(((..((((((((....)))))))).)))..)))))).)))..)))))..... ( -26.60, z-score =  -0.45, R)
>anoGam1.chr2R 23269641 101 - 62725911
GGCGGGCGGCGCCGGAAGCUGUGGCUGGUACGGUGGCACGUUCUGGCCGUGCAGUAGACCAUGCC-CGGGCGGUGC--CGCCAGCUGGUUCGGAUCUUGCGAGU---------
(((.(((((((((((..((((((((..(.(((......))).)..)))..)))))...))..((.-...)))))))--)))).)))..((((.......)))).--------- ( -48.90, z-score =  -0.28, R)
>consensus
_GGUGUCAGGGACUGGUGUUGCUGGUGGGGCGG___CGGUGGUGGUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCUAACUUGCGGUCCCAGGUUGU
............((((..((((.....(((.((.............)).))).((((((..((((((((...)))))))).))))))...........))))..))))..... (-18.43 = -20.08 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:55:31 2011