Locus 8948

Sequence ID	dm3.chr3R
Location	2,862,001 – 2,862,097
Length	96
Max. P	0.997948

overview

Window 5

Location	2,862,001 – 2,862,097
Length	96
Sequences	7
Columns	116
Reading direction	forward
Mean pairwise identity	62.60
Shannon entropy	0.68642
G+C content	0.51848
Mean single sequence MFE	-26.81
Consensus MFE	-14.39
Energy contribution	-14.27
Covariance contribution	-0.12
Combinations/Pair	1.12
Mean z-score	-1.93
Structure conservation index	0.54
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.22
SVM RNA-class probability	0.997948
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2862001 96 + 27905053
UGUACUUCUUCUUAGGGCAAAGUAUCCCACGGAUCCC-----ACAGUCUCCACCGCCGACGGCAAC-UU-CCCUGGUUCUCAAAUCCGUCGGCAGUUGUCACG-------------
...............(((((..........(((..(.-----...)..)))...((((((((.(((-(.-....)))).......))))))))..)))))...------------- ( -22.90, z-score =  -0.81, R)
>droSim1.chr3R 2901905 95 + 27517382
UGUACUUCUUCUUAAGGCAAAGUAUCCCACGGAUGC------ACAGUCUCCACCGCCGACGGCAAG-UU-CCCUGGUUCUCAAAUCCGUCGGCAAUUGUCACG-------------
...............(((((.((((((...))))))------............((((((((..((-..-(....)..)).....))))))))..)))))...------------- ( -28.30, z-score =  -3.10, R)
>droSec1.super_6 2952595 95 + 4358794
UGUACUUCUUCUUAGGGCAAAGUAUCCCACAGAUGC------ACAGUCUCCACAGCCGACGGCAAC-UU-CCCUGGUUCUCAAAUCCGUCGGCAAUUGUCACG-------------
...............(((((.(((((.....)))))------............((((((((.(((-(.-....)))).......))))))))..)))))...------------- ( -24.70, z-score =  -2.13, R)
>droYak2.chr3R 21295043 94 - 28832112
UGAAAUUCAUCUUGUGGCACAGUGUCGCAGUGAUGCACCUGAACAGUCUUCACCGCCGACGGCAAC-UU-ACCAUGUUCUCAAAUCCGUCGGCACG--------------------
.......(((((((((((.....))))))).))))....((((.....))))..((((((((....-..-...............))))))))...-------------------- ( -25.90, z-score =  -1.00, R)
>droEre2.scaffold_4770 3114574 100 + 17746568
GAUACUUCUUCUUAUGGCGAAGUAUCAGACGGAUGCACAUGAAGAGACUCCACCGCCGACGGCAAC-UU-CCA-GGUUUUCAAAUCCGUCGGCAGUUGUCACG-------------
((((((((.((....)).)))))))).((((((..(.(.....).)..)))...((((((((.(((-(.-...-)))).......))))))))....)))...------------- ( -31.90, z-score =  -2.50, R)
>droAna3.scaffold_13340 18496228 93 - 23697760
------UUUUCCUCUACUGAUGGUUUUUCCAGACACGC----ACUAUCUUACCAGCCGACGGUUUCGUCAUCCUCAGUUACAAAUCCGUCGGUAGCUGCCAUG-------------
------.......((((((((((.(((....(((..((----............)).((((....)))).......)))..))).))))))))))........------------- ( -19.20, z-score =  -1.34, R)
>dp4.chr2 11336467 100 - 30794189
----------CUUGGACU----UUUCCUCCUGCUUUUCCUGCACAGACG-CAAAGCCGACGGCUAUGUU-UCUUGAGACACAAAUCCGUCGGCAGUUGUCUGGCCCUCGAAAAGGU
----------...(((..----..))).....((((((..((.((((((-.(..((((((((...(((.-((....)).)))...))))))))..)))))))))....)))))).. ( -34.80, z-score =  -2.67, R)
>consensus
UGUACUUCUUCUUAGGGCAAAGUAUCCCACGGAUGC_C____ACAGUCUCCACCGCCGACGGCAAC_UU_CCCUGGUUCUCAAAUCCGUCGGCAGUUGUCACG_____________
......................................................((((((((.......................))))))))....................... (-14.39 = -14.27 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	2,862,001 – 2,862,097
Length	96
Sequences	7
Columns	116
Reading direction	reverse
Mean pairwise identity	62.60
Shannon entropy	0.68642
G+C content	0.51848
Mean single sequence MFE	-29.76
Consensus MFE	-13.89
Energy contribution	-14.03
Covariance contribution	0.14
Combinations/Pair	1.00
Mean z-score	-1.12
Structure conservation index	0.47
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.18
SVM RNA-class probability	0.905001
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2862001 96 - 27905053
-------------CGUGACAACUGCCGACGGAUUUGAGAACCAGGG-AA-GUUGCCGUCGGCGGUGGAGACUGU-----GGGAUCCGUGGGAUACUUUGCCCUAAGAAGAAGUACA
-------------.(((((.(((((((((((.((((.....)))).-..-....)))))))))))(((..(...-----.)..)))))(((........)))..........))). ( -30.40, z-score =  -0.86, R)
>droSim1.chr3R 2901905 95 - 27517382
-------------CGUGACAAUUGCCGACGGAUUUGAGAACCAGGG-AA-CUUGCCGUCGGCGGUGGAGACUGU------GCAUCCGUGGGAUACUUUGCCUUAAGAAGAAGUACA
-------------.(((.(....((((((((....(((..(....)-..-))).))))))))((..(((.(..(------(....))..)....)))..))..........)))). ( -28.10, z-score =  -0.73, R)
>droSec1.super_6 2952595 95 - 4358794
-------------CGUGACAAUUGCCGACGGAUUUGAGAACCAGGG-AA-GUUGCCGUCGGCUGUGGAGACUGU------GCAUCUGUGGGAUACUUUGCCCUAAGAAGAAGUACA
-------------.....((...((((((((.((((.....)))).-..-....))))))))..))......((------((.(((..(((........))).....))).)))). ( -27.90, z-score =  -0.90, R)
>droYak2.chr3R 21295043 94 + 28832112
--------------------CGUGCCGACGGAUUUGAGAACAUGGU-AA-GUUGCCGUCGGCGGUGAAGACUGUUCAGGUGCAUCACUGCGACACUGUGCCACAAGAUGAAUUUCA
--------------------.(((.(.((((............(((-..-...)))((((.((((((.((((.....))).).)))))))))).))))).)))............. ( -25.10, z-score =   0.90, R)
>droEre2.scaffold_4770 3114574 100 - 17746568
-------------CGUGACAACUGCCGACGGAUUUGAAAACC-UGG-AA-GUUGCCGUCGGCGGUGGAGUCUCUUCAUGUGCAUCCGUCUGAUACUUCGCCAUAAGAAGAAGUAUC
-------------...(((.(((((((((((.(((.(.....-).)-))-....)))))))))))(((....(.....)....)))))).((((((((..........)))))))) ( -35.20, z-score =  -2.64, R)
>droAna3.scaffold_13340 18496228 93 + 23697760
-------------CAUGGCAGCUACCGACGGAUUUGUAACUGAGGAUGACGAAACCGUCGGCUGGUAAGAUAGU----GCGUGUCUGGAAAAACCAUCAGUAGAGGAAAA------
-------------.((((..(((((((((((.(((((..(....)...))))).))))))).)))).(((((..----...))))).......)))).............------ ( -24.20, z-score =  -0.99, R)
>dp4.chr2 11336467 100 + 30794189
ACCUUUUCGAGGGCCAGACAACUGCCGACGGAUUUGUGUCUCAAGA-AACAUAGCCGUCGGCUUUG-CGUCUGUGCAGGAAAAGCAGGAGGAAA----AGUCCAAG----------
..((((((....(((((((....((((((((...(((.((....))-.)))...))))))))....-.))))).))..)))))).....(((..----..)))...---------- ( -37.40, z-score =  -2.61, R)
>consensus
_____________CGUGACAACUGCCGACGGAUUUGAGAACCAGGG_AA_GUUGCCGUCGGCGGUGGAGACUGU____G_GCAUCCGUGGGAUACUUUGCCAUAAGAAGAAGUACA
.......................((((((((.......................))))))))...................................................... (-13.89 = -14.03 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:55:16 2011