Locus 6524

Sequence ID dm3.chr3L
Location 7,345,257 – 7,345,397
Length 140
Max. P 0.976727
window8983 window8984

overview

Window 3

Location 7,345,257 – 7,345,397
Length 140
Sequences 6
Columns 141
Reading direction forward
Mean pairwise identity 64.29
Shannon entropy 0.66691
G+C content 0.46393
Mean single sequence MFE -31.39
Consensus MFE -20.55
Energy contribution -20.08
Covariance contribution -0.47
Combinations/Pair 1.38
Mean z-score -0.36
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.88
SVM RNA-class probability 0.842538
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7345257 140 + 24543557
AAAAGUAGAAAUUCGCACACAUCCCAUCGUUGCUACGUGUUUUGUGCUAAACUAAAGUAAUC-UCUCAACCCACACAGGUGGCUCGUUUGGGUAGCAAUCCGUACAUGGACCGCCUGCUCAACAAGCUGCUGUCGUGGAAG
..............(((((.....((.(((....)))))...)))))...............-.......(((((((.(..(((.(((.(((((((..((((....))))..).))))))))).)))..)))).))))... ( -36.20, z-score =  -0.47, R)
>droSim1.chr3L 6862708 140 + 22553184
AAAUGUAGAAAUUCGCACACAUCCCAUCGUUGCUACGUGUUUUGUGCUAAACUAAAGUAAUC-UCUCAACCCACACAGGUGGCUCGUCUGGGUAGUAAUCCGUACAUGGACCGCCUGCUCAACAAGCUGCUGUCGUGGAAG
...((.(((.....(((((.....((.(((....)))))...)))))...((....))....-)))))..(((((((.(..(((.((.(((((((...((((....))))....))))))))).)))..)))).))))... ( -35.70, z-score =  -0.46, R)
>droSec1.super_2 7269938 128 + 7591821
------------UCGCAAACAUCCCAUCGUUGCUACGUGUUUUGUGCUAAACUAAAGUAAUC-UCUCUACCCACACAGGUGGCUCGUCUGGGUAGCAAUCCGUACAUGGACCGCCUGCUCAACAAGCUGCUGUCGUGGAAG
------------................((((((....((((......))))...)))))).-.......(((((((.(..(((.((.((((((((..((((....))))..).))))))))).)))..)))).))))... ( -33.10, z-score =  -0.32, R)
>droYak2.chr3L 7950132 130 + 24197627
------AAAUUUAUGAUGUUUUCGCAUCAUUGGU-CGCAUGUAUCACCAA-CUAA--UAAAC-UCUCAACCCACACAGGUGGCCCGUCUGGGUAGCAAUCCGUACAUGGACCGCCUCCUCAACAAGCUGCUGUCGUGGAAG
------......(((((((....))))))).(((-(.(((((((((((..-....--.....-..............))))((((....))))........)))))))))))...(((.(.(((......))).).))).. ( -33.11, z-score =  -0.81, R)
>droWil1.scaffold_180698 9209510 114 + 11422946
---------------------------UUUUGUUUUUGUUUUUGGGCUCUAAUGUUCUAACGAUGUUAUUCCCCGCAGGUUACACGUUUAGGGGGCAAUCCCUAUAUGGAUCGGCUUUUGAAUAAGCUAUUGUCAUGGAAA
---------------------------........(((((...((((......)))).))))).....((((..((((......(((.((((((....)))))).)))....(((((......))))).))))...)))). ( -24.90, z-score =   0.30, R)
>droMoj3.scaffold_6680 5682094 107 + 24764193
---------------------------------UGCAAUCAUGUGACUAAUAUAUAAUUCUC-UUUAUUGCUUGGCAGUUGGCUCGUCUGGGUGGUAAUCCCUUCUUGGAUCGACUGCUCAAUAAGCUGUUGUCCUGGCAG
---------------------------------(((....((((.....))))(((((....-(((((((...(((((((((..((...(((.......)))....))..))))))))))))))))..)))))....))). ( -25.30, z-score =  -0.38, R)
>consensus
____________UCGCA_ACAUCCCAUCGUUGCUACGUGUUUUGUGCUAAACUAAAGUAAUC_UCUCAACCCACACAGGUGGCUCGUCUGGGUAGCAAUCCGUACAUGGACCGCCUGCUCAACAAGCUGCUGUCGUGGAAG
......................................................................((((((((.(((((.((.((((((((..(((......)))..).))))))))).))))))))).))))... (-20.55 = -20.08 +  -0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 7,345,257 – 7,345,397
Length 140
Sequences 6
Columns 141
Reading direction reverse
Mean pairwise identity 64.29
Shannon entropy 0.66691
G+C content 0.46393
Mean single sequence MFE -33.38
Consensus MFE -24.19
Energy contribution -24.28
Covariance contribution 0.09
Combinations/Pair 1.42
Mean z-score -0.81
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.96
SVM RNA-class probability 0.976727
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7345257 140 - 24543557
CUUCCACGACAGCAGCUUGUUGAGCAGGCGGUCCAUGUACGGAUUGCUACCCAAACGAGCCACCUGUGUGGGUUGAGA-GAUUACUUUAGUUUAGCACAAAACACGUAGCAACGAUGGGAUGUGUGCGAAUUUCUACUUUU
..(((((.((((..(((((((.....((((((((......)))))))).....)))))))...)))))))))...(((-((((((....))...(((((...(((((....))).)).....))))).)))))))...... ( -43.90, z-score =  -1.65, R)
>droSim1.chr3L 6862708 140 - 22553184
CUUCCACGACAGCAGCUUGUUGAGCAGGCGGUCCAUGUACGGAUUACUACCCAGACGAGCCACCUGUGUGGGUUGAGA-GAUUACUUUAGUUUAGCACAAAACACGUAGCAACGAUGGGAUGUGUGCGAAUUUCUACAUUU
..(((((.((((..(((((((.....((..((((......))))..)).....)))))))...))))))))).(((((-((((((....))...(((((...(((((....))).)).....))))).))))))).))... ( -40.30, z-score =  -0.99, R)
>droSec1.super_2 7269938 128 - 7591821
CUUCCACGACAGCAGCUUGUUGAGCAGGCGGUCCAUGUACGGAUUGCUACCCAGACGAGCCACCUGUGUGGGUAGAGA-GAUUACUUUAGUUUAGCACAAAACACGUAGCAACGAUGGGAUGUUUGCGA------------
......((((((....)))))).(((((((..(((((((((((((.(((((((.(((.......))).)))))))...-))))......((((......)))).))).)))....)))..)))))))..------------ ( -37.70, z-score =  -0.55, R)
>droYak2.chr3L 7950132 130 - 24197627
CUUCCACGACAGCAGCUUGUUGAGGAGGCGGUCCAUGUACGGAUUGCUACCCAGACGGGCCACCUGUGUGGGUUGAGA-GUUUA--UUAG-UUGGUGAUACAUGCG-ACCAAUGAUGCGAAAACAUCAUAAAUUU------
..(((((.((((..(((((((..((.((((((((......)))))))).))..)))))))...)))))))))....((-(((((--(..(-(((((..........-))))))((((......))))))))))))------ ( -44.80, z-score =  -2.65, R)
>droWil1.scaffold_180698 9209510 114 - 11422946
UUUCCAUGACAAUAGCUUAUUCAAAAGCCGAUCCAUAUAGGGAUUGCCCCCUAAACGUGUAACCUGCGGGGAAUAACAUCGUUAGAACAUUAGAGCCCAAAAACAAAAACAAAA---------------------------
....((((......((((......)))).........(((((......)))))..)))).........(((..(((..((....))...)))...)))................--------------------------- ( -17.00, z-score =   0.48, R)
>droMoj3.scaffold_6680 5682094 107 - 24764193
CUGCCAGGACAACAGCUUAUUGAGCAGUCGAUCCAAGAAGGGAUUACCACCCAGACGAGCCAACUGCCAAGCAAUAAA-GAGAAUUAUAUAUUAGUCACAUGAUUGCA---------------------------------
......((......(((..((.....(..(((((......)))))..).....))..)))......))..(((((...-(.((.(((.....))))).)...))))).--------------------------------- ( -16.60, z-score =   0.48, R)
>consensus
CUUCCACGACAGCAGCUUGUUGAGCAGGCGGUCCAUGUACGGAUUGCUACCCAGACGAGCCACCUGUGUGGGUUGAGA_GAUUACUUUAGUUUAGCACAAAACACGUAGCAACGAUGGGAUGU_UGCGA____________
..((((((.(((..(((((((.....((((((((......)))))))).....)))))))...)))))))))..................................................................... (-24.19 = -24.28 +   0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:09:27 2011