Locus 6515

Sequence ID dm3.chr3L
Location 7,223,380 – 7,223,515
Length 135
Max. P 0.979652
window8968 window8969 window8970 window8971

overview

Window 8

Location 7,223,380 – 7,223,496
Length 116
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 68.01
Shannon entropy 0.59078
G+C content 0.55289
Mean single sequence MFE -37.67
Consensus MFE -15.97
Energy contribution -18.18
Covariance contribution 2.21
Combinations/Pair 1.17
Mean z-score -1.23
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.517526
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7223380 116 + 24543557
GACGAAGGGGUGAGGGG--GGUGGACAUUUUAACAACCCAGGAUCGCAGGAUACUAGAAUCCCAGCAUUGCAACAUCCCAGCUUUCCAACAUCCUGGCGGCACAAGUUGCCAGUUGCC
......((((((.(((.--.((..........))..)))......((.((((......))))..)).......))))))..............((((((((....))))))))..... ( -35.00, z-score =  -0.12, R)
>droSim1.chr3L 6734907 114 + 22553184
GACGAAGGGGAGGGG-GUUGGGGGGCAUUUUAAC---CCAGGAUCGCAGGAUCCUAGAAUCCCAGCAUUGCAACAUCCCAGCUUUCCAGCAUCCUGGCGGCACAAGUUGCCAGUUGCC
......((..(((((-(((((((((........)---))((((((....)))))).....))))((...))...)))))..))..)).(((..((((((((....)))))))).))). ( -45.20, z-score =  -1.61, R)
>droSec1.super_2 7149617 118 + 7591821
GACGAAGGGGUGGGGAGUGGGGGGGCAUUUUAACAACCCAGGAUCGCAGGAUCCUAGAAUCCCAGCAGUGCAACAUCCCAGCUUUCCAGCAUCCUGGCGGCACAAGUUGCCAGUUGCC
......((((((((((..(((..(.........)..)))((((((....))))))....)))).((...))..)))))).........(((..((((((((....)))))))).))). ( -45.90, z-score =  -1.34, R)
>droYak2.chr3L 7823872 108 + 24197627
--------GAUGAAGGG--GAUGGGCAUUUUAACAACCCAGGAUCGCUGGAUCCUGGAAUCCCAACAACCCAACAUCCCAGCUUCACAGCAUCCUGGCGGCACAAGUUGCCAGUUGCC
--------..(((((((--((((((............((((((((....))))))))...........))))...))))..)))))..(((..((((((((....)))))))).))). ( -42.50, z-score =  -3.18, R)
>droEre2.scaffold_4784 21642326 100 - 25762168
--------GAUGAAGGG--GGUGGGCAUUUUAACAACCCAGGAUCGCAGCAUCCUGGAAUCCCAACA--------UCCCAGCUUCCCAGCAUCCUGGCGGCACAAGUUGCCAGUUGCC
--------((((..(((--((((((............(((((((......)))))))..........--------.)))).)))))...))))((((((((....))))))))..... ( -36.90, z-score =  -1.51, R)
>droWil1.scaffold_180698 7826472 87 + 11422946
-------UACACAGGGGUGGGGGGGCUGUCUAUUAAAGUGGG--UGUGGGUAACUGGGGUAAUAACAG-----------AACUUGCCAAUGU--UGCUAGUGUAAGGCA---------
-------...(((..((..((....((((.(((((...(.((--(.......))).)..)))))))))-----------..))..))..)))--((((.......))))--------- ( -20.50, z-score =   0.36, R)
>consensus
_______GGGUGAGGGG__GGGGGGCAUUUUAACAACCCAGGAUCGCAGGAUCCUAGAAUCCCAACAGUGCAACAUCCCAGCUUUCCAGCAUCCUGGCGGCACAAGUUGCCAGUUGCC
...................((..(((.............((((((....)))))).(........)..............)))..)).(((..((((((((....)))))))).))). (-15.97 = -18.18 +   2.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 7,223,380 – 7,223,496
Length 116
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 68.01
Shannon entropy 0.59078
G+C content 0.55289
Mean single sequence MFE -33.78
Consensus MFE -21.35
Energy contribution -23.92
Covariance contribution 2.56
Combinations/Pair 1.31
Mean z-score -0.48
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.651611
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7223380 116 - 24543557
GGCAACUGGCAACUUGUGCCGCCAGGAUGUUGGAAAGCUGGGAUGUUGCAAUGCUGGGAUUCUAGUAUCCUGCGAUCCUGGGUUGUUAAAAUGUCCACC--CCCCUCACCCCUUCGUC
((((((.((((.....)))).(((((((((.(((..((((((((.((((...)).)).)))))))).))).)).)))))))))))))............--................. ( -35.30, z-score =  -0.03, R)
>droSim1.chr3L 6734907 114 - 22553184
GGCAACUGGCAACUUGUGCCGCCAGGAUGCUGGAAAGCUGGGAUGUUGCAAUGCUGGGAUUCUAGGAUCCUGCGAUCCUGG---GUUAAAAUGCCCCCCAAC-CCCCUCCCCUUCGUC
((((...(....)...))))....(((.(((....))).(((..((......))((((.....((((((....))))))((---((......))))))))..-.))))))........ ( -37.10, z-score =  -0.07, R)
>droSec1.super_2 7149617 118 - 7591821
GGCAACUGGCAACUUGUGCCGCCAGGAUGCUGGAAAGCUGGGAUGUUGCACUGCUGGGAUUCUAGGAUCCUGCGAUCCUGGGUUGUUAAAAUGCCCCCCCACUCCCCACCCCUUCGUC
((((...(....)...))))...(((..(((....)))((((..((......))((((.....((((((....))))))((((.........)))).))))...))))..)))..... ( -36.60, z-score =   0.57, R)
>droYak2.chr3L 7823872 108 - 24197627
GGCAACUGGCAACUUGUGCCGCCAGGAUGCUGUGAAGCUGGGAUGUUGGGUUGUUGGGAUUCCAGGAUCCAGCGAUCCUGGGUUGUUAAAAUGCCCAUC--CCCUUCAUC--------
((((.(((((..........)))))..))))((((((..((((...(((((..((((.(..((((((((....))))))))..).))))...)))))))--)))))))).-------- ( -46.60, z-score =  -2.79, R)
>droEre2.scaffold_4784 21642326 100 + 25762168
GGCAACUGGCAACUUGUGCCGCCAGGAUGCUGGGAAGCUGGGA--------UGUUGGGAUUCCAGGAUGCUGCGAUCCUGGGUUGUUAAAAUGCCCACC--CCCUUCAUC--------
((((...(....)...)))).((((....))))((((..(((.--------....((((((.(((....))).))))))((((.........)))).))--).))))...-------- ( -36.90, z-score =  -0.59, R)
>droWil1.scaffold_180698 7826472 87 - 11422946
---------UGCCUUACACUAGCA--ACAUUGGCAAGUU-----------CUGUUAUUACCCCAGUUACCCACA--CCCACUUUAAUAGACAGCCCCCCCACCCCUGUGUA-------
---------.....(((((.....--.....(((....(-----------((((((........((.....)).--.......)))))))..)))...........)))))------- ( -10.19, z-score =   0.00, R)
>consensus
GGCAACUGGCAACUUGUGCCGCCAGGAUGCUGGAAAGCUGGGAUGUUGCAAUGCUGGGAUUCCAGGAUCCUGCGAUCCUGGGUUGUUAAAAUGCCCACC__CCCCUCACCC_______
((((...((((.....)))).(((((((((.(((...(((((((.((........)).)))))))..))).)).)))))))..........))))....................... (-21.35 = -23.92 +   2.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 7,223,418 – 7,223,515
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 91.96
Shannon entropy 0.14922
G+C content 0.54123
Mean single sequence MFE -35.47
Consensus MFE -27.50
Energy contribution -28.10
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -3.00
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979652
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7223418 97 + 24543557
GGAUCGCAGGAUACUAGAAUCCCAGCAUUGCAACAUCCCAGCUUUCCAACAUCCUGGCGGCACAAGUUGCCAGUUGCCAAUGCUGGCGACUAAUAGU
((.((((.((((......))))((((((((((((...((((............)))).((((.....)))).)))).))))))))))))))...... ( -34.00, z-score =  -2.93, R)
>droSim1.chr3L 6734943 97 + 22553184
GGAUCGCAGGAUCCUAGAAUCCCAGCAUUGCAACAUCCCAGCUUUCCAGCAUCCUGGCGGCACAAGUUGCCAGUUGCCAAUGCUGGCGACUAAUAGU
(((((....)))))(((..(((((((((((((((......(((....)))....(((((((....))))))))))).))))))))).)))))..... ( -39.40, z-score =  -3.97, R)
>droSec1.super_2 7149657 97 + 7591821
GGAUCGCAGGAUCCUAGAAUCCCAGCAGUGCAACAUCCCAGCUUUCCAGCAUCCUGGCGGCACAAGUUGCCAGUUGCCAAUGCUGGCGACUAAUAGU
(((((....)))))(((..((((((((..(((((......(((....)))....(((((((....))))))))))))...)))))).)))))..... ( -37.20, z-score =  -3.06, R)
>droYak2.chr3L 7823902 97 + 24197627
GGAUCGCUGGAUCCUGGAAUCCCAACAACCCAACAUCCCAGCUUCACAGCAUCCUGGCGGCACAAGUUGCCAGUUGCCAAUGCUGGCGACUAAUAGU
((((.((((((..((((....................))))..)).)))))))).((((((....))))))((((((((....))))))))...... ( -36.65, z-score =  -3.36, R)
>droEre2.scaffold_4784 21642356 89 - 25762168
GGAUCGCAGCAUCCUGGAAUCCCA--------ACAUCCCAGCUUCCCAGCAUCCUGGCGGCACAAGUUGCCAGUUGCCAAUGCUGGCGACUAAUAGU
((((..(((....)))..))))..--------...(((((((......(((..((((((((....)))))))).)))....))))).))........ ( -30.10, z-score =  -1.69, R)
>consensus
GGAUCGCAGGAUCCUAGAAUCCCAGCAUUGCAACAUCCCAGCUUUCCAGCAUCCUGGCGGCACAAGUUGCCAGUUGCCAAUGCUGGCGACUAAUAGU
(((((....))))).....................(((((((......(((..((((((((....)))))))).)))....))))).))........ (-27.50 = -28.10 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 7,223,418 – 7,223,515
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 91.96
Shannon entropy 0.14922
G+C content 0.54123
Mean single sequence MFE -36.58
Consensus MFE -29.96
Energy contribution -29.96
Covariance contribution 0.00
Combinations/Pair 1.08
Mean z-score -1.76
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.643235
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7223418 97 - 24543557
ACUAUUAGUCGCCAGCAUUGGCAACUGGCAACUUGUGCCGCCAGGAUGUUGGAAAGCUGGGAUGUUGCAAUGCUGGGAUUCUAGUAUCCUGCGAUCC
.......(((((((((((((.((((.((((.....)))).((((............))))...))))))))))))((((......)))).))))).. ( -34.80, z-score =  -1.58, R)
>droSim1.chr3L 6734943 97 - 22553184
ACUAUUAGUCGCCAGCAUUGGCAACUGGCAACUUGUGCCGCCAGGAUGCUGGAAAGCUGGGAUGUUGCAAUGCUGGGAUUCUAGGAUCCUGCGAUCC
.......(((((((((((((.((((.((((.....)))).(((....(((....))))))...))))))))))))(((((....))))).))))).. ( -38.70, z-score =  -2.30, R)
>droSec1.super_2 7149657 97 - 7591821
ACUAUUAGUCGCCAGCAUUGGCAACUGGCAACUUGUGCCGCCAGGAUGCUGGAAAGCUGGGAUGUUGCACUGCUGGGAUUCUAGGAUCCUGCGAUCC
.......((((((((((...(((((.((((.....)))).(((....(((....))))))...)))))..)))))(((((....))))).))))).. ( -36.50, z-score =  -1.57, R)
>droYak2.chr3L 7823902 97 - 24197627
ACUAUUAGUCGCCAGCAUUGGCAACUGGCAACUUGUGCCGCCAGGAUGCUGUGAAGCUGGGAUGUUGGGUUGUUGGGAUUCCAGGAUCCAGCGAUCC
.......(((.(((((..(((((.(((((..........)))))..)))))....))))))))...((((((((((.(((....))))))))))))) ( -37.60, z-score =  -1.62, R)
>droEre2.scaffold_4784 21642356 89 + 25762168
ACUAUUAGUCGCCAGCAUUGGCAACUGGCAACUUGUGCCGCCAGGAUGCUGGGAAGCUGGGAUGU--------UGGGAUUCCAGGAUGCUGCGAUCC
.......(((((.((((((((((...(....)...)))).((((....))))....(((((((..--------....)))))))))))))))))).. ( -35.30, z-score =  -1.72, R)
>consensus
ACUAUUAGUCGCCAGCAUUGGCAACUGGCAACUUGUGCCGCCAGGAUGCUGGAAAGCUGGGAUGUUGCAAUGCUGGGAUUCUAGGAUCCUGCGAUCC
.......(((.(((((...((((...(....)...)))).((((....))))...))))))))............(((((.(((....))).))))) (-29.96 = -29.96 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:09:15 2011