Locus 8908

Sequence ID dm3.chr3R
Location 2,645,933 – 2,646,093
Length 160
Max. P 0.981552
window12229 window12230

overview

Window 9

Location 2,645,933 – 2,646,053
Length 120
Sequences 13
Columns 120
Reading direction reverse
Mean pairwise identity 95.87
Shannon entropy 0.09676
G+C content 0.57115
Mean single sequence MFE -47.28
Consensus MFE -43.69
Energy contribution -43.75
Covariance contribution 0.05
Combinations/Pair 1.14
Mean z-score -2.52
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.08
SVM RNA-class probability 0.981552
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2645933 120 - 27905053
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......(((((((((((((....)))))))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -50.11, z-score =  -3.23, R)
>droSim1.chr3R 24838415 120 + 27517382
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......(((((((((((((....)))))))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -50.11, z-score =  -3.23, R)
>droSec1.super_6 2737087 120 - 4358794
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUACCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......(((((.(((((((....))))))).)))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -43.51, z-score =  -1.66, R)
>droYak2.chr3R 21064716 120 + 28832112
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......(((((((((((((....)))))))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -50.11, z-score =  -3.23, R)
>droEre2.scaffold_4770 2893871 120 - 17746568
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......(((((((((((((....)))))))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -50.11, z-score =  -3.23, R)
>droAna3.scaffold_13340 18289851 120 + 23697760
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCAAGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......((((((((.((((....)))).))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -46.21, z-score =  -2.43, R)
>dp4.chr2 11064733 120 + 30794189
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGCGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......((((((((.((((....)))).))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -45.51, z-score =  -1.83, R)
>droPer1.super_3 4910227 120 + 7375914
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGCGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......((((((((.((((....)))).))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -45.51, z-score =  -1.83, R)
>droWil1.scaffold_181089 12025040 120 - 12369635
UGACGGAACGUCCGCACUAAGCUUGACAUCAAUAUGGGUGCCAUGGAGGAGUCCACGGCAUUCAGGUUGGCCAAGGAGGGACGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((...((((...(((((.((((((((.((((....)))).)))))))).))))).)))).)))))))..)))(((....(((....)))....)))........ ( -44.40, z-score =  -2.04, R)
>droVir3.scaffold_13047 13141982 120 + 19223366
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCGCGGAGGAGUCCACGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......(((((((((.(((....))).)))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -48.01, z-score =  -2.49, R)
>droMoj3.scaffold_6540 17655583 120 + 34148556
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCGAGGAGGAGUCCACGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......(((((((((.(((....))).)))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -47.21, z-score =  -2.60, R)
>droGri2.scaffold_14906 2741966 120 + 14172833
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCGCGGAGGAGUCCACGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......(((((((((.(((....))).)))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ ( -48.01, z-score =  -2.49, R)
>anoGam1.chr3L 13644215 120 + 41284009
UGACGGGGCGUCCGCACUAAGCUGGCCGUCAAUAUGGGUGUCACGGAGGAGUCCGAGACAUUCAGGUUGGCUAAGGAGAGACACACCGAGCGAGGGGUGAAAACCAGCAGCUAAGAGUCU
.(((((.(.((((...((.(((..(((.......((((((((.((((....)))).)))))))))))..))).))..).))).).)).(((....(((....)))....)))....))). ( -45.81, z-score =  -2.44, R)
>consensus
UGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGCGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUC
...(((..(((((...((.((((.(((.......((((((((.((((....)))).))))))))))).)))).))...)))))..)))(((....(((....)))....)))........ (-43.69 = -43.75 +   0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 2,645,973 – 2,646,093
Length 120
Sequences 13
Columns 120
Reading direction forward
Mean pairwise identity 92.88
Shannon entropy 0.15806
G+C content 0.57266
Mean single sequence MFE -37.88
Consensus MFE -30.33
Energy contribution -30.13
Covariance contribution -0.20
Combinations/Pair 1.24
Mean z-score -1.74
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.570992
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2645973 120 + 27905053
CCCUCCUUAGCCAACCUGAAUGCCACGGACUCCUCCAUGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUGGUCCGCUACGCAGUAGAUCCCAGCCUCAGG
..............(((((.(((((.(((....))).)))))...........(((.((((((.(((((.....))).))...))))))((((..((....))..))))...)))))))) ( -39.00, z-score =  -1.92, R)
>droSim1.chr3R 24838455 120 - 27517382
CCCUCCUUAGCCAACCUGAAUGCCACGGACUCCUCCAUGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUAGUCCGCUACACAGUAGAUCCCAGCCUCAGG
..............(((((.(((((.(((....))).)))))...........(((.((((((.(((((.....))).))...)))))).(((..((....))..)))....)))))))) ( -36.60, z-score =  -2.15, R)
>droSec1.super_6 2737127 120 + 4358794
CCCUCCUUAGCCAACCUGAAUGCCACGGACUCCUCCAUGGUACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUAGUCCGCUACGCAGUAGAUCCCAGCCUCAGG
..............(((((.(((((.(((....))).)))))...........(((.((((((.(((((.....))).))...)))))).(((..((....))..)))....)))))))) ( -34.60, z-score =  -1.35, R)
>droYak2.chr3R 21064756 120 - 28832112
CCCUCCUUAGCCAACCUGAAUGCCACGGACUCCUCCAUGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUGGUCCGCUACGCAGUAAAUCCCAGCCUCAGG
..............(((((.(((((.(((....))).)))))....(((((.((((.((((((.(((((.....))).))...)))))).....))))..)))))..........))))) ( -35.00, z-score =  -1.13, R)
>droEre2.scaffold_4770 2893911 120 + 17746568
CCCUCCUUAGCCAACCUGAAUGCCACGGACUCCUCCAUGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUGGUCCGCUACGCAGUAGAUCCCAGCCUCAGG
..............(((((.(((((.(((....))).)))))...........(((.((((((.(((((.....))).))...))))))((((..((....))..))))...)))))))) ( -39.00, z-score =  -1.92, R)
>droAna3.scaffold_13340 18289891 120 - 23697760
CCCUCCUUAGCCAACCUGAAUGCCUUGGACUCCUCCAUGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUGGUCCGCUACACAGUGAAUCCCAGCCUCAGG
..............(((((.((((.((((....)))).))))...........(((.((((((.(((((.....))).))...))))))(((.((((....)))).)))...)))))))) ( -37.50, z-score =  -1.74, R)
>dp4.chr2 11064773 120 - 30794189
CCCUCCUUAGCCAACCUGAAUGCCGCGGACUCCUCCAUGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUGGUCCGUUACACAGUGAUUCCCAGCCUCAGG
..............(((((.(((((.(((....))).)))))...........(((.((((((.(((((.....))).))...))))))((...(((((...)))))..)).)))))))) ( -35.70, z-score =  -1.05, R)
>droPer1.super_3 4910267 120 - 7375914
CCCUCCUUAGCCAACCUGAAUGCCGCGGACUCCUCCAUGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUGGUCCGUUACACAGUGAUUCCCAGCCUCAGG
..............(((((.(((((.(((....))).)))))...........(((.((((((.(((((.....))).))...))))))((...(((((...)))))..)).)))))))) ( -35.70, z-score =  -1.05, R)
>droWil1.scaffold_181089 12025080 120 + 12369635
CCCUCCUUGGCCAACCUGAAUGCCGUGGACUCCUCCAUGGCACCCAUAUUGAUGUCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUGGUCCGCUACACAGUGAUUCCCAGCCUCAGG
.(((.(((((((((..((..(((((((((....)))))))))..))..)))..))))))....(((..((((...))))..)))(((((((..((((....))))....)))).)))))) ( -39.90, z-score =  -2.13, R)
>droVir3.scaffold_13047 13142022 119 - 19223366
CCCUCCUUAGCCAACCUGAAUGCCGUGGACUCCUCCGCGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUG-GCUGGUCCACUACACAGUGAUCCCCAGCCUCAGG
..............(((((.(((((((((....))))))))).......((.((((..((.....))((.....)))))).)).(-(((((..((((....))))....))))))))))) ( -43.30, z-score =  -2.94, R)
>droMoj3.scaffold_6540 17655623 119 - 34148556
CCCUCCUUAGCCAACCUGAAUGCCGUGGACUCCUCCUCGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUG-GCUGGUCCACUACACAGUGAUCCCCAGCCUCAGG
..............(((((.(((((.(((....))).))))).......((.((((..((.....))((.....)))))).)).(-(((((..((((....))))....))))))))))) ( -39.70, z-score =  -2.14, R)
>droGri2.scaffold_14906 2742006 119 - 14172833
CCCUCCUUAGCCAACCUGAAUGCCGUGGACUCCUCCGCGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUG-GCUGGUCCACUACACAGUGAUCCCCAGCCUCAGG
..............(((((.(((((((((....))))))))).......((.((((..((.....))((.....)))))).)).(-(((((..((((....))))....))))))))))) ( -43.30, z-score =  -2.94, R)
>anoGam1.chr3L 13644255 119 - 41284009
CUCUCCUUAGCCAACCUGAAUGUCUCGGACUCCUCCGUGACACCCAUAUUGACGGCCAGCUUAGUGCGGACGCCCCGUCAACAUGGCCUGGUCCGGUGCACAGUGA-UCCCGCCCUCAAA
.........(((.(((....((((.((((....)))).)))).((((.(((((((((.((.....)))).....))))))).))))...)))..))).....(((.-...)))....... ( -33.20, z-score =  -0.21, R)
>consensus
CCCUCCUUAGCCAACCUGAAUGCCGCGGACUCCUCCAUGGCACCCAUAUUGAUGGCAAGCUUAGUGCGGACGUUCCGUCAACAUGAGCUGGUCCGCUACACAGUGAAUCCCAGCCUCAGG
..............(((((.(((((.(((....))).)))))..(((.(((((((...((.....)).......))))))).))).(((((...(((....))).....))))).))))) (-30.33 = -30.13 +  -0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:54:29 2011