Locus 3164

Sequence ID dm3.chr2R
Location 3,000,575 – 3,000,683
Length 108
Max. P 0.860038
window4351 window4352

overview

Window 1

Location 3,000,575 – 3,000,683
Length 108
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 68.60
Shannon entropy 0.56796
G+C content 0.58082
Mean single sequence MFE -34.75
Consensus MFE -14.14
Energy contribution -15.75
Covariance contribution 1.61
Combinations/Pair 1.27
Mean z-score -1.42
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.550653
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3000575 108 + 21146708
ACUGCGGUCACGGCCAGCUGAAUAUCAGGGAAACCAGGCGACUGAAGGGACUGAGGUGACUGGAGUGACUCGGGUGAGCGGAGUGCAUUGCAACCGCAGGAAAGACAU
.((((((((((.(((...((.....))((....)).)))..((((.(..(((.((....)).).))..)))))))))((((......))))..))))))......... ( -36.50, z-score =  -1.39, R)
>droSim1.chr2R 1799487 101 + 19596830
ACCGCGGUCACGGCCAGCUGAAUAUGAGGGGAACCAGGGGACUGGGGGCACUG-------CGAGGUGACUCGGGUGAGCGGAGUGCAUUGCAACCGCAGGAAAGACAU
.((((((((((..((.(((..............((((....))))...((((.-------((((....))))))))))))).))).......))))).))........ ( -38.21, z-score =  -1.78, R)
>droSec1.super_1 669765 100 + 14215200
ACUGCGGUCACGGCCAGCUGAAUAUCAGGGGAACCAGGGGACUGAGGGGACUG-------CGAGGUGACUCGGGUGAGCGGAGUGCAUUGCAACCGCAGGAAA-ACAU
.((((((((((..((..(((.....))).))...(((....)))((....)).-------((((....)))).))))((((......))))..))))))....-.... ( -37.30, z-score =  -2.19, R)
>droYak2.chr2L 15712509 97 + 22324452
GCUGCGGUCACGGCCAGCUGAAU--CAGGGGAACCAGGUGACUGAGGUGAC---------CGAGGUGACUCGGGUGAAUGCACUGCAUUGCAACCGCAGGAAAGACAA
.((((((((((.(((........--..((....))((....))..)))..(---------((((....))))))))).((((......)))).))))))......... ( -40.00, z-score =  -2.66, R)
>droEre2.scaffold_4929 7074395 83 - 26641161
ACUGCGGUCACGGCCAGCUGAAU--CAGUGGCACCAGGCGACU-----------------CGAG------CGGGUGAGCGCAGUGCGCUGCAACCGCAGGAACGGCAA
.(((((((..((((..((((...--)))).((((...(((.((-----------------((..------....))))))).))))))))..)))))))......... ( -34.80, z-score =  -0.28, R)
>droWil1.scaffold_180700 2597327 87 + 6630534
AUCCCGGUCAUAGUCGAGUGAUUAGCAGUUGAAUGCAAUGCGUU---------------UUAUGGU----CAGCUGACUUU--UGCUUGGCAAGUGCAAAAACCACAA
.....((((((.((((((..(..(((((((((((((...)))).---------------......)----)))))).)).)--..))))))..))).....))).... ( -21.71, z-score =  -0.23, R)
>consensus
ACUGCGGUCACGGCCAGCUGAAUAUCAGGGGAACCAGGCGACUGAGGGGAC_________CGAGGUGACUCGGGUGAGCGGAGUGCAUUGCAACCGCAGGAAAGACAA
.(((((((..((..((.((((......((....))((....))..........................)))).))..))...(((...))))))))))......... (-14.14 = -15.75 +   1.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 3,000,575 – 3,000,683
Length 108
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 68.60
Shannon entropy 0.56796
G+C content 0.58082
Mean single sequence MFE -29.13
Consensus MFE -14.44
Energy contribution -16.13
Covariance contribution 1.70
Combinations/Pair 1.24
Mean z-score -1.39
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.860038
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3000575 108 - 21146708
AUGUCUUUCCUGCGGUUGCAAUGCACUCCGCUCACCCGAGUCACUCCAGUCACCUCAGUCCCUUCAGUCGCCUGGUUUCCCUGAUAUUCAGCUGGCCGUGACCGCAGU
.........(((((((..(..........((((....))))....(((((....((((.....((((....)))).....))))......)))))..)..))))))). ( -31.30, z-score =  -2.00, R)
>droSim1.chr2R 1799487 101 - 19596830
AUGUCUUUCCUGCGGUUGCAAUGCACUCCGCUCACCCGAGUCACCUCG-------CAGUGCCCCCAGUCCCCUGGUUCCCCUCAUAUUCAGCUGGCCGUGACCGCGGU
.........(((((((..(...(((((.(((((....)))......))-------.)))))..((((....((((............))))))))..)..))))))). ( -29.60, z-score =  -1.43, R)
>droSec1.super_1 669765 100 - 14215200
AUGU-UUUCCUGCGGUUGCAAUGCACUCCGCUCACCCGAGUCACCUCG-------CAGUCCCCUCAGUCCCCUGGUUCCCCUGAUAUUCAGCUGGCCGUGACCGCAGU
....-....(((((((..(..(((.....((((....))))......)-------))................((((...(((.....)))..)))))..))))))). ( -28.60, z-score =  -1.88, R)
>droYak2.chr2L 15712509 97 - 22324452
UUGUCUUUCCUGCGGUUGCAAUGCAGUGCAUUCACCCGAGUCACCUCG---------GUCACCUCAGUCACCUGGUUCCCCUG--AUUCAGCUGGCCGUGACCGCAGC
.........(((((((..(......(((.((((....)))))))...(---------((((.((.(((((...((....))))--))).)).))))))..))))))). ( -33.90, z-score =  -2.30, R)
>droEre2.scaffold_4929 7074395 83 + 26641161
UUGCCGUUCCUGCGGUUGCAGCGCACUGCGCUCACCCG------CUCG-----------------AGUCGCCUGGUGCCACUG--AUUCAGCUGGCCGUGACCGCAGU
.........(((((((..(.(((((((((((((.....------...)-----------------)).)))..)))))(((((--...))).)))).)..))))))). ( -34.40, z-score =  -0.97, R)
>droWil1.scaffold_180700 2597327 87 - 6630534
UUGUGGUUUUUGCACUUGCCAAGCA--AAAGUCAGCUG----ACCAUAA---------------AACGCAUUGCAUUCAACUGCUAAUCACUCGACUAUGACCGGGAU
((((((((.(((.((((((...)))--..))))))..)----)))))))---------------...((((((....))).)))......((((........)))).. ( -17.00, z-score =   0.22, R)
>consensus
AUGUCUUUCCUGCGGUUGCAAUGCACUCCGCUCACCCGAGUCACCUCG_________GUCCCCUCAGUCACCUGGUUCCCCUGAUAUUCAGCUGGCCGUGACCGCAGU
.........((((((((((..........((((....))))................................((((...(((.....)))..)))))))))))))). (-14.44 = -16.13 +   1.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:04:59 2011