Locus 3854

Sequence ID dm3.chr2R
Location 8,346,520 – 8,346,592
Length 72
Max. P 0.899456
window5281 window5282

overview

Window 1

Location 8,346,520 – 8,346,592
Length 72
Sequences 5
Columns 82
Reading direction forward
Mean pairwise identity 79.66
Shannon entropy 0.34416
G+C content 0.54080
Mean single sequence MFE -29.12
Consensus MFE -15.70
Energy contribution -17.06
Covariance contribution 1.36
Combinations/Pair 1.09
Mean z-score -2.46
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.899456
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8346520 72 + 21146708
------GGAGCUGCUUCUGCUUCUGGCGU-UGCAUCUACCAGGUGUU---CCUGGGCAAUCAAUGAAAGAAGCUGUCAGCGG
------...(((((....((((((..(((-((.((...(((((....---)))))...)))))))..)))))).).)))).. ( -29.00, z-score =  -2.51, R)
>droEre2.scaffold_4845 5146425 73 - 22589142
-----UCCUCCCGUUGCAGCUUCUGGCGU-UGCAUUUACCAGGUGUU---CCUGGGCAAUCAAUGAAAGAAGCUGUCAGCAG
-----.......((((((((((((..(((-((.(((..(((((....---)))))..))))))))..)))))))).)))).. ( -34.20, z-score =  -5.32, R)
>droYak2.chr2R 12550440 69 - 21139217
----------CAGCCGCUGGGUGCAGCUUCUGCAUUUACCAGGUGUU---CCUGGGCAAUCAAUGAAAGAAGCUGUCGGCGG
----------...((((((...(((((((((.((((..(((((....---)))))......))))..))))))))))))))) ( -31.10, z-score =  -3.29, R)
>droSec1.super_1 5896054 75 + 14215200
------GGAGCUGCUUCUUCUUCUGGCGU-UGCAUCUACCAGGUGUUGUUCCUGGGCAAUCAAUGAGAGAAGCUGUCACCGG
------((.((.((((((.(((...(.((-(((.....(((((.......)))))))))))...))))))))).))..)).. ( -23.40, z-score =  -0.59, R)
>droSim1.chr2R 6823869 81 + 19596830
GGAGCUGCUUCUGCUUCUGCUUCUGGCGU-UGCAUCUACCAGGUGUUGUUCCUGGGCAAUCAAUGAGAGAAGCUGUCAGCGG
(((((.......))))).((((((..(((-((.((...(((((.......)))))...)))))))..))))))......... ( -27.90, z-score =  -0.59, R)
>consensus
______GCAGCUGCUUCUGCUUCUGGCGU_UGCAUCUACCAGGUGUU___CCUGGGCAAUCAAUGAAAGAAGCUGUCAGCGG
..........(((((...((((((..(((.(((.....(((((.......))))))))....)))..))))))....))))) (-15.70 = -17.06 +   1.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 8,346,520 – 8,346,592
Length 72
Sequences 5
Columns 82
Reading direction reverse
Mean pairwise identity 79.66
Shannon entropy 0.34416
G+C content 0.54080
Mean single sequence MFE -23.68
Consensus MFE -13.74
Energy contribution -14.22
Covariance contribution 0.48
Combinations/Pair 1.16
Mean z-score -1.97
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.715805
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8346520 72 - 21146708
CCGCUGACAGCUUCUUUCAUUGAUUGCCCAGG---AACACCUGGUAGAUGCA-ACGCCAGAAGCAGAAGCAGCUCC------
..((((...((((((..(.((((((..(((((---....)))))..))).))-).)..)))))).....))))...------ ( -24.20, z-score =  -2.50, R)
>droEre2.scaffold_4845 5146425 73 + 22589142
CUGCUGACAGCUUCUUUCAUUGAUUGCCCAGG---AACACCUGGUAAAUGCA-ACGCCAGAAGCUGCAACGGGAGGA-----
(((.((.((((((((..(.((((((..(((((---....)))))..))).))-).)..)))))))))).))).....----- ( -26.50, z-score =  -2.67, R)
>droYak2.chr2R 12550440 69 + 21139217
CCGCCGACAGCUUCUUUCAUUGAUUGCCCAGG---AACACCUGGUAAAUGCAGAAGCUGCACCCAGCGGCUG----------
..((((.((((((((..((((......(((((---....)))))..)))).)))))))).......))))..---------- ( -25.00, z-score =  -2.89, R)
>droSec1.super_1 5896054 75 - 14215200
CCGGUGACAGCUUCUCUCAUUGAUUGCCCAGGAACAACACCUGGUAGAUGCA-ACGCCAGAAGAAGAAGCAGCUCC------
..(....).((((((((..(((.(((((((((.......))))).....)))-)...))).)).))))))......------ ( -19.40, z-score =  -0.64, R)
>droSim1.chr2R 6823869 81 - 19596830
CCGCUGACAGCUUCUCUCAUUGAUUGCCCAGGAACAACACCUGGUAGAUGCA-ACGCCAGAAGCAGAAGCAGAAGCAGCUCC
..((((...((((((....((((((..(((((.......)))))..))).))-).((.....)))))))).....))))... ( -23.30, z-score =  -1.13, R)
>consensus
CCGCUGACAGCUUCUUUCAUUGAUUGCCCAGG___AACACCUGGUAGAUGCA_ACGCCAGAAGCAGAAGCAGCACC______
..(((....((((((.....(((((..(((((.......)))))..))).))......))))))...)))............ (-13.74 = -14.22 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:18:03 2011