Locus 12241

Sequence ID dm3.chr3R
Location 26,722,693 – 26,722,782
Length 89
Max. P 0.979564
window16836 window16837

overview

Window 6

Location 26,722,693 – 26,722,782
Length 89
Sequences 7
Columns 102
Reading direction forward
Mean pairwise identity 57.03
Shannon entropy 0.79899
G+C content 0.55062
Mean single sequence MFE -25.06
Consensus MFE -14.18
Energy contribution -14.46
Covariance contribution 0.28
Combinations/Pair 1.70
Mean z-score -0.75
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979564
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26722693 89 + 27905053
------GAUGAAAGAGCGGCCCAGAGUCCCUCCGUUUCUCACCUGAGAAAUGCCCCACCUGA----UGAUCGCGAAA---UAGCGAUUCGCUAUUCGGGCGG
------.......(((.(((.....))).)))((((((((....))))))))..((.(((((----.((((((....---..))))))......))))).)) ( -28.00, z-score =  -1.50, R)
>droAna3.scaffold_12911 1132482 102 - 5364042
GACGAAGAGCUACCAACGGUCCAGCGGACCAAGAGCCGCCAAAAACCACCUGCCCCACCUGAGAAAUGGUCGCGAAACUGUGGCAGCGGCGUCAUCAGCCAG
(((..............(((((...)))))....(((((......((((.(((...(((........))).))).....))))..))))))))......... ( -27.50, z-score =  -0.04, R)
>droEre2.scaffold_4820 9202807 87 - 10470090
------GAUGAAAG--CGGCCCAGAGUCCCUCCAUUUCUCACCUGAGAAAUGCCCCACCUGA----UGGUCGCGAAA---UAGCGAUUCGCUUUUCGGGCGG
------.......(--((((((((.((.....((((((((....))))))))....))))).----.))))))((((---.((((...))))))))...... ( -28.10, z-score =  -1.44, R)
>droYak2.chr3R 27646886 69 + 28832112
--------------------------GAUGGAAGAGUCUCACCUGAGAAAUGCCCCACCUGA----UGGUCGCGAAA---UAGCGAUUCGCUUUUCGGGCGG
--------------------------...((.....((((....))))....))((.(((((----.((((((....---..))))))......))))).)) ( -20.50, z-score =  -0.59, R)
>droSec1.super_4 5548388 89 + 6179234
------GAUGAAAGAGCGGCCCAGAGUCCCUCCGUUUCUCACCUGAGAAAUGCCCCACCUGA----UGGUCGCGAAA---UAGCGAUUCGCUUUUCGGGCGG
------.........(((((((((.((.....((((((((....))))))))....))))).----.))))))((((---.((((...))))))))...... ( -27.70, z-score =  -0.70, R)
>droSim1.chr3R 26364296 89 + 27517382
------GAUGAAAGAGCGGCCCAGAGUCCCUCCGUUUCUCACCUGAGAAAUGCCCCACCUGA----UGGUCGCGAAA---UAGCGAUUCGCUUUUCGGGCGG
------.........(((((((((.((.....((((((((....))))))))....))))).----.))))))((((---.((((...))))))))...... ( -27.70, z-score =  -0.70, R)
>droVir3.scaffold_13047 11563192 73 + 19223366
----------------------GACCAAAGAGAGGGCCGCAAUAGCCGCUUGUCUUUUGGGUGUUGCGUUUAUUUUUUUAUAACAAUUCGUGUUG-------
----------------------....(((((((..(.(((((((.(((.........))).))))))).)..))))))).(((((.....)))))------- ( -15.90, z-score =  -0.30, R)
>consensus
______GAUGAAAGA_CGGCCCAGAGUCCCUCCGUUUCUCACCUGAGAAAUGCCCCACCUGA____UGGUCGCGAAA___UAGCGAUUCGCUUUUCGGGCGG
.................................(((((((....)))))))...((.(((((.....((((((.........))))))......))))).)) (-14.18 = -14.46 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 26,722,693 – 26,722,782
Length 89
Sequences 7
Columns 102
Reading direction reverse
Mean pairwise identity 57.03
Shannon entropy 0.79899
G+C content 0.55062
Mean single sequence MFE -27.16
Consensus MFE -10.95
Energy contribution -11.12
Covariance contribution 0.17
Combinations/Pair 1.71
Mean z-score -0.61
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.553858
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26722693 89 - 27905053
CCGCCCGAAUAGCGAAUCGCUA---UUUCGCGAUCA----UCAGGUGGGGCAUUUCUCAGGUGAGAAACGGAGGGACUCUGGGCCGCUCUUUCAUC------
(((((.((...(((((......---.))))).....----)).)))))(((.((((((....))))))(((((...))))).)))...........------ ( -30.00, z-score =  -0.71, R)
>droAna3.scaffold_12911 1132482 102 + 5364042
CUGGCUGAUGACGCCGCUGCCACAGUUUCGCGACCAUUUCUCAGGUGGGGCAGGUGGUUUUUGGCGGCUCUUGGUCCGCUGGACCGUUGGUAGCUCUUCGUC
..(((((..((((((((((((((.((..(((.............)))..))..)))))....))))))....(((((...))))))))..)))))....... ( -39.42, z-score =  -0.72, R)
>droEre2.scaffold_4820 9202807 87 + 10470090
CCGCCCGAAAAGCGAAUCGCUA---UUUCGCGACCA----UCAGGUGGGGCAUUUCUCAGGUGAGAAAUGGAGGGACUCUGGGCCG--CUUUCAUC------
(((((.((...(((((......---.))))).....----)).)))))((((((((((....)))))))((((...))))..))).--........------ ( -28.50, z-score =  -0.40, R)
>droYak2.chr3R 27646886 69 - 28832112
CCGCCCGAAAAGCGAAUCGCUA---UUUCGCGACCA----UCAGGUGGGGCAUUUCUCAGGUGAGACUCUUCCAUC--------------------------
..((((.....(((((......---.))))).(((.----...))).))))...((((....))))..........-------------------------- ( -20.60, z-score =  -0.97, R)
>droSec1.super_4 5548388 89 - 6179234
CCGCCCGAAAAGCGAAUCGCUA---UUUCGCGACCA----UCAGGUGGGGCAUUUCUCAGGUGAGAAACGGAGGGACUCUGGGCCGCUCUUUCAUC------
(((((.((...(((((......---.))))).....----)).)))))(((.((((((....))))))(((((...))))).)))...........------ ( -30.00, z-score =  -0.52, R)
>droSim1.chr3R 26364296 89 - 27517382
CCGCCCGAAAAGCGAAUCGCUA---UUUCGCGACCA----UCAGGUGGGGCAUUUCUCAGGUGAGAAACGGAGGGACUCUGGGCCGCUCUUUCAUC------
(((((.((...(((((......---.))))).....----)).)))))(((.((((((....))))))(((((...))))).)))...........------ ( -30.00, z-score =  -0.52, R)
>droVir3.scaffold_13047 11563192 73 - 19223366
-------CAACACGAAUUGUUAUAAAAAAAUAAACGCAACACCCAAAAGACAAGCGGCUAUUGCGGCCCUCUCUUUGGUC----------------------
-------.((((.....)))).....................((((((((...((.((....)).))..))).)))))..---------------------- ( -11.60, z-score =  -0.44, R)
>consensus
CCGCCCGAAAAGCGAAUCGCUA___UUUCGCGACCA____UCAGGUGGGGCAUUUCUCAGGUGAGAAACGGAGGGACUCUGGGCCG_UCUUUCAUC______
(((((.((........((((.........)))).......)).)))))....((((((....)))))).................................. (-10.95 = -11.12 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:58:29 2011