Locus 10980

Sequence ID dm3.chr3R
Location 17,915,553 – 17,915,701
Length 148
Max. P 0.995364
window15088 window15089 window15090

overview

Window 8

Location 17,915,553 – 17,915,663
Length 110
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 72.98
Shannon entropy 0.50819
G+C content 0.36147
Mean single sequence MFE -23.52
Consensus MFE -13.30
Energy contribution -13.67
Covariance contribution 0.37
Combinations/Pair 1.46
Mean z-score -1.06
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.619701
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17915553 110 + 27905053
AAAACGGAUGCUACAUAAAAAGUUUAUGGGGUGACAAGGUCACGAAAAGUAUGACAACUGCGAAAAACUUGAAGCUGACUUCUGCAGUAAUUCGCAAGUUAAACUUUGAA------
.............(((((.....)))))..(((((...)))))..(((((.((((...((((((..(((.((((....))))...)))..)))))).)))).)))))...------ ( -23.70, z-score =  -1.21, R)
>droSim1.chr3R_random 888262 110 + 1307089
AAAAUGGAUACAACAUAAAAAGUUUAUGGGGUGACAAGGUCACGAAAAGUAUGACAACUGCGAAAAACUUGAAGCUGACUUCUGCAGUAAUUCGCAAGUUAAACUUUGAA------
.............(((((.....)))))..(((((...)))))..(((((.((((...((((((..(((.((((....))))...)))..)))))).)))).)))))...------ ( -23.70, z-score =  -1.65, R)
>droSec1.super_0 18284346 110 + 21120651
AAAAUGGAUACAACAUAAAAAGUUUAUGGGGUGACAAGGUCACAAAAAGUAUGACAACUGCGAAAAACUUGAAGCUGACUUCUGCAGUAAUUCGCAAGUUAAACUUUGAA------
.............(((((.....)))))..(((((...)))))..(((((.((((...((((((..(((.((((....))))...)))..)))))).)))).)))))...------ ( -23.70, z-score =  -1.75, R)
>droYak2.chr3R 18755244 110 + 28832112
AAAAAGCAUGCUGUGUAAAAAGUUUAUGGGGUGACAAGGUCACGAAAAGUGUGACAACUGCGAAAAACUUGAAGCUGACUUCAGCAGUAACUCGCAAGUUAAACUUUGUU------
......(((.(((((.........))))).)))(((((((((((.....))))))((((((((...(((....((((....)))))))...)))).))))....))))).------ ( -26.10, z-score =  -0.55, R)
>droEre2.scaffold_4820 308382 108 - 10470090
AAAAGUAAGGCUAUGUAAAAG--UUAUGGGGUGACAAGGUCACGAAAACUGUGACAACUGCGAAAAACUUGGAGCUGACUUCUGCAGCAAUUCGCAAGUUAAACUUUGAA------
.(((((.......((((...(--((((((.(((((...))))).....)))))))...))))...((((((((((((.(....)))))...)).))))))..)))))...------ ( -23.80, z-score =  -0.43, R)
>droAna3.scaffold_13340 8919593 114 + 23697760
-ACGUAAAUGAUUC-CAUUGUGUUUCUUUGAUUAUCAUGCCUCAGGCUUUAAUAGAAAUAGAAAAACUUUAAACUUGACUUUCUGUUUCCAUAUUGAGUGGCAUUUAAUUUGUCAC
-......(((((..-((..(.....)..))...)))))(((...))).((((((((((((((((..(.........)..))))))))))..))))))((((((.......)))))) ( -20.10, z-score =  -0.76, R)
>consensus
AAAAUGGAUGCUACAUAAAAAGUUUAUGGGGUGACAAGGUCACGAAAAGUAUGACAACUGCGAAAAACUUGAAGCUGACUUCUGCAGUAAUUCGCAAGUUAAACUUUGAA______
..................((((((((....(((((...)))))...............((((((..(((.((((....))))...)))..))))))...))))))))......... (-13.30 = -13.67 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 17,915,553 – 17,915,663
Length 110
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 72.98
Shannon entropy 0.50819
G+C content 0.36147
Mean single sequence MFE -22.57
Consensus MFE -14.48
Energy contribution -15.85
Covariance contribution 1.37
Combinations/Pair 1.33
Mean z-score -2.23
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.79
SVM RNA-class probability 0.995364
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17915553 110 - 27905053
------UUCAAAGUUUAACUUGCGAAUUACUGCAGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCAUACUUUUCGUGACCUUGUCACCCCAUAAACUUUUUAUGUAGCAUCCGUUUU
------...(((((.(((((.(((((..(((...((((....)))).)))..))))))))))....)))))..(((((...)))))..(((((.....)))))............. ( -24.80, z-score =  -3.28, R)
>droSim1.chr3R_random 888262 110 - 1307089
------UUCAAAGUUUAACUUGCGAAUUACUGCAGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCAUACUUUUCGUGACCUUGUCACCCCAUAAACUUUUUAUGUUGUAUCCAUUUU
------...(((((.(((((.(((((..(((...((((....)))).)))..))))))))))....)))))..(((((...)))))..(((((.....)))))............. ( -24.80, z-score =  -3.60, R)
>droSec1.super_0 18284346 110 - 21120651
------UUCAAAGUUUAACUUGCGAAUUACUGCAGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCAUACUUUUUGUGACCUUGUCACCCCAUAAACUUUUUAUGUUGUAUCCAUUUU
------...((((((((..(((((((..(((...((((....)))).)))..)))))))..((((((.....))))))............)))))))).................. ( -24.80, z-score =  -3.38, R)
>droYak2.chr3R 18755244 110 - 28832112
------AACAAAGUUUAACUUGCGAGUUACUGCUGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCACACUUUUCGUGACCUUGUCACCCCAUAAACUUUUUACACAGCAUGCUUUUU
------...((((((((..(((((((..(((..(((((....))))))))..)))))))..(((((.......)))))............)))))))).................. ( -25.90, z-score =  -2.48, R)
>droEre2.scaffold_4820 308382 108 + 10470090
------UUCAAAGUUUAACUUGCGAAUUGCUGCAGAAGUCAGCUCCAAGUUUUUCGCAGUUGUCACAGUUUUCGUGACCUUGUCACCCCAUAA--CUUUUACAUAGCCUUACUUUU
------...((((((.((((.(((((..(((...((.(....)))..)))..)))))))))(((((.......))))).............))--))))................. ( -19.60, z-score =  -1.08, R)
>droAna3.scaffold_13340 8919593 114 - 23697760
GUGACAAAUUAAAUGCCACUCAAUAUGGAAACAGAAAGUCAAGUUUAAAGUUUUUCUAUUUCUAUUAAAGCCUGAGGCAUGAUAAUCAAAGAAACACAAUG-GAAUCAUUUACGU-
(((.........(((((.(.....(((((((.((((((.............)))))).)))))))........).)))))(.....).......)))....-.............- ( -15.54, z-score =   0.47, R)
>consensus
______UUCAAAGUUUAACUUGCGAAUUACUGCAGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCAUACUUUUCGUGACCUUGUCACCCCAUAAACUUUUUAUGUAGCAUCCAUUUU
.........((((((((..(((((((..(((...((((....)))).)))..)))))))..(((((.......)))))............)))))))).................. (-14.48 = -15.85 +   1.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 17,915,590 – 17,915,701
Length 111
Sequences 6
Columns 121
Reading direction reverse
Mean pairwise identity 69.01
Shannon entropy 0.55635
G+C content 0.38296
Mean single sequence MFE -21.69
Consensus MFE -12.81
Energy contribution -13.40
Covariance contribution 0.59
Combinations/Pair 1.33
Mean z-score -1.10
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.97
SVM RNA-class probability 0.864780
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17915590 111 - 27905053
----------GAGCUCUUUUUUCCUUUUUUUUUUGUUCGUGUAUGCCCUUCAAAGUUUAACUUGCGAAUUACUGCAGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCAUACUUUUCGUGACC
----------((((....................)))).............(((((.(((((.(((((..(((...((((....)))).)))..))))))))))....)))))........ ( -21.45, z-score =  -1.41, R)
>droSim1.chr3R_random 888299 108 - 1307089
----------GAGCUCUUUUUUCC---AUUUUUUGUUCGUGUAUGCCCUUCAAAGUUUAACUUGCGAAUUACUGCAGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCAUACUUUUCGUGACC
----------((((..........---.......)))).............(((((.(((((.(((((..(((...((((....)))).)))..))))))))))....)))))........ ( -21.63, z-score =  -1.44, R)
>droSec1.super_0 18284383 108 - 21120651
----------GAGCUCUUUUUUCC---AUUUUUUGUUCGUGUAUGCCCUUCAAAGUUUAACUUGCGAAUUACUGCAGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCAUACUUUUUGUGACC
----------((((..........---.......))))....................((((.(((((..(((...((((....)))).)))..)))))))))((((((.....)))))). ( -22.83, z-score =  -1.81, R)
>droYak2.chr3R 18755281 97 - 28832112
----------GAGCUCUUUUUCC----AUUUUUUUCACA----------ACAAAGUUUAACUUGCGAGUUACUGCUGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCACACUUUUCGUGACC
----------.............----.......((((.----------..(((((.(((((.(((((..(((..(((((....))))))))..))))))))))....)))))..)))).. ( -23.10, z-score =  -2.31, R)
>droEre2.scaffold_4820 308417 99 + 10470090
----------GAGCGCUGGUUGC----AUUUUUUGUUU--------CCUUCAAAGUUUAACUUGCGAAUUGCUGCAGAAGUCAGCUCCAAGUUUUUCGCAGUUGUCACAGUUUUCGUGACC
----------((((...((..((----(.....)))..--------))......))))((((.(((((..(((...((.(....)))..)))..)))))))))(((((.......))))). ( -23.10, z-score =  -0.26, R)
>droAna3.scaffold_13340 8919628 117 - 23697760
AAACUUACUGGAGGCCAUUUUUGAACGUACUAUUAUCUG----UGACAAAUUAAAUGCCACUCAAUAUGGAAACAGAAAGUCAAGUUUAAAGUUUUUCUAUUUCUAUUAAAGCCUGAGGCA
..........((((.(((((.......(((........)----)).......))))).).)))...(((((((.((((((.............)))))).)))))))....(((...))). ( -18.06, z-score =   0.67, R)
>consensus
__________GAGCUCUUUUUUCC___AUUUUUUGUUCG____UGCCCUUCAAAGUUUAACUUGCGAAUUACUGCAGAAGUCAGCUUCAAGUUUUUCGCAGUUGUCAUACUUUUCGUGACC
..........................................................((((.(((((..(((...((((....)))).)))..)))))))))(((((.......))))). (-12.81 = -13.40 +   0.59)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:34:08 2011