Locus 11302

Sequence ID dm3.chr3R
Location 20,202,209 – 20,202,314
Length 105
Max. P 0.666610
window15534 window15535

overview

Window 4

Location 20,202,209 – 20,202,311
Length 102
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 75.57
Shannon entropy 0.41709
G+C content 0.44863
Mean single sequence MFE -26.88
Consensus MFE -14.78
Energy contribution -16.42
Covariance contribution 1.64
Combinations/Pair 1.12
Mean z-score -1.66
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.666610
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20202209 102 + 27905053
GAGUCAUUGCGUAUCGAAG-----UAAGUGUUUCAGAUAGUUGGAAUGGCCACAGCUUCAGUUGCGGUUUCGAUGCUCAGUAUUCAUUUUGUCCAUUCGUUUUAGUA---------
((((.((((.((((((((.-----.....(((((((....))))))).(((.((((....)))).))))))))))).))))))))......................--------- ( -26.70, z-score =  -2.32, R)
>droSim1.chr3R 20037082 115 + 27517382
GAGGCAUUGCGAAUCGAAGCCACGUAAGUGUUCCAGAUAGUUGGAGUCGCCACAGCUUCAGUUGCGGUUUCGAUGUUCAGUAUUGAUUCUGCCCAUUCGUUUUA-UACAUACAUUU
(.((((....(((((((.(((((....))).....((..((((((..(((.((.......)).)))..))))))..)).)).))))))))))))..........-........... ( -29.80, z-score =  -1.45, R)
>droSec1.super_0 20540952 107 + 21120651
GAAGUAUUGCGUAUCGAAGCCACGUAAGUGUUCCAGAUAGUUGGAGUCGCCACAGCUUCAGUUGCAGUUUCGAUGUUCAGUAUUGAUUCUGCCGAUUCGUUUUAGUA---------
..(.((..(((.(((((((((((....)))((((((....))))))........)))))....((((..((((((.....))))))..)))).))).)))..)).).--------- ( -31.50, z-score =  -3.18, R)
>droYak2.chr3R 2529543 86 - 28832112
GAGGCAUUGCAUCUCGAAGCCACGUAAGCGUUCCAGGU------------------UCCAGUUGCGGUUUCGAUGUUCACUAUUGAUUCCAUCCAUUCAUUUUU------------
..((....(((.((.(((.(((((....)))....)))------------------)).)).)))((..((((((.....))))))..))..))..........------------ ( -17.60, z-score =  -0.60, R)
>droEre2.scaffold_4820 2612473 103 - 10470090
GAGGCAUUGCGGAUCGAAGCCACGUAAGUGUUCCAGAUAGUUGCAGUGGCCACAGCUUCAGUUGCGGUUUCGGUGCUCAGUAUUGAUUCCAUCCAAUCUUUUG-------------
..(((((((((.(((.....(((....))).....)))...)))))).))).((((....)))).((..(((((((...)))))))..)).............------------- ( -28.80, z-score =  -0.75, R)
>consensus
GAGGCAUUGCGUAUCGAAGCCACGUAAGUGUUCCAGAUAGUUGGAGUCGCCACAGCUUCAGUUGCGGUUUCGAUGUUCAGUAUUGAUUCUGUCCAUUCGUUUUA_UA_________
.....((((.(((((((((((..((((.((........(((((.........))))).)).))))))))))))))).))))................................... (-14.78 = -16.42 +   1.64)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,202,215 – 20,202,314
Length 99
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 74.10
Shannon entropy 0.44222
G+C content 0.43742
Mean single sequence MFE -25.58
Consensus MFE -13.34
Energy contribution -14.78
Covariance contribution 1.44
Combinations/Pair 1.12
Mean z-score -1.60
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.621619
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20202215 99 + 27905053
UUGCGUAUCGAAG-----UAAGUGUUUCAGAUAGUUGGAAUGGCCACAGCUUCAGUUGCGGUUUCGAUGCUCAGUAUUCAUUUUGUCCAUUCGUUUUAGUAGAA-----------
(((.((((((((.-----.....(((((((....))))))).(((.((((....)))).))))))))))).)))..............................----------- ( -21.80, z-score =  -0.82, R)
>droSim1.chr3R 20037088 115 + 27517382
UUGCGAAUCGAAGCCACGUAAGUGUUCCAGAUAGUUGGAGUCGCCACAGCUUCAGUUGCGGUUUCGAUGUUCAGUAUUGAUUCUGCCCAUUCGUUUUAUACAUACAUUUUAUACA
..((((((.((((((((....)))((((((....))))))........)))))....((((..((((((.....))))))..))))..))))))..................... ( -29.10, z-score =  -2.04, R)
>droSec1.super_0 20540958 104 + 21120651
UUGCGUAUCGAAGCCACGUAAGUGUUCCAGAUAGUUGGAGUCGCCACAGCUUCAGUUGCAGUUUCGAUGUUCAGUAUUGAUUCUGCCGAUUCGUUUUAGUAGCA-----------
..(((.(((((((((((....)))((((((....))))))........)))))....((((..((((((.....))))))..)))).))).)))..........----------- ( -29.90, z-score =  -2.62, R)
>droYak2.chr3R 2529549 83 - 28832112
UUGCAUCUCGAAGCCACGUAAGCGUUCCAGGU------------------UCCAGUUGCGGUUUCGAUGUUCACUAUUGAUUCCAUCCAUUCAUUUUUGAA--------------
..(((.((.(((.(((((....)))....)))------------------)).)).)))((..((((((.....))))))..)).....((((....))))-------------- ( -17.20, z-score =  -1.07, R)
>droEre2.scaffold_4820 2612479 100 - 10470090
UUGCGGAUCGAAGCCACGUAAGUGUUCCAGAUAGUUGCAGUGGCCACAGCUUCAGUUGCGGUUUCGGUGCUCAGUAUUGAUUCCAUCCAAUC-UUUUGGAA--------------
..((((...((((((((....))).........((.((....)).)).)))))..))))((..(((((((...)))))))..)).(((((..-..))))).-------------- ( -29.90, z-score =  -1.44, R)
>consensus
UUGCGUAUCGAAGCCACGUAAGUGUUCCAGAUAGUUGGAGUCGCCACAGCUUCAGUUGCGGUUUCGAUGUUCAGUAUUGAUUCUGUCCAUUCGUUUUAGAA__A___________
.((.(((((((((((..((((.((........(((((.........))))).)).))))))))))))))).)).......................................... (-13.34 = -14.78 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:40:20 2011