Locus 4263

Sequence ID dm3.chr2R
Location 11,751,213 – 11,751,313
Length 100
Max. P 0.947842
window5842 window5843

overview

Window 2

Location 11,751,213 – 11,751,313
Length 100
Sequences 6
Columns 127
Reading direction forward
Mean pairwise identity 82.17
Shannon entropy 0.29507
G+C content 0.54450
Mean single sequence MFE -38.75
Consensus MFE -29.90
Energy contribution -31.40
Covariance contribution 1.50
Combinations/Pair 1.16
Mean z-score -2.10
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.53
SVM RNA-class probability 0.947842
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11751213 100 + 21146708
AACCAGA------UAGGGUUGGGCCGGCACCAGUGGAGGUUUCUACGUGGA--------------------GCUUGCCCUCCACUGAAGGUGCCACUACCUGACCCCCAAAA-GUAUCCAGCAUAAU
.......------..((((..((..((((((.((((......))))(((((--------------------(......))))))....))))))....))..))))......-.............. ( -38.00, z-score =  -2.06, R)
>droSim1.chr2R 10493115 101 + 19596830
AACCAGA------UAGGGUUGGGCCGGCACCAGUGGAGGUUCCUACGUGGA--------------------GCUUGCCCUCCACUGAAGGUGCCACUGCCUGACCCCCAAAAAGUAUCCAGCAUAAU
.......------..((((..(((.((((((((((((((((((.....)))--------------------).....))))))))...))))))...)))..))))..................... ( -43.60, z-score =  -3.32, R)
>droSec1.super_1 9245727 101 + 14215200
AACCAGA------UAGGGUUGGGCCGGCACCAGUGGAGGUUCCUACGUGGA--------------------GCUUGCCCUCCACUGAAGGUGCCACUGCCUGACCCCCAAAAAGUAUCCAGCAUAAU
.......------..((((..(((.((((((((((((((((((.....)))--------------------).....))))))))...))))))...)))..))))..................... ( -43.60, z-score =  -3.32, R)
>droYak2.chr2R 3907324 105 - 21139217
AACCAGAUAGGAAUAGGGUUGGACCGGCACCAGUGGAGGUUCCUACGUGGA--------------------GCUUGCCCUCCACUGAAGGUGCCACUGCCUGACCCCCAAAA--UAUCCAGCAUAAU
.....((((......(((((((...((((((((((((((((((.....)))--------------------).....))))))))...))))))....)).)))))......--))))......... ( -39.20, z-score =  -2.34, R)
>droEre2.scaffold_4845 8481943 99 - 22589142
AACCAGA------UAGGGUUGGACCCACACCAGUGGAGGUUCUUACGUGGA--------------------GCUUGCCCUCCACUGAAGGUGCCACUGCCUGACCCCCAAAA--UAUCCAGCAUAGU
..((...------..))((((((.((((....)))).((((.....(((((--------------------(......))))))...((((......)))))))).......--..))))))..... ( -29.80, z-score =  -0.55, R)
>droAna3.scaffold_13266 7440600 120 - 19884421
GACCAGA------UAGGGUUGGGCAGGCACUACUGGAGGUGCCUAUGUACACAUUAUCUGUGUAGCCACCGGCAUGCCCUCCAAUGAAGGUGGAACAACUUGACCCCCAAAU-GUACACGUAAAAAU
.......------..((((..((.(((((((......)))))))...((((((.....)))))).(((((..(((........)))..))))).....))..))))......-.............. ( -38.30, z-score =  -1.00, R)
>consensus
AACCAGA______UAGGGUUGGGCCGGCACCAGUGGAGGUUCCUACGUGGA____________________GCUUGCCCUCCACUGAAGGUGCCACUGCCUGACCCCCAAAA_GUAUCCAGCAUAAU
...............((((..(((.((((((((((((((.(((.....)))....................(....)))))))))...))))))...)))..))))..................... (-29.90 = -31.40 +   1.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,751,213 – 11,751,313
Length 100
Sequences 6
Columns 127
Reading direction reverse
Mean pairwise identity 82.17
Shannon entropy 0.29507
G+C content 0.54450
Mean single sequence MFE -41.53
Consensus MFE -35.04
Energy contribution -35.27
Covariance contribution 0.23
Combinations/Pair 1.21
Mean z-score -1.60
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.893983
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11751213 100 - 21146708
AUUAUGCUGGAUAC-UUUUGGGGGUCAGGUAGUGGCACCUUCAGUGGAGGGCAAGC--------------------UCCACGUAGAAACCUCCACUGGUGCCGGCCCAACCCUA------UCUGGUU
.....((..(((.(-....)(((((..(((...((((((...((((((((....((--------------------.....)).....)))))))))))))).)))..))))))------))..)). ( -41.40, z-score =  -1.87, R)
>droSim1.chr2R 10493115 101 - 19596830
AUUAUGCUGGAUACUUUUUGGGGGUCAGGCAGUGGCACCUUCAGUGGAGGGCAAGC--------------------UCCACGUAGGAACCUCCACUGGUGCCGGCCCAACCCUA------UCUGGUU
.....((..((((((....))((((..(((...((((((...((((((((......--------------------(((.....))).)))))))))))))).)))..))))))------))..)). ( -44.90, z-score =  -2.38, R)
>droSec1.super_1 9245727 101 - 14215200
AUUAUGCUGGAUACUUUUUGGGGGUCAGGCAGUGGCACCUUCAGUGGAGGGCAAGC--------------------UCCACGUAGGAACCUCCACUGGUGCCGGCCCAACCCUA------UCUGGUU
.....((..((((((....))((((..(((...((((((...((((((((......--------------------(((.....))).)))))))))))))).)))..))))))------))..)). ( -44.90, z-score =  -2.38, R)
>droYak2.chr2R 3907324 105 + 21139217
AUUAUGCUGGAUA--UUUUGGGGGUCAGGCAGUGGCACCUUCAGUGGAGGGCAAGC--------------------UCCACGUAGGAACCUCCACUGGUGCCGGUCCAACCCUAUUCCUAUCUGGUU
.....((..((((--.....(((((..(((...((((((...((((((((......--------------------(((.....))).)))))))))))))).)))..))))).....))))..)). ( -45.70, z-score =  -2.67, R)
>droEre2.scaffold_4845 8481943 99 + 22589142
ACUAUGCUGGAUA--UUUUGGGGGUCAGGCAGUGGCACCUUCAGUGGAGGGCAAGC--------------------UCCACGUAAGAACCUCCACUGGUGUGGGUCCAACCCUA------UCUGGUU
.....((..(((.--.....(((((..(((....(((((...((((((((....((--------------------.....)).....)))))))))))))..)))..))))))------))..)). ( -35.10, z-score =  -0.15, R)
>droAna3.scaffold_13266 7440600 120 + 19884421
AUUUUUACGUGUAC-AUUUGGGGGUCAAGUUGUUCCACCUUCAUUGGAGGGCAUGCCGGUGGCUACACAGAUAAUGUGUACAUAGGCACCUCCAGUAGUGCCUGCCCAACCCUA------UCUGGUC
.............(-(..(((((..........((((.......))))((((..(((...)))((((((.....))))))...((((((........))))))))))..)))))------..))... ( -37.20, z-score =  -0.15, R)
>consensus
AUUAUGCUGGAUAC_UUUUGGGGGUCAGGCAGUGGCACCUUCAGUGGAGGGCAAGC____________________UCCACGUAGGAACCUCCACUGGUGCCGGCCCAACCCUA______UCUGGUU
.....((((((.........(((((..(((...((((((...((((((((......................................)))))))))))))).)))..))))).......)))))). (-35.04 = -35.27 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:25:49 2011