Locus 7078

Sequence ID dm3.chr3L
Location 12,007,832 – 12,007,931
Length 99
Max. P 0.999390
window9751 window9752

overview

Window 1

Location 12,007,832 – 12,007,931
Length 99
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 77.23
Shannon entropy 0.39919
G+C content 0.54440
Mean single sequence MFE -41.52
Consensus MFE -28.89
Energy contribution -30.45
Covariance contribution 1.56
Combinations/Pair 1.07
Mean z-score -3.60
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.85
SVM RNA-class probability 0.999390
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12007832 99 + 24543557
CUGAGUGCUCUGGUU-------CUCUUCCUCCAGCGGAUAUGUGGAUGUCUGCAAGUUCUUGAUCUUUCAGUCACGACUACGAGUCGCCCACUUCCGCUGGGGGAU---------
..(((.((....)).-------))).((((((((((((...((((.((.(((.(((........))).))).))((((.....)))).)))).)))))))))))).--------- ( -43.40, z-score =  -4.20, R)
>droSim1.chr3L 11377662 99 + 22553184
CUGAGUGCUCUGGUU-------CUCUUCCUCCAGCGGAUGUGUGGAUGUCUGCAAGUUCUUGAUCUUUCAGUCACGACCACGAGUCGCCCACUUCCGCUGGAGGAU---------
..(((.((....)).-------))).((((((((((((.(((.((.((.(((.(((........))).))).))((((.....))))))))).)))))))))))).--------- ( -43.90, z-score =  -4.02, R)
>droSec1.super_0 4193907 99 + 21120651
CUGAGUGCUCUGGUU-------CUCUUCCUCCAGCGGAUGUGUGGAUGUCUGCAAGUUCUUGAUCUUUCAGUCACGACUACGAGUCGCCCACUUCCGCUGGAGGAU---------
..(((.((....)).-------))).((((((((((((.(((.((.((.(((.(((........))).))).))((((.....))))))))).)))))))))))).--------- ( -44.60, z-score =  -4.43, R)
>droYak2.chr3L 12053870 106 + 24197627
CUGAGUGCUCUGGUUUCUGGUUCUCUUCCUCCAGCGGAUGUAUGCAUGUCUGGAAGUUCUUGAUCUUUCACUCACGACUAUGAGUCGCCCACUUCCGCUGGAGGAU---------
..(((.((.(........))).))).((((((((((((.((..((.((..((((((........))))))..)).(((.....)))))..)).)))))))))))).--------- ( -40.40, z-score =  -3.30, R)
>droEre2.scaffold_4784 11995453 98 + 25762168
-UGAGCGCUCUGGUU-------CUCUUGCUCCAGCGGAUACAUGGCUGUCUGGAAGCUCUUGUUCCUUCAGUCAUGACUAUGAGUCGCCCACUUCCGCUGGAGGAU---------
-.(((.((....)).-------)))...((((((((((...(((((((...((((.(....)))))..)))))))(((.....))).......))))))))))...--------- ( -38.80, z-score =  -2.46, R)
>droAna3.scaffold_13337 11387366 90 - 23293914
---------------------UGAACACCUCCAGCGGAUGUCUGGAUACCCCG----UUCUGGACUGGCAGUCACGACCACCAGUCGCCCACUUCCGCUGGAGGAUGUGCGACUA
---------------------.(.((((((((((((((.((..((.....)).----.....((((((..((....))..))))))....)).))))))))))).))).)..... ( -38.00, z-score =  -3.19, R)
>consensus
CUGAGUGCUCUGGUU_______CUCUUCCUCCAGCGGAUGUGUGGAUGUCUGCAAGUUCUUGAUCUUUCAGUCACGACUACGAGUCGCCCACUUCCGCUGGAGGAU_________
..........................((((((((((((....(((.((.(((.(((........))).))).))((((.....)))).)))..)))))))))))).......... (-28.89 = -30.45 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 12,007,832 – 12,007,931
Length 99
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 77.23
Shannon entropy 0.39919
G+C content 0.54440
Mean single sequence MFE -38.97
Consensus MFE -32.22
Energy contribution -33.63
Covariance contribution 1.42
Combinations/Pair 1.11
Mean z-score -3.41
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.68
SVM RNA-class probability 0.999167
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12007832 99 - 24543557
---------AUCCCCCAGCGGAAGUGGGCGACUCGUAGUCGUGACUGAAAGAUCAAGAACUUGCAGACAUCCACAUAUCCGCUGGAGGAAGAG-------AACCAGAGCACUCAG
---------.(((.((((((((.(((((((((.....)))))..(((.(((........))).)))....))))...)))))))).))).(((-------..........))).. ( -36.40, z-score =  -3.41, R)
>droSim1.chr3L 11377662 99 - 22553184
---------AUCCUCCAGCGGAAGUGGGCGACUCGUGGUCGUGACUGAAAGAUCAAGAACUUGCAGACAUCCACACAUCCGCUGGAGGAAGAG-------AACCAGAGCACUCAG
---------.((((((((((((.(((((((((.....)))))..(((.(((........))).)))....))))...)))))))))))).(((-------..........))).. ( -41.30, z-score =  -3.85, R)
>droSec1.super_0 4193907 99 - 21120651
---------AUCCUCCAGCGGAAGUGGGCGACUCGUAGUCGUGACUGAAAGAUCAAGAACUUGCAGACAUCCACACAUCCGCUGGAGGAAGAG-------AACCAGAGCACUCAG
---------.((((((((((((.(((((((((.....)))))..(((.(((........))).)))....))))...)))))))))))).(((-------..........))).. ( -41.20, z-score =  -4.37, R)
>droYak2.chr3L 12053870 106 - 24197627
---------AUCCUCCAGCGGAAGUGGGCGACUCAUAGUCGUGAGUGAAAGAUCAAGAACUUCCAGACAUGCAUACAUCCGCUGGAGGAAGAGAACCAGAAACCAGAGCACUCAG
---------.((((((((((((.(((.(((((((((....))))))(.(((........))).).....))).))).)))))))))))).(((..((........).)..))).. ( -36.80, z-score =  -3.35, R)
>droEre2.scaffold_4784 11995453 98 - 25762168
---------AUCCUCCAGCGGAAGUGGGCGACUCAUAGUCAUGACUGAAGGAACAAGAGCUUCCAGACAGCCAUGUAUCCGCUGGAGCAAGAG-------AACCAGAGCGCUCA-
---------...((((((((((....((((((.....))).((.(((.(((........))).))).))))).....))))))))))...(((-------..(....)..))).- ( -33.70, z-score =  -1.82, R)
>droAna3.scaffold_13337 11387366 90 + 23293914
UAGUCGCACAUCCUCCAGCGGAAGUGGGCGACUGGUGGUCGUGACUGCCAGUCCAGAA----CGGGGUAUCCAGACAUCCGCUGGAGGUGUUCA---------------------
.....(.(((.(((((((((((.((..(.((((((..((....))..)))))))...)----)((.....)).....)))))))))))))).).--------------------- ( -44.40, z-score =  -3.63, R)
>consensus
_________AUCCUCCAGCGGAAGUGGGCGACUCGUAGUCGUGACUGAAAGAUCAAGAACUUCCAGACAUCCACACAUCCGCUGGAGGAAGAG_______AACCAGAGCACUCAG
..........((((((((((((.(((((((((.....)))))..(((.(((........))).)))....))))...)))))))))))).......................... (-32.22 = -33.63 +   1.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:20:08 2011