Locus 9999

Sequence ID dm3.chr3R
Location 10,459,560 – 10,459,650
Length 90
Max. P 0.902482
window13741 window13742

overview

Window 1

Location 10,459,560 – 10,459,650
Length 90
Sequences 8
Columns 112
Reading direction forward
Mean pairwise identity 66.12
Shannon entropy 0.61324
G+C content 0.47234
Mean single sequence MFE -27.26
Consensus MFE -9.58
Energy contribution -9.66
Covariance contribution 0.08
Combinations/Pair 1.22
Mean z-score -2.07
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.902482
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10459560 90 + 27905053
----GCAUAUAUGCAUCUGCAUUUGACAGAUGCAGUCAUC---------GCUCUACAAAUGCAUUUUUCACACGCACCCC---CCUCUGUGAAAAGAUAAGCCGUU------
----((.....(((((((((....).))))))))(((...---------((.........))..((((((((........---....)))))))))))..))....------ ( -21.30, z-score =  -2.23, R)
>droPer1.super_0 9622958 96 + 11822988
GUAUCUGUGGCUGCAUCUGUAUCUGACAGAUGCAGUCAUC---------GCUAUGCACUUUUCACACGCGUACAUGAUCCG---CUGUGUGAGAAACCAAACGGAGAU----
...(((((((((((((((((.....))))))))))))...---------.........((((((((((((.........))---).))))))))).....)))))...---- ( -38.10, z-score =  -3.87, R)
>dp4.chr2 19942952 96 - 30794189
GUAUCUGUGGCUGCAUCUGUAUCUGACAGAUGCAGUCAUC---------GCUAUGCACUUUUCACACGCGUACAUGAUCCG---CUGUGUGAGAAACCAAACGGAGAU----
...(((((((((((((((((.....))))))))))))...---------.........((((((((((((.........))---).))))))))).....)))))...---- ( -38.10, z-score =  -3.87, R)
>droAna3.scaffold_13340 22551446 92 - 23697760
------GCAUGUGUUUCGGCAUCUGACAGAUGCUGUCAUCACAACUGCAGCGAUACAGAUGCGCUUUUCGCACGCCGGCU------UUGGGAAAAGAUAGGAUU--------
------(((((((...(((((((.....)))))))....))))..))).((((...((.....))..))))...((..((------((....))))...))...-------- ( -26.20, z-score =  -0.20, R)
>droEre2.scaffold_4770 9992976 95 + 17746568
--GCAUACAUAUGCAUCUGCAUUUGACAGAUGCAGUCAUC---------GCUCUACAAAUGCAUUUUUCACACGCAUCCCACGCCACUGCGAAAAGAUAAGCCGAU------
--((.......(((((((((....).))))))))(((...---------((.........))..(((((.((.((.......))...)).))))))))..))....------ ( -19.50, z-score =  -0.74, R)
>droYak2.chr3R 12858072 88 - 28832112
----GCAUAUAUGCAUCUGCAUUUGACAGAUGCAGUCAUC---------GCUCUACAAAUGCAUUUUUCACACGCACCCC---CCU--GUGAAAAGAUAAGCCGCA------
----((.....(((((((((....).))))))))(((...---------((.........))..((((((((.(......---).)--)))))))))).....)).------ ( -23.00, z-score =  -2.70, R)
>droSec1.super_0 9542933 96 - 21120651
----GCAUAUAUGCAUCUGCAUUUGACAGAUGCAGUCAUC---------GCUCUACAAAUGCAUUUUUCACACGCACCCC---CCGCUGUGAAAAGAUAAGCCAAAUGGGGG
----((((...(((((((((....).))))))))((....---------)).......)))).(((((((((.((.....---..))))))))))).....((....))... ( -25.30, z-score =  -1.21, R)
>droSim1.chr3R 16513455 88 - 27517382
----GCAUAUAUGCAUCUGCAUUUGACAGAUGCAGUCAUC---------GCUCUACAAAUGCAUUUUUCACACGCACCCC---CCGCUGUGCAAAGAGGGAGGG--------
----((.....(((((((((....).))))))))......---------((.........))...........)).((((---((.((......)).))).)))-------- ( -26.60, z-score =  -1.78, R)
>consensus
____GCAUAUAUGCAUCUGCAUUUGACAGAUGCAGUCAUC_________GCUCUACAAAUGCAUUUUUCACACGCACCCC___CCUCUGUGAAAAGAUAAGCCGA_______
...........(((((((((....).)))))))).............................................................................. ( -9.58 =  -9.66 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 10,459,560 – 10,459,650
Length 90
Sequences 8
Columns 112
Reading direction reverse
Mean pairwise identity 66.12
Shannon entropy 0.61324
G+C content 0.47234
Mean single sequence MFE -29.30
Consensus MFE -11.28
Energy contribution -11.81
Covariance contribution 0.53
Combinations/Pair 1.31
Mean z-score -1.49
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.652129
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10459560 90 - 27905053
------AACGGCUUAUCUUUUCACAGAGG---GGGGUGCGUGUGAAAAAUGCAUUUGUAGAGC---------GAUGACUGCAUCUGUCAAAUGCAGAUGCAUAUAUGC----
------....(((..((((......))))---..)))(((((((.....((((((((((((((---------(.....))).)))).))))))))......)))))))---- ( -25.80, z-score =  -1.22, R)
>droPer1.super_0 9622958 96 - 11822988
----AUCUCCGUUUGGUUUCUCACACAG---CGGAUCAUGUACGCGUGUGAAAAGUGCAUAGC---------GAUGACUGCAUCUGUCAGAUACAGAUGCAGCCACAGAUAC
----((((.((((..((...((((((.(---((.........))))))))).....))..)))---------).((.((((((((((.....)))))))))).)).)))).. ( -31.90, z-score =  -1.97, R)
>dp4.chr2 19942952 96 + 30794189
----AUCUCCGUUUGGUUUCUCACACAG---CGGAUCAUGUACGCGUGUGAAAAGUGCAUAGC---------GAUGACUGCAUCUGUCAGAUACAGAUGCAGCCACAGAUAC
----((((.((((..((...((((((.(---((.........))))))))).....))..)))---------).((.((((((((((.....)))))))))).)).)))).. ( -31.90, z-score =  -1.97, R)
>droAna3.scaffold_13340 22551446 92 + 23697760
--------AAUCCUAUCUUUUCCCAA------AGCCGGCGUGCGAAAAGCGCAUCUGUAUCGCUGCAGUUGUGAUGACAGCAUCUGUCAGAUGCCGAAACACAUGC------
--------..................------...((((((((.....))))((((..(((((.......)))))(((((...)))))))))))))..........------ ( -24.20, z-score =  -0.52, R)
>droEre2.scaffold_4770 9992976 95 - 17746568
------AUCGGCUUAUCUUUUCGCAGUGGCGUGGGAUGCGUGUGAAAAAUGCAUUUGUAGAGC---------GAUGACUGCAUCUGUCAAAUGCAGAUGCAUAUGUAUGC--
------........(((((..(((....))).)))))(((((((.....((((((((((((((---------(.....))).)))).))))))))....)))))))....-- ( -29.70, z-score =  -0.93, R)
>droYak2.chr3R 12858072 88 + 28832112
------UGCGGCUUAUCUUUUCAC--AGG---GGGGUGCGUGUGAAAAAUGCAUUUGUAGAGC---------GAUGACUGCAUCUGUCAAAUGCAGAUGCAUAUAUGC----
------((((.......(((((((--(.(---......).)))))))).((((((((((((((---------(.....))).)))).))))))))..)))).......---- ( -27.30, z-score =  -1.43, R)
>droSec1.super_0 9542933 96 + 21120651
CCCCCAUUUGGCUUAUCUUUUCACAGCGG---GGGGUGCGUGUGAAAAAUGCAUUUGUAGAGC---------GAUGACUGCAUCUGUCAAAUGCAGAUGCAUAUAUGC----
(((((..(((.............)))..)---)))).(((((((.....((((((((((((((---------(.....))).)))).))))))))......)))))))---- ( -31.42, z-score =  -1.55, R)
>droSim1.chr3R 16513455 88 + 27517382
--------CCCUCCCUCUUUGCACAGCGG---GGGGUGCGUGUGAAAAAUGCAUUUGUAGAGC---------GAUGACUGCAUCUGUCAAAUGCAGAUGCAUAUAUGC----
--------.((((((.((......)).))---)))).(((((((.....((((((((((((((---------(.....))).)))).))))))))......)))))))---- ( -32.20, z-score =  -2.35, R)
>consensus
_______UCGGCUUAUCUUUUCACAGAGG___GGGGUGCGUGUGAAAAAUGCAUUUGUAGAGC_________GAUGACUGCAUCUGUCAAAUGCAGAUGCAUAUAUGC____
.....................................((((.......))))..........................(((((((((.....)))))))))........... (-11.28 = -11.81 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:15:27 2011