Locus 15470

Sequence ID dm3.chrX
Location 19,218,369 – 19,218,498
Length 129
Max. P 0.932129
window21326 window21327 window21328

overview

Window 6

Location 19,218,369 – 19,218,468
Length 99
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 54.70
Shannon entropy 0.72542
G+C content 0.44621
Mean single sequence MFE -23.48
Consensus MFE -7.59
Energy contribution -8.28
Covariance contribution 0.69
Combinations/Pair 1.50
Mean z-score -1.65
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.830467
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19218369 99 - 22422827
AGCGAAUUUUUGCCUUCCAAUGCUGGUGU-GAUGUC-UCAUCGCCAUCCCCAUCAUCAUCAUUGCCAUCGUAGUGAAUGAAAUGAUGAU----GUAUUCGAUUUC-
.((((....))))..((.(((((((((((-((....-))).)))))....(((((((((((((((....)))))).))))..)))))..----))))).))....- ( -25.00, z-score =  -1.48, R)
>droEre2.scaffold_4690 9475139 76 - 18748788
AGCAAAU---UGCCUUCCUAUGCUG--GC-GAUGUC-CCAUCAGCGCCAUCGUGUU------------------GAAUGAAACGAUAAU----GUAUUCAAUAUC-
.....((---((((..........)--))-)))((.-.(((((((((....)))))------------------).)))..))((((.(----(....)).))))- ( -16.60, z-score =  -1.02, R)
>droSim1.chrX 14858114 79 - 17042790
AGCGCAUUUUUGCCUUCCUAUGCUG--GU-GAUGUC-UCAUCCUCAUCACCAUCAUC------------------AAUGAAAUGAUAAU----GUAUUCGAUUUC-
((.(((....)))))((..((((((--((-((((..-.......))))))))..(((------------------(......))))...----))))..))....- ( -16.30, z-score =  -1.45, R)
>droGri2.scaffold_15081 1610112 103 - 4274704
AGCUCAUUUCAGC--GACGACGGCGACGUCAACGUCAACGUCAACGUCGAC-UGAGAGAGCGGGCAGCAAGCACACAUCACAUGUUGACCUUGAUAUUCGCAUUCG
.((((.(((((((--(((((((..((((....))))..))))...)))).)-)))))))))((((((((.(.........).))))).)))............... ( -36.00, z-score =  -2.64, R)
>consensus
AGCGAAUUUUUGCCUUCCUAUGCUG__GU_GAUGUC_UCAUCAACAUCACCAUCAUC_________________GAAUGAAAUGAUAAU____GUAUUCGAUUUC_
.(((......)))......(((.((((((.((((....)))).)))))).)))..................................................... ( -7.59 =  -8.28 +   0.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,218,404 – 19,218,498
Length 94
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 53.68
Shannon entropy 0.70564
G+C content 0.50680
Mean single sequence MFE -27.59
Consensus MFE -10.10
Energy contribution -9.60
Covariance contribution -0.50
Combinations/Pair 1.36
Mean z-score -1.60
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.21
SVM RNA-class probability 0.909570
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19218404 94 + 22422827
-----GGCAAUGAUGAUGAUGGGGAUGGCGAUGA-GACAUCACACCAGCAUUGGAAGGCAAAAAUUCGCUGUGGGCCAUUGACUGGCUAACUUUUGCCAG----------
-----(((((....((((.(((.((((.(.....-).))))...))).))))....(((........)))((.(((((.....))))).))..)))))..---------- ( -26.40, z-score =  -0.64, R)
>droEre2.scaffold_4690 9475174 71 + 18748788
-----------------------GGCGCUGAUGG-GACAUCG--CCAGCAUAGGAAGGCAA---UUUGCUGUGGGCCAAUGACUGGCUAACUUUGGCCAG----------
-----------------------(((((((.(((-....)))--.))))((((.(((....---))).))))..))).....(((((((....)))))))---------- ( -24.20, z-score =  -0.79, R)
>droSim1.chrX 14858139 84 + 17042790
-------------UGAUGAUGGUGAUGAGGAUGA-GACAUCA--CCAGCAUAGGAAGGCAAAAAUGCGCUGUGGGCCAAUGACUGGCUAACUUUUGCCAG----------
-------------..(((.((((((((.......-..)))))--))).))).....(((((((.......((.(((((.....))))).)))))))))..---------- ( -27.31, z-score =  -2.55, R)
>droGri2.scaffold_15081 1610152 103 + 4274704
UGCCCGCUCUCUCAGUCGACGUUGACGUUGACGUUGACGUCG--CCGUCGUCG-----CUGAAAUGAGCUCUAAGAAAAUAAUUAAAUAGCAGCAGUCGGCAAACAAAAA
((((.(((...((((((((((.(((((((......)))))))--.)))))..)-----)))).....((((((..............))).)))))).))))........ ( -32.44, z-score =  -2.40, R)
>consensus
_____________UGAUGAUGGUGACGAUGAUGA_GACAUCA__CCAGCAUAGGAAGGCAAAAAUGCGCUGUGGGCCAAUGACUGGCUAACUUUUGCCAG__________
.............................((((....))))......((.......(((........)))....))......(((((........))))).......... (-10.10 =  -9.60 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,218,404 – 19,218,498
Length 94
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 53.68
Shannon entropy 0.70564
G+C content 0.50680
Mean single sequence MFE -25.88
Consensus MFE -9.00
Energy contribution -9.00
Covariance contribution 0.00
Combinations/Pair 1.31
Mean z-score -1.80
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.932129
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19218404 94 - 22422827
----------CUGGCAAAAGUUAGCCAGUCAAUGGCCCACAGCGAAUUUUUGCCUUCCAAUGCUGGUGUGAUGUC-UCAUCGCCAUCCCCAUCAUCAUCAUUGCC-----
----------..((((((((((.((((.....))))........))))))))))...(((((.(((((.((((.(-.....).)))).....))))).)))))..----- ( -25.50, z-score =  -1.75, R)
>droEre2.scaffold_4690 9475174 71 - 18748788
----------CUGGCCAAAGUUAGCCAGUCAUUGGCCCACAGCAAA---UUGCCUUCCUAUGCUGG--CGAUGUC-CCAUCAGCGCC-----------------------
----------..((((.......(((((.(((.((......((...---..))...)).)))))))--)((((..-.)))).).)))----------------------- ( -18.90, z-score =  -0.22, R)
>droSim1.chrX 14858139 84 - 17042790
----------CUGGCAAAAGUUAGCCAGUCAUUGGCCCACAGCGCAUUUUUGCCUUCCUAUGCUGG--UGAUGUC-UCAUCCUCAUCACCAUCAUCA-------------
----------..(((((((((..(((((...))))).........))))))))).....(((.(((--(((((..-.......)))))))).)))..------------- ( -23.90, z-score =  -2.54, R)
>droGri2.scaffold_15081 1610152 103 - 4274704
UUUUUGUUUGCCGACUGCUGCUAUUUAAUUAUUUUCUUAGAGCUCAUUUCAG-----CGACGACGG--CGACGUCAACGUCAACGUCAACGUCGACUGAGAGAGCGGGCA
........((((...........(((((........)))))((((.((((((-----((((((((.--.((((....))))..))))...)))).)))))))))).)))) ( -35.20, z-score =  -2.70, R)
>consensus
__________CUGGCAAAAGUUAGCCAGUCAUUGGCCCACAGCGAAUUUUUGCCUUCCUAUGCUGG__CGAUGUC_UCAUCAACAUCACCAUCAUCA_____________
..........(((((........((((.....)))).....(((......)))........)))))...((((....))))............................. ( -9.00 =  -9.00 +   0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:00:03 2011