Locus 14488

Sequence ID dm3.chrX
Location 13,628,219 – 13,628,478
Length 259
Max. P 0.739309
window19940 window19941 window19942 window19943

overview

Window 0

Location 13,628,219 – 13,628,337
Length 118
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 54.31
Shannon entropy 0.62748
G+C content 0.50126
Mean single sequence MFE -32.40
Consensus MFE -13.05
Energy contribution -14.12
Covariance contribution 1.07
Combinations/Pair 1.25
Mean z-score -1.28
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.618644
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 13628219 118 + 22422827
CCACACCCAGCGGUGUGGGCGUGGAACAAAGGUUGCUCCUUCGUUCGCCUUGUUUCCGCCGAUUCAGUUGUUAGCUUAACGGCUGUUGCUGUUUUAGUCCUUAUUGUCGCACUUGCCU
.((((((....))))))(((((((((..(((((.((......))..)))))..))))))(((..((((.....(((.((((((....))))))..)))....))))))).....))). ( -38.10, z-score =  -1.73, R)
>droSim1.chrX 10434695 107 + 17042790
CCACACCCAUCGGCGUGGGCGUGGGACAAAGGU-----------UCGCCUUGUUUCCGCCGAUUCAGUUGUUAGCUUAACGGCUGUUGCUGUUUUAGUCCUUAUUGUCGCACUUGCCU
...........((((((((((.(..((((.((.-----------...))))))..)))))((..((((.....(((.((((((....))))))..)))....)))))).)))..))). ( -33.70, z-score =  -0.97, R)
>droVir3.scaffold_12970 8005025 92 + 11907090
-----------------CAUCUGGCGCAAGGUUC------UGGUUUUUGUUAAUAGAGCUAAUUCGGA-AUUGUCCAGAGAGCGGAACUUGAUUCAGAUAG-GCUUUCACAUUGGCC-
-----------------.((((((..((((.(((------((.((((((.((((.(((....)))...-))))..)))))).)))))))))..)))))).(-(((........))))- ( -25.40, z-score =  -1.14, R)
>consensus
CCACACCCA_CGG_GUGGGCGUGGAACAAAGGU_______U_GUUCGCCUUGUUUCCGCCGAUUCAGUUGUUAGCUUAACGGCUGUUGCUGUUUUAGUCCUUAUUGUCGCACUUGCCU
(((((((....)))))))...((((((((((((.............)))))......((((.((.(((.....))).))))))......)))))))...................... (-13.05 = -14.12 +   1.07)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,628,219 – 13,628,337
Length 118
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 54.31
Shannon entropy 0.62748
G+C content 0.50126
Mean single sequence MFE -28.33
Consensus MFE -13.13
Energy contribution -14.63
Covariance contribution 1.51
Combinations/Pair 1.23
Mean z-score -1.03
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.677961
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 13628219 118 - 22422827
AGGCAAGUGCGACAAUAAGGACUAAAACAGCAACAGCCGUUAAGCUAACAACUGAAUCGGCGGAAACAAGGCGAACGAAGGAGCAACCUUUGUUCCACGCCCACACCGCUGGGUGUGG
.(((.(((.(........).)))......((....((((...((.......))....))))(....)...))(((((((((.....)))))))))...)))((((((....)))))). ( -38.60, z-score =  -2.20, R)
>droSim1.chrX 10434695 107 - 17042790
AGGCAAGUGCGACAAUAAGGACUAAAACAGCAACAGCCGUUAAGCUAACAACUGAAUCGGCGGAAACAAGGCGA-----------ACCUUUGUCCCACGCCCACGCCGAUGGGUGUGG
.(((..(((.(((((..(((...............((((...((.......))....))))(....).......-----------.)))))))).))))))((((((....)))))). ( -32.50, z-score =  -1.17, R)
>droVir3.scaffold_12970 8005025 92 - 11907090
-GGCCAAUGUGAAAGC-CUAUCUGAAUCAAGUUCCGCUCUCUGGACAAU-UCCGAAUUAGCUCUAUUAACAAAAACCA------GAACCUUGCGCCAGAUG-----------------
-((((((.((((.(((-....((......))....))).))((((....-))))........................------..)).))).))).....----------------- ( -13.90, z-score =   0.28, R)
>consensus
AGGCAAGUGCGACAAUAAGGACUAAAACAGCAACAGCCGUUAAGCUAACAACUGAAUCGGCGGAAACAAGGCGAAC_A_______ACCUUUGUCCCACGCCCAC_CCG_UGGGUGUGG
......(((.(((((....................((((...((.......))....))))(....)......................))))).)))..(((((((....))))))) (-13.13 = -14.63 +   1.51)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,628,337 – 13,628,456
Length 119
Sequences 7
Columns 120
Reading direction forward
Mean pairwise identity 62.20
Shannon entropy 0.75488
G+C content 0.51931
Mean single sequence MFE -30.23
Consensus MFE -13.55
Energy contribution -14.90
Covariance contribution 1.35
Combinations/Pair 1.52
Mean z-score -0.67
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.55
SVM RNA-class probability 0.739309
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 13628337 119 + 22422827
ACAAGGACCCCCCAUAUAUACCGACCGGCCGCCAGGCAAUUUGCAUCAAGUGCAGCCAUGCACUUGGUC-GACUUUGAAUGGCUGCCACCAGAAUCCGGUGCACAUCCAUGCACACGCAA
....((.....)).............(((.((((..(((.(((.((((((((((....)))))))))))-))..)))..)))).))).........(((((((......))))).))... ( -40.60, z-score =  -2.48, R)
>droSim1.chrX 10434802 115 + 17042790
ACAAGGACCC--CAUGUAUACCGCCCGGCC--CAGGCAAUUUGCAUCAAGUGCAGCCGUGCACUUGGUC-GACUUUGAAUGGCUGCCACCAGAAUCCGGUGCACAUCCAUGCACACGCAA
(((.((...)--).))).....((..((((--((..(((.(((.((((((((((....)))))))))))-))..)))..)))..)))...........(((((......)))))..)).. ( -34.80, z-score =  -0.08, R)
>droSec1.super_20 266727 115 + 1148123
ACAAGGACCC--CAUAUACACCGCCCGGCC--CAGGCAAUUUGCAUCAAGUGCAGCCGUGCACUUGGUC-GACUUUGAAUGGCUGCCACCAGAAUCCGGUGCACAUCCAUGCACACGCAA
..........--..........((..((((--((..(((.(((.((((((((((....)))))))))))-))..)))..)))..)))...........(((((......)))))..)).. ( -33.80, z-score =  -0.23, R)
>droYak2.chrX 7922362 108 + 21770863
ACAACUACCC---CCAUACCGCCGCCAGCU--CAGGCAAUUUGCAUCAAGUGCAGCCAGGCACUCGCUC-GACUUUGAAUGGCUGCCACCAGAAUCCGGUGCA------UGCACACGCAG
..........---.......((.(((....--..)))....(((((.....(((((((..((.((....-))...))..)))))))((((.......)))).)------))))...)).. ( -29.30, z-score =  -0.18, R)
>droEre2.scaffold_4690 5493418 104 - 18748788
ACAAGUACAC---C-AUACCUCC---AGCU--GAGGCAAUUUGCAUCAAGUGCAGCCAGGCACUUGGUC-GACUUUGAAUGGCUGCCACCAAAAUGCUGUGCA------UGCACACGCAA
....(((((.---.-...((((.---....--))))......((((...(((((((((..((...((..-..)).))..)))))).)))....))))))))).------(((....))). ( -30.00, z-score =   0.15, R)
>droAna3.scaffold_13248 2850188 91 + 4840945
ACAAGGACCU---CCCUACCCC-----------AGGCAAUUUGCGUCAAGUGCAAAAAGGCAUUUCGCCUGGCUUUCAGUGGC---AACUGGAAGCCGAAACAAGAAA------------
...(((....---.))).....-----------......((((((.....)))))).((((.....))))((((((((((...---.))))))))))...........------------ ( -27.50, z-score =  -1.14, R)
>droVir3.scaffold_12970 8005117 91 + 11907090
---------------------GGAAUAGCUGUGCGAACAUUUGCAAUAAGUGAAAUCUUCUUCGUAGAC--AUCAUUAAAGGU-AUACCAAGAAACCAAUAGGGUUACAUUUAAG-----
---------------------((.(((.((.(((((....)))))...(((((..(((.......))).--.)))))..)).)-)).))..(.((((.....)))).).......----- ( -15.60, z-score =  -0.72, R)
>consensus
ACAAGGACCC___AUAUACACCG_CCAGCC__CAGGCAAUUUGCAUCAAGUGCAGCCAUGCACUUGGUC_GACUUUGAAUGGCUGCCACCAGAAUCCGGUGCACAUCCAUGCACACGCAA
.........................(((((.....((.....))(((((((((......)))))))))............))))).............(((((......)))))...... (-13.55 = -14.90 +   1.35)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,628,377 – 13,628,478
Length 101
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 70.60
Shannon entropy 0.54322
G+C content 0.49398
Mean single sequence MFE -32.24
Consensus MFE -17.22
Energy contribution -16.62
Covariance contribution -0.60
Combinations/Pair 1.45
Mean z-score -0.96
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.540180
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 13628377 101 + 22422827
UUGCAUCAAGUGCAGCCAUGCACUUGGUCGACUUUGAAUGGCUGCCACCAGAAUCCGGUGCACAUCCAUGCACACGCAAUCAUCUGCACUGAUGAUUCUAA------------------
(((.((((((((((....)))))))))))))........((......))(((((((((((((.((...(((....)))...)).)))))))..))))))..------------------ ( -32.60, z-score =  -1.86, R)
>droSim1.chrX 10434838 119 + 17042790
UUGCAUCAAGUGCAGCCGUGCACUUGGUCGACUUUGAAUGGCUGCCACCAGAAUCCGGUGCACAUCCAUGCACACGCAAUCAUCUGCACUGCUGAUUCUAAUGCUAAGCCGUCGUCUUG
..(.((((((((((....)))))))))))(((...((.(((((..((..(((((((((((((.((...(((....)))...)).)))))))..))))))..))...))))))))))... ( -40.30, z-score =  -2.08, R)
>droSec1.super_20 266763 119 + 1148123
UUGCAUCAAGUGCAGCCGUGCACUUGGUCGACUUUGAAUGGCUGCCACCAGAAUCCGGUGCACAUCCAUGCACACGCAAUCAUCUGCACUGCUGAUUCUAAUGCUAAGCCGUCGUCUUG
..(.((((((((((....)))))))))))(((...((.(((((..((..(((((((((((((.((...(((....)))...)).)))))))..))))))..))...))))))))))... ( -40.30, z-score =  -2.08, R)
>droYak2.chrX 7922397 111 + 21770863
UUGCAUCAAGUGCAGCCAGGCACUCGCUCGACUUUGAAUGGCUGCCACCAGAAUCCGGUGCA------UGCACACGCAGUCAUCUGCACAGCUGCAUCUAACGCCAAGCCGUCGUCU--
..((.((..(((((((((..((.((....))...))..)))))).)))..))....((((((------.((....((((....))))...))))))))....)).............-- ( -32.10, z-score =   0.55, R)
>droEre2.scaffold_4690 5493449 111 - 18748788
UUGCAUCAAGUGCAGCCAGGCACUUGGUCGACUUUGAAUGGCUGCCACCAAAAUGCUGUGCA------UGCACACGCAAUCAUCUGCACUGCUUAAUCUAACGCCAAGCCGUCGUCC--
(((.(((((((((......))))))))))))....((.(((((((.........((.(((((------(((....)))......))))).))..........))..)))))))....-- ( -30.81, z-score =  -0.04, R)
>droVir3.scaffold_12970 8005136 98 + 11907090
UUGCAAUAAGUGAAAUCUUCUUCGUAGACAUCAUUAAAGGUAUACCA--AGAAACCAAUAGG------GUUACAUUUAAGUGAUU-UAUGGAUGGAUACCAACCCAU------------
........(((((..(((.......)))..)))))...(((((.(((--.....(((...((------(((((......))))))-).))).)))))))).......------------ ( -17.30, z-score =  -0.25, R)
>consensus
UUGCAUCAAGUGCAGCCAUGCACUUGGUCGACUUUGAAUGGCUGCCACCAGAAUCCGGUGCA______UGCACACGCAAUCAUCUGCACUGCUGAAUCUAACGCCAAGCCGUCGUCU__
((((.....(.((((((((.((.((....))...)).)))))))))...........(((((......)))))..))))........................................ (-17.22 = -16.62 +  -0.60)

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 01:41:02 2011