Locus 13991

Sequence ID dm3.chrX
Location 10,447,318 – 10,447,459
Length 141
Max. P 0.971403
window19244 window19245 window19246

overview

Window 4

Location 10,447,318 – 10,447,424
Length 106
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 68.53
Shannon entropy 0.56193
G+C content 0.34797
Mean single sequence MFE -23.30
Consensus MFE -10.18
Energy contribution -9.52
Covariance contribution -0.66
Combinations/Pair 1.45
Mean z-score -2.17
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.85
SVM RNA-class probability 0.971403
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 10447318 106 + 22422827
---------UUAACUUUGAGAGAUGAUGAUGAAGUAGAA---GUGGCCUUUGCCGAUGAUGAAUACAAGAUUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAAUUUAUGUGAACUG
---------...........((((.(..(((..(((...---((((((..((((((((((.........))))).)))))...)))))).)))..)))..)...)))).......... ( -25.80, z-score =  -2.74, R)
>droSim1.chrX_random 2969025 98 + 5698898
-----------------UUAAGAUGAUGAUGAUGUUGAA---GUGGCCUUUGCCGAUGAUGAAGACAAGAUUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAAUUUAUGUGAACUG
-----------------...((((....(..((((((..---((((((..((((((((((.........))))).)))))...))))))...))))))..)...)))).......... ( -29.00, z-score =  -4.18, R)
>droSec1.super_15 1145468 98 + 1954846
-----------------UUAAGAUGAUGAUGAAGUUGAA---GUGGCCUUUGCCGAUGAUGAAGACAAGAUUAUAUGGCAUCUGGCCAUAUGAAACAUUGUAUAAUUUAUGUGAACUG
-----------------...((((.(..(((...((.(.---((((((..((((((((((.........))))).)))))...)))))).).)).)))..)...)))).......... ( -23.00, z-score =  -2.73, R)
>droYak2.chrX 19012334 105 + 21770863
-------------UAGGAGACAAUGAUGAUGGAGUUGAUGAUGUAGUCUUUGCCGAUGAUGAAGACGAGAUUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAAUUUAUGUGAACUG
-------------..(....).......(((((....(..((((.((((((.........)))))).....((((((((.....))))))))..))))..)....)))))........ ( -22.90, z-score =  -1.14, R)
>droEre2.scaffold_4690 14062976 115 - 18748788
UAAUUCACAAAAAAAGGAGACAACGAUGAUGGAGUUGAU---GUAGCCUUUGCCGAUGAUGAAGUCAAGAUUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAGUUUAUGUGAACUG
...((((((...(((((..(((.((((......)))).)---))..)))))..(((((.((....))....((((((((.....))))))))...))))).........))))))... ( -29.00, z-score =  -2.17, R)
>apiMel3.Group16 3648293 84 + 5631066
-------------------UCGAAAACGAUGGAAUAGAA------ACGAUUAUCCAUUUU---------AUUACGCGAUAUUUAAUUCUAUAAAAUUUAGUUUAUUCUUUCCAAAUUC
-------------------(((....)))(((((.((((------..(((((...(((((---------((.....((........)).))))))).)))))..)))))))))..... ( -10.10, z-score =  -0.09, R)
>consensus
_________________AGAAGAUGAUGAUGAAGUUGAA___GUGGCCUUUGCCGAUGAUGAAGACAAGAUUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAAUUUAUGUGAACUG
.....................(((....(..(.((((........(((..((((((((((.........))))).)))))...)))......)))).)..)...)))........... (-10.18 =  -9.52 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,447,318 – 10,447,424
Length 106
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 68.53
Shannon entropy 0.56193
G+C content 0.34797
Mean single sequence MFE -16.27
Consensus MFE -8.37
Energy contribution -7.93
Covariance contribution -0.44
Combinations/Pair 1.56
Mean z-score -1.32
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.832348
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 10447318 106 - 22422827
CAGUUCACAUAAAUUUUACAAUGUUGCAUAUGGCCAGAUGCCAUAUAAUCUUGUAUUCAUCAUCGGCAAAGGCCAC---UUCUACUUCAUCAUCAUCUCUCAAAGUUAA---------
................(((((.(((..(((((((.....)))))))))).))))).........(((....)))..---..............................--------- ( -15.60, z-score =  -0.93, R)
>droSim1.chrX_random 2969025 98 - 5698898
CAGUUCACAUAAAUUUUACAAUGUUGCAUAUGGCCAGAUGCCAUAUAAUCUUGUCUUCAUCAUCGGCAAAGGCCAC---UUCAACAUCAUCAUCAUCUUAA-----------------
....................((((((.(..(((((.(((........)))(((((.........))))).))))).---.)))))))..............----------------- ( -18.00, z-score =  -2.22, R)
>droSec1.super_15 1145468 98 - 1954846
CAGUUCACAUAAAUUAUACAAUGUUUCAUAUGGCCAGAUGCCAUAUAAUCUUGUCUUCAUCAUCGGCAAAGGCCAC---UUCAACUUCAUCAUCAUCUUAA-----------------
.((((............((((.(((..(((((((.....)))))))))).))))..........(((....)))..---...))))...............----------------- ( -14.20, z-score =  -1.67, R)
>droYak2.chrX 19012334 105 - 21770863
CAGUUCACAUAAAUUUUACAAUGUUGCAUAUGGCCAGAUGCCAUAUAAUCUCGUCUUCAUCAUCGGCAAAGACUACAUCAUCAACUCCAUCAUCAUUGUCUCCUA-------------
.................((((((.((.(((((((.....)))))))......(((((..(.....)..))))).................)).))))))......------------- ( -16.30, z-score =  -1.68, R)
>droEre2.scaffold_4690 14062976 115 + 18748788
CAGUUCACAUAAACUUUACAAUGUUGCAUAUGGCCAGAUGCCAUAUAAUCUUGACUUCAUCAUCGGCAAAGGCUAC---AUCAACUCCAUCAUCGUUGUCUCCUUUUUUUGUGAAUUA
.((((((((.(((....((((((.((.(((((((.....)))))))..................(((....)))..---...........)).))))))......))).)))))))). ( -22.40, z-score =  -1.56, R)
>apiMel3.Group16 3648293 84 - 5631066
GAAUUUGGAAAGAAUAAACUAAAUUUUAUAGAAUUAAAUAUCGCGUAAU---------AAAAUGGAUAAUCGU------UUCUAUUCCAUCGUUUUCGA-------------------
(((..((((((((((.......))))).(((((.....((((.(((...---------...))))))).....------)))))))))).....)))..------------------- ( -11.10, z-score =   0.16, R)
>consensus
CAGUUCACAUAAAUUUUACAAUGUUGCAUAUGGCCAGAUGCCAUAUAAUCUUGUCUUCAUCAUCGGCAAAGGCCAC___UUCAACUCCAUCAUCAUCGUAA_________________
..............................(((((...((((......................))))..)))))........................................... ( -8.37 =  -7.93 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,447,346 – 10,447,459
Length 113
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 82.29
Shannon entropy 0.34309
G+C content 0.40084
Mean single sequence MFE -32.30
Consensus MFE -19.83
Energy contribution -22.42
Covariance contribution 2.59
Combinations/Pair 1.18
Mean z-score -1.81
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.668859
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10447346 113 + 22422827
AAGUGGCCUUUGCCGAUGAUGAAUACAAGA--UUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAAUUUAUGUGAACUGGUAUAUACGUGCGGUCCAUAAAUGGCAAAUGCAUU
..((((((..((((((((((.........)--)))).)))))...))))))(((((...((((...(((((((.((.(((.(((....))))))))))))))).)))).))))). ( -33.90, z-score =  -2.08, R)
>droSim1.chrX_random 2969045 113 + 5698898
AAGUGGCCUUUGCCGAUGAUGAAGACAAGA--UUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAAUUUAUGUGAACUGGUAUGUACGUGCGGUCCAUAAAUGGCAAAUGCAUC
..((((((..((((((((((.........)--)))).)))))...))))))(((((...((((...(((((((.((.(((.(((....))))))))))))))).)))).))))). ( -34.80, z-score =  -2.25, R)
>droSec1.super_15 1145488 113 + 1954846
AAGUGGCCUUUGCCGAUGAUGAAGACAAGA--UUAUAUGGCAUCUGGCCAUAUGAAACAUUGUAUAAUUUAUGUGAACUGGUAUGUACGUGCGGUCCAUAAAUGGCAAAUGCAUC
.....((.((((((..........((((..--(((((((((.....)))))))))....))))...(((((((.((.(((.(((....))))))))))))))))))))).))... ( -33.00, z-score =  -2.00, R)
>droYak2.chrX 19012361 113 + 21770863
AUGUAGUCUUUGCCGAUGAUGAAGACGAGA--UUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAAUUUAUGUGAACUGGUAUGUACGUGCGGUCCAUAAAUGGCAAAUGCAUU
.....((.((((((..........((((..--.((((((((.....)))))))).....))))...(((((((.((.(((.(((....))))))))))))))))))))).))... ( -29.80, z-score =  -0.88, R)
>droEre2.scaffold_4690 14063013 113 - 18748788
AUGUAGCCUUUGCCGAUGAUGAAGUCAAGA--UUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAGUUUAUGUGAACUGGUAUGUACGUGCGGUCCAUAAAUGGCAAAUGCAUU
.....((.((((((.(..(((..((.....--..(((((((.....)))))))))..)))..)...(((((((.((.(((.(((....))))))))))))))))))))).))... ( -31.41, z-score =  -0.91, R)
>droAna3.scaffold_13335 1076061 95 - 3335858
GAGUUGAUUUCGACGAUAAUGAAGCCAGAGAGUUGUAUGACAUCUGGC----UGUGGCACUGU----------------GGCAUGUAUGUAUGUGCCACAUAAGGAAAAUGCAUU
..((((....))))...((((.(((((((..(((....))).))))))----)(((((((...----------------.(((....)))..)))))))............)))) ( -30.90, z-score =  -2.74, R)
>consensus
AAGUGGCCUUUGCCGAUGAUGAAGACAAGA__UUAUAUGGCAUCUGGCCAUAUGCAACAUUGUAAAAUUUAUGUGAACUGGUAUGUACGUGCGGUCCAUAAAUGGCAAAUGCAUU
.....((.((((((..........((((.....((((((((.....)))))))).....))))...(((((((.((....((((....))))..))))))))))))))).))... (-19.83 = -22.42 +   2.59)

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 01:31:36 2011