Locus 14684

Sequence ID dm3.chrX
Location 14,793,590 – 14,793,756
Length 166
Max. P 0.937984
window20216 window20217 window20218

overview

Window 6

Location 14,793,590 – 14,793,690
Length 100
Sequences 7
Columns 113
Reading direction forward
Mean pairwise identity 70.51
Shannon entropy 0.54240
G+C content 0.50279
Mean single sequence MFE -29.60
Consensus MFE -8.84
Energy contribution -10.70
Covariance contribution 1.86
Combinations/Pair 1.17
Mean z-score -2.30
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.682074
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14793590 100 + 22422827
GCGUCACGGCGGACAAUUUCCGGCACUUACCACUUUUCAUACGAGUACUACCUAUGUACUAGACGC-------------AAUAUUUCUUUUGGGCCAAUUGCCCAAUCAACAA
(((((..(.((((.....)))).)...................(((((.......))))).)))))-------------..........((((((.....))))))....... ( -29.20, z-score =  -4.63, R)
>droSim1.chrX 11424577 113 + 17042790
GCGUCACGGCGGACAAUUUCCGGCACUAACCACUUUUCAUAUGAGUACUACCUAUGUACUAGACGCCCAUGCCAGACGCAAUACAUCUUUUGGGCCAAUUGCCCAAUCAACAA
(((((..((((((.....)))(((............((....))((((.......)))).....)))...))).)))))..........((((((.....))))))....... ( -32.00, z-score =  -3.56, R)
>droSec1.super_32 233953 113 + 562834
GCGUCACAGCGGACAAUUUCCGGCACUAACCACUUUUCAUAUGAGUACUACCUAUGUACUAGACGCCCAUGCCAGACGCAAUACAUCUUUUGGGCCAAUUGCCCAAUCAACAA
(((((.....(((.....)))((((...........((....))((((.......))))..........)))).)))))..........((((((.....))))))....... ( -29.00, z-score =  -3.10, R)
>droYak2.chrX 9005377 113 + 21770863
GCGUCACGGCGUACAAUUUCCGGCACUUACCACUUUUCAUAUGAGCACUACCUAUGUACUAGACGCCCAUGCCAGACGCAAUAUUUCUUUUGGGCCAAUUGCCCAAUCAACAA
(((((..((((((((......((......))....(((....))).........)))))..(.....)..))).)))))..........((((((.....))))))....... ( -25.70, z-score =  -1.84, R)
>droEre2.scaffold_4690 6541925 113 - 18748788
GCGUCACGGCGGACAAUUUCCGGCACUUACCACUUUUCAUACAAGUACUACCUAUGUGCUAGACGCCCAUGCCAGACGCAAUAUUUCUUUUGGGCCAAUUGCCCAAUCAACAA
(((((..((((((.....)))(((.......((((.......)))).(((.(.....).)))..)))...))).)))))..........((((((.....))))))....... ( -29.90, z-score =  -2.69, R)
>dp4.chrXL_group1a 5839474 89 + 9151740
GCCUUAUGGCCGACAGUUUCCGGCACUUACGGGGACCCAUGAUGGAACUGG----GGGCUGGAUG---------------GUGGGGGCUUGCG-----UUGCCCAAUCAACAA
(((....)))...((((..((((..((((.((....)).))).)...))))----..))))..((---------------((..((((.....-----..)))).)))).... ( -32.10, z-score =  -0.06, R)
>droPer1.super_63 267939 81 - 372969
GCCUUAUGGCCGACAGUUUCCGGCACUUACAGAGUCCCCUGAUGGAACGGG----GGAG-----------------------GGGGGCUUGGG-----UUGCCCAAUUAACAA
(((((...((((........))))..........(((((((......))))----))).-----------------------.)))))(((((-----...)))))....... ( -29.30, z-score =  -0.19, R)
>consensus
GCGUCACGGCGGACAAUUUCCGGCACUUACCACUUUUCAUAUGAGUACUACCUAUGUACUAGACGCCCAUGCCAGACGCAAUAUUUCUUUUGGGCCAAUUGCCCAAUCAACAA
(((((..(.((((.....)))).)...........((......))................))))).......................((((((.....))))))....... ( -8.84 = -10.70 +   1.86)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,793,628 – 14,793,729
Length 101
Sequences 8
Columns 117
Reading direction reverse
Mean pairwise identity 69.84
Shannon entropy 0.61112
G+C content 0.40640
Mean single sequence MFE -25.16
Consensus MFE -12.80
Energy contribution -13.36
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -1.38
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.42
SVM RNA-class probability 0.937984
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14793628 101 - 22422827
UCUAUUUUCACUUUUAAUUGCCCUCGAGCA-AAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAAAUAUU--------------GCGUCUAGUACAUA-GGUAGUACUCGUAU
..((((((.....((((((((((.((((((-(....)))))))......)))))))))).......)))))).(--------------(((..((.(((...-.))).))..)))). ( -23.70, z-score =  -1.79, R)
>droSim1.chrX 11424615 114 - 17042790
UCUAUUUUCACUUUUAAUUGCCCUCGAGCU-AAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAUGUAUUGCGU-CUGGCAUGGGCGUCUAGUACAUA-GGUAGUACUCAUAU
..............(((((((((.(((((.-.......)))))......)))))))))(((((..(((((.....)))-))....)))))....(((((...-....)))))..... ( -33.00, z-score =  -2.24, R)
>droSec1.super_32 233991 114 - 562834
UCUAUUUUCACUUUUAAUUGCCCUCGAGCU-AAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAUGUAUUGCGU-CUGGCAUGGGCGUCUAGUACAUA-GGUAGUACUCAUAU
..............(((((((((.(((((.-.......)))))......)))))))))(((((..(((((.....)))-))....)))))....(((((...-....)))))..... ( -33.00, z-score =  -2.24, R)
>droYak2.chrX 9005415 114 - 21770863
UCUAUUUUCACUUUUAAUUGCCCUCGAGCU-AAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAAAUAUUGCGU-CUGGCAUGGGCGUCUAGUACAUA-GGUAGUGCUCAUAU
..............(((((((((.(((((.-.......)))))......)))))))))(((((..(....)..(((..-...))))))))....(((((...-....)))))..... ( -28.20, z-score =  -0.62, R)
>droEre2.scaffold_4690 6541963 114 + 18748788
UCUAUUUUCACUUUUAAUUGCCCUCGAGCA-UAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAAAUAUUGCGU-CUGGCAUGGGCGUCUAGCACAUA-GGUAGUACUUGUAU
..............(((((((((.((((((-......))))))......)))))))))(((((..(....)..(((..-...))))))))(((((.(.....-).))).))...... ( -29.00, z-score =  -0.79, R)
>droAna3.scaffold_13335 668438 115 - 3335858
UCUAUUUUCACUUUUAAUUGCCCUCGAGCC--AAGUGUGUUUGCUUAUUGGGCAAUUGGCCCACAAGAAAUAUGGCCCACAUAUUCAGGUACUAUAUACAUAUGUUAGUACCCAUAG
.............((((((((((..((((.--(((....)))))))...)))))))))).......(((.((((.....))))))).((((((((((....))).)))))))..... ( -27.60, z-score =  -1.46, R)
>dp4.chrXL_group1a 5839512 90 - 9151740
ACUAUUUUCACUUUUAAUUGCCCGCGAGCU-AAAAUUUGUUUGUUGAUUGGGCAACGCAAGCCCCCACCAUCCAGCCC-CCAGUUCCAUCAU-------------------------
.......................(.(((((-.....(((..((.((...((((.......)))).)).))..)))...-..)))))).....------------------------- ( -14.10, z-score =  -0.38, R)
>droPer1.super_63 267977 83 + 372969
ACUAUUUUCACUUUUAAUUGCCCGCGAGCUAAAAAUUUGUUUGUUAAUUGGGCAACCCAAGCCCCCCUC--------C-CCCGUUCCAUCAG-------------------------
.................((((((((((((.........)))))).....))))))..............--------.-.............------------------------- ( -12.70, z-score =  -1.47, R)
>consensus
UCUAUUUUCACUUUUAAUUGCCCUCGAGCU_AAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAAAUAUUGCGU_CUGGCAUGGGCGUCUAGUACAUA_GGUAGUACUCAUAU
.............((((((((((.(((((.........)))))......)))))))))).......................................................... (-12.80 = -13.36 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,793,650 – 14,793,756
Length 106
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 86.56
Shannon entropy 0.25678
G+C content 0.35960
Mean single sequence MFE -26.03
Consensus MFE -19.82
Energy contribution -20.71
Covariance contribution 0.89
Combinations/Pair 1.04
Mean z-score -2.10
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.20
SVM RNA-class probability 0.908955
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14793650 106 - 22422827
CCAACUUCAUUU--------UUUUUUGGAGCCUCUUCUAUUUUCACUUUUAAUUGCCCUCGAGCAAAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAAAUAUUGCGUCU
..........((--------((((((((.(((..................((((((((.(((((((....)))))))......))))))))))))))))))))).......... ( -27.46, z-score =  -2.77, R)
>droSim1.chrX 11424650 114 - 17042790
CCAACUUCAUUUUAUUAUUUUUUUUUGGAGCCUCUUCUAUUUUCACUUUUAAUUGCCCUCGAGCUAAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAUGUAUUGCGUCU
......................((((((.(((..................((((((((.(((((........)))))......)))))))))))))))))((((.....)))). ( -25.86, z-score =  -2.41, R)
>droSec1.super_32 234026 114 - 562834
CCAACUUCAUUUUAUUAUUUUUUUUUUGAGCCUCUUCUAUUUUCACUUUUAAUUGCCCUCGAGCUAAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAUGUAUUGCGUCU
.......................(((((.(((..................((((((((.(((((........)))))......))))))))))).)))))((((.....)))). ( -22.76, z-score =  -1.81, R)
>droYak2.chrX 9005450 113 - 21770863
CCAACUUUAUUUUCAUA-UAUUUUUUGGAGCCUCUUCUAUUUUCACUUUUAAUUGCCCUCGAGCUAAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAAAUAUUGCGUCU
..............(((-(.((((((((.(((..................((((((((.(((((........)))))......))))))))))))))))))).))))....... ( -25.76, z-score =  -2.35, R)
>droEre2.scaffold_4690 6541998 113 + 18748788
CCAACUUUGCUUUAUU-UAUUUGUUCGGAGCCUCUUCUAUUUUCACUUUUAAUUGCCCUCGAGCAUAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAAAUAUUGCGUCU
........((..((((-(.(((....((.(((..................((((((((.((((((......))))))......))))))))))))).))).)))))..)).... ( -25.16, z-score =  -1.66, R)
>droAna3.scaffold_13335 668478 106 - 3335858
CCAACUUUUAUU----AUUACUUGGCAGGGCCUCUUCUAUUUUCACUUUUAAUUGCCCUCGAGCC-AAGUGUGUUUGCUUAUUGGGCAAUUGGCCCACAAGAAAUAUGGCC---
(((.........----..(((((((((((((.......................)))))...)))-)))))(((((.(((..(((((.....))))).)))))))))))..--- ( -29.20, z-score =  -1.62, R)
>consensus
CCAACUUCAUUUUAUUAUUUUUUUUUGGAGCCUCUUCUAUUUUCACUUUUAAUUGCCCUCGAGCUAAAAUUUGUUUGUUGAUUGGGCAAUUGGCCCAAAAGAAAUAUUGCGUCU
....................((((((((.(((..................((((((((.(((((........)))))......)))))))))))))))))))............ (-19.82 = -20.71 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:44:48 2011