Locus 13482

Sequence ID dm3.chrX
Location 6,812,433 – 6,812,566
Length 133
Max. P 0.997863
window18571 window18572 window18573 window18574

overview

Window 1

Location 6,812,433 – 6,812,526
Length 93
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 82.87
Shannon entropy 0.26755
G+C content 0.56141
Mean single sequence MFE -20.73
Consensus MFE -13.30
Energy contribution -14.30
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.97
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.979155
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6812433 93 + 22422827
ACCAAGGCAACCGCCGCCAUCCAACUGAUGCCCUCUCAGUCUCAGUCCCAGGCGCCCAUUUGCCAAAGUUGCCACCC-AGAAGUAACCACUUCU
.....((((((....(((.....(((((.((.......)).)))))....)))((......))....))))))....-((((((....)))))) ( -24.10, z-score =  -3.28, R)
>droYak2.chrX 7229238 76 - 21770863
ACCAAGGCAACCAAUGCCAACCAACUGAUACCCCCU-AGUC----------GACCAAAGUUGCCAAAGUUGCCACCCCAGACGUAAC-------
.....((((((...((.((((....((((.......-.)))----------)......)))).))..))))))..............------- ( -13.60, z-score =  -2.30, R)
>droSec1.super_24 26344 87 + 912625
ACCAAGGCAACCGCCGCCAUCCAACUGAUGCCCUCUCAGUC------CCAGGCGCCCAUUUGCCAAAGUUGCCACCC-AGAAGUAACCACUUCU
.....((((((....(((.....(((((.......))))).------...)))((......))....))))))....-((((((....)))))) ( -22.60, z-score =  -3.16, R)
>droSim1.chrX 5342909 87 + 17042790
ACCAAGGCAACCGCCGCCAUCCAACUGAUGCCCUCUCAGUC------CCAGGCGCCCAUUUGCCAAAGUUGCCACCC-AGAAGUAACCACUUCU
.....((((((....(((.....(((((.......))))).------...)))((......))....))))))....-((((((....)))))) ( -22.60, z-score =  -3.16, R)
>consensus
ACCAAGGCAACCGCCGCCAUCCAACUGAUGCCCUCUCAGUC______CCAGGCGCCCAUUUGCCAAAGUUGCCACCC_AGAAGUAACCACUUCU
.....((((((............(((((.......)))))..........((((......))))...))))))..................... (-13.30 = -14.30 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 6,812,433 – 6,812,526
Length 93
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 82.87
Shannon entropy 0.26755
G+C content 0.56141
Mean single sequence MFE -32.42
Consensus MFE -21.52
Energy contribution -23.02
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.886336
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6812433 93 - 22422827
AGAAGUGGUUACUUCU-GGGUGGCAACUUUGGCAAAUGGGCGCCUGGGACUGAGACUGAGAGGGCAUCAGUUGGAUGGCGGCGGUUGCCUUGGU
.(((((.((((((...-.)))))).)))))(((((.(.(.((((...((((((..((....))...))))))....)))).).))))))..... ( -36.30, z-score =  -2.47, R)
>droYak2.chrX 7229238 76 + 21770863
-------GUUACGUCUGGGGUGGCAACUUUGGCAACUUUGGUC----------GACU-AGGGGGUAUCAGUUGGUUGGCAUUGGUUGCCUUGGU
-------(((((.......))))).(((..(((((((...(((----------((((-((..(....)..)))))))))...)))))))..))) ( -28.40, z-score =  -3.29, R)
>droSec1.super_24 26344 87 - 912625
AGAAGUGGUUACUUCU-GGGUGGCAACUUUGGCAAAUGGGCGCCUGG------GACUGAGAGGGCAUCAGUUGGAUGGCGGCGGUUGCCUUGGU
.(((((.((((((...-.)))))).)))))(((((.(.(.((((...------((((((.......))))))....)))).).))))))..... ( -32.50, z-score =  -1.81, R)
>droSim1.chrX 5342909 87 - 17042790
AGAAGUGGUUACUUCU-GGGUGGCAACUUUGGCAAAUGGGCGCCUGG------GACUGAGAGGGCAUCAGUUGGAUGGCGGCGGUUGCCUUGGU
.(((((.((((((...-.)))))).)))))(((((.(.(.((((...------((((((.......))))))....)))).).))))))..... ( -32.50, z-score =  -1.81, R)
>consensus
AGAAGUGGUUACUUCU_GGGUGGCAACUUUGGCAAAUGGGCGCCUGG______GACUGAGAGGGCAUCAGUUGGAUGGCGGCGGUUGCCUUGGU
.......((((((.....)))))).(((..(((((.(.(.((((.........((((((.......))))))....)))).).))))))..))) (-21.52 = -23.02 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 6,812,449 – 6,812,566
Length 117
Sequences 5
Columns 123
Reading direction forward
Mean pairwise identity 75.73
Shannon entropy 0.41494
G+C content 0.50539
Mean single sequence MFE -32.40
Consensus MFE -15.38
Energy contribution -15.62
Covariance contribution 0.24
Combinations/Pair 1.20
Mean z-score -2.46
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.27
SVM RNA-class probability 0.919848
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6812449 117 + 22422827
CCAUCCAACUGAUGCCCUCUCAGUCUCAGUCCCAGGCGCCCAUUUGCCAAAGUUGCCACCCAGAA----GUAACCACUUCUGGCAGCCGCAC--UUCUGGCAAUUUGCGGCUGUUAAAUGAUU
.......(((((.((.......)).)))))..(((.(((....((((((((((.((...((((((----((....)))))))).....))))--)).))))))...))).))).......... ( -37.20, z-score =  -2.96, R)
>droAna3.scaffold_13117 1665492 88 - 5790199
-----------------------------------UCUUUUGUCUGGCACUGUGGCAACCAUAGACCAUGUUACCACAUCUGCCACACACACAAUUCUGGUAAUUUGCGGUUCUUAAAUGAUU
-----------------------------------.....(((.(((((.(((((.(((..........))).)))))..))))).))).................................. ( -16.30, z-score =   0.23, R)
>droEre2.scaffold_4690 15738130 111 + 18748788
CCACCCAACUGAUGCCCUAUCAG------UCGCAGGCGCCCAUUUGCCAAAGUUGCCAUCCAGAA----GUAACCACUUCUGGCAGCCGCAC--UUCUGGCAAUUUGCGACUGUUAAAUGAUU
....................(((------((((.((((......)))).(((((((((..(((((----((....)))))))((....))..--...)))))))))))))))).......... ( -37.10, z-score =  -3.77, R)
>droSec1.super_24 26360 111 + 912625
CCAUCCAACUGAUGCCCUCUCAG------UCCCAGGCGCCCAUUUGCCAAAGUUGCCACCCAGAA----GUAACCACUUCUGGCAGCCGCAC--UUCUGGCAAUUUGCGGCUGUUAAAUGAUU
.......(((((.......))))------)..(((.(((....((((((((((.((...((((((----((....)))))))).....))))--)).))))))...))).))).......... ( -35.70, z-score =  -2.89, R)
>droSim1.chrX 5342925 111 + 17042790
CCAUCCAACUGAUGCCCUCUCAG------UCCCAGGCGCCCAUUUGCCAAAGUUGCCACCCAGAA----GUAACCACUUCUGGCAGCCGCAC--UUCUGGCAAUUUGCGGCUGUUAAAUGAUU
.......(((((.......))))------)..(((.(((....((((((((((.((...((((((----((....)))))))).....))))--)).))))))...))).))).......... ( -35.70, z-score =  -2.89, R)
>consensus
CCAUCCAACUGAUGCCCUCUCAG______UCCCAGGCGCCCAUUUGCCAAAGUUGCCACCCAGAA____GUAACCACUUCUGGCAGCCGCAC__UUCUGGCAAUUUGCGGCUGUUAAAUGAUU
................................(((.(((.....(((((..(((((.............)))))......)))))((((........)))).....))).))).......... (-15.38 = -15.62 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 6,812,449 – 6,812,566
Length 117
Sequences 5
Columns 123
Reading direction reverse
Mean pairwise identity 75.73
Shannon entropy 0.41494
G+C content 0.50539
Mean single sequence MFE -43.14
Consensus MFE -25.05
Energy contribution -26.59
Covariance contribution 1.54
Combinations/Pair 1.18
Mean z-score -3.20
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.20
SVM RNA-class probability 0.997863
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6812449 117 - 22422827
AAUCAUUUAACAGCCGCAAAUUGCCAGAA--GUGCGGCUGCCAGAAGUGGUUAC----UUCUGGGUGGCAACUUUGGCAAAUGGGCGCCUGGGACUGAGACUGAGAGGGCAUCAGUUGGAUGG
...(((((..(((.(((...((((((((.--.(((.((..((((((((....))----)))))))).)))..))))))))....))).))).((((((..((....))...))))))))))). ( -49.20, z-score =  -3.58, R)
>droAna3.scaffold_13117 1665492 88 + 5790199
AAUCAUUUAAGAACCGCAAAUUACCAGAAUUGUGUGUGUGGCAGAUGUGGUAACAUGGUCUAUGGUUGCCACAGUGCCAGACAAAAGA-----------------------------------
..............(((((.((....)).)))))(((.(((((..(((((((((..........))))))))).))))).))).....----------------------------------- ( -27.30, z-score =  -2.35, R)
>droEre2.scaffold_4690 15738130 111 - 18748788
AAUCAUUUAACAGUCGCAAAUUGCCAGAA--GUGCGGCUGCCAGAAGUGGUUAC----UUCUGGAUGGCAACUUUGGCAAAUGGGCGCCUGCGA------CUGAUAGGGCAUCAGUUGGGUGG
...((((...(((.(((...((((((((.--((...((((((((((((....))----)))))).)))).))))))))))....))).)))(((------(((((.....)))))))))))). ( -44.40, z-score =  -3.07, R)
>droSec1.super_24 26360 111 - 912625
AAUCAUUUAACAGCCGCAAAUUGCCAGAA--GUGCGGCUGCCAGAAGUGGUUAC----UUCUGGGUGGCAACUUUGGCAAAUGGGCGCCUGGGA------CUGAGAGGGCAUCAGUUGGAUGG
...((((((((.(((.((..((((((((.--.(((.((..((((((((....))----)))))))).)))..)))))))).)))))((((....------......))))....)))))))). ( -47.40, z-score =  -3.50, R)
>droSim1.chrX 5342925 111 - 17042790
AAUCAUUUAACAGCCGCAAAUUGCCAGAA--GUGCGGCUGCCAGAAGUGGUUAC----UUCUGGGUGGCAACUUUGGCAAAUGGGCGCCUGGGA------CUGAGAGGGCAUCAGUUGGAUGG
...((((((((.(((.((..((((((((.--.(((.((..((((((((....))----)))))))).)))..)))))))).)))))((((....------......))))....)))))))). ( -47.40, z-score =  -3.50, R)
>consensus
AAUCAUUUAACAGCCGCAAAUUGCCAGAA__GUGCGGCUGCCAGAAGUGGUUAC____UUCUGGGUGGCAACUUUGGCAAAUGGGCGCCUGGGA______CUGAGAGGGCAUCAGUUGGAUGG
...(((((((((((((((...(......)...)))))))(((((.(((.(((((..........))))).))))))))........((((................))))....)))))))). (-25.05 = -26.59 +   1.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:22:20 2011