Locus 15910

Sequence ID dm3.chrYHet
Location 152,971 – 153,092
Length 121
Max. P 0.997018
window21918 window21919 window21920 window21921

overview

Window 8

Location 152,971 – 153,066
Length 95
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 70.29
Shannon entropy 0.46072
G+C content 0.36898
Mean single sequence MFE -19.57
Consensus MFE -11.14
Energy contribution -11.82
Covariance contribution 0.69
Combinations/Pair 1.14
Mean z-score -1.34
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.651832
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrYHet 152971 95 + 347038
UUAGGCUAAGAAACCAUUGUAUGUAGAUCAUA------------AGAGGAUUCACGAACUGACUUCGAAUGCAGCGGGACCUUCUCUGCUACU-UAAAUUGGAUAAAA---
...(((..((((.((.((((((((..(((...------------....)))..))(((.....)))..)))))).))....))))..)))...-..............--- ( -16.00, z-score =   0.46, R)
>droSim1.chrU 4593682 97 + 15797150
UUAGGCUAAGAAACCAUUGUAUUUAGAUCGCC------------AAAUGAUUGACGAAUUAACUUCGAAUGGAGCGGGACCUUCCCUGCUCCUACAAAU-AAAUAAAAAG-
...((........)).(((((.((((.(((.(------------((....))).))).))))........((((((((......)))))))))))))..-..........- ( -22.10, z-score =  -2.60, R)
>droSec1.super_94 39996 110 - 93855
UUAGGCUAAGAAACCAUUGUAUUUAGACCAUUGUAUUUAGAUUUAGAUUAUUGACGAAUUAACUUCGAAUGGAGCGGGACCUUCCCUGCUCCUACAAAUCAAAUAAAAAG-
...(((((((..((....)).))))).))....(((((.(((((..........((((.....))))...((((((((......))))))))...)))))))))).....- ( -24.70, z-score =  -2.55, R)
>droYak2.chrU 15191482 89 - 28119190
---GGCUAAAAAUCCUUUGUAUGGAGAACUCC------------AAGAUAUUCACAAAUUUACUUUGA-----GCGGGACCUUCCCAGCUCCA--GAAAUAAAUAAUUAAA
---..................((((....)))------------)............(((((.(((((-----(((((.....))).))))..--))).)))))....... ( -15.50, z-score =  -0.67, R)
>consensus
UUAGGCUAAGAAACCAUUGUAUGUAGAUCACC____________AAAUGAUUCACGAAUUAACUUCGAAUGGAGCGGGACCUUCCCUGCUCCU_CAAAUUAAAUAAAAAG_
...((........)).......................................((((.....))))...((((((((......))))))))................... (-11.14 = -11.82 +   0.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 152,971 – 153,066
Length 95
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 70.29
Shannon entropy 0.46072
G+C content 0.36898
Mean single sequence MFE -22.35
Consensus MFE -12.43
Energy contribution -13.05
Covariance contribution 0.62
Combinations/Pair 1.12
Mean z-score -1.53
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.773565
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrYHet 152971 95 - 347038
---UUUUAUCCAAUUUA-AGUAGCAGAGAAGGUCCCGCUGCAUUCGAAGUCAGUUCGUGAAUCCUCU------------UAUGAUCUACAUACAAUGGUUUCUUAGCCUAA
---..............-.(((((((....(....).)))).......((.((.((((((......)------------))))).)))).)))...((((....))))... ( -15.20, z-score =   0.28, R)
>droSim1.chrU 4593682 97 - 15797150
-CUUUUUAUUU-AUUUGUAGGAGCAGGGAAGGUCCCGCUCCAUUCGAAGUUAAUUCGUCAAUCAUUU------------GGCGAUCUAAAUACAAUGGUUUCUUAGCCUAA
-..........-..((((((((((.(((.....))))))))........(((..(((((((....))------------)))))..))).))))).((((....))))... ( -28.90, z-score =  -3.62, R)
>droSec1.super_94 39996 110 + 93855
-CUUUUUAUUUGAUUUGUAGGAGCAGGGAAGGUCCCGCUCCAUUCGAAGUUAAUUCGUCAAUAAUCUAAAUCUAAAUACAAUGGUCUAAAUACAAUGGUUUCUUAGCCUAA
-.....((((((((((((((((((.(((.....))))))))...((((.....))))...................)))))..))).)))))....((((....))))... ( -24.70, z-score =  -1.82, R)
>droYak2.chrU 15191482 89 + 28119190
UUUAAUUAUUUAUUUC--UGGAGCUGGGAAGGUCCCGC-----UCAAAGUAAAUUUGUGAAUAUCUU------------GGAGUUCUCCAUACAAAGGAUUUUUAGCC---
((((...((((((((.--..((((.(((.....)))))-----)).))))))))...))))...((.------------.(((((((........)))))))..))..--- ( -20.60, z-score =  -0.98, R)
>consensus
_CUUUUUAUUUAAUUUG_AGGAGCAGGGAAGGUCCCGCUCCAUUCGAAGUUAAUUCGUCAAUAAUCU____________GAUGAUCUAAAUACAAUGGUUUCUUAGCCUAA
...................(((((.(((.....))))))))...((((.....)))).......................................((((....))))... (-12.43 = -13.05 +   0.62)

alignment

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secondary structure

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dotplot

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Window 0

Location 152,996 – 153,092
Length 96
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 59.14
Shannon entropy 0.61849
G+C content 0.36382
Mean single sequence MFE -17.45
Consensus MFE -10.76
Energy contribution -11.45
Covariance contribution 0.69
Combinations/Pair 1.17
Mean z-score -1.87
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.02
SVM RNA-class probability 0.997018
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrYHet 152996 96 + 347038
------------GAUCAUAAGAGGAUUCACGAACUGACUUCGAAUGCAGCGGGACCUUCUCUGCUACU-UAA--AUUGGAUAAAAUAAAGAACAGCUCAAACACGAAUAAA---
------------........(((..(((.((((.....)))).....((((((......))))))...-...--...............)))...))).............--- ( -12.00, z-score =   0.55, R)
>droSim1.chrU 4593707 95 + 15797150
------------GAUCGCCAAAUGAUUGACGAAUUAACUUCGAAUGGAGCGGGACCUUCCCUGCUCCU-ACA--AAUAAAUAAAA-AGUGAAU---UCAAACUCAAAUAAUAAA
------------..((((...........((((.....))))...((((((((......)))))))).-...--...........-.))))..---.................. ( -20.60, z-score =  -3.34, R)
>droSec1.super_94 40021 106 - 93855
GACCAUUGUAUUUAGAUUUAGAUUAUUGACGAAUUAACUUCGAAUGGAGCGGGACCUUCCCUGCUCCUACAA--AUCAAAUAAAA-AGUGAAUA--UAAACUGAAAACCAA---
...((((.(((((.(((((..........((((.....))))...((((((((......))))))))...))--))))))))...-))))....--...............--- ( -24.60, z-score =  -3.85, R)
>droYak2.chrU 15191504 94 - 28119190
------------GAACUCCAAGAUAUUCACAAAUUUACUUUGA-----GCGGGACCUUCCCAGCUCCAGAAAUAAAUAAUUAAACAGAACGACAAACUAAAUGAGGCCUAU---
------------(..(((...(.....)....(((((.(((((-----(((((.....))).))))..))).))))).........................)))..)...--- ( -12.60, z-score =  -0.82, R)
>consensus
____________GAUCUCCAAAUGAUUCACGAAUUAACUUCGAAUGGAGCGGGACCUUCCCUGCUCCU_AAA__AAUAAAUAAAA_AAAGAACA__UCAAACGAAAACAAA___
.............................((((.....))))...((((((((......))))))))............................................... (-10.76 = -11.45 +   0.69)

alignment

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secondary structure

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dotplot

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Window 1

Location 152,996 – 153,092
Length 96
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 59.14
Shannon entropy 0.61849
G+C content 0.36382
Mean single sequence MFE -21.32
Consensus MFE -10.90
Energy contribution -11.28
Covariance contribution 0.38
Combinations/Pair 1.17
Mean z-score -1.48
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.960036
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrYHet 152996 96 - 347038
---UUUAUUCGUGUUUGAGCUGUUCUUUAUUUUAUCCAAU--UUA-AGUAGCAGAGAAGGUCCCGCUGCAUUCGAAGUCAGUUCGUGAAUCCUCUUAUGAUC------------
---...(((((....(((((((..((((...(((......--.))-)(((((.(.(.....)).)))))....)))).))))))))))))............------------ ( -15.50, z-score =   0.36, R)
>droSim1.chrU 4593707 95 - 15797150
UUUAUUAUUUGAGUUUGA---AUUCACU-UUUUAUUUAUU--UGU-AGGAGCAGGGAAGGUCCCGCUCCAUUCGAAGUUAAUUCGUCAAUCAUUUGGCGAUC------------
........((((.(((((---((.....-...(((.....--.))-)(((((.(((.....))))))))))))))).)))).(((((((....)))))))..------------ ( -28.20, z-score =  -4.06, R)
>droSec1.super_94 40021 106 + 93855
---UUGGUUUUCAGUUUA--UAUUCACU-UUUUAUUUGAU--UUGUAGGAGCAGGGAAGGUCCCGCUCCAUUCGAAGUUAAUUCGUCAAUAAUCUAAAUCUAAAUACAAUGGUC
---...............--.....(((-...((((((((--(((..(((((.(((.....))))))))...((((.....)))).........)))))).)))))....))). ( -21.90, z-score =  -1.54, R)
>droYak2.chrU 15191504 94 + 28119190
---AUAGGCCUCAUUUAGUUUGUCGUUCUGUUUAAUUAUUUAUUUCUGGAGCUGGGAAGGUCCCGC-----UCAAAGUAAAUUUGUGAAUAUCUUGGAGUUC------------
---...(..(((.....(.....)....((((((...((((((((...((((.(((.....)))))-----)).))))))))...)))))).....)))..)------------ ( -19.70, z-score =  -0.68, R)
>consensus
___AUUAUUCGCAUUUGA__UAUUCACU_UUUUAUUUAAU__UUU_AGGAGCAGGGAAGGUCCCGCUCCAUUCGAAGUUAAUUCGUCAAUAAUCUGAAGAUC____________
...............................................(((((.(((.....))))))))...((((.....))))............................. (-10.90 = -11.28 +   0.38)

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 02:08:08 2011