Locus 12007

Sequence ID dm3.chr3R
Location 25,056,878 – 25,057,011
Length 133
Max. P 0.992889
window16504 window16505

overview

Window 4

Location 25,056,878 – 25,056,977
Length 99
Sequences 12
Columns 105
Reading direction forward
Mean pairwise identity 64.56
Shannon entropy 0.77821
G+C content 0.58588
Mean single sequence MFE -35.48
Consensus MFE -11.47
Energy contribution -11.66
Covariance contribution 0.19
Combinations/Pair 1.30
Mean z-score -1.21
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.618751
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25056878 99 + 27905053
---CCCUGGAGGACUCAAAAGAACGCGGGGCAACAAGCUUCUAAAAGAGCU---CGAGAUCCAAUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAGGCGGA
---(((((..((((((...((((.((..(....)..))))))....(....---)))).)))...(((((....)))))(((((....)))))....)))).).. ( -42.30, z-score =  -3.15, R)
>droMoj3.scaffold_6540 26470595 99 + 34148556
CAACGUCAGCGGUAGAAAUCGCAAGCGUCGU------UCUAAGAUCGAGACCGAUUCUAAUUUCUCAGCGGAGACAGCAGCGGCCAUCGCUGCGGCUCAAAUCGA
..((((..(((((....)))))..))))...------.....(((.(((.((..........((((....))))..((((((.....)))))))))))..))).. ( -29.90, z-score =  -0.48, R)
>dp4.chr2 1897691 102 + 30794189
---UGCCGGUGGACGGAAUCGCACGCGACGCGGCAGGCUACUGAACGAGCUCGGUGAAAACUACGCCCCGGAAACAGCGGCCGCUAUUGCGGCGGCACAACUUGA
---..((((.((.((......(((.(((.((..(((....))).....)))))))).......)))))))).....((.(((((....))))).))......... ( -39.42, z-score =  -0.78, R)
>droWil1.scaffold_181108 1751082 90 + 4707319
---UAUUCGAGG---CAUUCGAAAGCGAAGAAACCAACUCCUCA------C---UGAAAUCUAUUCACCUGAAACCGAAGCGGCAAUUGCAGCAGCUCAACUCGA
---...(((((.---..((((..((.((.((.......)).)).------)---)........(((....)))..))))((.((....)).)).......))))) ( -15.20, z-score =   0.39, R)
>droGri2.scaffold_14624 3268585 102 + 4233967
---CGUCGGUUUUAGGAAUCGCAAGCGUCGCAACCGGCCUGAUCUCGAUACGUCGUCGAUCUUCUCGCCGGAGACGACGGCGGCAAUAGCGGCGGCCCAAAUUGA
---..(((((((..((...(....)((((((.....(((((....))....(((((((.(((((.....)))))))))))))))....))))))..))))))))) ( -34.80, z-score =   0.56, R)
>droVir3.scaffold_12822 2349893 96 + 4096053
---CGUCGGCGGUCGUAACCGAAAGCGUCGCAA------CAGGAUUGAGCUAGAUUUGAAUUUCUCAGCGGAGACAGCGGCGGCCAUUGCGGCAGCUCAAAUUGA
---....(((.(((((((.(....)((((((..------.........((((((........))).)))(....).))))))....))))))).)))........ ( -29.50, z-score =   0.21, R)
>droSim1.chr3R 24727783 99 + 27517382
---CGCUGGAGGACUCAAAAGAACGCGGGGCAACAAGCUUCUGAGAGAGCU---UGAGAUCCAAUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAGGCUGA
---..........(((...((((.((..(....)..))))))..)))((((---((.........(((((....)))))(((((....)))))....)))))).. ( -42.50, z-score =  -3.01, R)
>droSec1.super_4 3919662 99 + 6179234
---CGCUGGAGGACUCAAAAGAACGCGGGGCAACAAGCUUCUGAGAGAGCU---UGAGAUCCAAUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAGGCUGA
---..........(((...((((.((..(....)..))))))..)))((((---((.........(((((....)))))(((((....)))))....)))))).. ( -42.50, z-score =  -3.01, R)
>droYak2.chr3R 7391669 99 - 28832112
---CGCUGGAGGAAUCAAAAGGACGCGGGGCAACAAGCUUCUGAGAGAGAU---CGAGAUCUAUUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAGGCCGA
---.(((.((....((...((((.((..(....)..))))))..))....)---)..........(((((....)))))(((((....))))))))......... ( -36.00, z-score =  -1.31, R)
>droEre2.scaffold_4820 7496533 99 - 10470090
---CGCUGGAGGACUCAAAAGGACGCGCGGCAACAAGCUUCUGAGAGAGAU---CGAGAUACAUUCGCCGGAAACGGCGGCCGCAAUUGCGGCAGCACAGGCCGA
---.(((....(((((....(((.((..(....)..)).)))....))).)---)..........(((((....)))))(((((....))))))))......... ( -36.70, z-score =  -1.71, R)
>droAna3.scaffold_13340 9512284 101 - 23697760
-GGAGGAACGGGUCGGGCCAGGACACGCCGGAAUAAGCUAUUAAGCGAGCU---AGAGACCUACUCGCCAGAAACGGCGGCCGCCAUCGCGGCAGCACAACUCGA
-.......(((((.(.((.......(((((...(((....))).(((((.(---((....))))))))......)))))(((((....))))).)).).))))). ( -35.40, z-score =  -0.89, R)
>droPer1.super_7 2061226 102 + 4445127
---UGCCGGUGGACGUAAUCGCACGCGACGCGGCAGGCUACUGAACGAGCUCGGUGAAAACUACGCCCCGGAAACAGCGGCCGCUAUUGCGGCGGCACAACUUGA
---..((((.((.((((....(((.(((.((..(((....))).....)))))))).....)))))))))).....((.(((((....))))).))......... ( -41.50, z-score =  -1.39, R)
>consensus
___CGCUGGAGGACGCAAAAGAACGCGGCGCAACAAGCUUCUGAGAGAGCU___UGAGAUCUACUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAAGUUGA
....................................................................(((.....((.(((((....))))).)).....))). (-11.47 = -11.66 +   0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 25,056,909 – 25,057,011
Length 102
Sequences 12
Columns 111
Reading direction forward
Mean pairwise identity 59.60
Shannon entropy 0.81370
G+C content 0.57728
Mean single sequence MFE -37.60
Consensus MFE -11.95
Energy contribution -13.02
Covariance contribution 1.06
Combinations/Pair 1.23
Mean z-score -2.25
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.57
SVM RNA-class probability 0.992889
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25056909 102 + 27905053
AAGCUUCUAAAAGAGCUCG---AGAUCCAAUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAGGCGGAACUCAACGCCGCAGGAAAG------UCGGGAGCAGCAGGA
..(((((.....))(((((---((.(((...(((((....)))))(((((....))))).((....))))).)))....((((......)------.)))))))))).... ( -44.00, z-score =  -2.95, R)
>droMoj3.scaffold_6540 26470629 87 + 34148556
------AAGAUCGAGACCGAUUCUAAUUUCUCAGCGGAGACAGCAGCGGCCAUCGCUGCGGCUCAAAUCGAGCUUGAUUCGAAUAAACCGGCG------------------
------..(((((((..(((((......((((....))))..((((((.....))))))......)))))..)))))))..............------------------ ( -25.60, z-score =  -0.36, R)
>dp4.chr2 1897722 96 + 30794189
AGGCUACUGAACGAGCUCGGUGAAAACUACGCCCCGGAAACAGCGGCCGCUAUUGCGGCGGCACAACUUGAGCUCGAUUCGUCAGGGAAG------CCAUCA---------
.((((.((((.(((((((((((.......))))..(....).((.(((((....))))).)).......))))))).....))))...))------))....--------- ( -43.80, z-score =  -4.13, R)
>droWil1.scaffold_181108 1751110 87 + 4707319
---------CAACUCCUCACUGAAAUCUAUUCACCUGAAACCGAAGCGGCAAUUGCAGCAGCUCAACUCGAAUUAGACGCGACUGCCAAA------UCGAAU---------
---------.......(((.((((.....))))..)))...(((...((((.((((..(((.((.....)).)).)..)))).))))...------)))...--------- ( -12.70, z-score =   0.27, R)
>droGri2.scaffold_14624 3268616 93 + 4233967
CGGCCUGAUCUCGAUACGUCGUCGAUCUUCUCGCCGGAGACGACGGCGGCAAUAGCGGCGGCCCAAAUUGAGCUCGAUUCGGCCAAGCCGGUG------------------
..(((...........((((((((.(((((.....)))))))))))))((....))(((((((..(((((....))))).))))..)))))).------------------ ( -37.10, z-score =  -0.66, R)
>droVir3.scaffold_12822 2349924 87 + 4096053
------AGGAUUGAGCUAGAUUUGAAUUUCUCAGCGGAGACAGCGGCGGCCAUUGCGGCAGCUCAAAUUGAGCUUGAUUCGGGCAAACCGGUG------------------
------.((((..((((.(((((((...((((....))))..((.((.((....)).)).))))))))).))))..))))((.....))....------------------ ( -31.90, z-score =  -2.04, R)
>droSim1.chr3R 24727814 102 + 27517382
AAGCUUCUGAGAGAGCUUG---AGAUCCAAUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAGGCUGAACUUAACGCCGCCGGAAAG------UCGGGAGCAGCAGGA
..((((((((...((((((---.........(((((....)))))(((((....)))))....))))))...(((..((....))..)))------))))))))....... ( -44.70, z-score =  -2.55, R)
>droSec1.super_4 3919693 102 + 6179234
AAGCUUCUGAGAGAGCUUG---AGAUCCAAUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAGGCUGAACUCAACGCCGCCGGAAAG------UCGGGAGCAGCAGGA
..(((((((((((((((((---.........(((((....)))))(((((....)))))....))))))...)))..((....)).....------))))))))....... ( -44.60, z-score =  -2.27, R)
>droYak2.chr3R 7391700 102 - 28832112
AAGCUUCUGAGAGAGAUCG---AGAUCUAUUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAGGCCGAACUCAACGCCGCAGGAAAG------UCGGGAGCAGCAGGA
..((((((((..(((.(((---.(.(((...(((((....)))))(((((....))))).....))))))).)))....((...))....------))))))))....... ( -42.00, z-score =  -2.19, R)
>droEre2.scaffold_4820 7496564 108 - 10470090
AAGCUUCUGAGAGAGAUCG---AGAUACAUUCGCCGGAAACGGCGGCCGCAAUUGCGGCAGCACAGGCCGAACUCAACGCCGCAGGAAAGCAGCACUCGGGAGCAGCAGGA
..(((((((((.(((.(((---.........(((((....)))))(((((....))))).........))).)))...((.((......)).)).)))))))))....... ( -49.70, z-score =  -4.72, R)
>droAna3.scaffold_13340 9512317 96 - 23697760
AAGCUAUUAAGCGAGCUAG---AGACCUACUCGCCAGAAACGGCGGCCGCCAUCGCGGCAGCACAACUCGAGCUAGACGCCACAUCGAAA------CCGGGAGGA------
..........(((((.(((---....)))))))).......(((((((((....)))))(((.(.....).)))...)))).........------((....)).------ ( -31.30, z-score =  -1.23, R)
>droPer1.super_7 2061257 96 + 4445127
AGGCUACUGAACGAGCUCGGUGAAAACUACGCCCCGGAAACAGCGGCCGCUAUUGCGGCGGCACAACUUGAGCUCGAUUCGUCAGGGAAG------CCAUCA---------
.((((.((((.(((((((((((.......))))..(....).((.(((((....))))).)).......))))))).....))))...))------))....--------- ( -43.80, z-score =  -4.13, R)
>consensus
AAGCUUCUGAGAGAGCUCG___AGAUCUACUCGCCGGAAACGGCGGCCGCUAUUGCGGCAGCACAAGUUGAACUCGACGCCGCAGGAAAG______UCGGGA_________
............(((.((.................(....).((.(((((....))))).)).......)).))).................................... (-11.95 = -13.02 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:55 2011