Locus 11344

Sequence ID dm3.chr3R
Location 20,443,270 – 20,443,429
Length 159
Max. P 0.999172
window15600 window15601

overview

Window 0

Location 20,443,270 – 20,443,429
Length 159
Sequences 10
Columns 159
Reading direction forward
Mean pairwise identity 73.68
Shannon entropy 0.58101
G+C content 0.49127
Mean single sequence MFE -48.26
Consensus MFE -25.69
Energy contribution -25.15
Covariance contribution -0.54
Combinations/Pair 1.37
Mean z-score -2.80
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.69
SVM RNA-class probability 0.999172
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20443270 159 + 27905053
CGGAAACUGAGGCGGCCAAUCGUCAGUCCGCUGAUCCCAAGGAGUUUGCCCUGCGUCCCGAUGACGUGAACAACAACGAAAACGAUGAAAAUUUUUGCCAGAGUGCUACAGCAGAUAGCUUCAAUUCUGCUGUGGCACUCCGAACCAAUAAAAUUGAAG
.((.......(((((....(((((..(((..((....)).)))((((.....(((((.....)))))))))............)))))......))))).(((((((((((((((..........)))))))))))))))....))............. ( -49.00, z-score =  -2.59, R)
>droSim1.chr3R 20281022 159 + 27517382
CGGAGACUGAGGCGGCCAAUCGCCAGUCCGCUGAUCCCAAGGAGUUCCCCCUGCGCCCCGAUGACGUGAACAACAACGAAAACGAUGAAAAUUUUUGCCAGAGUGCUACAGCAGAUAGCUUCAAUUUUGCUGUGGCACUCCGAACCAAUAAAAUUGAAG
(((.((((..(((((....)))))))))(((((....))(((.......))))))..)))....(((........)))....((((.......((((...(((((((((((((((..........)))))))))))))))))))........))))... ( -43.86, z-score =  -1.56, R)
>droSec1.super_0 20776826 159 + 21120651
CGGAAACUGAGGCGGCCAAUCGCCAGUCCGCUGAUCCCAAGGAGUUCCCCCUGCGCCCCGAUGACGUGAACAACAACGAAAACGAUGAAAAUUUUUGCCAGGGUGCUACAGCAGAUAGCUUCAAUUCUGCUGUGGCACUCCGAACCAAUAAAAUUGAAG
((((......(((((....)))))..))))..........(((((...(((((.((........(((........))).....(((....)))...))))))).(((((((((((..........)))))))))))))))).................. ( -48.50, z-score =  -2.23, R)
>droYak2.chr3R 2776527 159 - 28832112
CAGAAACUGAAGAGCCCAAUCGCCAGUCCUUUUCGCCCAAGGAGUUUGCCCAGCGUCCCGAUGACGUCAAUAACAACGAAAACGAUGAAAAUUUUUGCCAGAGUGCUACAGCAGAUAGCUUCAAUGCUGCUGUGGCACUCCGAACCAAUAAAAUUGAAG
(((((((((..((......))..)))((.((((((.....((.(....))).(((((.....))))).........)))))).))......))))))...((((((((((((((.((.......))))))))))))))))................... ( -41.10, z-score =  -2.15, R)
>droEre2.scaffold_4820 2854631 159 - 10470090
CGGAAACUGAGACGGCCAAUCGCCAGUCCGCUUCGCCCAAGGAGUUCGCCAUGCGUCCCGAUGACGUGAACAACAACGAAAACGAUGAAAAUUUUUGCCAGAGUGCUACAGCAGAUAGCUUCAAUGCUGCUGUGGCACUCCGAACCAAUAAAAUUGAAG
.((.....(.((((((.....))).))))..((((..((((((((((((....(((....)))..))))))..((.((....)).))....))))))...((((((((((((((.((.......))))))))))))))))))))))............. ( -46.20, z-score =  -1.93, R)
>droAna3.scaffold_13088 484505 156 + 569066
---CGGAGGCGGGAGCGGAGUCGGAAGAGACCCGGGAGACGGCCACCACCCCCAAGUCCGAUGAUGUCAACAACAAUGCGAACGGUGAAAAUUUUUGCCAGAGUGCUACAGCAGAUAGCUUCAAUUCUGCUGUGGCACUCCGAACUGACGAUAUUGAAG
---.((.((.((..((((.(((......))))).(....).))..)).)).)).....(((((.(((((..............((..((....))..)).(((((((((((((((..........))))))))))))))).....))))).)))))... ( -61.40, z-score =  -4.06, R)
>droWil1.scaffold_181130 3411135 138 - 16660200
---CAUCAAAUGAGACCAAACCCACGUCUAGUGAUCCCAAGGAG------------------GAUAAGAAUAACAAUGCGAAAAAUGAAAAUUUUUGCCAGAGUGCUACAGCAGAUAGCUUCAAAUCUGCUGUGGCACUCUCAAAACCGUAUAUUGAAG
---..((((......((.....(((.....))).(((...))))------------------)............(((((((((((....))))))...(((((((((((((((((........)))))))))))))))))......))))).)))).. ( -43.70, z-score =  -5.60, R)
>droVir3.scaffold_13047 15004545 156 - 19223366
CGCAGGAGGAGGAAGAGCAUGCUCAAGAUGCCGAGCCUAAGGAGCCCA---CAGAGGCAGACGAUGUGAAUAACAAUGAGAAUAGUGAGAAUUUUUGCCAGAGUGCUACAGCAGAUAGCUUCAAUGCUGCUGUGGCACUCACAACCAAAAAAAUUGAAG
....((.(((((((...(((.((((.........((((..(.......---)..))))......(((.....))).))))....)))....))))).)).((((((((((((((.((.......))))))))))))))))....))............. ( -45.40, z-score =  -1.99, R)
>droMoj3.scaffold_6540 22132567 153 + 34148556
CCUUGGUGGAUA---CCGAGCAGCAGGAGACGGAGCCCAAGGAGCCAG---CGGAAGCGGACGAUGUGAACAACAAUGAGAAUGGCGAGAAUUUUUGCCAGAGUGCUACAGCAGAUAGCUUCAAUUCUGCUGUGGCACUCACAACCAACCAAAUUGAAG
..(((((((...---(((..(.((.(....)((..((...))..)).)---).)...)))....(((...............(((((((....)))))))(((((((((((((((..........)))))))))))))))))).)).)))))....... ( -57.30, z-score =  -4.57, R)
>droGri2.scaffold_14906 4452109 156 - 14172833
AGUUAGUCGACGAGUUGAAGAAACCGGAUGGGGAGCUCAAGGAGCCCG---UGGAAGCGGACGAUGUCAAUAACAAUGAGAAUGGCGAGAAUUUUUGCCAGAGUGCUACUGCAGAUAGCUUCAAUGCUGCUGUAGCACUCGCAACCAAACAAAUUGAAG
......((((((.(((.....)))))..((.((.((((...)))))).---(((..((.(((...)))..............(((((((....)))))))(((((((((.((((.((.......)))))).)))))))))))..)))..))..)))).. ( -46.10, z-score =  -1.34, R)
>consensus
CGGAAACUGAGGAGGCCAAUCGCCAGUCCGCUGAGCCCAAGGAGUUCGCCCUGCGUCCCGAUGACGUGAACAACAACGAAAACGAUGAAAAUUUUUGCCAGAGUGCUACAGCAGAUAGCUUCAAUUCUGCUGUGGCACUCCGAACCAAUAAAAUUGAAG
........................................((......................(((........)))......................((((((((((((((............))))))))))))))....))............. (-25.69 = -25.15 +  -0.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 20,443,270 – 20,443,429
Length 159
Sequences 10
Columns 159
Reading direction reverse
Mean pairwise identity 73.68
Shannon entropy 0.58101
G+C content 0.49127
Mean single sequence MFE -47.10
Consensus MFE -19.52
Energy contribution -19.82
Covariance contribution 0.30
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.579946
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20443270 159 - 27905053
CUUCAAUUUUAUUGGUUCGGAGUGCCACAGCAGAAUUGAAGCUAUCUGCUGUAGCACUCUGGCAAAAAUUUUCAUCGUUUUCGUUGUUGUUCACGUCAUCGGGACGCAGGGCAAACUCCUUGGGAUCAGCGGACUGACGAUUGGCCGCCUCAGUUUCCG
.............((((((((((((.((((((((..........)))))))).))))))))............(((((((((((((..((((.((((.....))))(((((......))))))))))))))))..)))))).))))............. ( -51.70, z-score =  -1.86, R)
>droSim1.chr3R 20281022 159 - 27517382
CUUCAAUUUUAUUGGUUCGGAGUGCCACAGCAAAAUUGAAGCUAUCUGCUGUAGCACUCUGGCAAAAAUUUUCAUCGUUUUCGUUGUUGUUCACGUCAUCGGGGCGCAGGGGGAACUCCUUGGGAUCAGCGGACUGGCGAUUGGCCGCCUCAGUCUCCG
............(((((((((((((.((((((..............)))))).)))))))................(((..(.((((.((((.((....)))))))))).)..)))......))))))(.(((((((((......))))..))))).). ( -50.34, z-score =  -0.91, R)
>droSec1.super_0 20776826 159 - 21120651
CUUCAAUUUUAUUGGUUCGGAGUGCCACAGCAGAAUUGAAGCUAUCUGCUGUAGCACCCUGGCAAAAAUUUUCAUCGUUUUCGUUGUUGUUCACGUCAUCGGGGCGCAGGGGGAACUCCUUGGGAUCAGCGGACUGGCGAUUGGCCGCCUCAGUUUCCG
.............((..(((.((((.((((((((..........)))))))).)))))).(((................(((((((..((((.((((.....))))((((((....)))))))))))))))))..(((.....))))))...)...)). ( -50.50, z-score =  -0.48, R)
>droYak2.chr3R 2776527 159 + 28832112
CUUCAAUUUUAUUGGUUCGGAGUGCCACAGCAGCAUUGAAGCUAUCUGCUGUAGCACUCUGGCAAAAAUUUUCAUCGUUUUCGUUGUUAUUGACGUCAUCGGGACGCUGGGCAAACUCCUUGGGCGAAAAGGACUGGCGAUUGGGCUCUUCAGUUUCUG
..........(((((..((((((((.(((((((.((.......))))))))).))))))))((...((((.(((((.((((((((........((((.....))))(.(((......))).))))))))).)).))).))))..))...)))))..... ( -46.50, z-score =  -0.81, R)
>droEre2.scaffold_4820 2854631 159 + 10470090
CUUCAAUUUUAUUGGUUCGGAGUGCCACAGCAGCAUUGAAGCUAUCUGCUGUAGCACUCUGGCAAAAAUUUUCAUCGUUUUCGUUGUUGUUCACGUCAUCGGGACGCAUGGCGAACUCCUUGGGCGAAGCGGACUGGCGAUUGGCCGUCUCAGUUUCCG
..............((.((((((((.(((((((.((.......))))))))).)))))))))).......((((..(..(((((..((((((.((....))))))).)..)))))..)..)))).(((((((((.(((.....)))))))..))))).. ( -52.10, z-score =  -1.53, R)
>droAna3.scaffold_13088 484505 156 - 569066
CUUCAAUAUCGUCAGUUCGGAGUGCCACAGCAGAAUUGAAGCUAUCUGCUGUAGCACUCUGGCAAAAAUUUUCACCGUUCGCAUUGUUGUUGACAUCAUCGGACUUGGGGGUGGUGGCCGUCUCCCGGGUCUCUUCCGACUCCGCUCCCGCCUCCG---
..........(((.((.((((((((.((((((((..........)))))))).)))))))))).............(((.(((....))).))).......)))..((((((((..((.(.....((((.....))))...).))..)))))))).--- ( -57.80, z-score =  -3.18, R)
>droWil1.scaffold_181130 3411135 138 + 16660200
CUUCAAUAUACGGUUUUGAGAGUGCCACAGCAGAUUUGAAGCUAUCUGCUGUAGCACUCUGGCAAAAAUUUUCAUUUUUCGCAUUGUUAUUCUUAUC------------------CUCCUUGGGAUCACUAGACGUGGGUUUGGUCUCAUUUGAUG---
..((((.....((....((((((((.(((((((((........))))))))).))))))..((((((((....)))))).))........))....)------------------)....((((((((...(((....))))))))))).))))..--- ( -40.10, z-score =  -2.69, R)
>droVir3.scaffold_13047 15004545 156 + 19223366
CUUCAAUUUUUUUGGUUGUGAGUGCCACAGCAGCAUUGAAGCUAUCUGCUGUAGCACUCUGGCAAAAAUUCUCACUAUUCUCAUUGUUAUUCACAUCGUCUGCCUCUG---UGGGCUCCUUAGGCUCGGCAUCUUGAGCAUGCUCUUCCUCCUCCUGCG
...(((((.....))))).((((((.(((((((.((.......))))))))).)))))).((((.................................(((..(....)---..))).......((((((....)))))).))))............... ( -36.30, z-score =   0.35, R)
>droMoj3.scaffold_6540 22132567 153 - 34148556
CUUCAAUUUGGUUGGUUGUGAGUGCCACAGCAGAAUUGAAGCUAUCUGCUGUAGCACUCUGGCAAAAAUUCUCGCCAUUCUCAUUGUUGUUCACAUCGUCCGCUUCCG---CUGGCUCCUUGGGCUCCGUCUCCUGCUGCUCGG---UAUCCACCAAGG
......((((((.((((((((((((.((((((((..........)))))))).))))))..))))........(((.....................(((.((....)---).))).....((((..((.....))..))))))---)..)))))))). ( -43.90, z-score =  -0.95, R)
>droGri2.scaffold_14906 4452109 156 + 14172833
CUUCAAUUUGUUUGGUUGCGAGUGCUACAGCAGCAUUGAAGCUAUCUGCAGUAGCACUCUGGCAAAAAUUCUCGCCAUUCUCAUUGUUAUUGACAUCGUCCGCUUCCA---CGGGCUCCUUGAGCUCCCCAUCCGGUUUCUUCAACUCGUCGACUAACU
...(((((.....))))).(((((((((.((((.((.......)))))).)))))))))((((..........))))........(((((((((...(((((......---)))))...(((((....((....))....)))))...))))).)))). ( -41.80, z-score =  -1.86, R)
>consensus
CUUCAAUUUUAUUGGUUCGGAGUGCCACAGCAGAAUUGAAGCUAUCUGCUGUAGCACUCUGGCAAAAAUUUUCAUCGUUCUCAUUGUUGUUCACAUCAUCGGGACGCAGGGCGAACUCCUUGGGCUCAGCGGACUGGCGAUUGGCCGCCUCAGUUUCCG
...................((((((.(((((((............))))))).)))))).................................................................................................... (-19.52 = -19.82 +   0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:41:14 2011