Locus 13208

Sequence ID dm3.chrX
Location 5,003,897 – 5,004,046
Length 149
Max. P 0.970412
window18167 window18168 window18169 window18170

overview

Window 7

Location 5,003,897 – 5,004,006
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 93.58
Shannon entropy 0.11149
G+C content 0.46789
Mean single sequence MFE -35.00
Consensus MFE -27.34
Energy contribution -27.30
Covariance contribution -0.04
Combinations/Pair 1.12
Mean z-score -2.03
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.582641
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5003897 109 + 22422827
AUGUGCCUAAGUAGUUGCUGCUCUGGUAAUCAUGUUCGACACGCCCCCAUUUCGGGGGCAUUGCCAACAUGCCGCACCAACGAUUGUUGUUAUUAUUGGUGUUUAUAUU
...((((..(((((...)))))..))))..((((((.(....((((((.....))))))....).))))))..(((((((..((.......))..)))))))....... ( -37.00, z-score =  -2.54, R)
>droSim1.chrX_random 1748465 109 + 5698898
AUGUGCCUAAGUAGUUGCUGCUCUGGUAAUCGUGUUCGACACGCCCCCUUUUCGGGGGCGUUGCCAACGUGCCGCACCUGCGAUUGUUGUUAUUAUUGCUGUUUAUAUU
..........((((.(((.((.((((((((.(((.....)))((((((.....)))))))))))))..).)).))).))))............................ ( -35.40, z-score =  -2.10, R)
>droSec1.super_4 4426522 109 - 6179234
AUGUGCCUAAGUAGUUGCUGCUCUGGUAAUCGUGUUCGACACGCCCCCAUUUCGGGGGCGUUGCCAACAUGCCGCACCUACGAUUGUUGUUAUUAUUGCUGUUUAUAUU
..........((((.(((.((..(((((((.(((.....)))((((((.....)))))))))))))....)).))).))))............................ ( -35.50, z-score =  -2.34, R)
>droYak2.chrX 18304749 109 - 21770863
AUGUGCCUAAGUAGUUGCUGCUCUGGUAAUCAUGUUCGACACGCCCCCAUUUUGGGGGCGUUGGCUACAUGCAGCACCUUCGAUUGUUGUUAUUAUUGCUGUUUAUAUU
...((((..(((((...)))))..))))..(((((.....((((((((.....)))))))).....)))))(((((.....(((....))).....)))))........ ( -35.30, z-score =  -2.28, R)
>droEre2.scaffold_4690 2356129 109 + 18748788
AUGUGCCUAAGUAGUUGCUGCUCUGGUAAUCAUGUACGACACGCCCCCAUUUUGUGGGCGGUGGCUACAUGCCGCACCAUCGAUUGUUGUUAUUAUUGCUGUUUAUAUU
...((((..(((((...)))))..)))).......(((((((((((.(.....).)))))(((((.....))))).........))))))................... ( -31.80, z-score =  -0.86, R)
>consensus
AUGUGCCUAAGUAGUUGCUGCUCUGGUAAUCAUGUUCGACACGCCCCCAUUUCGGGGGCGUUGCCAACAUGCCGCACCUACGAUUGUUGUUAUUAUUGCUGUUUAUAUU
...((((..(((((...)))))..))))..((((((.(.(((((((((.....))))))).)).)))))))...................................... (-27.34 = -27.30 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,003,897 – 5,004,006
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 93.58
Shannon entropy 0.11149
G+C content 0.46789
Mean single sequence MFE -31.23
Consensus MFE -26.60
Energy contribution -27.60
Covariance contribution 1.00
Combinations/Pair 1.08
Mean z-score -1.98
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.806993
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5003897 109 - 22422827
AAUAUAAACACCAAUAAUAACAACAAUCGUUGGUGCGGCAUGUUGGCAAUGCCCCCGAAAUGGGGGCGUGUCGAACAUGAUUACCAGAGCAGCAACUACUUAGGCACAU
........((((((..((.......))..))))))...((((((((((.(((((((.....))))))))))).))))))....((.(((.((...)).))).))..... ( -34.30, z-score =  -2.30, R)
>droSim1.chrX_random 1748465 109 - 5698898
AAUAUAAACAGCAAUAAUAACAACAAUCGCAGGUGCGGCACGUUGGCAACGCCCCCGAAAAGGGGGCGUGUCGAACACGAUUACCAGAGCAGCAACUACUUAGGCACAU
........................(((((...((.((((((...(....)((((((.....)))))))))))).)).))))).((.(((.((...)).))).))..... ( -32.90, z-score =  -2.72, R)
>droSec1.super_4 4426522 109 + 6179234
AAUAUAAACAGCAAUAAUAACAACAAUCGUAGGUGCGGCAUGUUGGCAACGCCCCCGAAAUGGGGGCGUGUCGAACACGAUUACCAGAGCAGCAACUACUUAGGCACAU
............................((((.(((.((...((((..((((((((.....))))))))((((....))))..)))).)).))).)))).......... ( -33.20, z-score =  -2.48, R)
>droYak2.chrX 18304749 109 + 21770863
AAUAUAAACAGCAAUAAUAACAACAAUCGAAGGUGCUGCAUGUAGCCAACGCCCCCAAAAUGGGGGCGUGUCGAACAUGAUUACCAGAGCAGCAACUACUUAGGCACAU
..........((...............(....)((((((((((.....((((((((.....)))))))).....))))(.....)...)))))).........)).... ( -30.60, z-score =  -2.37, R)
>droEre2.scaffold_4690 2356129 109 - 18748788
AAUAUAAACAGCAAUAAUAACAACAAUCGAUGGUGCGGCAUGUAGCCACCGCCCACAAAAUGGGGGCGUGUCGUACAUGAUUACCAGAGCAGCAACUACUUAGGCACAU
..........((...............(..(((((...((((((.(.(((((((.(.....).))))).)).)))))))..)))))..)..............)).... ( -25.15, z-score =  -0.04, R)
>consensus
AAUAUAAACAGCAAUAAUAACAACAAUCGAAGGUGCGGCAUGUUGGCAACGCCCCCGAAAUGGGGGCGUGUCGAACAUGAUUACCAGAGCAGCAACUACUUAGGCACAU
................................((((..((((((((((.(((((((.....))))))))))).)))))).......(((.((...)).)))..)))).. (-26.60 = -27.60 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,003,935 – 5,004,046
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 90.90
Shannon entropy 0.16085
G+C content 0.44486
Mean single sequence MFE -35.93
Consensus MFE -24.64
Energy contribution -26.32
Covariance contribution 1.68
Combinations/Pair 1.07
Mean z-score -3.18
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.83
SVM RNA-class probability 0.970412
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5003935 111 + 22422827
ACACGCCCCCAUUUCGGGGGCAUUGCCAACAUGCCGCACCAACGAUUGUUGUUAUUAUUGGUGUUUAUAUUGUUGCCGAAUUGUUAAUUGAUCUAAUUGAUAAAUUACCUG
....((((((.....)))))).(((.(((((....(((((((..((.......))..)))))))......))))).))).((((((((((...))))))))))........ ( -33.80, z-score =  -3.11, R)
>droSim1.chrX_random 1748503 111 + 5698898
ACACGCCCCCUUUUCGGGGGCGUUGCCAACGUGCCGCACCUGCGAUUGUUGUUAUUAUUGCUGUUUAUAUUGUUCCCGGCUUGGUAAUUGAUCUAAUUGAUGAAUUACCAG
..((((((((.....))))))))...(((((...(((....)))..)))))........((((.............)))).((((((((.(((.....))).)))))))). ( -39.02, z-score =  -3.98, R)
>droSec1.super_4 4426560 111 - 6179234
ACACGCCCCCAUUUCGGGGGCGUUGCCAACAUGCCGCACCUACGAUUGUUGUUAUUAUUGCUGUUUAUAUUGUUCCCGGCUUGGUAAUUGAUCUAAUUGAUGAAUUACCAG
..((((((((.....)))))))).........((((.....(((((....((.......)).......)))))...)))).((((((((.(((.....))).)))))))). ( -36.60, z-score =  -3.39, R)
>droYak2.chrX 18304787 111 - 21770863
ACACGCCCCCAUUUUGGGGGCGUUGGCUACAUGCAGCACCUUCGAUUGUUGUUAUUAUUGCUGUUUAUAUUGUUCCCGGCUUGGUAAUUGAUCUAAUUGAUGAACUGCCAG
....((((((.....))))))(((((..(((.((((((.....(((....))).....))))))......)))..))))).(((((.((.(((.....))).)).))))). ( -37.70, z-score =  -3.25, R)
>droEre2.scaffold_4690 2356167 109 + 18748788
ACACGCCCCCAUUUUGUGGGCGGUGGCUACAUGCCGCACCAUCGAUUGUUGUUAUUAUUGCUGUUUAUAUUGUUCCCGGCUUGGUAAUUGAUCUAAUUGAUGAACUACC--
...(((((.(.....).)))))(((((.....)))))..(((((((((..(((((((..((((.............)))).))))))).....))))))))).......-- ( -32.52, z-score =  -2.18, R)
>consensus
ACACGCCCCCAUUUCGGGGGCGUUGCCAACAUGCCGCACCUACGAUUGUUGUUAUUAUUGCUGUUUAUAUUGUUCCCGGCUUGGUAAUUGAUCUAAUUGAUGAAUUACCAG
.(((((((((.....))))))).)).(((((...((......))..)))))........((((.............))))..(((((((.(((.....))).))))))).. (-24.64 = -26.32 +   1.68)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,003,935 – 5,004,046
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 90.90
Shannon entropy 0.16085
G+C content 0.44486
Mean single sequence MFE -33.65
Consensus MFE -24.89
Energy contribution -25.73
Covariance contribution 0.84
Combinations/Pair 1.12
Mean z-score -2.67
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.34
SVM RNA-class probability 0.928958
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5003935 111 - 22422827
CAGGUAAUUUAUCAAUUAGAUCAAUUAACAAUUCGGCAACAAUAUAAACACCAAUAAUAACAACAAUCGUUGGUGCGGCAUGUUGGCAAUGCCCCCGAAAUGGGGGCGUGU
..(.(((((.(((.....))).))))).).....(.(((((.......((((((..((.......))..)))))).....))))).).((((((((.....)))))))).. ( -31.50, z-score =  -2.22, R)
>droSim1.chrX_random 1748503 111 - 5698898
CUGGUAAUUCAUCAAUUAGAUCAAUUACCAAGCCGGGAACAAUAUAAACAGCAAUAAUAACAACAAUCGCAGGUGCGGCACGUUGGCAACGCCCCCGAAAAGGGGGCGUGU
.((((((((.(((.....))).)))))))).((((....).....................(((..((((....))))...)))))).((((((((.....)))))))).. ( -38.30, z-score =  -4.09, R)
>droSec1.super_4 4426560 111 + 6179234
CUGGUAAUUCAUCAAUUAGAUCAAUUACCAAGCCGGGAACAAUAUAAACAGCAAUAAUAACAACAAUCGUAGGUGCGGCAUGUUGGCAACGCCCCCGAAAUGGGGGCGUGU
.((((((((.(((.....))).)))))))).((((....).....................((((.((((....))))..))))))).((((((((.....)))))))).. ( -36.50, z-score =  -3.06, R)
>droYak2.chrX 18304787 111 + 21770863
CUGGCAGUUCAUCAAUUAGAUCAAUUACCAAGCCGGGAACAAUAUAAACAGCAAUAAUAACAACAAUCGAAGGUGCUGCAUGUAGCCAACGCCCCCAAAAUGGGGGCGUGU
.((((.(((((((.....)))......((.....))))))..((((..(((((....................)))))..))))))))((((((((.....)))))))).. ( -34.35, z-score =  -2.94, R)
>droEre2.scaffold_4690 2356167 109 - 18748788
--GGUAGUUCAUCAAUUAGAUCAAUUACCAAGCCGGGAACAAUAUAAACAGCAAUAAUAACAACAAUCGAUGGUGCGGCAUGUAGCCACCGCCCACAAAAUGGGGGCGUGU
--(((((((.(((.....))).)))))))..(((((..............(((...((...........))..)))(((.....))).)).((((.....))))))).... ( -27.60, z-score =  -1.04, R)
>consensus
CUGGUAAUUCAUCAAUUAGAUCAAUUACCAAGCCGGGAACAAUAUAAACAGCAAUAAUAACAACAAUCGAAGGUGCGGCAUGUUGGCAACGCCCCCGAAAUGGGGGCGUGU
..(((((((.(((.....))).)))))))..((((....)..........(((....................)))))).........((((((((.....)))))))).. (-24.89 = -25.73 +   0.84)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:16:51 2011