Locus 9410

Sequence ID dm3.chr3R
Location 6,511,336 – 6,511,475
Length 139
Max. P 0.990861
window12901 window12902 window12903

overview

Window 1

Location 6,511,336 – 6,511,437
Length 101
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 68.84
Shannon entropy 0.56354
G+C content 0.35882
Mean single sequence MFE -15.32
Consensus MFE -7.66
Energy contribution -7.20
Covariance contribution -0.47
Combinations/Pair 1.50
Mean z-score -1.00
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.549501
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6511336 101 - 27905053
-------UCUUUCACCA-UUCACAUGGUAACUAAACAUUUAC-UUUUCGUUUCCUUAUAGCCAUGUGC-----UGUGCUUGCAGAUUACUCUAUUGACAUUAACUCGCCUUUUCG
-------....(((...-..((((((((((..((((......-.....))))..))...))))))))(-----(((....))))..........))).................. ( -12.70, z-score =  -0.86, R)
>droYak2.chr3R 10548834 106 - 28832112
-------UCUUUCACCA-UUCACAUGGUACCUAAACAUUUAU-UUUCCGUUUCCUUAUAGCCAUGUGCUGUUGUGUACUUGCAGAUUACUUUAUUGAUAUUGUCUCACCUUUUCG
-------.....(((.(-(.((((((((....((((......-.....)))).......))))))))..)).))).....((((((((......)))).))))............ ( -12.70, z-score =  -0.46, R)
>droEre2.scaffold_4770 2650973 106 + 17746568
-------UCUUCUACCA-CUCACAUGGCAACUAAGCGUUUAU-UUUCCGUUUCCUUAUAGCCAUGUGCUGUUGUGUACUGGCAGAUUAGUUUAUUGAUAUGGUCUCACCCUUUCG
-------......((((-..((((((((....(((((.....-....))))).......))))))))(((((.......)))))...............))))............ ( -19.40, z-score =  -0.45, R)
>droSec1.super_0 5690286 109 + 21120651
UCCUUUACCAUUCACAAUUUCACAUGGUAACUAAACAUUUAC-UUUUCGUUUCCUUAUAGCCAUGUGC-----UGUGCUUGCAGAUUACUUUAUAGACAUUAUCUCACCUUUUCG
........((..((((....((((((((((..((((......-.....))))..))...)))))))).-----))))..)).................................. ( -13.20, z-score =  -1.30, R)
>droSim1.chr3R 12665010 109 + 27517382
UCGUUCACCAUUCACAAUUUCACAUGGUAACUAAACAUUUAC-UUUUCGUUUCCUUAUAGCCAUGUGC-----UGUGCUUGCAGAUUACUUUAUUGACAUUAUCUCACCUUUUCG
....((..((..((((....((((((((((..((((......-.....))))..))...)))))))).-----))))..))..)).............................. ( -13.50, z-score =  -0.94, R)
>droGri2.scaffold_15203 448660 91 + 11997470
--------------UAUUUUUAUUGAGUUUAUGUAUAUUUACAUAUUCUUUUUAAAAUGGCUAAA---------GAGACUGGGCAUCUUUUUGAGGGUAGUAACUU-CCUGCUCA
--------------...(((((..(((..((((((....))))))..)))..)))))....((((---------((((.......)))))))).((((((......-.)))))). ( -20.40, z-score =  -2.00, R)
>consensus
_______UCUUUCACAA_UUCACAUGGUAACUAAACAUUUAC_UUUUCGUUUCCUUAUAGCCAUGUGC_____UGUGCUUGCAGAUUACUUUAUUGACAUUAUCUCACCUUUUCG
....................((((((((...............................))))))))................................................ ( -7.66 =  -7.20 +  -0.47)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,511,373 – 6,511,475
Length 102
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 82.10
Shannon entropy 0.29214
G+C content 0.35743
Mean single sequence MFE -20.04
Consensus MFE -12.20
Energy contribution -11.92
Covariance contribution -0.28
Combinations/Pair 1.17
Mean z-score -2.07
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.681420
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6511373 102 + 27905053
-----GCACAGCACAUGGCUAUAAGGAAACGAAAAGUAAAUGUUUAGUUACCAUGUGAA--------UGGUGAAAGAAACCGAAAGUAAAAUCAGAAAAAAAUAUGUUAAGGAAA-
-----.......((((((((....(....)....)))....((((..(((((((....)--------))))))...))))(....)................)))))........- ( -15.60, z-score =  -1.37, R)
>droYak2.chr3R 10548871 107 + 28832112
GUACACAACAGCACAUGGCUAUAAGGAAACGGAAAAUAAAUGUUUAGGUACCAUGUGAA--------UGGUGAAAGAAACCGAGAGUAAGAUCGCAAGAAA-UGUGUUAAGGGAAC
..(((((((..(((((((.(((....(((((.........)))))..))))))))))..--------((((.......))))...))....((....))..-)))))......... ( -23.00, z-score =  -2.71, R)
>droEre2.scaffold_4770 2651010 107 - 17746568
GUACACAACAGCACAUGGCUAUAAGGAAACGGAAAAUAAACGCUUAGUUGCCAUGUGAG--------UGGUAGAAGAAAUCGAAAGUAAAAUCGAAAAAAA-UGUGUUAAGGGAAG
..(((((.((.((((((((.....(....)........(((.....)))))))))))..--------))..........((((........))))......-)))))......... ( -24.00, z-score =  -3.26, R)
>droSec1.super_0 5690323 109 - 21120651
-----GCACAGCACAUGGCUAUAAGGAAACGAAAAGUAAAUGUUUAGUUACCAUGUGAAAUUGUGAAUGGUAAAGGAAACCGAAAGUAAAAUCGGAAAAAA-UACGUUAAGGAAG-
-----.((((.(((((((......(....)...((.(((....))).)).)))))))....))))..............((((........))))......-.............- ( -18.80, z-score =  -1.59, R)
>droSim1.chr3R 12665047 109 - 27517382
-----GCACAGCACAUGGCUAUAAGGAAACGAAAAGUAAAUGUUUAGUUACCAUGUGAAAUUGUGAAUGGUGAACGAAACCGAAAGUAAAAUCGGAAAAAA-UAUGUUAAGGAAG-
-----.((((.(((((((......(....)...((.(((....))).)).)))))))....))))..............((((........))))......-.............- ( -18.80, z-score =  -1.42, R)
>consensus
_____GCACAGCACAUGGCUAUAAGGAAACGAAAAGUAAAUGUUUAGUUACCAUGUGAA________UGGUGAAAGAAACCGAAAGUAAAAUCGGAAAAAA_UAUGUUAAGGAAA_
...........(((((((.((.....(((((.........)))))...)))))))))..........((((.......)))).................................. (-12.20 = -11.92 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,511,373 – 6,511,475
Length 102
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 82.10
Shannon entropy 0.29214
G+C content 0.35743
Mean single sequence MFE -16.60
Consensus MFE -12.92
Energy contribution -12.24
Covariance contribution -0.68
Combinations/Pair 1.26
Mean z-score -2.69
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.44
SVM RNA-class probability 0.990861
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6511373 102 - 27905053
-UUUCCUUAACAUAUUUUUUUCUGAUUUUACUUUCGGUUUCUUUCACCA--------UUCACAUGGUAACUAAACAUUUACUUUUCGUUUCCUUAUAGCCAUGUGCUGUGC-----
-....................((((........))))..........((--------(.((((((((((..((((...........))))..))...))))))))..))).----- ( -13.00, z-score =  -1.77, R)
>droYak2.chr3R 10548871 107 - 28832112
GUUCCCUUAACACA-UUUCUUGCGAUCUUACUCUCGGUUUCUUUCACCA--------UUCACAUGGUACCUAAACAUUUAUUUUCCGUUUCCUUAUAGCCAUGUGCUGUUGUGUAC
.........(((((-....................(((.......))).--------..((((((((....((((...........)))).......))))))))....))))).. ( -15.80, z-score =  -1.79, R)
>droEre2.scaffold_4770 2651010 107 + 17746568
CUUCCCUUAACACA-UUUUUUUCGAUUUUACUUUCGAUUUCUUCUACCA--------CUCACAUGGCAACUAAGCGUUUAUUUUCCGUUUCCUUAUAGCCAUGUGCUGUUGUGUAC
.........(((((-......((((........))))...........(--------(.((((((((....(((((.........))))).......))))))))..))))))).. ( -20.90, z-score =  -4.29, R)
>droSec1.super_0 5690323 109 + 21120651
-CUUCCUUAACGUA-UUUUUUCCGAUUUUACUUUCGGUUUCCUUUACCAUUCACAAUUUCACAUGGUAACUAAACAUUUACUUUUCGUUUCCUUAUAGCCAUGUGCUGUGC-----
-..........(((-......((((........)))).......)))....((((....((((((((((..((((...........))))..))...)))))))).)))).----- ( -17.32, z-score =  -3.11, R)
>droSim1.chr3R 12665047 109 + 27517382
-CUUCCUUAACAUA-UUUUUUCCGAUUUUACUUUCGGUUUCGUUCACCAUUCACAAUUUCACAUGGUAACUAAACAUUUACUUUUCGUUUCCUUAUAGCCAUGUGCUGUGC-----
-.............-......((((........))))..............((((....((((((((((..((((...........))))..))...)))))))).)))).----- ( -16.00, z-score =  -2.50, R)
>consensus
_UUUCCUUAACAUA_UUUUUUCCGAUUUUACUUUCGGUUUCUUUCACCA________UUCACAUGGUAACUAAACAUUUACUUUUCGUUUCCUUAUAGCCAUGUGCUGUGC_____
.........(((.........((((........))))......................((((((((....((((...........)))).......)))))))).)))....... (-12.92 = -12.24 +  -0.68)

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 00:03:52 2011