Locus 9550

Sequence ID dm3.chr3R
Location 7,333,591 – 7,333,752
Length 161
Max. P 0.708906
window13102 window13103 window13104

overview

Window 2

Location 7,333,591 – 7,333,693
Length 102
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 65.31
Shannon entropy 0.63130
G+C content 0.40176
Mean single sequence MFE -25.00
Consensus MFE -9.46
Energy contribution -12.30
Covariance contribution 2.84
Combinations/Pair 1.33
Mean z-score -1.27
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.515314
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7333591 102 + 27905053
----UUGAUCAAU----CAUGAUUAAUUUCCGCUUCCGAGGCUGUA-AAU--AAUAUAUACUCUUCGAAAGGCGGAAAGCAGU-AAGCCACCUUAUGUGGCGAUGUAGCAGGUU
----(((((((..----..)))))))(((((((((.(((((..(((-...--......))).)))))..)))))))))((..(-(.(((((.....)))))..))..))..... ( -30.60, z-score =  -2.60, R)
>droSim1.chr3R 13455828 102 - 27517382
----UUGAUCAAU----CAUGAUUAAUUUCCGUUUCCGAGGCAGUA-AAU--AAUAUAUUUCCCUCGAAAGGCGGAAAGCAGU-AAGCCGCCUUAUGUGGCGAGGUAGCAGGUA
----(((((((..----..)))))))(((((((((.(((((.((((-...--....))))..)))))..)))))))))((..(-..(((((.....)))))...)..))..... ( -29.50, z-score =  -2.15, R)
>droSec1.super_0 6489857 102 - 21120651
----UUGAUCAAU----CAUGAUUAAUUUCCGUUUCCGAGGCAGUA-AAU--AAUAUAUUUCCCUCGAAAGGCGGAAAGCAGU-AAGCCGCCUUAUGUGGCGAGGUAGCAGGUA
----(((((((..----..)))))))(((((((((.(((((.((((-...--....))))..)))))..)))))))))((..(-..(((((.....)))))...)..))..... ( -29.50, z-score =  -2.15, R)
>droYak2.chr3R 11368891 80 + 28832112
----UUGAUCAAU----CAUGAUUAAUUUCAGCUCCCGAGGCUGAA-CAU--AAUACAUAUCCCUCGAAAUGCGAAGAGAGGU-AGCAGGUA----------------------
----(((((((..----..))))))).(((((((.....)))))))-...--..(((.((((.(((..........))).)))-)....)))---------------------- ( -17.00, z-score =  -0.73, R)
>droEre2.scaffold_4770 3459967 103 - 17746568
----UGGAUCAAU----CAUAAUUAAUUUCAGUUCUCGAGGCUAAGUAAU--AAUAUAUAUCCCUCGAAGUGCCGAAAACAGU-AAGCCGCCUUAUGUGGCGAGGUAGCAGGUA
----...(((...----.........((((.((.(((((((.((.(((..--..))).))..))))).)).)).))))...((-.(.(((((......)))).).).)).))). ( -20.70, z-score =   0.10, R)
>droAna3.scaffold_13340 13772769 114 + 23697760
UAAAUUAAUCAAAAACAUACAUUUUAUUUAGCUUAUUGUUAUUUAUUGAUUUAAUUAGUGGGAUUGGAAUACCCAAAAGCGGCCAACUGGCUUUGUUAUGCCUGCUAGCAGGUA
.............((((.............((((.......(((((((((...))))))))).((((.....))))))))((((....)))).)))).((((((....)))))) ( -22.70, z-score =  -0.11, R)
>consensus
____UUGAUCAAU____CAUGAUUAAUUUCCGUUUCCGAGGCUGAA_AAU__AAUAUAUAUCCCUCGAAAGGCGGAAAGCAGU_AAGCCGCCUUAUGUGGCGAGGUAGCAGGUA
....(((((((........)))))))((((((((..(((((.....................)))))...))))))))..........((((......))))............ ( -9.46 = -12.30 +   2.84)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,333,591 – 7,333,693
Length 102
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 65.31
Shannon entropy 0.63130
G+C content 0.40176
Mean single sequence MFE -21.94
Consensus MFE -9.81
Energy contribution -11.28
Covariance contribution 1.48
Combinations/Pair 1.41
Mean z-score -1.08
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.43
SVM RNA-class probability 0.692286
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7333591 102 - 27905053
AACCUGCUACAUCGCCACAUAAGGUGGCUU-ACUGCUUUCCGCCUUUCGAAGAGUAUAUAUU--AUU-UACAGCCUCGGAAGCGGAAAUUAAUCAUG----AUUGAUCAA----
.....((......(((((.....)))))..-...))(((((((.((((((.(.(((......--...-)))..).)))))))))))))...((((..----..))))...---- ( -25.30, z-score =  -1.84, R)
>droSim1.chr3R 13455828 102 + 27517382
UACCUGCUACCUCGCCACAUAAGGCGGCUU-ACUGCUUUCCGCCUUUCGAGGGAAAUAUAUU--AUU-UACUGCCUCGGAAACGGAAAUUAAUCAUG----AUUGAUCAA----
.....((....(((((......)))))...-...))((((((..((((((((.(((((...)--)))-)....)))))))).))))))...((((..----..))))...---- ( -25.40, z-score =  -2.09, R)
>droSec1.super_0 6489857 102 + 21120651
UACCUGCUACCUCGCCACAUAAGGCGGCUU-ACUGCUUUCCGCCUUUCGAGGGAAAUAUAUU--AUU-UACUGCCUCGGAAACGGAAAUUAAUCAUG----AUUGAUCAA----
.....((....(((((......)))))...-...))((((((..((((((((.(((((...)--)))-)....)))))))).))))))...((((..----..))))...---- ( -25.40, z-score =  -2.09, R)
>droYak2.chr3R 11368891 80 - 28832112
----------------------UACCUGCU-ACCUCUCUUCGCAUUUCGAGGGAUAUGUAUU--AUG-UUCAGCCUCGGGAGCUGAAAUUAAUCAUG----AUUGAUCAA----
----------------------........-...((.(((((.....)))))))((((.(((--(..-(((((((....).))))))..))))))))----.........---- ( -15.60, z-score =   0.21, R)
>droEre2.scaffold_4770 3459967 103 + 17746568
UACCUGCUACCUCGCCACAUAAGGCGGCUU-ACUGUUUUCGGCACUUCGAGGGAUAUAUAUU--AUUACUUAGCCUCGAGAACUGAAAUUAAUUAUG----AUUGAUCCA----
...........(((((......)))))...-.....((((((...(((((((..((..((..--..))..)).)))))))..)))))).........----.........---- ( -20.10, z-score =  -0.46, R)
>droAna3.scaffold_13340 13772769 114 - 23697760
UACCUGCUAGCAGGCAUAACAAAGCCAGUUGGCCGCUUUUGGGUAUUCCAAUCCCACUAAUUAAAUCAAUAAAUAACAAUAAGCUAAAUAAAAUGUAUGUUUUUGAUUAAUUUA
((((((..(((.(((.((((.......))))))))))..))))))..................((((((.((((((((...............))).)))))))))))...... ( -19.86, z-score =  -0.20, R)
>consensus
UACCUGCUACCUCGCCACAUAAGGCGGCUU_ACUGCUUUCCGCCUUUCGAGGGAUAUAUAUU__AUU_UACAGCCUCGGAAACGGAAAUUAAUCAUG____AUUGAUCAA____
............((((......))))..........((((((...(((((((.....................)))))))..)))))).......................... ( -9.81 = -11.28 +   1.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,333,693 – 7,333,752
Length 59
Sequences 5
Columns 61
Reading direction forward
Mean pairwise identity 87.77
Shannon entropy 0.21522
G+C content 0.49825
Mean single sequence MFE -12.90
Consensus MFE -11.92
Energy contribution -11.52
Covariance contribution -0.40
Combinations/Pair 1.13
Mean z-score -1.12
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.708906
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 7333693 59 + 27905053
GUAAAAAGUGCGUAUACGCCCUGUGUUCGCCUUGUCUGCCGUGGUGUUGGUAUUCUUUC--
.....(((.(((.((((.....)))).))))))(..(((((......)))))..)....-- ( -12.10, z-score =  -1.38, R)
>droEre2.scaffold_4770 3460070 56 - 17746568
-GGAAAAGUGCGUAUACGCCCUGUGUUCGUCUUUUCUGCCGUGGUGUUGGUAUUGGU----
-(((((((.(((.((((.....)))).))))))))))((((......))))......---- ( -14.40, z-score =  -1.40, R)
>droYak2.chr3R 11368971 60 + 28832112
-GGGAAAGUGCGUAUACGCCCUGUGUUCGCCUUGUCUGCCGUGGUGUUGGUAUUAGUAUUG
-.((((((.(((.((((.....)))).)))))).)))((((......)))).......... ( -12.80, z-score =   0.32, R)
>droSec1.super_0 6489959 59 - 21120651
GUAAAAAGUGCGUAUACGCCCUGUGUUCGCCUUGUCUGCCAUGGUGUUGGUAUUCCUUC--
.....(((.(((.((((.....)))).))))))...(((((......))))).......-- ( -12.60, z-score =  -1.57, R)
>droSim1.chr3R 13455930 59 - 27517382
GUAAAAAGUGCGUAUACGCCCUGUGUUCGCCUUGUCUGCCAUGGUGUUGGUAUUCCUUC--
.....(((.(((.((((.....)))).))))))...(((((......))))).......-- ( -12.60, z-score =  -1.57, R)
>consensus
GUAAAAAGUGCGUAUACGCCCUGUGUUCGCCUUGUCUGCCGUGGUGUUGGUAUUCCUUC__
.....(((.(((.((((.....)))).))))))...(((((......)))))......... (-11.92 = -11.52 +  -0.40)

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 00:06:36 2011