Locus 4953

Sequence ID dm3.chr2R
Location 16,653,028 – 16,653,105
Length 77
Max. P 0.983040
window6809 window6810

overview

Window 9

Location 16,653,028 – 16,653,105
Length 77
Sequences 10
Columns 83
Reading direction forward
Mean pairwise identity 75.18
Shannon entropy 0.50527
G+C content 0.51710
Mean single sequence MFE -27.34
Consensus MFE -16.02
Energy contribution -15.88
Covariance contribution -0.14
Combinations/Pair 1.33
Mean z-score -1.98
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.12
SVM RNA-class probability 0.983040
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16653028 77 + 21146708
-----GCUGCAAGUGCUCAGAAUGUGGCUAGACAACAUAAAUCUGGCCAAUUGCAGCUGGGGCAACAGCUGCAAUUGCUGCU-
-----((.((((............((((((((.........)))))))).(((((((((......))))))))))))).)).- ( -32.80, z-score =  -2.70, R)
>droPer1.super_4 4783279 73 - 7162766
-----GACUUUCUACGUCAGAAUGCGGCUAGACGGCAUAAAUCUGGCCAGUUGCAG---GGGUAACAGCUGCAACCGCAGU--
-----(((.......)))....((((((((((.........))))))).(((((((---.(....)..))))))).)))..-- ( -25.10, z-score =  -1.85, R)
>dp4.chr3 11283395 73 - 19779522
-----GACUUUCUACGUCAGAAUGCGGCUAGACGGCAUAAAUCUGGCCAGUUGCAG---GGGUAACAGCUGCAACCGCAGU--
-----(((.......)))....((((((((((.........))))))).(((((((---.(....)..))))))).)))..-- ( -25.10, z-score =  -1.85, R)
>droAna3.scaffold_13266 15954161 75 - 19884421
GCUGGAGCGUAAUACCUCAGAGUGCGGCUAGACAGCAUAAAUCUGGCCAAUUGCUGGGUGUGCAGGGGCACUGCU--------
((....))...(((((.((((((..(((((((.........))))))).))).))))))))((((.....)))).-------- ( -26.10, z-score =  -0.29, R)
>droEre2.scaffold_4845 10797644 74 + 22589142
-----GCUGCAAGUGCUCAGAAUGCGGCUAGACAACAUAAAUCUGGCCAAUUGCAG---GGCCAACAGCUGCAACUGCAGCU-
-----.((((((..((.......))(((((((.........)))))))..))))))---.......((((((....))))))- ( -28.40, z-score =  -1.92, R)
>droYak2.chr2R 8595039 74 - 21139217
-----GCUGCAAGUGCUCAGAAUGCGGCUAGACAACAUAAAUCUGGCCAAUUGCAG---GGGUAACAGCUGCAAUUGCAGCU-
-----(((((....((.......))(((((((.........)))))))((((((((---.(....)..))))))))))))).- ( -29.20, z-score =  -2.60, R)
>droSec1.super_1 14200811 76 + 14215200
-----GCUGCAAGUGCUCAGAAUGCGGCUAGACAACAUAAAUCUGGCCAAUUGCAG-UGGGGCAACAGCUGCAAUUGCUGCU-
-----((.((....((.......))(((((((.........)))))))((((((((-(..(....).))))))))))).)).- ( -29.20, z-score =  -1.75, R)
>droSim1.chr2R 15308871 76 + 19596830
-----GCUGCAAGUGCUCAGAAUGCGGCUAGACAACAUAAAUCUGGCCAAUUGCAG-UGGGGCAACAGCUGCAAUUGCUGCU-
-----((.((....((.......))(((((((.........)))))))((((((((-(..(....).))))))))))).)).- ( -29.20, z-score =  -1.75, R)
>droVir3.scaffold_12823 405466 71 - 2474545
--------GCACA-GCUCGAAUUGCGGCUAGACAACAUAAAUCUGGCCAAUUGCAG---UGGCAACAGCUGCAACCAGCGACU
--------.....-.......(((((((((((.........)))))))..((((((---((....)).))))))...)))).. ( -24.40, z-score =  -2.48, R)
>droGri2.scaffold_15245 16014207 65 + 18325388
-----GCUGCAAUGCUUUAAAAUGCGGCUAGACAACAUAAAUCUGGCCAAUUGCAG---UGGCAACAGCUGCA----------
-----((((((((((........))(((((((.........))))))).)))))))---).(((.....))).---------- ( -23.90, z-score =  -2.60, R)
>consensus
_____GCUGCAAGUGCUCAGAAUGCGGCUAGACAACAUAAAUCUGGCCAAUUGCAG___GGGCAACAGCUGCAAUUGCAGCU_
.........................(((((((.........))))))).(((((((....(....)..)))))))........ (-16.02 = -15.88 +  -0.14)

alignment

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secondary structure

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dotplot

Postscript

Window 0

Location 16,653,028 – 16,653,105
Length 77
Sequences 10
Columns 83
Reading direction reverse
Mean pairwise identity 75.18
Shannon entropy 0.50527
G+C content 0.51710
Mean single sequence MFE -23.60
Consensus MFE -14.00
Energy contribution -14.13
Covariance contribution 0.13
Combinations/Pair 1.27
Mean z-score -1.05
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.662260
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16653028 77 - 21146708
-AGCAGCAAUUGCAGCUGUUGCCCCAGCUGCAAUUGGCCAGAUUUAUGUUGUCUAGCCACAUUCUGAGCACUUGCAGC-----
-.((((((((((((((((......))))))))))))((((((...((((.(.....).)))))))).))..))))...----- ( -30.80, z-score =  -2.75, R)
>droPer1.super_4 4783279 73 + 7162766
--ACUGCGGUUGCAGCUGUUACCC---CUGCAACUGGCCAGAUUUAUGCCGUCUAGCCGCAUUCUGACGUAGAAAGUC-----
--.((((((((((((.........---))))))).(((.((((.......)))).))).........)))))......----- ( -22.50, z-score =  -1.59, R)
>dp4.chr3 11283395 73 + 19779522
--ACUGCGGUUGCAGCUGUUACCC---CUGCAACUGGCCAGAUUUAUGCCGUCUAGCCGCAUUCUGACGUAGAAAGUC-----
--.((((((((((((.........---))))))).(((.((((.......)))).))).........)))))......----- ( -22.50, z-score =  -1.59, R)
>droAna3.scaffold_13266 15954161 75 + 19884421
--------AGCAGUGCCCCUGCACACCCAGCAAUUGGCCAGAUUUAUGCUGUCUAGCCGCACUCUGAGGUAUUACGCUCCAGC
--------(((.((((....))))((((((....((((.((((.......)))).))))....))).))).....)))..... ( -21.80, z-score =  -0.75, R)
>droEre2.scaffold_4845 10797644 74 - 22589142
-AGCUGCAGUUGCAGCUGUUGGCC---CUGCAAUUGGCCAGAUUUAUGUUGUCUAGCCGCAUUCUGAGCACUUGCAGC-----
-((((((....)))))).......---((((((..(((.((((.......)))).)))((.......))..)))))).----- ( -25.50, z-score =  -0.38, R)
>droYak2.chr2R 8595039 74 + 21139217
-AGCUGCAAUUGCAGCUGUUACCC---CUGCAAUUGGCCAGAUUUAUGUUGUCUAGCCGCAUUCUGAGCACUUGCAGC-----
-((((((....)))))).......---((((((..(((.((((.......)))).)))((.......))..)))))).----- ( -25.50, z-score =  -1.91, R)
>droSec1.super_1 14200811 76 - 14215200
-AGCAGCAAUUGCAGCUGUUGCCCCA-CUGCAAUUGGCCAGAUUUAUGUUGUCUAGCCGCAUUCUGAGCACUUGCAGC-----
-.(((((((((((((.((......))-)))))))))((((((...((((.(.....).)))))))).))..))))...----- ( -24.00, z-score =  -0.66, R)
>droSim1.chr2R 15308871 76 - 19596830
-AGCAGCAAUUGCAGCUGUUGCCCCA-CUGCAAUUGGCCAGAUUUAUGUUGUCUAGCCGCAUUCUGAGCACUUGCAGC-----
-.(((((((((((((.((......))-)))))))))((((((...((((.(.....).)))))))).))..))))...----- ( -24.00, z-score =  -0.66, R)
>droVir3.scaffold_12823 405466 71 + 2474545
AGUCGCUGGUUGCAGCUGUUGCCA---CUGCAAUUGGCCAGAUUUAUGUUGUCUAGCCGCAAUUCGAGC-UGUGC--------
....((..(((((((.((....))---)))))))..))(((.(((..(((((......)))))..))))-))...-------- ( -21.30, z-score =  -0.01, R)
>droGri2.scaffold_15245 16014207 65 - 18325388
----------UGCAGCUGUUGCCA---CUGCAAUUGGCCAGAUUUAUGUUGUCUAGCCGCAUUUUAAAGCAUUGCAGC-----
----------....((....))..---(((((((.(((.((((.......)))).)))((........))))))))).----- ( -18.10, z-score =  -0.26, R)
>consensus
_AGCUGCAAUUGCAGCUGUUGCCC___CUGCAAUUGGCCAGAUUUAUGUUGUCUAGCCGCAUUCUGAGCACUUGCAGC_____
.......((((((((............))))))))(((.((((.......)))).)))......................... (-14.00 = -14.13 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:39:10 2011