Locus 87

Sequence ID sy_sa.0
Location 2,287,061 – 2,287,178
Length 117
Max. P 0.999999
window431 window432 window433

overview

Window 1

Location 2,287,061 – 2,287,164
Length 103
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 58.17
Mean single sequence MFE -24.58
Consensus MFE -13.34
Energy contribution -13.34
Covariance contribution 0.00
Combinations/Pair 1.17
Mean z-score -1.64
Structure conservation index 0.54
SVM decision value 2.04
SVM RNA-class probability 0.986346
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2287061 103 + 2516575/0-120
AAAAGCACCCCUAACUU--------UAUUGUUAGAGGUGCUUUUGCACGGUUCCACUCUC-AUUUUA-----UAUAAGCAAUUGCCUAAAUCAAACUUUGUACUGAUU---GAUAUCAAG
(((((((((.(((((..--------....))))).)))))))))...((((.........-..((((-----..(((....)))..))))...........)))).((---(....))). ( -22.65)
>sy_au.0 2211593 119 - 2809422/0-120
AAAAGCACCACUAACAUACAAGUUGUAUUGUUAGAGGCGCUUCCGCACGGUUCCACUCUG-AAUUUAGCGAAUAACAUUAAUAAUAUUGCGGGCGCUUCCAAAUUAUCAAGGAAACUAAG
..((((.((.(((((((((.....))).)))))).)).))))(((((.(....).(.(((-....))).).................))))).................((....))... ( -24.50)
>sy_ha.0 2480264 106 + 2685015/0-120
AUUAGCGCCCCUAACAC-----UUAAGAUGCUAGAGGCGCUACUGCACGGUUCCACUCUGUAUUCUAG---AUAAAUGCAA----GCUAGUAUGUCUGUAUAACUAUA--GGUUACUAGA
..(((((((.(((.(((-----....).)).))).))))))).((((.(....)..((((.....)))---)....)))).----.((((((...(((((....))))--)..)))))). ( -26.60)
>consensus
AAAAGCACCCCUAACAU_____UU_UAUUGUUAGAGGCGCUUCUGCACGGUUCCACUCUG_AUUUUAG___AUAAAAGCAAU___AUUAAUAAAACUUUAUAAUUAUA__GGAUACUAAG
..(((((((.(((((..............))))).))))))).............................................................................. (-13.34 = -13.34 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,287,061 – 2,287,164
Length 103
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 58.17
Mean single sequence MFE -34.77
Consensus MFE -20.51
Energy contribution -19.74
Covariance contribution -0.77
Combinations/Pair 1.33
Mean z-score -3.84
Structure conservation index 0.59
SVM decision value 6.55
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2287061 103 + 2516575/0-120
CUUGAUAUC---AAUCAGUACAAAGUUUGAUUUAGGCAAUUGCUUAUA-----UAAAAU-GAGAGUGGAACCGUGCAAAAGCACCUCUAACAAUA--------AAGUUAGGGGUGCUUUU
..((((...---.))))((((...((((....(((((....)))))..-----..))))-......(....)))))(((((((((((((((....--------..))))))))))))))) ( -32.20)
>sy_au.0 2211593 119 - 2809422/0-120
CUUAGUUUCCUUGAUAAUUUGGAAGCGCCCGCAAUAUUAUUAAUGUUAUUCGCUAAAUU-CAGAGUGGAACCGUGCGGAAGCGCCUCUAACAAUACAACUUGUAUGUUAGUGGUGCUUUU
....((((((..........))))))..(((((((((.....))))).((((((.....-...)))))).....))))(((((((.((((((.(((.....))))))))).))))))).. ( -38.20)
>sy_ha.0 2480264 106 + 2685015/0-120
UCUAGUAACC--UAUAGUUAUACAGACAUACUAGC----UUGCAUUUAU---CUAGAAUACAGAGUGGAACCGUGCAGUAGCGCCUCUAGCAUCUUAA-----GUGUUAGGGGCGCUAAU
.((((((..(--(.((....)).))...)))))).----((((((...(---(((..........))))...))))))(((((((((((((((.....-----))))))))))))))).. ( -33.90)
>consensus
CUUAGUAUCC__AAUAAUUACAAAGACACACUAAC___AUUGCUUUUAU___CUAAAAU_CAGAGUGGAACCGUGCAGAAGCGCCUCUAACAAUA_AA_____AUGUUAGGGGUGCUUUU
..............................................................(..((....))..)(((((((((((((((..............))))))))))))))) (-20.51 = -19.74 +  -0.77) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,287,061 – 2,287,178
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 63.97
Mean single sequence MFE -21.63
Consensus MFE -18.83
Energy contribution -16.41
Covariance contribution -2.43
Combinations/Pair 1.58
Mean z-score -0.12
Structure conservation index 0.87
SVM decision value 0.61
SVM RNA-class probability 0.798280
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2287061 117 + 2516575/160-280
AACCUAUGAUUAACAUUGAAAUCAACAAAGGAUUAGUAUGUGA---UGGACGGUGUCAAGAGAGUGUGCGGUAGCUGUGAGCACAUCACUUAAAUUACAGAAUGCACCUUUGUGCAAAUA
......(((((........)))))(((((((.......(((((---(....((((........((((((...........))))))))))...)))))).......)))))))....... ( -24.24)
>sy_au.0 2211593 116 - 2809422/160-280
-AUGAAUAAAGUAUUUUAUAUAAAACGAAGGAUUAGUAAUUAAAUUUAUACGAUGC--AGAGAGUGUACGGUUGCUGUGAGUACAACGUAGAAAUUAAUGAAUGCACCUUCGUA-AAAUG
-.......................(((((((....((((......))))....(((--(...(((.((((..(((.....)))...))))...)))......))))))))))).-..... ( -18.00)
>sy_ha.0 2480264 116 + 2685015/160-280
AUUUUGGUAUGAGUAUUUAAA--GGCGAAGGAUUAGUAAAUAUUGGACUAUGAUAUC-AGAGAGUGUACGGAUGCUGUGAGUACGCCAUAGACGAUAUUGAAUGCACCUUUGUA-UAAUC
.....................--.(((((((.......(((((((..(((((.....-.....((((((...........))))))))))).))))))).......))))))).-..... ( -22.64)
>consensus
AAUCUAUAAUGAAUAUUAAAA__AACGAAGGAUUAGUAAAUAA___UAUACGAUGUC_AGAGAGUGUACGGUUGCUGUGAGUACAACAUAGAAAUUAAUGAAUGCACCUUUGUA_AAAUA
........................(((((((.......(((((...((((((...........((((((...........))))))))))))..))))).......)))))))....... (-18.83 = -16.41 +  -2.43) 
# Strand winner: reverse (0.98)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:56:35 2006