Locus 119

Sequence ID sy_ha.0
Location 2,623,378 – 2,623,470
Length 92
Max. P 0.999910
window756 window757 window758 window759

overview

Window 6

Location 2,623,378 – 2,623,470
Length 92
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 64.23
Mean single sequence MFE -30.38
Consensus MFE -21.70
Energy contribution -21.95
Covariance contribution 0.25
Combinations/Pair 1.26
Mean z-score -4.14
Structure conservation index 0.71
SVM decision value 4.50
SVM RNA-class probability 0.999910
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2623378 92 + 2685015
AGUGUUAUAAUUUAGACAACAAGAGCUUCGUGCAU-UAUAUGCACCAA-UCCCCUCACUACUCGCAAUAGUGAGGGGAUUUUUA--GGUGCUGGCU
..((((........))))......((.....))..-.....(((((((-(((((((((((.......)))))))))))))....--)))))..... ( -31.50)
>sy_au.0 902285 93 - 2809422
AGCAGUAUAAUUAAGACAACGAAAA-UAAGUAUUUACUUAUACACCAA-UCCCCUCACUAUUUGCGGUAGUGAGGGGAUUUUUAUUGGUGC-GGCU
(((.((((...(((((........(-(((((....))))))......(-((((((((((((.....))))))))))))))))))...))))-.))) ( -32.50)
>sy_sa.0 1702732 91 + 2516575
AGUGUUAUAAUGCAAUCAACAAAGA-UUAUCAGGCAUGUAUGCACCAAAUCCCCUUACUA-UGGCCGUAGUAAGGGGAUUUUUU--GGUGU-GACU
...(((...((((((((......))-)).....))))....(((((((((((((((((((-(....)))))))))))))...))--)))))-))). ( -33.20)
>sp_pn.0 72987 88 - 2038615
UAUGCUAAAAUGUAGUUAAUUGAUA----AGGUUCAUUAGAACACCAAAGCCCCUAACUA-UGGCCGUAGUUAAGGGCUUUUUU--GACGU-AUCU
..(((......)))(((((......----..((((....))))...(((((((.((((((-(....))))))).))))))).))--)))..-.... ( -24.30)
>consensus
AGUGUUAUAAUGUAGACAACAAAAA_UUAGUAUUCAUUUAUACACCAA_UCCCCUCACUA_UGGCCGUAGUGAGGGGAUUUUUA__GGUGC_GGCU
.........................................(((((((((((((((((((.......)))))))))))))).....)))))..... (-21.70 = -21.95 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,623,378 – 2,623,470
Length 92
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 64.23
Mean single sequence MFE -29.98
Consensus MFE -24.34
Energy contribution -23.28
Covariance contribution -1.06
Combinations/Pair 1.42
Mean z-score -4.75
Structure conservation index 0.81
SVM decision value 3.48
SVM RNA-class probability 0.999278
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2623378 92 + 2685015
AGCCAGCACC--UAAAAAUCCCCUCACUAUUGCGAGUAGUGAGGGGA-UUGGUGCAUAUA-AUGCACGAAGCUCUUGUUGUCUAAAUUAUAACACU
.....(((((--....((((((((((((((.....))))))))))))-))))))).((((-((......(((....)))......))))))..... ( -35.60)
>sy_au.0 902285 93 - 2809422
AGCC-GCACCAAUAAAAAUCCCCUCACUACCGCAAAUAGUGAGGGGA-UUGGUGUAUAAGUAAAUACUUA-UUUUCGUUGUCUUAAUUAUACUGCU
(((.-((((((......((((((((((((.......)))))))))))-)))))))((((((....)))))-).....................))) ( -30.60)
>sy_sa.0 1702732 91 + 2516575
AGUC-ACACC--AAAAAAUCCCCUUACUACGGCCA-UAGUAAGGGGAUUUGGUGCAUACAUGCCUGAUAA-UCUUUGUUGAUUGCAUUAUAACACU
.((.-.((((--((...((((((((((((......-))))))))))))))))))...)).....((.(((-((......))))))).......... ( -28.50)
>sp_pn.0 72987 88 - 2038615
AGAU-ACGUC--AAAAAAGCCCUUAACUACGGCCA-UAGUUAGGGGCUUUGGUGUUCUAAUGAACCU----UAUCAAUUAACUACAUUUUAGCAUA
.(((-(....--...((((((((((((((......-))))))))))))))((.((((....))))))----))))..................... ( -25.20)
>consensus
AGCC_ACACC__AAAAAAUCCCCUCACUACGGCCA_UAGUGAGGGGA_UUGGUGCAUAAAUAAACACUAA_UUUUUGUUGACUAAAUUAUAACACU
.....(((((.....((((((((((((((.......)))))))))))))))))))......................................... (-24.34 = -23.28 +  -1.06) 
# Strand winner: reverse (0.89)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,623,378 – 2,623,470
Length 92
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 64.23
Mean single sequence MFE -30.38
Consensus MFE -21.70
Energy contribution -21.95
Covariance contribution 0.25
Combinations/Pair 1.26
Mean z-score -4.14
Structure conservation index 0.71
SVM decision value 4.50
SVM RNA-class probability 0.999910
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2623378 92 + 2685015/0-96
AGUGUUAUAAUUUAGACAACAAGAGCUUCGUGCAU-UAUAUGCACCAA-UCCCCUCACUACUCGCAAUAGUGAGGGGAUUUUUA--GGUGCUGGCU
..((((........))))......((.....))..-.....(((((((-(((((((((((.......)))))))))))))....--)))))..... ( -31.50)
>sy_au.0 902285 93 - 2809422/0-96
AGCAGUAUAAUUAAGACAACGAAAA-UAAGUAUUUACUUAUACACCAA-UCCCCUCACUAUUUGCGGUAGUGAGGGGAUUUUUAUUGGUGC-GGCU
(((.((((...(((((........(-(((((....))))))......(-((((((((((((.....))))))))))))))))))...))))-.))) ( -32.50)
>sy_sa.0 1702732 91 + 2516575/0-96
AGUGUUAUAAUGCAAUCAACAAAGA-UUAUCAGGCAUGUAUGCACCAAAUCCCCUUACUA-UGGCCGUAGUAAGGGGAUUUUUU--GGUGU-GACU
...(((...((((((((......))-)).....))))....(((((((((((((((((((-(....)))))))))))))...))--)))))-))). ( -33.20)
>sp_pn.0 72987 88 - 2038615/0-96
UAUGCUAAAAUGUAGUUAAUUGAUA----AGGUUCAUUAGAACACCAAAGCCCCUAACUA-UGGCCGUAGUUAAGGGCUUUUUU--GACGU-AUCU
..(((......)))(((((......----..((((....))))...(((((((.((((((-(....))))))).))))))).))--)))..-.... ( -24.30)
>consensus
AGUGUUAUAAUGUAGACAACAAAAA_UUAGUAUUCAUUUAUACACCAA_UCCCCUCACUA_UGGCCGUAGUGAGGGGAUUUUUA__GGUGC_GGCU
.........................................(((((((((((((((((((.......)))))))))))))).....)))))..... (-21.70 = -21.95 +   0.25)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 9

Location 2,623,378 – 2,623,470
Length 92
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 64.23
Mean single sequence MFE -29.98
Consensus MFE -24.34
Energy contribution -23.28
Covariance contribution -1.06
Combinations/Pair 1.42
Mean z-score -4.75
Structure conservation index 0.81
SVM decision value 3.48
SVM RNA-class probability 0.999278
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2623378 92 + 2685015/0-96
AGCCAGCACC--UAAAAAUCCCCUCACUAUUGCGAGUAGUGAGGGGA-UUGGUGCAUAUA-AUGCACGAAGCUCUUGUUGUCUAAAUUAUAACACU
.....(((((--....((((((((((((((.....))))))))))))-))))))).((((-((......(((....)))......))))))..... ( -35.60)
>sy_au.0 902285 93 - 2809422/0-96
AGCC-GCACCAAUAAAAAUCCCCUCACUACCGCAAAUAGUGAGGGGA-UUGGUGUAUAAGUAAAUACUUA-UUUUCGUUGUCUUAAUUAUACUGCU
(((.-((((((......((((((((((((.......)))))))))))-)))))))((((((....)))))-).....................))) ( -30.60)
>sy_sa.0 1702732 91 + 2516575/0-96
AGUC-ACACC--AAAAAAUCCCCUUACUACGGCCA-UAGUAAGGGGAUUUGGUGCAUACAUGCCUGAUAA-UCUUUGUUGAUUGCAUUAUAACACU
.((.-.((((--((...((((((((((((......-))))))))))))))))))...)).....((.(((-((......))))))).......... ( -28.50)
>sp_pn.0 72987 88 - 2038615/0-96
AGAU-ACGUC--AAAAAAGCCCUUAACUACGGCCA-UAGUUAGGGGCUUUGGUGUUCUAAUGAACCU----UAUCAAUUAACUACAUUUUAGCAUA
.(((-(....--...((((((((((((((......-))))))))))))))((.((((....))))))----))))..................... ( -25.20)
>consensus
AGCC_ACACC__AAAAAAUCCCCUCACUACGGCCA_UAGUGAGGGGA_UUGGUGCAUAAAUAAACACUAA_UUUUUGUUGACUAAAUUAUAACACU
.....(((((.....((((((((((((((.......)))))))))))))))))))......................................... (-24.34 = -23.28 +  -1.06) 
# Strand winner: reverse (0.89)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:01:13 2006