Locus 63

Sequence ID sy_sa.0
Location 1,780,633 – 1,780,752
Length 119
Max. P 0.998953
window282 window283 window284 window285

overview

Window 2

Location 1,780,633 – 1,780,752
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.53
Mean single sequence MFE -26.00
Consensus MFE -22.39
Energy contribution -22.17
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -0.94
Structure conservation index 0.86
SVM decision value 0.44
SVM RNA-class probability 0.736742
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1780633 119 + 2516575/40-160
AAAUAAAUCAUUCGCACUAGGGGUGUUUUGUGACUGAGAUGAGGUAUACCCUCAAACCCUUUGAACCUGAUCUAGAUUAAACUAGCGUAGGAAAGUGUAUUGCGA-UAUCACUGAGUAAC
...........((((((.(((((((((....))).....(((((.....))))).)))))).)..((((..((((......))))..)))).........)))))-.............. ( -27.40)
>sy_au.0 1711988 111 - 2809422/40-160
AAAUAAAUCGCACACACUAGGGGUGUUUUAU-ACUGAGAUGAGGCUUGCCCUCAAACCCUUUGAACCUGAUCUAGCUUGAACUAGCGUAGGAAAGUG--UUACUA-UACAUAUG-----U
.........((((...(.(((((((((((..-...)))))((((.....))))..)))))).)..((((..((((......))))..))))...)))--).....-........-----. ( -23.90)
>sy_ha.0 1925530 114 + 2685015/40-160
AAAUAUA--AAAUGCACUAGGGGUGUGU-AU-ACUGAGAUGAGGUUUAACCUCGAACCCUUUGAACCUGAACUAGUUAAAACUAGCGUAGGAAAGUG--UUGCUAAUAUAAAUAAUUGUG
..((((.--....(((((((((((((..-..-)).....(((((.....))))).))))))....((((..(((((....)))))..))))..))))--).....))))........... ( -26.70)
>consensus
AAAUAAAUCAAACGCACUAGGGGUGUUUUAU_ACUGAGAUGAGGUUUACCCUCAAACCCUUUGAACCUGAUCUAGAUUAAACUAGCGUAGGAAAGUG__UUGCUA_UAUAAAUGA_U__C
..............((((((((((((......)).....(((((.....))))).))))))....((((..((((......))))..))))..))))....................... (-22.39 = -22.17 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,780,633 – 1,780,752
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.53
Mean single sequence MFE -23.63
Consensus MFE -18.50
Energy contribution -18.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.14
Structure conservation index 0.78
SVM decision value -0.00
SVM RNA-class probability 0.533027
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1780633 119 + 2516575/40-160
GUUACUCAGUGAUA-UCGCAAUACACUUUCCUACGCUAGUUUAAUCUAGAUCAGGUUCAAAGGGUUUGAGGGUAUACCUCAUCUCAGUCACAAAACACCCCUAGUGCGAAUGAUUUAUUU
(((((...))))).-(((((.........(((...((((......))))...))).....((((..(((((.....))))).....((......))..))))..)))))........... ( -24.70)
>sy_au.0 1711988 111 - 2809422/40-160
A-----CAUAUGUA-UAGUAA--CACUUUCCUACGCUAGUUCAAGCUAGAUCAGGUUCAAAGGGUUUGAGGGCAAGCCUCAUCUCAGU-AUAAAACACCCCUAGUGUGUGCGAUUUAUUU
.-----........-..((((--((((..(((...(((((....)))))...))).....((((..(((((.....))))).....((-.....))..))))))))).)))......... ( -24.30)
>sy_ha.0 1925530 114 + 2685015/40-160
CACAAUUAUUUAUAUUAGCAA--CACUUUCCUACGCUAGUUUUAACUAGUUCAGGUUCAAAGGGUUCGAGGUUAAACCUCAUCUCAGU-AU-ACACACCCCUAGUGCAUUU--UAUAUUU
.................(((.--......(((..((((((....))))))..))).....((((...((((.....))))......((-..-..))..))))..)))....--....... ( -21.90)
>consensus
A__A_UCAUUUAUA_UAGCAA__CACUUUCCUACGCUAGUUUAAACUAGAUCAGGUUCAAAGGGUUUGAGGGUAAACCUCAUCUCAGU_AUAAAACACCCCUAGUGCGUAUGAUUUAUUU
.......................((((..(((...((((......))))...))).....((((...((((.....))))......((......))..)))))))).............. (-18.50 = -18.50 +   0.00) 
# Strand winner: forward (1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,780,633 – 1,780,745
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 66.67
Mean single sequence MFE -28.83
Consensus MFE -14.63
Energy contribution -14.63
Covariance contribution 0.01
Combinations/Pair 1.13
Mean z-score -2.58
Structure conservation index 0.51
SVM decision value 3.30
SVM RNA-class probability 0.998953
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1780633 112 + 2516575/118-238
AAACUAGCGUAGGAAAGUGUAUUGCGA-UAUCACUGAGUAACUUUGGUAUCCGUAUGCCUAUAUAAAAA----CGCGCAACUUUC---UAGAAGGUUGUGCGUUUUUUAUAUUAGGAGGA
..(((((.((.....(((((((....)-)).)))).....)).))))).(((.....((((((((((((----(((((((((((.---...))))))))))).)))))))).)))).))) ( -34.30)
>sy_au.0 1711988 101 - 2809422/118-238
GAACUAGCGUAGGAAAGUG--UUACUA-UACAUAUG-----UUUUACUA-----AUAUAUAU-UGUGAA----CGCAUAACUUUCCUAUGGAUGGUUGUGCGUUUUUU-UAUUAGGAGGA
...((((.((((((..(((--(.....-.))))...-----))))))..-----........-...(((----(((((((((.(((...))).))))))))))))...-..))))..... ( -25.40)
>sy_ha.0 1925530 112 + 2685015/118-238
AAACUAGCGUAGGAAAGUG--UUGCUAAUAUAAAUAAUUGUGGUAAAUACAUAUAGCAUUUUAUUUAAAUUCACGCACAACUUUC-UACGGAUGGUUGUGCGUUUUUU-----AGGAGGA
....(((((..........--.)))))...(((((((.(((.(((......))).)))..))))))).....((((((((((.((-....)).)))))))))).....-----....... ( -26.80)
>consensus
AAACUAGCGUAGGAAAGUG__UUGCUA_UAUAAAUGA_U__CUUUAAUA____UAUAAAUAUAUAUAAA____CGCACAACUUUC_UAUGGAUGGUUGUGCGUUUUUU_UAUUAGGAGGA
...((((...((((((((.....))................................................(((((((((.((.....)).)))))))))))))))...))))..... (-14.63 = -14.63 +   0.01)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,780,633 – 1,780,745
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 66.67
Mean single sequence MFE -18.91
Consensus MFE -8.90
Energy contribution -9.57
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.47
SVM decision value 0.90
SVM RNA-class probability 0.878450
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1780633 112 + 2516575/118-238
UCCUCCUAAUAUAAAAAACGCACAACCUUCUA---GAAAGUUGCGCG----UUUUUAUAUAGGCAUACGGAUACCAAAGUUACUCAGUGAUA-UCGCAAUACACUUUCCUACGCUAGUUU
........(((((((((.(((.((((.((...---.)).)))).)))----))))))))).(((.((.(((.....((((......(((...-.))).....))))))))).)))..... ( -21.10)
>sy_au.0 1711988 101 - 2809422/118-238
UCCUCCUAAUA-AAAAAACGCACAACCAUCCAUAGGAAAGUUAUGCG----UUCACA-AUAUAUAU-----UAGUAAAA-----CAUAUGUA-UAGUAA--CACUUUCCUACGCUAGUUC
...........-....................(((((((((.....(----((.((.-((((((((-----........-----.)))))))-).))))--))))))))))......... ( -14.70)
>sy_ha.0 1925530 112 + 2685015/118-238
UCCUCCU-----AAAAAACGCACAACCAUCCGUA-GAAAGUUGUGCGUGAAUUUAAAUAAAAUGCUAUAUGUAUUUACCACAAUUAUUUAUAUUAGCAA--CACUUUCCUACGCUAGUUU
......(-----(((..(((((((((..((....-))..)))))))))...))))....((((((.....))))))...............((((((..--...........)))))).. ( -20.92)
>consensus
UCCUCCUAAUA_AAAAAACGCACAACCAUCCAUA_GAAAGUUGUGCG____UUUAAAUAUAAACAUA____UACUAAAA__A_UCAUUUAUA_UAGCAA__CACUUUCCUACGCUAGUUU
..................((((((((..((.....))..))))))))......................................................................... ( -8.90 =  -9.57 +   0.67) 
# Strand winner: forward (1.00)

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 18:54:32 2006