Locus 39

Sequence ID sy_sa.0
Location 1,148,686 – 1,148,805
Length 119
Max. P 0.999820
window190 window191 window192 window193

overview

Window 0

Location 1,148,686 – 1,148,805
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 64.64
Mean single sequence MFE -20.40
Consensus MFE -14.64
Energy contribution -12.20
Covariance contribution -2.44
Combinations/Pair 1.33
Mean z-score -1.78
Structure conservation index 0.72
SVM decision value 4.16
SVM RNA-class probability 0.999820
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1148686 119 + 2516575/120-240
CAAGCACUUAAUUACAUGAUUAACGCUCAAGCACGCUUUAACCUAUUAAACAGAUAUCUUCAUAUGAUUAGUGUUCAGUUAAAGUUCAAUGUGGGCUACCUUCA-AUAAGUUAAAUUGUA
...(((.((((((...(((.....(((((.....((((((((......((((...(((.......)))...))))..))))))))......))))).....)))-...))))))..))). ( -18.70)
>sy_ha.0 1298497 99 + 2685015/120-240
CUUGCACUUAAUU---UGAUUAACGCUCAAACACGCUUUUAUCUACUAA---------UUAAUG--------GUUCAAUAAAAGUUCAA-GUGGGCUACCUUCAGAUUGAAUGUUAUACA
...(((.((((((---(((.....(((((.....((((((((..((((.---------....))--------))...))))))))....-.))))).....))))))))).)))...... ( -23.90)
>sy_au.0 1066761 104 - 2809422/120-240
CAAGCACUCUAGAUUAUGAUUAACGCUCAAACACGUCUUAGCCUACUA----------UUAAUC------ACGUUCAGCUAAGAUACUCUGUGGGCUACCUUCAGUAAAAAUCAUUUACA
................(((.....(((((.....((((((((..((..----------......------..))...))))))))......))))).....)))(((((.....))))). ( -18.60)
>consensus
CAAGCACUUAAUU__AUGAUUAACGCUCAAACACGCUUUAACCUACUAA_________UUAAUA________GUUCAGUUAAAGUUCAAUGUGGGCUACCUUCAGAUAAAAUAAUUUACA
................(((.....(((((.....((((((((..((..........................))...))))))))......))))).....)))................ (-14.64 = -12.20 +  -2.44) 
# Strand winner: reverse (0.98)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,148,686 – 1,148,802
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 61.34
Mean single sequence MFE -30.80
Consensus MFE -10.58
Energy contribution -10.27
Covariance contribution -0.32
Combinations/Pair 1.45
Mean z-score -3.01
Structure conservation index 0.34
SVM decision value 1.04
SVM RNA-class probability 0.904832
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1148686 116 + 2516575/200-320
UAAAGCGUGCUUGAGCGUUAAUCAUGUAAUUAAGUGCUUGAA-AU-UAGUUUGUAAUUUCUUGAAUUUAGGUGGUACCACG--GAAUAUCCGUCCUAUUUUGAUAGGGCGGAUAUUUUUU
......(..(((((((((.....))))..)))))..)..(((-((-((.....)))))))..........(((....)))(--(((((((((((((((....)))))))))))))))).. ( -35.20)
>sy_ha.0 1298497 110 + 2685015/200-320
AAAAGCGUGUUUGAGCGUUAAUCA---AAUUAAGUGCAAGUAUAU-UAAUUUAUA----CUUGAAUUUAGGUGGUACCACG--GAACAUCCGUCCUAUAUUAUUUAGGAGGAUGUUUUUU
...(((((......))))).....---..((((((.((((((((.-.....))))----)))).))))))(((....)))(--((((((((.(((((.......)))))))))))))).. ( -34.50)
>sy_au.0 1066761 120 - 2809422/200-320
UAAGACGUGUUUGAGCGUUAAUCAUAAUCUAGAGUGCUUGAAGAGAUGAAGCAUUUCAAAUUUCACGAUGAUAGUAUUGGUAUGAUUAUUCCAAUUAUGUUAAAAGAGUGAAUUUGAUAU
...(((((......))))).............(((((((.(.....).)))))))(((((((.(((..(((((..(((((..........)))))..))))).....))))))))))... ( -22.70)
>consensus
UAAAGCGUGUUUGAGCGUUAAUCAU__AAUUAAGUGCUUGAA_AU_UAAUUUAUA____CUUGAAUUUAGGUGGUACCACG__GAAUAUCCGUCCUAUAUUAAUAGGGAGGAUAUUUUUU
...(((((......)))))...................................................(((....)))...((((((((.((((.........))))))))))))... (-10.58 = -10.27 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,148,686 – 1,148,796
Length 110
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 54.55
Mean single sequence MFE -29.43
Consensus MFE -6.57
Energy contribution -6.03
Covariance contribution -0.54
Combinations/Pair 1.50
Mean z-score -3.34
Structure conservation index 0.22
SVM decision value 0.44
SVM RNA-class probability 0.737751
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1148686 110 + 2516575/220-340
AUCAUGUAAUUAAGUGCUUGAA-AU-UAGUUUGUAAUUUCUUGAAUUUAGGUGGUACCACG--GAAUAUCCGUCCUAUUUUGAUAGGGCGGAUAUUUUUU-AUUUUU-----AAGGAGGA
.(((.(((......))).))).-..-..........(((((((((..((((((....)))(--(((((((((((((((....))))))))))))))))))-)..)))-----)))))).. ( -34.00)
>sy_ha.0 1298497 105 + 2685015/220-340
AUCA---AAUUAAGUGCAAGUAUAU-UAAUUUAUA----CUUGAAUUUAGGUGGUACCACG--GAACAUCCGUCCUAUAUUAUUUAGGAGGAUGUUUUUUUAAUUAU-----UAGGAGGU
....---..((((((.((((((((.-.....))))----)))).))))))(((....)))(--((((((((.(((((.......)))))))))))))).........-----........ ( -30.60)
>sy_au.0 1066761 120 - 2809422/220-340
AUCAUAAUCUAGAGUGCUUGAAGAGAUGAAGCAUUUCAAAUUUCACGAUGAUAGUAUUGGUAUGAUUAUUCCAAUUAUGUUAAAAGAGUGAAUUUGAUAUUAAUCAUCCUUCUUGAAUAU
................(..((((.(((((......(((((((.(((..(((((..(((((..........)))))..))))).....))))))))))......)))))))))..)..... ( -23.70)
>consensus
AUCAU__AAUUAAGUGCUUGAA_AU_UAAUUUAUA____CUUGAAUUUAGGUGGUACCACG__GAAUAUCCGUCCUAUAUUAAUAGGGAGGAUAUUUUUUUAAUUAU_____UAGGAGGU
.......................................(((........(((....)))...((((((((.((((.........))))))))))))..................))).. ( -6.57 =  -6.03 +  -0.54)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,148,686 – 1,148,796
Length 110
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 54.55
Mean single sequence MFE -21.63
Consensus MFE -3.23
Energy contribution -3.57
Covariance contribution 0.34
Combinations/Pair 1.40
Mean z-score -3.75
Structure conservation index 0.15
SVM decision value -0.03
SVM RNA-class probability 0.519057
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1148686 110 + 2516575/220-340
UCCUCCUU-----AAAAAU-AAAAAAUAUCCGCCCUAUCAAAAUAGGACGGAUAUUC--CGUGGUACCACCUAAAUUCAAGAAAUUACAAACUA-AU-UUCAAGCACUUAAUUACAUGAU
........-----......-....((((((((.(((((....))))).)))))))).--.(((....)))..........(((((((.....))-))-)))................... ( -21.10)
>sy_ha.0 1298497 105 + 2685015/220-340
ACCUCCUA-----AUAAUUAAAAAAACAUCCUCCUAAAUAAUAUAGGACGGAUGUUC--CGUGGUACCACCUAAAUUCAAG----UAUAAAUUA-AUAUACUUGCACUUAAUU---UGAU
........-----...((((((..((((((((((((.......))))).))))))).--.(((....))).......((((----((((.....-.)))))))).......))---)))) ( -23.40)
>sy_au.0 1066761 120 - 2809422/220-340
AUAUUCAAGAAGGAUGAUUAAUAUCAAAUUCACUCUUUUAACAUAAUUGGAAUAAUCAUACCAAUACUAUCAUCGUGAAAUUUGAAAUGCUUCAUCUCUUCAAGCACUCUAGAUUAUGAU
........(((((((((...((.((((((((((............(((((.((....)).))))).........))).))))))).))...))))).))))................... ( -20.40)
>consensus
ACCUCCUA_____AUAAUUAAAAAAAAAUCCACCCUAUUAAAAUAGGACGGAUAUUC__CGUGGUACCACCUAAAUUCAAG____UAUAAAUUA_AU_UUCAAGCACUUAAUU__AUGAU
........................((((((((((...........))).)))))))................................................................ ( -3.23 =  -3.57 +   0.34) 
# Strand winner: forward (0.91)

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 18:53:16 2006