Locus 91

Sequence ID sy_ha.0
Location 2,552,655 – 2,552,774
Length 119
Max. P 0.999640
window474 window475 window476

overview

Window 4

Location 2,552,655 – 2,552,774
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.16
Mean single sequence MFE -27.77
Consensus MFE -25.17
Energy contribution -24.73
Covariance contribution -0.44
Combinations/Pair 1.16
Mean z-score -1.98
Structure conservation index 0.91
SVM decision value 3.82
SVM RNA-class probability 0.999640
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2552655 119 + 2685015/0-120
UAAAAAAGACAAGUACUCAAUAUGUUAUAAAUUGAGUACUUGUCUUUUUUAUAUUUAUUAGUCUUGG-AUUUUAAUUAUAAUGGCGGAGGAAGAGGGAUUCGAACCCCCGCGGCCCGUUA
(((((((((((((((((((((.........)))))))))))))))))))))................-..........(((((((.(.((....(((.......))))).).).)))))) ( -36.80)
>sy_au.0 2289354 108 - 2809422/0-120
UAAAAAAGGUAAAUACUCAAAAU--------UUGAGCACUUACCUUCAUUAUAUAUAGAA---UUUA-AUAUAAAUAUUGAUGGCGGAGGAAGAGGGAUUCGAACCCCCGCGAGCCGUUA
......((((((...((((....--------.))))...))))))(((.(((.((((...---....-.)))).))).)))((((((.....(.(((........)))).....)))))) ( -23.00)
>sy_sa.0 2363694 116 + 2516575/0-120
UUAAAAAAGCAAGCAUCCAAAUUUUUC---AUUGAAUACUUGCUUUAUCUAUAU-CAUUAGUCUUGGUAUUUUAAAUAUAAUGGCGGAGGAAGAGGGAUUCGAACCCCCGCGGGCCGUUA
(((((((((((((.((.(((.......---.))).)).))))))))....((((-((.......)))))))))))...(((((((...((....(((.......)))))....))))))) ( -23.50)
>consensus
UAAAAAAGGCAAGUACUCAAAAU_UU____AUUGAGUACUUGCCUUAUUUAUAU_UAUUAGUCUUGG_AUUUUAAUUAUAAUGGCGGAGGAAGAGGGAUUCGAACCCCCGCGGGCCGUUA
.....(((((((((((((((...........)))))))))))))))...................................((((((.....(.(((........)))).....)))))) (-25.17 = -24.73 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 2,552,655 – 2,552,774
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.16
Mean single sequence MFE -34.63
Consensus MFE -35.82
Energy contribution -33.83
Covariance contribution -1.98
Combinations/Pair 1.34
Mean z-score -5.16
Structure conservation index 1.03
SVM decision value 2.43
SVM RNA-class probability 0.993914
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2552655 119 + 2685015/0-120
UAACGGGCCGCGGGGGUUCGAAUCCCUCUUCCUCCGCCAUUAUAAUUAAAAU-CCAAGACUAAUAAAUAUAAAAAAGACAAGUACUCAAUUUAUAACAUAUUGAGUACUUGUCUUUUUUA
....(((..(((((((...((.....))..)))))))..(((....)))..)-))..............(((((((((((((((((((((.........))))))))))))))))))))) ( -39.70)
>sy_au.0 2289354 108 - 2809422/0-120
UAACGGCUCGCGGGGGUUCGAAUCCCUCUUCCUCCGCCAUCAAUAUUUAUAU-UAAA---UUCUAUAUAUAAUGAAGGUAAGUGCUCAA--------AUUUUGAGUAUUUACCUUUUUUA
.........(((((((...((.....))..)))))))..........(((((-....---....)))))(((.(((((((((((((((.--------....))))))))))))))).))) ( -32.20)
>sy_sa.0 2363694 116 + 2516575/0-120
UAACGGCCCGCGGGGGUUCGAAUCCCUCUUCCUCCGCCAUUAUAUUUAAAAUACCAAGACUAAUG-AUAUAGAUAAAGCAAGUAUUCAAU---GAAAAAUUUGGAUGCUUGCUUUUUUAA
.........(((((((...((.....))..)))))))............................-...((((.(((((((((((((((.---.......))))))))))))))))))). ( -32.00)
>consensus
UAACGGCCCGCGGGGGUUCGAAUCCCUCUUCCUCCGCCAUUAUAAUUAAAAU_CCAAGACUAAUA_AUAUAAAAAAGGCAAGUACUCAAU____AA_AUUUUGAGUACUUGCCUUUUUUA
.........(((((((...((.....))..)))))))................................((((((((((((((((((((...........)))))))))))))))))))) (-35.82 = -33.83 +  -1.98) 
# Strand winner: reverse (1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 2,552,655 – 2,552,774
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.40
Mean single sequence MFE -33.20
Consensus MFE -30.31
Energy contribution -29.20
Covariance contribution -1.11
Combinations/Pair 1.12
Mean z-score -1.26
Structure conservation index 0.91
SVM decision value 0.47
SVM RNA-class probability 0.748780
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2552655 119 + 2685015/40-160
GUCCGGCUGAAGGGAUCGGUCUUGAAAACCGACAGGGCCUUAACGGGCCGCGGGGGUUCGAAUCCCUCUUCCUCCGCCAUUAUAAUUAAAAU-CCAAGACUAAUAAAUAUAAAAAAGACA
((((........)))).(((((((...........(((((....)))))(((((((...((.....))..)))))))...............-.)))))))................... ( -32.90)
>sy_au.0 2289354 116 - 2809422/40-160
GUCCGGCUGAAGGGAUCGGUCUUGAAAACCGACAGGGGCUUAACGGCUCGCGGGGGUUCGAAUCCCUCUUCCUCCGCCAUCAAUAUUUAUAU-UAAA---UUCUAUAUAUAAUGAAGGUA
..(((((.((.(((((((((.......)))))...(((((....)))))..(((((.......))))))))))).))).(((.(((.((((.-....---...)))).))).))).)).. ( -31.80)
>sy_sa.0 2363694 119 + 2516575/40-160
GUCCGGCUGAAGGGAUUGGUCUUGAAAACCAACAGGGGCUUAACGGCCCGCGGGGGUUCGAAUCCCUCUUCCUCCGCCAUUAUAUUUAAAAUACCAAGACUAAUG-AUAUAGAUAAAGCA
.(((.......)))((((((((((...........(((((....)))))(((((((...((.....))..))))))).................)))))))))).-.............. ( -34.90)
>consensus
GUCCGGCUGAAGGGAUCGGUCUUGAAAACCGACAGGGGCUUAACGGCCCGCGGGGGUUCGAAUCCCUCUUCCUCCGCCAUUAUAAUUAAAAU_CCAAGACUAAUA_AUAUAAAAAAGGCA
....(((.((.(((((((((.......)))))...(((((....)))))..(((((.......))))))))))).))).......................................... (-30.31 = -29.20 +  -1.11) 
# Strand winner: reverse (0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:57:10 2006