Locus 65

Sequence ID sy_sa.0
Location 1,825,917 – 1,826,026
Length 109
Max. P 0.978679
window303 window304 window305

overview

Window 3

Location 1,825,917 – 1,826,025
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.27
Mean single sequence MFE -35.87
Consensus MFE -32.08
Energy contribution -32.30
Covariance contribution 0.22
Combinations/Pair 1.03
Mean z-score -2.64
Structure conservation index 0.89
SVM decision value 1.82
SVM RNA-class probability 0.978679
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1825917 108 + 2516575/80-200
GUACGUUUCCA-AUGGCUCCACAGGUAGGACUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCUCUACCACUGAGCUACUGUGGAAUAAUGGGU---UGCUCUA---AU--C---AA
....((.((((-.((..((((((((((((.......))))).....((((((.....))))))(((((.......))))).))))))).)).)))).---.))....---..--.---.. ( -36.00)
>sy_au.0 1042231 113 + 2809422/80-200
GUACGUUUCCA-AUGGCUCCACAGGUAGGACUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCUCUACCACUGAGCUACUGUGGAUUAAUUUGUAUGUGUUUGA---AUAUC---AA
.(((((...((-(..(.((((((((((((.......))))).....((((((.....))))))(((((.......))))).))))))).)...))).))))).....---.....---.. ( -33.60)
>sy_ha.0 710687 120 - 2685015/80-200
GUACGUUUCCAUAUGGCUCCGCAGGUAGGAUUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCUCUACCACUGAGCUACUGCGGAAUAAUAUGUAUUUAUAUAAUGUAUCUCUAUGA
(((((((..(((((...((((((((((((.......))))).....((((((.....))))))(((((.......))))).)))))))...))))).........)))))))........ ( -38.00)
>consensus
GUACGUUUCCA_AUGGCUCCACAGGUAGGACUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCUCUACCACUGAGCUACUGUGGAAUAAUAUGUAU_UGUUUAA___AU_UC___AA
((((....((....)).((((((((((((.......))))).....((((((.....))))))(((((.......))))).))))))).......))))..................... (-32.08 = -32.30 +   0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,825,917 – 1,826,025
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.27
Mean single sequence MFE -32.27
Consensus MFE -30.48
Energy contribution -30.03
Covariance contribution -0.44
Combinations/Pair 1.04
Mean z-score -1.23
Structure conservation index 0.94
SVM decision value 0.72
SVM RNA-class probability 0.832700
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1825917 108 + 2516575/80-200
UU---G--AU---UAGAGCA---ACCCAUUAUUCCACAGUAGCUCAGUGGUAGAGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAGUCCUACCUGUGGAGCCAU-UGGAAACGUAC
..---.--..---.......---..(((...((((((((((((((.......))))))..(((((.........)))))(((((.......)))))))))))))....-)))........ ( -31.50)
>sy_au.0 1042231 113 + 2809422/80-200
UU---GAUAU---UCAAACACAUACAAAUUAAUCCACAGUAGCUCAGUGGUAGAGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAGUCCUACCUGUGGAGCCAU-UGGAAACGUAC
..---.....---.........(((.......(((((((((((((.......))))))..(((((.........)))))(((((.......)))))))))))).....-.(....)))). ( -30.80)
>sy_ha.0 710687 120 - 2685015/80-200
UCAUAGAGAUACAUUAUAUAAAUACAUAUUAUUCCGCAGUAGCUCAGUGGUAGAGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAAUCCUACCUGCGGAGCCAUAUGGAAACGUAC
........................(((((..((((((((((((((.......))))))..(((((.........)))))(((((.......)))))))))))))..)))))......... ( -34.50)
>consensus
UU___GA_AU___UAAAACA_AUACAAAUUAUUCCACAGUAGCUCAGUGGUAGAGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAGUCCUACCUGUGGAGCCAU_UGGAAACGUAC
................................(((((((((((((.......))))))..(((((.........)))))(((((.......)))))))))))).......(....).... (-30.48 = -30.03 +  -0.44) 
# Strand winner: forward (0.83)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,825,917 – 1,826,026
Length 109
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.38
Mean single sequence MFE -26.37
Consensus MFE -16.82
Energy contribution -16.60
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -2.26
Structure conservation index 0.64
SVM decision value 1.20
SVM RNA-class probability 0.930067
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1825917 109 + 2516575/120-240
CGACCGAUCGGUUAACAGCCGAUAGCUCUACCACUGAGCUACUGUGGAAUAAUGGGU---UGCUCUA---AU--C---AAGCACAAAUAUUAUUAUAUCAACUCUCGUUAAAUUUUCAAG
((((((((((((.....))))))(((((.......)))))....)))(((((((.((---.(((...---..--.---.)))))...)))))))..........)))............. ( -22.90)
>sy_au.0 1042231 113 + 2809422/120-240
CGACCGAUCGGUUAACAGCCGAUAGCUCUACCACUGAGCUACUGUGGAUUAAUUUGUAUGUGUUUGA---AUAUC---AAGCACAAAUAUUAUUAUAACAAGAUUAAGUUAAUUUGCAA-
......((((((.....))))))(((((.......)))))..((..((((((((((..((((((((.---....)---))))))).(((....)))........))))))))))..)).- ( -33.30)
>sy_ha.0 710687 120 - 2685015/120-240
CGACCGAUCGGUUAACAGCCGAUAGCUCUACCACUGAGCUACUGCGGAAUAAUAUGUAUUUAUAUAAUGUAUCUCUAUGAGCACAAAUAUUAUUAUAUCAAUAAACUUAAAAUUUGCAAG
.(((((((((((.....))))))(((((.......)))))....)))((((((((((.((((((...........)))))).)))..)))))))...))..................... ( -22.90)
>consensus
CGACCGAUCGGUUAACAGCCGAUAGCUCUACCACUGAGCUACUGUGGAAUAAUAUGUAU_UGUUUAA___AU_UC___AAGCACAAAUAUUAUUAUAUCAACAAUCAUUAAAUUUGCAAG
...(((((((((.....))))))(((((.......)))))....)))......................................................................... (-16.82 = -16.60 +  -0.22)

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 18:54:49 2006