Locus 98

Sequence ID sy_au.0
Location 2,228,414 – 2,228,491
Length 77
Max. P 0.998609
window503 window504 window505 window506

overview

Window 3

Location 2,228,414 – 2,228,491
Length 77
Sequences 4
Columns 79
Reading direction forward
Mean pairwise identity 84.62
Mean single sequence MFE -29.90
Consensus MFE -29.27
Energy contribution -26.77
Covariance contribution -2.50
Combinations/Pair 1.30
Mean z-score -4.53
Structure conservation index 0.98
SVM decision value 3.16
SVM RNA-class probability 0.998609
Prediction RNA

Download alignment: ClustalW | MAF

>sy_au.0 2228414 77 + 2809422
CUCCACAGGUAGGACUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCU-CUACCA-CUGAGCUACUGUGGAUUAAU
.((((((((((((.......))))).....((((((.....))))))((((-(.....-..))))).)))))))..... ( -30.80)
>sy_sa.0 1767823 77 - 2516575
CUCCACAGGUAGGACUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCU-CUACCA-CUGAGCUACUGUGGAAUAAU
.((((((((((((.......))))).....((((((.....))))))((((-(.....-..))))).)))))))..... ( -31.00)
>sy_ha.0 1800099 77 - 2685015
CUCCGCAGGUAGGAUUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCU-CUACCA-CUGAGCUACUGCGGAAUAAU
.((((((((((((.......))))).....((((((.....))))))((((-(.....-..))))).)))))))..... ( -32.50)
>sp_ag.0 1990025 79 - 2160267
CUCCGCCAGUAGGACUCGAACCUACGACAUCAUGAUUAACAGUCAUGCGCUACUACCAACUGAGCUAUGGCGGAUUAUA
.((((((((((((.......))))).....((((((.....)))))).(((.(........))))..)))))))..... ( -25.30)
>consensus
CUCCACAGGUAGGACUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCU_CUACCA_CUGAGCUACUGCGGAAUAAU
.((((((((((((.......))))).....((((((.....))))))((((.(........))))).)))))))..... (-29.27 = -26.77 +  -2.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 2,228,414 – 2,228,491
Length 77
Sequences 4
Columns 79
Reading direction reverse
Mean pairwise identity 84.62
Mean single sequence MFE -27.47
Consensus MFE -26.42
Energy contribution -23.30
Covariance contribution -3.12
Combinations/Pair 1.40
Mean z-score -2.39
Structure conservation index 0.96
SVM decision value 2.41
SVM RNA-class probability 0.993545
Prediction RNA

Download alignment: ClustalW | MAF

>sy_au.0 2228414 77 + 2809422
AUUAAUCCACAGUAGCUCAG-UGGUAG-AGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAGUCCUACCUGUGGAG
.....(((((((((((((..-.....)-)))))..(((((.........)))))(((((.......)))))))))))). ( -28.10)
>sy_sa.0 1767823 77 - 2516575
AUUAUUCCACAGUAGCUCAG-UGGUAG-AGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAGUCCUACCUGUGGAG
.....(((((((((((((..-.....)-)))))..(((((.........)))))(((((.......)))))))))))). ( -28.00)
>sy_ha.0 1800099 77 - 2685015
AUUAUUCCGCAGUAGCUCAG-UGGUAG-AGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAAUCCUACCUGCGGAG
.....(((((((((((((..-.....)-)))))..(((((.........)))))(((((.......)))))))))))). ( -29.50)
>sp_ag.0 1990025 79 - 2160267
UAUAAUCCGCCAUAGCUCAGUUGGUAGUAGCGCAUGACUGUUAAUCAUGAUGUCGUAGGUUCGAGUCCUACUGGCGGAG
.....(((((((..((((((((..((((........))))..)))..))).)).(((((.......)))))))))))). ( -24.30)
>consensus
AUUAAUCCACAGUAGCUCAG_UGGUAG_AGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAGUCCUACCUGCGGAG
.....(((((((.................((((((((.......))))).))).(((((.......)))))))))))). (-26.42 = -23.30 +  -3.12) 
# Strand winner: reverse (0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 2,228,414 – 2,228,491
Length 77
Sequences 4
Columns 79
Reading direction forward
Mean pairwise identity 84.62
Mean single sequence MFE -29.90
Consensus MFE -29.27
Energy contribution -26.77
Covariance contribution -2.50
Combinations/Pair 1.30
Mean z-score -4.53
Structure conservation index 0.98
SVM decision value 3.16
SVM RNA-class probability 0.998609
Prediction RNA

Download alignment: ClustalW | MAF

>sy_au.0 2228414 77 + 2809422/0-79
CUCCACAGGUAGGACUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCU-CUACCA-CUGAGCUACUGUGGAUUAAU
.((((((((((((.......))))).....((((((.....))))))((((-(.....-..))))).)))))))..... ( -30.80)
>sy_sa.0 1767823 77 - 2516575/0-79
CUCCACAGGUAGGACUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCU-CUACCA-CUGAGCUACUGUGGAAUAAU
.((((((((((((.......))))).....((((((.....))))))((((-(.....-..))))).)))))))..... ( -31.00)
>sy_ha.0 1800099 77 - 2685015/0-79
CUCCGCAGGUAGGAUUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCU-CUACCA-CUGAGCUACUGCGGAAUAAU
.((((((((((((.......))))).....((((((.....))))))((((-(.....-..))))).)))))))..... ( -32.50)
>sp_ag.0 1990025 79 - 2160267/0-79
CUCCGCCAGUAGGACUCGAACCUACGACAUCAUGAUUAACAGUCAUGCGCUACUACCAACUGAGCUAUGGCGGAUUAUA
.((((((((((((.......))))).....((((((.....)))))).(((.(........))))..)))))))..... ( -25.30)
>consensus
CUCCACAGGUAGGACUCGAACCUACGACCGAUCGGUUAACAGCCGAUAGCU_CUACCA_CUGAGCUACUGCGGAAUAAU
.((((((((((((.......))))).....((((((.....))))))((((.(........))))).)))))))..... (-29.27 = -26.77 +  -2.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 2,228,414 – 2,228,491
Length 77
Sequences 4
Columns 79
Reading direction reverse
Mean pairwise identity 84.62
Mean single sequence MFE -27.47
Consensus MFE -26.42
Energy contribution -23.30
Covariance contribution -3.12
Combinations/Pair 1.40
Mean z-score -2.39
Structure conservation index 0.96
SVM decision value 2.41
SVM RNA-class probability 0.993545
Prediction RNA

Download alignment: ClustalW | MAF

>sy_au.0 2228414 77 + 2809422/0-79
AUUAAUCCACAGUAGCUCAG-UGGUAG-AGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAGUCCUACCUGUGGAG
.....(((((((((((((..-.....)-)))))..(((((.........)))))(((((.......)))))))))))). ( -28.10)
>sy_sa.0 1767823 77 - 2516575/0-79
AUUAUUCCACAGUAGCUCAG-UGGUAG-AGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAGUCCUACCUGUGGAG
.....(((((((((((((..-.....)-)))))..(((((.........)))))(((((.......)))))))))))). ( -28.00)
>sy_ha.0 1800099 77 - 2685015/0-79
AUUAUUCCGCAGUAGCUCAG-UGGUAG-AGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAAUCCUACCUGCGGAG
.....(((((((((((((..-.....)-)))))..(((((.........)))))(((((.......)))))))))))). ( -29.50)
>sp_ag.0 1990025 79 - 2160267/0-79
UAUAAUCCGCCAUAGCUCAGUUGGUAGUAGCGCAUGACUGUUAAUCAUGAUGUCGUAGGUUCGAGUCCUACUGGCGGAG
.....(((((((..((((((((..((((........))))..)))..))).)).(((((.......)))))))))))). ( -24.30)
>consensus
AUUAAUCCACAGUAGCUCAG_UGGUAG_AGCUAUCGGCUGUUAACCGAUCGGUCGUAGGUUCGAGUCCUACCUGCGGAG
.....(((((((.................((((((((.......))))).))).(((((.......)))))))))))). (-26.42 = -23.30 +  -3.12) 
# Strand winner: reverse (0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:57:33 2006