Locus 31

Sequence ID sy_ha.0
Location 1,160,034 – 1,160,154
Length 120
Max. P 0.997901
window169 window170 window171

overview

Window 9

Location 1,160,034 – 1,160,154
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.37
Mean single sequence MFE -23.68
Consensus MFE -18.20
Energy contribution -18.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.77
SVM decision value 0.62
SVM RNA-class probability 0.800785
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1160034 120 + 2685015/120-240
AAGACGUCUCAUUCUUUCUCCCAUCCAGACUUUCACUGUCGGCUCUAGAAUCUCACUAGAUCAGCCAUCAAAGUUAUUACCUUUCACUUUGACAGGUCGCAGGCUUAUAUUACUGCCGGU
..(((((((.................)))).....(((((((((((((.......)))))...)))...(((((...........)))))))))))))((((..........)))).... ( -25.33)
>sy_au.0 933115 114 - 2809422/120-240
GAUAAUUAACAUUCUUUCUCCCAUCCAGACUUUAACUGUCGGCUCUAGAAUCUCACUAGAUCAGCCACUAA------UAUGAAACAUAUUAGCAGGUCGCAGGCUUUAUUUACUGCCGGU
....................((.....(((((........((((((((.......)))))...))).((((------((((...)))))))).)))))((((..........)))).)). ( -23.90)
>sy_sa.0 1025602 112 + 2516575/120-240
GUUAUACUUCAUUCUUUCUCCCAUCCAGACUUU-ACUGUCGGCUCUAGAAUCUCACUAGAUCAGCCAC-------AUUUAUACACAUAAAUGCAGGUCGCAGGCUUAAUUUACUGCCGGU
....................((.....(((((.-......((((((((.......)))))...))).(-------((((((....))))))).)))))((((..........)))).)). ( -21.80)
>consensus
GAUAAAUAUCAUUCUUUCUCCCAUCCAGACUUU_ACUGUCGGCUCUAGAAUCUCACUAGAUCAGCCAC_AA____AUUAACAAACAUAUUAGCAGGUCGCAGGCUUAAUUUACUGCCGGU
....................((..((.(((.......)))((((((((.......)))))...)))............................))..((((..........)))).)). (-18.20 = -18.20 +  -0.00) 
# Strand winner: forward (0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 1,160,034 – 1,160,149
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 68.66
Mean single sequence MFE -17.73
Consensus MFE -10.70
Energy contribution -10.70
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.60
SVM decision value 2.96
SVM RNA-class probability 0.997901
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1160034 115 + 2685015/160-280
UGU---GUAUGCUAAAUAACCGUC--AUAAUUAUCAAAUAAAGACGUCUCAUUCUUUCUCCCAUCCAGACUUUCACUGUCGGCUCUAGAAUCUCACUAGAUCAGCCAUCAAAGUUAUUAC
...---........((((((((((--................)))).....................(((.......)))((((((((.......)))))...)))......)))))).. ( -15.99)
>sy_au.0 933115 106 - 2809422/160-280
CAU---UUUUAC-AAAUACGCUAC--AUUAUCUUU--GUCGAUAAUUAACAUUCUUUCUCCCAUCCAGACUUUAACUGUCGGCUCUAGAAUCUCACUAGAUCAGCCACUAA------UAU
...---......-......(((..--.........--(((((((.((((...(((...........)))..)))).)))))))(((((.......)))))..)))......------... ( -13.90)
>sy_sa.0 1025602 112 + 2516575/160-280
UUUAUGGUAUGCCAAAUAAACACUUAAAAAGUGUUGUUUUGUUAUACUUCAUUCUUUCUCCCAUCCAGACUUU-ACUGUCGGCUCUAGAAUCUCACUAGAUCAGCCAC-------AUUUA
.....((((((.((((..((((((.....))))))..)))).))))))...................(((...-...)))((((((((.......)))))...)))..-------..... ( -23.30)
>consensus
UAU___GUAUGC_AAAUAAACAAC__AUAAUUAUU__AUAGAUAAAUAUCAUUCUUUCUCCCAUCCAGACUUU_ACUGUCGGCUCUAGAAUCUCACUAGAUCAGCCAC_AA____AUUAA
...................................................................(((.......)))((((((((.......)))))...))).............. (-10.70 = -10.70 +   0.00) 
# Strand winner: forward (0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 1,160,034 – 1,160,135
Length 101
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 50.88
Mean single sequence MFE -23.03
Consensus MFE -7.97
Energy contribution -7.76
Covariance contribution -0.21
Combinations/Pair 1.70
Mean z-score -2.34
Structure conservation index 0.35
SVM decision value 1.27
SVM RNA-class probability 0.938298
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>sy_ha.0 1160034 101 + 2685015/269-389
CAUAC---ACAUUUCUAAUGU---UGUAAGCUUAUUUGA------AUAUACAUUUGGUCUCCCUAUGCCUUU-AAGCACUUUAUUGGUAUAGGGAGUUUUAAUUUU------GAGGUGAU
.....---.((((((.(((((---.(((..(......).------.))))))))....(((((((((((..(-(((...))))..)))))))))))..........------)))))).. ( -26.70)
>sy_au.0 933115 91 - 2809422/269-389
UAAAA---AUGUGUACAA-------AUAGGCUUAUUUAA------CGAUAAAUUUU-UCUCCUUGCAUCUUA-AUUCA------UGAUGUGAGGAUUUUUGUUUAUA-----GAGGUGAU
.....---..........-------......((((((..------..((((((...-..((((..((((...-.....------.))))..)))).....)))))).-----.)))))). ( -18.10)
>sy_sa.0 1025602 120 + 2516575/269-389
CAUACCAUAAAUUUAAAAUUUAUGUAUAAGUGUGUCUAAUUUUUGCUAAUAAUGUUAUAUCAAUAGAUCCCACACCUGAAAUGUUCAUUUCAGGUGUUUUUUUUAUUAUUUAGAGGUGAU
((((((((((((.....))))))).....)))))(((((.....((.......))......((((((....(((((((((((....)))))))))))....))))))..)))))...... ( -24.30)
>consensus
CAUAC___AAAUUUAAAAU_U___UAUAAGCUUAUUUAA______CUAUAAAUUUU_UCUCCAUACAUCUUA_AACCA___U_UUGAUAUAAGGAGUUUUAUUUAU______GAGGUGAU
...........................................................((((((((((................))))))))))......................... ( -7.97 =  -7.76 +  -0.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:52:58 2006