Locus 61

Sequence ID sy_ha.0
Location 1,874,061 – 1,874,180
Length 119
Max. P 0.999933
window274 window275 window276 window277 window278 window279

overview

Window 4

Location 1,874,061 – 1,874,167
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 76.79
Mean single sequence MFE -24.77
Consensus MFE -13.79
Energy contribution -13.90
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -3.87
Structure conservation index 0.56
SVM decision value 3.26
SVM RNA-class probability 0.998865
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1874061 106 + 2685015/0-120
UCACUAUUUAUUGUUAACUUUUUUUCA-------UAAAAAAAGACUUCCAUCCC----AAAACU--GGGACGAAAGUC-UUUCCGUGGUACCACCCAAAUUUAUGCAUAUGCAUACACUU
...........................-------.....((((((((.(.((((----(....)--)))).).)))))-)))..(((....))).......(((((....)))))..... ( -22.20)
>sy_au.0 1653908 114 - 2809422/0-120
UUUCUAUUUAUCAUAUUUGUUGUUUAAC------UAAAAAAAGACUUUCAUCCUCUUAAAAAAUAAGGGACGAAAGUCAUUUCCGUGGUACCACCCAAAUUUAUGCCUAAGCAUACACUU
.................(((((((((..------........(((((((.(((.((((.....))))))).)))))))......(((....))).............)))))).)))... ( -23.40)
>sy_sa.0 1726369 113 + 2516575/0-120
UUUUAAGUUGUUAUAUUUAUAUUUUAAAAUUGCAUAAAAAAAGACUUCCAUCCCUU--AAAACU--GGGACGAA-GUC--UUCCGUGGUACCACCCAAAUUUAUGCCGUAGCAUACACUU
......((((((((.((((.....))))...(((((((..((((((((..((((..--......--)))).)))-)))--))..(((....))).....))))))).)))))).)).... ( -28.70)
>consensus
UUUCUAUUUAUUAUAUUUAUUUUUUAA_______UAAAAAAAGACUUCCAUCCC_U__AAAACU__GGGACGAAAGUC_UUUCCGUGGUACCACCCAAAUUUAUGCCUAAGCAUACACUU
..........................................(((((.(.((((............)))).).)))))......(((....))).......(((((....)))))..... (-13.79 = -13.90 +   0.11)

alignment

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secondary structure

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Window 5

Location 1,874,061 – 1,874,167
Length 106
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 76.79
Mean single sequence MFE -31.80
Consensus MFE -25.15
Energy contribution -26.77
Covariance contribution 1.61
Combinations/Pair 1.03
Mean z-score -3.87
Structure conservation index 0.79
SVM decision value 4.64
SVM RNA-class probability 0.999933
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1874061 106 + 2685015/0-120
AAGUGUAUGCAUAUGCAUAAAUUUGGGUGGUACCACGGAAA-GACUUUCGUCCC--AGUUUU----GGGAUGGAAGUCUUUUUUUA-------UGAAAAAAAGUUAACAAUAAAUAGUGA
((((.(((((....))))).))))..(((....)))(((((-((((((((((((--......----)))))))))))))))))...-------........................... ( -33.00)
>sy_au.0 1653908 114 - 2809422/0-120
AAGUGUAUGCUUAGGCAUAAAUUUGGGUGGUACCACGGAAAUGACUUUCGUCCCUUAUUUUUUAAGAGGAUGAAAGUCUUUUUUUA------GUUAAACAACAAAUAUGAUAAAUAGAAA
.....(((((....))))).(((((.(((....)))(((((.(((((((((((((((.....)))).))))))))))).)))))..------.........))))).............. ( -31.70)
>sy_sa.0 1726369 113 + 2516575/0-120
AAGUGUAUGCUACGGCAUAAAUUUGGGUGGUACCACGGAA--GAC-UUCGUCCC--AGUUUU--AAGGGAUGGAAGUCUUUUUUUAUGCAAUUUUAAAAUAUAAAUAUAACAACUUAAAA
((((((.(((....)))((((.(((.(((....)))((((--(((-((((((((--......--..))))).))))))))))......))).)))).............)).)))).... ( -30.70)
>consensus
AAGUGUAUGCUUAGGCAUAAAUUUGGGUGGUACCACGGAAA_GACUUUCGUCCC__AGUUUU__A_GGGAUGGAAGUCUUUUUUUA_______UUAAAAAAAAAAUAUAAUAAAUAGAAA
((((.(((((....))))).))))..(((....)))(((((.((((((((((((((........)))))))))))))).))))).................................... (-25.15 = -26.77 +   1.61) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,874,061 – 1,874,173
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.79
Mean single sequence MFE -28.24
Consensus MFE -17.31
Energy contribution -17.87
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -3.03
Structure conservation index 0.61
SVM decision value 1.78
SVM RNA-class probability 0.977133
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1874061 112 + 2685015/40-160
AAGACUUCCAUCCC----AAAACU--GGGACGAAAGUC-UUUCCGUGGUACCACCCAAAUUUAUGCAUAUGCAUACACUUGUA-AACGUUGCUAACGAAGACGUACUCCGACUUAAAUUU
(((((((.(.((((----(....)--)))).).)))))-))..((..((((..........(((((....))))).....((.-..(((.....)))...))))))..)).......... ( -27.50)
>sy_au.0 1653908 120 - 2809422/40-160
AAGACUUUCAUCCUCUUAAAAAAUAAGGGACGAAAGUCAUUUCCGUGGUACCACCCAAAUUUAUGCCUAAGCAUACACUUGUUUAAUAUUGAUAACGGAUUGUCUUUCCGACUUAAAUCU
..(((((((.(((.((((.....))))))).)))))))...(((((((((.............))))((((((......)))))).........)))))..(((.....)))........ ( -28.82)
>sy_sa.0 1726369 112 + 2516575/40-160
AAGACUUCCAUCCCUU--AAAACU--GGGACGAA-GUC--UUCCGUGGUACCACCCAAAUUUAUGCCGUAGCAUACACUUGUU-GUCAUUGAUAACGGAAAUGAUUUCCGACUUAAAUUU
((((((((..((((..--......--)))).)))-)))--))..(((....))).......(((((....))))).....(((-(((...))))))((((.....))))........... ( -28.40)
>consensus
AAGACUUCCAUCCC_U__AAAACU__GGGACGAAAGUC_UUUCCGUGGUACCACCCAAAUUUAUGCCUAAGCAUACACUUGUU_AACAUUGAUAACGGAAACGAUUUCCGACUUAAAUUU
..(((((.(.((((............)))).).)))))......(((....))).(((.(.(((((....))))).).)))..............(((((.....))))).......... (-17.31 = -17.87 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,874,061 – 1,874,173
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.79
Mean single sequence MFE -38.67
Consensus MFE -32.23
Energy contribution -33.40
Covariance contribution 1.17
Combinations/Pair 1.09
Mean z-score -4.19
Structure conservation index 0.83
SVM decision value 2.96
SVM RNA-class probability 0.997907
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1874061 112 + 2685015/40-160
AAAUUUAAGUCGGAGUACGUCUUCGUUAGCAACGUU-UACAAGUGUAUGCAUAUGCAUAAAUUUGGGUGGUACCACGGAAA-GACUUUCGUCCC--AGUUUU----GGGAUGGAAGUCUU
.........(((..((((.....(((.....)))..-..(((((.(((((....))))).)))))....))))..))).((-((((((((((((--......----)))))))))))))) ( -38.50)
>sy_au.0 1653908 120 - 2809422/40-160
AGAUUUAAGUCGGAAAGACAAUCCGUUAUCAAUAUUAAACAAGUGUAUGCUUAGGCAUAAAUUUGGGUGGUACCACGGAAAUGACUUUCGUCCCUUAUUUUUUAAGAGGAUGAAAGUCUU
........(((.....)))..(((((......(((((..(((((.(((((....))))).)))))..)))))..)))))...(((((((((((((((.....)))).))))))))))).. ( -40.90)
>sy_sa.0 1726369 112 + 2516575/40-160
AAAUUUAAGUCGGAAAUCAUUUCCGUUAUCAAUGAC-AACAAGUGUAUGCUACGGCAUAAAUUUGGGUGGUACCACGGAA--GAC-UUCGUCCC--AGUUUU--AAGGGAUGGAAGUCUU
........(((((((.....))))(....)...)))-..(((((.(((((....))))).))))).(((....)))..((--(((-((((((((--......--..))))).)))))))) ( -36.60)
>consensus
AAAUUUAAGUCGGAAAACAUAUCCGUUAUCAAUGUU_AACAAGUGUAUGCUUAGGCAUAAAUUUGGGUGGUACCACGGAAA_GACUUUCGUCCC__AGUUUU__A_GGGAUGGAAGUCUU
..........(((((.....)))))..............(((((.(((((....))))).))))).(((....)))......((((((((((((((........)))))))))))))).. (-32.23 = -33.40 +   1.17) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,874,061 – 1,874,180
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.78
Mean single sequence MFE -29.17
Consensus MFE -25.15
Energy contribution -24.93
Covariance contribution -0.21
Combinations/Pair 1.12
Mean z-score -2.02
Structure conservation index 0.86
SVM decision value 1.62
SVM RNA-class probability 0.967832
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1874061 119 + 2685015/80-200
AACAUGUAUUAGUUUCUUUCAUCUUUUUGGUUACUUAAAGAAAUUUAAGUCGGAGUACGUCUUCGUUAGCAACGUU-UACAAGUGUAUGCAUAUGCAUAAAUUUGGGUGGUACCACGGAA
...........(((.((..(............(((((((....))))))).((((.....)))))..)).)))...-..(((((.(((((....))))).))))).(((....))).... ( -24.00)
>sy_au.0 1653908 119 - 2809422/80-200
AAU-UAUUUAAAGUCUUUUCACCUUUUUGGUUACUUAAAGAGAUUUAAGUCGGAAAGACAAUCCGUUAUCAAUAUUAAACAAGUGUAUGCUUAGGCAUAAAUUUGGGUGGUACCACGGAA
...-........(((((((((((.....))).(((((((....))))))).))))))))..(((((......(((((..(((((.(((((....))))).)))))..)))))..))))). ( -33.90)
>sy_sa.0 1726369 118 + 2516575/80-200
GAUGUA-GUUAGUUUUUUUCACCUUUUUGGUUACUUAAAGAAAUUUAAGUCGGAAAUCAUUUCCGUUAUCAAUGAC-AACAAGUGUAUGCUACGGCAUAAAUUUGGGUGGUACCACGGAA
......-........((((((((.....))).(((((((....))))))).)))))....(((((((((((.....-..(((((.(((((....))))).)))))..)))))..)))))) ( -29.60)
>consensus
AAU_UAUAUUAGUUUUUUUCACCUUUUUGGUUACUUAAAGAAAUUUAAGUCGGAAAACAUAUCCGUUAUCAAUGUU_AACAAGUGUAUGCUUAGGCAUAAAUUUGGGUGGUACCACGGAA
..............(((((((((.....))).(((((((....))))))).))))))....(((((.............(((((.(((((....))))).)))))((.....))))))). (-25.15 = -24.93 +  -0.21) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,874,061 – 1,874,179
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.42
Mean single sequence MFE -21.96
Consensus MFE -14.74
Energy contribution -13.53
Covariance contribution -1.21
Combinations/Pair 1.32
Mean z-score -1.34
Structure conservation index 0.67
SVM decision value 0.54
SVM RNA-class probability 0.775761
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1874061 118 + 2685015/120-240
GUA-AACGUUGCUAACGAAGACGUACUCCGACUUAAAUUUCUUUAAGUAACCAAAAAGAUGAAAGAAACUAAUACAUGUUGGAGUAAAUUGCAGUCACGUUUACUCUCCCUGUA-CAACA
(((-(((((.(((..(((.....(((((((((.....(((((((.................))))))).........)))))))))..))).))).))))))))..........-..... ( -24.77)
>sy_au.0 1653908 119 - 2809422/120-240
GUUUAAUAUUGAUAACGGAUUGUCUUUCCGACUUAAAUCUCUUUAAGUAACCAAAAAGGUGAAAAGACUUUAAAUA-AUUGGAAUAACUUGCAGUCACGAUUAUUCUCCCUAAAACAAUU
((((......(((((((((((((..((((((((((((....))))))).(((.....)))................-..)))))......)))))).)).))))).......)))).... ( -19.32)
>sy_sa.0 1726369 118 + 2516575/120-240
GUU-GUCAUUGAUAACGGAAAUGAUUUCCGACUUAAAUUUCUUUAAGUAACCAAAAAGGUGAAAAAAACUAAC-UACAUCGGAUUAUCUUUCAGUCGUGGAUAAUCUCCCUUUUACUUCU
(((-(((...))))))((((.....)))).(((((((....))))))).....((((((.((..........(-......)((((((((.........))))))))))))))))...... ( -21.80)
>consensus
GUU_AACAUUGAUAACGGAAACGAUUUCCGACUUAAAUUUCUUUAAGUAACCAAAAAGGUGAAAAAAACUAAAAUA_AUUGGAAUAACUUGCAGUCACGAUUAAUCUCCCUAUAACAACU
......((((.....(((((.....)))))(((((((....))))))).........))))...................(((((((((.........)))))))))............. (-14.74 = -13.53 +  -1.21)

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 18:54:27 2006