Locus 29

Sequence ID sy_ha.0
Location 989,412 – 989,531
Length 119
Max. P 0.999042
window155 window156 window157 window158 window159

overview

Window 5

Location 989,412 – 989,531
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.03
Mean single sequence MFE -34.17
Consensus MFE -27.42
Energy contribution -26.87
Covariance contribution -0.55
Combinations/Pair 1.14
Mean z-score -5.66
Structure conservation index 0.80
SVM decision value 2.67
SVM RNA-class probability 0.996252
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 989412 119 + 2685015/0-120
UAAAACAUAAAAAGACGCCCCAAUUUAUGAUUGGGACGUCUAUAAGUCCCAUUCAAUGAGAAAUAGGACUUAAA-CAUUUAGUAACAGAUAAUUACUAAAGUUCCAGCCCUUGCGAGUAU
............(((((.(((((((...))))))).))))).(((((((..(((.....)))...)))))))((-(.((((((((.......)))))))))))...((....))...... ( -29.60)
>sy_au.0 708422 115 - 2809422/0-120
UAAAACAUAAAAAAACGUCCCAAU--AUUAUUGGGACGUUUACAAGUCCCAUUCAAACAGAAAUAGGACUUAAAGCGUUUAGUAA---AUAUUUACUAACGUUCGAGUCCUAAAGAGUAU
............((((((((((((--...))))))))))))......................((((((((..((((((.(((((---....))))))))))).))))))))........ ( -34.80)
>sy_sa.0 858419 116 + 2516575/0-120
UGAAAAUAAAAAAAGUGUCCCAAUAAAUUAUUGGGACACUUUAAAGCCCCAUUCAACUAGAAUAAGGACUUAAA-CGUUUAGUAGU--UUCUUUACUAAAGUUCCAGUCCU-AUGAGCAU
...........((((((((((((((...))))))))))))))...((...((((.....)))).((((((..((-(.((((((((.--....)))))))))))..))))))-....)).. ( -38.10)
>consensus
UAAAACAUAAAAAAACGUCCCAAU__AUUAUUGGGACGUUUAAAAGUCCCAUUCAAACAGAAAUAGGACUUAAA_CGUUUAGUAA___AUAUUUACUAAAGUUCCAGUCCU_AAGAGUAU
............((((((((((((.....)))))))))))).......................((((((..((...((((((((.......)))))))).))..))))))......... (-27.42 = -26.87 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 6

Location 989,412 – 989,531
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.03
Mean single sequence MFE -40.67
Consensus MFE -32.67
Energy contribution -31.57
Covariance contribution -1.10
Combinations/Pair 1.15
Mean z-score -6.23
Structure conservation index 0.80
SVM decision value 1.96
SVM RNA-class probability 0.983929
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 989412 119 + 2685015/0-120
AUACUCGCAAGGGCUGGAACUUUAGUAAUUAUCUGUUACUAAAUG-UUUAAGUCCUAUUUCUCAUUGAAUGGGACUUAUAGACGUCCCAAUCAUAAAUUGGGGCGUCUUUUUAUGUUUUA
...(((....)))...(((((((((((((.....))))))))).)-)))(((((((((((......)))))))))))..((((((((((((.....))))))))))))............ ( -44.10)
>sy_au.0 708422 115 - 2809422/0-120
AUACUCUUUAGGACUCGAACGUUAGUAAAUAU---UUACUAAACGCUUUAAGUCCUAUUUCUGUUUGAAUGGGACUUGUAAACGUCCCAAUAAU--AUUGGGACGUUUUUUUAUGUUUUA
........(((((((..(((((((((((....---))))).)))).))..)))))))............((((((.((.((((((((((((...--))))))))))))...)).)))))) ( -35.70)
>sy_sa.0 858419 116 + 2516575/0-120
AUGCUCAU-AGGACUGGAACUUUAGUAAAGAA--ACUACUAAACG-UUUAAGUCCUUAUUCUAGUUGAAUGGGGCUUUAAAGUGUCCCAAUAAUUUAUUGGGACACUUUUUUUAUUUUCA
..((((..-((((((.(((((((((((.....--..))))))).)-))).))))))(((((.....)))))))))...((((((((((((((...))))))))))))))........... ( -42.20)
>consensus
AUACUCAU_AGGACUGGAACUUUAGUAAAUAU___UUACUAAACG_UUUAAGUCCUAUUUCUAAUUGAAUGGGACUUAUAAACGUCCCAAUAAU__AUUGGGACGUUUUUUUAUGUUUUA
...(((...((((((..((.((((((((.......))))))))...))..))))))..(((.....))).)))......((((((((((((.....))))))))))))............ (-32.67 = -31.57 +  -1.10) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 989,412 – 989,520
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.01
Mean single sequence MFE -24.27
Consensus MFE -12.36
Energy contribution -12.70
Covariance contribution 0.34
Combinations/Pair 1.25
Mean z-score -2.14
Structure conservation index 0.51
SVM decision value 0.23
SVM RNA-class probability 0.644723
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 989412 108 + 2685015/40-160
UAUAAGUCCCAUUCAAUGAGAAAUAGGACUUAAA-CAUUUAGUAACAGAUAAUUACUAAAGUUCCAGCCCUUGCGAGUAUAAUAAAAUAAUUA----------AAUUGUCAGUUGG-GUU
..(((((((..(((.....)))...)))))))((-(.((((((((.......)))))))))))(((((....((((...((((......))))----------..))))..)))))-... ( -21.30)
>sy_au.0 708422 114 - 2809422/40-160
UACAAGUCCCAUUCAAACAGAAAUAGGACUUAAAGCGUUUAGUAA---AUAUUUACUAACGUUCGAGUCCUAAAGAGUAUAAUAAAAUAAUAAUA---UUUGAAGUUGUCGGUUGAUGUU
............((((...((..((((((((..((((((.(((((---....))))))))))).))))))))..((((((.((......)).)))---))).......))..)))).... ( -22.70)
>sy_sa.0 858419 116 + 2516575/40-160
UUAAAGCCCCAUUCAACUAGAAUAAGGACUUAAA-CGUUUAGUAGU--UUCUUUACUAAAGUUCCAGUCCU-AUGAGCAUAAUAAAAUGACUAAAAUAUUUGAAGUUGUUGGUUGAGCUU
...((((((((..(((((.(((((((((((..((-(.((((((((.--....)))))))))))..))))))-...(((((......))).))....)))))..))))).)))..).)))) ( -28.80)
>consensus
UAAAAGUCCCAUUCAAACAGAAAUAGGACUUAAA_CGUUUAGUAA___AUAUUUACUAAAGUUCCAGUCCU_AAGAGUAUAAUAAAAUAAUUA_A___UUUGAAGUUGUCGGUUGA_GUU
............((((((......((((((..((...((((((((.......)))))))).))..))))))...............((((((...........)))))).)))))).... (-12.36 = -12.70 +   0.34)

alignment

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secondary structure

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dotplot

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Window 8

Location 989,412 – 989,520
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.01
Mean single sequence MFE -25.93
Consensus MFE -14.06
Energy contribution -14.07
Covariance contribution 0.01
Combinations/Pair 1.14
Mean z-score -3.19
Structure conservation index 0.54
SVM decision value 3.34
SVM RNA-class probability 0.999042
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 989412 108 + 2685015/40-160
AAC-CCAACUGACAAUU----------UAAUUAUUUUAUUAUACUCGCAAGGGCUGGAACUUUAGUAAUUAUCUGUUACUAAAUG-UUUAAGUCCUAUUUCUCAUUGAAUGGGACUUAUA
...-(((..........----------((((......))))..(((....))).)))((((((((((((.....))))))))).)-))((((((((((((......)))))))))))).. ( -26.80)
>sy_au.0 708422 114 - 2809422/40-160
AACAUCAACCGACAACUUCAAA---UAUUAUUAUUUUAUUAUACUCUUUAGGACUCGAACGUUAGUAAAUAU---UUACUAAACGCUUUAAGUCCUAUUUCUGUUUGAAUGGGACUUGUA
.(((....(((.....((((((---((....(((......))).....(((((((..(((((((((((....---))))).)))).))..)))))))....)))))))))))....))). ( -24.20)
>sy_sa.0 858419 116 + 2516575/40-160
AAGCUCAACCAACAACUUCAAAUAUUUUAGUCAUUUUAUUAUGCUCAU-AGGACUGGAACUUUAGUAAAGAA--ACUACUAAACG-UUUAAGUCCUUAUUCUAGUUGAAUGGGGCUUUAA
((((((...((((...............((.(((......)))))...-((((((.(((((((((((.....--..))))))).)-))).)))))).......))))....))))))... ( -26.80)
>consensus
AAC_UCAACCGACAACUUCAAA___U_UAAUUAUUUUAUUAUACUCAU_AGGACUGGAACUUUAGUAAAUAU___UUACUAAACG_UUUAAGUCCUAUUUCUAAUUGAAUGGGACUUAUA
........(((......................................((((((..((.((((((((.......))))))))...))..))))))..(((.....))))))........ (-14.06 = -14.07 +   0.01) 
# Strand winner: reverse (0.81)

alignment

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secondary structure

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dotplot

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Window 9

Location 989,412 – 989,518
Length 106
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 68.27
Mean single sequence MFE -18.90
Consensus MFE -14.48
Energy contribution -14.93
Covariance contribution 0.45
Combinations/Pair 1.18
Mean z-score -1.53
Structure conservation index 0.77
SVM decision value 3.00
SVM RNA-class probability 0.998090
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 989412 106 + 2685015/80-200
AA--GGAAGGAGUAUAUUAAAAUGACAAAUCAA-ACAUAUAAC-CCAACUGACAAUU----------UAAUUAUUUUAUUAUACUCGCAAGGGCUGGAACUUUAGUAAUUAUCUGUUACU
..--.(((((((((((.((((((((........-.........-.............----------...)))))))).)))))))((....)).....))))((((((.....)))))) ( -16.21)
>sy_au.0 708422 112 - 2809422/80-200
AC--GGAAGGAGUAUAAUAAAAUGCUUAAUCAAUAUACUGAACAUCAACCGACAACUUCAAA---UAUUAUUAUUUUAUUAUACUCUUUAGGACUCGAACGUUAGUAAAUAU---UUACU
.(--..((((((((((((((((((.....(((......))).........((.....))...---......))))))))))))))))))..)...........(((((....---))))) ( -18.70)
>sy_sa.0 858419 117 + 2516575/80-200
UAUCGAGAGGAGUAUAAUAAAAUGACCAAACAUACAACGCAAGCUCAACCAACAACUUCAAAUAUUUUAGUCAUUUUAUUAUGCUCAU-AGGACUGGAACUUUAGUAAAGAA--ACUACU
..((.((..(((((((((((((((((...........(....).................((....)).)))))))))))))))))..-....)).))....((((......--)))).. ( -21.80)
>consensus
AA__GGAAGGAGUAUAAUAAAAUGACAAAUCAA_AAACACAAC_UCAACCGACAACUUCAAA___U_UAAUUAUUUUAUUAUACUCAU_AGGACUGGAACUUUAGUAAAUAU___UUACU
.........(((((((((((((((((...........................................)))))))))))))))))......(((((....))))).............. (-14.48 = -14.93 +   0.45) 
# Strand winner: reverse (0.97)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:52:47 2006