Locus 70

Sequence ID sy_sa.0
Location 1,948,487 – 1,948,602
Length 115
Max. P 0.999993
window361 window362 window363 window364

overview

Window 1

Location 1,948,487 – 1,948,602
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.94
Mean single sequence MFE -24.21
Consensus MFE -15.09
Energy contribution -13.93
Covariance contribution -1.15
Combinations/Pair 1.27
Mean z-score -2.24
Structure conservation index 0.62
SVM decision value 3.82
SVM RNA-class probability 0.999638
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1948487 115 + 2516575/0-120
AAAAAAUGCUUUCCCUAUGUUCAUUGAAGAAUAGAGAAAGCAACGUU-----UGCUUCUCUCAUCUUCUAAAGUUUCUAUGAACUUUAUGUGAAUUGGCACCAUUUCUGUUACAGACGGU
.............((...((((((.(((((..((((((.(((.....-----)))))))))..)))))((((((((....)))))))).)))))).)).(((...((((...)))).))) ( -26.70)
>sy_au.0 1908658 116 - 2809422/0-120
AAAAAAUGCUUUCUCAAUAUCGAUAGAAAAAUUGAGAAAGCAAUAGUAGUAUUGUUUCUCUCAUCUUCAAAAGUUA----AAACUUUAUGUGAAUUGGCACCAUUUCUAUAUAAGACGGU
......((((((((((((.((....))...))))))))))))........(((((((............(((((..----..)))))(((((((.((....)).))).)))).))))))) ( -23.30)
>sy_ha.0 2209611 106 - 2685015/0-120
AAAAAAUACUUUC----UAUUAUUUAA------GAGAAAGUAUCGAUAG---ACUUUCUCUUAUCUCUUAAAGUAU-UGUCUACUUUAUGUGAAUUAGCACCAUUUCGUUAAACGACGGU
....((((((((.----.......(((------((((((((........---)))))))))))......)))))))-)((((((.....)))..(((((........)))))..)))... ( -22.64)
>consensus
AAAAAAUGCUUUC_C_AUAUUAAUUGAA_AAU_GAGAAAGCAACGAUAG___UGUUUCUCUCAUCUUCUAAAGUUU_U_UAAACUUUAUGUGAAUUGGCACCAUUUCUAUAAAAGACGGU
......(((((((.((((.((....))...)))).)))))))...........(((....((((....(((((((......))))))).))))...)))(((...(((.....))).))) (-15.09 = -13.93 +  -1.15)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,948,487 – 1,948,602
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.94
Mean single sequence MFE -25.43
Consensus MFE -18.46
Energy contribution -18.30
Covariance contribution -0.16
Combinations/Pair 1.19
Mean z-score -2.56
Structure conservation index 0.73
SVM decision value 5.77
SVM RNA-class probability 0.999993
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1948487 115 + 2516575/0-120
ACCGUCUGUAACAGAAAUGGUGCCAAUUCACAUAAAGUUCAUAGAAACUUUAGAAGAUGAGAGAAGCA-----AACGUUGCUUUCUCUAUUCUUCAAUGAACAUAGGGAAAGCAUUUUUU
..(((((......(((.((....)).)))...(((((((......)))))))..))))).........-----.....((((((((((((((......))..))))))))))))...... ( -26.60)
>sy_au.0 1908658 116 - 2809422/0-120
ACCGUCUUAUAUAGAAAUGGUGCCAAUUCACAUAAAGUUU----UAACUUUUGAAGAUGAGAGAAACAAUACUACUAUUGCUUUCUCAAUUUUUCUAUCGAUAUUGAGAAAGCAUUUUUU
..((((((.....(((.((....)).))).((.(((((..----..)))))))))))))...................((((((((((((...((....)).))))))))))))...... ( -26.30)
>sy_ha.0 2209611 106 - 2685015/0-120
ACCGUCGUUUAACGAAAUGGUGCUAAUUCACAUAAAGUAGACA-AUACUUUAAGAGAUAAGAGAAAGU---CUAUCGAUACUUUCUC------UUAAAUAAUA----GAAAGUAUUUUUU
(((.(((.....)))...)))(((..(((...(((((((....-.))))))).....(((((((((((---........))))))))------))).......----))))))....... ( -23.40)
>consensus
ACCGUCUUUUAAAGAAAUGGUGCCAAUUCACAUAAAGUUCA_A_AAACUUUAGAAGAUGAGAGAAACA___CUAACGUUGCUUUCUC_AUU_UUCAAUCAAUAU_G_GAAAGCAUUUUUU
(((.(((.....)))...)))......((...(((((((......)))))))...)).....................((((((((((((............))))))))))))...... (-18.46 = -18.30 +  -0.16) 
# Strand winner: reverse (0.94)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,948,487 – 1,948,602
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.88
Mean single sequence MFE -29.50
Consensus MFE -20.50
Energy contribution -19.73
Covariance contribution -0.77
Combinations/Pair 1.16
Mean z-score -1.95
Structure conservation index 0.70
SVM decision value 2.44
SVM RNA-class probability 0.993971
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1948487 115 + 2516575/24-144
UGAAGAAUAGAGAAAGCAACGUU-----UGCUUCUCUCAUCUUCUAAAGUUUCUAUGAACUUUAUGUGAAUUGGCACCAUUUCUGUUACAGACGGUUGCCGGGCUUCAAAGGGCACAUCC
.(((((..((((((.(((.....-----)))))))))..)))))((((((((....))))))))(((...((((((((...((((...)))).)).))))))(((......))))))... ( -32.00)
>sy_au.0 1908658 116 - 2809422/24-144
AGAAAAAUUGAGAAAGCAAUAGUAGUAUUGUUUCUCUCAUCUUCAAAAGUUA----AAACUUUAUGUGAAUUGGCACCAUUUCUAUAUAAGACGGUUGCCGGGCUUCGUAGGGCACAUCC
.(((....(((((((((((((....)))))))).)))))..)))........----...(((((((....((((((((...(((.....))).)).))))))....)))))))....... ( -27.00)
>sy_ha.0 2209611 110 - 2685015/24-144
UAA------GAGAAAGUAUCGAUAG---ACUUUCUCUUAUCUCUUAAAGUAU-UGUCUACUUUAUGUGAAUUAGCACCAUUUCGUUAAACGACGGUUGCUGGGCUUCUUAGGGCACAUCC
(((------((((((((........---)))))))))))((.(.(((((((.-....))))))).).)).((((((((...(((.....))).)).))))))(((......)))...... ( -29.50)
>consensus
UGAA_AAU_GAGAAAGCAACGAUAG___UGUUUCUCUCAUCUUCUAAAGUUU_U_UAAACUUUAUGUGAAUUGGCACCAUUUCUAUAAAAGACGGUUGCCGGGCUUCAUAGGGCACAUCC
.........(((((((((..........))))).)))).((...(((((((......)))))))...)).((((((((...(((.....))).)).))))))(((......)))...... (-20.50 = -19.73 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,948,487 – 1,948,602
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.88
Mean single sequence MFE -27.63
Consensus MFE -21.25
Energy contribution -20.26
Covariance contribution -0.99
Combinations/Pair 1.21
Mean z-score -1.84
Structure conservation index 0.77
SVM decision value 2.56
SVM RNA-class probability 0.995293
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1948487 115 + 2516575/24-144
GGAUGUGCCCUUUGAAGCCCGGCAACCGUCUGUAACAGAAAUGGUGCCAAUUCACAUAAAGUUCAUAGAAACUUUAGAAGAUGAGAGAAGCA-----AACGUUGCUUUCUCUAUUCUUCA
((......))..((((....((((.((.((((...))))...))))))..))))..(((((((......)))))))(((((..(((((((((-----.....))).))))))..))))). ( -32.10)
>sy_au.0 1908658 116 - 2809422/24-144
GGAUGUGCCCUACGAAGCCCGGCAACCGUCUUAUAUAGAAAUGGUGCCAAUUCACAUAAAGUUU----UAACUUUUGAAGAUGAGAGAAACAAUACUACUAUUGCUUUCUCAAUUUUUCU
..(((((......(.....)((((.((.(((.....)))...))))))....)))))(((((..----..))))).(((((...(((((((((((....))))).))))))...))))). ( -23.90)
>sy_ha.0 2209611 110 - 2685015/24-144
GGAUGUGCCCUAAGAAGCCCAGCAACCGUCGUUUAACGAAAUGGUGCUAAUUCACAUAAAGUAGACA-AUACUUUAAGAGAUAAGAGAAAGU---CUAUCGAUACUUUCUC------UUA
((......))...(((....((((.((.(((.....)))...))))))..)))...(((((((....-.))))))).....(((((((((((---........))))))))------))) ( -26.90)
>consensus
GGAUGUGCCCUAAGAAGCCCGGCAACCGUCUUUUAAAGAAAUGGUGCCAAUUCACAUAAAGUUCA_A_AAACUUUAGAAGAUGAGAGAAACA___CUAACGUUGCUUUCUC_AUU_UUCA
(((((.((........)).)((((.((.(((.....)))...)))))).))))...(((((((......)))))))(((((...((((((...............))))))...))))). (-21.25 = -20.26 +  -0.99) 
# Strand winner: forward (0.69)

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 18:55:39 2006