Locus 131

Sequence ID sp_ag.0
Location 1,237,491 – 1,237,611
Length 120
Max. P 0.985208
window825 window826 window827

overview

Window 5

Location 1,237,491 – 1,237,611
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 65.72
Mean single sequence MFE -28.68
Consensus MFE -9.11
Energy contribution -6.86
Covariance contribution -2.25
Combinations/Pair 1.90
Mean z-score -2.70
Structure conservation index 0.32
SVM decision value 2.00
SVM RNA-class probability 0.985208
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 1237491 120 - 2160267/80-200
CAGUUAAAUAUAACUGCAAAAAAUACAAAUUCUUACGCAUUAGCUGCCUAAAAAACAGCCUGCGUGAUCUUCACAAGAUUGUUUGCGUUUUGCUAGAAGGUCUUAUUUAUCAGCAAACUA
.(((((....)))))((.................(((((...((((.........)))).)))))(((((((.((((((.......))))))...)))))))..........))...... ( -23.20)
>sp_pn.0 773591 118 + 2038615/80-200
CAGUUAAAUAUAACUGCAAAAAAUAACACUUCUUACGCUCUAGCUGCCUAAAAACCAGCAGGCGUGACCCGAUUUGGAUUGCUCGUGUUCAA-UGACAGGUCUUAUU-AUUAGCGAGAUA
((((((....))))))..............((((((((.((.((((.........))))))))))((((.(..((((((.......))))))-...).)))).....-......)))).. ( -24.40)
>sp_mu.0 891226 118 - 2030921/80-200
CAGUUAAAUAUAACUGCAAAAAAUACAAAUUCUUACGCAGUAGCUGCCUAAAAACCAGCCUGUGUGAUCAAUAACAAAUUGCUUGUGUUUGU-UGAUUGGUCUUAUU-GUUAACAAGCUA
((((((....))))))........((((......((((((..((((.........))))))))))((((((((((((((.......))))))-).)))))))...))-)).......... ( -25.90)
>sy_ha.0 550673 117 - 2685015/80-200
UCAGUAAAUAUAACUGACAAAUCAAACAAUAAUUUCGCAGUAGCUGCGUAAUAG-CACUCUGCAUCGCCUA-ACAGCAUCUCCUACGUGCUGUUAACGCGAUUCAACCCU-AGUAGGAUA
(((((.......)))))...(((..((.........((((.((.(((......)-))))))))(((((.((-(((((((.......)))))))))..)))))........-.))..))). ( -32.80)
>sy_sa.0 543911 117 - 2516575/80-200
-CAGUUAUAAUAACUGGCAAAGAAAACAAUAAUUUCGCAGUAGCUGCGUAAUAG-CACUCUGCAUCGCCUA-ACAGCAUCUCCUAUGUGCUGUUAACGCGAUUCAACCUUUAGUAGGAUA
-((((((...)))))).....(((............((((.((.(((......)-)))))))).((((.((-(((((((.......)))))))))..)))))))..(((.....)))... ( -33.30)
>sy_au.0 875945 117 + 2809422/80-200
CAGUUUAUAAUAACUGGCAAAUCAAACAAUAAUUUCGCAGUAGCUGCCUAAUCG-CACUCUGCAUCGCCUA-ACAGCAUUUCCUAUGUGCUGUUAACGCGAUUCAACCUU-AAUAGGAUA
(((((......)))))....................((((.((.(((......)-))))))))(((((.((-(((((((.......)))))))))..)))))....(((.-...)))... ( -32.50)
>consensus
CAGUUAAAUAUAACUGCAAAAAAAAACAAUAAUUACGCAGUAGCUGCCUAAAAA_CACCCUGCAUCACCUA_ACAGCAUUGCCUAUGUGCUGUUAACGCGACUCAACCAUUAGCAAGAUA
....................................((((...................)))).................((((((..........................)))))).. ( -9.11 =  -6.86 +  -2.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,237,491 – 1,237,609
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 64.49
Mean single sequence MFE -30.38
Consensus MFE -21.37
Energy contribution -17.24
Covariance contribution -4.13
Combinations/Pair 2.00
Mean z-score -0.93
Structure conservation index 0.70
SVM decision value 0.27
SVM RNA-class probability 0.663305
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 1237491 118 - 2160267/240-360
A--UAGACUCGCUAUGUGAGGGCUUGAGUUAUGUGUCAUCACCUAGUUAAAUCAAUACAUAACCUAUAGUUGUAGACAAAUAUAUUAGCAGAUGUUUGGACGUGGGUUCGACUCCCACCG
.--....(((((...)))))((((.(.(((((((((..................))))))))))...))))((...(((((((........))))))).))(((((.......))))).. ( -25.67)
>sp_pn.0 773591 118 + 2038615/240-360
A--UAGACUCGCAGUUUCUAGACUUGAGUUAUGUGUCGAGGGGCUGUUAAAAUAAUACAUAACCUAUGGUUGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCG
.--..((((((.((((....))))))))))..((.(((((.(.(((((((.(((....((((((...)))))).......))).))))))).).)))))))(((((.......))))).. ( -30.60)
>sp_mu.0 891226 118 - 2030921/240-360
A--CUGACUCGCAUCGUUAGAGUUUGAGUUAUGUAUUGUAACGGUGUUAAAUAAACACAUAACCUAUAGUUGUAGACAAAUGGGUUAGCAGAUGUUUGGACGUGGGUUCGACUCCCACCG
.--(((((.......))))).(((..((((((.....))))).(((((.....))))).((((((((..(((....)))))))))))........)..)))(((((.......))))).. ( -29.90)
>sy_ha.0 550673 118 - 2685015/240-360
AAUCAAACUAGCAUAAUACUGGUU--GUCUGUUGCUUACUAUUAUGCGAAAUUCAUCAAUAGACUACACACGUAGAAAGGUGUGUAUCAGGACCUCUGGACGCGGGUUCGAAUCCCGCCG
.....((((((.......))))))--(((((((((..........))((......)))))))))(((((((........)))))))((((.....))))..(((((.......))))).. ( -30.30)
>sy_sa.0 543911 118 - 2516575/240-360
AAUCAAACUAGCAUAAUGACGGAU--GUCUAUCACCUCCCAUUAUGCGAAACUCAUUGAUAGACUACGCACGUAGAAGUGCUAGUAUCAGAACCUCUGGACGCGGGUUCGAAUCCCGCCG
.(((((....((((((((..(((.--((.....)).)))))))))))(.....).)))))..((((.((((......)))))))).((((.....))))..(((((.......))))).. ( -34.80)
>sy_au.0 875945 118 + 2809422/240-360
AAUCAAACUAGCAUCAUGUUGGUU--GUUUAUCACUUUUCAUGAUGCGAAACCUAUCGAUAAACUACACACGUAGAAAGAUGUGUAUCAGGACCUUUGGACGCGGGUUCAAAUCCCGCCG
..(((((...((((((((..(((.--.......)))...))))))))((.((.((((......((((....))))...)))).)).))......)))))..(((((.......))))).. ( -31.00)
>consensus
A__CAAACUAGCAUAAUGAGGGUU__AGUUAUGUCUUAUCAUGAUGCGAAAUUAAUACAUAAACUACACACGUAGAAAAAUGUGUAUCAAGACCUUUGGACGCGGGUUCGAAUCCCACCG
..........((((((((..((.............))..))))))))................((((....))))..........................(((((.......))))).. (-21.37 = -17.24 +  -4.13)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 1,237,491 – 1,237,611
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 65.89
Mean single sequence MFE -32.24
Consensus MFE -24.30
Energy contribution -20.17
Covariance contribution -4.13
Combinations/Pair 1.83
Mean z-score -1.09
Structure conservation index 0.75
SVM decision value 0.95
SVM RNA-class probability 0.888260
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 1237491 120 - 2160267/247-367
CUCGCUAUGUGAGGGCUUGAGUUAUGUGUCAUCACCUAGUUAAAUCAAUACAUAACCUAUAGUUGUAGACAAAUAUAUUAGCAGAUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCAU
........(((.(((((...(((((((((..................)))))))))........((...(((((((........))))))).))(((((.......))))).)))))))) ( -25.67)
>sp_pn.0 773591 120 + 2038615/247-367
CUCGCAGUUUCUAGACUUGAGUUAUGUGUCGAGGGGCUGUUAAAAUAAUACAUAACCUAUGGUUGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCAU
((((.((((....))))))))...........(((((((................((.(((.((((.((((....)))).)))).)))..))..(((((.......)))))))))))).. ( -32.40)
>sp_mu.0 891226 120 - 2030921/247-367
CUCGCAUCGUUAGAGUUUGAGUUAUGUAUUGUAACGGUGUUAAAUAAACACAUAACCUAUAGUUGUAGACAAAUGGGUUAGCAGAUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCAU
...(((((((((.(((...........))).))))))))).....((((((.((((((((..(((....)))))))))))...).)))))(((.(((((.......)))))....))).. ( -30.70)
>sy_ha.0 550673 118 - 2685015/247-367
CUAGCAUAAUACUGGUU--GUCUGUUGCUUACUAUUAUGCGAAAUUCAUCAAUAGACUACACACGUAGAAAGGUGUGUAUCAGGACCUCUGGACGCGGGUUCGAAUCCCGCCGUCUCCAC
...((((((((..(((.--.......)))...))))))))..............((.(((((((........))))))))).(((......((((((((.......)))).))))))).. ( -33.50)
>sy_sa.0 543911 118 - 2516575/247-367
CUAGCAUAAUGACGGAU--GUCUAUCACCUCCCAUUAUGCGAAACUCAUUGAUAGACUACGCACGUAGAAGUGCUAGUAUCAGAACCUCUGGACGCGGGUUCGAAUCCCGCCGUCUCCAC
...((((((((..(((.--((.....)).)))))))))))........(((((..((((.((((......))))))))))))).......(((((((((.......)))).))))).... ( -36.90)
>sy_au.0 875945 118 + 2809422/247-367
CUAGCAUCAUGUUGGUU--GUUUAUCACUUUUCAUGAUGCGAAACCUAUCGAUAAACUACACACGUAGAAAGAUGUGUAUCAGGACCUUUGGACGCGGGUUCAAAUCCCGCCGUCUCCAU
...((((((((..(((.--.......)))...))))))))((.((.((((......((((....))))...)))).)).)).(((......((((((((.......)))).))))))).. ( -34.30)
>consensus
CUAGCAUAAUGAGGGUU__AGUUAUGUCUUAUCAUGAUGCGAAAUUAAUACAUAAACUACACACGUAGAAAAAUGUGUAUCAAGACCUUUGGACGCGGGUUCGAAUCCCACCGGCUCCAU
...((((((((..((.............))..))))))))................((((....)))).....................((((.(((((.......)))))....)))). (-24.30 = -20.17 +  -4.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:02:07 2006