Locus 5868

Sequence ID 3L_DroMel_CAF1
Location 15,811,464 – 15,811,592
Length 128
Max. P 0.949462
window9356 window9357 window9358

overview

Window 6

Location 15,811,464 – 15,811,559
Length 95
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 79.74
Mean single sequence MFE -22.00
Consensus MFE -15.16
Energy contribution -15.22
Covariance contribution 0.06
Combinations/Pair 1.17
Mean z-score -1.61
Structure conservation index 0.69
SVM decision value 0.10
SVM RNA-class probability 0.584909
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15811464 95 + 23771897
GGGCUCGUAAUAUCCUUAUAAUGGCACCAGCAGCUCUCCGGGGGCAUUAUUACUACAAUACUACUAUUCCAGCACUUUUCU-UUUUAGUGUGGGAA
((((.(((.(((....))).))))).))....((((.....)))).....................((((.(((((.....-....))))).)))) ( -20.10)
>DroSec_CAF1 18972 85 + 1
GGGCUCGUAAUAUCCUUAUAAUGGCACCAGCAGCUCUCCGGGGGCUUUAUUAC--------UACUAUUCCUGCACUU---UCUUUUAGUGUGGGAA
((((.(((.(((....))).))))).))...(((((.....))))).......--------.....((((..((((.---......))))..)))) ( -23.70)
>DroSim_CAF1 19382 88 + 1
UGGCUCGUAAUAUCCUUAUAAUGGCACCCCCCCCCCUCCAGGGGCAUUAUUAC--------UACUAUUCCAGCACUUUUCUCUUUUAGUGUGGGAA
......((((((.((.......))........((((....))))...))))))--------.....((((.(((((..........))))).)))) ( -19.10)
>DroYak_CAF1 57294 75 + 1
GGGCUCGUAAUAUCCUUAUAAUGGC-CUGG-----CACCAGGGGGAUUAUUGC--------UACUAUUCCCGCAU-------UUUUAGUGUGGGAA
......((((((((((........(-(((.-----...)))))))).))))))--------.....(((((((((-------.....))))))))) ( -25.10)
>consensus
GGGCUCGUAAUAUCCUUAUAAUGGCACCAGCAGCUCUCCAGGGGCAUUAUUAC________UACUAUUCCAGCACUU___U_UUUUAGUGUGGGAA
......((((((.((((....(((.............)))))))...)))))).............((((((((((..........)))))))))) (-15.16 = -15.22 +   0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,811,495 – 15,811,592
Length 97
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 82.69
Mean single sequence MFE -21.89
Consensus MFE -14.85
Energy contribution -15.21
Covariance contribution 0.36
Combinations/Pair 1.22
Mean z-score -2.48
Structure conservation index 0.68
SVM decision value 1.39
SVM RNA-class probability 0.949462
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15811495 97 + 23771897
AGCUCUCCGGGGGCAUUAUUACUACAAUACUACUAUUCCAGCACUUUUCU-UUUUAGUGUGGGAACAUUUCCUGGUGGUUAUUAAAUUUUAUUUGGAU
.((((.....))))...........((((((((((((((.(((((.....-....))))).)))).......)))))).))))............... ( -18.91)
>DroSec_CAF1 19003 87 + 1
AGCUCUCCGGGGGCUUUAUUAC--------UACUAUUCCUGCACUU---UCUUUUAGUGUGGGAACAUUUCCUGGUGGUUAUUAAUUUUUAUUUGGAU
(((((.....)))))(((..((--------(((((((((..((((.---......))))..)))).......)))))))...)))............. ( -22.41)
>DroSim_CAF1 19413 90 + 1
CCCCCUCCAGGGGCAUUAUUAC--------UACUAUUCCAGCACUUUUCUCUUUUAGUGUGGGAACAUUUCCUGGUGGUUAUUAAUUUUUAUUUGGAU
.((((....)))).((((..((--------(((((((((.(((((..........))))).)))).......)))))))...))))............ ( -21.31)
>DroEre_CAF1 18316 79 + 1
----CACCAGGGGGAUUAUUGC--------UACUAUUCCCGCGU-------UUUUAGUGUGGGAACAUUUCCCGGUGGUUAUUAAUUUUUAUUUGGAU
----((((.(((..((......--------.....((((((((.-------......)))))))).))..)))))))..................... ( -21.30)
>DroYak_CAF1 57323 79 + 1
----CACCAGGGGGAUUAUUGC--------UACUAUUCCCGCAU-------UUUUAGUGUGGGAACAUUUCCUGGUGGUUAUUAAUUUUUAUUUGGAU
----..(((((.((((((..((--------((((((((((((((-------.....))))))))).......)))))))...))))))...))))).. ( -25.51)
>consensus
__C_CUCCAGGGGCAUUAUUAC________UACUAUUCCAGCACUU___U_UUUUAGUGUGGGAACAUUUCCUGGUGGUUAUUAAUUUUUAUUUGGAU
....(.(((((((...................)).((((((((((..........)))))))))).....))))).)..................... (-14.85 = -15.21 +   0.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,811,495 – 15,811,592
Length 97
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 82.69
Mean single sequence MFE -18.30
Consensus MFE -8.88
Energy contribution -10.20
Covariance contribution 1.32
Combinations/Pair 1.06
Mean z-score -2.74
Structure conservation index 0.49
SVM decision value 0.73
SVM RNA-class probability 0.835867
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15811495 97 - 23771897
AUCCAAAUAAAAUUUAAUAACCACCAGGAAAUGUUCCCACACUAAAA-AGAAAAGUGCUGGAAUAGUAGUAUUGUAGUAAUAAUGCCCCCGGAGAGCU
.......................((.((...((((((..((((....-.....))))..))))))...(((((((....))))))).)).))...... ( -17.30)
>DroSec_CAF1 19003 87 - 1
AUCCAAAUAAAAAUUAAUAACCACCAGGAAAUGUUCCCACACUAAAAGA---AAGUGCAGGAAUAGUA--------GUAAUAAAGCCCCCGGAGAGCU
.(((................((....))...((((((..((((......---.))))..))))))...--------..............)))..... ( -14.10)
>DroSim_CAF1 19413 90 - 1
AUCCAAAUAAAAAUUAAUAACCACCAGGAAAUGUUCCCACACUAAAAGAGAAAAGUGCUGGAAUAGUA--------GUAAUAAUGCCCCUGGAGGGGG
....................((.(((((...((((((..((((..........))))..))))))(((--------.......))).))))).))... ( -20.80)
>DroEre_CAF1 18316 79 - 1
AUCCAAAUAAAAAUUAAUAACCACCGGGAAAUGUUCCCACACUAAAA-------ACGCGGGAAUAGUA--------GCAAUAAUCCCCCUGGUG----
.....................(((((((...(((((((.(.......-------..).))))))).((--------....)).....)))))))---- ( -18.70)
>DroYak_CAF1 57323 79 - 1
AUCCAAAUAAAAAUUAAUAACCACCAGGAAAUGUUCCCACACUAAAA-------AUGCGGGAAUAGUA--------GCAAUAAUCCCCCUGGUG----
.....................(((((((...(((((((.((......-------.)).))))))).((--------....)).....)))))))---- ( -20.60)
>consensus
AUCCAAAUAAAAAUUAAUAACCACCAGGAAAUGUUCCCACACUAAAA_A___AAGUGCGGGAAUAGUA________GUAAUAAUGCCCCUGGAG_G__
.......................(((((...((((((..((((..........))))..))))))...........(........).)))))...... ( -8.88 = -10.20 +   1.32)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:31 2006