Locus 1085

Sequence ID 2L_DroMel_CAF1
Location 2,993,357 – 2,993,512
Length 155
Max. P 0.973052
window1758 window1759 window1760

overview

Window 8

Location 2,993,357 – 2,993,475
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.45
Mean single sequence MFE -34.95
Consensus MFE -25.35
Energy contribution -27.22
Covariance contribution 1.87
Combinations/Pair 1.03
Mean z-score -1.55
Structure conservation index 0.73
SVM decision value 0.00
SVM RNA-class probability 0.534359
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2993357 118 + 22407834
AUCAAAUCUAAAUUCAUCAGGUGAGCGAGCAGCAGCAGCAACAACAACCACAGUGAGUGCCCAAAUAGGUGGGCACACGUACACAGGUGUGUGUG--UGGCUGUGUGCGUAAGUGUGUCA
.............((((...))))((..((....)).)).........((((.(..(((((((......)))))))((((((((((.(.......--.).)))))))))).).))))... ( -36.00)
>DroSec_CAF1 5126 107 + 1
AUCAAUUCCAAAUUCAUCAGGUGAGCGAGCAGC---AGAAACAACAACCACAGUGAGUGCCCAAAUAGGUGGGCACACGUACACAGGUAUGUGU----------GUGCGUAAGUGUGUCA
.((..........((((...))))((.....))---.)).........((((.(..(((((((......)))))))(((((((((......)))----------)))))).).))))... ( -31.20)
>DroSim_CAF1 5100 115 + 1
AUCAAAUCCAAAUUCAUCAGGUGAGCGAGCAGC---AGCAACAACAACCACAGAGAGUGCCCAAAUAGGUGGGCACACGUACACAGGUGUGUGUG--UGGCUGUGUGCGUAAGUGUGUCA
....................((..((.....))---.)).........((((....(((((((......)))))))((((((((((.(.......--.).))))))))))...))))... ( -34.20)
>DroYak_CAF1 5128 118 + 1
AUCAAAUCCAAAUUCAUCAGGUGAGCGAGCACCAGCAGCAACAACAACCACAC--AGUGCCCAAAUAGGUGGGCACACAUACACAGGUGUGUGUGAGCGGGUGUGUGCGUAAGUGUGUCA
...................((((......))))....(((.((...(((((((--((((((((......))))))).(((((((....)))))))......)))))).))...))))).. ( -38.40)
>consensus
AUCAAAUCCAAAUUCAUCAGGUGAGCGAGCAGC___AGCAACAACAACCACAGUGAGUGCCCAAAUAGGUGGGCACACGUACACAGGUGUGUGUG__UGGCUGUGUGCGUAAGUGUGUCA
............(((((...))))).....................(((((.....(((((((......)))))))((((((((((.((........)).))))))))))..))).)).. (-25.35 = -27.22 +   1.87)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,993,397 – 2,993,512
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.64
Mean single sequence MFE -38.12
Consensus MFE -30.64
Energy contribution -32.33
Covariance contribution 1.69
Combinations/Pair 1.06
Mean z-score -3.16
Structure conservation index 0.80
SVM decision value 1.70
SVM RNA-class probability 0.973052
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2993397 115 + 22407834
ACAACAACCACAGUGAGUGCCCAAAUAGGUGGGCACACGUACACAGGUGUGUGUG--UGGCUGUGUGCGUAAGUGUGUCACUUGUUGUUCUUGGG---AACAUUAGAGAAAAGUAAAUAG
........((((.(..(((((((......)))))))((((((((((.(.......--.).)))))))))).).))))...(((..(((((....)---))))...)))............ ( -39.10)
>DroSec_CAF1 5163 107 + 1
ACAACAACCACAGUGAGUGCCCAAAUAGGUGGGCACACGUACACAGGUAUGUGU----------GUGCGUAAGUGUGUCACUUGUUGUUCUUGGG---AACAUUAGAAAAAAGUAAAUAG
.(((((.....((((((((((((......)))))))(((((((((......)))----------)))))).......))))))))))((((((..---..))..))))............ ( -35.80)
>DroSim_CAF1 5137 115 + 1
ACAACAACCACAGAGAGUGCCCAAAUAGGUGGGCACACGUACACAGGUGUGUGUG--UGGCUGUGUGCGUAAGUGUGUCACUUGUUGUUCUUGGG---AACAUUAGAAAAAAGUAAAUAG
.((((((.((((....(((((((......)))))))((((((((((.(.......--.).))))))))))...))))....))))))((((((..---..))..))))............ ( -38.70)
>DroYak_CAF1 5168 118 + 1
ACAACAACCACAC--AGUGCCCAAAUAGGUGGGCACACAUACACAGGUGUGUGUGAGCGGGUGUGUGCGUAAGUGUGUCACUUGUUGUUCUUGGGCCGAGCAUUAGAAAAAAGUAAAUAG
.((((.(((((((--((((((((......))))))).(((((((....)))))))......)))))).))(((((...)))))))))((((...((...))...))))............ ( -38.90)
>consensus
ACAACAACCACAGUGAGUGCCCAAAUAGGUGGGCACACGUACACAGGUGUGUGUG__UGGCUGUGUGCGUAAGUGUGUCACUUGUUGUUCUUGGG___AACAUUAGAAAAAAGUAAAUAG
.((((((.((((....(((((((......)))))))((((((((((.((........)).))))))))))...))))....))))))((((..(......)...))))............ (-30.64 = -32.33 +   1.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,993,397 – 2,993,512
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.64
Mean single sequence MFE -34.35
Consensus MFE -27.48
Energy contribution -27.47
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -4.26
Structure conservation index 0.80
SVM decision value 1.48
SVM RNA-class probability 0.957635
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2993397 115 - 22407834
CUAUUUACUUUUCUCUAAUGUU---CCCAAGAACAACAAGUGACACACUUACGCACACAGCCA--CACACACACCUGUGUACGUGUGCCCACCUAUUUGGGCACUCACUGUGGUUGUUGU
..................((((---(....)))))..(((((...)))))..(((.(((((((--((.((((....))))..(.(((((((......))))))).)..)))))))))))) ( -36.50)
>DroSec_CAF1 5163 107 - 1
CUAUUUACUUUUUUCUAAUGUU---CCCAAGAACAACAAGUGACACACUUACGCAC----------ACACAUACCUGUGUACGUGUGCCCACCUAUUUGGGCACUCACUGUGGUUGUUGU
......................---......((((((.(((((.......(((.((----------(((......))))).)))(((((((......))))))))))))...)))))).. ( -31.70)
>DroSim_CAF1 5137 115 - 1
CUAUUUACUUUUUUCUAAUGUU---CCCAAGAACAACAAGUGACACACUUACGCACACAGCCA--CACACACACCUGUGUACGUGUGCCCACCUAUUUGGGCACUCUCUGUGGUUGUUGU
..................((((---(....)))))..(((((...)))))..(((.(((((((--((.((((....))))..(.(((((((......))))))).)..)))))))))))) ( -36.00)
>DroYak_CAF1 5168 118 - 1
CUAUUUACUUUUUUCUAAUGCUCGGCCCAAGAACAACAAGUGACACACUUACGCACACACCCGCUCACACACACCUGUGUAUGUGUGCCCACCUAUUUGGGCACU--GUGUGGUUGUUGU
...............................(((((((((((...)))))...((((((...((..(((((....)))))..))(((((((......))))))))--))))))))))).. ( -33.20)
>consensus
CUAUUUACUUUUUUCUAAUGUU___CCCAAGAACAACAAGUGACACACUUACGCACACAGCCA__CACACACACCUGUGUACGUGUGCCCACCUAUUUGGGCACUCACUGUGGUUGUUGU
...............................(((((((((((...))))).((((...........(((((....)))))....(((((((......)))))))....)))))))))).. (-27.48 = -27.47 +  -0.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:11 2006