Locus 2516

Sequence ID 2L_DroMel_CAF1
Location 6,956,312 – 6,956,448
Length 136
Max. P 0.972570
window4024 window4025 window4026

overview

Window 4

Location 6,956,312 – 6,956,419
Length 107
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 65.58
Mean single sequence MFE -19.36
Consensus MFE -10.68
Energy contribution -11.08
Covariance contribution 0.40
Combinations/Pair 1.14
Mean z-score -1.99
Structure conservation index 0.55
SVM decision value 1.70
SVM RNA-class probability 0.972570
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6956312 107 + 22407834
UAAAA-CCUCCUUAACUACACU-UU---AUAAACACAACACAUGUUUGCC------GAUCUAGCCAAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUA-UUAGUAAAAAGUUUUAA
(((((-(.......((((....-.(---(((....((((((..(((((.(------......).)))))((((((....))))))....).))))).))))-.)))).....)))))). ( -19.50)
>DroSec_CAF1 5779 104 + 1
CAAAA-CCUCCUUAACAC-------------AACACAAUAAACCUAUGCCAAUUGUGAUCUAGCCCAACACGGAUAAAAAUCCGCAUCCGCUGUUGCUAUA-UUAGUAAAAAGUAUUAA
.....-......(((.((-------------..((((((............))))))...((((..(((((((((..........))))).))))))))..-..........)).))). ( -14.60)
>DroSim_CAF1 5782 104 + 1
CAAAA-CCUCCUUAACAC-------------AACACAAUAAACCUAUGUCAAUUGUGAUCUAGCCCAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUA-UUAGUAAAAAGUAUUAA
.....-......(((.((-------------..((((((..((....))..))))))...((((.....((((((....))))))....))))((((((..-.))))))...)).))). ( -18.60)
>DroEre_CAF1 5836 102 + 1
UAAACAGAGAGGUAUUUGGGUAGUUUGGUUAAUCA-------UCUA---CUU------UCUUGACCCAUGCGAAUAAAAAUCCGCAUCCGCUGUAGCUAUU-UUAGUUAUAGGUAUUAA
........(.(((....((((((..(((....)))-------.)))---)))------.....))))(((((..........)))))...(((((((((..-.)))))))))....... ( -20.40)
>DroYak_CAF1 5795 102 + 1
UAACAAAAGCGUUAAUAAGGUU-UUUGGUUAAACA-------CCUA---CAU------UUACGACCCAUGCGGAUAAAAAUCCGCAUCCGCUGUAUCUAUAUAUAGUGAUAAGUAUUAG
...(((((((.(.....).)))-))))........-------....---...------.(((.....((((((((....)))))))).((((((((....))))))))....))).... ( -23.70)
>consensus
UAAAA_CCUCCUUAACAA_____UU____UAAACACAA_A_ACCUAUG_CAA____GAUCUAGCCCAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUA_UUAGUAAAAAGUAUUAA
.....................................................................((((((....))))))....(((..(((((....)))))...)))..... (-10.68 = -11.08 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 6,956,312 – 6,956,419
Length 107
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 65.58
Mean single sequence MFE -25.76
Consensus MFE -11.56
Energy contribution -11.40
Covariance contribution -0.16
Combinations/Pair 1.30
Mean z-score -2.09
Structure conservation index 0.45
SVM decision value 1.41
SVM RNA-class probability 0.951523
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6956312 107 - 22407834
UUAAAACUUUUUACUAA-UAUAGCAACAGCGGAUGCGGAUUUUUAUCCGCGUUUGGCUAGAUC------GGCAAACAUGUGUUGUGUUUAU---AA-AGUGUAGUUAAGGAGG-UUUUA
.(((((((((((((((.-(((((..((((((.((((((((....))))))(((((.(......------).))))))).))))))..))))---).-....))))..))))))-))))) ( -32.30)
>DroSec_CAF1 5779 104 - 1
UUAAUACUUUUUACUAA-UAUAGCAACAGCGGAUGCGGAUUUUUAUCCGUGUUGGGCUAGAUCACAAUUGGCAUAGGUUUAUUGUGUU-------------GUGUUAAGGAGG-UUUUG
.(((.(((((((..(((-((((((...(((.(((((((((....))))))))).).)).....(((((..((....))..))))))))-------------))))))))))))-).))) ( -27.50)
>DroSim_CAF1 5782 104 - 1
UUAAUACUUUUUACUAA-UAUAGCAACAGCGGAUGCGGAUUUUUAUCCGCGUUGGGCUAGAUCACAAUUGACAUAGGUUUAUUGUGUU-------------GUGUUAAGGAGG-UUUUG
.(((.(((((((..(((-((((((...(((.(((((((((....))))))))).).)).....(((((.(((....))).))))))))-------------))))))))))))-).))) ( -30.30)
>DroEre_CAF1 5836 102 - 1
UUAAUACCUAUAACUAA-AAUAGCUACAGCGGAUGCGGAUUUUUAUUCGCAUGGGUCAAGA------AAG---UAGA-------UGAUUAACCAAACUACCCAAAUACCUCUCUGUUUA
................(-(((((....((.((((((((((....))))))))((((.....------.((---(...-------((......)).))))))).....)).)))))))). ( -17.30)
>DroYak_CAF1 5795 102 - 1
CUAAUACUUAUCACUAUAUAUAGAUACAGCGGAUGCGGAUUUUUAUCCGCAUGGGUCGUAA------AUG---UAGG-------UGUUUAACCAAA-AACCUUAUUAACGCUUUUGUUA
.(((((............((((..(((.((..((((((((....))))))))..)).))).------.))---))((-------(.....)))...-.....)))))............ ( -21.40)
>consensus
UUAAUACUUUUUACUAA_UAUAGCAACAGCGGAUGCGGAUUUUUAUCCGCGUUGGGCUAGAUC____AUG_CAUAGGU_U_UUGUGUUUA____AA_____GUGUUAAGGAGG_UUUUA
.............................(.(((((((((....))))))))).)................................................................ (-11.56 = -11.40 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 6,956,347 – 6,956,448
Length 101
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 75.83
Mean single sequence MFE -21.46
Consensus MFE -12.06
Energy contribution -12.14
Covariance contribution 0.08
Combinations/Pair 1.19
Mean z-score -1.83
Structure conservation index 0.56
SVM decision value 0.53
SVM RNA-class probability 0.772888
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6956347 101 + 22407834
CAUGUUUGCC------GAUCUAGCCAAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUA-UUAGUAAAAAGUUUUAAAUAAGAGAAGGCAUAAAUUACUUUAUGAA
......((((------..((((((.....((((((....))))))....))).((((((..-.)))))).............)))...))))................ ( -21.30)
>DroSec_CAF1 5805 107 + 1
AACCUAUGCCAAUUGUGAUCUAGCCCAACACGGAUAAAAAUCCGCAUCCGCUGUUGCUAUA-UUAGUAAAAAGUAUUAAAUAGGAGAAUGAUUAAAUUACUAUUGGAA
........(((((.(((((.(((..((((((((((..........))))).)))))((((.-((((((.....))))))))))........))).))))).))))).. ( -21.80)
>DroSim_CAF1 5808 107 + 1
AACCUAUGUCAAUUGUGAUCUAGCCCAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUA-UUAGUAAAAAGUAUUAAAUAAGAGAAGGAUUAAAUUACUUUUGGAA
........((((..(((((.((..((...((((((....))))))....(((.((((((..-.))))))..)))..............))..)).)))))..)))).. ( -23.30)
>DroEre_CAF1 5871 96 + 1
--UCUA---CUU------UCUUGACCCAUGCGAAUAAAAAUCCGCAUCCGCUGUAGCUAUU-UUAGUUAUAGGUAUUAAAUAAGAAGAUGUUUCGAUCACUUUUGGAA
--(((.---(((------..((((..((((((..........)))))...(((((((((..-.))))))))))..))))..))).)))..((((((......)))))) ( -17.70)
>DroYak_CAF1 5829 97 + 1
--CCUA---CAU------UUACGACCCAUGCGGAUAAAAAUCCGCAUCCGCUGUAUCUAUAUAUAGUGAUAAGUAUUAGAUAAGAAAAUGUACAAAUCACUUUUGGAA
--..((---(((------((.(.....((((((((....)))))))).((((((((....))))))))...............).)))))))((((.....))))... ( -23.20)
>consensus
_ACCUAUG_CAA____GAUCUAGCCCAACGCGGAUAAAAAUCCGCAUCCGCUGUUGCUAUA_UUAGUAAAAAGUAUUAAAUAAGAGAAUGAUUAAAUUACUUUUGGAA
........................((...((((((....))))))....(((..(((((....)))))...)))..............................)).. (-12.06 = -12.14 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:44 2006