Locus 3124

Sequence ID 3L_DroMel_CAF1
Location 9,093,429 – 9,093,559
Length 130
Max. P 0.882129
window4871 window4872 window4873

overview

Window 1

Location 9,093,429 – 9,093,532
Length 103
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 81.69
Mean single sequence MFE -26.63
Consensus MFE -21.62
Energy contribution -21.73
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -1.92
Structure conservation index 0.81
SVM decision value 0.92
SVM RNA-class probability 0.882129
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9093429 103 + 23771897
CUUUAACUGAUUGUGUGUGUGUGUAGAUUGUAUGUGUAUGUGUGUAUAAAUAGUUGG-GGCAUGAAGACGCUGCUAACUAUUUCUGUAGACGCAGCUGAAUGUG
(((((((((.(((((..((..((((.((...)).))))..))..))))).)))))))-)).........(((((...((((....))))..)))))........ ( -23.40)
>DroSec_CAF1 12730 87 + 1
CUUUCACUGAUUGUGUGUGUG-----------------UGUGUGUAUACAUAGUUGGGGGCGUGAAGAAGCUGCCAACUAUUUCUGUAGACGCAGCUGAAUGUG
....(((.....)))......-----------------(((((.((((.((((((((.(((........))).))))))))...)))).))))).......... ( -26.20)
>DroSim_CAF1 16808 85 + 1
CUUUAACUUAUUGUGUGUG-------------------UGUCUGUAUACAUAGUUGGGGGCGUGAAGACGCUGCCAACUAUUUCUGUAGACGCAGCUGAAUGUG
........((((..((.((-------------------((((((((.(.((((((((.(((((....))))).)))))))).).))))))))))))..)))).. ( -30.30)
>consensus
CUUUAACUGAUUGUGUGUGUG_________________UGUGUGUAUACAUAGUUGGGGGCGUGAAGACGCUGCCAACUAUUUCUGUAGACGCAGCUGAAUGUG
......................................(((((.((((.((((((((.(((........))).))))))))...)))).))))).......... (-21.62 = -21.73 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 9,093,429 – 9,093,532
Length 103
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 81.69
Mean single sequence MFE -15.90
Consensus MFE -10.71
Energy contribution -11.27
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -1.99
Structure conservation index 0.67
SVM decision value 0.49
SVM RNA-class probability 0.756440
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9093429 103 - 23771897
CACAUUCAGCUGCGUCUACAGAAAUAGUUAGCAGCGUCUUCAUGCC-CCAACUAUUUAUACACACAUACACAUACAAUCUACACACACACACAAUCAGUUAAAG
........(((((..(((......)))...)))))...........-......................................................... ( -10.50)
>DroSec_CAF1 12730 87 - 1
CACAUUCAGCUGCGUCUACAGAAAUAGUUGGCAGCUUCUUCACGCCCCCAACUAUGUAUACACACA-----------------CACACACACAAUCAGUGAAAG
........(.((.((.((((....(((((((..((........))..))))))))))).)).))).-----------------......(((.....))).... ( -16.20)
>DroSim_CAF1 16808 85 - 1
CACAUUCAGCUGCGUCUACAGAAAUAGUUGGCAGCGUCUUCACGCCCCCAACUAUGUAUACAGACA-------------------CACACACAAUAAGUUAAAG
........(.((.((((......((((((((..((((....))))..))))))))......)))).-------------------)))................ ( -21.00)
>consensus
CACAUUCAGCUGCGUCUACAGAAAUAGUUGGCAGCGUCUUCACGCCCCCAACUAUGUAUACACACA_________________CACACACACAAUCAGUUAAAG
.........(((......)))..((((((((..((((....))))..))))))))................................................. (-10.71 = -11.27 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,093,462 – 9,093,559
Length 97
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 77.41
Mean single sequence MFE -25.06
Consensus MFE -14.94
Energy contribution -16.62
Covariance contribution 1.68
Combinations/Pair 1.18
Mean z-score -1.81
Structure conservation index 0.60
SVM decision value 0.48
SVM RNA-class probability 0.752142
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9093462 97 - 23771897
UGGCAACAAAGGAGGCAGCAGCAGUGGCACAUUCAGCUGCGUCUACAGAAAUAGUUAGCAGCGUCUUCAUGCC-CCAACUAUUUAUACACACAUACAC
.((((.....((((((....((....)).......(((((..(((......)))...))))))))))).))))-........................ ( -22.80)
>DroSec_CAF1 12751 93 - 1
UGGCAACAAAGGAGGCAGCAGCAGUGGCACAUUCAGCUGCGUCUACAGAAAUAGUUGGCAGCUUCUUCACGCCCCCAACUAUGUAUACACACA-----
((....))..(((.(((((.(.((((...))))).))))).)))......((((((((..((........))..))))))))...........----- ( -26.30)
>DroSim_CAF1 16827 93 - 1
UGGCAACAAAGGAGGCAGCAGCAGUGGCACAUUCAGCUGCGUCUACAGAAAUAGUUGGCAGCGUCUUCACGCCCCCAACUAUGUAUACAGACA-----
((....))......(((((.(.((((...))))).)))))((((......((((((((..((((....))))..))))))))......)))).----- ( -30.50)
>DroEre_CAF1 12486 96 - 1
UGGCAACAAAGGAGGCAGCAGCAGUAGCACAUUCAGCUGCGUCUACAGAAAUAGUUGGCAGCGUCUUCACGCCCCCAACUAUGUAUACACAUA--CAC
((....))..(((.(((((................))))).)))......((((((((..((((....))))..))))))))((((....)))--).. ( -29.19)
>DroWil_CAF1 14751 85 - 1
-----ACAAAGGCAACAGCAGCAGCUGCU---GGUGCUACGUUUGUAAAAAUAGUUGCUCCAUCCUUCAUCCGCCCUAACAUUUCACCAC-----CAC
-----.....(((..((((....)))).(---((.((.((((((....)))).)).)).)))..........)))...............-----... ( -16.50)
>consensus
UGGCAACAAAGGAGGCAGCAGCAGUGGCACAUUCAGCUGCGUCUACAGAAAUAGUUGGCAGCGUCUUCACGCCCCCAACUAUGUAUACACACA__CAC
..........(.((((.(((((.............))))))))).)....((((((((..((((....))))..))))))))................ (-14.94 = -16.62 +   1.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:09 2006