Locus 229

Sequence ID 3R_DroMel_CAF1
Location 923,423 – 923,529
Length 106
Max. P 0.953294
window411 window412

overview

Window 1

Location 923,423 – 923,529
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.37
Mean single sequence MFE -15.63
Consensus MFE -2.58
Energy contribution -2.38
Covariance contribution -0.20
Combinations/Pair 1.40
Mean z-score -1.67
Structure conservation index 0.17
SVM decision value 0.38
SVM RNA-class probability 0.713070
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 923423 106 + 27905053
CAUGAUAAUUGUCUAAACC------UUUCAUUCAACCACCUUCACCGGAAAUUCUUCAAACUCCACUUGUGAAAUUCAU----CAACUGCUU---UUUUCUACAAUCAUGAAAGGCUU-C
.................((------((((((...............(((............)))..((((((((.....----.........---.)))).))))..))))))))...-. ( -12.56)
>DroSec_CAF1 12415 113 + 1
CAUGAUAAUUGUCUAAACC------UUUCAUUCAACCACCUUCACCGGAAACUCUUCAAACUCCCCUUAUGAACUUUAUCGUUCAACUGUUUUUUUUUUCUACAAUCAUGAAGGGCUU-C
.................((------((((((...............(....).................(((((......)))))......................))))))))...-. ( -14.20)
>DroSim_CAF1 18306 113 + 1
CAUGAUAAUUGUCCAAACC------UUUCAUUCAACCACCUUCACCGGAAACUCUUCAAACACCACUUAUGAACUUUAUCGUUCAACUGUUUUUUUUUUCUACAAUCAUGAAGGGCUU-C
.................((------((((((...............(....).................(((((......)))))......................))))))))...-. ( -14.20)
>DroEre_CAF1 13624 97 + 1
UAUAAUAAAUGCCUAAACC------UUUCAUUUAAGCUCCGUCACUGUAAACUCUUCAGACUUCACUUGUGAAAUUUAGAGUUCAACGGUUUUUU----------------ACAGCUU-C
.....((((((........------...))))))((((.....(((((.((((((..(((.((((....)))).)))))))))..))))).....----------------..)))).-. ( -14.90)
>DroYak_CAF1 32594 106 + 1
------AGAUGCCUAAACUUACAAUUUUCAUUCAACCUCCGUCACCGGAAAUUC-UCAGAUUUCAAUUAUGAAAUUUAGAGUUAAACUGCUUUUAUU-------GUCAAGAAGGGCUUUA
------....((((...((((((((............((((....))))(((((-(.((((((((....))))))))))))))...........)))-------)).)))..)))).... ( -22.30)
>consensus
CAUGAUAAUUGUCUAAACC______UUUCAUUCAACCACCUUCACCGGAAACUCUUCAAACUCCACUUAUGAAAUUUAUAGUUCAACUGUUUUUUUUUUCUACAAUCAUGAAGGGCUU_C
..........((((.....................((.........))......((((...........)))).......................................)))).... ( -2.58 =  -2.38 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 923,423 – 923,529
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.37
Mean single sequence MFE -24.28
Consensus MFE -5.26
Energy contribution -6.86
Covariance contribution 1.60
Combinations/Pair 1.28
Mean z-score -2.09
Structure conservation index 0.22
SVM decision value 1.43
SVM RNA-class probability 0.953294
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 923423 106 - 27905053
G-AAGCCUUUCAUGAUUGUAGAAAA---AAGCAGUUG----AUGAAUUUCACAAGUGGAGUUUGAAGAAUUUCCGGUGAAGGUGGUUGAAUGAAA------GGUUUAGACAAUUAUCAUG
.-(((((((((((((((((......---..))))))(----((.(.((((((....(((((((...)))))))..)))))).).)))..))))))------))))).............. ( -25.40)
>DroSec_CAF1 12415 113 - 1
G-AAGCCCUUCAUGAUUGUAGAAAAAAAAAACAGUUGAACGAUAAAGUUCAUAAGGGGAGUUUGAAGAGUUUCCGGUGAAGGUGGUUGAAUGAAA------GGUUUAGACAAUUAUCAUG
(-((((.(((((.((((((...........))))))((((......))))............))))).))))).......((((((((..(((..------...)))..))))))))... ( -22.80)
>DroSim_CAF1 18306 113 - 1
G-AAGCCCUUCAUGAUUGUAGAAAAAAAAAACAGUUGAACGAUAAAGUUCAUAAGUGGUGUUUGAAGAGUUUCCGGUGAAGGUGGUUGAAUGAAA------GGUUUGGACAAUUAUCAUG
(-((((.(((((.((((((...........))))))((((......))))............))))).)))))..((((..((.(((.((.....------...)).))).))..)))). ( -22.10)
>DroEre_CAF1 13624 97 - 1
G-AAGCUGU----------------AAAAAACCGUUGAACUCUAAAUUUCACAAGUGAAGUCUGAAGAGUUUACAGUGACGGAGCUUAAAUGAAA------GGUUUAGGCAUUUAUUAUA
.-.....((----------------(((...((((((((((((..((((((....))))))....))))))).....))))).((((((((....------.)))))))).))))).... ( -23.20)
>DroYak_CAF1 32594 106 - 1
UAAAGCCCUUCUUGAC-------AAUAAAAGCAGUUUAACUCUAAAUUUCAUAAUUGAAAUCUGA-GAAUUUCCGGUGACGGAGGUUGAAUGAAAAUUGUAAGUUUAGGCAUCU------
....(((...((((.(-------(((.............(((...((((((....))))))..))-)((((((((....))))))))........))))))))....)))....------ ( -27.90)
>consensus
G_AAGCCCUUCAUGAUUGUAGAAAAAAAAAACAGUUGAACGAUAAAUUUCAUAAGUGGAGUUUGAAGAGUUUCCGGUGAAGGUGGUUGAAUGAAA______GGUUUAGACAAUUAUCAUG
....(((...................................(((((((((....)))))))))..(......))))...((((((((..((((.........))))..))))))))... ( -5.26 =  -6.86 +   1.60)

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 09:38:14 2006