Locus 10282

Sequence ID 3R_DroMel_CAF1
Location 27,563,761 – 27,563,966
Length 205
Max. P 0.969736
window16375 window16376 window16377

overview

Window 5

Location 27,563,761 – 27,563,863
Length 102
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 59.69
Mean single sequence MFE -19.24
Consensus MFE -9.54
Energy contribution -9.77
Covariance contribution 0.23
Combinations/Pair 1.25
Mean z-score -1.81
Structure conservation index 0.50
SVM decision value 1.65
SVM RNA-class probability 0.969736
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27563761 102 + 27905053
ACUGUUAAUUACAUUACAUUACUAUUAACAGUAUUUUUUCAAAUUCC--------------UUUCUAACAUUU-UUGUUCUGUCAAAUUUUCUAUUGUUCUGUCGUACGACAGGACG
(((((((((..............)))))))))...............--------------.....((((...-.)))).................((((((((....)))))))). ( -19.34)
>DroEre_CAF1 85933 103 + 1
AC---UAAUCAU---AAAUUCGAAGUAACGGUAUUU-UUCGAAUUCAUCAGCGGGACAACCAACUUUACAUUAAUUG--CUAUCGAACUUC-----AAUCUGUCGUACGACAGGGAG
..---...((..---...(((((((((((((.....-.)))...........((.....)).............)))--)).)))))....-----..((((((....)))))))). ( -18.40)
>DroYak_CAF1 84229 79 + 1
ACCGAUAAUUAU---AAAGUCGAAGUAACGGUAUUU-UUCGAAUUCA---------------------------UUG--CUGUCGAACUUA-----ACUCUGUCGUACGACAGGGUG
..(((((.....---....((((((..........)-))))).....---------------------------...--.)))))......-----((((((((....)))))))). ( -19.97)
>consensus
AC_G_UAAUUAU___AAAUUCGAAGUAACGGUAUUU_UUCGAAUUCA__________________U_ACAUU__UUG__CUGUCGAACUUA_____AAUCUGUCGUACGACAGGGAG
................................................................................................((((((((....)))))))). ( -9.54 =  -9.77 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 27,563,823 – 27,563,938
Length 115
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 75.53
Mean single sequence MFE -28.17
Consensus MFE -19.43
Energy contribution -19.67
Covariance contribution 0.23
Combinations/Pair 1.21
Mean z-score -1.54
Structure conservation index 0.69
SVM decision value 0.72
SVM RNA-class probability 0.833559
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27563823 115 + 27905053
UUCUGUCAAAUUUUCUAUUGUUCUGUCGUACGACAGGACGAGAGAGAGAGAAAGGAAGGAGCUUGCG-UCUUAUUUCAACGCAUAAGCGAAUAGUGUGCACAAUGUCUUUUGCAAU
((((.((...((((((.((((((((((....))))))))))...))))))....)).))))..((((-(.........)))))...(((((..(..(.....)..)..)))))... ( -31.30)
>DroEre_CAF1 86003 98 + 1
--CUAUCGAACUUC-----AAUCUGUCGUACGACAGGGAG-U----------AGAAAAGAGCUUGCGGUCUCAUUUCAACACACUUUCGAAUAGUGUGCACAAUGUCAAUUGCAAU
--...((..(((((-----...(((((....)))))))))-)----------.)).......(((((((..((((....((((((.......))))))...))))...))))))). ( -24.20)
>DroYak_CAF1 84275 99 + 1
--CUGUCGAACUUA-----ACUCUGUCGUACGACAGGGUGAG----------AGGAAAGAGCUUGCGGUCUCAUUUCAACGCACAUGCGAAUAGUGUGCAAAAUGUCAAUUGCAAU
--...((...(((.-----((((((((....))))))))..)----------))....))..(((((((..(((((....((((((.......)))))).)))))...))))))). ( -29.00)
>consensus
__CUGUCGAACUUA_____AAUCUGUCGUACGACAGGGAGAG__________AGGAAAGAGCUUGCGGUCUCAUUUCAACGCACAUGCGAAUAGUGUGCACAAUGUCAAUUGCAAU
...................((((((((....)))))))).......................(((((((..((((....(((((.........)))))...))))...))))))). (-19.43 = -19.67 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 27,563,863 – 27,563,966
Length 103
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 78.15
Mean single sequence MFE -24.30
Consensus MFE -15.50
Energy contribution -16.07
Covariance contribution 0.56
Combinations/Pair 1.17
Mean z-score -1.53
Structure conservation index 0.64
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27563863 103 + 27905053
AGAGAGAGAGAAAGGAAGGAGCUUGCG-UCUUAUUUCAACGCAUAAGCGAAUAGUGUGCACAAUGUCUUUUGCAAUUAGUGGUGAAUGUGCAUACUUUUAGUGA
.((((..((((.(((......)))...-)))).))))..(((....)))((.((((((((((...((..(..(.....)..).)).)))))))))).))..... ( -25.30)
>DroEre_CAF1 86036 93 + 1
-U----------AGAAAAGAGCUUGCGGUCUCAUUUCAACACACUUUCGAAUAGUGUGCACAAUGUCAAUUGCAAUUAGAGGUGAGUGUGCAUACUUGUAUUGU
-.----------......(((..((((..((((((((..((((((.......))))))..((((....))))......))))))))..))))..)))....... ( -24.70)
>DroYak_CAF1 84308 92 + 1
AG----------AGGAAAGAGCUUGCGGUCUCAUUUCAACGCACAUGCGAAUAGUGUGCAAAAUGUCAAUUGCAAUUAGAGGUGAGU--GCAUAAUUUUACUGG
..----------.((.((((...((((..((((((((..(((....)))..((((.(((((........))))))))))))))))))--)))...)))).)).. ( -22.90)
>consensus
AG__________AGGAAAGAGCUUGCGGUCUCAUUUCAACGCACAUGCGAAUAGUGUGCACAAUGUCAAUUGCAAUUAGAGGUGAGUGUGCAUACUUUUACUGA
................(((((..(((...((((((((..(((((.........))))).....(((.....)))....))))))))...)))..)))))..... (-15.50 = -16.07 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:53:14 2006