Locus 3979

Sequence ID 3L_DroMel_CAF1
Location 11,579,043 – 11,579,140
Length 97
Max. P 0.883145
window6198 window6199

overview

Window 8

Location 11,579,043 – 11,579,140
Length 97
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 79.55
Mean single sequence MFE -23.12
Consensus MFE -12.25
Energy contribution -12.62
Covariance contribution 0.36
Combinations/Pair 1.23
Mean z-score -2.44
Structure conservation index 0.53
SVM decision value 0.85
SVM RNA-class probability 0.865419
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11579043 97 + 23771897
UUUUAGUGAAAUGUAUUUUUCUACAAUUAGAAUCAAUGUUGUAUGGGGUAUGGUAUGUAUGUCGUCCAUAUGUACAUACA------------CUUGAACAC-----UGUUCACU
....((((((.(((....(((((....)))))((((.((.((((((.((((((.(((.....))))))))).).))))))------------)))))))).-----..)))))) ( -24.30)
>DroSec_CAF1 74613 95 + 1
UUUUAGUGAAAUGUAUUUUUCUACAAUUAGAAUCAAUGUUGUAUG--GUAUGGUAUGUAUGUCGUCCAUAUGUACAUACA------------CUUGAACAC-----UGUUCACU
....((((((.(((....(((((....)))))((((.((.(((((--((((((.(((.....)))))))))...))))))------------)))))))).-----..)))))) ( -22.50)
>DroSim_CAF1 76343 95 + 1
UUUUAGUGAAAUGUAUUUUUCUACAAUUAGAAUCAAUGUUGUAUG--GUAUGGUAUGUAUGUCGUCCAUAUGUACAUACA------------CUUGAACAC-----UGUUCACU
....((((((.(((....(((((....)))))((((.((.(((((--((((((.(((.....)))))))))...))))))------------)))))))).-----..)))))) ( -22.50)
>DroEre_CAF1 65882 101 + 1
UUUUAGUGAAAUGUAUUUUUCUACAAUUAGAAUCAAUGUUGUAU--------GUAUGUAUGUCGUCCAUAUGUACAUACACCUGUACGAAUACUUGAACAC-----UGUUCACU
...(((((....(((((((((((....))))).......(((((--------(((((((((.....)))))))))))))).......)))))).....)))-----))...... ( -24.10)
>DroYak_CAF1 80747 104 + 1
UUUUAGUGAAAUGUAUUUUUCUACAAUUAGAAUCAAUGUUGUGU-----AUGGUAUGUAUGUCGUCCAUAUGUACAUACACCUGUACGAAUACUUGAACAC-----UGUUCACU
....((((((.(((....(((((....)))))((((.((..(((-----((((..((((((((((....))).))))))).)))))))...))))))))).-----..)))))) ( -24.40)
>DroPer_CAF1 64024 95 + 1
UUUUAGUGAAAGGUAUUUUUUUACAAAUAGAACCCGUAUCGUAUG--GUAUGCAAUGCACAUG-----CCUGUACGAUUA------------CGUGAACACAUGAUUGUAAAAU
.....(((....(((......)))........(.(((((((((((--(((((.......))))-----)).)))))).))------------)).)..)))............. ( -20.90)
>consensus
UUUUAGUGAAAUGUAUUUUUCUACAAUUAGAAUCAAUGUUGUAUG__GUAUGGUAUGUAUGUCGUCCAUAUGUACAUACA____________CUUGAACAC_____UGUUCACU
.......((((......))))((((((..........)))))).........((((((((((.......))))))))))...............((((((......)))))).. (-12.25 = -12.62 +   0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,579,043 – 11,579,140
Length 97
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 79.55
Mean single sequence MFE -21.90
Consensus MFE -8.35
Energy contribution -8.93
Covariance contribution 0.58
Combinations/Pair 1.11
Mean z-score -3.20
Structure conservation index 0.38
SVM decision value 0.93
SVM RNA-class probability 0.883145
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11579043 97 - 23771897
AGUGAACA-----GUGUUCAAG------------UGUAUGUACAUAUGGACGACAUACAUACCAUACCCCAUACAACAUUGAUUCUAAUUGUAGAAAAAUACAUUUCACUAAAA
((((((..-----((((((((.------------((((((....(((((............)))))...))))))...))))(((((....)))))..))))..)))))).... ( -20.90)
>DroSec_CAF1 74613 95 - 1
AGUGAACA-----GUGUUCAAG------------UGUAUGUACAUAUGGACGACAUACAUACCAUAC--CAUACAACAUUGAUUCUAAUUGUAGAAAAAUACAUUUCACUAAAA
((((((((-----(((((....------------.(((((((..((((.....))))..)).)))))--.....))))))).(((((....)))))........)))))).... ( -20.60)
>DroSim_CAF1 76343 95 - 1
AGUGAACA-----GUGUUCAAG------------UGUAUGUACAUAUGGACGACAUACAUACCAUAC--CAUACAACAUUGAUUCUAAUUGUAGAAAAAUACAUUUCACUAAAA
((((((((-----(((((....------------.(((((((..((((.....))))..)).)))))--.....))))))).(((((....)))))........)))))).... ( -20.60)
>DroEre_CAF1 65882 101 - 1
AGUGAACA-----GUGUUCAAGUAUUCGUACAGGUGUAUGUACAUAUGGACGACAUACAUAC--------AUACAACAUUGAUUCUAAUUGUAGAAAAAUACAUUUCACUAAAA
((((((((-----(((((...(((....)))....(((((((..((((.....))))..)))--------))))))))))).(((((....)))))........)))))).... ( -25.00)
>DroYak_CAF1 80747 104 - 1
AGUGAACA-----GUGUUCAAGUAUUCGUACAGGUGUAUGUACAUAUGGACGACAUACAUACCAU-----ACACAACAUUGAUUCUAAUUGUAGAAAAAUACAUUUCACUAAAA
((((((((-----(((((...(((....)))..(((((((((..((((.....))))..)).)))-----))))))))))).(((((....)))))........)))))).... ( -25.50)
>DroPer_CAF1 64024 95 - 1
AUUUUACAAUCAUGUGUUCACG------------UAAUCGUACAGG-----CAUGUGCAUUGCAUAC--CAUACGAUACGGGUUCUAUUUGUAAAAAAAUACCUUUCACUAAAA
.((((((((....(...((.((------------((.(((((..((-----.((((.....)))).)--).)))))))))))..)...)))))))).................. ( -18.80)
>consensus
AGUGAACA_____GUGUUCAAG____________UGUAUGUACAUAUGGACGACAUACAUACCAUAC__CAUACAACAUUGAUUCUAAUUGUAGAAAAAUACAUUUCACUAAAA
..((((((......))))))..............(((((((...........))))))).......................(((((....))))).................. ( -8.35 =  -8.93 +   0.58)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:33 2006