Locus 8062

Sequence ID	3L_DroMel_CAF1
Location	21,258,599 – 21,258,731
Length	132
Max. P	0.922626

overview

Window 3

Location	21,258,599 – 21,258,700
Length	101
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	87.74
Mean single sequence MFE	-22.88
Consensus MFE	-15.77
Energy contribution	-16.90
Covariance contribution	1.13
Combinations/Pair	1.10
Mean z-score	-1.61
Structure conservation index	0.69
SVM decision value	0.06
SVM RNA-class probability	0.563103
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21258599 101 - 23771897
--------GUACAAGUAUGUCCUGUCCACGCAUACACACGCACAAGGGCACACAACCACCAAGAGGAAAGCAG-AACACACAGAUGUAAGGACACACUGACUUACAUUCA
--------......((.(((.((((((..((........))....((........)).......))...))))-.))).)).((((((((..........)))))))).. ( -19.30)
>DroSec_CAF1 16628 102 - 1
--------GUACAAGUAUGUCCUGCCCACGCAUACACACGCACAAGGGCACACAACCACCACGUGGAAACCAGGAGCACACAGAUGUAAGGACACACUGACUUACAUUCA
--------......((.((((((((((..((........))....))))......((((...)))).....)))).)).)).((((((((..........)))))))).. ( -24.90)
>DroSim_CAF1 16447 102 - 1
--------GUACAAGUAUGUCCUGCCCACGCAUACACACGCACAAGGGCACACAACCACCACGUGGAAACCAGGAGCACACAGAUGUAAGGACACACUGACUUACAUUCA
--------......((.((((((((((..((........))....))))......((((...)))).....)))).)).)).((((((((..........)))))))).. ( -24.90)
>DroEre_CAF1 17977 104 - 1
GUAAGUAUGUACGAGUAUGUCCUGCCCACGCAUACACACGCACAACAGCACACAACC---ACGGGGAAACCAGAA--ACACAGAUGUAAGG-CGCCCUGACUUACAUUCA
((((((.(((....((((((.........))))))....((......))..)))...---.(((((...((....--(((....)))..))-..)))))))))))..... ( -22.40)
>consensus
________GUACAAGUAUGUCCUGCCCACGCAUACACACGCACAAGGGCACACAACCACCACGUGGAAACCAGGAGCACACAGAUGUAAGGACACACUGACUUACAUUCA
........(((..(((.((((((((((..((........))....))))......(((.....)))......................)))))).)))....)))..... (-15.77 = -16.90 +   1.13)

alignment

secondary structure

dotplot

Window 4

Location	21,258,638 – 21,258,731
Length	93
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	87.41
Mean single sequence MFE	-35.55
Consensus MFE	-27.36
Energy contribution	-28.42
Covariance contribution	1.06
Combinations/Pair	1.10
Mean z-score	-2.27
Structure conservation index	0.77
SVM decision value	1.15
SVM RNA-class probability	0.922626
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21258638 93 + 23771897
CUUUCCUCUUGGUGGUUGUGUGCCCUUGUGCGUGUGUAUGCGUGGACAGGACAUACUUGUAC----------GCUUACACGAGCAUUCUGUACUGAGUGGGAG
..((((.((..(((((.....)))...((((.((((((.((((..(((((.....)))))))----------)).)))))).)))).....))..)).)))). ( -32.70)
>DroSec_CAF1 16668 93 + 1
GUUUCCACGUGGUGGUUGUGUGCCCUUGUGCGUGUGUAUGCGUGGGCAGGACAUACUUGUAC----------GCUUACAUGAGCAUUCUGUGCUGCGUGGGAG
..(((((((..(((((.....)))...((((..(((((.((((..(((((.....)))))))----------)).)))))..)))).....))..))))))). ( -36.10)
>DroSim_CAF1 16487 93 + 1
GUUUCCACGUGGUGGUUGUGUGCCCUUGUGCGUGUGUAUGCGUGGGCAGGACAUACUUGUAC----------GCUUACAUGAGCAUUCUGUGCUGCGUGGGAG
..(((((((..(((((.....)))...((((..(((((.((((..(((((.....)))))))----------)).)))))..)))).....))..))))))). ( -36.10)
>DroEre_CAF1 18014 100 + 1
GUUUCCCCGU---GGUUGUGUGCUGUUGUGCGUGUGUAUGCGUGGGCAGGACAUACUCGUACAUACUUACAUGCUUACAUGAGCAUUCUGAGCUGCGUGGGAG
...((((((.---.(((..(((((..((((((((((((((..((((.........))))..)))))..))))))..)))..)))))....)))..)).)))). ( -37.30)
>consensus
GUUUCCACGUGGUGGUUGUGUGCCCUUGUGCGUGUGUAUGCGUGGGCAGGACAUACUUGUAC__________GCUUACAUGAGCAUUCUGUGCUGCGUGGGAG
..(((((((((((....(((((((((..(((((....)))))..))..)).)))))................((((....)))).......))))))))))). (-27.36 = -28.42 +   1.06)

alignment

secondary structure

dotplot

Window 5

Location	21,258,638 – 21,258,731
Length	93
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	87.41
Mean single sequence MFE	-22.03
Consensus MFE	-14.86
Energy contribution	-15.43
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.56
Structure conservation index	0.67
SVM decision value	-0.02
SVM RNA-class probability	0.523876
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21258638 93 - 23771897
CUCCCACUCAGUACAGAAUGCUCGUGUAAGC----------GUACAAGUAUGUCCUGUCCACGCAUACACACGCACAAGGGCACACAACCACCAAGAGGAAAG
......(((.........(((..(((((.((----------(((((.(.....).)))..)))).)))))..)))...((........)).....)))..... ( -19.70)
>DroSec_CAF1 16668 93 - 1
CUCCCACGCAGCACAGAAUGCUCAUGUAAGC----------GUACAAGUAUGUCCUGCCCACGCAUACACACGCACAAGGGCACACAACCACCACGUGGAAAC
...(((((..........(((((.(((..((----------((....((((((.........))))))..))))))).)))))...........))))).... ( -23.10)
>DroSim_CAF1 16487 93 - 1
CUCCCACGCAGCACAGAAUGCUCAUGUAAGC----------GUACAAGUAUGUCCUGCCCACGCAUACACACGCACAAGGGCACACAACCACCACGUGGAAAC
...(((((..........(((((.(((..((----------((....((((((.........))))))..))))))).)))))...........))))).... ( -23.10)
>DroEre_CAF1 18014 100 - 1
CUCCCACGCAGCUCAGAAUGCUCAUGUAAGCAUGUAAGUAUGUACGAGUAUGUCCUGCCCACGCAUACACACGCACAACAGCACACAACC---ACGGGGAAAC
.((((.((..((((...(((((((((....))))..)))))....)))).(((.(((.....((........))....))).))).....---.))))))... ( -22.20)
>consensus
CUCCCACGCAGCACAGAAUGCUCAUGUAAGC__________GUACAAGUAUGUCCUGCCCACGCAUACACACGCACAAGGGCACACAACCACCACGUGGAAAC
...(((((..........(((((.(((..((((......))))....((((((.........))))))......))).)))))...........))))).... (-14.86 = -15.43 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:14 2006