Locus 8664

Sequence ID	3R_DroMel_CAF1
Location	23,153,983 – 23,154,143
Length	160
Max. P	0.857484

overview

Window 2

Location	23,153,983 – 23,154,103
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	98.47
Mean single sequence MFE	-44.98
Consensus MFE	-41.01
Energy contribution	-41.07
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.50
Structure conservation index	0.91
SVM decision value	0.81
SVM RNA-class probability	0.857484
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23153983 120 + 27905053
GCUACGGCAAAAUAUUAUUUCUGUGCAAAUGCACAACAUGGGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACC
((....)).............(((((....))))).((((((((.(((((((((((((((.((.(((.......))).)).)))))))))))))(((...))).)).))))))))..... ( -50.50)
>DroSec_CAF1 4798 120 + 1
GCUAUGGCAAAAUAUUAUUUCUGUUCAAAUGCACAACAUGGGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACC
((..(((((.((......)).)).)))...))....((((((((.(((((((((((((((.((.(((.......))).)).)))))))))))))(((...))).)).))))))))..... ( -42.40)
>DroSim_CAF1 9266 120 + 1
GCUAUGGCAAAAUAUUAUUUCUGUUCAAAUGCACAACAUGGGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACC
((..(((((.((......)).)).)))...))....((((((((.(((((((((((((((.((.(((.......))).)).)))))))))))))(((...))).)).))))))))..... ( -42.40)
>DroYak_CAF1 9241 120 + 1
GCUAGGGCAAAAUAUUAUUUCUGUUCAAAUGCACAACGUGGGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACC
....((((.............(((......)))...((.((((((.((((((((((((((.((.(((.......))).)).)))))))))))))).))))))))....))))........ ( -44.60)
>consensus
GCUAUGGCAAAAUAUUAUUUCUGUUCAAAUGCACAACAUGGGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACC
((...((((.((......)).)))).....))....((((((((.(((((((((((((((.((.(((.......))).)).)))))))))))))(((...))).)).))))))))..... (-41.01 = -41.07 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	23,154,023 – 23,154,143
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-43.44
Consensus MFE	-41.51
Energy contribution	-42.07
Covariance contribution	0.56
Combinations/Pair	1.02
Mean z-score	-1.62
Structure conservation index	0.96
SVM decision value	0.21
SVM RNA-class probability	0.635662
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23154023 120 + 27905053
GGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACCAAACUCUACUGAACAGCACUGCCCGCAGUUAGUUACUUUC
(((.((((((((((((((((.((.(((.......))).)).)))))))))(.(((((...))))).).)))))))..))).((((..((((....((...))...)))).))))...... ( -43.60)
>DroSec_CAF1 4838 120 + 1
GGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACCAAACUCAACUGAACAACACAGCCCGCAGUUAGUUACUCUC
(((.((((((((((((((((.((.(((.......))).)).)))))))))(.(((((...))))).).)))))))..))).((((.(((((..............)))))))))...... ( -43.14)
>DroSim_CAF1 9306 120 + 1
GGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACCAAACUCAACUGAACAGCACUGCCCGCAGUUAGUUACUCUC
(((.((((((((((((((((.((.(((.......))).)).)))))))))(.(((((...))))).).)))))))..))).((((.(((((....((...))...)))))))))...... ( -44.80)
>DroYak_CAF1 9281 120 + 1
GGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACCGAACUCCAUUGAACAGCACUGCCCGCAGUUAGUUACUCUC
(((.((((((((((((((((.((.(((.......))).)).)))))))))(.(((((...))))).).)))))))..)))..........((..(((((((....))))..)))..)).. ( -42.20)
>consensus
GGUGCAUGGGCUGCGGGCAUCCGAUUGAUAUAUGCAGAUGCGUGCUCGCAGUCCGAGUAUCUCGGUCCGCCCGUGAAACCAAACUCAACUGAACAGCACUGCCCGCAGUUAGUUACUCUC
(((.((((((((((((((((.((.(((.......))).)).)))))))))(.(((((...))))).).)))))))..))).((((.(((((....((...))...)))))))))...... (-41.51 = -42.07 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	23,154,023 – 23,154,143
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-44.28
Consensus MFE	-42.97
Energy contribution	-42.98
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.97
SVM decision value	0.00
SVM RNA-class probability	0.535068
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23154023 120 - 27905053
GAAAGUAACUAACUGCGGGCAGUGCUGUUCAGUAGAGUUUGGUUUCACGGGCGGACCGAGAUACUCGGACUGCGAGCACGCAUCUGCAUAUAUCAAUCGGAUGCCCGCAGCCCAUGCACC
....(((.....((((((((.(((.(((((.((((.(((((......)))))...(((((...))))).))))))))))))(((((.((......)))))))))))))))....)))... ( -44.10)
>DroSec_CAF1 4838 120 - 1
GAGAGUAACUAACUGCGGGCUGUGUUGUUCAGUUGAGUUUGGUUUCACGGGCGGACCGAGAUACUCGGACUGCGAGCACGCAUCUGCAUAUAUCAAUCGGAUGCCCGCAGCCCAUGCACC
.............(((((((((((.(((((.((.(((......)))))..((((.(((((...))))).))))))))).(((((((.((......))))))))).))))))))..))).. ( -44.20)
>DroSim_CAF1 9306 120 - 1
GAGAGUAACUAACUGCGGGCAGUGCUGUUCAGUUGAGUUUGGUUUCACGGGCGGACCGAGAUACUCGGACUGCGAGCACGCAUCUGCAUAUAUCAAUCGGAUGCCCGCAGCCCAUGCACC
....(((.....((((((((.(((.(((((.((.(((......)))))..((((.(((((...))))).))))))))))))(((((.((......)))))))))))))))....)))... ( -43.80)
>DroYak_CAF1 9281 120 - 1
GAGAGUAACUAACUGCGGGCAGUGCUGUUCAAUGGAGUUCGGUUUCACGGGCGGACCGAGAUACUCGGACUGCGAGCACGCAUCUGCAUAUAUCAAUCGGAUGCCCGCAGCCCAUGCACC
....(((.....((((((((.(((.(((((...(.((((((((.((.(((.....))).)).)).)))))).)))))))))(((((.((......)))))))))))))))....)))... ( -45.00)
>consensus
GAGAGUAACUAACUGCGGGCAGUGCUGUUCAGUUGAGUUUGGUUUCACGGGCGGACCGAGAUACUCGGACUGCGAGCACGCAUCUGCAUAUAUCAAUCGGAUGCCCGCAGCCCAUGCACC
....(((.....((((((((.(((.(((((....(((......)))....((((.(((((...))))).))))))))))))(((((.((......)))))))))))))))....)))... (-42.97 = -42.98 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:40 2006