Locus 8489

Sequence ID	3L_DroMel_CAF1
Location	22,283,322 – 22,283,482
Length	160
Max. P	0.999177

overview

Window 3

Location	22,283,322 – 22,283,442
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-42.10
Consensus MFE	-41.44
Energy contribution	-41.32
Covariance contribution	-0.12
Combinations/Pair	1.05
Mean z-score	-2.08
Structure conservation index	0.98
SVM decision value	3.42
SVM RNA-class probability	0.999177
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22283322 120 - 23771897
CAGCAGCUUCCGUUUGUGCCACAUGCGGCUGGCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAGAGAAGAGCAUUUAAAAAAUGUAUGCAGCGAAGGCCUUGACUGCAAAAUGUUG
(((((.(((((((((.((((((.(((((((......))).)))).(....))))).)).)))))))))......(((((.....))))).((((((((.....))).)))))...))))) ( -40.20)
>DroSec_CAF1 41692 120 - 1
CAGCAGCUUCCGUUUGUGCCACAUGCGGCUGGCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAGAGAAGAGCAUUUAAAAAAUGCAUGCAGCGAAGGCCUUGACUGCAAUAUGUUG
(((((.(((((((((.((((((.(((((((......))).)))).(....))))).)).)))))))))......(((((.....))))).((((((((.....))).)))))...))))) ( -42.50)
>DroSim_CAF1 33719 120 - 1
CAGCAGCUUCCGUUUGUGCCACAUGCGGCUGGCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAGAGAAGAGCAUUUAAAAAAUGCAUGCAGCGAAGGCCUUGACUGCAAUAUGUUG
(((((.(((((((((.((((((.(((((((......))).)))).(....))))).)).)))))))))......(((((.....))))).((((((((.....))).)))))...))))) ( -42.50)
>DroEre_CAF1 40263 120 - 1
CAGCAGCUUCCGUUUGUGCCACAUGCGGCUGUCGGAGGCAUGCAACACACGGUGGGCAGGAGCGGAAGAGGAGAGCAUUUAAAAAAUGCAUGCAGCAAAGGCCUUGACUGCAAUAUGUUG
(((((.(((((((((.((((...(((((((......))).)))).(((...))))))).)))))))))......(((((.....))))).((((((((.....))).)))))...))))) ( -45.00)
>DroYak_CAF1 6332 120 - 1
CAGCAGCUUCCGUUUGUGCCACAUGCGGCUGUCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAAAGGAGAGCAUUUAAAAAAUGCAUGCAGCGAAGGCCUUGACUGCAAUAUGUUG
(((((..((((((((.((((((.((..(((((.....))).))..))....)))).)).)))))))).......(((((.....))))).((((((((.....))).)))))...))))) ( -40.30)
>consensus
CAGCAGCUUCCGUUUGUGCCACAUGCGGCUGGCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAGAGAAGAGCAUUUAAAAAAUGCAUGCAGCGAAGGCCUUGACUGCAAUAUGUUG
(((((.(((((((((.((((((.(((((((......))).)))).(....))))).)).)))))))))......(((((.....))))).((((((((.....))).)))))...))))) (-41.44 = -41.32 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	22,283,362 – 22,283,482
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-43.80
Consensus MFE	-43.26
Energy contribution	-42.94
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-2.11
Structure conservation index	0.99
SVM decision value	3.16
SVM RNA-class probability	0.998599
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22283362 120 + 23771897
AAAUGCUCUUCUCUUCCGCUCCUGUCCACCGUGUGUUGCAUGCCUCCGCCAGCCGCAUGUGGCACAAACGGAAGCUGCUGUUUGGCUCGCAUAAAUAAUAACAAUGGCAGGAGACGGUGG
............((.(((((((((.(((((((((((..(((((...........)))))..))))..))))..((.(((....)))..))..............))))))))).))).)) ( -43.20)
>DroSec_CAF1 41732 120 + 1
AAAUGCUCUUCUCUUCCGCUCCUGUCCACCGUGUGUUGCAUGCCUCCGCCAGCCGCAUGUGGCACAAACGGAAGCUGCUGUUUGGCUCGCAUAAAUAAUAACAAUGGCAGGAGACGGUGG
............((.(((((((((.(((((((((((..(((((...........)))))..))))..))))..((.(((....)))..))..............))))))))).))).)) ( -43.20)
>DroSim_CAF1 33759 120 + 1
AAAUGCUCUUCUCUUCCGCUCCUGUCCACCGUGUGUUGCAUGCCUCCGCCAGCCGCAUGUGGCACAAACGGAAGCUGCUGUUUGGCUCGCAUAAAUAAUAACAAUGGCAGGAGACGGUGG
............((.(((((((((.(((((((((((..(((((...........)))))..))))..))))..((.(((....)))..))..............))))))))).))).)) ( -43.20)
>DroEre_CAF1 40303 120 + 1
AAAUGCUCUCCUCUUCCGCUCCUGCCCACCGUGUGUUGCAUGCCUCCGACAGCCGCAUGUGGCACAAACGGAAGCUGCUGUUUGGCUCGCAUAAAUAAUAACAAUGGCAGGAGACGGUGG
.........((....(((((((((((..((((((((..(((((...........)))))..))))..))))..((.(((....)))..))...............)))))))).))).)) ( -45.80)
>DroYak_CAF1 6372 120 + 1
AAAUGCUCUCCUUUUCCGCUCCUGUCCACCGUGUGUUGCAUGCCUCCGACAGCCGCAUGUGGCACAAACGGAAGCUGCUGUUUGGCUCGCAUAAAUAAUAACAAUGGCAGGAGACGGUGG
.........((....(((((((((.(((((((((((..(((((...........)))))..))))..))))..((.(((....)))..))..............))))))))).))).)) ( -43.60)
>consensus
AAAUGCUCUUCUCUUCCGCUCCUGUCCACCGUGUGUUGCAUGCCUCCGCCAGCCGCAUGUGGCACAAACGGAAGCUGCUGUUUGGCUCGCAUAAAUAAUAACAAUGGCAGGAGACGGUGG
............(..(((((((((((..((((((((..(((((...........)))))..))))..))))..((.(((....)))..))...............)))))))).)))..) (-43.26 = -42.94 +  -0.32)

alignment

secondary structure

dotplot

Window 5

Location	22,283,362 – 22,283,482
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-45.46
Consensus MFE	-44.82
Energy contribution	-45.22
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	0.99
SVM decision value	3.30
SVM RNA-class probability	0.998965
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22283362 120 - 23771897
CCACCGUCUCCUGCCAUUGUUAUUAUUUAUGCGAGCCAAACAGCAGCUUCCGUUUGUGCCACAUGCGGCUGGCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAGAGAAGAGCAUUU
...(((.(((((((((((((.........((((.((......)).(((((((((...(((......))).))))))))).))))....))))))).)))))))))............... ( -46.42)
>DroSec_CAF1 41732 120 - 1
CCACCGUCUCCUGCCAUUGUUAUUAUUUAUGCGAGCCAAACAGCAGCUUCCGUUUGUGCCACAUGCGGCUGGCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAGAGAAGAGCAUUU
...(((.(((((((((((((.........((((.((......)).(((((((((...(((......))).))))))))).))))....))))))).)))))))))............... ( -46.42)
>DroSim_CAF1 33759 120 - 1
CCACCGUCUCCUGCCAUUGUUAUUAUUUAUGCGAGCCAAACAGCAGCUUCCGUUUGUGCCACAUGCGGCUGGCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAGAGAAGAGCAUUU
...(((.(((((((((((((.........((((.((......)).(((((((((...(((......))).))))))))).))))....))))))).)))))))))............... ( -46.42)
>DroEre_CAF1 40303 120 - 1
CCACCGUCUCCUGCCAUUGUUAUUAUUUAUGCGAGCCAAACAGCAGCUUCCGUUUGUGCCACAUGCGGCUGUCGGAGGCAUGCAACACACGGUGGGCAGGAGCGGAAGAGGAGAGCAUUU
...(((.((((((((..............((((.((......)).(((((((.....(((......)))...))))))).)))).(((...))))))))))))))............... ( -44.50)
>DroYak_CAF1 6372 120 - 1
CCACCGUCUCCUGCCAUUGUUAUUAUUUAUGCGAGCCAAACAGCAGCUUCCGUUUGUGCCACAUGCGGCUGUCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAAAGGAGAGCAUUU
...(((.(((((((((((((.........((((.((......)).(((((((.....(((......)))...))))))).))))....))))))).)))))))))............... ( -43.52)
>consensus
CCACCGUCUCCUGCCAUUGUUAUUAUUUAUGCGAGCCAAACAGCAGCUUCCGUUUGUGCCACAUGCGGCUGGCGGAGGCAUGCAACACACGGUGGACAGGAGCGGAAGAGAAGAGCAUUU
...(((.(((((((((((((.........((((.((......)).(((((((((...(((......))).))))))))).))))....))))))).)))))))))............... (-44.82 = -45.22 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:55 2006