Locus 5601

Sequence ID	3R_DroMel_CAF1
Location	14,786,350 – 14,786,454
Length	104
Max. P	0.936146

overview

Window 7

Location	14,786,350 – 14,786,454
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.49
Mean single sequence MFE	-29.03
Consensus MFE	-19.28
Energy contribution	-19.54
Covariance contribution	0.25
Combinations/Pair	1.18
Mean z-score	-1.91
Structure conservation index	0.66
SVM decision value	1.25
SVM RNA-class probability	0.936146
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14786350 104 + 27905053
ACACCAGCACACUCGC----ACACUUUAUGGCCA---UUCAAUGCCUUGGCCAAAUUGAAGCUGACGGCAAAUGUCACGUUUUAUGACUGCGUUUGCAUAUCAACAGUGUG---------
.......(((((((((----(..(((((((((((---..........))))))...))))).)).))(((((((.((.(((....))))))))))))........))))))--------- ( -29.10)
>DroPse_CAF1 42687 103 + 1
ACGGCA-----UCCGCCACACGUAUUUAUGGCCAGUAGUCAAUGUCUUAGCCAAAUUGAAGUUGACGGCAAGUGUCACGUUUUAUGACUGCAUUUGCAUAUCAACGAA------------
..(((.-----...)))...........((((....((.......))..)))).......(((((..(((((((.((.(((....))))))))))))...)))))...------------ ( -25.50)
>DroSec_CAF1 44599 104 + 1
ACACCAGCACACUCGC----ACACUUUAUGGCCA---UUCAAUGCCUUGGCCAAAUUGAAGCUGACGGCAAAUGUCACGUUUUAUGACUGCGUUUGCAUAUCAACAGUGUG---------
.......(((((((((----(..(((((((((((---..........))))))...))))).)).))(((((((.((.(((....))))))))))))........))))))--------- ( -29.10)
>DroSim_CAF1 46599 95 + 1
---------CACUCGC----ACACUUUAUGGCCA---UUCAAUGCCUUGGCCAAAUUGAAGCUGACGGCAAAUGUCACGUUUUAUGACUGCGUUUGCAUAUCAACAGUGUG---------
---------....(((----((.(((((((((((---..........))))))...))))).(((..(((((((.((.(((....))))))))))))...)))...)))))--------- ( -28.20)
>DroAna_CAF1 47164 116 + 1
ACUCGUGUACACUGACGGCAAGCCUUUAUGGGCA---UUCAAUGCCUUGGCCAAAUUGAAGCUGACGGCAAAUGUCACGUUUUAUGACUGCGUUUGCAUAUCAACA-UGUACAUACAACC
....(((((((.((.((((..((((....)))).---((((((((....))...))))))))))...(((((((.((.(((....)))))))))))).......))-)))))))...... ( -35.40)
>DroPer_CAF1 42764 103 + 1
ACGUCA-----UCCGCCACACGUAUUUAUGGCCAGUAGUCAAUGCCUUGGCCAAAUUGAAGUUGACGGCAAGUGUCACGUUUUAUGACUGCAUUUGCAUAUGAACGAA------------
.(((((-----(........(((.(((((((((((((.....)))..))))))...))))....)))(((((((.((.(((....))))))))))))..))).)))..------------ ( -26.90)
>consensus
ACACCA___CACUCGC____ACACUUUAUGGCCA___UUCAAUGCCUUGGCCAAAUUGAAGCUGACGGCAAAUGUCACGUUUUAUGACUGCGUUUGCAUAUCAACAGUGUG_________
.......((((((...............((((((.............)))))).......(.(((..(((((((.((.(((....))))))))))))...))).)))))))......... (-19.28 = -19.54 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	14,786,350 – 14,786,454
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.49
Mean single sequence MFE	-28.65
Consensus MFE	-21.10
Energy contribution	-21.27
Covariance contribution	0.17
Combinations/Pair	1.19
Mean z-score	-1.15
Structure conservation index	0.74
SVM decision value	0.45
SVM RNA-class probability	0.741108
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14786350 104 - 27905053
---------CACACUGUUGAUAUGCAAACGCAGUCAUAAAACGUGACAUUUGCCGUCAGCUUCAAUUUGGCCAAGGCAUUGAA---UGGCCAUAAAGUGU----GCGAGUGUGCUGGUGU
---------.(((((((((((..(((((....(((((.....))))).))))).)))))).......((((((..........---))))))...)))))----((.((....)).)).. ( -29.20)
>DroPse_CAF1 42687 103 - 1
------------UUCGUUGAUAUGCAAAUGCAGUCAUAAAACGUGACACUUGCCGUCAACUUCAAUUUGGCUAAGACAUUGACUACUGGCCAUAAAUACGUGUGGCGGA-----UGCCGU
------------...((((((.(((....)))(((((.....))))).......))))))........(((.....((........))((((((......))))))...-----.))).. ( -24.80)
>DroSec_CAF1 44599 104 - 1
---------CACACUGUUGAUAUGCAAACGCAGUCAUAAAACGUGACAUUUGCCGUCAGCUUCAAUUUGGCCAAGGCAUUGAA---UGGCCAUAAAGUGU----GCGAGUGUGCUGGUGU
---------.(((((((((((..(((((....(((((.....))))).))))).)))))).......((((((..........---))))))...)))))----((.((....)).)).. ( -29.20)
>DroSim_CAF1 46599 95 - 1
---------CACACUGUUGAUAUGCAAACGCAGUCAUAAAACGUGACAUUUGCCGUCAGCUUCAAUUUGGCCAAGGCAUUGAA---UGGCCAUAAAGUGU----GCGAGUG---------
---------((((((((((((..(((((....(((((.....))))).))))).)))))).......((((((..........---))))))...)))))----)......--------- ( -28.60)
>DroAna_CAF1 47164 116 - 1
GGUUGUAUGUACA-UGUUGAUAUGCAAACGCAGUCAUAAAACGUGACAUUUGCCGUCAGCUUCAAUUUGGCCAAGGCAUUGAA---UGCCCAUAAAGGCUUGCCGUCAGUGUACACGAGU
.......((((((-(((((((..(((((....(((((.....))))).))))).)))))).......((((...((((.....---.(((......))).)))))))))))))))..... ( -31.30)
>DroPer_CAF1 42764 103 - 1
------------UUCGUUCAUAUGCAAAUGCAGUCAUAAAACGUGACACUUGCCGUCAACUUCAAUUUGGCCAAGGCAUUGACUACUGGCCAUAAAUACGUGUGGCGGA-----UGACGU
------------.((((((.......(((((.(((((.....))))).(((((((............))).)))))))))........((((((......)))))))))-----)))... ( -28.80)
>consensus
_________CACACUGUUGAUAUGCAAACGCAGUCAUAAAACGUGACAUUUGCCGUCAGCUUCAAUUUGGCCAAGGCAUUGAA___UGGCCAUAAAGUCU____GCGAGUG___UGGCGU
.........((((((((((((.(((....)))(((((.....))))).......)))))).......((((((.............))))))...............))))))....... (-21.10 = -21.27 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:06 2006