Locus 4587

Sequence ID	3R_DroMel_CAF1
Location	12,080,667 – 12,080,776
Length	109
Max. P	0.981722

overview

Window 4

Location	12,080,667 – 12,080,776
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.18
Mean single sequence MFE	-35.62
Consensus MFE	-30.16
Energy contribution	-30.32
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.85
SVM decision value	1.70
SVM RNA-class probability	0.973065
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12080667 109 + 27905053
--CUUGGUUUGG---------UUGGUUCGUUCCCAAAAGGGCGAACCAUCCGGAGUCCGGACGGCCAGCAUGUCUAGACUCGCUCCAGCCCCUAUACCAAAAAUAACACCGAAAAUACAG
--.(((((.(((---------.((((((((((......)))))))))).)))(((((..(((((....).))))..)))))((....))......))))).................... ( -35.30)
>DroSec_CAF1 17390 109 + 1
--CUUGGCUUGG---------UUGGUGCGUUCCCAAAAGGGCGAACCAUCCGGAGUCCGGACGGCCAGCAUGUCUAGACUCGCUCCAGCCCCUAUACCAAAAAUAACACCGAAAAUACAG
--.((((...((---------((((.((((((((.....)).))))......(((((..(((((....).))))..))))))).))))))......)))).................... ( -34.30)
>DroSim_CAF1 17578 109 + 1
--CGUGGCUUGG---------UUGGUUCGUUCCCAAAAGGGCGAACCAUCCGGAGUCCGGACGGCCAGCAUGUCUAGACUCGCUCCAGCCCCUAUACCAAAAAUAACACCGAAAAUACAG
--.(.(((((((---------.((((((((((......)))))))))).)))(((((..(((((....).))))..))))).....)))).)............................ ( -36.10)
>DroEre_CAF1 19443 109 + 1
--CUUGGUUUGG---------UUGGUUCGUUCCCAAAAGGGCGAACCAUCCGGAGUCCGGACGGCCAGCAUGUCUAGACUCGCUCCAGCCCCUAUACCAAAAAUAACACCGAAAAUACAG
--.(((((.(((---------.((((((((((......)))))))))).)))(((((..(((((....).))))..)))))((....))......))))).................... ( -35.30)
>DroYak_CAF1 19812 120 + 1
CUCUUGGUUUGGUUGGUUUGGUUGAUUCGGUCCCAAAAGGGCGAACCAUCCGGAGUCCGGACGGCCAGCAUGUCUAGACUCGCUCCAGCCCCUAUACCAAAAAUAACACCGAAAAUACAG
...(((((..((((((..(((.((.((((..(((....))))))).)).)))(((((..(((((....).))))..)))))...)))))).....))))).................... ( -37.10)
>consensus
__CUUGGUUUGG_________UUGGUUCGUUCCCAAAAGGGCGAACCAUCCGGAGUCCGGACGGCCAGCAUGUCUAGACUCGCUCCAGCCCCUAUACCAAAAAUAACACCGAAAAUACAG
.....((((.((..........(((((((..(((....))))))))))....(((((..(((((....).))))..)))))...)))))).............................. (-30.16 = -30.32 +   0.16)

alignment

secondary structure

dotplot

Window 5

Location	12,080,667 – 12,080,776
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.18
Mean single sequence MFE	-40.72
Consensus MFE	-36.20
Energy contribution	-36.20
Covariance contribution	-0.00
Combinations/Pair	1.06
Mean z-score	-1.75
Structure conservation index	0.89
SVM decision value	1.90
SVM RNA-class probability	0.981722
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12080667 109 - 27905053
CUGUAUUUUCGGUGUUAUUUUUGGUAUAGGGGCUGGAGCGAGUCUAGACAUGCUGGCCGUCCGGACUCCGGAUGGUUCGCCCUUUUGGGAACGAACCAA---------CCAAACCAAG--
(((......)))........(((((...(((((((((.((.(.((((.....)))))))))))).))))((.((((((((((....)))..))))))).---------))..))))).-- ( -41.20)
>DroSec_CAF1 17390 109 - 1
CUGUAUUUUCGGUGUUAUUUUUGGUAUAGGGGCUGGAGCGAGUCUAGACAUGCUGGCCGUCCGGACUCCGGAUGGUUCGCCCUUUUGGGAACGCACCAA---------CCAAGCCAAG--
(((......)))........(((((....((..(((.(((..((((((...((..(((((((((...)))))))))..))...))))))..))).))).---------))..))))).-- ( -39.90)
>DroSim_CAF1 17578 109 - 1
CUGUAUUUUCGGUGUUAUUUUUGGUAUAGGGGCUGGAGCGAGUCUAGACAUGCUGGCCGUCCGGACUCCGGAUGGUUCGCCCUUUUGGGAACGAACCAA---------CCAAGCCACG--
(((......))).........((((...(((((((((.((.(.((((.....)))))))))))).))))((.((((((((((....)))..))))))).---------))..))))..-- ( -40.30)
>DroEre_CAF1 19443 109 - 1
CUGUAUUUUCGGUGUUAUUUUUGGUAUAGGGGCUGGAGCGAGUCUAGACAUGCUGGCCGUCCGGACUCCGGAUGGUUCGCCCUUUUGGGAACGAACCAA---------CCAAACCAAG--
(((......)))........(((((...(((((((((.((.(.((((.....)))))))))))).))))((.((((((((((....)))..))))))).---------))..))))).-- ( -41.20)
>DroYak_CAF1 19812 120 - 1
CUGUAUUUUCGGUGUUAUUUUUGGUAUAGGGGCUGGAGCGAGUCUAGACAUGCUGGCCGUCCGGACUCCGGAUGGUUCGCCCUUUUGGGACCGAAUCAACCAAACCAACCAAACCAAGAG
..........(((.......(((((...(((((((((.((.(.((((.....)))))))))))).))))((.((((((((((....)))..))))))).))..)))))....)))..... ( -41.00)
>consensus
CUGUAUUUUCGGUGUUAUUUUUGGUAUAGGGGCUGGAGCGAGUCUAGACAUGCUGGCCGUCCGGACUCCGGAUGGUUCGCCCUUUUGGGAACGAACCAA_________CCAAACCAAG__
(((......))).......((((((...(((((((((.((.(.((((.....)))))))))))).))))...((((((((((....)))..)))))))..............)))))).. (-36.20 = -36.20 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:47 2006