Locus 1084

Sequence ID	3R_DroMel_CAF1
Location	3,304,455 – 3,304,604
Length	149
Max. P	0.582360

overview

Window 6

Location	3,304,455 – 3,304,564
Length	109
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	85.31
Mean single sequence MFE	-42.00
Consensus MFE	-28.07
Energy contribution	-28.73
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.67
SVM decision value	0.03
SVM RNA-class probability	0.547953
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3304455 109 + 27905053
CGCCAGCA---------GCAGCAGCAGUCAGGGCCAAAGCCGUGGCCAUAUCUG--CAGCUGGGGCACAGCGAUUUCUAUUCCAAUGCUGCCAAGGCUGCGCUCGAGGCCAAUAAAUAUU
.((((((.---------((((((((((....(((((......)))))....)))--).((((.....))))..............))))))....)))).)).................. ( -41.20)
>DroSec_CAF1 8533 120 + 1
CGCCAGCAGGAGCAGCAGCAGCACCAGUCAGGGCCAAAGCCGUGGCCAUAUCUGCGCAGCUGGGGCACAGCGAUUUCUAUUCCAAUGCUGCCAAGGCUGCGCUCGAGGCCAAUAAAUAUU
.(((.....((((....((((.....((((.(((....))).)))).....))))((((((..((((((..((.......))...)).))))..))))))))))..)))........... ( -45.70)
>DroYak_CAF1 18754 106 + 1
------------CAGCAGAAGCAGGAGUCAGGGCCAAAGCCGUGGCCAUAUCUG--CAGCUGGGGCACAGCGCUUUCUAUUCCAACGCUGCCAAGGCAGCGCUCCAGGCCAAUAAAUAUU
------------..(((((.....(.((((.(((....))).)))))...))))--)..(((((((..((......))........(((((....))))))))))))............. ( -39.10)
>consensus
CGCCAGCA____CAGCAGCAGCAGCAGUCAGGGCCAAAGCCGUGGCCAUAUCUG__CAGCUGGGGCACAGCGAUUUCUAUUCCAAUGCUGCCAAGGCUGCGCUCGAGGCCAAUAAAUAUU
.................(((((....((((.(((....))).))))............((((.....))))...............)))))...((((........)))).......... (-28.07 = -28.73 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	3,304,486 – 3,304,604
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.45
Mean single sequence MFE	-41.50
Consensus MFE	-32.26
Energy contribution	-33.07
Covariance contribution	0.81
Combinations/Pair	1.10
Mean z-score	-1.89
Structure conservation index	0.78
SVM decision value	0.10
SVM RNA-class probability	0.582360
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3304486 118 + 27905053
CGUGGCCAUAUCUG--CAGCUGGGGCACAGCGAUUUCUAUUCCAAUGCUGCCAAGGCUGCGCUCGAGGCCAAUAAAUAUUUUUUGGGGCACGCGAUUUUGUGCGCCACUUUGGUUUUCCU
..(((((.....((--(((((..((((((..((.......))...)).))))..))))))).....)))))............(((.(((((......))))).)))....((....)). ( -40.50)
>DroSec_CAF1 8573 120 + 1
CGUGGCCAUAUCUGCGCAGCUGGGGCACAGCGAUUUCUAUUCCAAUGCUGCCAAGGCUGCGCUCGAGGCCAAUAAAUAUUUUUUGGGGCACGCGAUUUUGUGCGGCACUUUGCCUUUUCU
..(((((......((((((((..((((((..((.......))...)).))))..))))))))....)))))................(((((......)))))(((.....)))...... ( -43.70)
>DroSim_CAF1 12182 120 + 1
CGUGGCCAUAUCUGCGCAGCUGGGGCACAGCGAUUUCUAUUCCAAUGCUGCCAAGGCUGCGCUCGAGGCCAAUAAAUAUUUUUUGGGGCACGCGAUUUUGUGCGGCACUUUGCCUUUUCU
..(((((......((((((((..((((((..((.......))...)).))))..))))))))....)))))................(((((......)))))(((.....)))...... ( -43.70)
>DroYak_CAF1 18782 116 + 1
CGUGGCCAUAUCUG--CAGCUGGGGCACAGCGCUUUCUAUUCCAACGCUGCCAAGGCAGCGCUCCAGGCCAAUAAAUAUUUUUUGGGGCACGCGAUUUUG--CGCCAUUUCGCUUUUCCU
.(((((((.(((.(--(..(((((((..((......))........(((((....))))))))))))(((...(((....)))...)))..)))))..))--.)))))............ ( -38.10)
>consensus
CGUGGCCAUAUCUG__CAGCUGGGGCACAGCGAUUUCUAUUCCAAUGCUGCCAAGGCUGCGCUCGAGGCCAAUAAAUAUUUUUUGGGGCACGCGAUUUUGUGCGCCACUUUGCCUUUCCU
(((((((......((((((((..((((..(((.............)))))))..))))))))......((((..........))))))).)))).........(((.....)))...... (-32.26 = -33.07 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:13 2006