Locus 4790

Sequence ID	3L_DroMel_CAF1
Location	13,425,351 – 13,425,510
Length	159
Max. P	0.530630

overview

Window 2

Location	13,425,351 – 13,425,470
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.07
Mean single sequence MFE	-30.96
Consensus MFE	-23.76
Energy contribution	-24.04
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-1.68
Structure conservation index	0.77
SVM decision value	-0.01
SVM RNA-class probability	0.530630
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13425351 119 + 23771897
AAUAGGUCUUAAUAGAGCUAACAAUUAUUU-UUGGUAGCCACGCUUCGCGAAGCUGGGCGCAAACAAAAAAGAACGCAAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAU
..(((.(((....))).))).........(-(((((((((..((((....))))..)))......................((((.((((..........))))..))))..))))))). ( -28.10)
>DroSec_CAF1 22394 120 + 1
AAUAGGUCUUAAUAGAGCUAACAAUUAUUUUUUGGUAGCCACGCUUCGCGGAGCUGGGCGCAAACAAAAAAGAACGCAAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAU
..(((.(((....))).)))..........((((((((((..((((....))))..)))......................((((.((((..........))))..))))..))))))). ( -29.00)
>DroSim_CAF1 24152 120 + 1
AAUAGGUCUUAAUAGAGCUAACAAUUAUUUGUUGGUAGCCACGCUUCGCGGAGCUGGGCGCAAACAAAAAAGAACGCAAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAU
....(((.((.((((.((((((((....)))))))).(((((((...))((((.(..(((..............)))..)))))))))))))).)).)))..((....)).......... ( -30.74)
>DroEre_CAF1 23454 119 + 1
AAUAGGUCUGCAUAGGCCAAACAAUUAUAU-UUGGUAGACACGCUUCGCGGAGCUGGGCGCGAAUAAAAAAGAACGCCAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAU
.(((((((.((....((((((........)-)))))......))...((((((...((((..............))))..))))))))))))).........((....)).......... ( -32.04)
>DroYak_CAF1 22507 119 + 1
CAUAGGUCUGCAUAGACCAAACAAUUAGAU-UUGGUAGCCACGCUUCGCGGAGCUGGGCGCAAACAAAAAAGAACGCCAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAU
..(((.((((...(((((...(((......-)))((((((((((...))((((...((((..............))))..)))))))).)))).......))))).))))....)))... ( -34.94)
>consensus
AAUAGGUCUUAAUAGAGCUAACAAUUAUUU_UUGGUAGCCACGCUUCGCGGAGCUGGGCGCAAACAAAAAAGAACGCAAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAU
..(((.(((....))).)))...........(((((((((..((((....))))..)))......................((((.((((..........))))..))))..)))))).. (-23.76 = -24.04 +   0.28)

alignment

secondary structure

dotplot

Window 3

Location	13,425,390 – 13,425,510
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.33
Mean single sequence MFE	-33.63
Consensus MFE	-28.46
Energy contribution	-28.74
Covariance contribution	0.28
Combinations/Pair	1.10
Mean z-score	-1.35
Structure conservation index	0.85
SVM decision value	-0.03
SVM RNA-class probability	0.519114
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13425390 120 + 23771897
ACGCUUCGCGAAGCUGGGCGCAAACAAAAAAGAACGCAAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAUCCAAUUGCAGUCCAAUUAGCAGUCGGACGCCAAUGAAGCG
.((((((((...))..((((.....................((((.((((..........))))..)))).........(((.(((((..........))))).)))))))...)))))) ( -32.00)
>DroSec_CAF1 22434 120 + 1
ACGCUUCGCGGAGCUGGGCGCAAACAAAAAAGAACGCAAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAUCCAAUUGCAGUCCAAUUAGCAGUCGGUCGUCAAUGAAGCG
.((((((((((((.(..(((..............)))..)))))))((((............((....)).............(((((..........))))).))))......)))))) ( -30.84)
>DroSim_CAF1 24192 120 + 1
ACGCUUCGCGGAGCUGGGCGCAAACAAAAAAGAACGCAAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAUCCAAUUGCAGUCCAAUUAGCAGUCGGGCGUCAAUGAAGCG
.(((((((((........)))..........((.(((....((((.((((..........))))..))))..........((.(((((..........))))).)))))))...)))))) ( -33.60)
>DroEre_CAF1 23493 120 + 1
ACGCUUCGCGGAGCUGGGCGCGAAUAAAAAAGAACGCCAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAUCCAAUUGCAGUCCAAUUAGCAGCCGAGCGCCAAUGAAGCG
.(((((((.((.(((.(((((....................((((.((((..........))))..))))............(((((.....))))).)).))).))).))..))))))) ( -36.00)
>DroYak_CAF1 22546 120 + 1
ACGCUUCGCGGAGCUGGGCGCAAACAAAAAAGAACGCCAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAUCCAAUUGCAGUCCAAUUAGCAGGCGAGCGCCAAUGAAGCG
.((((((((...))..(((((...(......)..((((...((((.((((..........))))..))))...............(((..........))))))).)))))...)))))) ( -35.70)
>consensus
ACGCUUCGCGGAGCUGGGCGCAAACAAAAAAGAACGCAAACUCCGUGGCCUAUAAAUAUCGGUCUUCGGAAUUACUAAAUCCAAUUGCAGUCCAAUUAGCAGUCGGGCGCCAAUGAAGCG
.(((((((.((.(((.(((((....................((((.((((..........))))..))))............(((((.....))))).)).))).))).))..))))))) (-28.46 = -28.74 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:22 2006