Locus 9413

Sequence ID	3R_DroMel_CAF1
Location	24,930,892 – 24,931,080
Length	188
Max. P	0.999002

overview

Window 1

Location	24,930,892 – 24,930,984
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	90.65
Mean single sequence MFE	-20.42
Consensus MFE	-17.10
Energy contribution	-17.90
Covariance contribution	0.80
Combinations/Pair	1.17
Mean z-score	-2.93
Structure conservation index	0.84
SVM decision value	3.32
SVM RNA-class probability	0.999002
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24930892 92 + 27905053
GAAACCAACAGCAUCUGCCCAUCAAUCGUCAACCGGCGCCACAGCAAUCACACUUCCUGGACAAUUCAAAUUCGAACAACAUGAUGGGCAAU
...............(((((((((...(((.....((......)).....((.....)))))..(((......))).....))))))))).. ( -20.00)
>DroSec_CAF1 1582 92 + 1
GAAACCAACAGCAUCUGCCCAUCAAUCGCCAACAGGCAACCCAGCAAUCACACUUCCUGGACAAUUCAAAUUCGAACAACAUGAUGGGCAAU
...............(((((((((...(((....)))...((((.((......)).)))).....................))))))))).. ( -24.40)
>DroSim_CAF1 1020 92 + 1
GAAACCAACAGCAUCUGCCCAUCAAUCGCCAACAGGCAACCCAGCAAUCACACUUCCUGGACAAUUCAAAUUCGAACAACAUGAUGGGCAAU
...............(((((((((...(((....)))...((((.((......)).)))).....................))))))))).. ( -24.40)
>DroEre_CAF1 1520 92 + 1
GAAACCAGCAGCAUCUGCCCAUUAAUCGCCAACCGGCGCCUCAGCAAUCGCACUUCAUGGACAACUCAAAUUCUAACAACAUGAUGGGCAAU
...............(((((((((..((((....)))).....((....))..............................))))))))).. ( -20.70)
>DroYak_CAF1 1532 92 + 1
GAAACCAGCAGCAUCUGCCCAUCAACCGACAAACGGCGCCCCAGCAAUCGCACUAUAUGGACAACUCAAAUUCUAACAACAUGAUGAGCAAU
...............(((.(((((.(((.....))).......((....))..............................))))).))).. ( -12.60)
>consensus
GAAACCAACAGCAUCUGCCCAUCAAUCGCCAACCGGCGCCCCAGCAAUCACACUUCCUGGACAAUUCAAAUUCGAACAACAUGAUGGGCAAU
...............(((((((((...(((....)))...((((.((......)).)))).....................))))))))).. (-17.10 = -17.90 +   0.80)

alignment

secondary structure

dotplot

Window 2

Location	24,930,984 – 24,931,080
Length	96
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	88.27
Mean single sequence MFE	-28.58
Consensus MFE	-19.44
Energy contribution	-20.04
Covariance contribution	0.60
Combinations/Pair	1.19
Mean z-score	-2.08
Structure conservation index	0.68
SVM decision value	0.13
SVM RNA-class probability	0.598731
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24930984 96 + 27905053
AGCAACCACAUGUCGGAUCUGUUCCCCAAUGGUUGCAUUGACAAGAGCAAUCAAAGCACCACCAGCAGCAGCAAUAGCAGUUGCGUUAG---CGAAAGC
.(((((((..((..(((.....))).)).)))))))..((((..((....))............(((((.((....)).)))))))))(---(....)) ( -29.30)
>DroSec_CAF1 1674 96 + 1
AGCAACCACAUGUCGGAUCUGUUCCCCAAUGGUUGCAUUGACAAGAGCAACCAGAGCACCACCAGCAGCAGCAAUAGCAGUUGCGUUAG---CGAAAGC
.(((((((..((..(((.....))).)).)))))))..((((....((.......)).......(((((.((....)).)))))))))(---(....)) ( -28.90)
>DroSim_CAF1 1112 96 + 1
AGCAACCACAUGUCGGAUCUGUUCCCCAAUGGUUGCAUUGACAAGAGCAACCAGAGCACCACCAGCAGCAGCAAUAGCAGUUGCGUUAG---CGAAAGC
.(((((((..((..(((.....))).)).)))))))..((((....((.......)).......(((((.((....)).)))))))))(---(....)) ( -28.90)
>DroWil_CAF1 1464 99 + 1
ACAAAUCACAUGGCCGAUCUCUUUCCCAAUGGCUGCAUUGACAAAAGCAAUCAGAGCAUUAGCAGCAGCAACAACAGCAGCUGUGCCAGUAGUGAGCAC
.....((((.((((.(((..((((..(((((....)))))...))))..))).........(((((.((.......)).)))))))))...)))).... ( -25.40)
>DroYak_CAF1 1624 96 + 1
AGCAACCACAUGUCGGAUCUGUUCCCCAAUGGUUGCAUCGACAAGAGCAACCAGAGCACCACCAGCAGCAGCAAUAGCAGUUGCGUUAG---CGAAAGC
.(((((....(((.((...(((((.....(((((((.((.....))))))))))))))...)).)))...((....)).)))))....(---(....)) ( -30.40)
>consensus
AGCAACCACAUGUCGGAUCUGUUCCCCAAUGGUUGCAUUGACAAGAGCAACCAGAGCACCACCAGCAGCAGCAAUAGCAGUUGCGUUAG___CGAAAGC
.(((((((..((..(((.....))).)).))))))).(((((....((.......)).......(((((.((....)).)))))))))).......... (-19.44 = -20.04 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:34:09 2006