Locus 4111

Sequence ID	2L_DroMel_CAF1
Location	11,806,286 – 11,806,426
Length	140
Max. P	0.573690

overview

Window 2

Location	11,806,286 – 11,806,386
Length	100
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	86.46
Mean single sequence MFE	-31.52
Consensus MFE	-23.08
Energy contribution	-24.88
Covariance contribution	1.80
Combinations/Pair	1.07
Mean z-score	-1.63
Structure conservation index	0.73
SVM decision value	0.08
SVM RNA-class probability	0.573690
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11806286 100 + 22407834
----------UUUCAGUUUUGGUUCCACUUCCACACACACACACAAACACAUGCAUACUUGCAUACGUGUGUGGGAAGAACGGACAGGGGGGCAAAAGCAAAUCAAGCGA
----------.....(((((.(((((.(((((.(((((((..........(((((....)))))..))))))))))))..(.....).))))).)))))........... ( -29.50)
>DroSec_CAF1 13606 110 + 1
CCAGUUUCGGUUUCAGUUUUGGUUCCACUUCCACACACACACACACAACCAUGCAUACUUGCAUACGUGUGUGGAAAGAGCGGAAAGGGGGGCGAAAGCAAAUCAAGCGA
...((((.(((((..(((((.(((((..((((.(.(...(((((((....(((((....)))))..)))))))....).).))))...))))).)))))))))))))).. ( -35.80)
>DroSim_CAF1 13534 108 + 1
CCAGUUUCGGUUUCAGUUUUGGUUCCACUUCCACACAC--ACACACAGCCAUGCAUACUUGCAUACGUGUGUGGAAAGAGCGGAAAGGGGGGCGAAAGCAAAUCAAGCGA
....(((((.(..(..((((.((((...((((((((((--.(.....)..(((((....)))))..)))))))))).)))).)))).)..).)))))((.......)).. ( -35.50)
>DroEre_CAF1 12542 104 + 1
CCAGUUUCGGUUUCAGUUUUGGUUCCACUUCCACACACUCAUA------CAUUCAUACUUGCAUACGUGUGUGGGAAAAGCGGACAGGGGGGCGAAAGCAAAUCAAGCGA
...((((.(((((..(((((.(((((..((((((((((..((.------((........)).))..))))))))))....(.....).))))).)))))))))))))).. ( -29.40)
>DroYak_CAF1 13460 101 + 1
CCAGUUUCGGUUUCAGUUUUGGUUCCACUUCCACAAA--CAUA------CCUACAUACUUGCAUACGUGUGUGGAAAGAGCGGAC-GGGGGGCGAAAGCAAAUCAAGCGA
...((((.(((((..(((((.(((((.(.(((.(...--....------.((((((((........)))))))).....).))).-).))))).)))))))))))))).. ( -27.42)
>consensus
CCAGUUUCGGUUUCAGUUUUGGUUCCACUUCCACACAC_CACACA_A__CAUGCAUACUUGCAUACGUGUGUGGAAAGAGCGGACAGGGGGGCGAAAGCAAAUCAAGCGA
....(((((.(..(....((.((((...((((((((((............(((((....)))))..)))))))))).)))).))...)..).)))))((.......)).. (-23.08 = -24.88 +   1.80)

alignment

secondary structure

dotplot

Window 3

Location	11,806,309 – 11,806,426
Length	117
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	91.17
Mean single sequence MFE	-27.93
Consensus MFE	-20.02
Energy contribution	-20.02
Covariance contribution	0.00
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.72
SVM decision value	-0.04
SVM RNA-class probability	0.514495
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11806309 117 + 22407834
CACACACACACAAACACAUGCAUACUUGCAUACGUGUGUGGGAAGAACGGACAGGGGGGCAAAAGCAAAUCAAGCGAAAAUUUAUUUGCAGUCAAUAUAUGUAUAUGUACAUCCAUA
....(((((((......(((((....)))))..)))))))(((......(((.((...((....))...))..(((((......))))).)))......((((....)))))))... ( -27.90)
>DroSec_CAF1 13639 117 + 1
CACACACACACACAACCAUGCAUACUUGCAUACGUGUGUGGAAAGAGCGGAAAGGGGGGCGAAAGCAAAUCAAGCGAAAAUUUAUUUGCAGUCAAUAUAUGUAUAUGUACAUCCAUA
......(((((((....(((((....)))))..)))))))........(((..((...((....))...))..(((((......)))))..........((((....)))))))... ( -29.20)
>DroSim_CAF1 13567 115 + 1
CACAC--ACACACAGCCAUGCAUACUUGCAUACGUGUGUGGAAAGAGCGGAAAGGGGGGCGAAAGCAAAUCAAGCGAAAAUUUAUUUGCAGUCAAUAUAUGUAUAUGUACAUCCAUA
....(--((((((....(((((....)))))..)))))))........(((..((...((....))...))..(((((......)))))..........((((....)))))))... ( -29.20)
>DroEre_CAF1 12575 111 + 1
CACACUCAUA------CAUUCAUACUUGCAUACGUGUGUGGGAAAAGCGGACAGGGGGGCGAAAGCAAAUCAAGCGAAAAUUUAUUUGCAGUCAAUAUAUGUAUAUGUACAUACAUG
....((((((------(((..............))))))))).......(((.((...((....))...))..(((((......))))).)))....(((((((......))))))) ( -25.44)
>consensus
CACACACACACACA_CCAUGCAUACUUGCAUACGUGUGUGGAAAGAGCGGAAAGGGGGGCGAAAGCAAAUCAAGCGAAAAUUUAUUUGCAGUCAAUAUAUGUAUAUGUACAUCCAUA
.(((...............(((....)))((((((((((.((...........((...((....))...))..(((((......)))))..)).)))))))))).)))......... (-20.02 = -20.02 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:54 2006