Locus 4711

Sequence ID	3R_DroMel_CAF1
Location	12,375,634 – 12,375,757
Length	123
Max. P	0.994218

overview

Window 1

Location	12,375,634 – 12,375,730
Length	96
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	88.77
Mean single sequence MFE	-29.32
Consensus MFE	-25.30
Energy contribution	-25.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.88
Structure conservation index	0.86
SVM decision value	1.98
SVM RNA-class probability	0.984544
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12375634 96 + 27905053
CGCCAUU-------CGCCAGCAGCUUCUCAGC-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAAC
.....((-------((..(((.(((....)))-.((((((((......))))))))...............)))...))))(((((((.....))))))).... ( -27.70)
>DroSec_CAF1 44030 95 + 1
CGCCAGC--------AGCAGCAGCUUCUCAGC-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAAC
.((.((.--------(((....))).))..))-.((((((((......)))))))).....((((((.......)))))).(((((((.....))))))).... ( -29.20)
>DroSim_CAF1 43383 95 + 1
CGCCAGC--------AGCAGCAGCUUCUCAGC-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAAUUGCGCAAAAAAC
.((.((.--------(((....))).))..))-.((((((((......)))))))).....((((((.......)))))).(((((((.....))))))).... ( -29.20)
>DroEre_CAF1 44397 103 + 1
CGCCACUAGCUAUACGCCAGCAGAUUCUCAGC-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAAG
.((.....)).....((..((((((((..(((-..(((((((......)))))))((((((...)))))).)))....))))))))((.....))))....... ( -28.70)
>DroYak_CAF1 40949 103 + 1
CGCCAUUCGCUAUUCGCCAGCAGCUUCUCAGC-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAAC
...((((.(((.......)))((((.......-..(((((((......)))))))((((((...)))))))))).))))..(((((((.....))))))).... ( -28.30)
>DroAna_CAF1 25759 93 + 1
CGCUGGG--------A---GCUUCUUCUCUCCGCCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAAC
.((((((--------(---(........))))..((((((((......)))))))).............))))........(((((((.....))))))).... ( -32.80)
>consensus
CGCCAGU________ACCAGCAGCUUCUCAGC_CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAAC
..................................((((((((......)))))))).....((((((.......)))))).(((((((.....))))))).... (-25.30 = -25.30 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	12,375,656 – 12,375,757
Length	101
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	87.39
Mean single sequence MFE	-29.75
Consensus MFE	-25.30
Energy contribution	-25.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-4.06
Structure conservation index	0.85
SVM decision value	2.46
SVM RNA-class probability	0.994218
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12375656 101 + 27905053
AG--C-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAACAACGC--CCAAAAAAGUAU--CUUAACAGCA
.(--(-.((((((((......)))))))).....((((((.......)))))).(((((((.....))))))).........--............--.......)). ( -26.60)
>DroPse_CAF1 41170 99 + 1
CGUCC-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAACAACGA--CCAAGAAGAUGG--C----CAGAA
((((.-.((((((((......))))))))....(((....((((......))))(((((((.....))))))).......))--)......)))).--.----..... ( -29.80)
>DroEre_CAF1 44426 103 + 1
AG--C-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAAGAACGC--CCAAAAAAGUGGCGCUUAACUGCA
..--.-.((((((((......))))))))....(((((((((((......))).(((((((.....))))))).........--.....))))))))((......)). ( -32.30)
>DroYak_CAF1 40978 101 + 1
AG--C-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAACAACGC--CCAAAAAAGUGG--CUAAACUGCA
.(--(-.((((((((......))))))))...((((((((((((......))).(((((((.....))))))).........--.....)))))))--)).....)). ( -32.50)
>DroAna_CAF1 25777 101 + 1
UC--CGCCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAACAACCCGACGAAAAAAAAAU--UAUAA---AA
..--...((((((((......))))))))....(((....((((......))))(((((((.....))))))).........)))...........--.....---.. ( -27.80)
>DroPer_CAF1 38253 99 + 1
CGUCC-CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAACAACGA--CCAAGAAAAUGG--C----CAGAA
.....-.((((((((......))))))))....(((((((((((......))).(((((((.....))))))).........--.....)))))))--)----..... ( -29.50)
>consensus
AG__C_CCGCAGCGUGACAAAAUGCUGCGAAAAGUCAUUUUUCAGCUAAAUGAAUUUGCGCCAACUGCGCAAAAAACAACGC__CCAAAAAAAUGG__CUUAACAGAA
.......((((((((......)))))))).....((((((.......)))))).(((((((.....)))))))................................... (-25.30 = -25.30 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:10 2006