Locus 5460

Sequence ID	X_DroMel_CAF1
Location	14,201,479 – 14,201,583
Length	104
Max. P	0.992989

overview

Window 3

Location	14,201,479 – 14,201,583
Length	104
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	76.78
Mean single sequence MFE	-44.28
Consensus MFE	-23.98
Energy contribution	-26.33
Covariance contribution	2.35
Combinations/Pair	1.23
Mean z-score	-2.84
Structure conservation index	0.54
SVM decision value	2.22
SVM RNA-class probability	0.990534
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14201479 104 + 22224390
AUCUGCUUCCUUCCGCUAUAUUUGCGCGGCAUAUUUACGCGACGCGAGGCGGGACGCUGCUGCCGCUGUCGGCG---------CAGCAGCUGCUGCUGAUAAGUGCAGCAGCC
.(((((((((.((.((.......))(((.........))))).).))))))))..(((((.((((....)))))---------)))).((((((((........)))))))). ( -48.30)
>DroPse_CAF1 124104 110 + 1
AUCUGCUUCCUUCCGCCAUAUUUGCGCGGCAUAUUUACGCGUUGCUGC---CGCCGUUGCCGUUGCCGUCAGCGUAGCAGCGGCAGCAGCUGCUGCUGAUAAGUGCAGCAGCC
....((......((((((....)).)))).........))..((((((---(((.(((((.((((....))))))))).)))))))))((((((((........)))))))). ( -50.46)
>DroSec_CAF1 111391 91 + 1
AUCUGCUUCCUUCCGCUAUAUUUGCG-------------CGAAGCGAGGCGGGACGCUGCUGCCGCUGUCGGCG---------CAGCAGCUGCUGCUGAUAAGUGCAGCAGCC
.(((((((((((((((.......)))-------------.)))).))))))))..(((((.((((....)))))---------)))).((((((((........)))))))). ( -52.00)
>DroEre_CAF1 100363 104 + 1
AUCUGCUUCCUUCCGCUAUAUUUGCGCGGCAUAUUUACGCGACGCGGGGCAGGACGUUGCCGCCGCUGUCGGCG---------CAGCAGCUGCUGCUGAUAAGUGCAGCAGCC
.(((((((((.((.((.......))(((.........))))).).))))))))..(((((.((((....)))))---------)))).((((((((........)))))))). ( -45.60)
>DroWil_CAF1 84973 82 + 1
AUCUGCUUCCUUCCGCCAUAUUUGCGCGGCAUAUUUACGCGUCGUGG-------------CUUCGCUGUUGGCG---------U---------CGCUGAUAAGUGCAGGCAGC
..((((((......(((((....(((((.........))))).))))-------------)..((((((..((.---------.---------.))..)).)))).)))))). ( -26.10)
>DroYak_CAF1 102638 104 + 1
AUCUGCUUCCUUCCGCUAUAUUUGCGCGGCAUAUUUACGCGACGCGAGGCAGGACGUUGCUGCCGCUGUCGACG---------CAGCAGCUGCUGCUGAUAAGUGCAGCAGCC
.(((((((((.((.((.......))(((.........))))).).))))))))..((((((((.(((((((..(---------((((....))))))))).))))))))))). ( -43.20)
>consensus
AUCUGCUUCCUUCCGCUAUAUUUGCGCGGCAUAUUUACGCGACGCGAGGC_GGACGUUGCCGCCGCUGUCGGCG_________CAGCAGCUGCUGCUGAUAAGUGCAGCAGCC
.((((((((.....((.......))(((.........))).....))))))))..((((.(((((....))))).........)))).((((((((........)))))))). (-23.98 = -26.33 +   2.35)

alignment

secondary structure

dotplot

Window 4

Location	14,201,479 – 14,201,583
Length	104
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	76.78
Mean single sequence MFE	-43.48
Consensus MFE	-21.92
Energy contribution	-24.22
Covariance contribution	2.29
Combinations/Pair	1.13
Mean z-score	-3.04
Structure conservation index	0.50
SVM decision value	2.37
SVM RNA-class probability	0.992989
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14201479 104 - 22224390
GGCUGCUGCACUUAUCAGCAGCAGCUGCUG---------CGCCGACAGCGGCAGCAGCGUCCCGCCUCGCGUCGCGUAAAUAUGCCGCGCAAAUAUAGCGGAAGGAAGCAGAU
(((((((((........)))))))))((((---------(((((....)))).))))).....((.((((((.((((....)))).))))........(....))).)).... ( -48.10)
>DroPse_CAF1 124104 110 - 1
GGCUGCUGCACUUAUCAGCAGCAGCUGCUGCCGCUGCUACGCUGACGGCAACGGCAACGGCG---GCAGCAACGCGUAAAUAUGCCGCGCAAAUAUGGCGGAAGGAAGCAGAU
(((((((((........)))))))))((((((((((((........)))).((....)))))---)))))...((.........((((.((....))))))......)).... ( -49.96)
>DroSec_CAF1 111391 91 - 1
GGCUGCUGCACUUAUCAGCAGCAGCUGCUG---------CGCCGACAGCGGCAGCAGCGUCCCGCCUCGCUUCG-------------CGCAAAUAUAGCGGAAGGAAGCAGAU
(((((((((........)))))))))((((---------(((((....)))).))))).....((.((.((((.-------------(((.......))))))))).)).... ( -45.40)
>DroEre_CAF1 100363 104 - 1
GGCUGCUGCACUUAUCAGCAGCAGCUGCUG---------CGCCGACAGCGGCGGCAACGUCCUGCCCCGCGUCGCGUAAAUAUGCCGCGCAAAUAUAGCGGAAGGAAGCAGAU
(((((((((........))))))))).(((---------(((((((.((((.((((......)))))))))))).)).......((((.........))))......)))).. ( -49.80)
>DroWil_CAF1 84973 82 - 1
GCUGCCUGCACUUAUCAGCG---------A---------CGCCAACAGCGAAG-------------CCACGACGCGUAAAUAUGCCGCGCAAAUAUGGCGGAAGGAAGCAGAU
(((.(((((........)).---------.---------(((((...(((...-------------...)).)((((.........)))).....)))))..))).))).... ( -21.20)
>DroYak_CAF1 102638 104 - 1
GGCUGCUGCACUUAUCAGCAGCAGCUGCUG---------CGUCGACAGCGGCAGCAACGUCCUGCCUCGCGUCGCGUAAAUAUGCCGCGCAAAUAUAGCGGAAGGAAGCAGAU
.(((((((.......))))))).(((((((---------(.......))))))))......((((.((((((.((((....)))).))))........(....))).)))).. ( -46.40)
>consensus
GGCUGCUGCACUUAUCAGCAGCAGCUGCUG_________CGCCGACAGCGGCAGCAACGUCC_GCCCCGCGUCGCGUAAAUAUGCCGCGCAAAUAUAGCGGAAGGAAGCAGAU
(((((((((........)))))))))..............((((....)))).((.............(((..((((....))))..)))........(....)...)).... (-21.92 = -24.22 +   2.29)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:25 2006