Locus 171

Sequence ID	X_DroMel_CAF1
Location	623,822 – 623,980
Length	158
Max. P	0.949208

overview

Window 3

Location	623,822 – 623,940
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.73
Mean single sequence MFE	-30.58
Consensus MFE	-20.88
Energy contribution	-22.00
Covariance contribution	1.12
Combinations/Pair	1.08
Mean z-score	-1.90
Structure conservation index	0.68
SVM decision value	0.28
SVM RNA-class probability	0.666124
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 623822 118 - 22224390
UUUCAACCGAAGCGAACCGCAGAUAAG-GGA-UAAAUGUCAAAAUUAUCUGCACACUCGCUCCCCACAUUAACCCAUGCCGUACGCACUAUCGUGCAACUGACCAAACCCAAGGUGAAGG
(((((.(((.(((((...((((((((.-.((-(....)))....))))))))....))))).).....................((((....))))................))))))). ( -28.20)
>DroSec_CAF1 8318 119 - 1
UUUCAACCGAAGCGAACCGCAGAUAAG-GGACUAAAUGUCAAAAUUAUCUGCACACUCGCUCCUCACAUUAACCCAUGGCGUACGCACUGUCGCGCAACUGACCAAACACAAGGUGGAGG
..........(((((...((((((((.-.(((.....)))....))))))))....)))))((((.............((((((.....)).)))).....(((........))).)))) ( -31.50)
>DroSim_CAF1 2578 120 - 1
UUUCAACCGAAGCGAACCGCAGAUAAGGGGACUAAAUGUCAAAAUUAUCUGCACACUCGCUCCUCACAUUAACCCAUGGCGUACGCACUGUCGUGCAACUGACCAAACCCAAGGUGGAGG
..........(((((...((((((((...(((.....)))....))))))))....)))))((((.((((......(((((...((((....))))...)).))).......)))))))) ( -33.82)
>DroEre_CAF1 8636 110 - 1
U-UCAGCCGAAACGAACUGCAGAUAAG-GGACUAAAUGUCAAAAUUAUCUGCACACUCGUUCCCCAUAUUAACCCAUGGCGUGCGCAUUGUCCCUCAGCUGCCCAAGCCCAA--------
.-......(.(((((..(((((((((.-.(((.....)))....)))))))))...))))).)..............(((.((.((((((.....))).))).)).)))...-------- ( -28.80)
>consensus
UUUCAACCGAAGCGAACCGCAGAUAAG_GGACUAAAUGUCAAAAUUAUCUGCACACUCGCUCCCCACAUUAACCCAUGGCGUACGCACUGUCGCGCAACUGACCAAACCCAAGGUGGAGG
.....((((.(((((...((((((((...(((.....)))....))))))))....))))).).................(((((......)))))................)))..... (-20.88 = -22.00 +   1.12)

alignment

secondary structure

dotplot

Window 4

Location	623,862 – 623,980
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.61
Mean single sequence MFE	-32.60
Consensus MFE	-27.02
Energy contribution	-28.27
Covariance contribution	1.25
Combinations/Pair	1.07
Mean z-score	-2.60
Structure conservation index	0.83
SVM decision value	1.39
SVM RNA-class probability	0.949208
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 623862 118 - 22224390
AAUCCGCAUGCGAACGCAAGGGGUUCCUCAGAAUUUCCAUUUUCAACCGAAGCGAACCGCAGAUAAG-GGA-UAAAUGUCAAAAUUAUCUGCACACUCGCUCCCCACAUUAACCCAUGCC
.....((((((....))..((((.......(((........)))......(((((...((((((((.-.((-(....)))....))))))))....)))))))))..........)))). ( -31.00)
>DroSec_CAF1 8358 119 - 1
AAUCCGCUUGCGAACGCGAGGGGUUCCACAGAAUUUCCAUUUUCAACCGAAGCGAACCGCAGAUAAG-GGACUAAAUGUCAAAAUUAUCUGCACACUCGCUCCUCACAUUAACCCAUGGC
...((((((((....)))))(((((.....(((........)))....(((((((...((((((((.-.(((.....)))....))))))))....)))))..)).....))))).))). ( -34.60)
>DroSim_CAF1 2618 120 - 1
AAUCCGCUUGCGAACGCGAGGGGUUCCACAGAAUUUCCAUUUUCAACCGAAGCGAACCGCAGAUAAGGGGACUAAAUGUCAAAAUUAUCUGCACACUCGCUCCUCACAUUAACCCAUGGC
...((((((((....)))))(((((.....(((........)))....(((((((...((((((((...(((.....)))....))))))))....)))))..)).....))))).))). ( -34.90)
>DroEre_CAF1 8668 116 - 1
AAUCCGCAGGCGAACG--AAGGGUUCCUCAGAAUUUCCAUU-UCAGCCGAAACGAACUGCAGAUAAG-GGACUAAAUGUCAAAAUUAUCUGCACACUCGUUCCCCAUAUUAACCCAUGGC
........(((((((.--....))))....(((.......)-)).)))(.(((((..(((((((((.-.(((.....)))....)))))))))...))))).)((((........)))). ( -29.90)
>consensus
AAUCCGCAUGCGAACGCGAGGGGUUCCACAGAAUUUCCAUUUUCAACCGAAGCGAACCGCAGAUAAG_GGACUAAAUGUCAAAAUUAUCUGCACACUCGCUCCCCACAUUAACCCAUGGC
......(((((....)))))(((((.....(((........)))....(.(((((...((((((((...(((.....)))....))))))))....))))).).......)))))..... (-27.02 = -28.27 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:02 2006