Locus 4830

Sequence ID	X_DroMel_CAF1
Location	12,544,423 – 12,544,645
Length	222
Max. P	0.682747

overview

Window 1

Location	12,544,423 – 12,544,525
Length	102
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	83.25
Mean single sequence MFE	-35.28
Consensus MFE	-22.49
Energy contribution	-22.05
Covariance contribution	-0.44
Combinations/Pair	1.17
Mean z-score	-1.88
Structure conservation index	0.64
SVM decision value	0.29
SVM RNA-class probability	0.669769
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12544423 102 - 22224390
AGGAUGGAUCGAUGAUGGCCAAAACAUCGAUGGCAUCCACAUCGUCGGCAUCGGUUGUUGUCACAUCUACGCCAUCGGCAUCCUCAUCGUCAUUGUCAUCCG
.((((((..(((((((((........((((((((.........(.(((((.....))))).)........))))))))........))))))))))))))). ( -32.52)
>DroSec_CAF1 8367 93 - 1
AGGAUGGAUCGA---UGGCCAAGACAUCGAUGGCAUGCACGUCGUCGGCUUCGGUUGUCGUCACAUCCACGCCAUCGGCAGCCUCAUCGU------CAUCCG
.((((((..(((---(((....((..((((((((......))))))))..))((((((((...............)))))))))))))))------))))). ( -36.26)
>DroSim_CAF1 6644 93 - 1
AGGAUGGAUCGA---UGGCCAAGACAUCGAUGGCAUCCACGUCGUCGGCUUCGGUUGUCGUCACAUCCACGCCAUCGGCAGCCUCAUCGU------CAUCCG
.((((((..(((---(((....((..((((((((......))))))))..))((((((((...............)))))))))))))))------))))). ( -36.26)
>DroEre_CAF1 9623 93 - 1
AGGAUGCAUCGA---UGGCCAAGGCUUCGAUGCCGUCCACGUCGUCGACAUCCGCUGCCGUCGCAUACACGCCACCGGCCUCCCCGGCGU------CAUCCG
.(((((...(((---((((...((..((((((.((....)).))))))...))...))))))).....(((((...((....)).)))))------))))). ( -36.10)
>consensus
AGGAUGGAUCGA___UGGCCAAGACAUCGAUGGCAUCCACGUCGUCGGCAUCGGUUGUCGUCACAUCCACGCCAUCGGCAGCCUCAUCGU______CAUCCG
.(((((.........((((...(((.((((((((......)))))))).....)))...)))).......(((...))).................))))). (-22.49 = -22.05 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	12,544,491 – 12,544,605
Length	114
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	90.52
Mean single sequence MFE	-38.22
Consensus MFE	-27.39
Energy contribution	-27.95
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.71
Structure conservation index	0.72
SVM decision value	-0.02
SVM RNA-class probability	0.523133
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12544491 114 - 22224390
UGCAACGUCAGCUAUGACCAAUAGCAGCACCAGUGGCAGCAUGAACAUCAGCAAUAGUCACGGAUUGAAGGCCAAUGCCAAGGAUGGAUCGAUGAUGGCCAAAACAUCGAUGGC
.((..((((.(((((.....)))))....((.(((((.((.((.....))))....)))))))......(((....)))...)))).(((((((.(......).))))))).)) ( -29.40)
>DroSec_CAF1 8429 111 - 1
CGCAACGGCGGCUAUGACCAAUAGCAGCACCAGUGGCAGCAUGAACAUCAGCAAUAGUCACGGCCUGAAGGCCAAUGCCAAGGAUGGAUCGA---UGGCCAAGACAUCGAUGGC
(((....)))(((((.....))))).((.(((.(((((((.((.....)))).........((((....))))..)))))....)))(((((---((.......))))))).)) ( -39.30)
>DroSim_CAF1 6706 111 - 1
CGCAACGGCGGCUAUGACCAAUAGCAGCACCAGUGGCAGCAUGAACAUCAGCAAUAGUCACGGCCUGAAGGCCAAUGCCAAGGAUGGAUCGA---UGGCCAAGACAUCGAUGGC
(((....)))(((((.....))))).((.(((.(((((((.((.....)))).........((((....))))..)))))....)))(((((---((.......))))))).)) ( -39.30)
>DroEre_CAF1 9685 111 - 1
CGCGGCGGCAGCUAUGGCCAAUAGCAGCGCCAGUGGCAGCAUGAGCAUCAGCAACAGUCACGGCCAGAAGGCCAGUGCCAAGGAUGCAUCGA---UGGCCAAGGCUUCGAUGCC
...((((.(.(((((.....))))).)))))..(((((((.((.....)))).........((((....))))..))))).....(((((((---.(((....)))))))))). ( -44.90)
>consensus
CGCAACGGCAGCUAUGACCAAUAGCAGCACCAGUGGCAGCAUGAACAUCAGCAAUAGUCACGGCCUGAAGGCCAAUGCCAAGGAUGGAUCGA___UGGCCAAGACAUCGAUGGC
......(((.(((((.....)))))....(((.(((((((.((.....)))).........((((....))))..)))))....)))..........))).............. (-27.39 = -27.95 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	12,544,525 – 12,544,645
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.28
Mean single sequence MFE	-42.08
Consensus MFE	-31.40
Energy contribution	-32.77
Covariance contribution	1.38
Combinations/Pair	1.09
Mean z-score	-1.85
Structure conservation index	0.75
SVM decision value	0.31
SVM RNA-class probability	0.682747
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12544525 120 - 22224390
GGAAACGAUUCGAACUGAAUUCCGGUGAGGCAGGUGGAAAUGCAACGUCAGCUAUGACCAAUAGCAGCACCAGUGGCAGCAUGAACAUCAGCAAUAGUCACGGAUUGAAGGCCAAUGCCA
.....(((((((.((((.....))))...((.((((...((((.......(((((.....))))).((.......)).))))...)))).))........)))))))..(((....))). ( -32.30)
>DroSec_CAF1 8460 120 - 1
GGAAGCGCUUCGAACUGAAUUCCGGUGAGGCAGCUGGGAACGCAACGGCGGCUAUGACCAAUAGCAGCACCAGUGGCAGCAUGAACAUCAGCAAUAGUCACGGCCUGAAGGCCAAUGCCA
......(((((..((((.....))))))))).(((((...(((....)))(((((.....)))))....)))))((((((.((.....)))).........((((....))))..)))). ( -42.10)
>DroSim_CAF1 6737 120 - 1
GGAAACGCUUCGAACUGAAUUCCGGUGAGGCGGCUGGAAACGCAACGGCGGCUAUGACCAAUAGCAGCACCAGUGGCAGCAUGAACAUCAGCAAUAGUCACGGCCUGAAGGCCAAUGCCA
.....((((((..((((.....))))))))))(((((...(((....)))(((((.....)))))....)))))((((((.((.....)))).........((((....))))..)))). ( -44.20)
>DroEre_CAF1 9716 120 - 1
GGAAACGCUUCGAGCUGAAUGCGGCUGAGGCAGCAGGAAACGCGGCGGCAGCUAUGGCCAAUAGCAGCGCCAGUGGCAGCAUGAGCAUCAGCAACAGUCACGGCCAGAAGGCCAGUGCCA
(....).......(((((.(((.((((..((.((.(....)))((((.(.(((((.....))))).))))).))..))))....))))))))....(.(((((((....)))).))).). ( -49.70)
>consensus
GGAAACGCUUCGAACUGAAUUCCGGUGAGGCAGCUGGAAACGCAACGGCAGCUAUGACCAAUAGCAGCACCAGUGGCAGCAUGAACAUCAGCAAUAGUCACGGCCUGAAGGCCAAUGCCA
(....)(((((..((((.....))))))))).(((((...(((....)))(((((.....)))))....)))))((((((.((.....)))).........((((....))))..)))). (-31.40 = -32.77 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:04 2006