Locus 5615

Sequence ID	X_DroMel_CAF1
Location	14,478,396 – 14,478,562
Length	166
Max. P	0.994829

overview

Window 1

Location	14,478,396 – 14,478,505
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.12
Mean single sequence MFE	-29.16
Consensus MFE	-28.45
Energy contribution	-28.05
Covariance contribution	-0.40
Combinations/Pair	1.07
Mean z-score	-1.65
Structure conservation index	0.98
SVM decision value	2.51
SVM RNA-class probability	0.994829
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14478396 109 - 22224390
GGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCCGCAGCACACUGCCA-ACUC---GCAACAACUUCUCAGUUCCUCAUCUGCGACUGC-------AACUGCAUCUUCAGCUCC
((((....(((((((.((.(.((((......))))).)).)))))))..)))).-....---((.......((.(((........))).)).(((-------....)))......))... ( -29.70)
>DroSec_CAF1 3599 109 - 1
GGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCCGCAGCACACUGCCA-ACUC---GCAACAACUUCUCAGUUCCUCAUCUGCAACUGC-------AACUGCAUCUUUAGCUCC
((((....(((((((.((.(.((((......))))).)).)))))))..)))).-....---(((..((((....)))).......(((....))-------)..)))............ ( -27.90)
>DroSim_CAF1 10099 109 - 1
GGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCCGCAGCACACUGCCA-ACUC---GCAACAACUUCUCAGUUCCUCAUCUGCAACUGC-------AUCUGCAUCUUCAGCUCC
((((....(((((((.((.(.((((......))))).)).)))))))..)))).-....---(((..((((....)))).......(((....))-------)..)))............ ( -27.70)
>DroEre_CAF1 2197 109 - 1
GGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCAGCAACACACUGCCA-ACUC---GCAACAACUUCUCAGUUCCUCAUCUGCAACUGC-------AACUGCAUCUUUGGCUCC
((((....(((((((.((.(.((((......))))).)).)))))))..)))).-....---(((..((((....)))).......(((....))-------)..)))............ ( -27.90)
>DroYak_CAF1 6277 120 - 1
GGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCAGCAACACACUGCCACACUCGCCGCAACAACUUCUCAGUUCCUCAUCGGCAACUGCAACUUGCAACUGCAUCUUUAGCUCC
((((....(((((((.((.(.((((......))))).)).)))))))..)))).........((..........(((((((.....)).))))).....(((....)))......))... ( -32.60)
>consensus
GGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCCGCAGCACACUGCCA_ACUC___GCAACAACUUCUCAGUUCCUCAUCUGCAACUGC_______AACUGCAUCUUUAGCUCC
((((....(((((((.((.(.((((......))))).)).)))))))..)))).........(((.........(((((.(......).)))))...........)))............ (-28.45 = -28.05 +  -0.40)

alignment

secondary structure

dotplot

Window 2

Location	14,478,429 – 14,478,524
Length	95
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.83
Mean single sequence MFE	-36.32
Consensus MFE	-24.80
Energy contribution	-24.91
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.09
Structure conservation index	0.68
SVM decision value	0.33
SVM RNA-class probability	0.693083
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14478429 95 + 22224390
GAACUGAGAAGUUGUUGC---GAGU-UGGCAGUGUGCUGCGGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUG---------------------CAAGAUGCAAUAUG
.((((....)))).((((---(...-((((((((((((((..((((((........))))))))))).))))....)))))..))---------------------)))........... ( -31.40)
>DroSec_CAF1 3632 95 + 1
GAACUGAGAAGUUGUUGC---GAGU-UGGCAGUGUGCUGCGGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUG---------------------CAAGAUGCAAUAUG
.((((....)))).((((---(...-((((((((((((((..((((((........))))))))))).))))....)))))..))---------------------)))........... ( -31.40)
>DroSim_CAF1 10132 95 + 1
GAACUGAGAAGUUGUUGC---GAGU-UGGCAGUGUGCUGCGGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUG---------------------CAAGAUGCAAUAUG
.((((....)))).((((---(...-((((((((((((((..((((((........))))))))))).))))....)))))..))---------------------)))........... ( -31.40)
>DroEre_CAF1 2230 102 + 1
GAACUGAGAAGUUGUUGC---GAGU-UGGCAGUGUGUUGCUGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUGCAA--------------GCUGCAAGCUGCAAGAUG
.((((....)))).((((---.(((-(.((((((((((((((((((((........))))).))))))))))..((..(...)..)).--------------))))).)))))))).... ( -39.90)
>DroYak_CAF1 6317 120 + 1
GAACUGAGAAGUUGUUGCGGCGAGUGUGGCAGUGUGUUGCUGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUGCCAUGUGCAAUGGGAGAUGUGCAAGAUGCAAUAUC
.((((....))))(((((((((...(((((((((((((((((((((((........))))).))))))))).))).)))))).)))).((..((........))..))....)))))... ( -47.50)
>consensus
GAACUGAGAAGUUGUUGC___GAGU_UGGCAGUGUGCUGCGGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUG_____________________CAAGAUGCAAUAUG
.((((....))))(((((........((((((((((((((..((((((........))))))))))).))))....)))))..(((...................)))....)))))... (-24.80 = -24.91 +   0.11)

alignment

secondary structure

dotplot

Window 3

Location	14,478,429 – 14,478,524
Length	95
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.83
Mean single sequence MFE	-28.44
Consensus MFE	-24.22
Energy contribution	-24.13
Covariance contribution	-0.09
Combinations/Pair	1.04
Mean z-score	-2.10
Structure conservation index	0.85
SVM decision value	1.68
SVM RNA-class probability	0.971579
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14478429 95 - 22224390
CAUAUUGCAUCUUG---------------------CACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCCGCAGCACACUGCCA-ACUC---GCAACAACUUCUCAGUUC
...........(((---------------------(...(((((....(((((((.((.(.((((......))))).)).)))))))..)))))-....---)))).............. ( -26.40)
>DroSec_CAF1 3632 95 - 1
CAUAUUGCAUCUUG---------------------CACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCCGCAGCACACUGCCA-ACUC---GCAACAACUUCUCAGUUC
...........(((---------------------(...(((((....(((((((.((.(.((((......))))).)).)))))))..)))))-....---)))).............. ( -26.40)
>DroSim_CAF1 10132 95 - 1
CAUAUUGCAUCUUG---------------------CACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCCGCAGCACACUGCCA-ACUC---GCAACAACUUCUCAGUUC
...........(((---------------------(...(((((....(((((((.((.(.((((......))))).)).)))))))..)))))-....---)))).............. ( -26.40)
>DroEre_CAF1 2230 102 - 1
CAUCUUGCAGCUUGCAGC--------------UUGCACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCAGCAACACACUGCCA-ACUC---GCAACAACUUCUCAGUUC
....((((....(((...--------------..)))..(((((....(((((((.((.(.((((......))))).)).)))))))..)))))-....---)))).............. ( -29.70)
>DroYak_CAF1 6317 120 - 1
GAUAUUGCAUCUUGCACAUCUCCCAUUGCACAUGGCACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCAGCAACACACUGCCACACUCGCCGCAACAACUUCUCAGUUC
....((((....((((..........))))...(((...(((((....(((((((.((.(.((((......))))).)).)))))))..))))).....))))))).............. ( -33.30)
>consensus
CAUAUUGCAUCUUG_____________________CACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCCGCAGCACACUGCCA_ACUC___GCAACAACUUCUCAGUUC
....((((....(((...................)))..(((((....(((((((.((.(.((((......))))).)).)))))))..)))))........)))).............. (-24.22 = -24.13 +  -0.09)

alignment

secondary structure

dotplot

Window 4

Location	14,478,465 – 14,478,562
Length	97
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	85.88
Mean single sequence MFE	-33.77
Consensus MFE	-22.41
Energy contribution	-24.10
Covariance contribution	1.69
Combinations/Pair	1.00
Mean z-score	-2.41
Structure conservation index	0.66
SVM decision value	0.84
SVM RNA-class probability	0.863865
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14478465 97 + 22224390
GGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUG-------CAAGAUGCAAUAUGCAAUGUUGCUGCUUCUGCUGC--CUGCUGCCUGCAUAAUU
(((((((.((((((((((...((.(....).))...(((....((-------(.....)))....)))))))))..)))).))))))--)(((.....)))..... ( -34.60)
>DroSec_CAF1 3668 90 + 1
GGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUG-------CAAGAUGCAAUAUGCAAUGUUGCUGCUUCUGCU---------GCCUGCAUAAUU
(((((((.((((((((((...((.(....).))...(((....((-------(.....)))....)))))))))..)))).))))---------)))......... ( -32.50)
>DroSim_CAF1 10168 97 + 1
GGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUG-------CAAGAUGCAAUAUGCAAUGUUGCUGCUUCUGCUGC--CUGCUGCCUGCAUAAUU
(((((((.((((((((((...((.(....).))...(((....((-------(.....)))....)))))))))..)))).))))))--)(((.....)))..... ( -34.60)
>DroEre_CAF1 2266 97 + 1
UGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUGCAAGCUGCAAGCUGCAAGAUGCAAUGUUGC---------UGCUGCUACUGCCUGCAUAAUU
(((((((...(....)..(.(((((((((((.....(((....((((.((.....))))))....))).))))))---------))))))...)))).)))..... ( -33.40)
>consensus
GGCGGCAUAAGUCAACAUGUCGGCGGCAACACCAUGUGCCAUGUG_______CAAGAUGCAAUAUGCAAUGUUGCUGCUUCUGCUGC__CUGCUGCCUGCAUAAUU
((((((((........)))))((((((((((.(((((((....(((.....)))....)).)))))...))))))))))...............)))......... (-22.41 = -24.10 +   1.69)

alignment

secondary structure

dotplot

Window 5

Location	14,478,465 – 14,478,562
Length	97
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	85.88
Mean single sequence MFE	-30.62
Consensus MFE	-21.48
Energy contribution	-23.22
Covariance contribution	1.75
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.70
SVM decision value	0.16
SVM RNA-class probability	0.611358
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14478465 97 - 22224390
AAUUAUGCAGGCAGCAG--GCAGCAGAAGCAGCAACAUUGCAUAUUGCAUCUUG-------CACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCC
......((.((((..((--((((((...((.((((((((((....(((.....)-------))....)))....))))))).)).....))))).))).)))))). ( -32.00)
>DroSec_CAF1 3668 90 - 1
AAUUAUGCAGGC---------AGCAGAAGCAGCAACAUUGCAUAUUGCAUCUUG-------CACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCC
.........(((---------.(((.(((((((..((((((....(((.....)-------))....))).)))((((((....)))))))))).))).))).))) ( -26.70)
>DroSim_CAF1 10168 97 - 1
AAUUAUGCAGGCAGCAG--GCAGCAGAAGCAGCAACAUUGCAUAUUGCAUCUUG-------CACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCC
......((.((((..((--((((((...((.((((((((((....(((.....)-------))....)))....))))))).)).....))))).))).)))))). ( -32.00)
>DroEre_CAF1 2266 97 - 1
AAUUAUGCAGGCAGUAGCAGCA---------GCAACAUUGCAUCUUGCAGCUUGCAGCUUGCACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCA
.....(((.((((.(((((((.---------(((((((((((..((((.....))))..))))((((...))))))))))).)).....))))).....))))))) ( -31.80)
>consensus
AAUUAUGCAGGCAGCAG__GCAGCAGAAGCAGCAACAUUGCAUAUUGCAUCUUG_______CACAUGGCACAUGGUGUUGCCGCCGACAUGUUGACUUAUGCCGCC
......((.((((.......(((((...((.((((((((((.....)))..............((((...))))))))))).)).....))))).....)))))). (-21.48 = -23.22 +   1.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:24 2006