Locus 4692

Sequence ID	3R_DroMel_CAF1
Location	12,343,056 – 12,343,195
Length	139
Max. P	0.989957

overview

Window 6

Location	12,343,056 – 12,343,155
Length	99
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	93.59
Mean single sequence MFE	-21.17
Consensus MFE	-18.79
Energy contribution	-18.79
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.89
SVM decision value	2.19
SVM RNA-class probability	0.989957
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12343056 99 + 27905053
CAUAACACCGAGUGGAUAUACUCCAUAUAUCAGCUAUGCUCUCCUG------AUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCAACUCCUCCC
.........(((((((.....)))......(((((((((....(((------.....))).........))))).))))..((((((...))))))))))..... ( -20.52)
>DroSec_CAF1 11833 99 + 1
CAUAACACCGAGUGGAUAUACUCCAUAUAUCAGCUAUGCUCUCCUG------AUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCAACUCCUCCC
.........(((((((.....)))......(((((((((....(((------.....))).........))))).))))..((((((...))))))))))..... ( -20.52)
>DroSim_CAF1 10967 99 + 1
CAUAACACCGAGUGGAUAUACUCCAUAUAUCAGCUAUGCUCUCCUG------AUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCAACUCCUCCC
.........(((((((.....)))......(((((((((....(((------.....))).........))))).))))..((((((...))))))))))..... ( -20.52)
>DroEre_CAF1 11678 103 + 1
CAUAACACCGAGUGGAUAUACUCCAUAUAUCAGCUAUGCUCUCCUGAUCCUGAUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCACCAC--CCC
...........((((...............(((((((((......((..(((.....)))..)).....))))).))))..((((((...))))))))))--... ( -22.30)
>DroYak_CAF1 7674 101 + 1
CAUAACACCGAGUGGAUAUACUCCAUAUAUCAGCUAUGCUCUCCUGAUUCUGAUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCA--AC--CCC
...........(((((.....)))))....(((((((((......((..(((.....)))..)).....))))).)))).(((((((...))))))--).--... ( -22.00)
>consensus
CAUAACACCGAGUGGAUAUACUCCAUAUAUCAGCUAUGCUCUCCUG______AUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCAACUCCUCCC
...........(((((.....)))))....(((((((((..............................))))).))))..((((((...))))))......... (-18.79 = -18.79 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	12,343,056 – 12,343,155
Length	99
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	93.59
Mean single sequence MFE	-27.48
Consensus MFE	-23.50
Energy contribution	-23.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.30
Structure conservation index	0.86
SVM decision value	0.21
SVM RNA-class probability	0.634536
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12343056 99 - 27905053
GGGAGGAGUUGGCAGGUGCUACCAAACAGCAUAUGCAGAGAAAGGCCGGGAAU------CAGGAGAGCAUAGCUGAUAUAUGGAGUAUAUCCACUCGGUGUUAUG
...........(((.(((((.......))))).))).....((.((((((.((------(((..........)))))...((((.....)))))))))).))... ( -26.20)
>DroSec_CAF1 11833 99 - 1
GGGAGGAGUUGGCAGGUGCUACCAAACAGCAUAUGCAGAGAAAGGCCGGGAAU------CAGGAGAGCAUAGCUGAUAUAUGGAGUAUAUCCACUCGGUGUUAUG
...........(((.(((((.......))))).))).....((.((((((.((------(((..........)))))...((((.....)))))))))).))... ( -26.20)
>DroSim_CAF1 10967 99 - 1
GGGAGGAGUUGGCAGGUGCUACCAAACAGCAUAUGCAGAGAAAGGCCGGGAAU------CAGGAGAGCAUAGCUGAUAUAUGGAGUAUAUCCACUCGGUGUUAUG
...........(((.(((((.......))))).))).....((.((((((.((------(((..........)))))...((((.....)))))))))).))... ( -26.20)
>DroEre_CAF1 11678 103 - 1
GGG--GUGGUGGCAGGUGCUACCAAACAGCAUAUGCAGAGAAAGGCCGGGAAUCAGGAUCAGGAGAGCAUAGCUGAUAUAUGGAGUAUAUCCACUCGGUGUUAUG
.(.--.(((((((....)))))))..).((....)).....((.((((((.......(((((..........)))))...((((.....)))))))))).))... ( -32.00)
>DroYak_CAF1 7674 101 - 1
GGG--GU--UGGCAGGUGCUACCAAACAGCAUAUGCAGAGAAAGGCCGGGAAUCAGAAUCAGGAGAGCAUAGCUGAUAUAUGGAGUAUAUCCACUCGGUGUUAUG
...--..--..(((.(((((.......))))).))).....((.((((((.(((((..((....))......)))))...((((.....)))))))))).))... ( -26.80)
>consensus
GGGAGGAGUUGGCAGGUGCUACCAAACAGCAUAUGCAGAGAAAGGCCGGGAAU______CAGGAGAGCAUAGCUGAUAUAUGGAGUAUAUCCACUCGGUGUUAUG
...........(((.(((((.......))))).))).....((.((((((...............(((...)))......((((.....)))))))))).))... (-23.50 = -23.50 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	12,343,086 – 12,343,195
Length	109
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	91.67
Mean single sequence MFE	-22.39
Consensus MFE	-16.80
Energy contribution	-16.64
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.60
Structure conservation index	0.75
SVM decision value	-0.04
SVM RNA-class probability	0.513719
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12343086 109 + 27905053
CAGCUAUGCUCUCCUG------AUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCAACUCCUCCCUCAUCGUCUUUCAUUUUUUGCUACUGGCUGUCAGUGCACA
(((((((((....(((------.....))).........))))).)))).(((((((...)))))))..........................(((.((((.....))))))).. ( -21.62)
>DroSec_CAF1 11863 109 + 1
CAGCUAUGCUCUCCUG------AUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCAACUCCUCCCUCAUCGUCUUUCAUUUUUUUCAGCUGGCUGUCAGUGCACA
......(((....(((------((..(((((........((....))...(((((((...)))))))..............................)))))..))))).))).. ( -24.00)
>DroSim_CAF1 10997 109 + 1
CAGCUAUGCUCUCCUG------AUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCAACUCCUCCCUCAUCGUCUUUCAUUUUUUUCAGCUGGCUGUCAGUGCACA
......(((....(((------((..(((((........((....))...(((((((...)))))))..............................)))))..))))).))).. ( -24.00)
>DroEre_CAF1 11708 111 + 1
CAGCUAUGCUCUCCUGAUCCUGAUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCACCAC--CCCUCAUCGUCUUUCAUUUU-UUCC-CUGGCUGUCAGUGCACA
(((((((((......((..(((.....)))..)).....))))).))))....((.((((.((.(((((.--....................-....-.))).)).)))))))). ( -19.57)
>DroYak_CAF1 7704 110 + 1
CAGCUAUGCUCUCCUGAUUCUGAUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCA--AC--CCCUCAUCGUCUUUCAUUUUUUUCU-CUGGUUGUCAGUGCACA
(((((((((......((..(((.....)))..)).....))))).))))....((.((((.((.((--((--(........................-..))))).)))))))). ( -22.77)
>consensus
CAGCUAUGCUCUCCUG______AUUCCCGGCCUUUCUCUGCAUAUGCUGUUUGGUAGCACCUGCCAACUCCUCCCUCAUCGUCUUUCAUUUUUUUCA_CUGGCUGUCAGUGCACA
(((((((((..............................))))).))))....((.((((..((((.................................)))).....)))))). (-16.80 = -16.64 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:38 2006