Locus 6225

Sequence ID	3R_DroMel_CAF1
Location	16,271,798 – 16,271,926
Length	128
Max. P	0.894024

overview

Window 0

Location	16,271,798 – 16,271,898
Length	100
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	90.35
Mean single sequence MFE	-25.78
Consensus MFE	-21.46
Energy contribution	-21.46
Covariance contribution	0.00
Combinations/Pair	1.17
Mean z-score	-1.70
Structure conservation index	0.83
SVM decision value	0.98
SVM RNA-class probability	0.894024
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16271798 100 + 27905053
GACGGCCAAUACUAAUCACACAUAAAUCAAAAAAUGACAUAAAGUGUACCA-ACAGCAGCUGGCUG---GGUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAA
((((((((.((((....((((.....(((.....)))......))))....-.((((.....))))---))))...)))))))).....((((.....)))).. ( -25.80)
>DroSec_CAF1 72077 100 + 1
GACGGCCAAUACUAAUCACACAUAAAUCAAAAAAUGACAUAAAGUGUACCA-ACAGCAGCUGGCUG---GGUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAA
((((((((.((((....((((.....(((.....)))......))))....-.((((.....))))---))))...)))))))).....((((.....)))).. ( -25.80)
>DroEre_CAF1 73366 100 + 1
GACGGCCAAUACUAAUCACACAUAAAUCAAAAAAUGACAUAAAGUGUACCA-ACAGCAGCUGGCUG---GCUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAA
....((((.........((((.....(((.....)))......))))....-......((..((((---.(((((......))))).))))..))...)))).. ( -30.70)
>DroYak_CAF1 57696 100 + 1
GACAGCCAAUACUAAUCACACAUAAAUCAAAAAAUGACAUAAAGUGUACCA-ACAGCAGCUGGCUG---GGUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAA
((((((((.((((....((((.....(((.....)))......))))....-.((((.....))))---))))...)))))))).....((((.....)))).. ( -26.50)
>DroAna_CAF1 88897 98 + 1
UACACCCAACACUAAUCACACAUAAAUCAAAAAAUGACAUAAAGUGUAGCAAAUAGCAGCUGGUUGUCAGGUUGUCUGGCUGUCGAGU--UUGG----UGGCAA
..((((.(((.......((((.....(((.....)))......))))........(((((..(............)..)))))...))--).))----)).... ( -20.10)
>consensus
GACGGCCAAUACUAAUCACACAUAAAUCAAAAAAUGACAUAAAGUGUACCA_ACAGCAGCUGGCUG___GGUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAA
....((((.........((((.....(((.....)))......)))).........((((((.(((...(((......)))..))).)))))).....)))).. (-21.46 = -21.46 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	16,271,829 – 16,271,926
Length	97
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	88.82
Mean single sequence MFE	-27.80
Consensus MFE	-23.04
Energy contribution	-22.84
Covariance contribution	-0.20
Combinations/Pair	1.20
Mean z-score	-1.65
Structure conservation index	0.83
SVM decision value	0.70
SVM RNA-class probability	0.826596
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16271829 97 + 27905053
AAAUGACAUAAAGUGUACCA-ACAGCAGCUGGCUG---GGUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAAACUGCCGACA----UGUAACACGGAAUCAAAA
...(((......(((((((.-.((((.....))))---)))......((((((.(((((...((.....))...)))))))))----.)).))))....)))... ( -26.80)
>DroSec_CAF1 72108 97 + 1
AAAUGACAUAAAGUGUACCA-ACAGCAGCUGGCUG---GGUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAAACUGCCGACA----UGUAACACGGAAUGAAAA
......(((...(((((((.-.((((.....))))---)))......((((((.(((((...((.....))...)))))))))----.)).))))...))).... ( -28.00)
>DroEre_CAF1 73397 97 + 1
AAAUGACAUAAAGUGUACCA-ACAGCAGCUGGCUG---GCUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAAACUGCCGACA----UGUAACACGGAAUCAAAA
...(((......((((..((-......((..((((---.(((((......))))).))))..))...((((.....))))...----))..))))....)))... ( -31.80)
>DroYak_CAF1 57727 97 + 1
AAAUGACAUAAAGUGUACCA-ACAGCAGCUGGCUG---GGUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAAACUGCCGACA----UGUAACACGGAAUCAAAA
...(((......(((((((.-.((((.....))))---)))......((((((.(((((...((.....))...)))))))))----.)).))))....)))... ( -26.80)
>DroAna_CAF1 88928 99 + 1
AAAUGACAUAAAGUGUAGCAAAUAGCAGCUGGUUGUCAGGUUGUCUGGCUGUCGAGU--UUGG----UGGCAAACUGCCGACACACCUAUAACACGAAAUCGAAA
....((((...(((...((.....)).)))...))))((((((((.(((.....(((--(((.----...))))))))))))).))))......((....))... ( -25.60)
>consensus
AAAUGACAUAAAGUGUACCA_ACAGCAGCUGGCUG___GGUGAUCUGGCUGUCAGGCAGCUGGCACAUGGCAAACUGCCGACA____UGUAACACGGAAUCAAAA
............((((.........((((((.(((...(((......)))..))).)))))).....((((.....))))...........)))).......... (-23.04 = -22.84 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:00 2006