Locus 5058

Sequence ID	2R_DroMel_CAF1
Location	16,432,190 – 16,432,331
Length	141
Max. P	0.975859

overview

Window 3

Location	16,432,190 – 16,432,291
Length	101
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	79.48
Mean single sequence MFE	-38.10
Consensus MFE	-20.62
Energy contribution	-22.66
Covariance contribution	2.04
Combinations/Pair	1.04
Mean z-score	-1.82
Structure conservation index	0.54
SVM decision value	-0.00
SVM RNA-class probability	0.531089
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16432190 101 + 20766785
UGCUCCUUUAUGCGACUGCGACUUUGGGCCAACAG---CCGUCAGUGUGGCAAUGUAGCAAUGUGGCUAUGU--------GGCAAUGUGGCGAUAUGGCGGGAUGCCAUGUC
.((..(....(((.(((((.((.((((((.....)---))..))).)).)))..(((((......)))))))--------.)))..)..))((((((((.....)))))))) ( -34.10)
>DroSec_CAF1 107811 101 + 1
UGCUCCUUUAUGGGACUGCGACUUUGGGCCACCAG---CCGCCAGUGUGGCAAUGUAGCAAUGUGGCUAUGU--------GGCAAUGUGGCGAUAUGGCGGGAUGCCAUGUC
.((((((....))))..))........(((((..(---(((((.....))).(((((((......)))))))--------)))...)))))((((((((.....)))))))) ( -40.20)
>DroSim_CAF1 103559 101 + 1
UGCUCCUUUAUGCGACUGCGACUUUGGGCCACCAG---CCGCCAGUGUGGCAAUGUAGCAAUGUGGCUAUGU--------GGCAAUGUGGCGAUAUGGCGGGAUGCCAUGUC
.((........))....((.((.....(((((..(---((((....)))))...(((((......)))))))--------)))...)).))((((((((.....)))))))) ( -38.30)
>DroEre_CAF1 107684 78 + 1
UGCUCC-----------ACGACUUUGGGGCAC-------UGCCAGUGCGGCGAUGUGGCAAUGUG----------------GCAAUGUGGCGAUAUGGCGGGAUGCCAUGUC
((((((-----------(......))))))).-------.((((.(((.(((.((...)).))).----------------)))...))))((((((((.....)))))))) ( -32.40)
>DroYak_CAF1 108452 101 + 1
UGCUCC-----------ACGAGUUUGGGGCACGGGGCAUCGCCAGUGUGGCGAUGUAGCAAUGUGGCAAUGUGGCAUUGUGGCAAUGUGGCGAUAUGGCGGGAUGCCAUGUC
.(((((-----------(......))))))(((.((((((((((.(((.(((.(((.(((((((.((...)).))))))).))).))).)))...))))..)))))).))). ( -45.50)
>consensus
UGCUCCUUUAUG_GACUGCGACUUUGGGCCACCAG___CCGCCAGUGUGGCAAUGUAGCAAUGUGGCUAUGU________GGCAAUGUGGCGAUAUGGCGGGAUGCCAUGUC
...........................(((((........(((.....))).(((((((......)))))))..............)))))((((((((.....)))))))) (-20.62 = -22.66 +   2.04)

alignment

secondary structure

dotplot

Window 4

Location	16,432,190 – 16,432,291
Length	101
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	79.48
Mean single sequence MFE	-30.08
Consensus MFE	-16.06
Energy contribution	-18.06
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.53
SVM decision value	0.61
SVM RNA-class probability	0.800105
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16432190 101 - 20766785
GACAUGGCAUCCCGCCAUAUCGCCACAUUGCC--------ACAUAGCCACAUUGCUACAUUGCCACACUGACGG---CUGUUGGCCCAAAGUCGCAGUCGCAUAAAGGAGCA
((((((((.....)))))...((.((...(((--------(.((((((.....((......))(.....)..))---)))))))).....)).)).)))((........)). ( -27.30)
>DroSec_CAF1 107811 101 - 1
GACAUGGCAUCCCGCCAUAUCGCCACAUUGCC--------ACAUAGCCACAUUGCUACAUUGCCACACUGGCGG---CUGGUGGCCCAAAGUCGCAGUCCCAUAAAGGAGCA
((((((((.....)))))...(((((...(((--------...((((......))))....(((.....)))))---)..))))).....)))((..(((......))))). ( -36.10)
>DroSim_CAF1 103559 101 - 1
GACAUGGCAUCCCGCCAUAUCGCCACAUUGCC--------ACAUAGCCACAUUGCUACAUUGCCACACUGGCGG---CUGGUGGCCCAAAGUCGCAGUCGCAUAAAGGAGCA
((((((((.....)))))...(((((...(((--------...((((......))))....(((.....)))))---)..))))).....)))((....))........... ( -34.00)
>DroEre_CAF1 107684 78 - 1
GACAUGGCAUCCCGCCAUAUCGCCACAUUGC----------------CACAUUGCCACAUCGCCGCACUGGCA-------GUGCCCCAAAGUCGU-----------GGAGCA
((.(((((.....))))).))((..((((((----------------((...(((.........))).)))))-------)))..(((......)-----------)).)). ( -23.50)
>DroYak_CAF1 108452 101 - 1
GACAUGGCAUCCCGCCAUAUCGCCACAUUGCCACAAUGCCACAUUGCCACAUUGCUACAUCGCCACACUGGCGAUGCCCCGUGCCCCAAACUCGU-----------GGAGCA
((.(((((.....))))).))((..(((((...)))))((((...((......))..(((((((.....))))))).................))-----------)).)). ( -29.50)
>consensus
GACAUGGCAUCCCGCCAUAUCGCCACAUUGCC________ACAUAGCCACAUUGCUACAUUGCCACACUGGCGG___CUGGUGGCCCAAAGUCGCAGUC_CAUAAAGGAGCA
((((((((.....)))))...(((((.................((((......))))....(((.....)))........))))).....)))................... (-16.06 = -18.06 +   2.00)

alignment

secondary structure

dotplot

Window 5

Location	16,432,227 – 16,432,331
Length	104
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	77.63
Mean single sequence MFE	-39.05
Consensus MFE	-24.34
Energy contribution	-24.07
Covariance contribution	-0.28
Combinations/Pair	1.13
Mean z-score	-2.46
Structure conservation index	0.62
SVM decision value	1.76
SVM RNA-class probability	0.975859
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16432227 104 + 20766785
GUCAGUGUGGCAAU----GUAGCAAUGUGGCUAUGU--------GGCAAUGUGGCGAUAUGGCGGGAUGCCAUGUCUGGCAGCCAUUCGUUUCGGGUGGCAAAUUGUGACGUGAAC
((((((((((((..----...((.((((.(((((((--------....))))))).)))).))....))))))).))))).((((((((...))))))))................ ( -40.50)
>DroPse_CAF1 137238 96 + 1
-----UGUGGCUGUGUCAGUGGCAAUGU----CUGA--------GGCAGUGUGGCAGGAUGCC---AUGCCAUGUCUGGCAGCCAUUCGUUUCGGGUGGCAAAUUGUGACGUGAAC
-----(((.((((...)))).)))((((----(...--------(.((((((((((((...))---.))))))).))).).((((((((...)))))))).......))))).... ( -36.40)
>DroEre_CAF1 107706 96 + 1
GCCAGUGCGGCGAU----GUGGCAAUGUG----------------GCAAUGUGGCGAUAUGGCGGGAUGCCAUGUCUGGCAGCCAUUCGUUUCGGGUGGCAAAUUGUGACGUGAAC
((((..((.(((.(----((.((...)).----------------))).))).))((((((((.....)))))))))))).((((((((...))))))))................ ( -38.90)
>DroYak_CAF1 108481 112 + 1
GCCAGUGUGGCGAU----GUAGCAAUGUGGCAAUGUGGCAUUGUGGCAAUGUGGCGAUAUGGCGGGAUGCCAUGUCUGGGAGCCAUUCGUUUCGGGUGGCAAAUUGUGACGUGAAC
(((.....)))..(----((.(((((((.((...)).))))))).)))((((.((((((((((.....)))))))).....((((((((...)))))))).....)).)))).... ( -44.50)
>DroAna_CAF1 103055 93 + 1
AA---AGU-----A----GUGGCAGUAUGCC-CGGU--------GGCAGUGUGCCGG--UGGCAGGAUGCCAUGUCUGGCAGCCAUUCGUUUCGGGUGGCAAAUUGUGACGUGAAC
..---...-----.----((.(((((.((((-.(((--------((((.(.((((..--.)))).).))))))..).))))((((((((...))))))))..))))).))...... ( -37.60)
>DroPer_CAF1 138334 96 + 1
-----UGUGGCUGUGUCAGUGGCAAUGU----CUGA--------GGCAGUGUGGCAGGAUGCC---AUGCCAUGUCUGGCAGCCAUUCGUUUCGGGUGGCAAAUUGUGACGUGAAC
-----(((.((((...)))).)))((((----(...--------(.((((((((((((...))---.))))))).))).).((((((((...)))))))).......))))).... ( -36.40)
>consensus
G____UGUGGCGAU____GUGGCAAUGUG___CUGU________GGCAAUGUGGCGAUAUGGCGGGAUGCCAUGUCUGGCAGCCAUUCGUUUCGGGUGGCAAAUUGUGACGUGAAC
..................((.(((((...................((.(..(((((...........)))))..)...)).((((((((...))))))))..))))).))...... (-24.34 = -24.07 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:26 2006