Locus 1908

Sequence ID	3L_DroMel_CAF1
Location	5,346,227 – 5,346,397
Length	170
Max. P	0.999216

overview

Window 3

Location	5,346,227 – 5,346,339
Length	112
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	78.24
Mean single sequence MFE	-31.26
Consensus MFE	-22.96
Energy contribution	-23.00
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.71
Structure conservation index	0.73
SVM decision value	0.83
SVM RNA-class probability	0.862278
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5346227 112 + 23771897
UUUGGGCAAUUUUGAGAGACUGCGCCAAAGGUCGGCGCGUCUAAAUCAAUGCGCAAAAAAUGCAGCCAU---CGAGUGGAGUUCCCGAAAAAUGGGCAAAAGCUGUAGUAAU---CCC
((((.(((...((((.((((.(((((.......)))))))))...))))))).))))...((((((..(---(.....))...((((.....)))).....)))))).....---... ( -33.90)
>DroSec_CAF1 94132 94 + 1
UUUGGGCAAUUUUGAGAGACUGCGCCAAAGGUCGGCGCGUCUAAAUCAAUGCGCAAAAAAUGCAGCCAU---CGAGUGGAGCUCC------------------AGUAGUAAU---CCC
....(((....((((.((((.(((((.......)))))))))...))))...(((.....))).)))..---..(.(((....))------------------).)......---... ( -28.00)
>DroSim_CAF1 95904 94 + 1
UUUGGGCAAUUUUGAGAGACUGCGCCAAAGGUCGGCGCGUCUAAAUCAAUGCGCAAAAAAUGCAGCCAU---CGAGUGGAGUUCC------------------AGUAGUAAU---CCC
....(((....((((.((((.(((((.......)))))))))...))))...(((.....))).)))..---..(.(((....))------------------).)......---... ( -28.00)
>DroEre_CAF1 94158 118 + 1
UUUGGGCAAUUUUGAAAGACUGCGCCAAAGGUCGGCGCGUCUAAAUCAAUGCGGAAAAAAUGCAGCCAUCCUCCAGUGGAGCUCCAGAAAAAUGGGCAGAAGCUGUAGUAAUCGGCGG
...........((((.((((.(((((.......)))))))))...))))(((.((.....((((((..(((......)))((.(((......)))))....))))))....)).))). ( -37.30)
>DroYak_CAF1 102846 99 + 1
UUUGGGCAAUUUUGAGAGACUGCGCCAAAGGUCGGUGCGUCUAAAUCAAUGCGGAAAAAAUGCAGC------------------CAGAAAAAUGGGCAAAAGCUCUAGUA-UAAGCCC
....(((....((((.((((.(((((.......)))))))))...))))((((.......))))))------------------)........((((....((....)).-...)))) ( -29.10)
>consensus
UUUGGGCAAUUUUGAGAGACUGCGCCAAAGGUCGGCGCGUCUAAAUCAAUGCGCAAAAAAUGCAGCCAU___CGAGUGGAGCUCC_GAAAAAUGGGCA_AAGCUGUAGUAAU___CCC
....(((....((((.((((.(((((.......)))))))))...))))((((.......)))))))................................................... (-22.96 = -23.00 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	5,346,227 – 5,346,339
Length	112
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	78.24
Mean single sequence MFE	-29.67
Consensus MFE	-19.12
Energy contribution	-20.12
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.64
SVM decision value	0.62
SVM RNA-class probability	0.800824
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5346227 112 - 23771897
GGG---AUUACUACAGCUUUUGCCCAUUUUUCGGGAACUCCACUCG---AUGGCUGCAUUUUUUGCGCAUUGAUUUAGACGCGCCGACCUUUGGCGCAGUCUCUCAAAAUUGCCCAAA
(((---.........((....(((......(((((.......))))---).))).(((.....))))).((((...(((((((((((...))))))).)))).)))).....)))... ( -32.90)
>DroSec_CAF1 94132 94 - 1
GGG---AUUACUACU------------------GGAGCUCCACUCG---AUGGCUGCAUUUUUUGCGCAUUGAUUUAGACGCGCCGACCUUUGGCGCAGUCUCUCAAAAUUGCCCAAA
(((---........(------------------((....))).(((---(((.(.(((.....))))))))))...(((((((((((...))))))).))))..........)))... ( -28.40)
>DroSim_CAF1 95904 94 - 1
GGG---AUUACUACU------------------GGAACUCCACUCG---AUGGCUGCAUUUUUUGCGCAUUGAUUUAGACGCGCCGACCUUUGGCGCAGUCUCUCAAAAUUGCCCAAA
(((---........(------------------((....))).(((---(((.(.(((.....))))))))))...(((((((((((...))))))).))))..........)))... ( -28.40)
>DroEre_CAF1 94158 118 - 1
CCGCCGAUUACUACAGCUUCUGCCCAUUUUUCUGGAGCUCCACUGGAGGAUGGCUGCAUUUUUUCCGCAUUGAUUUAGACGCGCCGACCUUUGGCGCAGUCUUUCAAAAUUGCCCAAA
..((.((......(((((((((((((......))).))(((...)))))).))))).......)).)).((((...(((((((((((...))))))).)))).))))........... ( -33.42)
>DroYak_CAF1 102846 99 - 1
GGGCUUA-UACUAGAGCUUUUGCCCAUUUUUCUG------------------GCUGCAUUUUUUCCGCAUUGAUUUAGACGCACCGACCUUUGGCGCAGUCUCUCAAAAUUGCCCAAA
((((...-....((((...(((((((....((.(------------------(.(((.(((..((......))...))).)))))))....))).)))).)))).......))))... ( -25.24)
>consensus
GGG___AUUACUACAGCUU_UGCCCAUUUUUC_GGAACUCCACUCG___AUGGCUGCAUUUUUUGCGCAUUGAUUUAGACGCGCCGACCUUUGGCGCAGUCUCUCAAAAUUGCCCAAA
(((.................................................((.(((.....))))).((((...(((((((((((...))))))).)))).)))).....)))... (-19.12 = -20.12 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	5,346,302 – 5,346,397
Length	95
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	72.86
Mean single sequence MFE	-20.64
Consensus MFE	-10.42
Energy contribution	-12.42
Covariance contribution	2.00
Combinations/Pair	1.10
Mean z-score	-2.78
Structure conservation index	0.50
SVM decision value	3.44
SVM RNA-class probability	0.999216
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5346302 95 + 23771897
GAGUUCCCGAAAAAUGGGCAAAAGCUGUAGUAAU---CCCAACUGCAGCUCAAUCAAAAUGCUCAGCGGAAUUUAAAUCAAAAUUCAAAUUGAGCAUC
((...((((.....))))....(((((((((...---....)))))))))...))...((((((((..((((((......))))))...)))))))). ( -27.90)
>DroSec_CAF1 94207 76 + 1
GAGCUCC------------------AGUAGUAAU---CCCACCUGCAGUUCAACCAAAAUGCUCAGAGGAAUUUAAAUCAAAA-UCAAAUUGAGCAUC
(((((.(------------------((..(....---..)..))).))))).......((((((((..((.(((.....))).-))...)))))))). ( -16.30)
>DroSim_CAF1 95979 76 + 1
GAGUUCC------------------AGUAGUAAU---CCCACCUGCAGCUCAACCAAAAUGCUCAGCGGAAUUUAAAUCAAAA-UCAAAUUGAGCAUC
(((((.(------------------((..(....---..)..))).))))).......((((((((..((.(((.....))).-))...)))))))). ( -16.30)
>DroEre_CAF1 94236 97 + 1
GAGCUCCAGAAAAAUGGGCAGAAGCUGUAGUAAUCGGCGGGAUUACAGCUCUACCCAAAUGCUCAUCGGAAUUUAAAGCAAAA-UCGAAUUGAGCAUC
..............((((.(((.((((((((..........))))))))))).)))).((((((((((..((((......)))-))))..))))))). ( -27.00)
>DroYak_CAF1 102912 90 + 1
------CAGAAAAAUGGGCAAAAGCUCUAGUA-UAAGCCCUACUACAGCUCUACCAAAAUGCUCAUCGGAAUUUGAAUCGAAA-UCAAAUUGAACAUC
------.......(((((((..((((.(((((-.......))))).)))).........)))))))...(((((((.......-)))))))....... ( -15.70)
>consensus
GAGCUCC_GAAAAAUGGGCA_AAGCUGUAGUAAU___CCCAACUGCAGCUCAACCAAAAUGCUCAGCGGAAUUUAAAUCAAAA_UCAAAUUGAGCAUC
.......................((((((((..........)))))))).........((((((((..((.(((......))).))...)))))))). (-10.42 = -12.42 +   2.00)

alignment

secondary structure

dotplot

Window 6

Location	5,346,302 – 5,346,397
Length	95
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	72.86
Mean single sequence MFE	-22.94
Consensus MFE	-8.46
Energy contribution	-8.34
Covariance contribution	-0.12
Combinations/Pair	1.14
Mean z-score	-1.92
Structure conservation index	0.37
SVM decision value	0.75
SVM RNA-class probability	0.839463
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5346302 95 - 23771897
GAUGCUCAAUUUGAAUUUUGAUUUAAAUUCCGCUGAGCAUUUUGAUUGAGCUGCAGUUGGG---AUUACUACAGCUUUUGCCCAUUUUUCGGGAACUC
((((((((....((((((......))))))...))))))))......((((((.(((....---...))).))))))...(((.......)))..... ( -24.70)
>DroSec_CAF1 94207 76 - 1
GAUGCUCAAUUUGA-UUUUGAUUUAAAUUCCUCUGAGCAUUUUGGUUGAACUGCAGGUGGG---AUUACUACU------------------GGAGCUC
((((((((....((-(((......)))))....))))))))......((.((.(((.(((.---....)))))------------------).)).)) ( -16.90)
>DroSim_CAF1 95979 76 - 1
GAUGCUCAAUUUGA-UUUUGAUUUAAAUUCCGCUGAGCAUUUUGGUUGAGCUGCAGGUGGG---AUUACUACU------------------GGAACUC
((((((((....((-(((......)))))....))))))))......(((.(.(((.(((.---....)))))------------------).).))) ( -16.90)
>DroEre_CAF1 94236 97 - 1
GAUGCUCAAUUCGA-UUUUGCUUUAAAUUCCGAUGAGCAUUUGGGUAGAGCUGUAAUCCCGCCGAUUACUACAGCUUCUGCCCAUUUUUCUGGAGCUC
((((((((..((((-(((......))))..)))))))))))(((((((((((((((((.....)))...)))))).)))))))).............. ( -31.10)
>DroYak_CAF1 102912 90 - 1
GAUGUUCAAUUUGA-UUUCGAUUCAAAUUCCGAUGAGCAUUUUGGUAGAGCUGUAGUAGGGCUUA-UACUAGAGCUUUUGCCCAUUUUUCUG------
((((((((((((((-.......)))))).....))))))))..(((((((((.(((((.......-))))).))).))))))..........------ ( -25.10)
>consensus
GAUGCUCAAUUUGA_UUUUGAUUUAAAUUCCGCUGAGCAUUUUGGUUGAGCUGCAGUUGGG___AUUACUACAGCUU_UGCCCAUUUUUC_GGAACUC
((((((((((((((........)))))).....))))))))......................................................... ( -8.46 =  -8.34 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:42 2006