Locus 5068

Sequence ID	2R_DroMel_CAF1
Location	16,459,754 – 16,459,847
Length	93
Max. P	0.980166

overview

Window 1

Location	16,459,754 – 16,459,847
Length	93
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	74.73
Mean single sequence MFE	-24.93
Consensus MFE	-14.93
Energy contribution	-15.93
Covariance contribution	1.01
Combinations/Pair	1.33
Mean z-score	-1.67
Structure conservation index	0.60
SVM decision value	0.85
SVM RNA-class probability	0.867128
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16459754 93 + 20766785
CGCAGCGCCCUUGUGUCCUUUUUUUU--UUUUUUUGUGUGGCAU-UGGCAGUAAAUGCCGGCAAAAUGGCGCUCAUUAGGUAUAUUCCUUGUGCAA-
.((((((((.((.((((.........--......((.....)).-.((((.....)))))))).)).)))))).((.(((......))).))))..- ( -24.40)
>DroSec_CAF1 135070 84 + 1
CACAGCGCCCUUGUGUCCUUU-----------UUUGUGUGGCAU-UGGCCGUAAAUGCCGGCAAAAUGGCGCUCAUUAGACAUAUUCCUUGUGCAA-
....((((...((((((....-----------..((.(((.(((-(.((((.......))))..)))).))).))...))))))......))))..- ( -24.70)
>DroSim_CAF1 131878 84 + 1
CACAGCGCCCUUGUGUCCUUU-----------UUUGUGUGGCAU-UGGCAGUAAAUGCCGGCAAAAUGGCGCUCAUUAGGCAUAUUCCUUGUGCAA-
...((((((.((.(((((...-----------...)...(((((-(.......)))))))))).)).))))))......(((((.....)))))..- ( -25.80)
>DroEre_CAF1 136168 85 + 1
GACAGCGCCCUUGUGUCC-----------UUUUUUGUGCGGCAUUUGGCAGUAAAUGCCAUGAAAAUGGCGCUCAUUAGGCAUAUACCUUGUGCAA-
....((((...((((.((-----------(....((.(((.(((((((((.....)))))....)))).))).))..)))))))......))))..- ( -28.00)
>DroYak_CAF1 136584 95 + 1
UGCAGCGCCCUUGUGUCCUUUUUAUGUCCUUUUUUGUGCGGCAU-UGGCAGUAAAUGCCAUGAAAAUGGCGCUCAUUAGGCAGAUUCCUUGUGCAA-
((((((((....))))........((.(((....((.(((.(((-(((((.....))))).....))).))).))..))))).........)))).- ( -24.90)
>DroAna_CAF1 131732 72 + 1
UGAAGCGCCCCUCUUCUA-----------CCUUUUGUGUGGC-------------UGCCA-CAAAAUGGCGCUCAUUAAGGCGCUUCCUUUGGUCCU
.((((((((......(((-----------((....).)))).-------------.((((-.....)))).........)))))))).......... ( -21.80)
>consensus
CACAGCGCCCUUGUGUCCUUU________UUUUUUGUGUGGCAU_UGGCAGUAAAUGCCAGCAAAAUGGCGCUCAUUAGGCAUAUUCCUUGUGCAA_
...((((((...(((((......................))))).(((((.....))))).......))))))......(((((.....)))))... (-14.93 = -15.93 +   1.01)

alignment

secondary structure

dotplot

Window 2

Location	16,459,754 – 16,459,847
Length	93
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	74.73
Mean single sequence MFE	-23.62
Consensus MFE	-16.43
Energy contribution	-16.08
Covariance contribution	-0.34
Combinations/Pair	1.20
Mean z-score	-1.96
Structure conservation index	0.70
SVM decision value	1.85
SVM RNA-class probability	0.980166
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16459754 93 - 20766785
-UUGCACAAGGAAUAUACCUAAUGAGCGCCAUUUUGCCGGCAUUUACUGCCA-AUGCCACACAAAAAAA--AAAAAAAAGGACACAAGGGCGCUGCG
-..((...(((......)))....((((((.((.((((((((.....)))).-.((.....))......--........)).)).)).)))))))). ( -23.10)
>DroSec_CAF1 135070 84 - 1
-UUGCACAAGGAAUAUGUCUAAUGAGCGCCAUUUUGCCGGCAUUUACGGCCA-AUGCCACACAAA-----------AAAGGACACAAGGGCGCUGUG
-...(((..(((.....)))....((((((.(((((..((((((.......)-)))))...))))-----------)..(....)...))))))))) ( -20.40)
>DroSim_CAF1 131878 84 - 1
-UUGCACAAGGAAUAUGCCUAAUGAGCGCCAUUUUGCCGGCAUUUACUGCCA-AUGCCACACAAA-----------AAAGGACACAAGGGCGCUGUG
-...(((.(((......)))....((((((.((.((((((((.....)))).-.((.....))..-----------...)).)).)).))))))))) ( -22.70)
>DroEre_CAF1 136168 85 - 1
-UUGCACAAGGUAUAUGCCUAAUGAGCGCCAUUUUCAUGGCAUUUACUGCCAAAUGCCGCACAAAAAA-----------GGACACAAGGGCGCUGUC
-...((..((((....))))..))((((((.......(((((.....)))))..((((..........-----------)).))....))))))... ( -23.20)
>DroYak_CAF1 136584 95 - 1
-UUGCACAAGGAAUCUGCCUAAUGAGCGCCAUUUUCAUGGCAUUUACUGCCA-AUGCCGCACAAAAAAGGACAUAAAAAGGACACAAGGGCGCUGCA
-.(((...(((......)))....((((((.......(((((.....)))))-(((((..........)).)))..............))))))))) ( -24.90)
>DroAna_CAF1 131732 72 - 1
AGGACCAAAGGAAGCGCCUUAAUGAGCGCCAUUUUG-UGGCA-------------GCCACACAAAAGG-----------UAGAAGAGGGGCGCUUCA
..........((((((((((..(....(((.(((((-((...-------------....)))))))))-----------)...)..)))))))))). ( -27.40)
>consensus
_UUGCACAAGGAAUAUGCCUAAUGAGCGCCAUUUUGCCGGCAUUUACUGCCA_AUGCCACACAAAAAA________AAAGGACACAAGGGCGCUGCG
........(((......)))....((((((........(((((..........))))).....................(....)...))))))... (-16.43 = -16.08 +  -0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:42 2006