Locus 7487

Sequence ID	3L_DroMel_CAF1
Location	20,093,147 – 20,093,270
Length	123
Max. P	0.978015

overview

Window 2

Location	20,093,147 – 20,093,241
Length	94
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	92.70
Mean single sequence MFE	-34.36
Consensus MFE	-27.60
Energy contribution	-27.88
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-2.32
Structure conservation index	0.80
SVM decision value	1.80
SVM RNA-class probability	0.978015
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20093147 94 + 23771897
AGGGCGUUGCAGGACAAUGAAAAGUGUUCCGGCAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUGGGUAA------AACUGGGCAAC
...((((((((((.((((......(((.(((((....)))))))).......))))))))))))..(((.(((.....)))..------.)))..))... ( -33.52)
>DroSec_CAF1 7736 100 + 1
AGGGCGUUGCAGGACAAUGAAAAGUGUUCCGGCAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUGGGUAAUGUGGCAACUAGGCAAC
...((((((((((.((((......(((.(((((....)))))))).......))))))))))))..(((.((((.(........))))).)))..))... ( -36.32)
>DroSim_CAF1 7990 100 + 1
AGGGCGUUGCAGGACAAUGAAAAGUGUUCCGGCAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUGGGUAAUGUGGCAACUAGGCAAC
...((((((((((.((((......(((.(((((....)))))))).......))))))))))))..(((.((((.(........))))).)))..))... ( -36.32)
>DroEre_CAF1 7639 99 + 1
CGCGCGUUGCAGGACAAUGAAAAGUGUUUGGGCAUUCGCCGGGCAAAAAUAAAUUGCUUGCAGCGG-GCGGCCAACUGGGUAAUGUGGCAACUAGGCAAC
(((.(((((((((.((((......(((((((.......))))))).......))))))))))))).-)))((((.(........)))))........... ( -36.92)
>DroYak_CAF1 7762 100 + 1
CGGGCGUUGCAGGACAAUGAAAAGUGUUCAGACAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUUGGUAAUGUGGCAACUAGGCAAC
.....(((((.(((((.(....).)))))......(((((((((((.......)))))..))))))(((.((((.(........))))).)))..))))) ( -28.70)
>consensus
AGGGCGUUGCAGGACAAUGAAAAGUGUUCCGGCAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUGGGUAAUGUGGCAACUAGGCAAC
....(((((((((.((((......(((.(((((....)))))))).......))))))))))))).....(((.....(((.........))).)))... (-27.60 = -27.88 +   0.28)

alignment

secondary structure

dotplot

Window 3

Location	20,093,147 – 20,093,241
Length	94
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	92.70
Mean single sequence MFE	-24.12
Consensus MFE	-20.26
Energy contribution	-20.54
Covariance contribution	0.28
Combinations/Pair	1.10
Mean z-score	-1.30
Structure conservation index	0.84
SVM decision value	0.10
SVM RNA-class probability	0.585056
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20093147 94 - 23771897
GUUGCCCAGUU------UUACCCAGUUGGCCACCCCGCCGCAAGCAAUUUAUUUUUGCCCGGCAAAUGCCGGAACACUUUUCAUUGUCCUGCAACGCCCU
(((((......------..........(((......)))((((((((.......))))(((((....)))))...........))))...)))))..... ( -24.40)
>DroSec_CAF1 7736 100 - 1
GUUGCCUAGUUGCCACAUUACCCAGUUGGCCACCCCGCCGCAAGCAAUUUAUUUUUGCCCGGCAAAUGCCGGAACACUUUUCAUUGUCCUGCAACGCCCU
(((((...((.(((((........).)))).))......((((((((.......))))(((((....)))))...........))))...)))))..... ( -25.70)
>DroSim_CAF1 7990 100 - 1
GUUGCCUAGUUGCCACAUUACCCAGUUGGCCACCCCGCCGCAAGCAAUUUAUUUUUGCCCGGCAAAUGCCGGAACACUUUUCAUUGUCCUGCAACGCCCU
(((((...((.(((((........).)))).))......((((((((.......))))(((((....)))))...........))))...)))))..... ( -25.70)
>DroEre_CAF1 7639 99 - 1
GUUGCCUAGUUGCCACAUUACCCAGUUGGCCGC-CCGCUGCAAGCAAUUUAUUUUUGCCCGGCGAAUGCCCAAACACUUUUCAUUGUCCUGCAACGCGCG
...((...(((((.(((......((((((.((.-.(((((...((((.......)))).)))))..)).)))...)))......)))...)))))..)). ( -23.10)
>DroYak_CAF1 7762 100 - 1
GUUGCCUAGUUGCCACAUUACCAAGUUGGCCACCCCGCCGCAAGCAAUUUAUUUUUGCCCGGCAAAUGUCUGAACACUUUUCAUUGUCCUGCAACGCCCG
(((((...((.(((((........).)))).))...((((...((((.......)))).))))...........................)))))..... ( -21.70)
>consensus
GUUGCCUAGUUGCCACAUUACCCAGUUGGCCACCCCGCCGCAAGCAAUUUAUUUUUGCCCGGCAAAUGCCGGAACACUUUUCAUUGUCCUGCAACGCCCU
(((((......................(((......)))((((((((.......))))(((((....)))))...........))))...)))))..... (-20.26 = -20.54 +   0.28)

alignment

secondary structure

dotplot

Window 4

Location	20,093,173 – 20,093,270
Length	97
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	78.82
Mean single sequence MFE	-37.70
Consensus MFE	-20.84
Energy contribution	-21.60
Covariance contribution	0.76
Combinations/Pair	1.14
Mean z-score	-1.84
Structure conservation index	0.55
SVM decision value	0.15
SVM RNA-class probability	0.609276
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20093173 97 + 23771897
UUCCGGCAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUGGGUAA------AACUGGGCAACUUGGC---UAG--------GCAACCAGGCAACCAGGCAUC
.((((((....))))))...........((((((..((..(((.(((..(..(....------..)..)((......))---..)--------)).)))..))...)))))).. ( -35.10)
>DroSec_CAF1 7762 114 + 1
UUCCGGCAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUGGGUAAUGUGGCAACUAGGCAACUGGGCAACUAGGAAACCCGGCAACCCGUCAGCCAGGCAUC
.((((((....))))))...........(((((((((((((...(((....((((..(.(((...((((....))))....))).)..)))))))..)))))).).)))))).. ( -47.50)
>DroSim_CAF1 8016 114 + 1
UUCCGGCAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUGGGUAAUGUGGCAACUAGGCAACUGGGCAACUAGGCAACUAGGCAACCCGGCAGCCGGGCAUC
.((((((...(((((((..........((((((((.(((...((.((....)).)).))).))))((((....))))))))((((....))))....))))))))))))).... ( -51.70)
>DroEre_CAF1 7665 88 + 1
UUUGGGCAUUCGCCGGGCAAAAAUAAAUUGCUUGCAGCGG-GCGGCCAACUGGGUAAUGUGGCAACUAGGCAACC-------------------------AGCAACCAGGCAUC
.((((.(.((((((((((((.......)))))))..))))-).).))))((((....((..((......))...)-------------------------)....))))..... ( -26.10)
>DroYak_CAF1 7788 98 + 1
UUCAGACAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUUGGUAAUGUGGCAACUAGGCAACUUGGCACCUA----------------GGCAACCAGGCAUC
..........((((((((((.......))))((((....(((((((((.(........)))))..(.((....)).).))))).----------------.)))))).)))).. ( -28.10)
>consensus
UUCCGGCAUUUGCCGGGCAAAAAUAAAUUGCUUGCGGCGGGGUGGCCAACUGGGUAAUGUGGCAACUAGGCAACUGGGCA_CUAG________GCAACC_GGCAACCAGGCAUC
....(((.((((((((((((.......)))))..)))))))...)))..((((.......(....).((....))..............................))))..... (-20.84 = -21.60 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:27 2006