Locus 679

Sequence ID	3R_DroMel_CAF1
Location	2,455,471 – 2,455,591
Length	120
Max. P	0.999991

overview

Window 3

Location	2,455,471 – 2,455,591
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-31.10
Consensus MFE	-28.25
Energy contribution	-28.83
Covariance contribution	0.59
Combinations/Pair	1.06
Mean z-score	-2.93
Structure conservation index	0.91
SVM decision value	3.75
SVM RNA-class probability	0.999581
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2455471 120 + 27905053
AGAUUCCGAACAUUUGUUACCCCAAACAAAAUGGCUACACAGCCAUUUCCGACGAAUUUCCACAUGGAAGGCUUUACACCCAUCUCAGCGCUUUUGUUUGGAUUAUUAUAUUCGCGUUUC
............((((((......))))))((((((....))))))...((.(((((.((((.(..(((((((.............))).))))..).)))).......))))))).... ( -24.92)
>DroSec_CAF1 14468 120 + 1
AGAUUCCGAACAUUUGUUACCCCAAACAAAAUGGCUACACAGCCAUUUCCGCCGAAUUUCCACAUGGAAGGCUUUACACCCAUCUCGGCGCUUUUGUUUGGAUUAUUAUAUUCGCGUUUC
.((..(((((.((....((..(((((((((((((((....)))))....((((((..((((....))))((........))...)))))).))))))))))..))..)).)))).)..)) ( -33.80)
>DroSim_CAF1 11187 120 + 1
AGAUUCCGAACAUUUGUUACCCCAAACAAAAUGGCUACACAGCCAUUUCCGCCGAAUUUCCACAUGGAAGGCUUUACACCCAUCUCGGCGCUUUUGUUUGGAUUAUUAUAUUCGCGUUUC
.((..(((((.((....((..(((((((((((((((....)))))....((((((..((((....))))((........))...)))))).))))))))))..))..)).)))).)..)) ( -33.80)
>DroEre_CAF1 15428 120 + 1
AGAUUCCGAACAUUUGUUACCCCGAACAAAAUGGCUACACAGCCAUUUCCGCCGAAUUUCCACAUGGAAGGCUUUACACCCAUCUCGGCGCUUUUGUUUGGAUUAUUAUAUUCGCGUUUC
.((..(((((.((....((..(((((((((((((((....)))))....((((((..((((....))))((........))...)))))).))))))))))..))..)).)))).)..)) ( -33.50)
>DroYak_CAF1 15286 120 + 1
AGAUUCCGAACAUUUGUUACCCCAAACAAAAUGGCUACACAGCCAUUUCCGCUGAAUUUCCACAUGGAAGGCUUUACACCCAUCGCGGCGCUUUUGUUUGGAUUAUUAUAUUCGCGUUUC
.((..(((((.((....((..(((((((((((((((....)))))....(((((...((((....))))((........))....))))).))))))))))..))..)).)))).)..)) ( -30.10)
>DroAna_CAF1 14796 120 + 1
GCAGACCAAACAUUUGUUACCCCAAACAAAAUGGCUACAUAGCCAUUUCCGCCAAAUUUCCACAUGGAAGGCUUUACACCCAUCUCGGCGCUUUUGUUUGGAUUAUUAUAUUCGCGUUUC
((......(((....)))...(((((((((((((((....)))))....((((....((((....))))((........)).....)))).))))))))))............))..... ( -30.50)
>consensus
AGAUUCCGAACAUUUGUUACCCCAAACAAAAUGGCUACACAGCCAUUUCCGCCGAAUUUCCACAUGGAAGGCUUUACACCCAUCUCGGCGCUUUUGUUUGGAUUAUUAUAUUCGCGUUUC
....((((((((((((((......))))))((((((....))))))...((((((..((((....))))((........))...))))))....)))))))).................. (-28.25 = -28.83 +   0.59)

alignment

secondary structure

dotplot

Window 4

Location	2,455,471 – 2,455,591
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-38.90
Consensus MFE	-38.24
Energy contribution	-38.52
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-3.23
Structure conservation index	0.98
SVM decision value	5.65
SVM RNA-class probability	0.999991
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2455471 120 - 27905053
GAAACGCGAAUAUAAUAAUCCAAACAAAAGCGCUGAGAUGGGUGUAAAGCCUUCCAUGUGGAAAUUCGUCGGAAAUGGCUGUGUAGCCAUUUUGUUUGGGGUAACAAAUGUUCGGAAUCU
......(((((((.....(((((((...........(((((((.....)))((((....))))...)))).(((((((((....)))))))))))))))).......)))))))...... ( -34.30)
>DroSec_CAF1 14468 120 - 1
GAAACGCGAAUAUAAUAAUCCAAACAAAAGCGCCGAGAUGGGUGUAAAGCCUUCCAUGUGGAAAUUCGGCGGAAAUGGCUGUGUAGCCAUUUUGUUUGGGGUAACAAAUGUUCGGAAUCU
......(((((((.....(((((((.....(((((((...(((.....)))((((....)))).)))))))(((((((((....)))))))))))))))).......)))))))...... ( -42.40)
>DroSim_CAF1 11187 120 - 1
GAAACGCGAAUAUAAUAAUCCAAACAAAAGCGCCGAGAUGGGUGUAAAGCCUUCCAUGUGGAAAUUCGGCGGAAAUGGCUGUGUAGCCAUUUUGUUUGGGGUAACAAAUGUUCGGAAUCU
......(((((((.....(((((((.....(((((((...(((.....)))((((....)))).)))))))(((((((((....)))))))))))))))).......)))))))...... ( -42.40)
>DroEre_CAF1 15428 120 - 1
GAAACGCGAAUAUAAUAAUCCAAACAAAAGCGCCGAGAUGGGUGUAAAGCCUUCCAUGUGGAAAUUCGGCGGAAAUGGCUGUGUAGCCAUUUUGUUCGGGGUAACAAAUGUUCGGAAUCU
......(((((((.....(((.(((.....(((((((...(((.....)))((((....)))).)))))))(((((((((....)))))))))))).))).......)))))))...... ( -38.30)
>DroYak_CAF1 15286 120 - 1
GAAACGCGAAUAUAAUAAUCCAAACAAAAGCGCCGCGAUGGGUGUAAAGCCUUCCAUGUGGAAAUUCAGCGGAAAUGGCUGUGUAGCCAUUUUGUUUGGGGUAACAAAUGUUCGGAAUCU
......(((((((.....(((((((((((...((((....(((.....)))((((....)))).....))))...(((((....)))))))))))))))).......)))))))...... ( -37.40)
>DroAna_CAF1 14796 120 - 1
GAAACGCGAAUAUAAUAAUCCAAACAAAAGCGCCGAGAUGGGUGUAAAGCCUUCCAUGUGGAAAUUUGGCGGAAAUGGCUAUGUAGCCAUUUUGUUUGGGGUAACAAAUGUUUGGUCUGC
...((.(((((((.....(((((((.....(((((((...(((.....)))((((....)))).)))))))(((((((((....)))))))))))))))).......))))))))).... ( -38.60)
>consensus
GAAACGCGAAUAUAAUAAUCCAAACAAAAGCGCCGAGAUGGGUGUAAAGCCUUCCAUGUGGAAAUUCGGCGGAAAUGGCUGUGUAGCCAUUUUGUUUGGGGUAACAAAUGUUCGGAAUCU
......(((((((.....(((((((.....(((((((...(((.....)))((((....)))).)))))))(((((((((....)))))))))))))))).......)))))))...... (-38.24 = -38.52 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:07 2006