Locus 3322

Sequence ID	X_DroMel_CAF1
Location	8,878,531 – 8,878,626
Length	95
Max. P	0.999951

overview

Window 5

Location	8,878,531 – 8,878,626
Length	95
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	72.40
Mean single sequence MFE	-29.40
Consensus MFE	-12.84
Energy contribution	-13.08
Covariance contribution	0.24
Combinations/Pair	1.26
Mean z-score	-4.15
Structure conservation index	0.44
SVM decision value	4.79
SVM RNA-class probability	0.999951
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8878531 95 + 22224390
-------------------AAAAGUAAAGGGGGAGCACAAACCUCAUUCAAAUGAGGUUUGCGGAAGAAAAAGAAAAGAAAUUUUCAAAGGAGGAAAAGU-UACUUAGCUCUCCG
-------------------..........(((((((.((((((((((....))))))))))(....).....(((((....)))))..............-......))))))). ( -31.50)
>DroSec_CAF1 8841 93 + 1
-------------------AAAAGAAAAGGGG--GCACAAACCUCAUUCAAAUGAGGUUCGCGGAAGGAAAAUAAACGAAAUUUUCAAAGGAGGAAAAAU-UUCUUAGCUCUCCG
-------------------.........((((--((...((((((((....))))))))..(....)((((((.......)))))).((((((......)-))))).)).)))). ( -22.90)
>DroSim_CAF1 9148 93 + 1
-------------------AAAAGAAAAGGGG--GCACAAACCUCAUUCAAAUGAGGUUCGCGGAAGGAAAAUAAACGAAAUUUUCAAAGGAGGAAAAGU-UUCUUAGCUCUCCG
-------------------.........((((--((...((((((((....))))))))..(....)((((((.......)))))).((((((......)-))))).)).)))). ( -22.30)
>DroEre_CAF1 8314 106 + 1
AAAAAUGAGAUGGAAAAGA------AAAGGGG--GCACAAACCUCAUUCAAAUGAGGUUCGCGGAAGGAAAAGAAACGAAAUUUCCAAAGGAGGAAAAGU-UUCUUAGCUCUCCG
...................------...((((--((....(((((((....)))))))((.(....))).(((((((....(((((......))))).))-))))).)).)))). ( -29.00)
>DroAna_CAF1 13477 98 + 1
GAAA----GACUGCG----AA-----GAGU-G--GGAGGGAGCUCAUUCAAAUGGGGUUCGCGGAAGGAAACUCCA-GCGAGCUUCGAAGGAGGAAAGCCACUUUCAGGGGUCCG
....----((((.(.----.(-----((((-(--((((....))).(((...(((((((((((((.(....)))).-))))))))))...))).....)))))))..).)))).. ( -41.30)
>consensus
___________________AAAAG_AAAGGGG__GCACAAACCUCAUUCAAAUGAGGUUCGCGGAAGGAAAAUAAACGAAAUUUUCAAAGGAGGAAAAGU_UUCUUAGCUCUCCG
..................................((...((((((((....)))))))).))(((.(((((..........)))))....(((((......))))).....))). (-12.84 = -13.08 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	8,878,531 – 8,878,626
Length	95
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	72.40
Mean single sequence MFE	-26.64
Consensus MFE	-16.32
Energy contribution	-16.92
Covariance contribution	0.60
Combinations/Pair	1.32
Mean z-score	-4.39
Structure conservation index	0.61
SVM decision value	4.36
SVM RNA-class probability	0.999880
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8878531 95 - 22224390
CGGAGAGCUAAGUA-ACUUUUCCUCCUUUGAAAAUUUCUUUUCUUUUUCUUCCGCAAACCUCAUUUGAAUGAGGUUUGUGCUCCCCCUUUACUUUU-------------------
.((.((((......-..............(((((....)))))..........(((((((((((....))))))))))))))).))..........------------------- ( -24.40)
>DroSec_CAF1 8841 93 - 1
CGGAGAGCUAAGAA-AUUUUUCCUCCUUUGAAAAUUUCGUUUAUUUUCCUUCCGCGAACCUCAUUUGAAUGAGGUUUGUGC--CCCCUUUUCUUUU-------------------
.((((((..(((((-((((((........))))))))).))..))))))...((((((((((((....)))))))))))).--.............------------------- ( -27.00)
>DroSim_CAF1 9148 93 - 1
CGGAGAGCUAAGAA-ACUUUUCCUCCUUUGAAAAUUUCGUUUAUUUUCCUUCCGCGAACCUCAUUUGAAUGAGGUUUGUGC--CCCCUUUUCUUUU-------------------
.((((((..(((((-(.(((((.......))))))))).))..))))))...((((((((((((....)))))))))))).--.............------------------- ( -24.80)
>DroEre_CAF1 8314 106 - 1
CGGAGAGCUAAGAA-ACUUUUCCUCCUUUGGAAAUUUCGUUUCUUUUCCUUCCGCGAACCUCAUUUGAAUGAGGUUUGUGC--CCCCUUU------UCUUUUCCAUCUCAUUUUU
.((((((..(((((-((.(((((......)))))....))))))).......((((((((((((....)))))))))))).--.......------..))))))........... ( -31.80)
>DroAna_CAF1 13477 98 - 1
CGGACCCCUGAAAGUGGCUUUCCUCCUUCGAAGCUCGC-UGGAGUUUCCUUCCGCGAACCCCAUUUGAAUGAGCUCCCUCC--C-ACUC-----UU----CGCAGUC----UUUC
.((((...(((((((((.....(((.((((((..((((-.((((....)))).))))......)))))).))).......)--)-))).-----))----))..)))----)... ( -25.20)
>consensus
CGGAGAGCUAAGAA_ACUUUUCCUCCUUUGAAAAUUUCGUUUAUUUUCCUUCCGCGAACCUCAUUUGAAUGAGGUUUGUGC__CCCCUUU_CUUUU___________________
.((((....(((....)))...))))...((((((.......))))))....((((((((((((....))))))))))))................................... (-16.32 = -16.92 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:25 2006