Locus 7753

Sequence ID	3L_DroMel_CAF1
Location	20,671,829 – 20,671,967
Length	138
Max. P	0.997432

overview

Window 5

Location	20,671,829 – 20,671,948
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	74.76
Mean single sequence MFE	-24.93
Consensus MFE	-13.60
Energy contribution	-15.60
Covariance contribution	2.00
Combinations/Pair	1.15
Mean z-score	-2.27
Structure conservation index	0.55
SVM decision value	1.40
SVM RNA-class probability	0.950423
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20671829 119 - 23771897
UUAAUAAGUGCCAUUUAUAUUCAGCAGGUGUUGAUUGUAAAUCGCACUUCAUAAAAUAGUUAUCGAAAGUGAUUGGAAUACCUAAAUAACUCCGACUGUGAUCGAAACA-AACAGUAAUC
.....((((((.(((((((.(((((....))))).))))))).)))))).......((((((.(....)))))))...................(((((..........-.))))).... ( -26.50)
>DroSec_CAF1 43378 119 - 1
UUAAUUAGUGCCAUUUAUAUUCAGCAGGUGUUGAUUGUAAAUCGCACUUCAUAAAAUAGUUAUCGAAAGUGAUUGGAAUACCUAAAUAACUCCGACUGUGAUCGAAACA-AAAAGUAAUC
......(((((.(((((((.(((((....))))).))))))).)))))..........(((.((((..((..(((((.............)))))..))..))))))).-.......... ( -25.12)
>DroSim_CAF1 49578 120 - 1
UUAAUAAGUGCCAUUUAUAUUCAGCAGGUGUUGAUUGUAAAUCGCACUUCAUAAAAUAGUUAUCGAAAGUGAUUGGAAUAUCUAAACAACUUCGACUGUGAUCGAAACAGAAAAGUAAUC
.....((((((.(((((((.(((((....))))).))))))).)))))).............(((((..((.((((.....)))).))..)))))((((.......)))).......... ( -30.60)
>DroAna_CAF1 46579 93 - 1
AUA----AUAUUAUUUAUAUUCCGCACAGGCCCCUCGUAAAUCGCACUUCAUAAAAAAGAUAUUAGGUAUGAGGGGAAUAAU--AAUAACUUCUAAUGA---------------------
...----.(((((((......((.....))((((((((..(((.....((........)).....)))))))))))))))))--)..............--------------------- ( -17.50)
>consensus
UUAAUAAGUGCCAUUUAUAUUCAGCAGGUGUUGAUUGUAAAUCGCACUUCAUAAAAUAGUUAUCGAAAGUGAUUGGAAUACCUAAAUAACUCCGACUGUGAUCGAAACA_AAAAGUAAUC
......(((((.(((((((.(((((....))))).))))))).)))))..............((((......(((((.............)))))......))))............... (-13.60 = -15.60 +   2.00)

alignment

secondary structure

dotplot

Window 6

Location	20,671,868 – 20,671,967
Length	99
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	73.06
Mean single sequence MFE	-25.52
Consensus MFE	-12.77
Energy contribution	-15.03
Covariance contribution	2.25
Combinations/Pair	1.11
Mean z-score	-2.94
Structure conservation index	0.50
SVM decision value	2.86
SVM RNA-class probability	0.997432
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20671868 99 - 23771897
U---------AGAACAAUUUGGUUUU------------AUUUAAUAAGUGCCAUUUAUAUUCAGCAGGUGUUGAUUGUAAAUCGCACUUCAUAAAAUAGUUAUCGAAAGUGAUUGGAAUA
(---------(((((......)))))------------)((((..((((((.(((((((.(((((....))))).))))))).))))))..)))).((((((.(....)))))))..... ( -25.70)
>DroSec_CAF1 43417 99 - 1
U---------AGGACAAAUAGGUUUA------------AUUUAAUUAGUGCCAUUUAUAUUCAGCAGGUGUUGAUUGUAAAUCGCACUUCAUAAAAUAGUUAUCGAAAGUGAUUGGAAUA
.---------.((((......)))).------------.((((...(((((.(((((((.(((((....))))).))))))).)))))...)))).((((((.(....)))))))..... ( -23.30)
>DroSim_CAF1 49618 99 - 1
U---------UGGACAAAUUUGUUUA------------AUUUAAUAAGUGCCAUUUAUAUUCAGCAGGUGUUGAUUGUAAAUCGCACUUCAUAAAAUAGUUAUCGAAAGUGAUUGGAAUA
(---------((((((....))))))------------)((((..((((((.(((((((.(((((....))))).))))))).))))))..)))).((((((.(....)))))))..... ( -26.10)
>DroAna_CAF1 46596 116 - 1
UAGGUUGUGCCAGAAAAAUGGGUUUAUAGAAAAGAAGAAUAUA----AUAUUAUUUAUAUUCCGCACAGGCCCCUCGUAAAUCGCACUUCAUAAAAAAGAUAUUAGGUAUGAGGGGAAUA
....((((((((......))................(((((((----(......)))))))).)))))).((((((((..(((.....((........)).....))))))))))).... ( -27.00)
>consensus
U_________AGGACAAAUUGGUUUA____________AUUUAAUAAGUGCCAUUUAUAUUCAGCAGGUGUUGAUUGUAAAUCGCACUUCAUAAAAUAGUUAUCGAAAGUGAUUGGAAUA
.......................................((((...(((((.(((((((.(((((....))))).))))))).)))))...)))).((((((.(....)))))))..... (-12.77 = -15.03 +   2.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:06 2006