Locus 1632

Sequence ID	3L_DroMel_CAF1
Location	4,757,319 – 4,757,548
Length	229
Max. P	0.988595

overview

Window 6

Location	4,757,319 – 4,757,428
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.37
Mean single sequence MFE	-26.40
Consensus MFE	-17.36
Energy contribution	-17.52
Covariance contribution	0.16
Combinations/Pair	1.22
Mean z-score	-1.86
Structure conservation index	0.66
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4757319 109 - 23771897
CGAGUCUCCUGACUUUUUUUUCACUUUGC---------UCGCCUUUGUUGCCGAAUCA--AAGUGACUUUUGCUUGAAGUCGCCGACGACAACACAACAUUUUGUAAUUUUCGUCAUAUU
.(((((....))))).......((((((.---------(((.(......).)))..))--))))((((((.....))))))...(((((....((((....)))).....)))))..... ( -23.70)
>DroSec_CAF1 20024 108 - 1
CGAGUCUCCAGGCUUU-UCUUCACUUUGC---------UCGCCUUUGUGGCCGAAACA--AAGUGACUUUUGCUUGAAGUCGCCGACGACGACACAACAUUUUGUAAUUUUCGUCAUAUU
((((((..(((((...-...((((((((.---------(((((.....)).)))..))--)))))).....)))))..((((....)))))))((((....)))).....)))....... ( -29.60)
>DroSim_CAF1 17357 108 - 1
CGAGUCUCCUGGCUUU-UCUUCACUUUGC---------UCGCCUUUGUGGCCGAAACA--AAGUGACUUUUGCUUGAAGUCGCCGACAACGACACAACAUUUUGUAAUUUUCGUCAUAUU
((((((...((((...-.....((((((.---------(((((.....)).)))..))--))))((((((.....)))))))))).....)))((((....)))).....)))....... ( -24.60)
>DroEre_CAF1 9228 108 - 1
CGAGUCUGCUGGCUUU-UCUUCACUUGGC---------UCGCCUUUGUGGCCGAAUCA--AAGUGACUUUUGCUUGAAGUCACCGACGACGACACAACAUUUUGUAAUUUUCGUCAUAUU
.(((((....))))).-.......(((((---------.(((....))))))))....--..((((((((.....)))))))).(((((.((.((((....))))..)).)))))..... ( -28.50)
>DroYak_CAF1 15991 117 - 1
CGAGUCUCUUGGCUUU-UCUUCACUUUGUGGUCCUUUGUGGUCUUUGUGGCCGAAUCA--AAGUGACUUUUGCUUGAAGUUGCCGACGACGACACAACAUUUUGUAAUUUUCGUCAUAUU
(((((((((((((...-.(((((......((((((((((((((.....)))))...))--))).))))......)))))..))))).)).)))((((....)))).....)))....... ( -32.60)
>DroAna_CAF1 9986 92 - 1
-----------------UUUUCACUCGCCG--------GCUCCUUUAUGGCCAAAUCAAAAAGUGACUUUUGCUUGAAGUUGCCGAC---GACACAGCUUUUUGUAAUUUUCGUCAUAUU
-----------------............(--------((..(((((.(((.((((((.....))).))).))))))))..)))(((---((....((.....)).....)))))..... ( -19.40)
>consensus
CGAGUCUCCUGGCUUU_UCUUCACUUUGC_________UCGCCUUUGUGGCCGAAUCA__AAGUGACUUUUGCUUGAAGUCGCCGACGACGACACAACAUUUUGUAAUUUUCGUCAUAUU
.(((((....))))).........................(((.....)))...........((((((((.....)))))))).(((((.((.((((....))))..)).)))))..... (-17.36 = -17.52 +   0.16)

alignment

secondary structure

dotplot

Window 7

Location	4,757,428 – 4,757,548
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.94
Mean single sequence MFE	-38.33
Consensus MFE	-36.78
Energy contribution	-36.83
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.46
Structure conservation index	0.96
SVM decision value	2.13
SVM RNA-class probability	0.988595
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4757428 120 - 23771897
GGACGGAAGUCGGUGUCAAGUGUCGCGGAAGCUUUCUGGCACUUCAUCAACUUUGAAGUAAACGUCCGCCCGCCAGGUGGAGCCACAAAUCAGAUAAGCGAGCACGCGAUUAAUAUUUUU
.(((....)))..........(((((((..(((((((((.((((((.......)))))).....((((((.....))))))........))))).))))...).)))))).......... ( -38.60)
>DroSec_CAF1 20132 120 - 1
GGACGGAAGUCGGUGUCAAGUGUCGCGGAAGCUUUCUGGCACUUCAUCAACUUUGAAGUAAACGUCCGCCCGCCAGGUGGAGCCACAAAUCAGAUAAGCGAGCACGCGAUUAAUAUUUUU
.(((....)))..........(((((((..(((((((((.((((((.......)))))).....((((((.....))))))........))))).))))...).)))))).......... ( -38.60)
>DroSim_CAF1 17465 120 - 1
GGACGGAAGUCGGUGUCAAGUGUCGCGGAAGCUUUCUGGCACUUCAUCAACUUUGAAGUAAACGUCCGCCCGCCAGGUGGAGCCACAAAUCAGAUAAGCGAGCACGCGAUUAAUAUUUUU
.(((....)))..........(((((((..(((((((((.((((((.......)))))).....((((((.....))))))........))))).))))...).)))))).......... ( -38.60)
>DroEre_CAF1 9336 120 - 1
GGACGGAAGUCGGUGUCAAGUGUCGCGGAAGCUUUCUGGCACUUCAUCAACUUUGAAGUAAGCGUCCGCCCGCCAGGUGGAGCCACAAAUCAGAUAAGCGAGCACGCGAUUAAUAUUUUU
.(((....)))..........(((((((..(((((((((.((((((.......))))))..((.((((((.....))))))))......))))).))))...).)))))).......... ( -40.80)
>DroYak_CAF1 16108 120 - 1
GGACGGAAGUCGGUGUCAAGUGUCGCGGAAGCUUUCUGGCACUUCAUCAACUUUGAAGUAAACGUCCGCCCGCCAGGUGGAGCCACAAAUCAGAUAAGGGCGCACGCGAUUAAUAUUUUU
.(((....))).(((((...((((((....))(((.((((((((((.......)))))).....((((((.....)))))))))).)))...))))..)))))................. ( -41.90)
>DroAna_CAF1 10078 118 - 1
GAACGGAAGUUGGUGUCAAGUGUCGCGGAAGCUUUCUGGCACUUCAUCAACUUUGAAGUAAACGUCCGCCCAAGA-AUGGAGCCACAAAUCAGAUAAGCGAGCACGCGAUUAAUAUUUU-
.....((((((((((..(((((((((....)).....)))))))))))))))))((((((...(((.(((((...-.))).))..............(((....))))))...))))))- ( -31.50)
>consensus
GGACGGAAGUCGGUGUCAAGUGUCGCGGAAGCUUUCUGGCACUUCAUCAACUUUGAAGUAAACGUCCGCCCGCCAGGUGGAGCCACAAAUCAGAUAAGCGAGCACGCGAUUAAUAUUUUU
.(((....))).((((....((((((....))(((.((((((((((.......)))))).....((((((.....)))))))))).)))...)))).....))))............... (-36.78 = -36.83 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:26 2006