Locus 1964

Sequence ID	X_DroMel_CAF1
Location	5,380,303 – 5,380,526
Length	223
Max. P	0.943690

overview

Window 4

Location	5,380,303 – 5,380,395
Length	92
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	81.32
Mean single sequence MFE	-17.80
Consensus MFE	-14.48
Energy contribution	-14.10
Covariance contribution	-0.38
Combinations/Pair	1.11
Mean z-score	-1.70
Structure conservation index	0.81
SVM decision value	0.55
SVM RNA-class probability	0.778828
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5380303 92 - 22224390
-----------------------GCAUAUGCAAUUUGCAAUUCGCAAUUUUGCAGCCCCAGUGAGCAAAUAUUCGCCACCCACCCAAGCCAGCAAUCCGCAAACCAUAAUACCCG---
-----------------------((...(((((.((((.....))))..)))))......(((.((........)))))........))..((.....))...............--- ( -15.50)
>DroSec_CAF1 61645 89 - 1
-----------------------GCAUAUGCAAUUUGCAAUUCGCAAUUUUGCAGCCCCAGUGAGCAAAUAUUCGCCACCCAC--AAGCCAGCAAUCCGCA-UCCAUAAUACCCG---
-----------------------((...(((((.((((.....))))..)))))......(((.((........)))))....--..))..((.....)).-.............--- ( -15.50)
>DroSim_CAF1 48618 89 - 1
-----------------------GCAUAUGCAAUUUGCAAUUCGCAAUUUUGCAGCCCCAGUGAGCAAAUAUUCGCCACCCAC--CAGCCAGCAAUCCGCA-UCCAUAAUACCCG---
-----------------------((...(((((.((((.....))))..)))))......(((.((........)))))....--..))..((.....)).-.............--- ( -15.50)
>DroYak_CAF1 54244 115 - 1
CCAUUGCCGUUGCCAUUGCCAUUGCAUAUGCAAUUUGCAAUUCGCAAUUUUGCAGCACCAGCGAGCAAAUAUUCGCCACCCAC--AAGUCCGCAAUCUGCA-CCCAUAAUACCAACAC
..(((((.(((((.(((((.((((((.........))))))..)))))...)))))....(((((......))))).......--......))))).....-................ ( -24.70)
>consensus
_______________________GCAUAUGCAAUUUGCAAUUCGCAAUUUUGCAGCCCCAGUGAGCAAAUAUUCGCCACCCAC__AAGCCAGCAAUCCGCA_UCCAUAAUACCCG___
.......................((...(((((.((((.....))))..)))))......(((((......)))))...........))..((.....)).................. (-14.48 = -14.10 +  -0.38)

alignment

secondary structure

dotplot

Window 5

Location	5,380,395 – 5,380,486
Length	91
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.74
Mean single sequence MFE	-35.30
Consensus MFE	-27.71
Energy contribution	-27.75
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.76
Structure conservation index	0.78
SVM decision value	0.53
SVM RNA-class probability	0.770915
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5380395 91 + 22224390
-------AACGGGUCGCAGGAC------UUGUCGUCCUUUUCAGGUGACAUGUGCAC----------------CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGA
-------..(((((((((((((------.(((((.(((....)))))))).))...)----------------))))).))))).((((((((.......))))))))............ ( -31.30)
>DroSec_CAF1 61734 91 + 1
-------AACGGGUCGCAGGAC------UCGUCGUCCUUUUCAGGUGACAUGUGCAC----------------CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGA
-------.((((((((((((((------.....))))......(....).)))).))----------------))))(((.....((((((((.......))))))))...)))...... ( -30.60)
>DroSim_CAF1 48707 91 + 1
-------AACGGGUCGCAGGAC------UCGUCGUCCUUUUCAGGUGACAUGUGCAC----------------CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGA
-------.((((((((((((((------.....))))......(....).)))).))----------------))))(((.....((((((((.......))))))))...)))...... ( -30.60)
>DroEre_CAF1 54827 106 + 1
-------AGCGGGUCGCAGGAC------UCGUCGUCCUUUUCAGGUGACAUGUGCACCUGUGCACCUGUGCACCUGUGCAUUCGAUUUUGC-CUGCACUCGGGCGGGAAUUUGCCUUUGA
-------..(((((.(((((..------..((((.......(((((((((.(((((....))))).))).))))))......))))....)-)))))))))(((((....)))))..... ( -44.82)
>DroYak_CAF1 54359 104 + 1
CAACAGCAACGGGUCGCAGGAGUCGCAGUCGUCGUCCUUUUCAGGUGACAUGUGCAC----------------CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGA
(((..(((((((((((((((.(.((((...((((.(((....))))))).))))).)----------------))))).))))).((((((((.......))))))))..))))..))). ( -39.20)
>consensus
_______AACGGGUCGCAGGAC______UCGUCGUCCUUUUCAGGUGACAUGUGCAC________________CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGA
.........(((((.(((((..........((((.(((....)))))))..((((((..................))))))..........))))))))))(((((....)))))..... (-27.71 = -27.75 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	5,380,395 – 5,380,486
Length	91
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.74
Mean single sequence MFE	-31.24
Consensus MFE	-26.65
Energy contribution	-26.89
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.95
Structure conservation index	0.85
SVM decision value	1.34
SVM RNA-class probability	0.943690
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5380395 91 - 22224390
UCAAAGGCAAAUUCCCGCCCGAAUGCAGGGCAAAAUCGAAUGCACAG----------------GUGCACAUGUCACCUGAAAAGGACGACAA------GUCCUGCGACCCGUU-------
.....(((........)))....((((((((.........((((...----------------.))))..((((.(((....)))..)))).------)))))))).......------- ( -29.40)
>DroSec_CAF1 61734 91 - 1
UCAAAGGCAAAUUCCCGCCCGAAUGCAGGGCAAAAUCGAAUGCACAG----------------GUGCACAUGUCACCUGAAAAGGACGACGA------GUCCUGCGACCCGUU-------
.....(((........)))....((((((((.........((((...----------------.))))..((((.(((....)))..)))).------)))))))).......------- ( -28.70)
>DroSim_CAF1 48707 91 - 1
UCAAAGGCAAAUUCCCGCCCGAAUGCAGGGCAAAAUCGAAUGCACAG----------------GUGCACAUGUCACCUGAAAAGGACGACGA------GUCCUGCGACCCGUU-------
.....(((........)))....((((((((.........((((...----------------.))))..((((.(((....)))..)))).------)))))))).......------- ( -28.70)
>DroEre_CAF1 54827 106 - 1
UCAAAGGCAAAUUCCCGCCCGAGUGCAG-GCAAAAUCGAAUGCACAGGUGCACAGGUGCACAGGUGCACAUGUCACCUGAAAAGGACGACGA------GUCCUGCGACCCGCU-------
.....(((........)))((.((((((-((.........(((((..(((((....)))))..)))))..((((.(((....)))..)))).------).))))).)).))..------- ( -38.30)
>DroYak_CAF1 54359 104 - 1
UCAAAGGCAAAUUCCCGCCCGAAUGCAGGGCAAAAUCGAAUGCACAG----------------GUGCACAUGUCACCUGAAAAGGACGACGACUGCGACUCCUGCGACCCGUUGCUGUUG
.(((.(((((......((((.......)))).........((((..(----------------(((((..((((.(((....)))..))))..))).)))..)))).....))))).))) ( -31.10)
>consensus
UCAAAGGCAAAUUCCCGCCCGAAUGCAGGGCAAAAUCGAAUGCACAG________________GUGCACAUGUCACCUGAAAAGGACGACGA______GUCCUGCGACCCGUU_______
.....(((........)))....((((((((.........(((((..................)))))..((((.(((....)))..)))).......)))))))).............. (-26.65 = -26.89 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	5,380,422 – 5,380,526
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.48
Mean single sequence MFE	-33.46
Consensus MFE	-28.81
Energy contribution	-29.01
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.48
Structure conservation index	0.86
SVM decision value	0.80
SVM RNA-class probability	0.853811
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5380422 104 + 22224390
UCAGGUGACAUGUGCAC----------------CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGAGUUCGUGUGCGGCCUUUAUUGGUUUACUUCAUCAACUCGA
.((((((.(....))))----------------))).(((.....((((((((.......))))))))...)))..(((((((.(((...((((......)))).....))).))))))) ( -31.20)
>DroSec_CAF1 61761 104 + 1
UCAGGUGACAUGUGCAC----------------CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGAGUUCGUGUGCGGCCUUUAUUGGUUUACUUCAUCAACUCGA
.((((((.(....))))----------------))).(((.....((((((((.......))))))))...)))..(((((((.(((...((((......)))).....))).))))))) ( -31.20)
>DroSim_CAF1 48734 104 + 1
UCAGGUGACAUGUGCAC----------------CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGAGUUCGUGUGCGGCCUUUAUUGGUUUACUUCAUCAACUCGA
.((((((.(....))))----------------))).(((.....((((((((.......))))))))...)))..(((((((.(((...((((......)))).....))).))))))) ( -31.20)
>DroEre_CAF1 54854 119 + 1
UCAGGUGACAUGUGCACCUGUGCACCUGUGCACCUGUGCAUUCGAUUUUGC-CUGCACUCGGGCGGGAAUUUGCCUUUGAGUUCGUGUGCGGCCUUUAUUGGUUUACUUCAUCAACUCGA
.(((((((((.(((((....))))).))).)))))).(((.....((((((-(((....)))))))))...)))..(((((((.(((...((((......)))).....))).))))))) ( -42.50)
>DroYak_CAF1 54399 104 + 1
UCAGGUGACAUGUGCAC----------------CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGAGUUCGUGUGCGGCCUUUAUUGGUUUACUUCAUCAACUCGA
.((((((.(....))))----------------))).(((.....((((((((.......))))))))...)))..(((((((.(((...((((......)))).....))).))))))) ( -31.20)
>consensus
UCAGGUGACAUGUGCAC________________CUGUGCAUUCGAUUUUGCCCUGCAUUCGGGCGGGAAUUUGCCUUUGAGUUCGUGUGCGGCCUUUAUUGGUUUACUUCAUCAACUCGA
..(((..((..((((((..................))))))..).((((((((.......))))))))..)..)))(((((((.(((...((((......)))).....))).))))))) (-28.81 = -29.01 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:00 2006