Locus 2862

Sequence ID	3R_DroMel_CAF1
Location	7,685,109 – 7,685,362
Length	253
Max. P	0.999896

overview

Window 3

Location	7,685,109 – 7,685,228
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	76.36
Mean single sequence MFE	-36.36
Consensus MFE	-23.32
Energy contribution	-25.80
Covariance contribution	2.48
Combinations/Pair	1.19
Mean z-score	-2.42
Structure conservation index	0.64
SVM decision value	2.36
SVM RNA-class probability	0.992882
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7685109 119 + 27905053
AGACCGAAACACAAUGGAAAUGUUUGGUUUUGUGGGGCUUCGAGGAUUUCGCGGGCAGAUGCCAUGGUGGCUAUGGGAUGUCUACGGAGUUCUAUAAGCCCCGCUUUAUAACUCAUAUG
((((((((.....((....)).)))))))).(((((((((..(((((((((..((((....((((((...))))))..))))..)))))))))..)))))))))............... ( -45.90)
>DroSec_CAF1 34992 100 + 1
AGACCGAAACACAAUGGAAAUGUUUGGUUUUGUGGGGCUUCGAGGAUUUCGCGGGCAGA-------------------UGUCUACGGAGUUCUAUAAGCUGCGCUUUAUAACUCAUAUG
((((((((.....((....)).)))))))).(((.(((((..(((((((((..(((...-------------------.)))..)))))))))..))))).)))............... ( -31.90)
>DroSim_CAF1 34993 100 + 1
AGACCGAAACACAAUGGAAAUGUUUGGUUUUGUGGGGCUUCGAGGAUUUCGCGGGCAGA-------------------UGUCUACGGAGUUCUAUAAGCUCCGCUUUAUAACUCAUAUG
((((((((.....((....)).)))))))).(((((((((..(((((((((..(((...-------------------.)))..)))))))))..)))))))))............... ( -35.70)
>DroEre_CAF1 35547 116 + 1
AGACCGAAACACAAUGGAAAUGUUUGGUUUUGUGGGGCUUCGAGGAUUUCGCGGGCGAAUGCCAUG---GCUAUGGGGUGUCUACGGAGUUCUAUAAGCUCCGCUUUAUAACUCAUAUG
((((((((.....((....)).)))))))).(((((((((..(((((((((..(((..((.((((.---...)))).)))))..)))))))))..)))))))))............... ( -39.70)
>DroAna_CAF1 37572 102 + 1
A--UGAAAACACAAUGCGAAUGCGGGAGUGGGAGC-GGGUGGUGGACUGAGGGGACC------------AGCAUGG--AGUCUUCAGUGUUCUAUAAGCCGAGCUUUAUAACUCAUAUG
.--...........(((....))).((((.(((((-.(((.((((((((((((..((------------.....))--..)))))))...)))))..)))..)))))...))))..... ( -28.60)
>consensus
AGACCGAAACACAAUGGAAAUGUUUGGUUUUGUGGGGCUUCGAGGAUUUCGCGGGCAGA_____________AUGG__UGUCUACGGAGUUCUAUAAGCUCCGCUUUAUAACUCAUAUG
(((((.(((((.........)))))))))).(((((((((..(((((((((..((((.....................))))..)))))))))..)))))))))............... (-23.32 = -25.80 +   2.48)

alignment

secondary structure

dotplot

Window 4

Location	7,685,228 – 7,685,347
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.31
Mean single sequence MFE	-30.28
Consensus MFE	-26.80
Energy contribution	-26.88
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.77
Structure conservation index	0.89
SVM decision value	1.63
SVM RNA-class probability	0.968760
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7685228 119 + 27905053
GGCUUGUUAUGUGCCAUGUUAUCGUCUUGUCGCUGCACGCAUUUGUCUUGAUACCCAACUCGUUU-UUUAUUGCCCUUUUUUGGGCUUUAUAAUAAUGAGCUUCCCACAGGGUAUUAUGA
.((.(((...(((.((...........)).))).))).)).....((.((((((((((((((((.-.((((.((((......))))...)))).)))))).))......)))))))).)) ( -29.00)
>DroSec_CAF1 35092 119 + 1
GGCUUGUUAUGUGCCAUGUUAUCGUCUUGUCGCUCCACGCAUUUGUCUUGAUACCCAACUCGUUU-UUUAUUGCCCUUUUUUGGGCUUUAAAAUAAUGAGCUUCCGACAGGGUAUUAUGA
(((.........)))................((.....)).....((.((((((((..(((((((-((((..((((......))))..))))).))))))(....)...)))))))).)) ( -30.80)
>DroSim_CAF1 35093 120 + 1
GGCUUGUUAUGUGCCAUGUUAUCGUCUUGUCGCUGCACGCAUUUGUCUUGAUACCCAACUCGUUUUUUUAUUGCCCUUUUUUGGGCUUUAAAAUAAUGAGCUUCCGACAGGGUAUUAUGA
.((.(((...(((.((...........)).))).))).)).....((.((((((((..((((((.(((((..((((......))))..))))).))))))(....)...)))))))).)) ( -33.70)
>DroEre_CAF1 35663 119 + 1
GGCUUGUUAUGUGCCAUGUUAUCGUCUUGUCGCUGUACGCAUUUGUCUUGAUACCCAACUCGUUU-UUUAUUGCCCUUUUUUGGGCUUUAUAAUAAUGAGCUCCCGACAGGGUAUUGUGA
(((.........)))..............((((.((((.(...(((((((.....)))((((((.-.((((.((((......))))...)))).)))))).....))))).)))).)))) ( -28.70)
>DroYak_CAF1 35491 119 + 1
GGCUUGUUAUGUGCCAUGUUAUCGUGUUGUCGCUGUACGCAUUUGUCUUGAUACCCAACUCGUUU-UUUAUUGCCCUUUUUUGGGCUUUAUAAUAAUGAGCUUCCGACAGGGUAUGAUGG
(((.........)))....((((((((((((((.....))..................((((((.-.((((.((((......))))...)))).)))))).....)))))..))))))). ( -29.20)
>consensus
GGCUUGUUAUGUGCCAUGUUAUCGUCUUGUCGCUGCACGCAUUUGUCUUGAUACCCAACUCGUUU_UUUAUUGCCCUUUUUUGGGCUUUAUAAUAAUGAGCUUCCGACAGGGUAUUAUGA
(((.........)))................((.....)).....((.((((((((..((((((....((..((((......))))..))....))))))(....)...)))))))).)) (-26.80 = -26.88 +   0.08)

alignment

secondary structure

dotplot

Window 5

Location	7,685,268 – 7,685,362
Length	94
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	95.76
Mean single sequence MFE	-34.18
Consensus MFE	-32.24
Energy contribution	-32.08
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-5.28
Structure conservation index	0.94
SVM decision value	3.68
SVM RNA-class probability	0.999520
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7685268 94 + 27905053
AUUUGUCUUGAUACCCAACUCGUUU-UUUAUUGCCCUUUUUUGGGCUUUAUAAUAAUGAGCUUCCCACAGGGUAUUAUGAAGGGUAUACAGGAUA
...(((((((((((((..((((((.-.((((.((((......))))...)))).))))))...(((...))).........)))))).))))))) ( -32.30)
>DroSec_CAF1 35132 94 + 1
AUUUGUCUUGAUACCCAACUCGUUU-UUUAUUGCCCUUUUUUGGGCUUUAAAAUAAUGAGCUUCCGACAGGGUAUUAUGAAGGGUAUGCAGGAUA
...(((((((((((((..(((((((-((((..((((......))))..))))).))))))..(((....))).........)))))).))))))) ( -34.80)
>DroSim_CAF1 35133 95 + 1
AUUUGUCUUGAUACCCAACUCGUUUUUUUAUUGCCCUUUUUUGGGCUUUAAAAUAAUGAGCUUCCGACAGGGUAUUAUGAAGGGUAUGCAGGAUA
...(((((((((((((..((((((.(((((..((((......))))..))))).))))))..(((....))).........)))))).))))))) ( -36.20)
>DroEre_CAF1 35703 94 + 1
AUUUGUCUUGAUACCCAACUCGUUU-UUUAUUGCCCUUUUUUGGGCUUUAUAAUAAUGAGCUCCCGACAGGGUAUUGUGAAGGGUAUGCAGGAUU
....((((((((((((..((((((.-.((((.((((......))))...)))).))))))..(((....))).........)))))).)))))). ( -33.70)
>DroYak_CAF1 35531 94 + 1
AUUUGUCUUGAUACCCAACUCGUUU-UUUAUUGCCCUUUUUUGGGCUUUAUAAUAAUGAGCUUCCGACAGGGUAUGAUGGAGGGUAUGCAGGAUU
....((((((((((((..((((((.-.((((.((((......))))...)))).))))))..((((.((.....)).)))))))))).)))))). ( -33.90)
>consensus
AUUUGUCUUGAUACCCAACUCGUUU_UUUAUUGCCCUUUUUUGGGCUUUAUAAUAAUGAGCUUCCGACAGGGUAUUAUGAAGGGUAUGCAGGAUA
....((((((((((((..((((((....((..((((......))))..))....))))))..(((....))).........)))))).)))))). (-32.24 = -32.08 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	7,685,268 – 7,685,362
Length	94
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	95.76
Mean single sequence MFE	-23.98
Consensus MFE	-21.61
Energy contribution	-21.61
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.83
Structure conservation index	0.90
SVM decision value	4.43
SVM RNA-class probability	0.999896
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7685268 94 - 27905053
UAUCCUGUAUACCCUUCAUAAUACCCUGUGGGAAGCUCAUUAUUAUAAAGCCCAAAAAAGGGCAAUAAA-AAACGAGUUGGGUAUCAAGACAAAU
..((.((.((((((.........(((...))).(((((....((((...((((......)))).)))).-....))))))))))))).))..... ( -23.10)
>DroSec_CAF1 35132 94 - 1
UAUCCUGCAUACCCUUCAUAAUACCCUGUCGGAAGCUCAUUAUUUUAAAGCCCAAAAAAGGGCAAUAAA-AAACGAGUUGGGUAUCAAGACAAAU
..((.((.((((((..........((....)).(((((.((.(((((..((((......))))..))))-))).))))))))))))).))..... ( -23.70)
>DroSim_CAF1 35133 95 - 1
UAUCCUGCAUACCCUUCAUAAUACCCUGUCGGAAGCUCAUUAUUUUAAAGCCCAAAAAAGGGCAAUAAAAAAACGAGUUGGGUAUCAAGACAAAU
..((.((.((((((..........((....)).(((((.((.(((((..((((......))))..))))).)).))))))))))))).))..... ( -24.90)
>DroEre_CAF1 35703 94 - 1
AAUCCUGCAUACCCUUCACAAUACCCUGUCGGGAGCUCAUUAUUAUAAAGCCCAAAAAAGGGCAAUAAA-AAACGAGUUGGGUAUCAAGACAAAU
..((.((.((((((.........(((....)))(((((....((((...((((......)))).)))).-....))))))))))))).))..... ( -24.70)
>DroYak_CAF1 35531 94 - 1
AAUCCUGCAUACCCUCCAUCAUACCCUGUCGGAAGCUCAUUAUUAUAAAGCCCAAAAAAGGGCAAUAAA-AAACGAGUUGGGUAUCAAGACAAAU
..((.((.(((((((((..((.....))..)))(((((....((((...((((......)))).)))).-....))))))))))))).))..... ( -23.50)
>consensus
UAUCCUGCAUACCCUUCAUAAUACCCUGUCGGAAGCUCAUUAUUAUAAAGCCCAAAAAAGGGCAAUAAA_AAACGAGUUGGGUAUCAAGACAAAU
..((.((.((((((.........((.....)).(((((...........((((......))))...........))))))))))))).))..... (-21.61 = -21.61 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:32 2006