Locus 1504

Sequence ID	3R_DroMel_CAF1
Location	4,317,899 – 4,318,169
Length	270
Max. P	0.909575

overview

Window 9

Location	4,317,899 – 4,318,015
Length	116
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	87.92
Mean single sequence MFE	-24.00
Consensus MFE	-20.40
Energy contribution	-20.74
Covariance contribution	0.34
Combinations/Pair	1.09
Mean z-score	-1.65
Structure conservation index	0.85
SVM decision value	0.01
SVM RNA-class probability	0.537663
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4317899 116 - 27905053
AAUUUUGUUUGCGUAUUUCAAUUCGGAUUUUGAUUUCGCAUUUGAUUGCCAAAAGCGAUUUUUACAGUUAGAGUUCCACUCACUUGUGCACUCGAACAAAAUA----AAAAAAAUUGCAG
.((((((((((.((..........(((((((((((((((.((((.....)))).)))).......)))))))))))(((......))).)).)))))))))).----............. ( -25.31)
>DroSec_CAF1 5269 119 - 1
AAUUUUGUUUGCGUAUUUCAAUUCGGAUUUUGAUUUCGCAUUUGAUUGCCAAAAGCGAUUUUU-CAGUUAGAGUUCCACUCACUCGUGCACUCAAACAAAAUAUAAAAAAAAAAUUACAG
.((((((((((.((..........(((((((((((((((.((((.....)))).)))).....-.)))))))))))(((......))).)).)))))))))).................. ( -25.20)
>DroEre_CAF1 5294 109 - 1
AAUUUUGUUUGCGUAUUUCAAUUCGGAUUUUGAUUUCGCAUUUGAUUGCCAAAAGCGAUUUUUACAGUUAGAGUUUCACUCACUUAUGCACUCGGAAAAAACC----GAAAAA-------
.........((((((..........((((.(((..((((.((((.....)))).))))...))).)))).(((.....)))...)))))).((((......))----))....------- ( -21.50)
>consensus
AAUUUUGUUUGCGUAUUUCAAUUCGGAUUUUGAUUUCGCAUUUGAUUGCCAAAAGCGAUUUUUACAGUUAGAGUUCCACUCACUUGUGCACUCGAACAAAAUA____AAAAAAAUU_CAG
.((((((((((.((..........(((((((((((((((.((((.....)))).)))).......)))))))))))(((......))).)).)))))))))).................. (-20.40 = -20.74 +   0.34)

alignment

secondary structure

dotplot

Window 0

Location	4,317,975 – 4,318,095
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-25.93
Consensus MFE	-25.17
Energy contribution	-25.51
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.97
SVM decision value	0.10
SVM RNA-class probability	0.584702
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4317975 120 - 27905053
CCAAUUCCGGUAGCCAACUUUUGGCAGCCGGCGGAUGCACAAACGAAUUUUAAACACUUUCGACAUCAAAUCCACUUUACAAUUUUGUUUGCGUAUUUCAAUUCGGAUUUUGAUUUCGCA
......(((((.((((.....)))).))))).((((.......((((...........)))).......))))................((((.(..((((........))))..))))) ( -27.44)
>DroSec_CAF1 5348 120 - 1
CCAAUUCCGGUAGCCAACUUUUGGCAGCCGGCGGAUGCACAAACGAAUUUUAAACACUUUCGACAUCAAAUCCACUUUACAAUUUUGUUUGCGUAUUUCAAUUCGGAUUUUGAUUUCGCA
......(((((.((((.....)))).))))).((((.......((((...........)))).......))))................((((.(..((((........))))..))))) ( -27.44)
>DroEre_CAF1 5363 120 - 1
CCAAUUCCGAUAGCCAACUUUUGGCAGCCGGCGGAUGCACAAACGAAUUUUAAACACUUUCGACAUCAAAUCCACUUUACAAUUUUGUUUGCGUAUUUCAAUUCGGAUUUUGAUUUCGCA
.(((.(((((..((((.....)))).......((((((.((((((((....................................)))))))).))))))....)))))..)))........ ( -22.92)
>consensus
CCAAUUCCGGUAGCCAACUUUUGGCAGCCGGCGGAUGCACAAACGAAUUUUAAACACUUUCGACAUCAAAUCCACUUUACAAUUUUGUUUGCGUAUUUCAAUUCGGAUUUUGAUUUCGCA
......(((((.((((.....)))).))))).((((.......((((...........)))).......))))................((((.(..((((........))))..))))) (-25.17 = -25.51 +   0.33)

alignment

secondary structure

dotplot

Window 1

Location	4,318,015 – 4,318,129
Length	114
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.09
Mean single sequence MFE	-26.22
Consensus MFE	-20.92
Energy contribution	-21.25
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.86
Structure conservation index	0.80
SVM decision value	1.07
SVM RNA-class probability	0.909575
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4318015 114 - 27905053
ACGGAACCACCAGCAUCCCCACCG------AUACCACAUCCCAAUUCCGGUAGCCAACUUUUGGCAGCCGGCGGAUGCACAAACGAAUUUUAAACACUUUCGACAUCAAAUCCACUUUAC
..(((.......((((((.....(------((.....)))......(((((.((((.....)))).))))).)))))).....((((...........))))........)))....... ( -29.90)
>DroSec_CAF1 5388 120 - 1
ACUGAACCACCGGCAUCCCCACCAUCCCACAUCCCACAUCCCAAUUCCGGUAGCCAACUUUUGGCAGCCGGCGGAUGCACAAACGAAUUUUAAACACUUUCGACAUCAAAUCCACUUUAC
..(((.......((((((............................(((((.((((.....)))).))))).)))))).....((((...........))))...)))............ ( -23.95)
>DroEre_CAF1 5403 112 - 1
ACGGCACCACCAGCAUCC--ACCG------AUCCCACAUCCCAAUUCCGAUAGCCAACUUUUGGCAGCCGGCGGAUGCACAAACGAAUUUUAAACACUUUCGACAUCAAAUCCACUUUAC
..((........((((((--.(((------.......(((........))).((((.....))))...))).)))))).....((((...........)))).........))....... ( -24.80)
>consensus
ACGGAACCACCAGCAUCCCCACCG______AUCCCACAUCCCAAUUCCGGUAGCCAACUUUUGGCAGCCGGCGGAUGCACAAACGAAUUUUAAACACUUUCGACAUCAAAUCCACUUUAC
............((((((............................(((((.((((.....)))).))))).)))))).....((((...........)))).................. (-20.92 = -21.25 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	4,318,055 – 4,318,169
Length	114
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	90.68
Mean single sequence MFE	-42.23
Consensus MFE	-37.72
Energy contribution	-37.83
Covariance contribution	0.12
Combinations/Pair	1.08
Mean z-score	-1.90
Structure conservation index	0.89
SVM decision value	0.45
SVM RNA-class probability	0.740512
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4318055 114 + 27905053
GUGCAUCCGCCGGCUGCCAAAAGUUGGCUACCGGAAUUGGGAUGUGGUAU------CGGUGGGGAUGCUGGUGGUUCCGUGUGAAUGUGGCAUUAAGUGCUAACUACUGGCGUGAAAACU
..((((((.((((..((((.....))))..)))).....)))))).....------.(((....((((..(((((..(((....)))((((((...)))))))))))..))))....))) ( -39.60)
>DroSec_CAF1 5428 120 + 1
GUGCAUCCGCCGGCUGCCAAAAGUUGGCUACCGGAAUUGGGAUGUGGGAUGUGGGAUGGUGGGGAUGCCGGUGGUUCAGUGUGAAUGUGGCAUUAAGUGCUAACUACCGGCGGGAAAACU
..((((((.((((..((((.....))))..)))).....))))))............(((.....(((((((((((.((..(.((((...))))..)..))))))))))))).....))) ( -43.90)
>DroEre_CAF1 5443 112 + 1
GUGCAUCCGCCGGCUGCCAAAAGUUGGCUAUCGGAAUUGGGAUGUGGGAU------CGGU--GGAUGCUGGUGGUGCCGUGUGAAUGUGGCAUUAAGUGCUAACUACGGGCGGGAAAACU
..(((((((((((((((((.....))))((((........))))..)).)------))))--)))))).(((..(.((((.((....((((((...))))))....)).)))).)..))) ( -43.20)
>consensus
GUGCAUCCGCCGGCUGCCAAAAGUUGGCUACCGGAAUUGGGAUGUGGGAU______CGGUGGGGAUGCUGGUGGUUCCGUGUGAAUGUGGCAUUAAGUGCUAACUACCGGCGGGAAAACU
..((((((.((((..((((.....))))..)))).....))))))............(((.....((((((((((..(((....)))((((((...)))))))))))))))).....))) (-37.72 = -37.83 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:18 2006