Locus 667

Sequence ID	2L_DroMel_CAF1
Location	1,966,242 – 1,966,374
Length	132
Max. P	0.966759

overview

Window 2

Location	1,966,242 – 1,966,335
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	92.15
Mean single sequence MFE	-28.58
Consensus MFE	-21.92
Energy contribution	-23.72
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.77
SVM decision value	0.70
SVM RNA-class probability	0.828018
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1966242 93 + 22407834
CCGCCAUUUUGUUUCGCCGGGUUGCGCCUUCAAAUGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
((((......(..((((..((((((((........))))))))...))))..)..)))).........(((((((....)))))))....... ( -32.30)
>DroSec_CAF1 8713 93 + 1
CCGCCAUUUUGUUUCGUCGGGUUGCGCCUUCAAAUGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
((((......(..((((..((((((((........))))))))...))))..)..)))).........(((((((....)))))))....... ( -30.70)
>DroSim_CAF1 12859 93 + 1
CCGCCAUUUUGUUUCGUCGGGUUGCGCCUUCAAAUGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
((((......(..((((..((((((((........))))))))...))))..)..)))).........(((((((....)))))))....... ( -30.70)
>DroEre_CAF1 17833 83 + 1
CCGCCAUUUUGUCAC----------GCCUUCAAAAGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
((((..(((((....----------.....))))).((.((((.....)))).)))))).........(((((((....)))))))....... ( -20.20)
>DroYak_CAF1 15768 93 + 1
CCGCCAUUUUGUCUCGCCGCGUUGCGCCUUCAAAUGUGCAACCAUCGCGCUUCCAGCGGCCCCAACCUAGACCCCAAGUUGGGGUUUAAAAAU
..(((..........((...(((((((........)))))))....))((.....))))).......((((((((.....))))))))..... ( -29.00)
>consensus
CCGCCAUUUUGUUUCGCCGGGUUGCGCCUUCAAAUGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
..(((..............((((((((........))))))))...((.......)))))........(((((((....)))))))....... (-21.92 = -23.72 +   1.80)

alignment

secondary structure

dotplot

Window 3

Location	1,966,281 – 1,966,374
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	97.85
Mean single sequence MFE	-27.92
Consensus MFE	-23.92
Energy contribution	-24.52
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.14
Structure conservation index	0.86
SVM decision value	1.60
SVM RNA-class probability	0.966759
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1966281 93 + 22407834
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAUUCCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((..(.(((((((((.((((....))))..))))))))).).))))......)))).))).... ( -28.30)
>DroSec_CAF1 8752 93 + 1
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAUUCCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((..(.(((((((((.((((....))))..))))))))).).))))......)))).))).... ( -28.30)
>DroSim_CAF1 12898 93 + 1
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAUUCCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((..(.(((((((((.((((....))))..))))))))).).))))......)))).))).... ( -28.30)
>DroEre_CAF1 17862 92 + 1
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAU-CCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((..(.(((((((((.((((....)))).-))))))))).).))))......)))).))).... ( -29.30)
>DroYak_CAF1 15807 93 + 1
AACCAUCGCGCUUCCAGCGGCCCCAACCUAGACCCCAAGUUGGGGUUUAAAAAUAAAUUCCCCAUUUGCGAGUGGUAAUUUGCCGACUGUCUG
..............(((((((.......((((((((.....)))))))).....(((((..(((((....))))).))))))))).))).... ( -25.40)
>consensus
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAUUCCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((....(((((((((..((.......))..)))))))))...))))......)))).))).... (-23.92 = -24.52 +   0.60)

alignment

secondary structure

dotplot

Window 4

Location	1,966,281 – 1,966,374
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	97.85
Mean single sequence MFE	-31.12
Consensus MFE	-27.06
Energy contribution	-27.66
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.87
SVM decision value	0.91
SVM RNA-class probability	0.880750
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1966281 93 - 22407834
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGGAAUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((..((((....)))).))))).))).)).)).)))....))))))).((((.....)))) ( -31.20)
>DroSec_CAF1 8752 93 - 1
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGGAAUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((..((((....)))).))))).))).)).)).)))....))))))).((((.....)))) ( -31.20)
>DroSim_CAF1 12898 93 - 1
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGGAAUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((..((((....)))).))))).))).)).)).)))....))))))).((((.....)))) ( -31.20)
>DroEre_CAF1 17862 92 - 1
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGG-AUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((-.((((....)))).))))).))).)).)).)))....))))))).((((.....)))) ( -33.30)
>DroYak_CAF1 15807 93 - 1
CAGACAGUCGGCAAAUUACCACUCGCAAAUGGGGAAUUUAUUUUUAAACCCCAACUUGGGGUCUAGGUUGGGGCCGCUGGAAGCGCGAUGGUU
.................((((.((((.....((...((((....))))(((((((((((...)))))))))))))((.....)))))))))). ( -28.70)
>consensus
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGGAAUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((..((((....)))).))))).))).)).)).)))....))))))).((((.....)))) (-27.06 = -27.66 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:26 2006