Locus 1401

Sequence ID	3R_DroMel_CAF1
Location	4,091,190 – 4,091,350
Length	160
Max. P	0.998694

overview

Window 4

Location	4,091,190 – 4,091,310
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-42.90
Consensus MFE	-41.12
Energy contribution	-41.08
Covariance contribution	-0.04
Combinations/Pair	1.09
Mean z-score	-2.13
Structure conservation index	0.96
SVM decision value	3.19
SVM RNA-class probability	0.998694
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4091190 120 + 27905053
GUCCGAUGAUGAGGACGACGUUGGACCCCGGGCCAAGAGACGAGCUGGCGAGAAGGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUUGAAAACCUGGAGGAUACCAA
((((........))))....((((.((((((((((....((.(((((.(.....).)))))))))))..((((((...((((.....))))...))))))......)))).))...)))) ( -40.60)
>DroSec_CAF1 3104 120 + 1
GUCCGAUGAUGAGGACGACGUGGGACCCCGGGCCAAGAGACGAGCUGGCGAGAAGGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAA
((((........))))....(((..((((((((((....((.(((((.(.....).)))))))))))..((((((...((((.....))))...))))))......)))).))...))). ( -44.40)
>DroSim_CAF1 3143 120 + 1
GUCCGAUGAUGAGGACGACGUGGGACCCCGGGCCAAGAGACGAGCUGGCGAGAAGGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAA
((((........))))....(((..((((((((((....((.(((((.(.....).)))))))))))..((((((...((((.....))))...))))))......)))).))...))). ( -44.40)
>DroEre_CAF1 3159 120 + 1
GUCCGAUGAUGAGGACGACGUGGGACCCCGGGCCAAAAGACGAGCUGGCGAGAAAGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAA
((((........))))....(((..(((((((((((......(((((.(......)))))).)))))..((((((...((((.....))))...))))))......)))).))...))). ( -42.10)
>DroYak_CAF1 3092 120 + 1
GUCCGAUGAUGAGGACGACGUGGGACCCCGGGCCAAGAGACGAGCUGGUGAGAAGGCAGCUGUUGGUGAGGUAGAAGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAA
((((........))))....(((..(((((((.((...(((.(((((.(.....).))))))))..)).((((((...((((.....))))...)))))).....))))).))...))). ( -43.00)
>consensus
GUCCGAUGAUGAGGACGACGUGGGACCCCGGGCCAAGAGACGAGCUGGCGAGAAGGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAA
((((........))))....(((..((((((((((....((.(((((.(.....).)))))))))))..((((((...((((.....))))...))))))......)))).))...))). (-41.12 = -41.08 +  -0.04)

alignment

secondary structure

dotplot

Window 5

Location	4,091,230 – 4,091,350
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-38.22
Consensus MFE	-36.96
Energy contribution	-36.72
Covariance contribution	-0.24
Combinations/Pair	1.09
Mean z-score	-1.63
Structure conservation index	0.97
SVM decision value	2.01
SVM RNA-class probability	0.985486
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4091230 120 + 27905053
CGAGCUGGCGAGAAGGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUUGAAAACCUGGAGGAUACCAAGGGACACUCAACUAAAGAGUGGGUCAGUAUGCUAGGACCA
..(((((.(.....).)))))..(((...((((((...((((.....))))...)))))).....(((((...((((...((..(((((.......)))))..)).)))).))))).))) ( -36.30)
>DroSec_CAF1 3144 120 + 1
CGAGCUGGCGAGAAGGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAAGGGACACUCAACCAAAGAGUGGGUCAGUAUGCUAGGACCA
..(((((.(.....).)))))..(((...((((((...((((.....))))...)))))).....(((((...((((...((..(((((.......)))))..)).)))).))))).))) ( -38.70)
>DroSim_CAF1 3183 120 + 1
CGAGCUGGCGAGAAGGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAAGGGACACUCAACCAAAGAGUGGGUCAGUAUGCUAGGACCA
..(((((.(.....).)))))..(((...((((((...((((.....))))...)))))).....(((((...((((...((..(((((.......)))))..)).)))).))))).))) ( -38.70)
>DroEre_CAF1 3199 120 + 1
CGAGCUGGCGAGAAAGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAAGGGACACUCUACCAAAGAGUGGGUCAGUAUGCUAGGACCA
..(((((.(......))))))..(((...((((((...((((.....))))...)))))).....(((((...((((...((..((((((.....))))))..)).)))).))))).))) ( -37.80)
>DroYak_CAF1 3132 120 + 1
CGAGCUGGUGAGAAGGCAGCUGUUGGUGAGGUAGAAGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAAGGGACACUCUACCAAAGAGUGGGUCAGUAUGCUGGGACCA
..(((((.(.....).)))))..((((..((((((...((((.....))))...)))))).....((..(...((((...((..((((((.....))))))..)).)))).)..)))))) ( -39.60)
>consensus
CGAGCUGGCGAGAAGGCAGCUGUUGGCGAGGUAGAGGACACCGAGAUGGUGGAGUCUAUCGAAAACCUGGAGGAUACCAAGGGACACUCAACCAAAGAGUGGGUCAGUAUGCUAGGACCA
..(((((.(.....).)))))..(((...((((((...((((.....))))...)))))).....(((((...((((...((..(((((.......)))))..)).)))).))))).))) (-36.96 = -36.72 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:16 2006