Locus 4447

Sequence ID	3R_DroMel_CAF1
Location	11,759,093 – 11,759,232
Length	139
Max. P	0.986948

overview

Window 1

Location	11,759,093 – 11,759,198
Length	105
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	77.20
Mean single sequence MFE	-40.90
Consensus MFE	-27.83
Energy contribution	-28.92
Covariance contribution	1.09
Combinations/Pair	1.29
Mean z-score	-2.68
Structure conservation index	0.68
SVM decision value	2.06
SVM RNA-class probability	0.986948
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11759093 105 + 27905053
CUCCAUCAGUCGCACCUGCUCAUCCAAACUGCUCAAGGGCAGCUUUCGCAUUAUGCGGCGC----AGCUGCUUGCGCUUUUUGGGCGUGAGCAGGUGGUGGUGCUUCUG
...(((((..(.((((((((((((((((..((.((..(((((((.((((.....))))...----))))))))).))..)))))..)))))))))))))))))...... ( -46.50)
>DroSec_CAF1 91942 102 + 1
CUCCAUCAGUCGCACCUGCUCAUCCAAACUGCUCAAGGGCAGCUUUCGCAUUAUGCGGCGC----AGCUGCUUGCGCUUUUUGGGCGUGAGCAGGUGGUUGUGC---UG
......((((((((((((((((((((((..((.((..(((((((.((((.....))))...----))))))))).))..)))))..)))))))))))..)).))---)) ( -45.10)
>DroSim_CAF1 93702 102 + 1
CUCCAUCAGUCGCACCUGCUCAUCCAAACUGCUCAAGGGCAGCUUUCGCAUUAUGCGGCGC----AGCUGCUUGCGCUUUUUGGGCGUGAGCAGGUGGUUGUGC---UG
......((((((((((((((((((((((..((.((..(((((((.((((.....))))...----))))))))).))..)))))..)))))))))))..)).))---)) ( -45.10)
>DroEre_CAF1 92356 105 + 1
CUCCAUCAGACGCACCUGCUCCUCCAAGGUGCUCAUGGGCAGCUUUCGUAUUAUGCGACGC----AGUUGCUUUUUCUUCUUGGGCGAGAGGAGGUGCUUGUGCUUCUG
......((((.((((..((.(((((....((((((.((((((((.((((.....))))...----))))))))........))))))...))))).))..)))).)))) ( -41.80)
>DroYak_CAF1 96191 105 + 1
UUCCAUUAGACGCACCUGCUCCUCCAAGGUGCUCAUGGGCAGCUUUCCUAUUAUGCGGCGC----AGUUGCUUGUGCUUUUUGGGCGAGAGUAGGUGCUUGUUCUUCCU
...........((((((((((((((((((....((..(((((((..((........))...----)))))))..))..))))))).).))))))))))........... ( -39.80)
>DroPer_CAF1 99130 105 + 1
CUCCAUUAUUCUCACACGCUCCUCCAGCGAGUGGACGGGCAUCUUC----UUCUGUAGUGCCGUUAGUUGCUGCCUCUUUUUUGGUGUCAGCGAAUGCUUUGUGCGCUC
.................(((.....)))(((((.(((((((.((.(----....).))))))((...((((((.(.((.....)).).))))))..))..))).))))) ( -27.10)
>consensus
CUCCAUCAGUCGCACCUGCUCAUCCAAACUGCUCAAGGGCAGCUUUCGCAUUAUGCGGCGC____AGCUGCUUGCGCUUUUUGGGCGUGAGCAGGUGCUUGUGCUUCUG
............(((((((((.((((((..((....((((((((..(((........))).....))))))))..))..))))))...)))))))))............ (-27.83 = -28.92 +   1.09)

alignment

secondary structure

dotplot

Window 2

Location	11,759,093 – 11,759,198
Length	105
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	77.20
Mean single sequence MFE	-35.45
Consensus MFE	-19.87
Energy contribution	-21.57
Covariance contribution	1.70
Combinations/Pair	1.22
Mean z-score	-2.09
Structure conservation index	0.56
SVM decision value	1.05
SVM RNA-class probability	0.907498
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11759093 105 - 27905053
CAGAAGCACCACCACCUGCUCACGCCCAAAAAGCGCAAGCAGCU----GCGCCGCAUAAUGCGAAAGCUGCCCUUGAGCAGUUUGGAUGAGCAGGUGCGACUGAUGGAG
........((((((((((((((...(((((..((.(((((((((----....(((.....)))..))))))..))).))..))))).)))))))))).).....))).. ( -42.50)
>DroSec_CAF1 91942 102 - 1
CA---GCACAACCACCUGCUCACGCCCAAAAAGCGCAAGCAGCU----GCGCCGCAUAAUGCGAAAGCUGCCCUUGAGCAGUUUGGAUGAGCAGGUGCGACUGAUGGAG
((---(......((((((((((...(((((..((.(((((((((----....(((.....)))..))))))..))).))..))))).))))))))))...)))...... ( -41.90)
>DroSim_CAF1 93702 102 - 1
CA---GCACAACCACCUGCUCACGCCCAAAAAGCGCAAGCAGCU----GCGCCGCAUAAUGCGAAAGCUGCCCUUGAGCAGUUUGGAUGAGCAGGUGCGACUGAUGGAG
((---(......((((((((((...(((((..((.(((((((((----....(((.....)))..))))))..))).))..))))).))))))))))...)))...... ( -41.90)
>DroEre_CAF1 92356 105 - 1
CAGAAGCACAAGCACCUCCUCUCGCCCAAGAAGAAAAAGCAACU----GCGUCGCAUAAUACGAAAGCUGCCCAUGAGCACCUUGGAGGAGCAGGUGCGUCUGAUGGAG
((((.((((..((.(((((..(((........((....((....----)).))........)))(((.(((......))).)))))))).))..)))).))))...... ( -31.69)
>DroYak_CAF1 96191 105 - 1
AGGAAGAACAAGCACCUACUCUCGCCCAAAAAGCACAAGCAACU----GCGCCGCAUAAUAGGAAAGCUGCCCAUGAGCACCUUGGAGGAGCAGGUGCGUCUAAUGGAA
....(((....((((((.(((.(..((((...((.((.(((.((----...((........))..)).)))...)).))...)))).)))).)))))).)))....... ( -29.50)
>DroPer_CAF1 99130 105 - 1
GAGCGCACAAAGCAUUCGCUGACACCAAAAAAGAGGCAGCAACUAACGGCACUACAGAA----GAAGAUGCCCGUCCACUCGCUGGAGGAGCGUGUGAGAAUAAUGGAG
(((.((.....)).)))((((.(..(......)..)))))..(((..((((((......----..)).))))..(((((.((((.....)))).))).))....))).. ( -25.20)
>consensus
CAGAAGCACAACCACCUGCUCACGCCCAAAAAGCGCAAGCAACU____GCGCCGCAUAAUGCGAAAGCUGCCCUUGAGCACUUUGGAGGAGCAGGUGCGACUGAUGGAG
............((((((((((...(((((..((.((.(((.((.....(((........)))..)).)))...)).))..))))).))))))))))............ (-19.87 = -21.57 +   1.70)

alignment

secondary structure

dotplot

Window 3

Location	11,759,130 – 11,759,232
Length	102
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	76.75
Mean single sequence MFE	-36.88
Consensus MFE	-21.46
Energy contribution	-22.97
Covariance contribution	1.51
Combinations/Pair	1.38
Mean z-score	-1.60
Structure conservation index	0.58
SVM decision value	0.30
SVM RNA-class probability	0.678554
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11759130 102 + 27905053
GGCAGCUUUCGCAUUAUGCGGCGC----AGCUGCUUGCGCUUUUUGGGCGUGAGCAGGUGGUGGUGCUUCUGAAAGCGCUCCACUCCGC--GGUGCAAGUUCUCCAUC
((.(((((..((((..(((((...----..(((((..((((.....))))..)))))((((.(((((((....))))))))))).))))--))))))))))..))... ( -45.80)
>DroPse_CAF1 103339 100 + 1
GGCAUCUUC----UUCUGUAGUGCCGUUAGUUGCUGCCUCUUUUUUGGUGUCAACGUAUGCUUUGUGCGCUCAAGGCGAUCCAAUUCUUCUCGUAUAAGGUCUA----
((((.((.(----....).))))))....((((.((((........)))).))))....((((((((((....(((.((......)).)))))))))))))...---- ( -24.90)
>DroSec_CAF1 91979 99 + 1
GGCAGCUUUCGCAUUAUGCGGCGC----AGCUGCUUGCGCUUUUUGGGCGUGAGCAGGUGGUUGUGC---UGAAAGCGCUCCACUCCGC--GGUGCAAGUUCUCCAUC
((.(((((..((((..(((((...----..(((((..((((.....))))..)))))((((..((((---.....)))).)))).))))--))))))))))..))... ( -43.30)
>DroSim_CAF1 93739 99 + 1
GGCAGCUUUCGCAUUAUGCGGCGC----AGCUGCUUGCGCUUUUUGGGCGUGAGCAGGUGGUUGUGC---UGAAAGCGCUCCACUCCGC--GGUGCAAGUUCUCCAUC
((.(((((..((((..(((((...----..(((((..((((.....))))..)))))((((..((((---.....)))).)))).))))--))))))))))..))... ( -43.30)
>DroEre_CAF1 92393 102 + 1
GGCAGCUUUCGUAUUAUGCGACGC----AGUUGCUUUUUCUUCUUGGGCGAGAGGAGGUGCUUGUGCUUCUGAAAGCGCUCCACCCCGC--GGUGCAAGUUCUCCAUC
(((((((.((((.....))))...----))))))).......((((.((..(.((.((((...((((((....))))))..)))))).)--.)).))))......... ( -32.80)
>DroYak_CAF1 96228 102 + 1
GGCAGCUUUCCUAUUAUGCGGCGC----AGUUGCUUGUGCUUUUUGGGCGAGAGUAGGUGCUUGUUCUUCCUAAAGCGCUCCACUCUGC--GGUGCAAGUUUUCCAUC
((.((((.........((((.(((----((......(((((((..(((((((........))))))).....)))))))......))))--).))))))))..))... ( -31.20)
>consensus
GGCAGCUUUCGCAUUAUGCGGCGC____AGCUGCUUGCGCUUUUUGGGCGUGAGCAGGUGCUUGUGCUUCUGAAAGCGCUCCACUCCGC__GGUGCAAGUUCUCCAUC
((.(((((..((((...((((.........(((((((((((.....)))))))))))(((...(((((......)))))..))).))))...)))))))))..))... (-21.46 = -22.97 +   1.51)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:33 2006