Locus 553

Sequence ID	3R_DroMel_CAF1
Location	2,060,860 – 2,060,969
Length	109
Max. P	0.998793

overview

Window 2

Location	2,060,860 – 2,060,969
Length	109
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	81.69
Mean single sequence MFE	-28.79
Consensus MFE	-18.98
Energy contribution	-20.18
Covariance contribution	1.20
Combinations/Pair	1.19
Mean z-score	-3.96
Structure conservation index	0.66
SVM decision value	3.23
SVM RNA-class probability	0.998793
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2060860 109 + 27905053
UUCUUUACAGCUUCCUGUCAAGCUGCAACUAU-UUCGCAAUAAUCAAUUUUGAAAAGAGUGUGUAGUUUGCCAAACACAAUUGACACCUGACAGGAAGAUGUGAA-AACAA
...((((((.((((((((((((((((((((.(-((((.(((.....))).)))))..))).))))))))..(((......)))......))))))))).))))))-..... ( -32.00)
>DroSec_CAF1 204800 98 + 1
UUCUUUACAGCUUCCUGUCGAGCUGAAAUUAU-UUCCCAAUAAUCAAUAUUUAAAAGAGUGUGUAAUUUGCCACAUACAAUUGACACCUGACAGGAAGA------------
..........(((((((((.((.((..(((((-(....))))))..............((((((........))))))......)).))))))))))).------------ ( -22.40)
>DroSim_CAF1 209880 110 + 1
UUCUUUACAGCUUCCUGUCGAGCUGCAAUUAU-UUCGCAAUAAUCAAUAUUUAAAAGAGUGUGUAAUUUGCCAGAUACAAUUGACACCUGACAGGAAGAUGUGAAAAACAA
...((((((.(((((((((.((.(((((((((-((.((((......((((((....)))))).....)))).)))))..)))).)).))))))))))).))))))...... ( -33.10)
>DroEre_CAF1 204710 104 + 1
UUCUUCGCAGCUUCCUGUCAU-----AAUAAUAAUCACAAUAAUCAAUGUUUAAUAGAGUGUGCAGUCUACCAGCUAAAAUUGA--CCUGACAGGAAGAUGUGAAAAUCAA
...((((((.((((((((((.-----.........((((....((.((.....)).)).))))..(((..............))--).)))))))))).))))))...... ( -27.14)
>DroYak_CAF1 207853 110 + 1
UUCUUCACAGCUUCCUGUCAAGCUGCAAUUAU-UUCACAAUAAUCUAUAUUUAACAGAGUGUUCAGCCUACCAGAUACAAUUGACACCUGACAGGAAGAUGUGAAAAUCAA
...((((((.((((((((((.(.(((((((..-..........(((.........)))(((((..(....)..)))))))))).))).)))))))))).))))))...... ( -29.30)
>consensus
UUCUUUACAGCUUCCUGUCAAGCUGCAAUUAU_UUCACAAUAAUCAAUAUUUAAAAGAGUGUGUAGUUUGCCAGAUACAAUUGACACCUGACAGGAAGAUGUGAAAAACAA
...((((((.((((((((((.......................((...........))((((.(((((..........))))))))).)))))))))).))))))...... (-18.98 = -20.18 +   1.20)

alignment

secondary structure

dotplot

Window 3

Location	2,060,860 – 2,060,969
Length	109
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	81.69
Mean single sequence MFE	-32.01
Consensus MFE	-19.97
Energy contribution	-21.98
Covariance contribution	2.01
Combinations/Pair	1.12
Mean z-score	-3.83
Structure conservation index	0.62
SVM decision value	3.03
SVM RNA-class probability	0.998197
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2060860 109 - 27905053
UUGUU-UUCACAUCUUCCUGUCAGGUGUCAAUUGUGUUUGGCAAACUACACACUCUUUUCAAAAUUGAUUAUUGCGAA-AUAGUUGCAGCUUGACAGGAAGCUGUAAAGAA
...((-((.(((.((((((((((((((((((((((((.(((....))).)))).........)))))))...(((((.-....)))))))))))))))))).))).)))). ( -35.60)
>DroSec_CAF1 204800 98 - 1
------------UCUUCCUGUCAGGUGUCAAUUGUAUGUGGCAAAUUACACACUCUUUUAAAUAUUGAUUAUUGGGAA-AUAAUUUCAGCUCGACAGGAAGCUGUAAAGAA
------------.(((((((((..((...((((((.((((........))))...(((..((((.....))))..)))-))))))...))..))))))))).......... ( -24.70)
>DroSim_CAF1 209880 110 - 1
UUGUUUUUCACAUCUUCCUGUCAGGUGUCAAUUGUAUCUGGCAAAUUACACACUCUUUUAAAUAUUGAUUAUUGCGAA-AUAAUUGCAGCUCGACAGGAAGCUGUAAAGAA
...(((((.(((.(((((((((((.((.(((((((.((..((((...........................)))))).-))))))))).)).))))))))).)))))))). ( -29.93)
>DroEre_CAF1 204710 104 - 1
UUGAUUUUCACAUCUUCCUGUCAGG--UCAAUUUUAGCUGGUAGACUGCACACUCUAUUAAACAUUGAUUAUUGUGAUUAUUAUU-----AUGACAGGAAGCUGCGAAGAA
....(((((.((.(((((((((.((--(((((.((...(((((((........))))))))).)))))))...(((((....)))-----))))))))))).)).))))). ( -29.40)
>DroYak_CAF1 207853 110 - 1
UUGAUUUUCACAUCUUCCUGUCAGGUGUCAAUUGUAUCUGGUAGGCUGAACACUCUGUUAAAUAUAGAUUAUUGUGAA-AUAAUUGCAGCUUGACAGGAAGCUGUGAAGAA
....((((((((.(((((((((((((..(((((((.((((((((......)..(((((.....))))).))))).)).-)))))))..))))))))))))).)))))))). ( -40.40)
>consensus
UUGAUUUUCACAUCUUCCUGUCAGGUGUCAAUUGUAUCUGGCAAACUACACACUCUUUUAAAUAUUGAUUAUUGCGAA_AUAAUUGCAGCUUGACAGGAAGCUGUAAAGAA
.........(((.(((((((((((((((((........))))..............................(((((......)))))))))))))))))).)))...... (-19.97 = -21.98 +   2.01)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:57 2006