Locus 9968

Sequence ID	3R_DroMel_CAF1
Location	26,687,361 – 26,687,628
Length	267
Max. P	0.996670

overview

Window 7

Location	26,687,361 – 26,687,473
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.83
Mean single sequence MFE	-31.94
Consensus MFE	-29.50
Energy contribution	-30.34
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.33
Structure conservation index	0.92
SVM decision value	0.90
SVM RNA-class probability	0.877979
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26687361 112 + 27905053
--------UGCGCUUUGGUCUCUGACCGAGACCCGUAAUAAUUGAAACCAAUUAGCUUGGAAAAACCUUUUAAUUGUGUGUUCAAUGCCCGGUCUUAAGUAAAUAUUUUCAUGGGCGCAG
--------(((((((.((((...))))((((((.(.....(((((((((((((((...((.....))..))))))).)).))))))..).))))))................))))))). ( -31.00)
>DroSec_CAF1 278115 120 + 1
UCGGAUUCUGCGCUUUGGUCUCUGACCGAGACCCGUAAUAAUUGAAACCAAUUAGCUUGGAAAAACCUUUUAAUUGUGUGUUCAAUGCCCGGUCUUAAGUAAAUAUUUUCAUGGGCGCAG
.......((((((((.((((...))))((((((.(.....(((((((((((((((...((.....))..))))))).)).))))))..).))))))................)))))))) ( -32.90)
>DroSim_CAF1 274872 120 + 1
UCGGAUUCUGCGCUUUGGUCUCUGACCGAGACCCGUUAUAAUUGAAACCAAUUAGCUUGGAAAAACCUUUUAAUAGUGUGUUCAAUGCCCGGUCUUAAGUAAAUAUUUUCAUGGGCGCAG
.......((((((((.((((...))))((((((.....((((((....))))))(((((((...((((......)).)).))))).))..))))))................)))))))) ( -32.10)
>DroEre_CAF1 294069 120 + 1
GCGGAUUCUGCGCUUUGGUCUCUGGCCGAGACCCGUAAUAAUUGAAACCAAUUAGCUUGGAAAAACCUUUUAAUUGUGUGCUCAAUGCCCGGUCUUAAGUAAAUAUUUUCAUGGGCGCAG
.......((((((((.(((.....)))((((((.(.....(((((.(((((((((...((.....))..))))))).))..)))))..).))))))................)))))))) ( -32.50)
>DroYak_CAF1 283078 120 + 1
GCGGAUUCUGCGCUUUGGUGUCUGACCGAGACCCGUAAUAAUUGAAACCAAUUAGCUUGGAAAAACCUUUUAAUUGUGUGCUCAAUGCCUGGUCUUAAGUAAAUAUUUUCAUGGGCGCAG
.......((((((((.(((.....)))((((((.(.....(((((.(((((((((...((.....))..))))))).))..)))))..).))))))................)))))))) ( -31.20)
>consensus
GCGGAUUCUGCGCUUUGGUCUCUGACCGAGACCCGUAAUAAUUGAAACCAAUUAGCUUGGAAAAACCUUUUAAUUGUGUGUUCAAUGCCCGGUCUUAAGUAAAUAUUUUCAUGGGCGCAG
.......((((((((.((((...))))((((((.(.....(((((((((((((((...((.....))..))))))).)).))))))..).))))))................)))))))) (-29.50 = -30.34 +   0.84)

alignment

secondary structure

dotplot

Window 8

Location	26,687,361 – 26,687,473
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.83
Mean single sequence MFE	-30.12
Consensus MFE	-29.24
Energy contribution	-29.84
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.97
SVM decision value	2.73
SVM RNA-class probability	0.996670
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26687361 112 - 27905053
CUGCGCCCAUGAAAAUAUUUACUUAAGACCGGGCAUUGAACACACAAUUAAAAGGUUUUUCCAAGCUAAUUGGUUUCAAUUAUUACGGGUCUCGGUCAGAGACCAAAGCGCA--------
..((((...(((((..........((((((....((((......)))).....)))))).((((.....))))))))).........((((((.....))))))...)))).-------- ( -28.70)
>DroSec_CAF1 278115 120 - 1
CUGCGCCCAUGAAAAUAUUUACUUAAGACCGGGCAUUGAACACACAAUUAAAAGGUUUUUCCAAGCUAAUUGGUUUCAAUUAUUACGGGUCUCGGUCAGAGACCAAAGCGCAGAAUCCGA
((((((...(((((..........((((((....((((......)))).....)))))).((((.....))))))))).........((((((.....))))))...))))))....... ( -32.30)
>DroSim_CAF1 274872 120 - 1
CUGCGCCCAUGAAAAUAUUUACUUAAGACCGGGCAUUGAACACACUAUUAAAAGGUUUUUCCAAGCUAAUUGGUUUCAAUUAUAACGGGUCUCGGUCAGAGACCAAAGCGCAGAAUCCGA
((((((...(((((..........((((((.......................)))))).((((.....))))))))).........((((((.....))))))...))))))....... ( -29.80)
>DroEre_CAF1 294069 120 - 1
CUGCGCCCAUGAAAAUAUUUACUUAAGACCGGGCAUUGAGCACACAAUUAAAAGGUUUUUCCAAGCUAAUUGGUUUCAAUUAUUACGGGUCUCGGCCAGAGACCAAAGCGCAGAAUCCGC
((((((...(((((..........((((((....((((......)))).....)))))).((((.....))))))))).........((((((.....))))))...))))))....... ( -32.30)
>DroYak_CAF1 283078 120 - 1
CUGCGCCCAUGAAAAUAUUUACUUAAGACCAGGCAUUGAGCACACAAUUAAAAGGUUUUUCCAAGCUAAUUGGUUUCAAUUAUUACGGGUCUCGGUCAGACACCAAAGCGCAGAAUCCGC
((((((...................(((((.(..((((((.((.((((((...((.....))....)))))))))))))).....).))))).(((.....)))...))))))....... ( -27.50)
>consensus
CUGCGCCCAUGAAAAUAUUUACUUAAGACCGGGCAUUGAACACACAAUUAAAAGGUUUUUCCAAGCUAAUUGGUUUCAAUUAUUACGGGUCUCGGUCAGAGACCAAAGCGCAGAAUCCGA
((((((...(((((..........((((((....((((......)))).....)))))).((((.....))))))))).........((((((.....))))))...))))))....... (-29.24 = -29.84 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	26,687,473 – 26,687,593
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.17
Mean single sequence MFE	-31.52
Consensus MFE	-26.22
Energy contribution	-27.26
Covariance contribution	1.04
Combinations/Pair	1.12
Mean z-score	-1.66
Structure conservation index	0.83
SVM decision value	0.87
SVM RNA-class probability	0.869862
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26687473 120 + 27905053
GACAAUGCGAGGAUGUGAGAACAUGGCAAUGACCAAAAUAAUCCUGCUCCGUCCGUAGGAUAUAUUGUAGUGAAUGUUACCAGCGAAAGCGGUGCAAAGAAAUUGCCAUAUAAUUGCCAG
............((((....))))((((((...........((((((.......))))))(((((.(((((...(((.(((.((....)))))))).....))))).))))))))))).. ( -32.50)
>DroSec_CAF1 278235 120 + 1
GACAAUGCGAGGAUGUGAGAACAUGGCAAUGACCAAAAUAAUCCUGCUCCGUUCGUAGCAUAUAUUGUAGUGAAUGUUACCAGCGAAAGCGGUCUAAAGAAAUUGCCAAAUAAUUGCCAG
......((((..((((....))))((((((((((...............((((((..(((.....)))..))))))......((....)))))).......))))))......))))... ( -29.51)
>DroSim_CAF1 274992 120 + 1
GACAAUGCGAGGAUGUGAGAACAUGGCAAUGACCAAAAUAAUCCUGCUCCGUUCGUAGGAUAUAUUGUAGUGAAUGUUACCAGCGAAAGCGGUCUAAAGAAAUUGCCAAAUAAUUGCCAG
......((((..((((....))))((((((((((..(((((((((((.......))))))).))))................((....)))))).......))))))......))))... ( -31.11)
>DroEre_CAF1 294189 120 + 1
GACAAUGCGAGGAUGUGAGAACAUGGCAAUGACCAAAAUAAUCCUGCUCCGUCCGCUGGAUAUGUUGUAGUGAAUGUUGCCAGCGAAAGCGGUAAGAAGAAAUUGCCAUAUAAUUGCCAG
(((...((.(((((((....)).(((......))).....)))))))...)))..((((.(((((.(((((...(.(((((.((....))))))).)....))))).)))))....)))) ( -32.70)
>DroYak_CAF1 283198 120 + 1
GACAAUGCGAGGAUGUGAGAACAUGGCAAUGACCAAAAUAAUCCUGCUCCGUACGCAGCAUAUAUGGUAGUGAAUGCUAACAGCGAAAGCGGUAAAAAGAAAUUGCCAUAUAAUUGCCAG
............((((....))))((((((.............((((.......))))..(((((((((((........((.((....)).))........))))))))))))))))).. ( -31.79)
>consensus
GACAAUGCGAGGAUGUGAGAACAUGGCAAUGACCAAAAUAAUCCUGCUCCGUCCGUAGGAUAUAUUGUAGUGAAUGUUACCAGCGAAAGCGGUAAAAAGAAAUUGCCAUAUAAUUGCCAG
............((((....))))((((((...........((((((.......))))))(((((.(((((......((((.((....)))))).......))))).))))))))))).. (-26.22 = -27.26 +   1.04)

alignment

secondary structure

dotplot

Window 0

Location	26,687,513 – 26,687,628
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.86
Mean single sequence MFE	-31.45
Consensus MFE	-20.38
Energy contribution	-21.66
Covariance contribution	1.28
Combinations/Pair	1.11
Mean z-score	-2.74
Structure conservation index	0.65
SVM decision value	0.19
SVM RNA-class probability	0.627343
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26687513 115 + 27905053
AUCCUGCUCCGUCCGUAGGAUAUAUUGUAGUGAAUGUUACCAGCGAAAGCGGUGCAAAGAAAUUGCCAUAUAAUUGCCAGGAAAAAAAACCAAGACAAAGGCA-----GUGCAGAAUGGA
...(((((((.......)))(((((.(((((...(((.(((.((....)))))))).....))))).)))))((((((.....................))))-----))))))...... ( -28.00)
>DroSec_CAF1 278275 113 + 1
AUCCUGCUCCGUUCGUAGCAUAUAUUGUAGUGAAUGUUACCAGCGAAAGCGGUCUAAAGAAAUUGCCAAAUAAUUGCCAGGAAAA--AAGCAAGACAAAGGCU-----CUGGAGAAUGGA
.(((..((((.((((((((((.(((....))).)))))))..((....))........)))...(((......((((........--..))))......))).-----..))))...))) ( -29.00)
>DroSim_CAF1 275032 118 + 1
AUCCUGCUCCGUUCGUAGGAUAUAUUGUAGUGAAUGUUACCAGCGAAAGCGGUCUAAAGAAAUUGCCAAAUAAUUGCCAGGAAAA--AAGCAAGACAAAGAAUAGAGAAUGGAGAAUGGA
.(((..((((((((..........((((..((....((.((.((....))(((...((....)))))............)).)).--...))..))))........))))))))...))) ( -28.47)
>DroEre_CAF1 294229 113 + 1
AUCCUGCUCCGUCCGCUGGAUAUGUUGUAGUGAAUGUUGCCAGCGAAAGCGGUAAGAAGAAAUUGCCAUAUAAUUGCCAGGAAAA--AAGCAAGACAAAGGCG-----GUGGAGAAUGGA
.(((..(((((.(((((...(((((.(((((...(.(((((.((....))))))).)....))))).))))).((((........--..))))......))))-----))))))...))) ( -38.00)
>DroYak_CAF1 283238 113 + 1
AUCCUGCUCCGUACGCAGCAUAUAUGGUAGUGAAUGCUAACAGCGAAAGCGGUAAAAAGAAAUUGCCAUAUAAUUGCCAGGAAAA--AAGCAAGACAAAGGCG-----GUGGAGAAUGGA
.(((..((((...(((....(((((((((((........((.((....)).))........))))))))))).((((........--..)))).......)))-----..))))...))) ( -33.79)
>consensus
AUCCUGCUCCGUCCGUAGGAUAUAUUGUAGUGAAUGUUACCAGCGAAAGCGGUAAAAAGAAAUUGCCAUAUAAUUGCCAGGAAAA__AAGCAAGACAAAGGCG_____GUGGAGAAUGGA
.(((..(((((.........(((((.(((((......((((.((....)))))).......))))).)))))...(((.....................))).......)))))...))) (-20.38 = -21.66 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:46:01 2006