Locus 3573

Sequence ID	2R_DroMel_CAF1
Location	11,893,083 – 11,893,217
Length	134
Max. P	0.984912

overview

Window 1

Location	11,893,083 – 11,893,198
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.42
Mean single sequence MFE	-27.82
Consensus MFE	-25.05
Energy contribution	-25.19
Covariance contribution	0.14
Combinations/Pair	1.07
Mean z-score	-1.95
Structure conservation index	0.90
SVM decision value	1.99
SVM RNA-class probability	0.984912
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11893083 115 - 20766785
AAAAAGUGCAAAAAUAUGUUGCACAUAAAUUCGUAUUAAGUUUGGCCCGCUGUCACUUUUUCU---UCGGCCGCC--UAAGCAAUGCGGGCAGACAGAAUAACGACAUAAUCAUAAAUUU
.....((((((.......))))))......(((((((..(((((.(((((...........(.---...)..((.--...))...))))))))))..))).))))............... ( -28.00)
>DroPse_CAF1 31669 120 - 1
AAAAAGUGCAAAAAUAUGUUGCACAUAAAUUUGUAUUAAGUUUGGCCCGCUGUCACUUUUUCUUCUUCGGCCGCCUCUAAGCAAUGCGGGCAGACAGCAUAACGACAUAAUCAUAAAUUU
.....((((((.......))))))..((((((((((((.(((.(....((((((..........(....)..((((...(....)..)))).))))))....)))).)))).)))))))) ( -27.80)
>DroSec_CAF1 33605 115 - 1
AAAAAGUGCAAAAAUAUGUUGCACAUAAAUUCGUAUUAAGUUUGGCCCGCUGUCACUUUUUCU---UCGGCCGCC--UAAGCAAUGCGGGCAGACAGAAUAACGACAUAAUCAUAAAUUU
.....((((((.......))))))......(((((((..(((((.(((((...........(.---...)..((.--...))...))))))))))..))).))))............... ( -28.00)
>DroSim_CAF1 33954 113 - 1
AAAAAGUGCAAAAAUAUGUUGCACAUAAAUUCGUAUUAAGUUUGGCCCGCUGUCACUUUUUCU---UCGGCCGCC--UAAGC-AUGCGGGCAGACAGAAUAACGACAUA-UCAUAAAUUU
.....((((((.......))))))......(((((((..(((((.((((((((........(.---...).....--...))-).))))))))))..))).))))....-.......... ( -29.29)
>DroEre_CAF1 35540 114 - 1
AGAAAGUGCAAAAAUAUGUUGCACAUAAAUUCGUAUUAAGUUUGGCCCGCUGUCACUUUUUCU---UCG-CCGCC--UAAGCAAUGCGGGCAGACAGAGUAACGACAUAAUCAUAAAUUU
.((..((((((.......))))))......(((((((..(((((.(((((.....(((...(.---...-..)..--.)))....))))))))))..))).)))).....))........ ( -26.00)
>DroPer_CAF1 32995 120 - 1
AAAAAGUGCAAAAAUAUGUUGCACAUAAAUUUGUAUUAAGUUUGGCCCGCUGUCACUUUUUCUUCUUCGGCCGCCUCUAAGCAAUGCGGGCAGACAGCAUAACGACAUAAUCAUAAAUUU
.....((((((.......))))))..((((((((((((.(((.(....((((((..........(....)..((((...(....)..)))).))))))....)))).)))).)))))))) ( -27.80)
>consensus
AAAAAGUGCAAAAAUAUGUUGCACAUAAAUUCGUAUUAAGUUUGGCCCGCUGUCACUUUUUCU___UCGGCCGCC__UAAGCAAUGCGGGCAGACAGAAUAACGACAUAAUCAUAAAUUU
.....((((((.......))))))......(((((((..(((((.(((((.(((..............))).((......))...))))))))))..))).))))............... (-25.05 = -25.19 +   0.14)

alignment

secondary structure

dotplot

Window 2

Location	11,893,123 – 11,893,217
Length	94
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.43
Mean single sequence MFE	-26.39
Consensus MFE	-19.42
Energy contribution	-19.09
Covariance contribution	-0.33
Combinations/Pair	1.12
Mean z-score	-1.26
Structure conservation index	0.74
SVM decision value	0.04
SVM RNA-class probability	0.554763
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11893123 94 + 20766785
UUA--GGCGGCCGA---AGAAAAAGUGACAGCGGGCCAAACUUAAUACGAAUUUAUGUGCAACAUAUUUUUGCACUUUUUU---CC--CCGCCC----------UUUGAAGCAU------
...--(((((....---.(((((((((.....((......)).....((((..((((.....))))..)))))))))))))---..--))))).----------..........------ ( -20.70)
>DroPse_CAF1 31709 117 + 1
UUAGAGGCGGCCGAAGAAGAAAAAGUGACAGCGGGCCAAACUUAAUACAAAUUUAUGUGCAACAUAUUUUUGCACUUUUUU---UUUGUUGCCUUUGGUGUGCCUUUGGUGUAUGCCCAG
..(((((((((....((((((((((((.....((......)).....((((..((((.....))))..)))))))))))))---))))))))))))((((((((....).)))))))... ( -33.10)
>DroSim_CAF1 33992 94 + 1
UUA--GGCGGCCGA---AGAAAAAGUGACAGCGGGCCAAACUUAAUACGAAUUUAUGUGCAACAUAUUUUUGCACUUUUUU---CC--CCGGCG----------UUUGCAGCAU------
.((--((((.(((.---.(((((((((.....((......)).....((((..((((.....))))..)))))))))))))---..--.)))))----------))))......------ ( -21.20)
>DroEre_CAF1 35580 93 + 1
UUA--GGCGG-CGA---AGAAAAAGUGACAGCGGGCCAAACUUAAUACGAAUUUAUGUGCAACAUAUUUUUGCACUUUCUU---CC--CCGCCA----------UUUGCUGCAC------
...--(((((-.((---(((((..((((...((..............))...))))((((((.......))))))))))))---).--))))).----------..........------ ( -25.94)
>DroYak_CAF1 34083 97 + 1
UUA--GGCGGCCGA---AGAAAAAGUGACAGCGGGCCAAACUUAAUACGAAUUUAUGUGCAACAUAUUUUUGCACUUUUUUUCGCC--CCGCCU----------UUUGCUGCAU------
...--.(((((.((---((...........(((((............((((.....((((((.......)))))).....)))).)--))))))----------)).)))))..------ ( -25.72)
>DroPer_CAF1 33035 117 + 1
UUAGAGGCGGCCGAAGAAGAAAAAGUGACAGCGGGCCAAACUUAAUACAAAUUUAUGUGCAACAUAUUUUUGCACUUUUUU---UUUGUUGCCUUUGGUGUGCCUUUGGUGUGUGCCCAG
..(((((((((....((((((((((((.....((......)).....((((..((((.....))))..)))))))))))))---))))))))))))((((..((....).)..))))... ( -31.70)
>consensus
UUA__GGCGGCCGA___AGAAAAAGUGACAGCGGGCCAAACUUAAUACGAAUUUAUGUGCAACAUAUUUUUGCACUUUUUU___CC__CCGCCU__________UUUGCUGCAU______
.....(((((........(((((((((.....((......)).....((((..((((.....))))..))))))))))))).......)))))........................... (-19.42 = -19.09 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:55 2006