Locus 3897

Sequence ID	3L_DroMel_CAF1
Location	11,282,987 – 11,283,128
Length	141
Max. P	0.900685

overview

Window 8

Location	11,282,987 – 11,283,095
Length	108
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	89.13
Mean single sequence MFE	-21.95
Consensus MFE	-19.91
Energy contribution	-19.73
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.78
Structure conservation index	0.91
SVM decision value	1.01
SVM RNA-class probability	0.900685
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11282987 108 + 23771897
CAAGAUGACGGCACACAAGUUGACCGCAACCAAUCCGAAUUAGUUUCGGAUUAUCUCCUACACAAUUGCACAAGAUAAUUGAGGUAGCAGGGCAUAUAUAUACAUAUA
....(((.((((......)))).((((.(((((((((((.....))))))))..........(((((((....).)))))).))).)).))...........)))... ( -23.30)
>DroSec_CAF1 7215 104 + 1
AAAGAUGACGGCACACAACUUGACCGCAACCAAUCCGAAUUAGUUUCGGAUUAUCUCCUACACAAUUGCACAAGAUAAUUGAGGUAGCAGGACAUAC----AAACAUA
.....((.(((((.......)).)))))...((((((((.....)))))))).(((.((((.(((((((....).))))))..)))).)))......----....... ( -21.60)
>DroSim_CAF1 9999 95 + 1
AAAGAUGACGGCACACAACUUGACCGCAACCAAUCCGAAUUAGUUUCGGAUUAUCUCCUACACAAUUGCACAAGAUAAUUGAGGUAGC-------------AAACAUA
....(((..((((.......)).))((.(((((((((((.....))))))))..........(((((((....).)))))).))).))-------------...))). ( -20.80)
>DroEre_CAF1 7441 100 + 1
AAAGAUGACGGCACACAACUUGACCGCAACCAAUCCGAAUUAGUUUCGGAUUAUCUCUUACACAAUUGCACCAGAUAAUUGAGGUAGCAGGGCAUA--------CAUA
....(((...((.((.....)).((((.(((((((((((.....))))))))..........(((((((....).)))))).))).)).))))...--------))). ( -22.10)
>consensus
AAAGAUGACGGCACACAACUUGACCGCAACCAAUCCGAAUUAGUUUCGGAUUAUCUCCUACACAAUUGCACAAGAUAAUUGAGGUAGCAGGGCAUA_____AAACAUA
....(((..((((.......)).))((.(((((((((((.....))))))))..........(((((((....).)))))).))).))................))). (-19.91 = -19.73 +  -0.19)

alignment

secondary structure

dotplot

Window 9

Location	11,282,987 – 11,283,095
Length	108
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	89.13
Mean single sequence MFE	-27.40
Consensus MFE	-24.00
Energy contribution	-24.25
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.88
SVM decision value	0.73
SVM RNA-class probability	0.834180
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11282987 108 - 23771897
UAUAUGUAUAUAUAUGCCCUGCUACCUCAAUUAUCUUGUGCAAUUGUGUAGGAGAUAAUCCGAAACUAAUUCGGAUUGGUUGCGGUCAACUUGUGUGCCGUCAUCUUG
.....(((((((......((((.(((....(((((((.((((....)))).)))))))((((((.....))))))..))).))))......))))))).......... ( -31.00)
>DroSec_CAF1 7215 104 - 1
UAUGUUU----GUAUGUCCUGCUACCUCAAUUAUCUUGUGCAAUUGUGUAGGAGAUAAUCCGAAACUAAUUCGGAUUGGUUGCGGUCAAGUUGUGUGCCGUCAUCUUU
.(((...----(((..(...((((((.((((((((((.((((....)))).)))))((((((((.....))))))))))))).)))..))).)..)))...))).... ( -27.40)
>DroSim_CAF1 9999 95 - 1
UAUGUUU-------------GCUACCUCAAUUAUCUUGUGCAAUUGUGUAGGAGAUAAUCCGAAACUAAUUCGGAUUGGUUGCGGUCAAGUUGUGUGCCGUCAUCUUU
.......-------------((.(((....(((((((.((((....)))).)))))))((((((.....))))))..))).))(((((.....)).)))......... ( -25.10)
>DroEre_CAF1 7441 100 - 1
UAUG--------UAUGCCCUGCUACCUCAAUUAUCUGGUGCAAUUGUGUAAGAGAUAAUCCGAAACUAAUUCGGAUUGGUUGCGGUCAAGUUGUGUGCCGUCAUCUUU
...(--------(((((...((((((.(((((((((..((((....))))..))))((((((((.....))))))))))))).)))..))).)))))).......... ( -26.10)
>consensus
UAUGUUU_____UAUGCCCUGCUACCUCAAUUAUCUUGUGCAAUUGUGUAGGAGAUAAUCCGAAACUAAUUCGGAUUGGUUGCGGUCAAGUUGUGUGCCGUCAUCUUU
....................((.(((....(((((((.((((....)))).)))))))((((((.....))))))..))).))(((((.....)).)))......... (-24.00 = -24.25 +   0.25)

alignment

secondary structure

dotplot

Window 0

Location	11,283,027 – 11,283,128
Length	101
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	82.17
Mean single sequence MFE	-23.25
Consensus MFE	-16.51
Energy contribution	-18.20
Covariance contribution	1.69
Combinations/Pair	1.04
Mean z-score	-1.55
Structure conservation index	0.71
SVM decision value	0.06
SVM RNA-class probability	0.563079
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11283027 101 - 23771897
UUGGGCCUUCCAC-----C-AAAUC-CGAGUGGUUUGAUAUAUAUGUAUAUAUAUGCCCUGCUACCUCAAUUAUCUUGUGCAAUUGUGUAGGAGAUAAUCCGAAACUA
..((((...((((-----(-.....-.).))))....(((((((....))))))))))).......((.((((((((.((((....)))).))))))))..))..... ( -25.00)
>DroSec_CAF1 7255 91 - 1
UUGGGC------------CAAAAUC-CGAGUGGUUUGAUAUAUGUUU----GUAUGUCCUGCUACCUCAAUUAUCUUGUGCAAUUGUGUAGGAGAUAAUCCGAAACUA
((((..------------.......-.(((((((..(((((((....----)))))))..)))).))).((((((((.((((....)))).))))))))))))..... ( -26.90)
>DroSim_CAF1 10039 90 - 1
UUGGGCCUUCCAC-----CAAAAUCACGAGUGGUUUGAUAUAUGUUU-------------GCUACCUCAAUUAUCUUGUGCAAUUGUGUAGGAGAUAAUCCGAAACUA
((((........)-----)))..((..(((((((..(((....))).-------------)))).))).((((((((.((((....)))).))))))))..))..... ( -20.00)
>DroEre_CAF1 7481 99 - 1
UUGGGCCUUCCACUCCCUCCAACUC-CGAGUGGUUUGAUAUAUG--------UAUGCCCUGCUACCUCAAUUAUCUGGUGCAAUUGUGUAAGAGAUAAUCCGAAACUA
..((((...((((((..........-.))))))....(((....--------))))))).......((.(((((((..((((....))))..)))))))..))..... ( -21.10)
>consensus
UUGGGCCUUCCAC_____CAAAAUC_CGAGUGGUUUGAUAUAUGUUU_____UAUGCCCUGCUACCUCAAUUAUCUUGUGCAAUUGUGUAGGAGAUAAUCCGAAACUA
((((.......................(((((((....(((((........)))))....)))).))).((((((((.((((....)))).))))))))))))..... (-16.51 = -18.20 +   1.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:29 2006