Locus 3906

Sequence ID	2L_DroMel_CAF1
Location	11,417,032 – 11,417,126
Length	94
Max. P	0.749866

overview

Window 7

Location	11,417,032 – 11,417,126
Length	94
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	77.75
Mean single sequence MFE	-16.37
Consensus MFE	-2.58
Energy contribution	-5.22
Covariance contribution	2.64
Combinations/Pair	1.16
Mean z-score	-1.81
Structure conservation index	0.16
SVM decision value	0.47
SVM RNA-class probability	0.749866
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11417032 94 + 22407834
AAAAUCCAAGCAAAUACUGUU-UUUAAUAACAUAUGAAAAAGAUCCGCAUUCUUGUGACCUUUUAUAUUCUUACACAGAAAGUAUAAGCUUGAGU
......(((((..(((((...-...............(((((...((((....))))..)))))...((((.....)))))))))..)))))... ( -15.50)
>DroSec_CAF1 134539 94 + 1
AAAAUUCAAGCAAAUACUUUU-UUUAAUGUCAUAUAAAUAAGAUCCGCAUUCUUAUGACCUUUUAUAUGCUUACACAGAAAGUAUAAGCUUGAGU
...((((((((..((((((((-(.....(.(((((((((((((.......))))))......))))))))......)))))))))..)))))))) ( -23.00)
>DroSim_CAF1 141340 94 + 1
AAAAUCCAAGCAAAUACUGUU-UUUAAUGCCAUAUAAAUAAGAUCCGCAUUCUUCUGACCUUUUAUAUGCUUACACAGAAAGUAUAAGCUUGAGU
......(((((..(((((...-........((((((((..(((..........))).....))))))))...........)))))..)))))... ( -16.15)
>DroEre_CAF1 142155 81 + 1
GAAAUCGUAGCAAAUAUUCUU-UUUAAUACCAAUUGAACAAGAUCCGCAUUCUUGCAAACUUUUUUCUUCGGACUUAGAAAA-------------
.................((((-((((((....)))))).))))...(((....)))......((((((........))))))------------- (  -8.00)
>DroYak_CAF1 139048 95 + 1
AAAAUCCUAUCAAAUAUUCUUGUUUAAUUCCCAUUGAACAAGAUCCGCAUUCCUGUAGCCUUUUCUAUUCGGACACAGAAAGUAUAGGCUUGAGU
.....((((((......(((((((((((....))))))))))).........((((..((..........))..))))...).)))))....... ( -19.20)
>consensus
AAAAUCCAAGCAAAUACUCUU_UUUAAUACCAUAUGAACAAGAUCCGCAUUCUUGUGACCUUUUAUAUUCUUACACAGAAAGUAUAAGCUUGAGU
......(((((..(((((...................((((((.......))))))...........(((.......))))))))..)))))... ( -2.58 =  -5.22 +   2.64)

alignment

secondary structure

dotplot

Window 8

Location	11,417,032 – 11,417,126
Length	94
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	77.75
Mean single sequence MFE	-19.39
Consensus MFE	-4.20
Energy contribution	-6.44
Covariance contribution	2.24
Combinations/Pair	1.30
Mean z-score	-1.69
Structure conservation index	0.22
SVM decision value	-0.04
SVM RNA-class probability	0.513142
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11417032 94 - 22407834
ACUCAAGCUUAUACUUUCUGUGUAAGAAUAUAAAAGGUCACAAGAAUGCGGAUCUUUUUCAUAUGUUAUUAAA-AACAGUAUUUGCUUGGAUUUU
..((((((..(((((......((((..((((((((((((.(........)))))))))..)))).))))....-...)))))..))))))..... ( -19.32)
>DroSec_CAF1 134539 94 - 1
ACUCAAGCUUAUACUUUCUGUGUAAGCAUAUAAAAGGUCAUAAGAAUGCGGAUCUUAUUUAUAUGACAUUAAA-AAAAGUAUUUGCUUGAAUUUU
..((((((..(((((((..((((...(((((((((((((...........)))))..))))))))))))....-.)))))))..))))))..... ( -24.20)
>DroSim_CAF1 141340 94 - 1
ACUCAAGCUUAUACUUUCUGUGUAAGCAUAUAAAAGGUCAGAAGAAUGCGGAUCUUAUUUAUAUGGCAUUAAA-AACAGUAUUUGCUUGGAUUUU
..((((((..(((((((..((((...(((((((((((((.(.......).)))))..))))))))))))..))-...)))))..))))))..... ( -21.60)
>DroEre_CAF1 142155 81 - 1
-------------UUUUCUAAGUCCGAAGAAAAAAGUUUGCAAGAAUGCGGAUCUUGUUCAAUUGGUAUUAAA-AAGAAUAUUUGCUACGAUUUC
-------------......(((((....(((.((..((((((....))))))..)).)))...(((((.....-.........))))).))))). ( -10.24)
>DroYak_CAF1 139048 95 - 1
ACUCAAGCCUAUACUUUCUGUGUCCGAAUAGAAAAGGCUACAGGAAUGCGGAUCUUGUUCAAUGGGAAUUAAACAAGAAUAUUUGAUAGGAUUUU
.......(((((..((((((((.((..........)).))))))))......(((((((.(((....))).))))))).......)))))..... ( -21.60)
>consensus
ACUCAAGCUUAUACUUUCUGUGUAAGAAUAUAAAAGGUCACAAGAAUGCGGAUCUUAUUCAUAUGGCAUUAAA_AACAGUAUUUGCUUGGAUUUU
..((((((..(((((((((...((......))..))...((((((.......)))))).................)))))))..))))))..... ( -4.20 =  -6.44 +   2.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:25 2006