Locus 4272

Sequence ID X_DroMel_CAF1
Location 11,236,434 – 11,236,550
Length 116
Max. P 0.699734
window7023 window7024

overview

Window 3

Location 11,236,434 – 11,236,550
Length 116
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 78.04
Mean single sequence MFE -23.59
Consensus MFE -15.17
Energy contribution -15.54
Covariance contribution 0.37
Combinations/Pair 1.10
Mean z-score -1.62
Structure conservation index 0.64
SVM decision value -0.01
SVM RNA-class probability 0.529613
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11236434 116 + 22224390
UUUUUUUACGCAUAGAACUACGCAUAUAGAACUAAGUUCUAUAUUUUUGCCCACCACUGUGCGC--ACACUCGCACUCACACAGUUUGGUGCGUUGUCAUCAUUCUAGCGUCUUUGCA
.........(((.(((....((((((((((((...)))))))))....(((((..((((((.((--......)).....)))))).))).))...............)))))).))). ( -28.60)
>DroSec_CAF1 23349 101 + 1
UUUUUUUU---------UUACGCAACUUUGAAUAAGUUUUAUAUUUUUGCCCACCACUGUGCGC--ACAC------UCACACAGUUAGGUGCGUUGUCAACAUUUUAGCGUCUUUGCA
........---------..(((((((((.....)))))..........((.((((((((((.(.--....------.).))))))..)))).)).............))))....... ( -18.60)
>DroEre_CAF1 23167 106 + 1
UUUUUUUC----------CCCGCAACUUUCAAUAGGAACUAUACUUUUGCCCUACACUGUGCGC--ACACUCGCACUCACACAGUUGGGUGCGUUGUCAUCAUUUUGGCGUCUUUGCA
........----------...((((.......((((..............))))......((((--(((..((((((((......)))))))).)))((......))))))..)))). ( -22.74)
>DroYak_CAF1 15350 107 + 1
UCUUUUUA-----------GCGCAACUCUAAAUGGGAACUAUACUAUUGCCCUCCAUUGUGCACACACACUCGCACUCACACAGUUGGGUGCGUUGUCAUCAUUUUAGCGUCUUUGCA
........-----------((((((.....(((((........)))))........))))))....(((..((((((((......)))))))).)))..........(((....))). ( -24.42)
>consensus
UUUUUUUA__________UACGCAACUUUAAAUAAGAACUAUACUUUUGCCCACCACUGUGCGC__ACACUCGCACUCACACAGUUGGGUGCGUUGUCAUCAUUUUAGCGUCUUUGCA
.....................((((.......................((((...((((((..................)))))).))))((((((.........))))))..)))). (-15.17 = -15.54 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,236,434 – 11,236,550
Length 116
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 78.04
Mean single sequence MFE -28.08
Consensus MFE -16.56
Energy contribution -17.12
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.92
Structure conservation index 0.59
SVM decision value 0.35
SVM RNA-class probability 0.699734
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11236434 116 - 22224390
UGCAAAGACGCUAGAAUGAUGACAACGCACCAAACUGUGUGAGUGCGAGUGU--GCGCACAGUGGUGGGCAAAAAUAUAGAACUUAGUUCUAUAUGCGUAGUUCUAUGCGUAAAAAAA
.......((((((((((.(((.(...((.(((.((((((((...((....))--.))))))))..)))))....(((((((((...))))))))))))).)))))).))))....... ( -38.70)
>DroSec_CAF1 23349 101 - 1
UGCAAAGACGCUAAAAUGUUGACAACGCACCUAACUGUGUGA------GUGU--GCGCACAGUGGUGGGCAAAAAUAUAAAACUUAUUCAAAGUUGCGUAA---------AAAAAAAA
.......((((....(((((.....(.((((..((((((((.------....--.)))))))))))).)....)))))..(((((.....)))))))))..---------........ ( -25.60)
>DroEre_CAF1 23167 106 - 1
UGCAAAGACGCCAAAAUGAUGACAACGCACCCAACUGUGUGAGUGCGAGUGU--GCGCACAGUGUAGGGCAAAAGUAUAGUUCCUAUUGAAAGUUGCGGG----------GAAAAAAA
(((....((((..............(((((......))))).(((((.....--.))))).))))...))).........(((((..(....).....))----------)))..... ( -23.30)
>DroYak_CAF1 15350 107 - 1
UGCAAAGACGCUAAAAUGAUGACAACGCACCCAACUGUGUGAGUGCGAGUGUGUGUGCACAAUGGAGGGCAAUAGUAUAGUUCCCAUUUAGAGUUGCGC-----------UAAAAAGA
.((......))..............(((((......)))))(((((((((((....))))(((((.((((.........))))))))).....))))))-----------)....... ( -24.70)
>consensus
UGCAAAGACGCUAAAAUGAUGACAACGCACCCAACUGUGUGAGUGCGAGUGU__GCGCACAGUGGAGGGCAAAAAUAUAGAACCUAUUUAAAGUUGCGUA__________UAAAAAAA
........(((.....((....))..((.((..((((((((...((....))...))))))))...)))).........................))).................... (-16.56 = -17.12 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:54 2006