Locus 5354

Sequence ID 3R_DroMel_CAF1
Location 14,051,848 – 14,051,982
Length 134
Max. P 0.737710
window8729 window8730

overview

Window 9

Location 14,051,848 – 14,051,944
Length 96
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 79.05
Mean single sequence MFE -20.24
Consensus MFE -8.20
Energy contribution -7.76
Covariance contribution -0.44
Combinations/Pair 1.31
Mean z-score -1.98
Structure conservation index 0.41
SVM decision value 0.04
SVM RNA-class probability 0.555286
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14051848 96 + 27905053
GCUCCAUUUGAUUUGUAUCGAUA--UGCAGGCUCAAAUUUAAAUUUGCUGCAUCUAAAUAUGCUGCACUGCAACUGCAAUUUAAAUAUUUCCAUACGA
.......(((((((((((....)--)))))).))))((((((((((((.((((......)))).)))..((....)))))))))))............ ( -17.30)
>DroSec_CAF1 4511 88 + 1
GCUCCAUUUGAUAUGUAUCGAUA--UGCAGGCUCAAAUUCAAAUUA--------UGAAUAUGCUGCACUGCAAUUGCAAUUUAAAUAUUUGCAUGCGA
((.....(((((....)))))..--(((((((.((.(((((.....--------))))).))..)).)))))..(((((.........))))).)).. ( -19.50)
>DroSim_CAF1 4546 88 + 1
GCUCCAUUUGAUAUGUAUCGAUA--UGCAGGCUCAAAUUCAAAUUU--------UGAAUAUGCUGCACUGCAGCUGCAAUUUAAAUAUUUGCAUGCGA
.......(((((....)))))..--(((((((.((.(((((.....--------))))).))..)).)))))(((((((.........))))).)).. ( -21.50)
>DroEre_CAF1 4510 82 + 1
GCUCCAUUCGAUUUGUAUCGAUAAGUGC------AAAUUGAAAUGUU-------CGAAU---CUUCACUGCAACUGCAAUUUAAAUUGUUGCAUGAAA
......((((((((((((......))))------)))))))).....-------.....---.((((.((((((.............)))))))))). ( -20.32)
>DroYak_CAF1 4503 91 + 1
GCUCCAUUCAAUUUGUAUCGAUAGUUGCAAGCUCAAAUUCCAAUUUU-------UGAAUUUGCUUCGCUGCAACUGCAAUUUAGAUAGGUGCAUGAAG
((.((((..((.((((......(((((((.((.(((((((.......-------.)))))))....))))))))))))).))..)).)).))...... ( -22.60)
>consensus
GCUCCAUUUGAUUUGUAUCGAUA__UGCAGGCUCAAAUUCAAAUUU________UGAAUAUGCUGCACUGCAACUGCAAUUUAAAUAUUUGCAUGCGA
((.....(((((....))))).....))...................................((((.(((((...............))))))))). ( -8.20 =  -7.76 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 14,051,866 – 14,051,982
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.87
Mean single sequence MFE -24.12
Consensus MFE -8.67
Energy contribution -9.72
Covariance contribution 1.05
Combinations/Pair 1.10
Mean z-score -1.87
Structure conservation index 0.36
SVM decision value 0.44
SVM RNA-class probability 0.737710
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14051866 116 + 27905053
CGAUA--UGCAGGCUCAAAUUUAAAUUUGCUGCAUCUAAAUAUGCUGCACUGCAACUGCAAUUUAAAUAUUUCCAUACGAAAGUAUGCUUUUCCUUAAUAUUGCAAGCAUAUGGC--CAA
(.(((--(((..((....((((((((((((.((((......)))).)))..((....))))))))))).....(((((....)))))...............))..)))))).).--... ( -28.70)
>DroSec_CAF1 4529 107 + 1
CGAUA--UGCAGGCUCAAAUUCAAAUUA--------UGAAUAUGCUGCACUGCAAUUGCAAUUUAAAUAUUUGCAUGCGAAAUGGUGCUUUUCCUAAAAAUUGCAAGU---UGGCUACAA
((((.--(((((((.((.(((((.....--------))))).))..)).))))).(((((((((........((((........)))).........)))))))))))---))....... ( -25.53)
>DroSim_CAF1 4564 107 + 1
CGAUA--UGCAGGCUCAAAUUCAAAUUU--------UGAAUAUGCUGCACUGCAGCUGCAAUUUAAAUAUUUGCAUGCGAAAUGAUGCUUUUCCUAAACAUUGCAAGU---UGGCUAUAA
((((.--(((((((.((.(((((.....--------))))).))..)).)))))..((((((..........((((........))))...........)))))).))---))....... ( -22.50)
>DroEre_CAF1 4528 102 + 1
CGAUAAGUGC------AAAUUGAAAUGUU-------CGAAU---CUUCACUGCAACUGCAAUUUAAAUUGUUGCAUGAAAAAUUAUGCAUUUCCGAAGCAUUGCAAGCAUAUAAC--CAA
.(...(((((------.....(((((((.-------.....---.((((.((((((.............)))))))))).......)))))))....))))).)...........--... ( -20.36)
>DroYak_CAF1 4521 111 + 1
CGAUAGUUGCAAGCUCAAAUUCCAAUUUU-------UGAAUUUGCUUCGCUGCAACUGCAAUUUAGAUAGGUGCAUGAAGAAGAAUGCUAUUCCGAAACAUGGCAAGCAUAUACG--CAA
.(.((((((((.((.(((((((.......-------.)))))))....)))))))))))..........((.((((........))))....))............((......)--).. ( -23.50)
>consensus
CGAUA__UGCAGGCUCAAAUUCAAAUUU________UGAAUAUGCUGCACUGCAACUGCAAUUUAAAUAUUUGCAUGCGAAAUGAUGCUUUUCCUAAACAUUGCAAGCAUAUGGC__CAA
.......(((((...((.((((...............)))).)).....)))))..((((((..........((((........))))...........))))))............... ( -8.67 =  -9.72 +   1.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:46 2006