Locus 2415

Sequence ID 3L_DroMel_CAF1
Location 6,789,109 – 6,789,268
Length 159
Max. P 0.791357
window3732 window3733

overview

Window 2

Location 6,789,109 – 6,789,205
Length 96
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 79.58
Mean single sequence MFE -30.25
Consensus MFE -17.10
Energy contribution -19.55
Covariance contribution 2.45
Combinations/Pair 1.12
Mean z-score -2.10
Structure conservation index 0.57
SVM decision value 0.59
SVM RNA-class probability 0.791357
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6789109 96 + 23771897
UGCCUGAAUGCAUAAAAUAUUUCUUGUUGUGUGCUUUUGGGCGCCAUUUUGAAGCUGC---CUGGAAAAAUGGCGCUGGGU--GGAAAAUGGUGCUAAAAG
.(((..((.(((((.((((.....)))).))))).))..)))((((((((....(..(---(..(..........)..)).--.)))))))))........ ( -31.50)
>DroPse_CAF1 62748 96 + 1
CCC-----CCCAAAAAACAUUUCCUGUUGUAUGCUUUUGGGCGCCAUUUUGAAGCUGCAAACUGGAAUAGGGGCUUGGGGUUUGGGGUUUGGGGUUUGGGG
(((-----((((((...((..(((((......(((((((....(((.((((......)))).)))..))))))).)))))..))...)))))))...)).. ( -28.90)
>DroSec_CAF1 49857 96 + 1
UGCCUGAAUGCAUAAAAUAUUUCUUGUUGUGUGCUUUUGAGCGCCAUUUUGAAGCUGC---CUGGAAAAAUGGCGCCGGGU--GGAAAAUGGUGCUAAAAG
.....(((.(((((.((((.....)))).))))).))).(((((((((((....(..(---((((..........))))).--.))))))))))))..... ( -30.90)
>DroEre_CAF1 63079 96 + 1
UGGCUGAAUGCAUAAAAUAUUUCUUGUUGUGUGCUUUUGGGCGCCAUUUUGAAGCUGC---CUGGAAAAAUGGCGUUGGGU--GGAAAAUGGGGCGGAAAG
...(..((.(((((.((((.....)))).))))).))..)((.(((((((....(..(---(..(..........)..)).--.)))))))).))...... ( -26.70)
>DroYak_CAF1 53637 96 + 1
UGCCUGAAUGCAUAAAAUAUUUCUUGUUGUGUGCUUUUGGGCGCCAUUUUGAAGUUGC---CUGGAAAAAUGGCGUUGGGU--GGAAAAUCGGGCUAAAAG
.(((..((.(((((.((((.....)))).))))).))..)))((((((((..((....---))...))))))))(((.(((--.....))).)))...... ( -31.50)
>DroAna_CAF1 60403 91 + 1
UGCCUGCCUGCAUAAAAUAUUUCUUGUUGUGUGCUUUUGGGCGCCAUUUUGAAGCUGG--GCUGAAGUCCUGGCUGGGGGC--GGUGGGUGGUG------G
.(((..((.(((((.((((.....)))).)))))......((.((.......(((..(--((....).))..))).)).))--))..)))....------. ( -32.00)
>consensus
UGCCUGAAUGCAUAAAAUAUUUCUUGUUGUGUGCUUUUGGGCGCCAUUUUGAAGCUGC___CUGGAAAAAUGGCGUUGGGU__GGAAAAUGGGGCUAAAAG
.(((((((.(((((.((((.....)))).))))).)))))))((((((((..((.......))...))))))))........................... (-17.10 = -19.55 +   2.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 6,789,170 – 6,789,268
Length 98
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 69.53
Mean single sequence MFE -19.00
Consensus MFE -5.79
Energy contribution -6.57
Covariance contribution 0.78
Combinations/Pair 1.11
Mean z-score -1.95
Structure conservation index 0.30
SVM decision value 0.09
SVM RNA-class probability 0.579774
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6789170 98 - 23771897
UCAG-GCAACUUCACC---AA-AAAGU-----GCAUCACGCAAUGGCCACUACGGCAUGCUA-UGCACCACCCA------CUUUUAGCACCAUUUUCC--ACCCAGCGCCAUUUUUC
...(-((.........---..-...((-----((((...(((...(((.....))).))).)-)))))......------......((..........--.....)))))....... ( -20.16)
>DroPse_CAF1 62807 108 - 1
UCAC-UCAACUUUUACUGCAA-GAACUCUGCGGCCACACGCUAUAG-------GGGGUGUUGUUGCAACACCACCCCGAACCCCAAACCCCAAACCCCAAACCCCAAGCCCCUAUUC
....-............((..-.......(((......)))....(-------(((((((((...))))))).)))...............................))........ ( -19.70)
>DroSec_CAF1 49918 99 - 1
UCAG-GCAACUUCACC---AAAAAAGU-----GCAUCACGCAAUUGCCACCACGGCAUGCUA-UGCACCACCCA------CUUUUAGCACCAUUUUCC--ACCCGGCGCCAUUUUUC
...(-((.........---......((-----((((...(((..((((.....))))))).)-)))))......------......((..........--.....)))))....... ( -20.66)
>DroSim_CAF1 52493 99 - 1
UCAG-GCAACUUCACC---AAAAAAGU-----GCAUCACGCAAUGGCCACAACGGCAUGCUA-UGCACCACCCA------CUUUUAGCACCAUUUUCC--ACCCGGCGCCAUUUUUC
...(-((.........---......((-----((((...(((...(((.....))).))).)-)))))......------......((..........--.....)))))....... ( -20.06)
>DroYak_CAF1 53698 99 - 1
UCAGCACAACUUCACC---GG-AAAGU-----GCAUCACGCAAUGGCCACCACGGCAUGCUA-UGCACCACCCA------CUUUUAGCCCGAUUUUCC--ACCCAACGCCAUUUUUC
................---((-(((((-----((((...(((...(((.....))).))).)-)))))......------.............)))))--................. ( -16.70)
>DroAna_CAF1 60465 92 - 1
UCAA-GCAGCUCCACC---AA-AAAGU-----GCAGCACGCAAUGGCCGAGCUAGCAUGUCA-UGCAUCACCAC------C------CACCACCCACC--GCCCCCAGCCAGGACUU
....-(((((((..((---(.-....(-----((.....))).)))..))))).))..(((.-.((........------.------...........--.......))...))).. ( -16.73)
>consensus
UCAG_GCAACUUCACC___AA_AAAGU_____GCAUCACGCAAUGGCCACCACGGCAUGCUA_UGCACCACCCA______CUUUUAGCACCAUUUUCC__ACCCAGCGCCAUUUUUC
................................(((....(((...(((.....))).)))...)))................................................... ( -5.79 =  -6.57 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:52 2006