Locus 4477

Sequence ID 3R_DroMel_CAF1
Location 11,836,299 – 11,836,405
Length 106
Max. P 0.737651
window7319 window7320

overview

Window 9

Location 11,836,299 – 11,836,405
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.83
Mean single sequence MFE -36.95
Consensus MFE -23.81
Energy contribution -24.10
Covariance contribution 0.29
Combinations/Pair 1.35
Mean z-score -2.53
Structure conservation index 0.64
SVM decision value 0.44
SVM RNA-class probability 0.737651
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11836299 106 + 27905053
ACUCUGUC--UGUUUCGCCGCCCCUAAGUCUUCCGUCUUAGGGUCGUAAAUUCGCCGGC-AAAGCA---------CCUAAAGCUAGGCGCGGCGGUGCCAUCAAU--UAGGGUAUUAAUU
((((((..--((...(((((((((((((.(....).))))))((((.........))))-...((.---------((((....)))).)))))))))....))..--))))))....... ( -37.90)
>DroSim_CAF1 17677 106 + 1
ACUCUGUC--UGUUUCGCCGCCCCUAAGUCUUCCGUCUUAGGGUCAUAAAUUCGCCGGC-AAAGCA---------CCUAAAGCUAGGCGCGGCGGUGCCAUCAAU--UAGGGUAUUAAUU
((((((..--((...(((((.(((((((.(....).))))))).)........((((((-..(((.---------......)))..)).))))))))....))..--))))))....... ( -37.50)
>DroEre_CAF1 20128 106 + 1
ACUCUGUC--UGUUUCGCCGCCCCUAAGUCUUCCGUCUUAGGGUCGUAAAUUCGUUGGC-AAAGCA---------CCUAAAGCUAGGCGCGGCGGUGCCAUCAAU--UAGGGUAUUAAUU
((((((..--((...(((((((((((((.(....).))))))((((.........))))-...((.---------((((....)))).)))))))))....))..--))))))....... ( -37.00)
>DroYak_CAF1 20699 106 + 1
ACUCUGUC--UGUUUCGCCGCCCCUAAGUCUUCCGUCUUAGGGUCGUAAAUUCGCUGGC-AAAGCA---------CCUAAAGCUAGGCGCGGCGGUACCAUCAAU--UAGGGUAUUAAUU
((((((..--((..((((((((((((((.(....).)))))))..........(((...-..))).---------((((....)))).)))))))......))..--))))))....... ( -34.80)
>DroMoj_CAF1 19780 106 + 1
AUUCCUUA--GUUUGUGCCGCCAAUAAGUCUUGCGUCUUAUGGCCAUAAAUUUG--GGCUUCAAUA---------UUUUAAGCUAGGCG-GCUUGUGUCAUCAAUGUUGGGGUAUUAAUU
...((..(--(((((((..((((.((((.(....).)))))))))))))))).)--)(((((((((---------((.((((((....)-))))).......)))))))))))....... ( -27.90)
>DroAna_CAF1 15443 117 + 1
GCCCUGUCUCUGGUCUGCCGCCCCUAAGUCUUCCGUCUUAGGGCCGUAAAUUCUCCGCC-AAAGCAGUCAAAGCGGCCAAAGCUAGGCGCGGCGGUACCAUCAAU--UAGGGUAUUAAUU
((((((....((((((((((((((((((.(....).)))))((((((.....((.(...-...).)).....)))))).......)).))))))).)))).....--))))))....... ( -46.60)
>consensus
ACUCUGUC__UGUUUCGCCGCCCCUAAGUCUUCCGUCUUAGGGUCGUAAAUUCGCCGGC_AAAGCA_________CCUAAAGCUAGGCGCGGCGGUGCCAUCAAU__UAGGGUAUUAAUU
((((((....((..((((((((((((((.(....).)))))))..........((((((...((............))...))).))))))))))......))....))))))....... (-23.81 = -24.10 +   0.29)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 11,836,299 – 11,836,405
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.83
Mean single sequence MFE -34.47
Consensus MFE -22.14
Energy contribution -23.06
Covariance contribution 0.92
Combinations/Pair 1.08
Mean z-score -1.94
Structure conservation index 0.64
SVM decision value 0.05
SVM RNA-class probability 0.560124
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11836299 106 - 27905053
AAUUAAUACCCUA--AUUGAUGGCACCGCCGCGCCUAGCUUUAGG---------UGCUUU-GCCGGCGAAUUUACGACCCUAAGACGGAAGACUUAGGGGCGGCGAAACA--GACAGAGU
.((((((......--))))))(((...)))(((((((....))))---------)))(((-((((.((......)).(((((((.(....).))))))).)))))))...--........ ( -36.40)
>DroSim_CAF1 17677 106 - 1
AAUUAAUACCCUA--AUUGAUGGCACCGCCGCGCCUAGCUUUAGG---------UGCUUU-GCCGGCGAAUUUAUGACCCUAAGACGGAAGACUUAGGGGCGGCGAAACA--GACAGAGU
.((((((......--)))))).....(((((((((.(((......---------.)))..-...)))..........(((((((.(....).))))))))))))).....--........ ( -34.30)
>DroEre_CAF1 20128 106 - 1
AAUUAAUACCCUA--AUUGAUGGCACCGCCGCGCCUAGCUUUAGG---------UGCUUU-GCCAACGAAUUUACGACCCUAAGACGGAAGACUUAGGGGCGGCGAAACA--GACAGAGU
.((((((......--))))))(((...)))(((((((....))))---------)))(((-(((..((......)).(((((((.(....).)))))))..))))))...--........ ( -34.80)
>DroYak_CAF1 20699 106 - 1
AAUUAAUACCCUA--AUUGAUGGUACCGCCGCGCCUAGCUUUAGG---------UGCUUU-GCCAGCGAAUUUACGACCCUAAGACGGAAGACUUAGGGGCGGCGAAACA--GACAGAGU
.((((((......--)))))).((..(((((((((((....))))---------)))...-(((..((......))..((((((.(....).)))))))))))))..)).--........ ( -34.30)
>DroMoj_CAF1 19780 106 - 1
AAUUAAUACCCCAACAUUGAUGACACAAGC-CGCCUAGCUUAAAA---------UAUUGAAGCC--CAAAUUUAUGGCCAUAAGACGCAAGACUUAUUGGCGGCACAAAC--UAAGGAAU
..........((....(((......)))((-((((..(((..(((---------(.(((.....--)))))))..))).(((((.(....).))))).))))))......--...))... ( -22.20)
>DroAna_CAF1 15443 117 - 1
AAUUAAUACCCUA--AUUGAUGGUACCGCCGCGCCUAGCUUUGGCCGCUUUGACUGCUUU-GGCGGAGAAUUUACGGCCCUAAGACGGAAGACUUAGGGGCGGCAGACCAGAGACAGGGC
........((((.--.((..((((.(.(((((((((((.(((..(((((...........-))))).))).))).)))((((((.(....).)))))).))))).)))))..)).)))). ( -44.80)
>consensus
AAUUAAUACCCUA__AUUGAUGGCACCGCCGCGCCUAGCUUUAGG_________UGCUUU_GCCGGCGAAUUUACGACCCUAAGACGGAAGACUUAGGGGCGGCGAAACA__GACAGAGU
.((((((........)))))).....((((((((..(((................)))...))..............(((((((.(....).)))))))))))))............... (-22.14 = -23.06 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:20 2006