Locus 1648

Sequence ID 3R_DroMel_CAF1
Location 4,782,096 – 4,782,270
Length 174
Max. P 0.838067
window2719 window2720

overview

Window 9

Location 4,782,096 – 4,782,215
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.09
Mean single sequence MFE -28.70
Consensus MFE -23.75
Energy contribution -24.42
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.83
SVM decision value 0.70
SVM RNA-class probability 0.826709
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4782096 119 - 27905053
CGGUGGGCAUUCAAAUGCAAACGGACCAGCACAACACCGUUACAAUGUGGCUCAUUAAAA-GCAAAAUGCUCAUGUACCAGGCACAAUAAAACGCCGGCCAAACAAAAAUGUGUAAAAUC
.(((.(((...........(((((............)))))....((((.((...((..(-((.....)))..))....)).)))).......))).))).................... ( -24.80)
>DroSec_CAF1 17401 119 - 1
CGGUGGGCAUUCAAAUGCAAACGGACCAGCACAACACCGUUACAAUGUGGCUCAUUAAAA-GCAAAAUGCUCAUGUAGCAGCCACAAUAAAACGCCGGCCAAACAAAAAUGUGUAAAAUC
.(((.(((...........(((((............)))))....((((((((..((..(-((.....)))..))..).))))))).......))).))).................... ( -29.50)
>DroSim_CAF1 12823 119 - 1
CGGUGGGCAUUCAAAUGCAAACGGACCAGCACAACACCGUUACAAUGUGGCUCAUUAAAA-GCAAAAUGCUCAUGUAGCAGCCACAAUAAAACGCCGGCCAAACAAAAAUGUGUAAAAUC
.(((.(((...........(((((............)))))....((((((((..((..(-((.....)))..))..).))))))).......))).))).................... ( -29.50)
>DroEre_CAF1 17605 119 - 1
UGGUGGGCAUUCAAAUGCAAACGGACCAGCACAACACCGUUACAAUGUGGCUCAUUAAAA-GCAAAAUGCUCAUGUAGCAGCCACAGUAAAACGCCGGCCAAACAAAAAUGUGUAAAAUC
((((.(((...........(((((............)))))....((((((((..((..(-((.....)))..))..).))))))).......))).))))................... ( -29.90)
>DroYak_CAF1 17793 119 - 1
CGGUGGGCAUUCAAAUGCAAACGGACCAGCACAACACCGUUACAAUGUGGCUCAUUAAAA-GCAAAAUGCUCAUGUAGCAGCCACAAUAAAACGCCGGCCAAACAAAAAUGUGUAAAAUC
.(((.(((...........(((((............)))))....((((((((..((..(-((.....)))..))..).))))))).......))).))).................... ( -29.50)
>DroAna_CAF1 17255 120 - 1
CGGUGGGCAUUCAAAUGCAAACGGAGCAGCGGACCACCGUUACAAUGUGGCUCAUUAAAACACAAACUGCUCAUGUAGCAGCAACAAUAAAACGCCGGGCAAACAGAAAUGUGUAAAAUC
(((((.((((....))))..((((((((((((....)))......((((...........))))..)))))).)))................))))).....(((....)))........ ( -29.00)
>consensus
CGGUGGGCAUUCAAAUGCAAACGGACCAGCACAACACCGUUACAAUGUGGCUCAUUAAAA_GCAAAAUGCUCAUGUAGCAGCCACAAUAAAACGCCGGCCAAACAAAAAUGUGUAAAAUC
.(((.(((...........(((((............)))))....(((((((.........((.....)).........))))))).......))).))).................... (-23.75 = -24.42 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 4,782,175 – 4,782,270
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.47
Mean single sequence MFE -20.59
Consensus MFE -12.37
Energy contribution -12.48
Covariance contribution 0.11
Combinations/Pair 1.17
Mean z-score -1.79
Structure conservation index 0.60
SVM decision value 0.74
SVM RNA-class probability 0.838067
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4782175 95 + 27905053
ACGGUGUUGUGCUGGUCCGUUUGCAUUUGAAUGCCCACCGUCC--CACUCACACAC--------------ACACACACAGACU--UGG-----AAGACCCCAACACCAUCAC-ACA-AAU
..(((((((((.(((..((...((((....))))....))..)--))..)))....--------------.............--.((-----......)))))))).....-...-... ( -20.10)
>DroSec_CAF1 17480 96 + 1
ACGGUGUUGUGCUGGUCCGUUUGCAUUUGAAUGCCCACCGUCC--CACUCACACAC--------------ACACACACCCACUU-UGG-----AAGACUCCAACACCAUCAC-ACA-AAU
..(((((((((.(((..((...((((....))))....))..)--))..)))....--------------..............-.((-----(....))))))))).....-...-... ( -21.30)
>DroSim_CAF1 12902 94 + 1
ACGGUGUUGUGCUGGUCCGUUUGCAUUUGAAUGCCCACCGUCC--CACUCACACAC----------------ACACACCCACUU-CGG-----AAGACUCCAACACCAUCAC-ACA-AAU
..(((((((((.(((..((...((((....))))....))..)--))..)))....----------------............-.((-----(....))))))))).....-...-... ( -21.60)
>DroEre_CAF1 17684 113 + 1
ACGGUGUUGUGCUGGUCCGUUUGCAUUUGAAUGCCCACCAUCUCCCACUCACACACACUCACGCUCACACUCACACACCCACUUGUGG-----AAGACCCCAACACCAUCAC-ACG-UUU
..(((((((.(..((((.((..((((....))))..))................................((.((((......)))))-----).)))))))))))).....-...-... ( -21.80)
>DroYak_CAF1 17872 105 + 1
ACGGUGUUGUGCUGGUCCGUUUGCAUUUGAAUGCCCACCGUCCCACACUAACGCACACUC------ACACACACACACCCACUU--GG-----AAGACCCCAACACCAUCAC-ACG-AUU
..(((((((((((((..((...((((....))))....))..))).......))))....------..................--((-----......)))))))).....-...-... ( -21.41)
>DroAna_CAF1 17335 101 + 1
ACGGUGGUCCGCUGCUCCGUUUGCAUUUGAAUGCCCACCGCC---AACAUACCGCC----------------ACAGAUACAUUUUCAGAUACAGAUACACGCACACCAUCGCUACGCUAU
.(((((((..((((....(((((.(((((((.((.....)).---.......(...----------------...).......))))))).))))).)).))..)))))))......... ( -17.30)
>consensus
ACGGUGUUGUGCUGGUCCGUUUGCAUUUGAAUGCCCACCGUCC__CACUCACACAC______________ACACACACCCACUU_UGG_____AAGACCCCAACACCAUCAC_ACA_AAU
..(((((((....((((.((..((((....))))..))...........................................(....)........)))).)))))))............. (-12.37 = -12.48 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:51 2006