Locus 4538

Sequence ID 3R_DroMel_CAF1
Location 12,041,286 – 12,041,516
Length 230
Max. P 0.996348
window7409 window7410 window7411

overview

Window 9

Location 12,041,286 – 12,041,401
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.29
Mean single sequence MFE -25.03
Consensus MFE -19.76
Energy contribution -21.36
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -2.92
Structure conservation index 0.79
SVM decision value 2.48
SVM RNA-class probability 0.994445
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12041286 115 - 27905053
UGGAAUAUAUUUUCGGGCUCUGUGCUGCUACCAGCACGAGUCCUGCAACCCCAAGUCCUUUCCUUGGCC----CCA-UCCCAGCUCGACCUAACAUCAAUUCCUUCCACCGACCGCCUCU
.(((((........((((((.((((((....)))))))))))).......(((((.......)))))..----...-.....................)))))................. ( -27.90)
>DroSec_CAF1 12662 115 - 1
UGGAAUAUAUUUUCGGGCUCUGUGCUGCUACCAGCACGAGUCCUGCAACCCCAAGUCCUUUCCUUGGCC----CCA-UCCCAGCUCGACCUAACAUCAAUUCCUUCCACCGACCACCUCU
.(((((........((((((.((((((....)))))))))))).......(((((.......)))))..----...-.....................)))))................. ( -27.90)
>DroEre_CAF1 11865 115 - 1
UGGAAUAUAUUUUCGGUCUCUGUGCUGCUACCAGCACGAGUCCUGCCACCCCAAGUCCUUUCCUUUGCC----CCA-UCCCAGCUCGACCUAACAUCAAUUCCUUCCACCGACCUCCUCU
.(((((........((((...((((((....))))))((((..........((((........))))..----...-.....))))))))........)))))................. ( -22.04)
>DroYak_CAF1 12142 115 - 1
UGGAAUAUAUUUUCGGUCUCUGUGCUGCUACCAGCACGAGUCCUGCAACCCCAAGUCCUUUCCUUGGCC----CCA-UCCCAGCUCGACCUAACAUCAAUUCCUUCCACCGACCCCCUCA
.(((((........((((...((((((....))))))((((.........(((((.......)))))..----...-.....))))))))........)))))................. ( -26.80)
>DroAna_CAF1 11209 104 - 1
UGGAAUAUAUUUC--GGCUCUGUGCUGCUACCAGCAAGAGUCCUCCAACCCCAGGUCCUUU---UUGCCCAUUCCAUUCCAAGCUCAACCUAACAUCAAUUCCUUCUAC-----------
((((((.......--((((((.(((((....)))))))))))...........(((.....---..)))......))))))............................----------- ( -20.50)
>consensus
UGGAAUAUAUUUUCGGGCUCUGUGCUGCUACCAGCACGAGUCCUGCAACCCCAAGUCCUUUCCUUGGCC____CCA_UCCCAGCUCGACCUAACAUCAAUUCCUUCCACCGACC_CCUCU
.(((((........((((((.((((((....)))))))))))).......(((((.......)))))...............................)))))................. (-19.76 = -21.36 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 12,041,326 – 12,041,438
Length 112
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 92.46
Mean single sequence MFE -25.74
Consensus MFE -18.56
Energy contribution -19.96
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.72
SVM decision value 0.11
SVM RNA-class probability 0.587107
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12041326 112 - 27905053
CUAGCUUAAAUGCCAGAAAUUUAAUAAACAAUUCUAGUGGAAUAUAUUUUCGGGCUCUGUGCUGCUACCAGCACGAGUCCUGCAACCCCAAGUCCUUUCCUUGGCC----CCA-UCC
((.((......)).))....................((((...........((((((.((((((....)))))))))))).......(((((.......)))))..----)))-).. ( -28.70)
>DroSec_CAF1 12702 112 - 1
CCAGCUUAAAUGCCAGAAAUUUAAUAAACAAUUCUAGUGGAAUAUAUUUUCGGGCUCUGUGCUGCUACCAGCACGAGUCCUGCAACCCCAAGUCCUUUCCUUGGCC----CCA-UCC
...((......)).......................((((...........((((((.((((((....)))))))))))).......(((((.......)))))..----)))-).. ( -27.60)
>DroEre_CAF1 11905 112 - 1
CCAGCUUAAAUGCCAGAAAUUUAAUAAACAAUUCUAGUGGAAUAUAUUUUCGGUCUCUGUGCUGCUACCAGCACGAGUCCUGCCACCCCAAGUCCUUUCCUUUGCC----CCA-UCC
...((((((((.......))))))............((((((......)))((.(((.((((((....))))))))).))...))).................)).----...-... ( -20.40)
>DroYak_CAF1 12182 112 - 1
CCAGCUUAAAUGCCAGAAAUUUAAUAAACAAUUCUAGUGGAAUAUAUUUUCGGUCUCUGUGCUGCUACCAGCACGAGUCCUGCAACCCCAAGUCCUUUCCUUGGCC----CCA-UCC
...((......)).......................((((...........((.(((.((((((....))))))))).)).......(((((.......)))))..----)))-).. ( -24.30)
>DroAna_CAF1 11238 111 - 1
-UGGCUUAAAUGCCAGAAAUUUAAUAAACAAUUCUAGUGGAAUAUAUUUC--GGCUCUGUGCUGCUACCAGCAAGAGUCCUCCAACCCCAGGUCCUUU---UUGCCCAUUCCAUUCC
-((((......))))....................((((((((.......--((((((.(((((....)))))))))))...........(((.....---..))).)))))))).. ( -27.70)
>consensus
CCAGCUUAAAUGCCAGAAAUUUAAUAAACAAUUCUAGUGGAAUAUAUUUUCGGGCUCUGUGCUGCUACCAGCACGAGUCCUGCAACCCCAAGUCCUUUCCUUGGCC____CCA_UCC
...........(((((..............((((.....))))........((((((.((((((....))))))))))))....................)))))............ (-18.56 = -19.96 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 12,041,401 – 12,041,516
Length 115
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 87.83
Mean single sequence MFE -31.29
Consensus MFE -25.40
Energy contribution -25.64
Covariance contribution 0.24
Combinations/Pair 1.26
Mean z-score -2.85
Structure conservation index 0.81
SVM decision value 2.69
SVM RNA-class probability 0.996348
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12041401 115 + 27905053
CUAGAAUUGUUUAUUAAAUUUCUGGCAUUUAAGCUAGAGCUGUUGUUUGGAAUUGG-GAAAACCGACGCUCUAGACAAAGCAAAGCACAAGAACAAAAUCAAAAUGCAAUCUAGCA
(((((.((((..........((((((......))))))(((.(((((((((.((((-.....))))...))))))))))))........................))))))))).. ( -29.70)
>DroSec_CAF1 12777 115 + 1
CUAGAAUUGUUUAUUAAAUUUCUGGCAUUUAAGCUGGAGCUGUUGUUUGGAAUUGG-GAAAACCGACGCUCUAGACAAAGCAAAGCACAAGAACAGAAUCAAAAUGCAAUCUAGCA
(((((.((((.........(((((........(((...(((.(((((((((.((((-.....))))...))))))))))))..))).......))))).......))))))))).. ( -29.75)
>DroEre_CAF1 11980 116 + 1
CUAGAAUUGUUUAUUAAAUUUCUGGCAUUUAAGCUGGAGCUGUUGUUUGGAAUCGGGGAAAACCGACGCUCUAGACAAAGCAAAGCUCAAGAACAGAAUCAAAAUGCAAUCUAGCA
(((((.((((.........(((((((......))..(((((.(((((((((.((((......))))...))))))))).....))))).....))))).......))))))))).. ( -34.59)
>DroYak_CAF1 12257 116 + 1
CUAGAAUUGUUUAUUAAAUUUCUGGCAUUUAAGCUGGAGCUGUUGUUUGGAAUUGGGGAAAACCGACGCUCUAAACAAAGCAAAGCACAAGAACAGAAUCAAAGUGCAAUCUAGCA
((((((.............)))))).......(((((((((.(((((((((.((((......))))...))))))))))))...((((..((......))...))))..)))))). ( -32.62)
>DroAna_CAF1 11313 113 + 1
CUAGAAUUGUUUAUUAAAUUUCUGGCAUUUAAGCCA--GCUUGACGCUAGAAUUGGUGAAAACCAAAGCACCGGACAGAGCGAACCAGGGGAAUGGAAUCAAAUUGCAAUCUGGG-
(((((.((((...........(((((......))))--).((((((((....((((((..........))))))....))))..(((......)))..))))...))))))))).- ( -29.80)
>consensus
CUAGAAUUGUUUAUUAAAUUUCUGGCAUUUAAGCUGGAGCUGUUGUUUGGAAUUGG_GAAAACCGACGCUCUAGACAAAGCAAAGCACAAGAACAGAAUCAAAAUGCAAUCUAGCA
(((((.((((..........((((((......))))))(((.(((((((((.((((......))))...))))))))))))........................))))))))).. (-25.40 = -25.64 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:47 2006