Locus 5728

Sequence ID 3L_DroMel_CAF1
Location 15,604,353 – 15,604,506
Length 153
Max. P 0.935853
window9073 window9074

overview

Window 3

Location 15,604,353 – 15,604,466
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.19
Mean single sequence MFE -28.26
Consensus MFE -23.94
Energy contribution -25.10
Covariance contribution 1.16
Combinations/Pair 1.06
Mean z-score -1.72
Structure conservation index 0.85
SVM decision value 1.25
SVM RNA-class probability 0.935853
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15604353 113 - 23771897
UUUAAAUUUAUUCAACAAGGAGCGGAAGCGAUCAAAAACGCCUCAUUAGGUCGCUUCUGGUCAGUUUCGGUUCCAGUUUUCGA-------UUCUUUUCGUAUAAUAAAAUACGAAAUAGA
..................(((((.((((((((((.((.(((((....))).)).)).))))).))))).))))).........-------.(((((((((((......)))))))).))) ( -32.00)
>DroSec_CAF1 27472 113 - 1
UUUAAAUUUAUUCAACAAGUAGCGGAAGCGAUCAAAAACGCCUCAUUAGGUCGCUGCUGGUCAGGUUGGGUUCCAGUUUUCGA-------UUCUUUUCGUAUAAUAAAAUACGAAAUAGA
...(((((.(((((((.....((....))(((((..(.(((((....))).)).)..)))))..)))))))...)))))....-------.(((((((((((......)))))))).))) ( -26.90)
>DroSim_CAF1 27385 113 - 1
UUUAAAUUUAUUCAACAAGGAGCGGAAGCGAUCAAAAACGCCUCAUUAGGUCGGUGCUGGUCAGUUUCGGUUCCAGUUUACGA-------UUCUUUUCGUAUAAUAAAAUACGAAAUAGA
..................(((((.((((((((((....(((((....))).))....))))).))))).))))).........-------.(((((((((((......)))))))).))) ( -32.00)
>DroEre_CAF1 27371 120 - 1
UUUAAAUUUAUUCAACACGAAGCGGAAGCGAUCAAAAACGCCUCAUUAGGCCGCUGCUGGUCAGUUUUGGUUCCAGUUUUCGGUUUCCAGUUCUUUUCGGCUAAUAAAAUACGAAAUAGA
..........(((.....((.((....))..))......((((....))))....(((((..((..((((..((.......))...))))..))..)))))...........)))..... ( -24.80)
>DroYak_CAF1 29506 113 - 1
UUUAAAUUUAUUCAACAAGGAGCGGAAGCGAUCAAAAACGGCUCAUUAGCUCGCUGCUGGUCAGUUUCAGUUCCAGUUUUCGG-------UUCUUUUCGUCCAAUAAAAAACGAAAUAGA
..................(((((.((((((((((..(.(((((....))).)).)..))))).))))).))))).........-------.(((((((((..........)))))).))) ( -25.60)
>consensus
UUUAAAUUUAUUCAACAAGGAGCGGAAGCGAUCAAAAACGCCUCAUUAGGUCGCUGCUGGUCAGUUUCGGUUCCAGUUUUCGA_______UUCUUUUCGUAUAAUAAAAUACGAAAUAGA
..................(((((.((((((((((..(.(((((....))).)).)..))))).))))).))))).................(((((((((((......)))))))).))) (-23.94 = -25.10 +   1.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,604,386 – 15,604,506
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.92
Mean single sequence MFE -29.16
Consensus MFE -24.12
Energy contribution -24.68
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.31
Structure conservation index 0.83
SVM decision value 0.04
SVM RNA-class probability 0.551789
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15604386 120 - 23771897
ACAUUAAGACGAUUUGUUCAAUAUUUGACCCUAAUGAGUAUUUAAAUUUAUUCAACAAGGAGCGGAAGCGAUCAAAAACGCCUCAUUAGGUCGCUUCUGGUCAGUUUCGGUUCCAGUUUU
.....(((((...(((((((.....)))......((((((........))))))))))(((((.((((((((((.((.(((((....))).)).)).))))).))))).))))).))))) ( -30.70)
>DroSec_CAF1 27505 120 - 1
ACAUUAAGACGAUUUGUUCAAUAUUUUCCCUUAAUGAGUAUUUAAAUUUAUUCAACAAGUAGCGGAAGCGAUCAAAAACGCCUCAUUAGGUCGCUGCUGGUCAGGUUGGGUUCCAGUUUU
.(((((((..((..(((...)))..))..))))))).......(((((.(((((((.....((....))(((((..(.(((((....))).)).)..)))))..)))))))...))))). ( -24.40)
>DroSim_CAF1 27418 120 - 1
ACAUUAAGACGAUUUGUUCAAUAUUUGCCCCUAAUGAGUAUUUAAAUUUAUUCAACAAGGAGCGGAAGCGAUCAAAAACGCCUCAUUAGGUCGGUGCUGGUCAGUUUCGGUUCCAGUUUA
......((((........................((((((........))))))....(((((.((((((((((....(((((....))).))....))))).))))).))))).)))). ( -30.20)
>DroEre_CAF1 27411 120 - 1
ACAUUAAGACGAUUCGUUCAAUAUUCGGAGCUAAUGAGUAUUUAAAUUUAUUCAACACGAAGCGGAAGCGAUCAAAAACGCCUCAUUAGGCCGCUGCUGGUCAGUUUUGGUUCCAGUUUU
.....(((((((.....)).......((((((((((((((........)))))).......((....))(((((.....((((....))))......)))))....)))))))).))))) ( -29.60)
>DroYak_CAF1 29539 120 - 1
ACAUUAAGACGAUUUGUUCAAUAUUUGGCUCUAAUGAGUAUUUAAAUUUAUUCAACAAGGAGCGGAAGCGAUCAAAAACGGCUCAUUAGCUCGCUGCUGGUCAGUUUCAGUUCCAGUUUU
.....(((((...(((((.((((..(.((((....))))......)..)))).)))))(((((.((((((((((..(.(((((....))).)).)..))))).))))).))))).))))) ( -30.90)
>consensus
ACAUUAAGACGAUUUGUUCAAUAUUUGCCCCUAAUGAGUAUUUAAAUUUAUUCAACAAGGAGCGGAAGCGAUCAAAAACGCCUCAUUAGGUCGCUGCUGGUCAGUUUCGGUUCCAGUUUU
.....(((((........................((((((........))))))....(((((.((((((((((..(.(((((....))).)).)..))))).))))).))))).))))) (-24.12 = -24.68 +   0.56)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:58 2006