Locus 1718

Sequence ID 3R_DroMel_CAF1
Location 4,936,585 – 4,936,723
Length 138
Max. P 0.704377
window2828 window2829

overview

Window 8

Location 4,936,585 – 4,936,697
Length 112
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 88.21
Mean single sequence MFE -22.87
Consensus MFE -16.22
Energy contribution -17.34
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -2.03
Structure conservation index 0.71
SVM decision value 0.36
SVM RNA-class probability 0.704377
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4936585 112 + 27905053
UGUCGAGCUGCCCUGAAACGCACCCAGCUAAAACGGAAACAACACACUGAAUUUUCACAACACUGAAGGAAAAGUGCGAAAAGUAAAUAGAUAAAUUUCUAAGUUUGAAAUA
..(((((((.........(((((.(((.......(....)......)))..((((((......))))))....))))).........((((......))))))))))).... ( -20.92)
>DroSec_CAF1 44020 112 + 1
UGUCAAGCUGCCCUGAAACGCACCCAGCUAAAACGGAAACAACGCACUGAAUUUUCACAACACUGAAGGAAAAGUGUGAAAAGUAAAUAGAUACAACAUUCAGUUUGAAAUA
..((((((((...((....((.....))....(((....)..((((((...((((((......))))))...))))))....))............))..)))))))).... ( -22.80)
>DroSim_CAF1 44154 112 + 1
UGUCAAGCUGCCCUGAAACGCACCCAGCUAAAACGGAAACAACGCACUGAAUUUUCACAACACUGAAGGAAAAGUGUGAAAAGUAAAUAGAUACAAAGUUCAGUUUGAAAUA
..((((((((..((............(((.....(....)..((((((...((((((......))))))...))))))...)))............))..)))))))).... ( -24.75)
>DroEre_CAF1 44296 112 + 1
UGUCGAGCUGCCCUGAAACGCACCCAGCUAAAACGGAAACAACGCACUGAAUAUUCACAACACUGAAGGAAAAGUGUGAACAAAAAAUAUAGUUAUAUUUUAGUUGGCAAUA
........(((........))).((((((((((.(....)..((((((.....((((......)))).....))))))...................))))))))))..... ( -24.10)
>DroYak_CAF1 44936 111 + 1
UGUCAAGCUGCCCCGAAACGCACCCAGCUAAAACGGAAACAACGCACUGAAUAUUCACCACACUGAAGGAAAAGUGUG-ACAAAAACUAUCAAUAUUUUGUAGUUUCAAAUA
((((.(((((...((...))....))))).....(....)...(((((.....((((......)))).....))))))-))).((((((.(((....)))))))))...... ( -21.80)
>consensus
UGUCAAGCUGCCCUGAAACGCACCCAGCUAAAACGGAAACAACGCACUGAAUUUUCACAACACUGAAGGAAAAGUGUGAAAAGUAAAUAGAUACAUAUUUCAGUUUGAAAUA
..((((((((.........((.....))......(....)..((((((...((((((......))))))...))))))......................)))))))).... (-16.22 = -17.34 +   1.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,936,619 – 4,936,723
Length 104
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 76.12
Mean single sequence MFE -16.66
Consensus MFE -10.36
Energy contribution -10.96
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.62
SVM decision value 0.12
SVM RNA-class probability 0.594059
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4936619 104 + 27905053
GGAAACAACACACUGAAUUUUCACAACACUGAAGGAAAAGUGCGAAAAGUAAAUAGAUAAAUUUCUAAGUUUGAAAUAGUACUCUAA-AAACGAGAAACCAGAAU-------------
((((((..(.((((...((((((......))))))...)))).).........((((......)))).)))).........(((...-....)))...)).....------------- ( -15.00)
>DroSec_CAF1 44054 104 + 1
GGAAACAACGCACUGAAUUUUCACAACACUGAAGGAAAAGUGUGAAAAGUAAAUAGAUACAACAUUCAGUUUGAAAUAUUACUCUUA-AAACAGGAAACCAGAAG-------------
(....)..((.(((((((((((((...(((........))))))))))(((......)))....)))))).))..............-.....(....)......------------- ( -15.80)
>DroSim_CAF1 44188 104 + 1
GGAAACAACGCACUGAAUUUUCACAACACUGAAGGAAAAGUGUGAAAAGUAAAUAGAUACAAAGUUCAGUUUGAAAUAUUACUCUUA-AAACAGGAAACCAGAUG-------------
(....)..((.((((((((((....(((((........))))).....(((......))))))))))))).))..............-.....(....)......------------- ( -17.60)
>DroEre_CAF1 44330 102 + 1
GGAAACAACGCACUGAAUAUUCACAACACUGAAGGAAAAGUGUGAACAAAAAAUAUAGUUAUAUUUUAGUUGGCAAUAUAACUCCUA-AAACUAGAA---------------AACUCA
(((.....((((((.....((((......)))).....)))))).............((((((((.........)))))))))))..-.........---------------...... ( -17.00)
>DroYak_CAF1 44970 117 + 1
GGAAACAACGCACUGAAUAUUCACCACACUGAAGGAAAAGUGUG-ACAAAAACUAUCAAUAUUUUGUAGUUUCAAAUAUUACUCUUACAAACAAGAAACUGGAACUUUAAUUAACUAA
.(((((..((((((.....((((......)))).....))))))-((((((..........)))))).))))).........((((......))))...................... ( -17.90)
>consensus
GGAAACAACGCACUGAAUUUUCACAACACUGAAGGAAAAGUGUGAAAAGUAAAUAGAUACAUAUUUCAGUUUGAAAUAUUACUCUUA_AAACAAGAAACCAGAAG_____________
(....)..((((((...((((((......))))))...)))))).......................................................................... (-10.36 = -10.96 +   0.60)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:38 2006