Locus 1399

Sequence ID 3R_DroMel_CAF1
Location 4,082,057 – 4,082,197
Length 140
Max. P 0.807922
window2309 window2310

overview

Window 9

Location 4,082,057 – 4,082,157
Length 100
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 75.64
Mean single sequence MFE -26.63
Consensus MFE -17.07
Energy contribution -18.73
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.64
SVM decision value 0.43
SVM RNA-class probability 0.733133
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4082057 100 - 27905053
UAAUGGCAAGCCAUUAUGUGCGAGUGGCACAUGUUGCCAAUUGUGGUAAUCGUUUUAGAUGAUACAC--AGGCAAAAAUUAUGG-------C----UAAAACUAUCUUAAAGU-------
........(((((((((((((.....)))))))(((((...((((...((((((...)))))).)))--)))))).....))))-------)----)................------- ( -27.90)
>DroEre_CAF1 10830 120 - 1
UAAUGGCAAGCCAUUAUCUGCGAGUGGCACAUGUUGCCAAUUCUGGUAAUCGUUUUAGAUGAUACACUUGGACAAAAAUUAUGAACUAUGGCCCAGUAAAAGCAUAUUAAAAUACCUCCU
((((((....))))))..(((.(.(((..((((((((((....))))))).(((..((........))..)))..............)))..))).)....)))................ ( -22.20)
>DroYak_CAF1 7717 101 - 1
UAAUGGCAAGCCAUUAUGUGCGAGUGGCACAUGUUGCCAAUUGUGGUAAUCGUUUUAGAUGAUACACUUGGCCAAAAAUGACGGACUGUGGCCCAGUUAAA-------------------
....(((.((((..(((((((.....)))))))..(((((.((((...(((......)))..)))).)))))..........)).))...)))........------------------- ( -29.80)
>consensus
UAAUGGCAAGCCAUUAUGUGCGAGUGGCACAUGUUGCCAAUUGUGGUAAUCGUUUUAGAUGAUACACUUGGACAAAAAUUAUGGACU_UGGCCCAGUAAAA__AU_UUAAA_U_______
.(((((....)))))((((((.....)))))).(((((((.((((...(((......)))..)))).)))).)))............................................. (-17.07 = -18.73 +   1.67)

alignment

Postscript

secondary structure

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dotplot

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Window 0

Location 4,082,079 – 4,082,197
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -35.53
Consensus MFE -31.27
Energy contribution -31.60
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.88
SVM decision value 0.64
SVM RNA-class probability 0.807922
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4082079 118 - 27905053
AUAUUCAUGGAGCAGCAUUUGAAACCGAUUCUAAGGCGGCUAAUGGCAAGCCAUUAUGUGCGAGUGGCACAUGUUGCCAAUUGUGGUAAUCGUUUUAGAUGAUACAC--AGGCAAAAAUU
...........((..((((((((((.(((((((.((((((.(((((....)))))((((((.....)))))))))))).....))).))))))))))))))......--..))....... ( -34.10)
>DroEre_CAF1 10870 120 - 1
AUAUUCAUGGAGCAGCAUUUGAAACCGAUUCUAAGGCGGCUAAUGGCAAGCCAUUAUCUGCGAGUGGCACAUGUUGCCAAUUCUGGUAAUCGUUUUAGAUGAUACACUUGGACAAAAAUU
...((((.(......((((((((((.(((((((..((((.((((((....)))))).))))((((((((.....)))).))))))).)))))))))))))).....).))))........ ( -35.70)
>DroYak_CAF1 7738 120 - 1
ACAUUCAUGGAGCAGCAUUUGAAACCGAUUCUAAGGCGGCUAAUGGCAAGCCAUUAUGUGCGAGUGGCACAUGUUGCCAAUUGUGGUAAUCGUUUUAGAUGAUACACUUGGCCAAAAAUG
.((((..(((..(((((((((((((.(((((((.((((((.(((((....)))))((((((.....)))))))))))).....))).))))))))))))))......))).)))..)))) ( -36.80)
>consensus
AUAUUCAUGGAGCAGCAUUUGAAACCGAUUCUAAGGCGGCUAAUGGCAAGCCAUUAUGUGCGAGUGGCACAUGUUGCCAAUUGUGGUAAUCGUUUUAGAUGAUACACUUGGACAAAAAUU
...............((((((((((.(((((((.((((((.(((((....)))))((((((.....)))))))))))).....))).))))))))))))))................... (-31.27 = -31.60 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:11 2006