Locus 2699

Sequence ID 3R_DroMel_CAF1
Location 7,265,001 – 7,265,175
Length 174
Max. P 0.783196
window4384 window4385

overview

Window 4

Location 7,265,001 – 7,265,104
Length 103
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 76.05
Mean single sequence MFE -19.46
Consensus MFE -3.73
Energy contribution -4.33
Covariance contribution 0.60
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.19
SVM decision value 0.56
SVM RNA-class probability 0.783196
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7265001 103 - 27905053
A-GAGAAAGCGAAAAAUGAAAUUCAAAACUGACCAUAUUUUAUCAAAGCUCAAUUUGUAUUAAAUUUCGGAAGCCAUA-------CUUUUCAA-GUAAGGUGCCUUCAUCCC
.-..(((.((..................((((....((((...((((......))))....)))).))))..(((.((-------((.....)-))).))))).)))..... ( -14.10)
>DroSec_CAF1 1390 103 - 1
A-GGGAAACCGAAAAAUUAAAUUCAAAACUGACCAUGUUUUAUCAAAUCUCAAUUUGUAUUUCAUUUCGGAAGCCAUA-------CUCUUCAA-GUAAGGUGCCUUCAUCCC
.-((((..((((((..........(((((.......)))))..(((((....))))).......))))))..(((.((-------((.....)-))).))).......)))) ( -19.90)
>DroSim_CAF1 3279 103 - 1
A-GGGAAACCGAAAAAUGAAAUUCAAAACUGACCAUGUUUUAUCAAAGCUCGAUUUGUAUUUCAUUUCGGAAGCCAUA-------CUUUUCAA-GUAAGGUGCCUUCAUCCC
.-((((..(((((..(((((((.((((..((((..((......))..).))).)))).))))))))))))..(((.((-------((.....)-))).))).......)))) ( -23.60)
>DroEre_CAF1 1379 79 - 1
A-UGGCAACCGAAAAAUUAAAUUUGAAA-------------------------AUUGUAUUUCAUUUCGGAAGCCAUA-------AUUUUCAAAGUAUAGAGGGUUCAUCCC
(-((((..((((((.........(((((-------------------------......)))))))))))..))))).-------................(((.....))) ( -17.60)
>DroYak_CAF1 1414 107 - 1
AAAGGCAACCGAAAAAUGAAAUUCGAAACUGACCAUGUUUUAUCAAAGCUCAAUUUGUAUUUCAUGUCGGAAGCCAUACUUCAUACUUUUCAAA-----GAUGGUUCAUCCC
...(((..((((...(((((((.((((..((((..((......))..).))).)))).))))))).))))..))).....((((.(((....))-----)))))........ ( -22.10)
>consensus
A_GGGAAACCGAAAAAUGAAAUUCAAAACUGACCAUGUUUUAUCAAAGCUCAAUUUGUAUUUCAUUUCGGAAGCCAUA_______CUUUUCAA_GUAAGGUGCCUUCAUCCC
...((...((((((....((((.((((..........................)))).))))..))))))...))..................................... ( -3.73 =  -4.33 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,265,073 – 7,265,175
Length 102
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 76.17
Mean single sequence MFE -15.34
Consensus MFE -1.46
Energy contribution -3.06
Covariance contribution 1.60
Combinations/Pair 1.33
Mean z-score -1.34
Structure conservation index 0.10
SVM decision value -0.04
SVM RNA-class probability 0.510957
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7265073 102 - 27905053
UCUGAUUGAAGCCAGCAGACAGCUUGCUGUUGAGAAGGAAUCAGACAAGUUGAAUAGUAAAAUUAUUAUCAA-GAGAAAGCGAAAAAUGAAAUUCAAAACUGA
(((((((....(((((((.(.....))))))).)....)))))))....((((.(((((....)))))))))-.............................. ( -16.30)
>DroSec_CAF1 1462 102 - 1
UCUGAUUGCACGCAGCAGACAGCAUGUAGUUGAAAAGGAAUCAAAAAAGUUGAAUAUUAAAAUUAUUCACAA-GGGAAACCGAAAAAUUAAAUUCAAAACUGA
.(((.((((.....)))).)))....(((((......((((.......((.(((((.......)))))))..-((....))..........))))..))))). ( -17.50)
>DroSim_CAF1 3351 96 - 1
------UACAUGCAGCAGACAGCAUGUAGUUGAAAAGGAAUCAAAAAAGUAGAAUAUUAAAAUUAUUCACAA-GGGAAACCGAAAAAUGAAAUUCAAAACUGA
------(((((((........))))))).(((((..............((.(((((.......)))))))..-((....))...........)))))...... ( -19.50)
>DroEre_CAF1 1431 90 - 1
UCUGAUUGAAUGCAGCAUACAGCUUGGUGUA--------ACAUGCCAAGAUGAAUAUUAAAAUUAUUGACAA-UGGCAACCGAAAAAUUAAAUUUGAAA----
((.((((...((((.((.......)).))))--------...(((((...(.((((.......)))).)...-)))))............)))).))..---- ( -12.30)
>DroYak_CAF1 1489 103 - 1
UCUGAUUGAAUGCAGUAUACAACAUGAUGUAGAGACGGAAUCAGACAAACUGAAUAUUAAAAUAAUUCACAAAAGGCAACCGAAAAAUGAAAUUCGAAACUGA
............((((.((((......))))....((((.((((.....))))............((((.....((...))......)))).))))..)))). ( -11.10)
>consensus
UCUGAUUGAAUGCAGCAGACAGCAUGUUGUUGAAAAGGAAUCAGACAAGUUGAAUAUUAAAAUUAUUCACAA_GGGAAACCGAAAAAUGAAAUUCAAAACUGA
..........(((((((.......)))))))..........................................((....))...................... ( -1.46 =  -3.06 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:37 2006