Locus 3530

Sequence ID X_DroMel_CAF1
Location 9,451,018 – 9,451,174
Length 156
Max. P 0.680519
window5778 window5779 window5780

overview

Window 8

Location 9,451,018 – 9,451,136
Length 118
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 79.98
Mean single sequence MFE -37.50
Consensus MFE -21.83
Energy contribution -22.83
Covariance contribution 1.00
Combinations/Pair 1.12
Mean z-score -1.85
Structure conservation index 0.58
SVM decision value 0.26
SVM RNA-class probability 0.655738
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9451018 118 + 22224390
GCCCGUGUGCGCCUGCCACACCUUAAUGGUGUGGUCAUAACCACCGGUGGCCAGGAUCAGCUGCUGUUGGUCCCCCAUCCUGUGAUUGCACAGAUUAAUUGACAAUUUCCGCGUUUUU
.....(((((....((((((((.....))))))))......(((.(((((...((((((((....)))))))).))).)).)))...))))).......................... ( -41.20)
>DroPse_CAF1 6853 103 + 1
GCCGGUAUGGGCUUGCCACACCUUGAUUGUGUGAUCGUAUCCACCGGUGGCCAGUAUUAG------UUGGUCCCCCAU--------UGCUUCCAUUAAUCGUCAAUUAG-GCGAUUCU
((((((..(((..((.(((((.......)))))..))..)))))))))((((((......------))))))......--------..........(((((((.....)-)))))).. ( -29.00)
>DroSec_CAF1 4643 118 + 1
GCCCGUGUGCGCCUGCCACACCUUUAUGGUGUGGUCAUAACCACCGGUGGCCAGGAUCAGCUGCUGUUGGUCCCCCAUCCUGUGACUGCACGGAUUAAUUGACAAUUUCCGCGUUUUU
...(((((((....((((((((.....))))))))......(((.(((((...((((((((....)))))))).))).)).)))...))))(((.............))))))..... ( -44.02)
>DroEre_CAF1 4884 116 + 1
GCCCGUGUGCGCUUGCCACACCUUUAUGGUGUGGUCAUAGCCACCGGUGGCCAGGAUCAGCUGUUGUUGGUCCCCCAUCCUGUGAU--UACGGAUUAAUUGACAAUUUUCGCUUUUUU
..(((((...(((.((((((((.....))))))))...)))(((.(((((...((((((((....)))))))).))).)).)))..--)))))......................... ( -43.20)
>DroYak_CAF1 4634 116 + 1
GCCCGUGUGCGCCUGCCACACCUUUAUUGUGUGGUCAUAGCCGCCGGUGGCCAGGAUCAGCUGCUGUUGGUCCCCCAUCCUGUGUU--CACGGAUUAAUUGACAAUUUCCGCUUUUUU
..(((((.((((..(((((((.......)))))))..........(((((...((((((((....)))))))).)))))..)))).--)))))......................... ( -38.90)
>DroPer_CAF1 4974 103 + 1
GCCGGUAUGGGCUUGCCAAACCUUGAUUGUGUGAUCGUAUCCACCGGUGGCCAGUAUUAG------UUGGUCCCCCAU--------UGCUUCCAUUAAUCGUCAAUUAG-GCGAUUCU
...((.(((((...(((((......((((.((.((((.......)))).)))))).....------)))))..)))))--------.....))...(((((((.....)-)))))).. ( -28.70)
>consensus
GCCCGUGUGCGCCUGCCACACCUUUAUGGUGUGGUCAUAACCACCGGUGGCCAGGAUCAGCUGCUGUUGGUCCCCCAUCCUGUGAUUGCACGGAUUAAUUGACAAUUUCCGCGUUUUU
(((.(((.((....(((((((.......)))))))....))))).)))((...((((((((....)))))))).)).......................................... (-21.83 = -22.83 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,451,018 – 9,451,136
Length 118
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 79.98
Mean single sequence MFE -35.67
Consensus MFE -21.96
Energy contribution -22.85
Covariance contribution 0.89
Combinations/Pair 1.24
Mean z-score -1.69
Structure conservation index 0.62
SVM decision value 0.27
SVM RNA-class probability 0.660479
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9451018 118 - 22224390
AAAAACGCGGAAAUUGUCAAUUAAUCUGUGCAAUCACAGGAUGGGGGACCAACAGCAGCUGAUCCUGGCCACCGGUGGUUAUGACCACACCAUUAAGGUGUGGCAGGCGCACACGGGC
.....((((((..(((.....)))))))))......((((((((....))..(((...)))))))))....(((((((((.((.(((((((.....)))))))))))).))).))).. ( -41.40)
>DroPse_CAF1 6853 103 - 1
AGAAUCGC-CUAAUUGACGAUUAAUGGAAGCA--------AUGGGGGACCAA------CUAAUACUGGCCACCGGUGGAUACGAUCACACAAUCAAGGUGUGGCAAGCCCAUACCGGC
......((-(........((((....((....--------.(((....))).------....((((((...)))))).......))....))))..(((((((.....)))))))))) ( -27.80)
>DroSec_CAF1 4643 118 - 1
AAAAACGCGGAAAUUGUCAAUUAAUCCGUGCAGUCACAGGAUGGGGGACCAACAGCAGCUGAUCCUGGCCACCGGUGGUUAUGACCACACCAUAAAGGUGUGGCAGGCGCACACGGGC
.....((((((..(((.....)))))))))......((((((((....))..(((...)))))))))....(((((((((.((.(((((((.....)))))))))))).))).))).. ( -43.60)
>DroEre_CAF1 4884 116 - 1
AAAAAAGCGAAAAUUGUCAAUUAAUCCGUA--AUCACAGGAUGGGGGACCAACAACAGCUGAUCCUGGCCACCGGUGGCUAUGACCACACCAUAAAGGUGUGGCAAGCGCACACGGGC
......((((......))............--....((((((((....))..((.....))))))))))..(((((((((.((.(((((((.....)))))))))))).))).))).. ( -39.20)
>DroYak_CAF1 4634 116 - 1
AAAAAAGCGGAAAUUGUCAAUUAAUCCGUG--AACACAGGAUGGGGGACCAACAGCAGCUGAUCCUGGCCACCGGCGGCUAUGACCACACAAUAAAGGUGUGGCAGGCGCACACGGGC
......(((((..(((.....)))))))).--....((((((((....))..(((...)))))))))(((....(((.((..(.((((((.......))))))))).))).....))) ( -38.10)
>DroPer_CAF1 4974 103 - 1
AGAAUCGC-CUAAUUGACGAUUAAUGGAAGCA--------AUGGGGGACCAA------CUAAUACUGGCCACCGGUGGAUACGAUCACACAAUCAAGGUUUGGCAAGCCCAUACCGGC
......((-(........((((....((....--------.(((....))).------....((((((...)))))).......))....))))..(((.(((.....))).)))))) ( -23.90)
>consensus
AAAAACGCGGAAAUUGUCAAUUAAUCCGUGCAAUCACAGGAUGGGGGACCAACAGCAGCUGAUCCUGGCCACCGGUGGAUAUGACCACACAAUAAAGGUGUGGCAAGCGCACACGGGC
........................((((((...........(((....)))......(((.....((((((....)))))).(.((((((.......))))))).)))...)))))). (-21.96 = -22.85 +   0.89)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,451,058 – 9,451,174
Length 116
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 79.98
Mean single sequence MFE -30.72
Consensus MFE -19.37
Energy contribution -20.58
Covariance contribution 1.21
Combinations/Pair 1.19
Mean z-score -1.65
Structure conservation index 0.63
SVM decision value 0.30
SVM RNA-class probability 0.680519
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9451058 116 + 22224390
CCACCGGUGGCCAGGAUCAGCUGCUGUUGGUCCCCCAUCCUGUGAUUGCACAGAUUAAUUGACAAUUUCCGCGUUUUUUUGCCCCAAUGUUUUCAUUUCACCAGACCUAUCGGUCC
.....(((((...((((((((....))))))))......(((((....)))))......(((.(((....(((......)))......))).)))..))))).((((....)))). ( -30.20)
>DroSec_CAF1 4683 116 + 1
CCACCGGUGGCCAGGAUCAGCUGCUGUUGGUCCCCCAUCCUGUGACUGCACGGAUUAAUUGACAAUUUCCGCGUUUUUCUCGCCAAAUGUUUUCAUUUGACCACGCCUAUCGGUCC
..(((((((((..((((((((....))))))))........(((...((.((((.............)))).)).........((((((....))))))..)))))).)))))).. ( -35.72)
>DroSim_CAF1 961 116 + 1
CCACCGGUGGCCAGGAUCAGCUGCUGUUGGUCCCCCAUCCUGUGAUUGCACGGAUUAAUUGACAAUUUCCGCGUUUUUCUCGCCAAAUGUUUUCAUUUGACCAAGCCUAUCGGUCC
..(((((((((..((((((((....))))))))...((((.(((....)))))))...(((.........(((.......)))((((((....))))))..)))))).)))))).. ( -35.50)
>DroEre_CAF1 4924 114 + 1
CCACCGGUGGCCAGGAUCAGCUGUUGUUGGUCCCCCAUCCUGUGAU--UACGGAUUAAUUGACAAUUUUCGCUUUUUUCUCCGCCAAUGUUUUCAUUUGGCCGAACCUAUCGGUUC
.(((.(((((...((((((((....)))))))).))).)).)))..--...(((..((.(((......)))....))..)))(((((((....)).))))).(((((....))))) ( -32.50)
>DroYak_CAF1 4674 114 + 1
CCGCCGGUGGCCAGGAUCAGCUGCUGUUGGUCCCCCAUCCUGUGUU--CACGGAUUAAUUGACAAUUUCCGCUUUUUUCUCCGGCAAUGUUUUCAUUUGGCCAAACCUAUCGGUCC
..(((((((((((((((((((....))))))))...((((.((...--.)))))).....((((.((.(((..........))).))))))......))))))......))))).. ( -30.60)
>DroPer_CAF1 5014 93 + 1
CCACCGGUGGCCAGUAUUAG------UUGGUCCCCCAU--------UGCUUCCAUUAAUCGUCAAUUAG-GCGAUUCUGUUA--UUUUGUUAUCAUUUAAUCAG------CGGUCA
..(((((.((((((......------))))))))....--------.(((......(((((((.....)-))))))..((((--...((....))..)))).))------)))).. ( -19.80)
>consensus
CCACCGGUGGCCAGGAUCAGCUGCUGUUGGUCCCCCAUCCUGUGAUUGCACGGAUUAAUUGACAAUUUCCGCGUUUUUCUCCCCCAAUGUUUUCAUUUGACCAAACCUAUCGGUCC
..((((((((...((((((((....))))))))......(((((....))))).....................................................)))))))).. (-19.37 = -20.58 +   1.21)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:43 2006