Locus 3148

Sequence ID 3R_DroMel_CAF1
Location 8,346,445 – 8,346,595
Length 150
Max. P 0.994556
window5099 window5100 window5101

overview

Window 9

Location 8,346,445 – 8,346,540
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.42
Mean single sequence MFE -24.22
Consensus MFE -12.28
Energy contribution -14.28
Covariance contribution 2.00
Combinations/Pair 1.15
Mean z-score -2.54
Structure conservation index 0.51
SVM decision value 2.49
SVM RNA-class probability 0.994556
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8346445 95 + 27905053
UC--U-----------------------CCCCACAUCUAACCACUUGUCACAGCGCAAAACCACGCCAAACGUAAUGGCAUAUGGCAUGCAUCAUAUGUGCACAUGCCGCUGUACUAAGC
..--.-----------------------...............((((..(((((..........((((.......))))....(((((((((.....)))))..)))))))))..)))). ( -24.90)
>DroSec_CAF1 8542 95 + 1
UC--C-----------------------CCCACCAUCUAACCACCUGUCACAGCGCAAAACCACGCCAAACGUAAUGGCAUAUGGCAUGCAUCAUAUGUGCACAUGCCGCUGUACUAAGC
..--.-----------------------..................((.(((((..........((((.......))))....(((((((((.....)))))..)))))))))))..... ( -23.40)
>DroSim_CAF1 5485 95 + 1
UC--C-----------------------CCCACUAUCUAACCACCUGUCACAGCGCAAAACCACGCCAAACGUAAUGGCAUAUGGCAUGCAUCAUAUGUGCACAUGCCGCUGUACUAAGC
..--.-----------------------..................((.(((((..........((((.......))))....(((((((((.....)))))..)))))))))))..... ( -23.40)
>DroEre_CAF1 9731 120 + 1
CCUAGCUCCUAGCUCCUAGCUCCUAACUCCUAACCCCUAACCACUCGUCACGGAGCAAAACCACGCCAAACGUAAUAGCAUAUGGCAUGCAUCAUAUGUGCAGAGUCCGUUGGACUAAGC
..(((.(((..((((...(((((............................)))))........((((...((....))...)))).(((((.....))))))))).....))))))... ( -23.59)
>DroYak_CAF1 8413 118 + 1
UC--CCUCCCAACUUCCAACUCCCACCUCCUAACCACUAACCACUCGUCACAGUGCAAAGCCACGCCAAAUGUAAUGGCAUAUGGCAUUCAUCAUAUGUGCCGAGUCCGGUAGACUAAGC
..--................................(((.(((((((.(((((((......)))((((.((((....)))).))))..........)))).)))))..)))))....... ( -25.80)
>consensus
UC__C_______________________CCCAACAUCUAACCACUUGUCACAGCGCAAAACCACGCCAAACGUAAUGGCAUAUGGCAUGCAUCAUAUGUGCACAUGCCGCUGUACUAAGC
..............................................((.(((((..........((((.......))))....(((((((((.....)))))..)))))))))))..... (-12.28 = -14.28 +   2.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,346,500 – 8,346,595
Length 95
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 81.76
Mean single sequence MFE -28.60
Consensus MFE -15.49
Energy contribution -16.26
Covariance contribution 0.77
Combinations/Pair 1.11
Mean z-score -3.01
Structure conservation index 0.54
SVM decision value 1.76
SVM RNA-class probability 0.976057
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8346500 95 + 27905053
UAUGGCAUGCAUCAUAUGUGCACAUGCCGCUGUACUAAGCGCUUUGGUUGGCUCCUUCCGUUGGCCAAGCAGUGCACCACUGCUUUCCAU------UUCCU
.((((...(((......((((((.(((((((......))))..(((((..((.......))..))))))))))))))...)))...))))------..... ( -32.90)
>DroSec_CAF1 8597 99 + 1
UAUGGCAUGCAUCAUAUGUGCACAUGCCGCUGUACUAAGCUCUUUGGCC--UUCCUUCCGUUGGCCAAGCAGUGCACCACUGCUUUCCAUUUCCAUUUCCU
.((((...(((......((((((.(((.(((......)))...((((((--...........)))))))))))))))...)))...))))........... ( -30.00)
>DroSim_CAF1 5540 99 + 1
UAUGGCAUGCAUCAUAUGUGCACAUGCCGCUGUACUAAGCUCUUUGGCC--UUCCUUCCGUUGGCCAAGCAGUGCACCACUGCUUUCCAUUUCCAUUUCUU
.((((...(((......((((((.(((.(((......)))...((((((--...........)))))))))))))))...)))...))))........... ( -30.00)
>DroEre_CAF1 9811 83 + 1
UAUGGCAUGCAUCAUAUGUGCAGAGUCCGUUGGACUAAGCU------------CCUUCCGCUGGCCAAGCUG------GCUGUUUUCCAGUUCCAUUUCUU
..((((.(((((.....))))).(((((...))))).(((.------------......))).))))(((((------(.......))))))......... ( -21.60)
>DroYak_CAF1 8491 99 + 1
UAUGGCAUUCAUCAUAUGUGCCGAGUCCGGUAGACUAAGCUCUUUGGCC--UUCCUUCCGUGGGCCAAGCAGUGCACCACUGCUUUCCAUUUCCAUUUCCU
...(((((.........)))))((((..((....))..)))).((((((--(.........)))))))((((((...)))))).................. ( -28.50)
>consensus
UAUGGCAUGCAUCAUAUGUGCACAUGCCGCUGUACUAAGCUCUUUGGCC__UUCCUUCCGUUGGCCAAGCAGUGCACCACUGCUUUCCAUUUCCAUUUCCU
..((((.(((((.....)))))......(((......))).......................))))(((((((...)))))))................. (-15.49 = -16.26 +   0.77)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,346,500 – 8,346,595
Length 95
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 81.76
Mean single sequence MFE -31.64
Consensus MFE -16.59
Energy contribution -18.84
Covariance contribution 2.25
Combinations/Pair 1.00
Mean z-score -3.08
Structure conservation index 0.52
SVM decision value 1.78
SVM RNA-class probability 0.976810
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8346500 95 - 27905053
AGGAA------AUGGAAAGCAGUGGUGCACUGCUUGGCCAACGGAAGGAGCCAACCAAAGCGCUUAGUACAGCGGCAUGUGCACAUAUGAUGCAUGCCAUA
.....------((((...(((...((((((((((((((...(....)..)))))......((((......))))))).))))))......)))...)))). ( -33.90)
>DroSec_CAF1 8597 99 - 1
AGGAAAUGGAAAUGGAAAGCAGUGGUGCACUGCUUGGCCAACGGAAGGAA--GGCCAAAGAGCUUAGUACAGCGGCAUGUGCACAUAUGAUGCAUGCCAUA
...........((((...(((...(((((((((((((((..(....)...--)))))....(((......))))))).))))))......)))...)))). ( -35.50)
>DroSim_CAF1 5540 99 - 1
AAGAAAUGGAAAUGGAAAGCAGUGGUGCACUGCUUGGCCAACGGAAGGAA--GGCCAAAGAGCUUAGUACAGCGGCAUGUGCACAUAUGAUGCAUGCCAUA
...........((((...(((...(((((((((((((((..(....)...--)))))....(((......))))))).))))))......)))...)))). ( -35.50)
>DroEre_CAF1 9811 83 - 1
AAGAAAUGGAACUGGAAAACAGC------CAGCUUGGCCAGCGGAAGG------------AGCUUAGUCCAACGGACUCUGCACAUAUGAUGCAUGCCAUA
(((...(((..(((.....))))------)).)))(((..(((..(.(------------.((..(((((...)))))..)).)...)..)))..)))... ( -21.60)
>DroYak_CAF1 8491 99 - 1
AGGAAAUGGAAAUGGAAAGCAGUGGUGCACUGCUUGGCCCACGGAAGGAA--GGCCAAAGAGCUUAGUCUACCGGACUCGGCACAUAUGAUGAAUGCCAUA
...........((((.((((((((...))))))))((((..(....)...--)))).....(((.((((.....)))).)))..............)))). ( -31.70)
>consensus
AGGAAAUGGAAAUGGAAAGCAGUGGUGCACUGCUUGGCCAACGGAAGGAA__GGCCAAAGAGCUUAGUACAGCGGCAUGUGCACAUAUGAUGCAUGCCAUA
............(((.((((((((...))))))))..))).(....)..........................((((((((((....)).))))))))... (-16.59 = -18.84 +   2.25)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:14 2006