Locus 4473

Sequence ID 2L_DroMel_CAF1
Location 12,816,037 – 12,816,190
Length 153
Max. P 0.941445
window7035 window7036 window7037

overview

Window 5

Location 12,816,037 – 12,816,152
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.32
Mean single sequence MFE -49.65
Consensus MFE -45.53
Energy contribution -46.03
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 0.92
SVM decision value 1.32
SVM RNA-class probability 0.941445
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12816037 115 + 22407834
-----GAGCUUCGGGGUGGCGGGCGGUUGAGCCCAGACAGUUUGGCAUGGCCGCACGCCAUGAUAUAAUCUGGCACUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCA
-----...(....).(.((((((.(((((.((((((.(((.(((.((((((.....))))))...))).)))...)))))).((((((.....)))).)).......)))))))))))). ( -50.20)
>DroSec_CAF1 81991 115 + 1
-----GAGCUUCGGGGUGGCGGGCGGUUGAGCCUAGACAGUUUGGCAUGGCCGCACGCCAUGAUAUAAUCUGGCACUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCA
-----...(....).(.((((((.(((((.(((.(((..((....((((((.....))))))..))..))))))..(((((.((((((.....)))).)).))))).)))))))))))). ( -49.40)
>DroSim_CAF1 85311 115 + 1
-----GAGCUUCGGGGUGGCGGGCGGUUGAGCCCAGACAGUUUGGCAUGGCCGCACGCCAUGAUAUAAUCUGGCAGUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCA
-----........((((((.((((......)))).....(((.((((.((((.(((((((.(((...))))))).)))))))((((((.....)))).)))))).))).....)))))). ( -53.00)
>DroYak_CAF1 85819 119 + 1
GUCCGGAGCUUUG-GGUGGCGGGCGGUUGAGCCCAGACAGUUUGGCAUAGCCGCACGCCAUGAUAUAAUCUCGCACUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCA
....((.((...(-(((((((.(((((((.(((..........))).))))))).)))))................(((((.((((((.....)))).)).)))))......))))))). ( -46.00)
>consensus
_____GAGCUUCGGGGUGGCGGGCGGUUGAGCCCAGACAGUUUGGCAUGGCCGCACGCCAUGAUAUAAUCUGGCACUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCA
...............(.((((((.(((((.(((.(((..((....((((((.....))))))..))..))))))..(((((.((((((.....)))).)).))))).)))))))))))). (-45.53 = -46.03 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,816,037 – 12,816,152
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.32
Mean single sequence MFE -47.10
Consensus MFE -45.45
Energy contribution -45.33
Covariance contribution -0.13
Combinations/Pair 1.05
Mean z-score -1.63
Structure conservation index 0.96
SVM decision value 0.62
SVM RNA-class probability 0.802388
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12816037 115 - 22407834
UGGGCGGGAGUUGUUAGGCAGCGCGUAAUAUAUACGGCGGCCCAGUGCCAGAUUAUAUCAUGGCGUGCGGCCAUGCCAAACUGUCUGGGCUCAACCGCCCGCCACCCCGAAGCUC-----
.(((..((((..(((.((((((.((((.....))))))((((((.((((((((...))).))))))).)))).)))).)))...))((((......)))).))..))).......----- ( -47.60)
>DroSec_CAF1 81991 115 - 1
UGGGCGGGAGUUGUUAGGCAGCGCGUAAUAUAUACGGCGGCCCAGUGCCAGAUUAUAUCAUGGCGUGCGGCCAUGCCAAACUGUCUAGGCUCAACCGCCCGCCACCCCGAAGCUC-----
.((((((((((..((((((((...(((.....)))(((((((((.((((((((...))).))))))).))))..)))...))))))))))))..))))))...............----- ( -47.40)
>DroSim_CAF1 85311 115 - 1
UGGGCGGGAGUUGUUAGGCAGCGCGUAAUAUAUACGGCGGCCCACUGCCAGAUUAUAUCAUGGCGUGCGGCCAUGCCAAACUGUCUGGGCUCAACCGCCCGCCACCCCGAAGCUC-----
.(((..((((..(((.((((((.((((.....))))))(((((((.(((((((...))).))))))).)))).)))).)))...))((((......)))).))..))).......----- ( -49.40)
>DroYak_CAF1 85819 119 - 1
UGGGCGGGAGUUGUUAGGCAGCGCGUAAUAUAUACGGCGGCCCAGUGCGAGAUUAUAUCAUGGCGUGCGGCUAUGCCAAACUGUCUGGGCUCAACCGCCCGCCACC-CAAAGCUCCGGAC
..((((((.((((.......((.((((.....))))))(((((((.((((.......)).(((((((....)))))))....)))))))))))))..))))))..(-(........)).. ( -44.00)
>consensus
UGGGCGGGAGUUGUUAGGCAGCGCGUAAUAUAUACGGCGGCCCAGUGCCAGAUUAUAUCAUGGCGUGCGGCCAUGCCAAACUGUCUGGGCUCAACCGCCCGCCACCCCGAAGCUC_____
.((((((((((..((((((((...(((.....)))(((((((((.((((((((...))).))))))).))))..)))...))))))))))))..)))))).................... (-45.45 = -45.33 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,816,072 – 12,816,190
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.14
Mean single sequence MFE -33.52
Consensus MFE -27.98
Energy contribution -28.22
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.83
SVM decision value 0.74
SVM RNA-class probability 0.838500
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12816072 118 + 22407834
UUUGGCAUGGCCGCACGCCAUGAUAUAAUCUGGCACUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCACAACACCUCCUCACCGGAGGCAACUCA--UCCACAAAUGU
..(((.((((..((..((((.(((...)))))))..(((((.((((((.....)))).)).))))).........))........(((((.....)))))....)))--))))....... ( -34.60)
>DroSec_CAF1 82026 118 + 1
UUUGGCAUGGCCGCACGCCAUGAUAUAAUCUGGCACUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCACAACAGCUCCUCACCGGAGGCACCUCA--UCCACAAGCGU
..(((.((((((((..((((.(((...)))))))..(((((.((((((.....)))).)).)))))...................))(((.....))))))....))--))))....... ( -32.40)
>DroSim_CAF1 85346 118 + 1
UUUGGCAUGGCCGCACGCCAUGAUAUAAUCUGGCAGUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCACAACACCGCCUCACCAGAGGCACCUCA--UCCACAAACGU
...((((.((((.(((((((.(((...))))))).)))))))((((((.....)))).)))))).......................(((((....)))))......--........... ( -39.00)
>DroYak_CAF1 85858 120 + 1
UUUGGCAUAGCCGCACGCCAUGAUAUAAUCUCGCACUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCACAGCCCCUCCUCACCGGAGGCACCUCAAACCCCCAAAUGG
(((((.......((..((...(((...)))..))..(((((.((((((.....)))).)).))))).........))........(((((.....)))))............)))))... ( -28.10)
>consensus
UUUGGCAUGGCCGCACGCCAUGAUAUAAUCUGGCACUGGGCCGCCGUAUAUAUUACGCGCUGCCUAACAACUCCCGCCCACAACACCUCCUCACCGGAGGCACCUCA__UCCACAAACGU
...(((..........((((.(((...)))))))..(((((.((((((.....)))).)).))))).........)))..........((((....)))).................... (-27.98 = -28.22 +   0.25)

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 11:18:39 2006