Locus 6771

Sequence ID 3R_DroMel_CAF1
Location 17,862,055 – 17,862,190
Length 135
Max. P 0.928695
window10994 window10995 window10996

overview

Window 4

Location 17,862,055 – 17,862,155
Length 100
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 78.91
Mean single sequence MFE -24.28
Consensus MFE -18.26
Energy contribution -19.48
Covariance contribution 1.23
Combinations/Pair 1.28
Mean z-score -1.89
Structure conservation index 0.75
SVM decision value 1.19
SVM RNA-class probability 0.928695
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17862055 100 + 27905053
AACUACCAAUAAUAAUGAUGAUUUUUAAAGGCGAAUUUGAGCAGCUCUGGUGCAGCGAGUUAAUGUUGCCCAGGGCAGGCAUGAAAUCCAUUUAAAAAC--C-
.....................((((((((.(.((.((((.((.(((((((.((((((......)))))))))))))..)).)))).))).)))))))).--.- ( -27.10)
>DroSec_CAF1 3908 100 + 1
AGCUACAUAUAAUAAUGAUGAUUUUUAAAGGCGAAUUUGAGCAGCUCUGGAGCAGCGAGUUAAUGUUGCCCAGGGCAGGCAUGAAAUCCAUUUAAAAAC--C-
.....................((((((((.(.((.((((.((.(((((((.((((((......)))))))))))))..)).)))).))).)))))))).--.- ( -27.10)
>DroSim_CAF1 3888 100 + 1
AACUACAUAUAGUAAUGAUGAUUUUUAAAGGCGAAUUUGAGCAGCUCUGGAGCAGCGAGUUAAUGUUGCCCAGGGCAGGCAUGAAAUCCAUUUAAAAAC--C-
.((((....))))........((((((((.(.((.((((.((.(((((((.((((((......)))))))))))))..)).)))).))).)))))))).--.- ( -27.70)
>DroEre_CAF1 4296 100 + 1
GACUACCAACAACAAUGAUGAUUUUUAAAGGCGAAUUUGAGCAGCCCUGAAGCAGCGAGUUAAUGUUGCCCAGAGCAGGCAUGAAAUCCAUUUAAAAAC--C-
.....................((((((((.(.((.((((.((.((.(((..((((((......)))))).))).))..)).)))).))).)))))))).--.- ( -18.10)
>DroWil_CAF1 2956 94 + 1
AUCU------UUAAAUGAUGAU--UCAAAGGCGAAUUUGAUUAGCCCAAGAGCAGCGAGUUAAUGUUGCCUUGGGCGGAAAUGAAAUCUAUUUAAAUAUUUA-
...(------(((((((((...--(((((......)))))...(((((((.((((((......))))))))))))).........))).)))))))......- ( -27.10)
>DroMoj_CAF1 3140 88 + 1
---------AUUUAAGGAUGAU--UCAAAGGCGAAUUCGAUUUGCUCUGGAGCAGCGAGUUAAUGUUGCCAAUUGCAGGCAUGAGAUACCC--AAAAAA--UA
---------......((.((.(--(((..(((((....(((((((((....).))))))))....)))))...((....)))))).)).))--......--.. ( -18.60)
>consensus
AACUAC__AUAAUAAUGAUGAUUUUUAAAGGCGAAUUUGAGCAGCUCUGGAGCAGCGAGUUAAUGUUGCCCAGGGCAGGCAUGAAAUCCAUUUAAAAAC__C_
.....................((((((((...((.((((.((.(((((((.((((((......)))))))))))))..)).)))).))..))))))))..... (-18.26 = -19.48 +   1.23)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,862,055 – 17,862,155
Length 100
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 78.91
Mean single sequence MFE -23.48
Consensus MFE -12.77
Energy contribution -13.58
Covariance contribution 0.81
Combinations/Pair 1.32
Mean z-score -2.42
Structure conservation index 0.54
SVM decision value 1.09
SVM RNA-class probability 0.913091
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17862055 100 - 27905053
-G--GUUUUUAAAUGGAUUUCAUGCCUGCCCUGGGCAACAUUAACUCGCUGCACCAGAGCUGCUCAAAUUCGCCUUUAAAAAUCAUCAUUAUUAUUGGUAGUU
-(--((((((((((((((((...((..((.(((((((.(........).))).)))).)).))..)))))))..))))))))))((((.......)))).... ( -25.50)
>DroSec_CAF1 3908 100 - 1
-G--GUUUUUAAAUGGAUUUCAUGCCUGCCCUGGGCAACAUUAACUCGCUGCUCCAGAGCUGCUCAAAUUCGCCUUUAAAAAUCAUCAUUAUUAUAUGUAGCU
-(--((((((((((((((((...((..((.(((((((.(........).))).)))).)).))..)))))))..))))))))))................... ( -24.80)
>DroSim_CAF1 3888 100 - 1
-G--GUUUUUAAAUGGAUUUCAUGCCUGCCCUGGGCAACAUUAACUCGCUGCUCCAGAGCUGCUCAAAUUCGCCUUUAAAAAUCAUCAUUACUAUAUGUAGUU
-(--((((((((((((((((...((..((.(((((((.(........).))).)))).)).))..)))))))..))))))))))...(((((.....))))). ( -26.60)
>DroEre_CAF1 4296 100 - 1
-G--GUUUUUAAAUGGAUUUCAUGCCUGCUCUGGGCAACAUUAACUCGCUGCUUCAGGGCUGCUCAAAUUCGCCUUUAAAAAUCAUCAUUGUUGUUGGUAGUC
-(--((((((((((((((((...((..((((((((((.(........).))).))))))).))..)))))))..))))))))))((((.......)))).... ( -26.40)
>DroWil_CAF1 2956 94 - 1
-UAAAUAUUUAAAUAGAUUUCAUUUCCGCCCAAGGCAACAUUAACUCGCUGCUCUUGGGCUAAUCAAAUUCGCCUUUGA--AUCAUCAUUUAA------AGAU
-......(((((((.(((.........((((((((((.(........).))).)))))))...(((((......)))))--...)))))))))------)... ( -21.90)
>DroMoj_CAF1 3140 88 - 1
UA--UUUUUU--GGGUAUCUCAUGCCUGCAAUUGGCAACAUUAACUCGCUGCUCCAGAGCAAAUCGAAUUCGCCUUUGA--AUCAUCCUUAAAU---------
..--.(((..--((((......((((.......))))........(((.((((....))))...)))....))))..))--)............--------- ( -15.70)
>consensus
_G__GUUUUUAAAUGGAUUUCAUGCCUGCCCUGGGCAACAUUAACUCGCUGCUCCAGAGCUGCUCAAAUUCGCCUUUAAAAAUCAUCAUUAUUAU__GUAGUU
....((((((((((((((((...((..((.(((((((.(........).))).)))).)).))..)))))))..))))))))).................... (-12.77 = -13.58 +   0.81)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,862,080 – 17,862,190
Length 110
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 83.31
Mean single sequence MFE -24.72
Consensus MFE -19.85
Energy contribution -19.05
Covariance contribution -0.80
Combinations/Pair 1.32
Mean z-score -1.43
Structure conservation index 0.80
SVM decision value 0.02
SVM RNA-class probability 0.542476
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17862080 110 + 27905053
UAAAGGCGAAUUUGAGCAGCUCUGGUGCAGCGAGUUAAUGUUGCCCAGGGCAGGCAUGAAAUCCAUUUAAAAAC--CAACUGAAUUAUAUAAAAUACUAAAAAACUGUAUCC
((((.(.((.((((.((.(((((((.((((((......)))))))))))))..)).)))).))).)))).....--.................((((.........)))).. ( -23.60)
>DroSec_CAF1 3933 110 + 1
UAAAGGCGAAUUUGAGCAGCUCUGGAGCAGCGAGUUAAUGUUGCCCAGGGCAGGCAUGAAAUCCAUUUAAAAAC--CAACUGAAUUAUAUCAAAUAUUGGAAUACUGUAUUC
((((.(.((.((((.((.(((((((.((((((......)))))))))))))..)).)))).))).))))....(--(((.(((......)))....))))............ ( -26.10)
>DroSim_CAF1 3913 110 + 1
UAAAGGCGAAUUUGAGCAGCUCUGGAGCAGCGAGUUAAUGUUGCCCAGGGCAGGCAUGAAAUCCAUUUAAAAAC--CAACUGAAUUAUAUCAAAUAUUGAAAUACUUUAUCC
(((((.(((((((((((.(((((((.((((((......)))))))))))))..))(((.....)))........--.............)))))).))).....)))))... ( -27.80)
>DroEre_CAF1 4321 110 + 1
UAAAGGCGAAUUUGAGCAGCCCUGAAGCAGCGAGUUAAUGUUGCCCAGAGCAGGCAUGAAAUCCAUUUAAAAAC--CAACUGAAUUAAAUCAAACGUGUAUUUACUGUAGCC
....(((...(((((((.((.(((..((((((......)))))).))).))..))(((.....)))........--.............))))).(((....)))....))) ( -19.10)
>DroWil_CAF1 2973 111 + 1
CAAAGGCGAAUUUGAUUAGCCCAAGAGCAGCGAGUUAAUGUUGCCUUGGGCGGAAAUGAAAUCUAUUUAAAUAUUUAAACUGAU-UAUAAAAAUGAUACCUAGAAUUCAUAU
.......((((((.(((((((((((.((((((......)))))))))))))........((((..(((((....)))))..)))-).......)))).....)))))).... ( -28.40)
>DroYak_CAF1 4345 110 + 1
UAAAGGCGAAUUUGAGCAGCCCUGAAGCAACGAGUUAAUGUUGCCCAGAGCAGGCAUGAAAUCCAGUUAAAAAC--CAACUGAAUUACAUCAAACGUUUAAUUACUGUAGCC
....(((....((((((.((.(((..((((((......)))))).))).))..(.(((.(((.(((((......--.))))).))).))))....))))))........))) ( -23.30)
>consensus
UAAAGGCGAAUUUGAGCAGCCCUGGAGCAGCGAGUUAAUGUUGCCCAGGGCAGGCAUGAAAUCCAUUUAAAAAC__CAACUGAAUUAUAUCAAAUAUUGAAAUACUGUAUCC
....((...((((.(((.(((((((.((((((......)))))))))))))..)).).))))))................................................ (-19.85 = -19.05 +  -0.80)

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 12:29:34 2006