Locus 6148

Sequence ID 3L_DroMel_CAF1
Location 16,266,464 – 16,266,597
Length 133
Max. P 0.982242
window9877 window9878 window9879 window9880

overview

Window 7

Location 16,266,464 – 16,266,560
Length 96
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 79.20
Mean single sequence MFE -33.46
Consensus MFE -22.78
Energy contribution -22.86
Covariance contribution 0.08
Combinations/Pair 1.11
Mean z-score -1.99
Structure conservation index 0.68
SVM decision value 1.06
SVM RNA-class probability 0.907838
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16266464 96 + 23771897
-----------CUUUAGCCUCGCCUCGGCCGAAAGCCGCUCGCUCAGUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGCCUGGGAAUUGGC--------UUGAGGAAAAAC
-----------......((((((....))...((((((....(((((....(((((.((((.(((....))).)))).))))))))))...))))--------))))))...... ( -38.40)
>DroSec_CAF1 17805 84 + 1
-----------UUUUAGCCUCGCCUCGGCCGAAA------------GUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGCUUGGGAAUUGGC--------UUGAGGAAAAAC
-----------...........((((((((((..------------.(((.(((((.((((.(((....))).)))).))))).)))...)))))--------.)))))...... ( -32.10)
>DroSim_CAF1 16337 96 + 1
-----------UUUUAGCCUCGCCUCGGCCGAAAGCCGCUCGCUCAGUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGCUUGGGAAUUGGC--------UUGAGGAAAAAC
-----------......((((((....))...((((((....(((((....(((((.((((.(((....))).)))).))))))))))...))))--------))))))...... ( -36.40)
>DroEre_CAF1 17786 105 + 1
UUCAGCCACAGUUUUAGCCUCGCCUCGACCA-AAGCCGCUCGCUCAGUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGUCUGGGAAUUGGC--------UUGAGGAAA-AC
......................(((((....-.(((((....(((((....(((((.((((.(((....))).)))).))))))))))...))))--------))))))...-.. ( -33.10)
>DroAna_CAF1 16687 109 + 1
-----CUUGGCUUUCAGCCUCGCCUUGGUCCAAA-CUGCUCGCUCAGUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGUCUGGGAAAUACACAAACAUAGUCGAGGAAAAAC
-----(((((((....((...))((..(.(((..-..(((((...(((...((((....)))).)))..)))))....))).)..))..............)))))))....... ( -27.30)
>consensus
___________UUUUAGCCUCGCCUCGGCCGAAAGCCGCUCGCUCAGUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGCUUGGGAAUUGGC________UUGAGGAAAAAC
.................((((((....))......................(((((.((((.(((....))).)))).)))))......................))))...... (-22.78 = -22.86 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 16,266,464 – 16,266,560
Length 96
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 79.20
Mean single sequence MFE -36.05
Consensus MFE -26.28
Energy contribution -27.46
Covariance contribution 1.18
Combinations/Pair 1.07
Mean z-score -2.34
Structure conservation index 0.73
SVM decision value 1.91
SVM RNA-class probability 0.982242
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16266464 96 - 23771897
GUUUUUCCUCAA--------GCCAAUUCCCAGGCCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAACUGAGCGAGCGGCUUUCGGCCGAGGCGAGGCUAAAG-----------
.(((..((((..--------(((..(((((((((((((((((.(((....))).))))))))))....))).).)))((((.....)))).)))))))..))).----------- ( -38.60)
>DroSec_CAF1 17805 84 - 1
GUUUUUCCUCAA--------GCCAAUUCCCAAGCCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAAC------------UUUCGGCCGAGGCGAGGCUAAAA-----------
(((((.((((..--------(((.........((((((((((.(((....))).)))))))))).....------------....))).)))).))))).....----------- ( -34.07)
>DroSim_CAF1 16337 96 - 1
GUUUUUCCUCAA--------GCCAAUUCCCAAGCCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAACUGAGCGAGCGGCUUUCGGCCGAGGCGAGGCUAAAA-----------
(((((.((((..--------(((.........((((((((((.(((....))).))))))))))......((((.....))))..))).)))).))))).....----------- ( -38.00)
>DroEre_CAF1 17786 105 - 1
GU-UUUCCUCAA--------GCCAAUUCCCAGACCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAACUGAGCGAGCGGCUU-UGGUCGAGGCGAGGCUAAAACUGUGGCUGAA
..-((.((((..--------(((((..(((...(((((((((.(((....))).)))))))))(((......))).).))..)-)))).)))).))(((((......)))))... ( -35.20)
>DroAna_CAF1 16687 109 - 1
GUUUUUCCUCGACUAUGUUUGUGUAUUUCCCAGACCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAACUGAGCGAGCAG-UUUGGACCAAGGCGAGGCUGAAAGCCAAG-----
(((((((((((.((.((((((.(.....).))))((((((.((((.(((((..(((....)))....)))))..)))).)-)))))..)).)))))))..))))))....----- ( -34.40)
>consensus
GUUUUUCCUCAA________GCCAAUUCCCAAGCCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAACUGAGCGAGCGGCUUUCGGCCGAGGCGAGGCUAAAA___________
(((((.((((......................((((((((((.(((....))).))))))))))((....((((.....))))...)).)))).)))))................ (-26.28 = -27.46 +   1.18)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 16,266,492 – 16,266,597
Length 105
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 87.44
Mean single sequence MFE -23.83
Consensus MFE -19.30
Energy contribution -18.61
Covariance contribution -0.69
Combinations/Pair 1.24
Mean z-score -2.10
Structure conservation index 0.81
SVM decision value 1.11
SVM RNA-class probability 0.916844
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16266492 105 + 23771897
UCGCUCAGUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGCCUGGGAAUUGGCUUGAGGAAAAACGC---AAAAAACAUCAGUAUGGCAAAAACAAAAAAAAAAA
...(((((....(((((.((((.(((....))).)))).)))))))))).....(((((.(......).)---))....(((....)))))................. ( -24.00)
>DroSec_CAF1 17828 95 + 1
-------GUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGCUUGGGAAUUGGCUUGAGGAAAAACGC---AAAAAACACUAGUAUGGCAAAAACAAAAAA---AA
-------((((.(((((.((((.(((....))).)))).)))))(..((......))..)..........---..............))))............---.. ( -21.10)
>DroSim_CAF1 16365 100 + 1
UCGCUCAGUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGCUUGGGAAUUGGCUUGAGGAAAAACGC---AAAAAACACUAGUAUGGCAAAAACAAAAA-----A
..(((....((((((((.((((.(((....))).)))).)))))(..((......))..)..........---...........))).)))...........-----. ( -24.00)
>DroEre_CAF1 17824 100 + 1
UCGCUCAGUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGUCUGGGAAUUGGCUUGAGGAAA-ACGCAACAAAAAACACAAGCAUAGCAAAA-CAAA------AA
..((((((((..(((((.((((.(((....))).)))).))))).....)))))(((((.(....-.............).)))))..)))....-....------.. ( -26.23)
>consensus
UCGCUCAGUUACGCCCAAAUGGGUCACUAAUGAGCCAUCUGGGCCUGGGAAUUGGCUUGAGGAAAAACGC___AAAAAACACUAGUAUGGCAAAAACAAAAA____AA
.......((((.(((((.((((.(((....))).)))).)))))((((............(......).............))))..))))................. (-19.30 = -18.61 +  -0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 16,266,492 – 16,266,597
Length 105
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 87.44
Mean single sequence MFE -25.92
Consensus MFE -19.95
Energy contribution -20.20
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.31
Structure conservation index 0.77
SVM decision value 1.19
SVM RNA-class probability 0.928071
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16266492 105 - 23771897
UUUUUUUUUUUGUUUUUGCCAUACUGAUGUUUUUU---GCGUUUUUCCUCAAGCCAAUUCCCAGGCCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAACUGAGCGA
.........((((((((((....(((.......((---(.((((......)))))))....)))((((((((((.(((....))).))))))))))))))..)))))) ( -27.60)
>DroSec_CAF1 17828 95 - 1
UU---UUUUUUGUUUUUGCCAUACUAGUGUUUUUU---GCGUUUUUCCUCAAGCCAAUUCCCAAGCCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAAC-------
..---..........((((..............((---(.((((......))))))).......((((((((((.(((....))).)))))))))))))).------- ( -23.40)
>DroSim_CAF1 16365 100 - 1
U-----UUUUUGUUUUUGCCAUACUAGUGUUUUUU---GCGUUUUUCCUCAAGCCAAUUCCCAAGCCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAACUGAGCGA
.-----.........(((((((((.........((---(.((((......))))))).......((((((((((.(((....))).)))))))))))))..)).)))) ( -26.30)
>DroEre_CAF1 17824 100 - 1
UU------UUUG-UUUUGCUAUGCUUGUGUUUUUUGUUGCGU-UUUCCUCAAGCCAAUUCCCAGACCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAACUGAGCGA
..------.(((-(((.(.(((((....((((...((((.((-((.....))))))))....))))((((((((.(((....))).))))))))))))).).)))))) ( -26.40)
>consensus
UU____UUUUUGUUUUUGCCAUACUAGUGUUUUUU___GCGUUUUUCCUCAAGCCAAUUCCCAAGCCCAGAUGGCUCAUUAGUGACCCAUUUGGGCGUAACUGAGCGA
...............((((...................((............))..........((((((((((.(((....))).))))))))))))))........ (-19.95 = -20.20 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:22 2006