Locus 5565

Sequence ID X_DroMel_CAF1
Location 14,382,696 – 14,382,827
Length 131
Max. P 0.998486
window9030 window9031 window9032

overview

Window 0

Location 14,382,696 – 14,382,787
Length 91
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 64.46
Mean single sequence MFE -31.30
Consensus MFE -12.73
Energy contribution -15.60
Covariance contribution 2.87
Combinations/Pair 1.19
Mean z-score -3.89
Structure conservation index 0.41
SVM decision value 3.12
SVM RNA-class probability 0.998486
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14382696 91 - 22224390
UUCUUUGGCUGGCCAUAAAAUUCUGCUCAAUUUGCAUGGCCAACUUGGC--CAGCGAA-----CUGAAGUGGCCAAGUAAACAAAAACUUGGCUAACG
(((.((.((((((((......(((((.......))).))......))))--)))).))-----..))).(((((((((........)))))))))... ( -33.60)
>DroYak_CAF1 100606 96 - 1
UCAUUUAGUAGGCCAUCACAUUCUGCUCAAUUUGCGUGGCUAACUUGGC--CAGCGAAGGCCACUGAAGUGGCCAAGUAAACAAAAACUUGGCCAACG
...((((((.((((.((.(.....((.......)).(((((.....)))--))).)).)))))))))).(((((((((........)))))))))... ( -37.70)
>DroAna_CAF1 164671 83 - 1
UCGUUUACUCGGCCCUCAAAU---------UUUGUGUUGCCUACUUGGCAGCGCCGAC-----UUCGAGUAUCUAAGCGAAAACAAAACUUUCUAAG-
(((((((...((..(((.((.---------((.((((((((.....)))))))).)).-----)).)))..))))))))).................- ( -22.60)
>consensus
UCAUUUAGUAGGCCAUCAAAUUCUGCUCAAUUUGCGUGGCCAACUUGGC__CAGCGAA_____CUGAAGUGGCCAAGUAAACAAAAACUUGGCUAACG
..........((((((((((((......)))))).))))))............................(((((((((........)))))))))... (-12.73 = -15.60 +   2.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 14,382,723 – 14,382,827
Length 104
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 73.38
Mean single sequence MFE -26.28
Consensus MFE -10.69
Energy contribution -12.75
Covariance contribution 2.06
Combinations/Pair 1.05
Mean z-score -2.79
Structure conservation index 0.41
SVM decision value 1.03
SVM RNA-class probability 0.903555
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14382723 104 + 22224390
CACUUCAG-----UUCGCUGGCCAAGUUGGCCAUGCAAAUUGAGCAGAAUUUUAUGGCCAGCCAAAGAAGGCUAAUUUGGUAAAUUUUUUUUUACUUGGCUUAAAAUUU
...(((((-----((.(((((((.....))))).)).)))))))..((((((((.((((((((......)))).....((((((......)))))).)))))))))))) ( -35.10)
>DroSec_CAF1 98834 81 + 1
CACUUCAG-----UUCGCUGG-----------------------CAGAGUUUUAUGGCCAGCUAAAGAAGGCUAAUUUCGUAAAUUUAUUUUUACUUGGUUUAAAAUUU
..((((..-----((.(((((-----------------------(...........)))))).)).))))(((((....(((((......))))))))))......... ( -17.10)
>DroSim_CAF1 92933 81 + 1
CACUUCAG-----UUCGCUGG-----------------------CAGAAUUUUAUGGCCAGCUAAAGAAGGCUAAUUUCGUAAAUUUAUUUUUACUUGGCUUAAAAUUU
..((((..-----((.(((((-----------------------(...........)))))).)).))))(((((....(((((......))))))))))......... ( -19.20)
>DroYak_CAF1 100633 107 + 1
CACUUCAGUGGCCUUCGCUGGCCAAGUUAGCCACGCAAAUUGAGCAGAAUGUGAUGGCCUACUAAAUGAGGCUAAUUUUGUAAAUUUGUU--CACUUGGCUUACAAAUG
........(((((......))))).((.(((((.(((((((..(((((((....((((((........))))))))))))).))))))).--....))))).))..... ( -33.70)
>consensus
CACUUCAG_____UUCGCUGG_______________________CAGAAUUUUAUGGCCAGCUAAAGAAGGCUAAUUUCGUAAAUUUAUUUUUACUUGGCUUAAAAUUU
................(((((((................................)))))))......(((((((....(((((......))))))))))))....... (-10.69 = -12.75 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 14,382,723 – 14,382,827
Length 104
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 73.38
Mean single sequence MFE -22.45
Consensus MFE -8.69
Energy contribution -10.56
Covariance contribution 1.87
Combinations/Pair 1.10
Mean z-score -2.48
Structure conservation index 0.39
SVM decision value 0.06
SVM RNA-class probability 0.561531
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14382723 104 - 22224390
AAAUUUUAAGCCAAGUAAAAAAAAAUUUACCAAAUUAGCCUUCUUUGGCUGGCCAUAAAAUUCUGCUCAAUUUGCAUGGCCAACUUGGCCAGCGAA-----CUGAAGUG
.(((((((.(((..(((((......)))))......((((......)))))))..)))))))..(((((.(((((.(((((.....))))))))))-----.)).))). ( -31.40)
>DroSec_CAF1 98834 81 - 1
AAAUUUUAAACCAAGUAAAAAUAAAUUUACGAAAUUAGCCUUCUUUAGCUGGCCAUAAAACUCUG-----------------------CCAGCGAA-----CUGAAGUG
..............(((((......))))).........((((....((((((...........)-----------------------)))))...-----..)))).. ( -15.80)
>DroSim_CAF1 92933 81 - 1
AAAUUUUAAGCCAAGUAAAAAUAAAUUUACGAAAUUAGCCUUCUUUAGCUGGCCAUAAAAUUCUG-----------------------CCAGCGAA-----CUGAAGUG
..............(((((......))))).........((((....((((((...........)-----------------------)))))...-----..)))).. ( -15.80)
>DroYak_CAF1 100633 107 - 1
CAUUUGUAAGCCAAGUG--AACAAAUUUACAAAAUUAGCCUCAUUUAGUAGGCCAUCACAUUCUGCUCAAUUUGCGUGGCUAACUUGGCCAGCGAAGGCCACUGAAGUG
..((((((((....(..--..)...))))))))..........((((((.((((.((.(.....((.......)).(((((.....)))))).)).))))))))))... ( -26.80)
>consensus
AAAUUUUAAGCCAAGUAAAAAUAAAUUUACGAAAUUAGCCUUCUUUAGCUGGCCAUAAAAUUCUG_______________________CCAGCGAA_____CUGAAGUG
..............(((((......)))))....((((.....(((.((((((((..............................))))))))))).....)))).... ( -8.69 = -10.56 +   1.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:03 2006