Locus 3168

Sequence ID 3R_DroMel_CAF1
Location 8,394,685 – 8,394,775
Length 90
Max. P 0.912035
window5135 window5136

overview

Window 5

Location 8,394,685 – 8,394,775
Length 90
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 80.89
Mean single sequence MFE -21.80
Consensus MFE -15.49
Energy contribution -16.43
Covariance contribution 0.95
Combinations/Pair 1.14
Mean z-score -1.44
Structure conservation index 0.71
SVM decision value 0.26
SVM RNA-class probability 0.659514
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8394685 90 + 27905053
GCCACACA-CACACGA-----UUUUUC---CGCUUUCCACGCUGGCUUUUCGCAUUCCACGCGUGGCCAGCGAUUUUCGCCGCUCUGCGUUU-UGAUUAU
........-.......-----......---.........((((((((...(((.......))).)))))))).....(((......)))...-....... ( -21.70)
>DroSec_CAF1 56558 90 + 1
GCCACACA-CACAUGA-----AUUUUC---CGCUUUCCACGCUGGCUUUUCGCAUUCCACGCGUGGCCAGCGAUUUUCGCCGCUCUGCGUUU-UGAUUAU
........-.......-----......---.........((((((((...(((.......))).)))))))).....(((......)))...-....... ( -21.70)
>DroSim_CAF1 55865 81 + 1
----------ACAUGA-----AUUUUC---CGCUUUCCACGCUGGCUUUUCGCAUUCCACGCGUGGCCAGCGAUUUUCGCCGCUCUGCGUUU-UGAUUAU
----------......-----......---.........((((((((...(((.......))).)))))))).....(((......)))...-....... ( -21.70)
>DroEre_CAF1 58427 91 + 1
GCCACACA---UACGA-----AUUUUUCCACGCUUUCCACGCUGGCUUCUCGCAUUCCACGCGUGGCCAGCGAUUUUCCCUGCUCUGCGUUU-UGAUUAU
........---.....-----........((((....((((((((((...(((.......))).))))))))........))....))))..-....... ( -21.40)
>DroYak_CAF1 58172 78 + 1
GCCACACA---CACGA-----AUUUUUCCACGCUUUCCACGCUGGCUUUUCGCAUUCCACGCGUGGCC-------------GCUCUGCGUUU-UGAUUAU
(((((...---...((-----(.....(((.((.......)))))...)))((.......)))))))(-------------((...)))...-....... ( -15.80)
>DroAna_CAF1 58933 95 + 1
GCCGCACAGCGUUCGACUGAGAAUUUC---CACUUGCCA--CUGGCUUUUCGCAUUCCACGCGUGGCCGGCGAUUUUCGCCGCUUUGCGUUUCUGAUUAU
..((((.(((((((......))))...---.........--..((((...(((.......))).))))((((.....))))))).))))........... ( -28.50)
>consensus
GCCACACA__ACACGA_____AUUUUC___CGCUUUCCACGCUGGCUUUUCGCAUUCCACGCGUGGCCAGCGAUUUUCGCCGCUCUGCGUUU_UGAUUAU
.......................................((((((((...(((.......))).))))))))........(((...)))........... (-15.49 = -16.43 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 6

Location 8,394,685 – 8,394,775
Length 90
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 80.89
Mean single sequence MFE -27.52
Consensus MFE -20.03
Energy contribution -20.33
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -2.35
Structure conservation index 0.73
SVM decision value 1.08
SVM RNA-class probability 0.912035
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8394685 90 - 27905053
AUAAUCA-AAACGCAGAGCGGCGAAAAUCGCUGGCCACGCGUGGAAUGCGAAAAGCCAGCGUGGAAAGCG---GAAAAA-----UCGUGUG-UGUGUGGC
.......-..(((((..(((.(((...(((((..((((((.(((..(.....)..)))))))))..))))---).....-----)))))).-)))))... ( -31.00)
>DroSec_CAF1 56558 90 - 1
AUAAUCA-AAACGCAGAGCGGCGAAAAUCGCUGGCCACGCGUGGAAUGCGAAAAGCCAGCGUGGAAAGCG---GAAAAU-----UCAUGUG-UGUGUGGC
.......-..(((((..(((..(((..(((((..((((((.(((..(.....)..)))))))))..))))---)....)-----)).))).-)))))... ( -29.70)
>DroSim_CAF1 55865 81 - 1
AUAAUCA-AAACGCAGAGCGGCGAAAAUCGCUGGCCACGCGUGGAAUGCGAAAAGCCAGCGUGGAAAGCG---GAAAAU-----UCAUGU----------
.......-...(((......)))....(((((..((((((.(((..(.....)..)))))))))..))))---).....-----......---------- ( -25.90)
>DroEre_CAF1 58427 91 - 1
AUAAUCA-AAACGCAGAGCAGGGAAAAUCGCUGGCCACGCGUGGAAUGCGAGAAGCCAGCGUGGAAAGCGUGGAAAAAU-----UCGUA---UGUGUGGC
.......-..(((((..((..(......((((..((((((.(((...........)))))))))..))))........)-----..)).---)))))... ( -26.34)
>DroYak_CAF1 58172 78 - 1
AUAAUCA-AAACGCAGAGC-------------GGCCACGCGUGGAAUGCGAAAAGCCAGCGUGGAAAGCGUGGAAAAAU-----UCGUG---UGUGUGGC
.......-...(((...))-------------)(((((((.....(((((((...(((.(((.....)))))).....)-----)))))---)))))))) ( -22.60)
>DroAna_CAF1 58933 95 - 1
AUAAUCAGAAACGCAAAGCGGCGAAAAUCGCCGGCCACGCGUGGAAUGCGAAAAGCCAG--UGGCAAGUG---GAAAUUCUCAGUCGAACGCUGUGCGGC
...........((((.(((((((.....))))..((((((((...)))).....(((..--.)))..)))---)................))).)))).. ( -29.60)
>consensus
AUAAUCA_AAACGCAGAGCGGCGAAAAUCGCUGGCCACGCGUGGAAUGCGAAAAGCCAGCGUGGAAAGCG___GAAAAU_____UCGUGU__UGUGUGGC
...........(((....(((((.....))))).((((((.(((..(.....)..)))))))))...))).............................. (-20.03 = -20.33 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:46 2006