Locus 7967

Sequence ID 3R_DroMel_CAF1
Location 21,362,571 – 21,362,711
Length 140
Max. P 0.967003
window12826 window12827 window12828

overview

Window 6

Location 21,362,571 – 21,362,671
Length 100
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 78.93
Mean single sequence MFE -29.89
Consensus MFE -19.58
Energy contribution -20.75
Covariance contribution 1.17
Combinations/Pair 1.00
Mean z-score -2.58
Structure conservation index 0.66
SVM decision value 1.60
SVM RNA-class probability 0.967003
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21362571 100 + 27905053
CAUCAGCUGUCAGCAGCUUU------GGCUGCUGUCUGCCUAAAUAUUUGCCAGCUGCGUAAUUGCAGCCGAAACUACGGAGCAAAAAA-----UAAGACAGAGUCGACAA
....(((((....)))))((------((((.((((((.........(((((..((((((....)))))).....(....).)))))...-----..))))))))))))... ( -32.44)
>DroPse_CAF1 66744 89 + 1
CAUCAACUGUCAACAGCCUUUGCUUCUGCUGCUGUCUGCGUAAAUAUUUGCCAGCUGCGUAAUUGCAGCUGAAACCG------AAAAAA----------------CUACAG
......((((..(((((....((....)).)))))..(((........)))((((((((....))))))))......------......----------------..)))) ( -23.20)
>DroSim_CAF1 52415 99 + 1
CAUCAGCUGUCAGCAGCUUU------GGCUGCUGUCUGCCUAAAUAUUUGCCAGCUGCGUAAUUGCAGCCGAAACUGCGGAGCAAAAAA-----UAAGACAGUGUCGACA-
.....((((((((((((...------.)))))).............((((((.((((((....))))))((......))).)))))...-----...)))))).......- ( -32.20)
>DroEre_CAF1 54817 105 + 1
CAUCAGCUGUCAGCAGCUUU------GGCUGCUGUCUGCCUAAAUAUUUGCCAGCUGCGUAAUUGCAGGCGAAACUAGGGAGGUAAAAAUAAAAAGAGCUAGUGUCUACAA
(((.((((..(((((((...------.)))))))(((.((((....((((((...((((....))))))))))..)))).))).............)))).)))....... ( -34.30)
>DroYak_CAF1 55080 101 + 1
CAUCAGCUGUCAGCAGCUUU------GGCUGCUGUCUGCCUAAAUAUUUGCCAGCUGCGUAAUUGCAGCCGAAACUGCGGUGGAAAAAA----AUAAGACAGUGUCUACAA
.....((((((((((((...------.)))))).((..((......((((...((((((....)))))))))).....))..)).....----....))))))........ ( -34.00)
>DroPer_CAF1 88644 89 + 1
CAUCAACUGUCAACAGCCUUUGCUUCUGCUGCUGUCUGCGUAAAUAUUUGCCAGCUGCGUAAUUGCAGCUGAAACCG------AAAAAA----------------CUACAG
......((((..(((((....((....)).)))))..(((........)))((((((((....))))))))......------......----------------..)))) ( -23.20)
>consensus
CAUCAGCUGUCAGCAGCUUU______GGCUGCUGUCUGCCUAAAUAUUUGCCAGCUGCGUAAUUGCAGCCGAAACUGCGGAG_AAAAAA_____UAAGACAGUGUCUACAA
..((.((.(.((((((((........)))))))).).))..............((((((....)))))).))....................................... (-19.58 = -20.75 +   1.17)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,362,571 – 21,362,671
Length 100
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.93
Mean single sequence MFE -30.67
Consensus MFE -24.34
Energy contribution -23.40
Covariance contribution -0.94
Combinations/Pair 1.25
Mean z-score -2.36
Structure conservation index 0.79
SVM decision value 1.55
SVM RNA-class probability 0.962948
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21362571 100 - 27905053
UUGUCGACUCUGUCUUA-----UUUUUUGCUCCGUAGUUUCGGCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAGCAGCC------AAAGCUGCUGACAGCUGAUG
..((((..(((((((..-----...((((((.((......))(((((......))))).)))))).....)))))))(((((((.------...))))))).....)))). ( -36.90)
>DroPse_CAF1 66744 89 - 1
CUGUAG----------------UUUUUU------CGGUUUCAGCUGCAAUUACGCAGCUGGCAAAUAUUUACGCAGACAGCAGCAGAAGCAAAGGCUGUUGACAGUUGAUG
((((.(----------------(.....------.....((((((((......)))))))).........)))))).(((((((..........))))))).......... ( -25.31)
>DroSim_CAF1 52415 99 - 1
-UGUCGACACUGUCUUA-----UUUUUUGCUCCGCAGUUUCGGCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAGCAGCC------AAAGCUGCUGACAGCUGAUG
-.((((.(.((((((..-----...(((((..........(((((((......)))))))))))).....)))))).(((((((.------...)))))))...).)))). ( -36.40)
>DroEre_CAF1 54817 105 - 1
UUGUAGACACUAGCUCUUUUUAUUUUUACCUCCCUAGUUUCGCCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAGCAGCC------AAAGCUGCUGACAGCUGAUG
.......((.(((((..............((.(((((.((.(((.((.........)).))).))...))))).)).(((((((.------...)))))))..))))).)) ( -28.60)
>DroYak_CAF1 55080 101 - 1
UUGUAGACACUGUCUUAU----UUUUUUCCACCGCAGUUUCGGCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAGCAGCC------AAAGCUGCUGACAGCUGAUG
((((.....((((((...----..(((.(((.((......))(((((......)))))))).))).....)))))).(((((((.------...)))))))))))...... ( -31.50)
>DroPer_CAF1 88644 89 - 1
CUGUAG----------------UUUUUU------CGGUUUCAGCUGCAAUUACGCAGCUGGCAAAUAUUUACGCAGACAGCAGCAGAAGCAAAGGCUGUUGACAGUUGAUG
((((.(----------------(.....------.....((((((((......)))))))).........)))))).(((((((..........))))))).......... ( -25.31)
>consensus
UUGUAGACACUGUCUUA_____UUUUUU_CUCCGCAGUUUCGGCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAGCAGCC______AAAGCUGCUGACAGCUGAUG
..................................(((((((((((((......))))))))................(((((((..........)))))))..)))))... (-24.34 = -23.40 +  -0.94)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,362,596 – 21,362,711
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.94
Mean single sequence MFE -23.68
Consensus MFE -19.39
Energy contribution -19.87
Covariance contribution 0.48
Combinations/Pair 1.12
Mean z-score -1.49
Structure conservation index 0.82
SVM decision value 0.03
SVM RNA-class probability 0.546297
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21362596 115 - 27905053
AAAUAUAUGUUUGUUUUAGCCUCUUUCUUUUUUUUUUUUUUUGUCGACUCUGUCUUA-----UUUUUUGCUCCGUAGUUUCGGCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAG
................................................(((((((..-----...((((((.((......))(((((......))))).)))))).....)))))))... ( -23.30)
>DroSec_CAF1 55366 110 - 1
AAAUAUAUGUUUGUUUUAGCCUCAUU-----UUUUUUUUUUCGUCGACACUGUCUUA-----UUUUUUGCUCCGUAGUUUCGGCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAG
..........................-----..................((((((..-----...((((((.((......))(((((......))))).)))))).....)))))).... ( -22.40)
>DroSim_CAF1 52440 105 - 1
GAAUAUAUGUUUGUUUUAGCCUCAUU-----UUUUU-----UGUCGACACUGUCUUA-----UUUUUUGCUCCGCAGUUUCGGCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAG
...........(((((..((((....-----...((-----((((((.(((((....-----...........))))).))((((((......)))))))))))).....))))))))). ( -27.26)
>DroEre_CAF1 54842 107 - 1
AAAUAUAUGUAUGUUUUAGCCUCUUU-------------UUUGUAGACACUAGCUCUUUUUAUUUUUACCUCCCUAGUUUCGCCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAG
...........(((((..((((....-------------(((((.((.(((((....................))))).))((.(((......)))))..))))).....))))))))). ( -19.65)
>DroYak_CAF1 55105 104 - 1
ACAUUUAUGUGUGUGCUAGCCGCUUU------------UUUUGUAGACACUGUCUUAU----UUUUUUCCACCGCAGUUUCGGCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAG
((((....))))((.((.(((.....------------.(((((.((.(((((.....----...........))))).))((((((......)))))).)))))......))))))).. ( -25.79)
>consensus
AAAUAUAUGUUUGUUUUAGCCUCUUU_____UUUUU__UUUUGUCGACACUGUCUUA_____UUUUUUGCUCCGUAGUUUCGGCUGCAAUUACGCAGCUGGCAAAUAUUUAGGCAGACAG
.......(((((((((..(((........................((.(((((....................))))).))((((((......)))))))))........))))))))). (-19.39 = -19.87 +   0.48)

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 12:59:11 2006