Locus 8842

Sequence ID 3R_DroMel_CAF1
Location 23,681,113 – 23,681,228
Length 115
Max. P 0.997364
window14195 window14196 window14197 window14198

overview

Window 5

Location 23,681,113 – 23,681,206
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 85.33
Mean single sequence MFE -32.20
Consensus MFE -20.91
Energy contribution -21.97
Covariance contribution 1.06
Combinations/Pair 1.08
Mean z-score -4.05
Structure conservation index 0.65
SVM decision value 1.80
SVM RNA-class probability 0.977930
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23681113 93 + 27905053
UCCAGGACAUCAGGAUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUGCUGUUCCUGCUGCUGCUGUGU
..(((.(((.((((((((((((((.......))))....)))))....((((((((((((....))))))))))))))))).)).).)))... ( -32.80)
>DroSec_CAF1 142724 87 + 1
UCCAUGACAUCAGGAUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUG------CUGUUGCUGCUGUGU
((((.((.((....)).))))))............((((((....(((((((((((((((....))))))))------)))))))..)))))) ( -35.70)
>DroSim_CAF1 142575 93 + 1
UCCAGGACAUCAGGAUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUGCUGUUGCUGUUGCUGCUGUGU
((((((...........))))))............((((((....((((((((((((((((.......).)))))))))))))))..)))))) ( -37.00)
>DroYak_CAF1 149261 72 + 1
UUCAGGAUAUCAGGAUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCU---------------------GCUGCUGUGU
(((.((((((....)))))).)))..........(((........)))(((((((((....)---------------------)))))))).. ( -23.30)
>consensus
UCCAGGACAUCAGGAUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUG______CUGUUGCUGCUGUGU
((((.((.((....)).))))))...........(((........)))((((((((((((.....((....))......)))))))))))).. (-20.91 = -21.97 +   1.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 23,681,113 – 23,681,206
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 85.33
Mean single sequence MFE -29.71
Consensus MFE -21.20
Energy contribution -21.51
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -4.12
Structure conservation index 0.71
SVM decision value 2.30
SVM RNA-class probability 0.991926
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23681113 93 - 27905053
ACACAGCAGCAGCAGGAACAGCAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAUCCUGAUGUCCUGGA
..(((((((((((.(......)....((....)))))))))))))(((((....)))))...........(((((((((....)))).))))) ( -32.40)
>DroSec_CAF1 142724 87 - 1
ACACAGCAGCAACAG------CAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAUCCUGAUGUCAUGGA
.....((((((((((------((.((((......)))).))))))))).......)))............(((((((((....))))).)))) ( -30.51)
>DroSim_CAF1 142575 93 - 1
ACACAGCAGCAACAGCAACAGCAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAUCCUGAUGUCCUGGA
.....(((......(((((((((.((((......)))).))))))))).......)))............(((((((((....)))).))))) ( -33.82)
>DroYak_CAF1 149261 72 - 1
ACACAGCAGC---------------------AGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAUCCUGAUAUCCUGAA
..((((((((---------------------(....)))))))))(((((....)))))..........(((..(((((....)))))..))) ( -22.10)
>consensus
ACACAGCAGCAACAG______CAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAUCCUGAUGUCCUGGA
..(((((((((.........................)))))))))(((((....)))))...........(((((((((....))))).)))) (-21.20 = -21.51 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 23,681,127 – 23,681,228
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 85.57
Mean single sequence MFE -31.06
Consensus MFE -20.95
Energy contribution -23.07
Covariance contribution 2.12
Combinations/Pair 1.03
Mean z-score -3.40
Structure conservation index 0.67
SVM decision value 1.90
SVM RNA-class probability 0.982019
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23681127 101 + 27905053
AUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUGCUGUUCCUGCUGCUGCUGUGUGCGAUAUGAAAAAUGCAAAGGG
...(((((((......))))(((((..(((((((((((((((((((.....((....))......)))))))))))).)))).))).....))))).))). ( -33.60)
>DroSec_CAF1 142738 95 + 1
AUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUG------CUGUUGCUGCUGUGUGCGAUAUGAAAAAUGCAAAGGG
(((((.((((.......))))((((((....(((((((((((((((....))))))))------)))))))..))))))..)))))............... ( -36.60)
>DroSim_CAF1 142589 101 + 1
AUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUGCUGUUGCUGUUGCUGCUGUGUGCGAUAUGAAAAAUGCAAAGGG
...(((((((......))))(((((......(((((((((((((((....)))))))))))))))((((((........))))))......))))).))). ( -37.30)
>DroEre_CAF1 149669 77 + 1
AUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCU---------------------G---CUGUGUGCGAUAUGAAAAAUGCAAAGGG
...(((((((......))))(((((..(((((((((((((((...)))---------------------)---)))).)))).))).....))))).))). ( -22.20)
>DroYak_CAF1 149275 80 + 1
AUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCU---------------------GCUGCUGUGUGCGAUAUGAAAAAUGCAAAGGG
...(((((((......))))(((((..((((((((((((((((....)---------------------)))))))).)))).))).....))))).))). ( -25.60)
>consensus
AUAUCUGGAAUUUAAUUUUCUGCAUAGAUACGCAACAGCAGCAGCGCUCUUGCUGUUG______CUG_UGCUGCUGUGUGCGAUAUGAAAAAUGCAAAGGG
...(((((((......))))(((((..(((((((((((((((((((...................)))))))))))).)))).))).....))))).))). (-20.95 = -23.07 +   2.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 23,681,127 – 23,681,228
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 85.57
Mean single sequence MFE -29.28
Consensus MFE -20.81
Energy contribution -21.81
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -4.53
Structure conservation index 0.71
SVM decision value 2.85
SVM RNA-class probability 0.997364
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23681127 101 - 27905053
CCCUUUGCAUUUUUCAUAUCGCACACAGCAGCAGCAGGAACAGCAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAU
...(((((((.....(((.((((.(((((((((((.(......)....((....))))))))))))))))))))..))))))).................. ( -33.90)
>DroSec_CAF1 142738 95 - 1
CCCUUUGCAUUUUUCAUAUCGCACACAGCAGCAACAG------CAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAU
...(((((((....(.....((.....)).(((((((------((.((((......)))).)))))))))).....))))))).................. ( -30.30)
>DroSim_CAF1 142589 101 - 1
CCCUUUGCAUUUUUCAUAUCGCACACAGCAGCAACAGCAACAGCAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAU
...(((((((.....(((.((((.(((((((((.(.((....))....((....))).))))))))))))))))..))))))).................. ( -30.60)
>DroEre_CAF1 149669 77 - 1
CCCUUUGCAUUUUUCAUAUCGCACACAG---C---------------------AGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAU
...(((((((.....(((.((((.((((---(---------------------(((...)))))))))))))))..))))))).................. ( -24.10)
>DroYak_CAF1 149275 80 - 1
CCCUUUGCAUUUUUCAUAUCGCACACAGCAGC---------------------AGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAU
...(((((((.....(((.((((.((((((((---------------------(....))))))))))))))))..))))))).................. ( -27.50)
>consensus
CCCUUUGCAUUUUUCAUAUCGCACACAGCAGCA_CAG______CAACAGCAAGAGCGCUGCUGCUGUUGCGUAUCUAUGCAGAAAAUUAAAUUCCAGAUAU
...(((((((.....(((.((((.(((((((((.........................))))))))))))))))..))))))).................. (-20.81 = -21.81 +   1.00)

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 13:21:03 2006