Locus 5157

Sequence ID 3R_DroMel_CAF1
Location 13,542,128 – 13,542,428
Length 300
Max. P 0.999953
window8421 window8422 window8423 window8424 window8425 window8426 window8427 window8428

overview

Window 1

Location 13,542,128 – 13,542,227
Length 99
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 78.36
Mean single sequence MFE -26.95
Consensus MFE -10.79
Energy contribution -12.71
Covariance contribution 1.92
Combinations/Pair 1.17
Mean z-score -2.61
Structure conservation index 0.40
SVM decision value 0.59
SVM RNA-class probability 0.791281
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13542128 99 - 27905053
GCUGCAGUCAUG---CACUAUCAUCAUCUGCACCAGCAGCAACAGCAGCAUCCGCCACCACCCCAUAUGCAGCAACAGC------AGCACCACGGCGGACCUGCACCA
(((((.....((---((...........))))...)))))....((((..((((((...........(((.((....))------.)))....)))))).)))).... ( -28.26)
>DroVir_CAF1 6802 102 - 1
GCAACAGCUAUGUCACACUAUCACCAUUUACAUCAACAACAACAG---CAGCCACAGGGGCCGCCUCUUCCACCACACA---UGCAGCACCACGGUGGACCACCGCCA
((((((....)))...............................(---(.(((.....))).))...............---)))........(((((....))))). ( -17.40)
>DroSec_CAF1 16874 99 - 1
GCUGCAGUCAUG---CACUAUCAUCAUCUGCACCAGCAACAACAGCAGCAUCCGCCACCACCCCAUAUGCAGCAACAGC------AGCACCACGGCGGACCUGCACCA
(((((((..(((---......)))...))))...))).......((((..((((((...........(((.((....))------.)))....)))))).)))).... ( -25.46)
>DroSim_CAF1 13888 99 - 1
GCUGCAGUCAUG---CACUAUCAUCAUCUGCACCAGCAGCAACAGCAGCAUCCGCCACCACCCCAUAUGCAGCAACAGC------AGCACCACGGCGGACCUGCACCA
(((((.....((---((...........))))...)))))....((((..((((((...........(((.((....))------.)))....)))))).)))).... ( -28.26)
>DroYak_CAF1 20680 93 - 1
GCUGCAGUCAUG---CACUAUCAUCAUUUACACCAG---------CAGCAUCCGCCACCACCCCAUAUGCAGCAACAGC---AGCAGCACCACGGCGGACCUGCACCA
..((((....))---))..................(---------(((..((((((...........(((.((....))---.)))(.....))))))).)))).... ( -23.60)
>DroAna_CAF1 14590 102 - 1
GCUGCUGUCAUG---CAUUAUCAUCACCUGCACCAGCAGC---AGCAGCACCCGCCGCCGCCUCACAUGCAGCAACAACAACAGCCGCACCACGGCGGACCGGCGCCA
((((((((..((---((...........))))...)))))---)))......((((((((((.....(((.((..........)).)))....)))))..)))))... ( -38.70)
>consensus
GCUGCAGUCAUG___CACUAUCAUCAUCUGCACCAGCAGCAACAGCAGCAUCCGCCACCACCCCAUAUGCAGCAACAGC______AGCACCACGGCGGACCUGCACCA
((((((((........)))........((((....)))).....))))).((((((.....................................))))))......... (-10.79 = -12.71 +   1.92) 

alignment

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secondary structure

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dotplot

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Window 2

Location 13,542,162 – 13,542,267
Length 105
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 73.09
Mean single sequence MFE -40.82
Consensus MFE -21.83
Energy contribution -24.88
Covariance contribution 3.06
Combinations/Pair 1.34
Mean z-score -1.96
Structure conservation index 0.53
SVM decision value 1.27
SVM RNA-class probability 0.938802
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13542162 105 + 27905053
AUAUGGGGUGGUGGCGGAUGCUGCUGUUGCUGCUGGUGCAGAUGAUGAUAGUG---CAUGACUGCAGCUGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGG
......((..(..((((......))))..)..))(.(((((.(.(((......---))).)))))).).(((((.((((((((.......)))))))).))))).... ( -46.40)
>DroVir_CAF1 6839 87 + 1
AGAGGCGGCCCCUGUGGCUG---CUGUUGUUGUUGAUGUAAAUGGUGAUAGUGUGACAUAGCUGUUGCUGAGUCGG------GAGUUGA------------ACCUGGC
((..(((((...(((.((.(---((((..(..((......))..)..))))))).)))..)))))..))..(((((------(......------------.)))))) ( -28.90)
>DroSec_CAF1 16908 105 + 1
AUAUGGGGUGGUGGCGGAUGCUGCUGUUGUUGCUGGUGCAGAUGAUGAUAGUG---CAUGACUGCAGCUGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGG
......((..(..((((......))))..)..))(.(((((.(.(((......---))).)))))).).(((((.((((((((.......)))))))).))))).... ( -44.50)
>DroSim_CAF1 13922 105 + 1
AUAUGGGGUGGUGGCGGAUGCUGCUGUUGCUGCUGGUGCAGAUGAUGAUAGUG---CAUGACUGCAGCUGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGG
......((..(..((((......))))..)..))(.(((((.(.(((......---))).)))))).).(((((.((((((((.......)))))))).))))).... ( -46.40)
>DroYak_CAF1 20717 96 + 1
AUAUGGGGUGGUGGCGGAUGCUG---------CUGGUGUAAAUGAUGAUAGUG---CAUGACUGCAGCUGGAUCCGGUCCUGGUGGUCCUCCGGGACCAGAUCCUGGG
.........(((.((((((((.(---------(((..((.....))..)))))---)))..)))).)))(((((.((((((((.......)))))))).))))).... ( -35.50)
>DroAna_CAF1 14630 96 + 1
AUGUGAGGCGGCGGCGGGUGCUGCU---GCUGCUGGUGCAGGUGAUGAUAAUG---CAUGACAGCAGCCGGGUC------UGGCGGACCGCCGGGUGCGGAGCCAGGG
......(((((((((....))))))---))).(((((((..((.(((......---))).)).))).)))).((------((((...((((.....)))).)))))). ( -43.20)
>consensus
AUAUGGGGUGGUGGCGGAUGCUGCUGUUGCUGCUGGUGCAGAUGAUGAUAGUG___CAUGACUGCAGCUGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGG
......((((((..(((......)))..))))))(.(((((.(.(((.........))).)))))).).(((((.((((((((.......)))))))).))))).... (-21.83 = -24.88 +   3.06) 

alignment

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secondary structure

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dotplot

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Window 3

Location 13,542,162 – 13,542,267
Length 105
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 73.09
Mean single sequence MFE -31.49
Consensus MFE -15.34
Energy contribution -18.93
Covariance contribution 3.60
Combinations/Pair 1.12
Mean z-score -3.14
Structure conservation index 0.49
SVM decision value 3.16
SVM RNA-class probability 0.998627
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13542162 105 - 27905053
CCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCAGCUGCAGUCAUG---CACUAUCAUCAUCUGCACCAGCAGCAACAGCAGCAUCCGCCACCACCCCAUAU
....((.(((((((((((.......))))))))))).)).((((((((....---.)))........((((....)))).....)))))................... ( -37.40)
>DroVir_CAF1 6839 87 - 1
GCCAGGU------------UCAACUC------CCGACUCAGCAACAGCUAUGUCACACUAUCACCAUUUACAUCAACAACAACAG---CAGCCACAGGGGCCGCCUCU
....(((------------.......------..(((..(((....)))..)))........)))...................(---(.(((.....))).)).... ( -14.43)
>DroSec_CAF1 16908 105 - 1
CCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCAGCUGCAGUCAUG---CACUAUCAUCAUCUGCACCAGCAACAACAGCAGCAUCCGCCACCACCCCAUAU
....((.(((((((((((.......))))))))))).)).((((((((....---.))).........(((....)))......)))))................... ( -35.20)
>DroSim_CAF1 13922 105 - 1
CCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCAGCUGCAGUCAUG---CACUAUCAUCAUCUGCACCAGCAGCAACAGCAGCAUCCGCCACCACCCCAUAU
....((.(((((((((((.......))))))))))).)).((((((((....---.)))........((((....)))).....)))))................... ( -37.40)
>DroYak_CAF1 20717 96 - 1
CCCAGGAUCUGGUCCCGGAGGACCACCAGGACCGGAUCCAGCUGCAGUCAUG---CACUAUCAUCAUUUACACCAG---------CAGCAUCCGCCACCACCCCAUAU
....(((((((((((.((.......)).))))))))))).(((((.......---....................)---------))))................... ( -30.73)
>DroAna_CAF1 14630 96 - 1
CCCUGGCUCCGCACCCGGCGGUCCGCCA------GACCCGGCUGCUGUCAUG---CAUUAUCAUCACCUGCACCAGCAGC---AGCAGCACCCGCCGCCGCCUCACAU
..(((((.((((.....))))...))))------)....(((((((((..((---((...........))))...)))))---)((.((....)).)).)))...... ( -33.80)
>consensus
CCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCAGCUGCAGUCAUG___CACUAUCAUCAUCUGCACCAGCAGCAACAGCAGCAUCCGCCACCACCCCAUAU
....((.((((((((.((.......)).)))))))).)).((((((((........)))........((((....)))).....)))))................... (-15.34 = -18.93 +   3.60) 

alignment

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secondary structure

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dotplot

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Window 4

Location 13,542,193 – 13,542,297
Length 104
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 75.74
Mean single sequence MFE -43.90
Consensus MFE -25.72
Energy contribution -27.00
Covariance contribution 1.28
Combinations/Pair 1.35
Mean z-score -1.92
Structure conservation index 0.59
SVM decision value 1.15
SVM RNA-class probability 0.922251
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13542193 104 + 27905053
GCUGGUGCAGAUGAUGAUAGUG---CAUGACUGCAGC---UGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGGGGCGGUGGUGCGCCGUAUGGAUGUGGGGCA-
((((...((.....)).))))(---(((.(((((..(---((((((.((((((((.......)))))))).))))).))..))))).))))(((.(((....))).))).- ( -49.70)
>DroGri_CAF1 11154 93 + 1
GUUGAUGUAGAUGGUGAUAGUGGGACAUGGCUGCGGCAGCCGGAUCAU------UUGGUGC------------ACCUGGCGCUGGUGGCCCGCCAUAGGGAUGGGGCAAGG
......((....((((..(((((....((((((...))))))..))))------).....)------------)))..)).....((.((((((....)).)))).))... ( -27.80)
>DroSec_CAF1 16939 104 + 1
GCUGGUGCAGAUGAUGAUAGUG---CAUGACUGCAGC---UGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGGGGCGGUGGUGCGCCGUAUGGAUGUGGGGCA-
((((...((.....)).))))(---(((.(((((..(---((((((.((((((((.......)))))))).))))).))..))))).))))(((.(((....))).))).- ( -49.70)
>DroSim_CAF1 13953 104 + 1
GCUGGUGCAGAUGAUGAUAGUG---CAUGACUGCAGC---UGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGGGGCGGUGGUGCGCCGUAUGGAUGUGGGGCA-
((((...((.....)).))))(---(((.(((((..(---((((((.((((((((.......)))))))).))))).))..))))).))))(((.(((....))).))).- ( -49.70)
>DroYak_CAF1 20740 103 + 1
-CUGGUGUAAAUGAUGAUAGUG---CAUGACUGCAGC---UGGAUCCGGUCCUGGUGGUCCUCCGGGACCAGAUCCUGGGGGCAGUGGUGCGCCAUAUGGAUGUGGCGCA-
-..................(((---(((.(((((..(---((((((.((((((((.......)))))))).))))).))..))))).))))((((((....)))))))).- ( -49.10)
>DroAna_CAF1 14658 98 + 1
GCUGGUGCAGGUGAUGAUAAUG---CAUGACAGCAGC---CGGGUC------UGGCGGACCGCCGGGUGCGGAGCCAGGGGGUGGUGGGGCACCAUAGGGGUGAGGCGCU-
(((((((((...........))---)))..)))).((---(.((((------.....)))).((.(((((...((((.....))))...)))))...)).....)))...- ( -37.40)
>consensus
GCUGGUGCAGAUGAUGAUAGUG___CAUGACUGCAGC___UGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGGGGCGGUGGUGCGCCAUAUGGAUGUGGCGCA_
((((.(((((.(.(((.........))).))))))......(((((.((((((((.......)))))))).)))))......))))..(((.(((((....))))).))). (-25.72 = -27.00 +   1.28) 

alignment

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secondary structure

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dotplot

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Window 5

Location 13,542,193 – 13,542,297
Length 104
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 75.74
Mean single sequence MFE -33.08
Consensus MFE -16.16
Energy contribution -18.15
Covariance contribution 1.99
Combinations/Pair 1.21
Mean z-score -2.51
Structure conservation index 0.49
SVM decision value 1.76
SVM RNA-class probability 0.976025
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13542193 104 - 27905053
-UGCCCCACAUCCAUACGGCGCACCACCGCCCCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCA---GCUGCAGUCAUG---CACUAUCAUCAUCUGCACCAGC
-.((.............((((......))))....((.(((((((((((.......))))))))))).)).---))(((((..(((---......)))...)))))..... ( -36.20)
>DroGri_CAF1 11154 93 - 1
CCUUGCCCCAUCCCUAUGGCGGGCCACCAGCGCCAGGU------------GCACCAA------AUGAUCCGGCUGCCGCAGCCAUGUCCCACUAUCACCAUCUACAUCAAC
................(((((.........)))))(((------------(......------..(((..(((((...)))))..))).......))))............ ( -19.76)
>DroSec_CAF1 16939 104 - 1
-UGCCCCACAUCCAUACGGCGCACCACCGCCCCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCA---GCUGCAGUCAUG---CACUAUCAUCAUCUGCACCAGC
-.((.............((((......))))....((.(((((((((((.......))))))))))).)).---))(((((..(((---......)))...)))))..... ( -36.20)
>DroSim_CAF1 13953 104 - 1
-UGCCCCACAUCCAUACGGCGCACCACCGCCCCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCA---GCUGCAGUCAUG---CACUAUCAUCAUCUGCACCAGC
-.((.............((((......))))....((.(((((((((((.......))))))))))).)).---))(((((..(((---......)))...)))))..... ( -36.20)
>DroYak_CAF1 20740 103 - 1
-UGCGCCACAUCCAUAUGGCGCACCACUGCCCCCAGGAUCUGGUCCCGGAGGACCACCAGGACCGGAUCCA---GCUGCAGUCAUG---CACUAUCAUCAUUUACACCAG-
-(((((((........)))))))..(((((.....(((((((((((.((.......)).))))))))))).---...)))))....---.....................- ( -40.00)
>DroAna_CAF1 14658 98 - 1
-AGCGCCUCACCCCUAUGGUGCCCCACCACCCCCUGGCUCCGCACCCGGCGGUCCGCCA------GACCCG---GCUGCUGUCAUG---CAUUAUCAUCACCUGCACCAGC
-...(((.........(((((...)))))....(((((.((((.....))))...))))------)....)---)).((((...((---((...........)))).)))) ( -30.10)
>consensus
_UGCCCCACAUCCAUACGGCGCACCACCGCCCCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCA___GCUGCAGUCAUG___CACUAUCAUCAUCUGCACCAGC
.(((.............((((......))))....((.((((((((.((.......)).)))))))).)).......)))............................... (-16.16 = -18.15 +   1.99) 

alignment

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secondary structure

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dotplot

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Window 6

Location 13,542,227 – 13,542,323
Length 96
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 75.69
Mean single sequence MFE -43.60
Consensus MFE -31.55
Energy contribution -31.90
Covariance contribution 0.35
Combinations/Pair 1.21
Mean z-score -2.54
Structure conservation index 0.72
SVM decision value 3.61
SVM RNA-class probability 0.999444
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13542227 96 + 27905053
UGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGGGGCGGUGGUGCGCCGUAUGGAUGUGGGGCAACAUUUUGUUGUUGCUGCUGGAUGCU
.(.((((((((((((.......))))).(((.((((..(.((((......)))).)..)))).)))(((((((......)))))))))))))).). ( -45.40)
>DroSim_CAF1 13987 96 + 1
UGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGGGGCGGUGGUGCGCCGUAUGGAUGUGGGGCAACAUUUUGUUGUUGCUGCUGGAUGCU
.(.((((((((((((.......))))).(((.((((..(.((((......)))).)..)))).)))(((((((......)))))))))))))).). ( -45.40)
>DroAna_CAF1 14692 84 + 1
CGGGUC------UGGCGGACCGCCGGGUGCGGAGCCAGGGGGUGGUGGGGCACCAUAGGGGUGAGGCGCUAUACUCU------GCUGCUGGACGCU
.(.(((------..((((.((((.....))))...(((((..(((((...((((.....))))...)))))..))))------)))))..))).). ( -40.00)
>consensus
UGGGUCCGGUCCUGGUGGUCCUCCAGGACCAGAUCCUGGGGGCGGUGGUGCGCCGUAUGGAUGUGGGGCAACAUUUUGUUGUUGCUGCUGGAUGCU
.(.(((((((...(((.((((.((((((.....))))))))))((((.(((.(((((....))))).))).))))........)))))))))).). (-31.55 = -31.90 +   0.35) 

alignment

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secondary structure

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dotplot

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Window 7

Location 13,542,227 – 13,542,323
Length 96
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 75.69
Mean single sequence MFE -32.87
Consensus MFE -25.44
Energy contribution -28.67
Covariance contribution 3.22
Combinations/Pair 1.04
Mean z-score -3.17
Structure conservation index 0.77
SVM decision value 4.82
SVM RNA-class probability 0.999953
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13542227 96 - 27905053
AGCAUCCAGCAGCAACAACAAAAUGUUGCCCCACAUCCAUACGGCGCACCACCGCCCCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCA
.((.....)).((((((......)))))).............((((......))))....((.(((((((((((.......))))))))))).)). ( -37.20)
>DroSim_CAF1 13987 96 - 1
AGCAUCCAGCAGCAACAACAAAAUGUUGCCCCACAUCCAUACGGCGCACCACCGCCCCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCA
.((.....)).((((((......)))))).............((((......))))....((.(((((((((((.......))))))))))).)). ( -37.20)
>DroAna_CAF1 14692 84 - 1
AGCGUCCAGCAGC------AGAGUAUAGCGCCUCACCCCUAUGGUGCCCCACCACCCCCUGGCUCCGCACCCGGCGGUCCGCCA------GACCCG
.((.....))...------........(((((..........)))))...........(((((.((((.....))))...))))------)..... ( -24.20)
>consensus
AGCAUCCAGCAGCAACAACAAAAUGUUGCCCCACAUCCAUACGGCGCACCACCGCCCCCAGGAUCUGGUCCUGGAGGACCACCAGGACCGGACCCA
.((.....)).((((((......)))))).............((((......))))....((.(((((((((((.......))))))))))).)). (-25.44 = -28.67 +   3.22) 

alignment

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secondary structure

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dotplot

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Window 8

Location 13,542,323 – 13,542,428
Length 105
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 68.52
Mean single sequence MFE -34.50
Consensus MFE -15.93
Energy contribution -16.68
Covariance contribution 0.75
Combinations/Pair 1.22
Mean z-score -2.08
Structure conservation index 0.46
SVM decision value 0.87
SVM RNA-class probability 0.870801
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13542323 105 - 27905053
CCUGCUGC------CACGCCCCCAUCGGCUGGAGCGGCUCCUGGUGCCGCUACACCGCCAACCUCGGGCCCGCCCACACCCAACAACAACAGCAACAACGGUAGCGAUCCC
..((((((------(..(((......)))(((.(((((((..(((...((......))..)))..))).))))))).......................)))))))..... ( -34.90)
>DroVir_CAF1 6985 99 - 1
GCGACUGGUGCAAGCGCAUCCCCAACUGUGGCAGCCAGUGCAGGUGGCGCUACACCACCAACCGCGGGUCCACCCACACCGAA------------CAACGGCAACGAUUCU
(((..(((((..(((((..((...((((.(....)))))...))..)))))....)))))..)))(((....)))........------------...((....))..... ( -33.80)
>DroSim_CAF1 14083 105 - 1
CCUGCUGC------CACGCCCCCAUCGGCUGGAGCGGCACCUGGUGGCGCUACACCGCCAACCUCGGGCCCGCCCACGCCCAACAAUAACAGCAACAACGGCAGCGAUCCC
..((((((------(..(((......)))(((.((((..((.(((((((......)))).)))..))..))))))).......................)))))))..... ( -40.90)
>DroAna_CAF1 14776 93 - 1
CCCUCUGC------CACGCCCCCGUCGGC------GGCA------GGUGCCACACCGCCAACUUCGGGCCCGCCCACUCCCAAUAAUAACAGUAACAACGGCAGUGACCCC
..(.((((------(..(((......)))------(((.------((((...)))))))......(((....)))........................))))).)..... ( -28.40)
>consensus
CCUGCUGC______CACGCCCCCAUCGGCUGGAGCGGCACCUGGUGGCGCUACACCGCCAACCUCGGGCCCGCCCACACCCAACAAUAACAGCAACAACGGCAGCGAUCCC
................(((..((...(((.(((.....))).((((......)))))))......(((....)))........................))..)))..... (-15.93 = -16.68 +   0.75) 

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 11:47:57 2006