Locus 6825

Sequence ID X_DroMel_CAF1
Location 16,979,518 – 16,979,821
Length 303
Max. P 0.996507
window11173 window11174 window11175 window11176 window11177

overview

Window 3

Location 16,979,518 – 16,979,623
Length 105
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 83.13
Mean single sequence MFE -26.50
Consensus MFE -21.80
Energy contribution -20.44
Covariance contribution -1.36
Combinations/Pair 1.31
Mean z-score -1.82
Structure conservation index 0.82
SVM decision value 0.53
SVM RNA-class probability 0.770359
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16979518 105 - 22224390
CUAAAACUGCAGCGUUGAUCCUUACAGGGUUGUGGUAUUCAACUGGACCAUAAUAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGCCUCAAAAAUGC-AAC
.......((((...((((........((((((((((..........))))))....))))........(((((((((....)))).))))).))))...)))-).. ( -24.70)
>DroVir_CAF1 6501 106 - 1
CUAAAACCGCAUCAGUGAUUUACACGCUGGCGUGGUAUUCAAUUGGACUACAUAAAAGCCCAUGAUUAACUAUUCCUCUUAAGGGCAUUGGCUCGAAGAUGCAAAC
........(((((.(((.....)))((..(.(((((..........)))))......((((.(((.............))).)))).)..)).....))))).... ( -24.32)
>DroGri_CAF1 5680 106 - 1
CUAAAACCGCAUCAGUGAUUCACACGCUGAUGUGGUAUUCAAUUGGACUACAUCAAAGCCCAUGAUUUACUAUUCCUCUUAAGGGCAUUGGCUAAAAGAUGCGAAC
.......((((((.(((.....)))(((((((((((..........))))))))...((((.(((.............))).))))...))).....))))))... ( -30.12)
>DroSim_CAF1 6453 105 - 1
CUAAAACUGCAGCGUUGAUCUCUACAGCGUUGUGGUAUUCAACUGGACCACAAUAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGCCUCAAAAAUGA-AAC
.....((..((((((((.......))))))))..)).((((..(((.............)))(((...(((((((((....)))).))))).)))....)))-).. ( -25.72)
>DroMoj_CAF1 5860 106 - 1
CUAAAACCGCAUCAGUGACCCACACGCUGGUGUGGUAUUCAAUUGGACUACAUUGAACCCCAUGGUUAACUAUUCCUCUUAAGGGCAUUGGCUAAAAGAUGCAUUC
........(((((.(((.....)))((..((((((..((((((.(.....)))))))..)).............(((....)))))))..)).....))))).... ( -28.70)
>DroAna_CAF1 9496 106 - 1
CUAAAACUGCAGCGUUGAUCCUCACAGCGUUGUGGUAUUCAAUUGGACCAAAAUGAACCCCAUGGUUAACUAUUCCUCUUAAGGGCAUUGCCUCAAAAAUGCGAAC
.....((..((((((((.......))))))))..)).(((....(((........((((....))))......)))........(((((........)))))))). ( -25.44)
>consensus
CUAAAACCGCAGCAGUGAUCCACACACUGUUGUGGUAUUCAAUUGGACCACAAUAAACCCCAUGAUUAACUAUUCCUCUUAAGGGCAUUGCCUCAAAAAUGC_AAC
.....((((((((((((.......))))))))))))..(((..(((.............)))))).........(((....)))(((((........))))).... (-21.80 = -20.44 +  -1.36)

alignment

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secondary structure

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Window 4

Location 16,979,557 – 16,979,651
Length 94
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 70.53
Mean single sequence MFE -23.04
Consensus MFE -22.67
Energy contribution -21.11
Covariance contribution -1.56
Combinations/Pair 1.35
Mean z-score -2.76
Structure conservation index 0.98
SVM decision value 1.59
SVM RNA-class probability 0.966231
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16979557 94 - 22224390
---CACCAAGGGUAUCAUUAUCCGUCCAAAACUAAAACUGCAGCGUUGAUCCUUACAGGGUUGUGGUAUUCAACUGGACCAUAAUAAACCCCAUGAU
---......((((...(((((..(((((........((..((((.(((.......))).))))..)).......))))).)))))..))))...... ( -23.06)
>DroVir_CAF1 6541 88 - 1
A-------ACACU--CGAUUUAUGUCCAAAACUAAAACCGCAUCAGUGAUUUACACGCUGGCGUGGUAUUCAAUUGGACUACAUAAAAGCCCAUGAU
.-------.....--........((((((.......(((((..(((((.......)))))..)))))......)))))).................. ( -20.72)
>DroGri_CAF1 5720 75 - 1
----------------------UGUCCAAAACUAAAACCGCAUCAGUGAUUCACACGCUGAUGUGGUAUUCAAUUGGACUACAUCAAAGCCCAUGAU
----------------------.((((((.......((((((((((((.......))))))))))))......)))))).................. ( -25.72)
>DroSim_CAF1 6492 94 - 1
---CACCAAGAGUAUCAUUAUCCGUCCAAAACUAAAACUGCAGCGUUGAUCUCUACAGCGUUGUGGUAUUCAACUGGACCACAAUAAACCCCAUGAU
---....................(((((........((..((((((((.......))))))))..)).......))))).................. ( -20.86)
>DroMoj_CAF1 5900 95 - 1
AUCUAUCAGAGAU--UGGCUUAUGUCCACAACUAAAACCGCAUCAGUGACCCACACGCUGGUGUGGUAUUCAAUUGGACUACAUUGAACCCCAUGGU
....((((.....--.((.(((.(((((........((((((((((((.......)))))))))))).......))))).....))).))...)))) ( -25.26)
>DroAna_CAF1 9536 88 - 1
---UGUAAA------CGAUAUCCGUCCAAAACUAAAACUGCAGCGUUGAUCCUCACAGCGUUGUGGUAUUCAAUUGGACCAAAAUGAACCCCAUGGU
---......------......((((((((.......((..((((((((.......))))))))..))......))))))....(((.....))))). ( -22.62)
>consensus
____A_CAA___U__CGAUAUCCGUCCAAAACUAAAACCGCAGCAGUGAUCCACACACUGUUGUGGUAUUCAAUUGGACCACAAUAAACCCCAUGAU
.......................(((((........((((((((((((.......)))))))))))).......))))).................. (-22.67 = -21.11 +  -1.56)

alignment

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secondary structure

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Window 5

Location 16,979,651 – 16,979,756
Length 105
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 72.68
Mean single sequence MFE -18.45
Consensus MFE -12.90
Energy contribution -13.07
Covariance contribution 0.17
Combinations/Pair 1.16
Mean z-score -1.11
Structure conservation index 0.70
SVM decision value 0.65
SVM RNA-class probability 0.812162
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16979651 105 - 22224390
UGGACUAAUAUCAAUUGAAAUUGUUUUAACUAUCCUUGUGCUUGAAGAUAUAA---GCCACUUCCUGCUCUCCUGGAAAUUAAAACAACACUAAAGU-----UAAGCAUUAUU-
..((((....((....))..(((((((((...(((..(.((..((((......---....))))..)).)....)))..)))))))))......)))-----)..........- ( -15.30)
>DroVir_CAF1 6629 104 - 1
UGGACUCAUAAUAAAU-AUAGGGUUUUAA-UAUCCUAGUGCCUGAAGAUCUCA---UUCUCUUCCCGCUCUCUUGGAACUUAAAACCACAUUACGCU----AUGCUCUUUUUG-
.(((..((((......-....((((((((-..(((.((.((..(((((.....---...)))))..))...)).)))..)))))))).........)----))).))).....- ( -19.61)
>DroPse_CAF1 6341 100 - 1
UGGACU-----CAAAGGAAACGGUUUUAA-UAUCCUAGUGCUUGAAGAACCAUAUCCCCUCUUCCCGCUCUCUUGGAACUUAAAACAACAUUU--------GUAAGCCCCAUCA
.((...-----(((((....).(((((((-..(((.((.((..(((((...........)))))..))...)).)))..)))))))....)))--------)....))...... ( -19.60)
>DroSim_CAF1 6586 105 - 1
UGGACUAAUAUCAAUUGAAAUUGUUUUAACUAUCCUUGUGCCUGAAGAUAUAA---GCCACUUCCUGCUCUCCUGGAAAUUAAAACAACACUAUAGU-----UAAGCAUUAUU-
..(((((...((....))..(((((((((...(((..(.((..((((......---....))))..)).)....)))..))))))))).....))))-----)..........- ( -15.80)
>DroMoj_CAF1 5995 108 - 1
UGGACUGAUAUUAAAU-AUGAGGUUUUAA-UAUCCUAGUGCUUGAAGAUUAGA---CUCUCUUCCCGCUCUCUUGGAACUUAAAAUCACAUUUAUCUGAAUGUAAUCUUCAUU-
..((..(((.......-....((((((((-..(((.((.((..(((((.....---...)))))..))...)).)))..))))))))((((((....)))))).))).))...- ( -20.90)
>DroPer_CAF1 6349 100 - 1
UGGACU-----CAAAGGAAACGGUUUUAA-UAUCCUAGUGCUUGAAGAUACAUAUCCCCUCUUCCCGCUCUCUUGGAACUUAAGACAACAUUU--------GUAAGCCCCACCA
.((...-----(((((....).(((((((-..(((.((.((..(((((...........)))))..))...)).)))..)))))))....)))--------)....))...... ( -19.50)
>consensus
UGGACU_AUAUCAAAUGAAACGGUUUUAA_UAUCCUAGUGCUUGAAGAUAUAA___CCCUCUUCCCGCUCUCUUGGAACUUAAAACAACAUUA___U____GUAAGCAUCAUU_
.....................((((((((...(((.((.((..((((.............))))..))...)).)))..))))))))........................... (-12.90 = -13.07 +   0.17)

alignment

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secondary structure

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Window 6

Location 16,979,721 – 16,979,821
Length 100
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 69.32
Mean single sequence MFE -29.99
Consensus MFE -19.12
Energy contribution -18.60
Covariance contribution -0.52
Combinations/Pair 1.42
Mean z-score -3.12
Structure conservation index 0.64
SVM decision value 2.71
SVM RNA-class probability 0.996507
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16979721 100 + 22224390
GGAUAGUUAAAACAAUUUCAAUUGAUAUUAGUCCAUUUUUGGU-UAUGCUCAGUAUGGCAUCGUAUUUUUAA--GCCAUCUGGCAUUGAGGUGGACUGACACG
............((((....))))...((((((((((((....-.((((.(((.(((((.............--)))))))))))).)))))))))))).... ( -28.42)
>DroVir_CAF1 6700 96 + 1
GGAUA-UUAAAACCCUAU-AUUUAUUAUGAGUCCAAUUGAAAUGUAUGCUUAGCUCAGCAUGGAAA-A-CAA--GCUGGCUGGCAUUGAGGUGGACUAAGAU-
.....-............-..........((((((..........(((((.(((.((((.((....-.-)).--)))))))))))).....)))))).....- ( -23.96)
>DroPse_CAF1 6412 94 + 1
GGAUA-UUAAAACCGUUUCCUUUG-----AGUCCAUUUUUAGUGGAUGCGCAGCU-GGGAAGGGGUUUUCCU--UUCAGCUGGCAUUGAGGUGGACUGACAAA
(((..-...........)))....-----((((((((((.....(((((.(((((-((.(((((....))))--)))))))))))))))))))))))...... ( -33.12)
>DroSim_CAF1 6656 99 + 1
GGAUAGUUAAAACAAUUUCAAUUGAUAUUAGUCCAUUUUU-UU-UAUGCUCAGUAUGGCAUGGUAUUUUUAA--GCCGUCUGGCAUUGAGGUGGACUGAAACG
.....(((....((((....))))...((((((((((((.-..-.((((.(((.(((((.(((.....))).--)))))))))))).))))))))))))))). ( -31.10)
>DroMoj_CAF1 6070 92 + 1
GGAUA-UUAAAACCUCAU-AUUUAAUAUCAGUCCAAUUGAGAU----GCGCAGUGCAG--UGGAAA-A-UAAUACUUGCCUGGCAUUGAGGUGGACUAACUU-
.((((-(((((.......-.)))))))))((((((.....(((----((.(((.((((--((....-.-...))).)))))))))))....)))))).....- ( -30.20)
>DroPer_CAF1 6420 94 + 1
GGAUA-UUAAAACCGUUUCCUUUG-----AGUCCAUUUUUAGUGGAUGCGCAGCU-GGGAAGGGGUUUUCCU--UUCAGCUGGCAUUGAGGUGGACUGACAAA
(((..-...........)))....-----((((((((((.....(((((.(((((-((.(((((....))))--)))))))))))))))))))))))...... ( -33.12)
>consensus
GGAUA_UUAAAACCAUUUCAUUUGAUAU_AGUCCAUUUUUAGU_UAUGCGCAGCU_GGCAUGGAAUUUUCAA__GCCAGCUGGCAUUGAGGUGGACUGACAA_
.............................((((((((((......((((.(((.(((((....((....))...)))))))))))).))))))))))...... (-19.12 = -18.60 +  -0.52)

alignment

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secondary structure

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Window 7

Location 16,979,721 – 16,979,821
Length 100
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 69.32
Mean single sequence MFE -22.20
Consensus MFE -8.16
Energy contribution -8.66
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.82
Structure conservation index 0.37
SVM decision value 2.64
SVM RNA-class probability 0.996030
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16979721 100 - 22224390
CGUGUCAGUCCACCUCAAUGCCAGAUGGC--UUAAAAAUACGAUGCCAUACUGAGCAUA-ACCAAAAAUGGACUAAUAUCAAUUGAAAUUGUUUUAACUAUCC
.((((.((((((.....((((((((((((--.............))))).))).)))).-........)))))).))))........................ ( -21.86)
>DroVir_CAF1 6700 96 - 1
-AUCUUAGUCCACCUCAAUGCCAGCCAGC--UUG-U-UUUCCAUGCUGAGCUAAGCAUACAUUUCAAUUGGACUCAUAAUAAAU-AUAGGGUUUUAA-UAUCC
-.....((((((.....((((.(((((((--.((-.-....)).)))).)))..))))..........))))))..........-...((((.....-.)))) ( -19.36)
>DroPse_CAF1 6412 94 - 1
UUUGUCAGUCCACCUCAAUGCCAGCUGAA--AGGAAAACCCCUUCCC-AGCUGCGCAUCCACUAAAAAUGGACU-----CAAAGGAAACGGUUUUAA-UAUCC
((((..((((((.....((((((((((.(--(((......))))..)-))))).))))..........))))))-----))))(....)........-..... ( -25.66)
>DroSim_CAF1 6656 99 - 1
CGUUUCAGUCCACCUCAAUGCCAGACGGC--UUAAAAAUACCAUGCCAUACUGAGCAUA-AA-AAAAAUGGACUAAUAUCAAUUGAAAUUGUUUUAACUAUCC
......((((((.....(((((((..(((--.............)))...))).)))).-..-.....))))))............................. ( -16.84)
>DroMoj_CAF1 6070 92 - 1
-AAGUUAGUCCACCUCAAUGCCAGGCAAGUAUUA-U-UUUCCA--CUGCACUGCGC----AUCUCAAUUGGACUGAUAUUAAAU-AUGAGGUUUUAA-UAUCC
-.....((((((.....((((((((((.((....-.-.....)--)))).))).))----))......))))))(((((((((.-.......)))))-)))). ( -23.80)
>DroPer_CAF1 6420 94 - 1
UUUGUCAGUCCACCUCAAUGCCAGCUGAA--AGGAAAACCCCUUCCC-AGCUGCGCAUCCACUAAAAAUGGACU-----CAAAGGAAACGGUUUUAA-UAUCC
((((..((((((.....((((((((((.(--(((......))))..)-))))).))))..........))))))-----))))(....)........-..... ( -25.66)
>consensus
_AUGUCAGUCCACCUCAAUGCCAGCCGAC__UUAAAAAUACCAUGCC_AACUGAGCAUA_ACUAAAAAUGGACU_AUAUCAAAUGAAACGGUUUUAA_UAUCC
......((((((.....(((((((..........................))).))))..........))))))............................. ( -8.16 =  -8.66 +   0.50)

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 12:23:52 2006