Locus 3418

Sequence ID 2L_DroMel_CAF1
Location 9,887,417 – 9,887,620
Length 203
Max. P 0.925176
window5410 window5411 window5412 window5413 window5414

overview

Window 0

Location 9,887,417 – 9,887,529
Length 112
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 95.50
Mean single sequence MFE -25.34
Consensus MFE -20.03
Energy contribution -20.19
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -2.11
Structure conservation index 0.79
SVM decision value 0.83
SVM RNA-class probability 0.862531
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9887417 112 + 22407834
AUUUCUGUUGCUCUUGCGCUGGCAUACGAAAUUGGAAGUUGGCACUGCCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUA-
.......(((((((((.(((((((.....(((.....))).....))))...))))))))))))....(((((((((((.................))))))))))).....- ( -26.83)
>DroSec_CAF1 95289 110 + 1
AUUU-UGUUGCUCUUG--CUGGCAUGCGAAAUUGGAAGUUGGCACUGCCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUAC
....-..(((((((((--(((((((((.((........)).))).))))...)).)))))))))....(((((((((((.................)))))))))))...... ( -28.43)
>DroSim_CAF1 102107 110 + 1
AUUU-UGUUGCUCUUG--CUGGCAUGCGAAAUUGGAAGUUGGCACUGCCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUAC
....-..(((((((((--(((((((((.((........)).))).))))...)).)))))))))....(((((((((((.................)))))))))))...... ( -28.43)
>DroEre_CAF1 100267 109 + 1
AUUU-UGUUGCUCUUG--CUGGCUUACGAAA-UGGAAGUUGGCACUGUCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUAC
....-..(((((((((--(..((((.(....-..)))))..)).((......))..))))))))....(((((((((((.................)))))))))))...... ( -23.93)
>DroYak_CAF1 101387 109 + 1
AUUU-UGUUACUCUUG--CUGGCAUACGAAA-UGGAUGUUGGCACUGUCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUAUGAUGCAUAC
.(((-(((((....((--(..((((.(....-..)))))..))).........(((...)))..............)))))))).........(.((((....)))).).... ( -19.10)
>consensus
AUUU_UGUUGCUCUUG__CUGGCAUACGAAAUUGGAAGUUGGCACUGCCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUAC
.......((((((((....((.....)).....((...(((((...)))))...))))))))))....(((((((((((.................)))))))))))...... (-20.03 = -20.19 +   0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,887,417 – 9,887,529
Length 112
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -24.76
Consensus MFE -19.46
Energy contribution -20.50
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -2.07
Structure conservation index 0.79
SVM decision value 0.67
SVM RNA-class probability 0.818186
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9887417 112 - 22407834
-UAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGGCAGUGCCAACUUCCAAUUUCGUAUGCCAGCGCAAGAGCAACAGAAAU
-..(((((((((((((((...............))))))))))))..((((((.((.(((..((((.(((....))).))))........))))).)))))))))........ ( -26.86)
>DroSec_CAF1 95289 110 - 1
GUAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGGCAGUGCCAACUUCCAAUUUCGCAUGCCAG--CAAGAGCAACA-AAAU
((.(((((((((((((((...............))))))))))))..((((((...((((..((((.(((....))).))))........)))))--)))))))))).-.... ( -25.76)
>DroSim_CAF1 102107 110 - 1
GUAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGGCAGUGCCAACUUCCAAUUUCGCAUGCCAG--CAAGAGCAACA-AAAU
((.(((((((((((((((...............))))))))))))..((((((...((((..((((.(((....))).))))........)))))--)))))))))).-.... ( -25.76)
>DroEre_CAF1 100267 109 - 1
GUAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGACAGUGCCAACUUCCA-UUUCGUAAGCCAG--CAAGAGCAACA-AAAU
((.(((((((((((((((...............))))))))))))..((((((...((((((.(((.((((........))-))))).)))))))--)))))))))).-.... ( -26.66)
>DroYak_CAF1 101387 109 - 1
GUAUGCAUCAUAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGACAGUGCCAACAUCCA-UUUCGUAUGCCAG--CAAGAGUAACA-AAAU
((.(((((((.(((((((...............))))))).))))..((((((...((((...(((.((((........))-)))))...)))))--)))))))))).-.... ( -18.76)
>consensus
GUAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGGCAGUGCCAACUUCCAAUUUCGUAUGCCAG__CAAGAGCAACA_AAAU
...(((((((((((((((...............))))))))))))..(((((...(((((..((((.(((....))).))))........)))))..))))))))........ (-19.46 = -20.50 +   1.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,887,450 – 9,887,553
Length 103
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 95.45
Mean single sequence MFE -21.34
Consensus MFE -18.64
Energy contribution -18.60
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.61
Structure conservation index 0.87
SVM decision value 1.17
SVM RNA-class probability 0.925176
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9887450 103 + 22407834
GGAAGUUGGCACUGCCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUA-------CACUUAUAGGGAUGCACAUGCAAU
((...(((((...)))))...))....(((.....(((((((((((.................)))))))))))((((.-------..((....)).))))...)))... ( -22.53)
>DroSec_CAF1 95319 110 + 1
GGAAGUUGGCACUGCCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUACUGCACACACUUAUAGGGAUGCACAUGCAUU
((...(((((...)))))...))............(((((((((((.................)))))))))))((((..((((..(........)..)))).))))... ( -23.23)
>DroSim_CAF1 102137 110 + 1
GGAAGUUGGCACUGCCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUACUGCACACACUUAUAGGGAUGCACAUGCAUU
((...(((((...)))))...))............(((((((((((.................)))))))))))((((..((((..(........)..)))).))))... ( -23.23)
>DroEre_CAF1 100296 110 + 1
GGAAGUUGGCACUGUCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUACUGCACACACUUAUAGAGAUGCACAUGCAUU
..(((((((((.((((....(((...)))......(((((((((((.................)))))))))))).))).))).)).)))).....(((((....))))) ( -19.83)
>DroYak_CAF1 101416 110 + 1
GGAUGUUGGCACUGUCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUAUGAUGCAUACUGCACACACUUAUAGGGAUGCACAUGCAUU
((...(((((...)))))...)).........((((((...(((..........)))....))))))....(((((((..((((..(........)..)))).))))))) ( -17.90)
>consensus
GGAAGUUGGCACUGCCAAAAGCCAAGGGCAAAAUAAUCAAAUAUAACAAAAACGAUAACAGGAUUAUAUUUGAUGCAUACUGCACACACUUAUAGGGAUGCACAUGCAUU
((...(((((...)))))...))....(((.....(((((((((((.................)))))))))))((((...................))))...)))... (-18.64 = -18.60 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,887,450 – 9,887,553
Length 103
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 95.45
Mean single sequence MFE -22.86
Consensus MFE -19.38
Energy contribution -20.42
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.46
Structure conservation index 0.85
SVM decision value 0.43
SVM RNA-class probability 0.735163
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9887450 103 - 22407834
AUUGCAUGUGCAUCCCUAUAAGUG-------UAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGGCAGUGCCAACUUCC
..((((((..(..........)..-------))))))(((((((((((...............))))))))))).......(((...)))..(((((...)))))..... ( -21.76)
>DroSec_CAF1 95319 110 - 1
AAUGCAUGUGCAUCCCUAUAAGUGUGUGCAGUAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGGCAGUGCCAACUUCC
..((((((((((..((.....).)..)))).))))))(((((((((((...............))))))))))).......(((...)))..(((((...)))))..... ( -24.66)
>DroSim_CAF1 102137 110 - 1
AAUGCAUGUGCAUCCCUAUAAGUGUGUGCAGUAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGGCAGUGCCAACUUCC
..((((((((((..((.....).)..)))).))))))(((((((((((...............))))))))))).......(((...)))..(((((...)))))..... ( -24.66)
>DroEre_CAF1 100296 110 - 1
AAUGCAUGUGCAUCUCUAUAAGUGUGUGCAGUAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGACAGUGCCAACUUCC
..((((((((((((.(.....).).))))).))))))(((((((((((...............)))))))))))...........(((((..........)))))..... ( -22.96)
>DroYak_CAF1 101416 110 - 1
AAUGCAUGUGCAUCCCUAUAAGUGUGUGCAGUAUGCAUCAUAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGACAGUGCCAACAUCC
..((((((((((..((.....).)..)))).))))))(((.(((((((...............))))))).)))...........(((((..........)))))..... ( -20.26)
>consensus
AAUGCAUGUGCAUCCCUAUAAGUGUGUGCAGUAUGCAUCAAAUAUAAUCCUGUUAUCGUUUUUGUUAUAUUUGAUUAUUUUGCCCUUGGCUUUUGGCAGUGCCAACUUCC
..(((((((((((.((.....).).))))).))))))(((((((((((...............)))))))))))...........(((((..........)))))..... (-19.38 = -20.42 +   1.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,887,529 – 9,887,620
Length 91
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 84.16
Mean single sequence MFE -26.96
Consensus MFE -21.04
Energy contribution -22.04
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.92
Structure conservation index 0.78
SVM decision value 0.76
SVM RNA-class probability 0.842469
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9887529 91 + 22407834
------CACUUAUAGGGAUGCACAUGCAAUCAUAAAGCCGCUGGGCAGAUUACAUUUGGAGAGCACUGUGUGUGUGUGUGUGUUGUUGUUGUAGCCG
------.((..((((.((((((((((((........(((....)))....(((((.((.....))..))))))))))))))))).)))).))..... ( -23.70)
>DroSec_CAF1 95399 86 + 1
UGCACACACUUAUAGGGAUGCACAUGCAUUCA-AAAGCCGCUGGGCAGAUUACAUUUGGAGAGCACUGUGUGUGUGUG-------UUGUUGGA---G
.((((((((.(((((((((((....)))))).-...(((....)))...................))))).)))))))-------).......---. ( -28.70)
>DroSim_CAF1 102217 86 + 1
UGCACACACUUAUAGGGAUGCACAUGCAUUCA-AAAGCCGCUGGGCAGAUUACAUUUGGAGAGCACUGUGUGUGUGUG-------UUGUUGGA---G
.((((((((.(((((((((((....)))))).-...(((....)))...................))))).)))))))-------).......---. ( -28.70)
>DroEre_CAF1 100376 85 + 1
UGCACACACUUAUAGAGAUGCACAUGCAUUCA-AAAGCCGCUGGGCAGAUUACAUUUGAGAAACACUGUGUGUGUGUA-------G-CUCAGA---A
.((((((((.(((((.(((((....)))))..-...(((....)))...................))))).)))))).-------)-).....---. ( -23.70)
>DroYak_CAF1 101496 85 + 1
UGCACACACUUAUAGGGAUGCACAUGCAUUCG-AAAGCCGCUGGGCAGAUUACAUUUGUGGAGCACUGUGUGUGUGUA-------G-CUUGGA---A
.((((((((.(((((((((((....)))))).-......(((..((((((...))))))..))).))))).)))))).-------)-).....---. ( -30.00)
>consensus
UGCACACACUUAUAGGGAUGCACAUGCAUUCA_AAAGCCGCUGGGCAGAUUACAUUUGGAGAGCACUGUGUGUGUGUG_______UUGUUGGA___G
...((((((.(((((((((((....)))))).....(((....)))...................))))).)))))).................... (-21.04 = -22.04 +   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 10:52:04 2006