Locus 3238

Sequence ID X_DroMel_CAF1
Location 8,555,075 – 8,555,233
Length 158
Max. P 0.792034
window5317 window5318 window5319

overview

Window 7

Location 8,555,075 – 8,555,195
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.40
Mean single sequence MFE -50.59
Consensus MFE -37.62
Energy contribution -38.94
Covariance contribution 1.32
Combinations/Pair 1.15
Mean z-score -1.44
Structure conservation index 0.74
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8555075 120 + 22224390
GCUUUUGCUCUGCUGUUGGAUCGCUGCUGCUAUUAUCCCUAUUAUCCUUCGCGGUCGGCGCUGCGCUGACGCGGGCAGAUGACGUCGGCAGCGACGCCGACGCCGGCAGCGCCAGCAGGU
((....))....(((((((..((((((((............(((((.((((((.((((((...))))))))))))..)))))(((((((......))))))).))))))))))))))).. ( -56.20)
>DroSec_CAF1 15832 120 + 1
GCUUCUGCUCUGCCGUUGCAUCGAUGCUGCUAUUAUCCUUAUUAUCCUUCGCGGUCGGCGCAGCGCUGACGCGGGCAGAUGACGUCGGCAGCGACGCCGACGCCGGCAGCGCCAGCAGGU
...(((((((((((((.(((....))).))....................(((.((((((..(((((((((((......)).))))))).))..))))))))).)))))....)))))). ( -50.80)
>DroSim_CAF1 23042 120 + 1
GCUUCUGCUCUGCCGUUUCAUCGCUGCUGCUUUUAUCCUUAUUAUCCUUCGCGGUCGGCGCUGCGCUGACGCGGGCAGAUGACGUCGGCAGCGACGCCGACGCCGGCAGCGCCAGCAGGU
...((((((((((((..(((((((((((((....................)))).))))(((.(((....)))))).)))))(((((((......))))))).))))))....)))))). ( -51.95)
>DroEre_CAF1 16717 108 + 1
GCUUCUGCUCUGCUGCUGCUUCGCUGCUUCUU------------UGCUUUGCGGUCGGCGCAGCGCUGACGCGGGCAGAUGAUGCCGGCAGCGACGUCGACGCCGGCAGCGCCAGCAGGU
...((((((.(((((((((..(((.((.....------------.))...)))(((((((...((((...((.((((.....)))).)))))).)))))))).))))))))..)))))). ( -52.60)
>DroYak_CAF1 17978 100 + 1
AUUUUAGAUCUUAUC--------CUGCUGCUU------------UGCUUCGCGGUCGGCGCUGCGCUGACGCGGGCAGAUGACGGCGACAGUGACGUUGACGCCGGCAGCGCCAGUAGGU
.........(((((.--------.((((((((------------((((.((((.((((((...))))))))))))))))...(((((.(((.....))).)))))))))))...))))). ( -41.40)
>consensus
GCUUCUGCUCUGCUGUUGCAUCGCUGCUGCUUUUAUCC_UAUUAUCCUUCGCGGUCGGCGCUGCGCUGACGCGGGCAGAUGACGUCGGCAGCGACGCCGACGCCGGCAGCGCCAGCAGGU
........(((((((......((((((((..................((((((.((((((...)))))))))))).......(((((((......))))))).)))))))).))))))). (-37.62 = -38.94 +   1.32)

alignment

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secondary structure

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Window 8

Location 8,555,075 – 8,555,195
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.40
Mean single sequence MFE -47.96
Consensus MFE -36.64
Energy contribution -37.64
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -1.77
Structure conservation index 0.76
SVM decision value 0.59
SVM RNA-class probability 0.792034
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8555075 120 - 22224390
ACCUGCUGGCGCUGCCGGCGUCGGCGUCGCUGCCGACGUCAUCUGCCCGCGUCAGCGCAGCGCCGACCGCGAAGGAUAAUAGGGAUAAUAGCAGCAGCGAUCCAACAGCAGAGCAAAAGC
..(((((((((((((.((((((((((....))))))))))........((....))))))))))..((.....)).......((((....((....)).))))...)))))......... ( -52.60)
>DroSec_CAF1 15832 120 - 1
ACCUGCUGGCGCUGCCGGCGUCGGCGUCGCUGCCGACGUCAUCUGCCCGCGUCAGCGCUGCGCCGACCGCGAAGGAUAAUAAGGAUAAUAGCAGCAUCGAUGCAACGGCAGAGCAGAAGC
..((((.(((...)))((((((((((....)))))))))).((((((.(((((...(((((.((.....(....).......))......)))))...)))))...)))))))))).... ( -52.90)
>DroSim_CAF1 23042 120 - 1
ACCUGCUGGCGCUGCCGGCGUCGGCGUCGCUGCCGACGUCAUCUGCCCGCGUCAGCGCAGCGCCGACCGCGAAGGAUAAUAAGGAUAAAAGCAGCAGCGAUGAAACGGCAGAGCAGAAGC
..((((((.((((((.((((((((((....))))))))))((((...((((((.(((...))).)).))))..))))................))))))......))))))......... ( -50.90)
>DroEre_CAF1 16717 108 - 1
ACCUGCUGGCGCUGCCGGCGUCGACGUCGCUGCCGGCAUCAUCUGCCCGCGUCAGCGCUGCGCCGACCGCAAAGCA------------AAGAAGCAGCGAAGCAGCAGCAGAGCAGAAGC
..(((((.(((((((((((((.(.(((.(.(((.((((.....)))).))).).)))).))))))..(((...((.------------.....)).)))..))))).))..))))).... ( -47.40)
>DroYak_CAF1 17978 100 - 1
ACCUACUGGCGCUGCCGGCGUCAACGUCACUGUCGCCGUCAUCUGCCCGCGUCAGCGCAGCGCCGACCGCGAAGCA------------AAGCAGCAG--------GAUAAGAUCUAAAAU
.(((.(((((((((((((((.((.......)).)))))..........((....))))))))))....((......------------..)))).))--------).............. ( -36.00)
>consensus
ACCUGCUGGCGCUGCCGGCGUCGGCGUCGCUGCCGACGUCAUCUGCCCGCGUCAGCGCAGCGCCGACCGCGAAGGAUAAUA_GGAUAAAAGCAGCAGCGAUGCAACAGCAGAGCAGAAGC
..(((((((((((((.((((((((((....))))))))))........((....))))))))))....((.......................))...........)))))......... (-36.64 = -37.64 +   1.00)

alignment

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secondary structure

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Window 9

Location 8,555,115 – 8,555,233
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.67
Mean single sequence MFE -44.00
Consensus MFE -36.20
Energy contribution -37.08
Covariance contribution 0.88
Combinations/Pair 1.11
Mean z-score -1.42
Structure conservation index 0.82
SVM decision value 0.24
SVM RNA-class probability 0.650714
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8555115 118 - 22224390
CUUGUUGCACUGAUU--UCCUUUAUGAAGCAAAGACACAAACCUGCUGGCGCUGCCGGCGUCGGCGUCGCUGCCGACGUCAUCUGCCCGCGUCAGCGCAGCGCCGACCGCGAAGGAUAAU
...............--(((((..((.((((............))))((((((((.((((((((((....))))))))))........((....))))))))))...))..))))).... ( -47.90)
>DroSec_CAF1 15872 120 - 1
CUUGUUGCACUAGUUGCUCCUUUAUUAAGCAAAGACACAAACCUGCUGGCGCUGCCGGCGUCGGCGUCGCUGCCGACGUCAUCUGCCCGCGUCAGCGCUGCGCCGACCGCGAAGGAUAAU
......(((.....)))((((((....(((..((........))((((((((.((.((((((((((....))))))))))....))..)))))))))))(((.....))))))))).... ( -45.10)
>DroSim_CAF1 23082 120 - 1
CUUGUUGCACUAGUUGCUCCUUUAUUAAGCAAAGACACAAACCUGCUGGCGCUGCCGGCGUCGGCGUCGCUGCCGACGUCAUCUGCCCGCGUCAGCGCAGCGCCGACCGCGAAGGAUAAU
......(((.....)))((((((....((((............))))((((((((.((((((((((....))))))))))........((....))))))))))......)))))).... ( -47.80)
>DroEre_CAF1 16749 114 - 1
CUUGUUGCACUGGUU--UCCUUUAUUAAGCAGAGACACAAACCUGCUGGCGCUGCCGGCGUCGACGUCGCUGCCGGCAUCAUCUGCCCGCGUCAGCGCUGCGCCGACCGCAAAGCA----
....((((...((((--..........(((((..........)))))(((((((((((((.((....)).))))))))..........(((....))).)))))))))))))....---- ( -43.00)
>DroYak_CAF1 18002 114 - 1
CUUGUUGCACUGGUU--UCCUUAAUUAAGCAAAGACACGAACCUACUGGCGCUGCCGGCGUCAACGUCACUGUCGCCGUCAUCUGCCCGCGUCAGCGCAGCGCCGACCGCGAAGCA----
....((((...((((--(.(((.........)))....)))))...((((((((((((((.((.......)).)))))..........((....)))))))))))...))))....---- ( -36.20)
>consensus
CUUGUUGCACUGGUU__UCCUUUAUUAAGCAAAGACACAAACCUGCUGGCGCUGCCGGCGUCGGCGUCGCUGCCGACGUCAUCUGCCCGCGUCAGCGCAGCGCCGACCGCGAAGGAUAAU
....((((...................((((............))))((((((((.((((((((((....))))))))))........((....))))))))))....))))........ (-36.20 = -37.08 +   0.88)

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 10:54:39 2006