Locus 4258

Sequence ID X_DroMel_CAF1
Location 11,184,987 – 11,185,139
Length 152
Max. P 0.969494
window6996 window6997 window6998 window6999

overview

Window 6

Location 11,184,987 – 11,185,099
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 86.61
Mean single sequence MFE -43.82
Consensus MFE -33.08
Energy contribution -32.45
Covariance contribution -0.63
Combinations/Pair 1.19
Mean z-score -2.70
Structure conservation index 0.75
SVM decision value 1.62
SVM RNA-class probability 0.967965
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11184987 112 + 22224390
CUAGAAACAGGUGUGAUUAGCCAAGAGAGCAUCACUGUUCUGUUCUGGGUGCCAAGAACCAAAGUCUGGCAACGACUGCAGCCAGAACAGCUGGGCCGGCGUUGCCAGGUGC
((((((.((((.(((((..(((....).)))))))...))))))))))(..((.(((.......)))(((((((.(((...((((.....))))..)))))))))).))..) ( -40.10)
>DroSim_CAF1 4967 112 + 1
CUAGAAAAAGCGGUGAUUAGCCAAGAGAGCAUCACUAUUCUGUUCUGGCUGCCAAGAACCAAAGUCCGGCAACGACUGCAGCCAGAACAGCUGGGCCGGCGUUGCCAGGUGC
((((.......((((((..(((....).))))))))...(((((((((((((..........((((.(....))))))))))))))))))))))((((((...))).))).. ( -43.00)
>DroEre_CAF1 4918 110 + 1
CUAGGAAA-GCUGUAAAUGGCCAUUACAGCAUCACUGUUGUGUUCUUGCUGCCAAGAACCGAAGUCUGGCAACGACCGCGGCCAGAACAGCUG-GCCGGCGUUGCCAGGCGU
.(((..(.-(((((((.......))))))).)..)))(((.(((((((....)))))))))).(((((((((((....(((((((.....)))-)))).))))))))))).. ( -51.80)
>DroYak_CAF1 4913 112 + 1
CUAGAAAAACCUGUAAUUUGCCAUUAGAGCAUCACUGUUCUGUUCUUGCUGCUAAGAACCGAAGUCUGGCAGCGCCCGCAGCCAGAACAGCUGGGCUGGCGUUGCCAGGUGU
................((((.....((((((....))))))(((((((....))))))))))).((((((((((((.((..((((.....)))))).))))))))))))... ( -40.40)
>consensus
CUAGAAAAAGCUGUAAUUAGCCAAGAGAGCAUCACUGUUCUGUUCUGGCUGCCAAGAACCAAAGUCUGGCAACGACCGCAGCCAGAACAGCUGGGCCGGCGUUGCCAGGUGC
...................(((...((((((....))))))(((((((....)))))))........(((((((.(((..(((((.....))).)))))))))))).))).. (-33.08 = -32.45 +  -0.63)

alignment

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secondary structure

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Window 7

Location 11,184,987 – 11,185,099
Length 112
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 86.61
Mean single sequence MFE -41.02
Consensus MFE -32.51
Energy contribution -32.95
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -2.07
Structure conservation index 0.79
SVM decision value 1.02
SVM RNA-class probability 0.902373
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11184987 112 - 22224390
GCACCUGGCAACGCCGGCCCAGCUGUUCUGGCUGCAGUCGUUGCCAGACUUUGGUUCUUGGCACCCAGAACAGAACAGUGAUGCUCUCUUGGCUAAUCACACCUGUUUCUAG
....(((((...)))))..((((((((((((.(((.......(((((...))))).....))).)))))))))....((((((((.....)))..)))))..)))....... ( -35.30)
>DroSim_CAF1 4967 112 - 1
GCACCUGGCAACGCCGGCCCAGCUGUUCUGGCUGCAGUCGUUGCCGGACUUUGGUUCUUGGCAGCCAGAACAGAAUAGUGAUGCUCUCUUGGCUAAUCACCGCUUUUUCUAG
((..(((((...))))).....(((((((((((((.......((((.....)))).....)))))))))))))....((((((((.....)))..))))).))......... ( -40.70)
>DroEre_CAF1 4918 110 - 1
ACGCCUGGCAACGCCGGC-CAGCUGUUCUGGCCGCGGUCGUUGCCAGACUUCGGUUCUUGGCAGCAAGAACACAACAGUGAUGCUGUAAUGGCCAUUUACAGC-UUUCCUAG
.(((((((((((((((((-(((.....))))))..)).)))))))))......(((((((....)))))))......)))..(((((((.......)))))))-........ ( -47.50)
>DroYak_CAF1 4913 112 - 1
ACACCUGGCAACGCCAGCCCAGCUGUUCUGGCUGCGGGCGCUGCCAGACUUCGGUUCUUAGCAGCAAGAACAGAACAGUGAUGCUCUAAUGGCAAAUUACAGGUUUUUCUAG
..(((((.....((((((...(((((((((((.....))(((((..(((....)))....))))).....)))))))))...)).....))))......)))))........ ( -40.60)
>consensus
ACACCUGGCAACGCCGGCCCAGCUGUUCUGGCUGCAGUCGUUGCCAGACUUCGGUUCUUGGCAGCAAGAACAGAACAGUGAUGCUCUAAUGGCUAAUCACAGCUUUUUCUAG
....((((((((((((((.(((.....)))))))..).)))))))))......(((((((....)))))))......((((((((.....)))..)))))............ (-32.51 = -32.95 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,185,025 – 11,185,139
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 89.47
Mean single sequence MFE -41.73
Consensus MFE -32.20
Energy contribution -32.58
Covariance contribution 0.37
Combinations/Pair 1.18
Mean z-score -3.42
Structure conservation index 0.77
SVM decision value 1.64
SVM RNA-class probability 0.969494
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11185025 114 + 22224390
UCUGUUCUGGGUGCCAAGAACCAAAGUCUGGCAACGACUGCAGCCAGAACAGCUGGGCCGGCGUUGCCAGGUGCAAAGAACGUAGAUGAGCAACAGAAAAGCAAACGAAAUGGA
..((((((((.(((..........((((.(....)))))))).))))))))((((...))))(((((((..(((.......)))..)).))))).................... ( -34.80)
>DroSim_CAF1 5005 114 + 1
UCUGUUCUGGCUGCCAAGAACCAAAGUCCGGCAACGACUGCAGCCAGAACAGCUGGGCCGGCGUUGCCAGGUGCAAAUAACGUAGAUGAGCAACAGAAAAGAAAACGAAAUGAA
..((((((((((((..........((((.(....)))))))))))))))))((((...))))(((((((..(((.......)))..)).))))).................... ( -39.30)
>DroEre_CAF1 4955 113 + 1
UGUGUUCUUGCUGCCAAGAACCGAAGUCUGGCAACGACCGCGGCCAGAACAGCUG-GCCGGCGUUGCCAGGCGUAAAGAACGCAGAAGAGCAACAGAAAAGCAAGCGAAAUGAA
(((((((((.((((...........(((((((((((....(((((((.....)))-)))).)))))))))))((.....)))))))))))).)))................... ( -47.70)
>DroYak_CAF1 4951 114 + 1
UCUGUUCUUGCUGCUAAGAACCGAAGUCUGGCAGCGCCCGCAGCCAGAACAGCUGGGCUGGCGUUGCCAGGUGUAAAGAACGUAGGCGAGCAACAGAGAAGCAAACGAAAUGAA
((((((((((((...........(..((((((((((((.((..((((.....)))))).))))))))))))..)..........)))))).))))))................. ( -45.10)
>consensus
UCUGUUCUGGCUGCCAAGAACCAAAGUCUGGCAACGACCGCAGCCAGAACAGCUGGGCCGGCGUUGCCAGGUGCAAAGAACGUAGAUGAGCAACAGAAAAGCAAACGAAAUGAA
((((((((((((((...........(((((((((((.(((..(((((.....))).)))))))))))))))).........)))).)))).))))))................. (-32.20 = -32.58 +   0.37)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,185,025 – 11,185,139
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 89.47
Mean single sequence MFE -38.04
Consensus MFE -31.59
Energy contribution -31.40
Covariance contribution -0.19
Combinations/Pair 1.18
Mean z-score -2.42
Structure conservation index 0.83
SVM decision value 1.57
SVM RNA-class probability 0.964445
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11185025 114 - 22224390
UCCAUUUCGUUUGCUUUUCUGUUGCUCAUCUACGUUCUUUGCACCUGGCAACGCCGGCCCAGCUGUUCUGGCUGCAGUCGUUGCCAGACUUUGGUUCUUGGCACCCAGAACAGA
.............((.(((((.(((.((...((((.....))..(((((((((.(....(((((.....)))))..).)))))))))......))...)))))..))))).)). ( -32.70)
>DroSim_CAF1 5005 114 - 1
UUCAUUUCGUUUUCUUUUCUGUUGCUCAUCUACGUUAUUUGCACCUGGCAACGCCGGCCCAGCUGUUCUGGCUGCAGUCGUUGCCGGACUUUGGUUCUUGGCAGCCAGAACAGA
..................(((.(((...............))).(((((...)))))..)))(((((((((((((.......((((.....)))).....))))))))))))). ( -35.46)
>DroEre_CAF1 4955 113 - 1
UUCAUUUCGCUUGCUUUUCUGUUGCUCUUCUGCGUUCUUUACGCCUGGCAACGCCGGC-CAGCUGUUCUGGCCGCGGUCGUUGCCAGACUUCGGUUCUUGGCAGCAAGAACACA
................((((((((((.....((((.....))))((((((((((((((-(((.....))))))..)).)))))))))((....))....)))))).)))).... ( -43.90)
>DroYak_CAF1 4951 114 - 1
UUCAUUUCGUUUGCUUCUCUGUUGCUCGCCUACGUUCUUUACACCUGGCAACGCCAGCCCAGCUGUUCUGGCUGCGGGCGCUGCCAGACUUCGGUUCUUAGCAGCAAGAACAGA
.........((((.((((.(((((((.(((...((.....))..((((((.((((....(((((.....)))))..)))).)))))).....)))....))))))))))))))) ( -40.10)
>consensus
UUCAUUUCGUUUGCUUUUCUGUUGCUCAUCUACGUUCUUUACACCUGGCAACGCCGGCCCAGCUGUUCUGGCUGCAGUCGUUGCCAGACUUCGGUUCUUGGCAGCAAGAACAGA
.............((.((((((((((.....((((.....))..((((((((((((((.(((.....)))))))..).)))))))))......))....)))))).)))).)). (-31.59 = -31.40 +  -0.19)

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 11:20:30 2006