Locus 1885

Sequence ID X_DroMel_CAF1
Location 5,228,370 – 5,228,570
Length 200
Max. P 0.995661
window3061 window3062 window3063

overview

Window 1

Location 5,228,370 – 5,228,490
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.61
Mean single sequence MFE -29.04
Consensus MFE -28.02
Energy contribution -28.13
Covariance contribution 0.11
Combinations/Pair 1.07
Mean z-score -1.01
Structure conservation index 0.96
SVM decision value 0.93
SVM RNA-class probability 0.884415
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5228370 120 - 22224390
GCUACGUCAUAUGGCACCAUUUCGGUGCCAAUUGUUUUAUUCUUAUUGGCCAAUUUCGUCGUCCACUGGAAAUAGUAUUCGCCAGGAAUUGGAUGUAUAGCGCAUAUAAAAAGUUCUAAC
((((...(((.(((((((.....)))))))...................((((((((..((...((((....))))...))...)))))))))))..))))................... ( -30.50)
>DroVir_CAF1 7957 120 - 1
GCUACGUCGUAUGGCACCAUUUCAGUGCCAAUUGUUUUAUUUUUAUUGGCCAAUUUCGUCGUCCACUGGAAAUAGUAUUCACCAGGAAUUGGAUGUAUAGCGCAUAUAAAAAGUUCUAAA
((((...(((.((((((.......))))))...................((((((((.......((((....))))........)))))))))))..))))................... ( -23.76)
>DroGri_CAF1 7579 120 - 1
GCUACGUCGUAUGGCACCAUUUCGGUGCCAAUUGUUUUAUUUUUAUUGGCCAAUUUUGUCGUCCACUGGAAAUAGUAUUCGCCAGGAAUUGGAUGUAUAGCGCAUAUAAAAAGUUCUAAC
((((((((...(((((((.....)))))))...............(((((.(((.((((..(((...))).)))).))).)))))......)))))..)))................... ( -29.90)
>DroWil_CAF1 6553 120 - 1
GCUACGUCAUAUGGCACCAGUUCGGUGCCAAUUGUUUUGUUCUUAUUGGCCAAUUUCGUCGUCCACUGGAAAUAGUAUUCGCCAGGAAUUGGAUGUAUAGCGCAUAUAAAAAGUUCUAAU
((((...(((.(((((((.....)))))))...................((((((((..((...((((....))))...))...)))))))))))..))))................... ( -30.50)
>DroMoj_CAF1 9550 120 - 1
GCUACGUCGUAGGGCACCAUUUCGGUGCCAAUUGUUUUAUUUUUAUUGGCCAAUUUCGUCGUCCACUGGAAAUAGUAUUCGCCAGGAAUUGGAUGUAUAGCGCAUAUAAAAAGUUCUAAC
((((...(((..((((((.....))))))....................((((((((..((...((((....))))...))...)))))))))))..))))................... ( -29.10)
>DroAna_CAF1 6495 120 - 1
GCUACGUCAUAUGGCACCAAUUCGGUGCCAAUUGUUUUAUUCUUAUUGGCCAAUUUCGUCGUCCACUGGAAAUAGUAUUCGCCAGGAAUUGGAUGUAUAGCGCAUAUAAAAAGUUCUAAC
((((...(((.(((((((.....)))))))...................((((((((..((...((((....))))...))...)))))))))))..))))................... ( -30.50)
>consensus
GCUACGUCAUAUGGCACCAUUUCGGUGCCAAUUGUUUUAUUCUUAUUGGCCAAUUUCGUCGUCCACUGGAAAUAGUAUUCGCCAGGAAUUGGAUGUAUAGCGCAUAUAAAAAGUUCUAAC
((((...(((.(((((((.....)))))))...................((((((((..((...((((....))))...))...)))))))))))..))))................... (-28.02 = -28.13 +   0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,228,450 – 5,228,570
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.89
Mean single sequence MFE -26.70
Consensus MFE -24.94
Energy contribution -24.63
Covariance contribution -0.30
Combinations/Pair 1.15
Mean z-score -1.88
Structure conservation index 0.93
SVM decision value 2.60
SVM RNA-class probability 0.995661
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5228450 120 + 22224390
AUAAAACAAUUGGCACCGAAAUGGUGCCAUAUGACGUAGCUUUAUCAUUACCUAUGUUCCUUCGAUUAUAUUUAAUCUGCCGCGUAAUGCUGCUGCAUUCAAAGCUAUUCACAGAUGCAU
..........(((((((.....)))))))..(((.((((((((....................(((((....)))))(((.(((......))).)))...)))))))))))......... ( -29.50)
>DroVir_CAF1 8037 120 + 1
AUAAAACAAUUGGCACUGAAAUGGUGCCAUACGACGUAGCUUUAUCAUUACCUAUGUUCCUUCGAUUAUAUUUAAUCUGCCGCGUUAUGCUGCUUCAUUCAAAGCUAUUCACAGACGCAU
..........(((((((.....)))))))...(((((((.(........).))))))).....(((((....)))))....(((((.((..((((......))))....))..))))).. ( -25.70)
>DroGri_CAF1 7659 120 + 1
AUAAAACAAUUGGCACCGAAAUGGUGCCAUACGACGUAGCUUUAUCACUACCUAUGUUCCUUCGAUUAUAUUUAAUCUGCCGUGUUAUGCUGCUUCAUUCAAAGCUAUUCACAGACGCAU
..........(((((((.....)))))))...((.((((((((....................(((((....))))).((.((.....)).)).......)))))))))).......... ( -25.90)
>DroWil_CAF1 6633 120 + 1
ACAAAACAAUUGGCACCGAACUGGUGCCAUAUGACGUAGCUUUAUCAUUACCUAUGUUCCUUCGAUUAUAUUUAAUCUGCCGCGUAAUGCUGUUACAUUCAAAGCUAUUCACAGACGCAU
..........(((((((.....)))))))..(((.((((((((....................(((((....)))))......(((((...)))))....)))))))))))......... ( -26.10)
>DroMoj_CAF1 9630 120 + 1
AUAAAACAAUUGGCACCGAAAUGGUGCCCUACGACGUAGCUUUAUCACUACCUAUGUUCCUUCGAUUAUAUUUAAUCUGCCGUGUCAUGCUGCUACAUUCAAAGCUAUUCACAGACGCAU
...........((((((.....))))))....(((((((.(........).))))))).....(((((....)))))....(((((.((..(((........)))....))..))))).. ( -24.80)
>DroAna_CAF1 6575 120 + 1
AUAAAACAAUUGGCACCGAAUUGGUGCCAUAUGACGUAGCUUUAUCAUUACCUAUGUUCCUUCGAUUAUAUUUAAUCUGCCGCGUAAUGCUGCUGCAUUCGAAACUAUUCACAGACGCAU
..........(((((((.....)))))))...(((((((.(........).))))))).....(((((....)))))....(((((((((....))))).(((....)))....)))).. ( -28.20)
>consensus
AUAAAACAAUUGGCACCGAAAUGGUGCCAUACGACGUAGCUUUAUCAUUACCUAUGUUCCUUCGAUUAUAUUUAAUCUGCCGCGUAAUGCUGCUACAUUCAAAGCUAUUCACAGACGCAU
..........(((((((.....)))))))...((.((((((((....................(((((....))))).((.((.....)).)).......)))))))))).......... (-24.94 = -24.63 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,228,450 – 5,228,570
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.89
Mean single sequence MFE -32.08
Consensus MFE -26.19
Energy contribution -26.08
Covariance contribution -0.11
Combinations/Pair 1.10
Mean z-score -1.93
Structure conservation index 0.82
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5228450 120 - 22224390
AUGCAUCUGUGAAUAGCUUUGAAUGCAGCAGCAUUACGCGGCAGAUUAAAUAUAAUCGAAGGAACAUAGGUAAUGAUAAAGCUACGUCAUAUGGCACCAUUUCGGUGCCAAUUGUUUUAU
..(((..(((((.((((((((..(((.((........)).))).((((..(((..((....))..)))..))))..))))))))..)))))(((((((.....)))))))..)))..... ( -33.80)
>DroVir_CAF1 8037 120 - 1
AUGCGUCUGUGAAUAGCUUUGAAUGAAGCAGCAUAACGCGGCAGAUUAAAUAUAAUCGAAGGAACAUAGGUAAUGAUAAAGCUACGUCGUAUGGCACCAUUUCAGUGCCAAUUGUUUUAU
.(((((.((((....(((((....)))))..)))))))))...(((((....)))))...((((((......(((((........))))).((((((.......))))))..)))))).. ( -28.60)
>DroGri_CAF1 7659 120 - 1
AUGCGUCUGUGAAUAGCUUUGAAUGAAGCAGCAUAACACGGCAGAUUAAAUAUAAUCGAAGGAACAUAGGUAGUGAUAAAGCUACGUCGUAUGGCACCAUUUCGGUGCCAAUUGUUUUAU
....((.((((....(((((....)))))..))))))(((((.(((((....)))))............(((((......)))))))))).(((((((.....))))))).......... ( -33.60)
>DroWil_CAF1 6633 120 - 1
AUGCGUCUGUGAAUAGCUUUGAAUGUAACAGCAUUACGCGGCAGAUUAAAUAUAAUCGAAGGAACAUAGGUAAUGAUAAAGCUACGUCAUAUGGCACCAGUUCGGUGCCAAUUGUUUUGU
.......(((((.((((((((..(((....((.....)).))).((((..(((..((....))..)))..))))..))))))))..)))))(((((((.....))))))).......... ( -31.40)
>DroMoj_CAF1 9630 120 - 1
AUGCGUCUGUGAAUAGCUUUGAAUGUAGCAGCAUGACACGGCAGAUUAAAUAUAAUCGAAGGAACAUAGGUAGUGAUAAAGCUACGUCGUAGGGCACCAUUUCGGUGCCAAUUGUUUUAU
.((((.(((((....(((.((.((((....))))..)).))).(((((....))))).......)))))(((((......)))))..)))).((((((.....))))))........... ( -33.60)
>DroAna_CAF1 6575 120 - 1
AUGCGUCUGUGAAUAGUUUCGAAUGCAGCAGCAUUACGCGGCAGAUUAAAUAUAAUCGAAGGAACAUAGGUAAUGAUAAAGCUACGUCAUAUGGCACCAAUUCGGUGCCAAUUGUUUUAU
.....((((((....((..(((((((....))))).))..)).(((((....))))).......))))))..(((((........))))).(((((((.....))))))).......... ( -31.50)
>consensus
AUGCGUCUGUGAAUAGCUUUGAAUGAAGCAGCAUUACGCGGCAGAUUAAAUAUAAUCGAAGGAACAUAGGUAAUGAUAAAGCUACGUCAUAUGGCACCAUUUCGGUGCCAAUUGUUUUAU
.......(((((.((((((((.........((........))..((((..(((..((....))..)))..))))..))))))))..)))))(((((((.....))))))).......... (-26.19 = -26.08 +  -0.11)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:01 2006