Locus 3163

Sequence ID X_DroMel_CAF1
Location 8,403,568 – 8,403,805
Length 237
Max. P 0.973080
window5190 window5191 window5192 window5193 window5194

overview

Window 0

Location 8,403,568 – 8,403,685
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.61
Mean single sequence MFE -46.60
Consensus MFE -37.70
Energy contribution -38.45
Covariance contribution 0.75
Combinations/Pair 1.11
Mean z-score -1.74
Structure conservation index 0.81
SVM decision value 0.55
SVM RNA-class probability 0.777487
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8403568 117 + 22224390
GUCCUCAUAGGAUAUCUCAUCGGUUAUCUUGACCAAGAGCUCCAGCAGUUCCCUGCUAUUCGCGGCCGUCAUUGGGGGAGCUCCAGUCGC---CGCAGCCGGCGGAUUUCCGAUGACACC
((((.....))))...(((((((..((((.(((...((((((((((((....)))))........(((....))).)))))))..)))((---((....))))))))..))))))).... ( -48.10)
>DroSec_CAF1 2774 117 + 1
GUCCUCGUAGGAUAUCUCAUCGGUGAUCUUGACCAAGAGCUCCAGCAGUUCUCUGCUAUUAGCGGCUGUCAUUGGAGGAGCUCCAGUCGC---CGCAGCCGGCGGAUUUCCGAUGACACC
((((.....))))...(((((((.(((((.(.((....(((..(((((....)))))...)))((((((.(((((((...)))))))...---.)))))))))))))).))))))).... ( -47.10)
>DroEre_CAF1 6221 117 + 1
GUCCUCGUAGGAUAUCUCAUCGGUGAUCUUGACCAAGAGCUCCAGCAGUUCCCUGCUGUUGCCGGCGGUCAUUUGGGGAGCUCCCGUCGC---CGCGGCCGGCUGAUUUCCGAGGGCAGC
((((((...(((.(((.....((((((..(((((..(.((..((((((....))))))..)))...)))))....(((....))))))))---)((.....)).))).)))))))))... ( -47.70)
>DroYak_CAF1 5859 120 + 1
GUCCUCGUAGGAUAUCUCAUCGGUGAUUUUGACCAAUAGCUCCAGUAGUUCCCUGCUAUUGCCGGCCGUCAUUUGAGGAGCACCCGUCGCUGUCGCGGCCGGUGGAUUUCCGAGGGCAGC
((((((...(((.(((.((((((((((..((((.....((((((((((....)))))...........((....)))))))....))))..)))...)))))))))).)))))))))... ( -43.50)
>consensus
GUCCUCGUAGGAUAUCUCAUCGGUGAUCUUGACCAAGAGCUCCAGCAGUUCCCUGCUAUUGCCGGCCGUCAUUGGAGGAGCUCCAGUCGC___CGCAGCCGGCGGAUUUCCGAGGACACC
((((((...(((.(((.(.(((((......(((...((((((((((((....)))))........(((....))).)))))))..)))((....)).))))).)))).)))))))))... (-37.70 = -38.45 +   0.75)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,403,568 – 8,403,685
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.61
Mean single sequence MFE -45.20
Consensus MFE -31.66
Energy contribution -33.73
Covariance contribution 2.06
Combinations/Pair 1.05
Mean z-score -1.72
Structure conservation index 0.70
SVM decision value 0.13
SVM RNA-class probability 0.600281
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8403568 117 - 22224390
GGUGUCAUCGGAAAUCCGCCGGCUGCG---GCGACUGGAGCUCCCCCAAUGACGGCCGCGAAUAGCAGGGAACUGCUGGAGCUCUUGGUCAAGAUAACCGAUGAGAUAUCCUAUGAGGAC
.((.(((((((..(((.((((....))---))((((((((((((.((......))........(((((....)))))))))))).)))))..)))..))))))).)).(((.....))). ( -50.00)
>DroSec_CAF1 2774 117 - 1
GGUGUCAUCGGAAAUCCGCCGGCUGCG---GCGACUGGAGCUCCUCCAAUGACAGCCGCUAAUAGCAGAGAACUGCUGGAGCUCUUGGUCAAGAUCACCGAUGAGAUAUCCUACGAGGAC
.((.(((((((..(((.((((....))---))((((((((((((((....))...........(((((....)))))))))))).)))))..)))..))))))).)).(((.....))). ( -45.60)
>DroEre_CAF1 6221 117 - 1
GCUGCCCUCGGAAAUCAGCCGGCCGCG---GCGACGGGAGCUCCCCAAAUGACCGCCGGCAACAGCAGGGAACUGCUGGAGCUCUUGGUCAAGAUCACCGAUGAGAUAUCCUACGAGGAC
.....(((((((.(((.((((....))---))((((((.....)))...((((((..(((..((((((....))))))..)))..)))))).).))........))).)))...)))).. ( -47.60)
>DroYak_CAF1 5859 120 - 1
GCUGCCCUCGGAAAUCCACCGGCCGCGACAGCGACGGGUGCUCCUCAAAUGACGGCCGGCAAUAGCAGGGAACUACUGGAGCUAUUGGUCAAAAUCACCGAUGAGAUAUCCUACGAGGAC
.....(((((((.(((((((((((((....))((.((.....)))).......))))))(((((((.((......))...)))))))..............)).))).)))...)))).. ( -37.60)
>consensus
GCUGCCAUCGGAAAUCCGCCGGCCGCG___GCGACGGGAGCUCCCCAAAUGACGGCCGCCAAUAGCAGGGAACUGCUGGAGCUCUUGGUCAAGAUCACCGAUGAGAUAUCCUACGAGGAC
...(((((((((.(((((.(((.(((....))).((((((((((.....((.....)).....(((((....)))))))))))))))..........))).)).))).)))...)))))) (-31.66 = -33.73 +   2.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,403,608 – 8,403,725
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.25
Mean single sequence MFE -50.28
Consensus MFE -39.46
Energy contribution -39.90
Covariance contribution 0.44
Combinations/Pair 1.16
Mean z-score -1.71
Structure conservation index 0.78
SVM decision value 0.44
SVM RNA-class probability 0.737640
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8403608 117 - 22224390
CACUGGGACACCAGUUGCUUCGACGGGAGCCCCGUCAACAGGUGUCAUCGGAAAUCCGCCGGCUGCG---GCGACUGGAGCUCCCCCAAUGACGGCCGCGAAUAGCAGGGAACUGCUGGA
..((((....))))((((...((((((...))))))....((((((((.((.....(((((....))---)))...((....)).)).))))).))))))).((((((....)))))).. ( -49.80)
>DroSec_CAF1 2814 117 - 1
CACUGGGACACCAGUUGCUUCAACGGGAGCUCCGUCAAUAGGUGUCAUCGGAAAUCCGCCGGCUGCG---GCGACUGGAGCUCCUCCAAUGACAGCCGCUAAUAGCAGAGAACUGCUGGA
.(((((....))))).((((((..((((((((((((....((..((....))...))((((....))---))))).)))))))))....))).)))......((((((....)))))).. ( -47.50)
>DroEre_CAF1 6261 117 - 1
CACUGGGGCACCUGUUGCUCUAACGGGCGCCCCGUCCUCCGCUGCCCUCGGAAAUCAGCCGGCCGCG---GCGACGGGAGCUCCCCAAAUGACCGCCGGCAACAGCAGGGAACUGCUGGA
....(((((.(((((((...))))))).)))))....((((.......)))).....((((((...(---....)(((.....)))........))))))..((((((....)))))).. ( -54.10)
>DroYak_CAF1 5899 120 - 1
CACUGGAGCACCUGUUGCUCCAACGGGCGCCCCGUCCUCCGCUGCCCUCGGAAAUCCACCGGCCGCGACAGCGACGGGUGCUCCUCAAAUGACGGCCGGCAAUAGCAGGGAACUACUGGA
....(((((((((((((((.....(((((...)))))..(((.(((...((....))...))).)))..)))))))))))))))...........((.((....)).))........... ( -49.70)
>consensus
CACUGGGACACCAGUUGCUCCAACGGGAGCCCCGUCAACAGCUGCCAUCGGAAAUCCGCCGGCCGCG___GCGACGGGAGCUCCCCAAAUGACGGCCGCCAAUAGCAGGGAACUGCUGGA
....(((((.((((((((....(((((...))))).....((.(((..(((....)))..))).))....)))))))).)))))..................((((((....)))))).. (-39.46 = -39.90 +   0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,403,685 – 8,403,805
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.75
Mean single sequence MFE -55.97
Consensus MFE -47.42
Energy contribution -47.92
Covariance contribution 0.50
Combinations/Pair 1.14
Mean z-score -1.74
Structure conservation index 0.85
SVM decision value 0.67
SVM RNA-class probability 0.817351
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8403685 120 + 22224390
UGUUGACGGGGCUCCCGUCGAAGCAACUGGUGUCCCAGUGGGCAGGACCAACGCACCGGCGGGCAGGUUGCCCACAUAGGCGUCCAAUUGGUUGAGCGCCGUCAGCUUGCGCUCCACAUU
.((((((((.((((((((((..((.(((((....)))))((......))...))..))))))...((.((((......)))).))........)))).)))))))).............. ( -51.30)
>DroSec_CAF1 2891 120 + 1
UAUUGACGGAGCUCCCGUUGAAGCAACUGGUGUCCCAGUGGGCAGGACCAACGCGCCGGAGGGCAGGUUGCCCACAUAGGCGUCCAGUUGGUUGAGCGCCGUCAGCUUGCGCUCCACAUU
...((((((.((((........((.(((((....)))))..))..((((((((((((.(.((((.....)))).)...)))))...))))))))))).))))))((....))........ ( -52.70)
>DroEre_CAF1 6338 120 + 1
GGAGGACGGGGCGCCCGUUAGAGCAACAGGUGCCCCAGUGGGCAGGACCAACGAUCCGGCGGGCAGGUUGCCCACAUAGGCGUCCAGUUGGCUGAGCGCCGUUAGCUUGCGCUCUUCAUU
((((..(((((((((.(((.....))).)))))))).(..(((.(((.......)))(((((((.....)))).....((((..(((....)))..))))))).)))..))..))))... ( -58.70)
>DroYak_CAF1 5979 120 + 1
GGAGGACGGGGCGCCCGUUGGAGCAACAGGUGCUCCAGUGGGCAGGACCAGCGCUCCGGCGGGGAGGUUGCCCACAUAGGCGUCCAGUUGGCUGAGCGCCGUCAGCUUACGCUCCGCAUU
((((....(((((((...(((((((.....)))))))((((((((..((..(((....))).))...))))))))...))))))).((.((((((......)))))).)).))))..... ( -61.20)
>consensus
GGAGGACGGGGCGCCCGUUGAAGCAACAGGUGCCCCAGUGGGCAGGACCAACGCUCCGGCGGGCAGGUUGCCCACAUAGGCGUCCAGUUGGCUGAGCGCCGUCAGCUUGCGCUCCACAUU
....(((((((((((.(((.....))).)))))))).(((((((..(((..(((....)))....))))))))))...((((..(((....)))..)))))))(((....)))....... (-47.42 = -47.92 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,403,685 – 8,403,805
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.75
Mean single sequence MFE -54.58
Consensus MFE -45.64
Energy contribution -47.07
Covariance contribution 1.44
Combinations/Pair 1.13
Mean z-score -2.47
Structure conservation index 0.84
SVM decision value 1.70
SVM RNA-class probability 0.973080
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8403685 120 - 22224390
AAUGUGGAGCGCAAGCUGACGGCGCUCAACCAAUUGGACGCCUAUGUGGGCAACCUGCCCGCCGGUGCGUUGGUCCUGCCCACUGGGACACCAGUUGCUUCGACGGGAGCCCCGUCAACA
.......(((....)))(((((.((((..((.....(((((((..((((((.....)))))).)).))))).(((..((..(((((....))))).))...))))))))).))))).... ( -53.20)
>DroSec_CAF1 2891 120 - 1
AAUGUGGAGCGCAAGCUGACGGCGCUCAACCAACUGGACGCCUAUGUGGGCAACCUGCCCUCCGGCGCGUUGGUCCUGCCCACUGGGACACCAGUUGCUUCAACGGGAGCUCCGUCAAUA
.......(((....)))(((((.((((...(((((((...((((.((((((((((((((....))))....)))..)))))))))))...)))))))((.....)))))).))))).... ( -55.40)
>DroEre_CAF1 6338 120 - 1
AAUGAAGAGCGCAAGCUAACGGCGCUCAGCCAACUGGACGCCUAUGUGGGCAACCUGCCCGCCGGAUCGUUGGUCCUGCCCACUGGGGCACCUGUUGCUCUAACGGGCGCCCCGUCCUCC
.......(((....)))...((((..(((....)))..))))...((((((.....)))))).((((.((.((.....)).)).(((((.(((((((...))))))).)))))))))... ( -54.90)
>DroYak_CAF1 5979 120 - 1
AAUGCGGAGCGUAAGCUGACGGCGCUCAGCCAACUGGACGCCUAUGUGGGCAACCUCCCCGCCGGAGCGCUGGUCCUGCCCACUGGAGCACCUGUUGCUCCAACGGGCGCCCCGUCCUCC
...(((((((....)))...((((..(((....)))..)))).....((....))...)))).((((.((.((...(((((..(((((((.....)))))))..))))).)).)).)))) ( -54.80)
>consensus
AAUGUGGAGCGCAAGCUGACGGCGCUCAACCAACUGGACGCCUAUGUGGGCAACCUGCCCGCCGGAGCGUUGGUCCUGCCCACUGGGACACCAGUUGCUCCAACGGGAGCCCCGUCAACA
.......(((....)))(((((((..(((....)))..))))...((((((((((.(((....))).....)))..))))))).(((((.(((((((...))))))).)))))))).... (-45.64 = -47.07 +   1.44)

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 10:52:46 2006