Locus 5633

Sequence ID 3R_DroMel_CAF1
Location 14,827,687 – 14,827,887
Length 200
Max. P 0.963843
window9183 window9184 window9185 window9186 window9187

overview

Window 3

Location 14,827,687 – 14,827,807
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.20
Mean single sequence MFE -35.54
Consensus MFE -34.61
Energy contribution -34.61
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.97
SVM decision value 0.02
SVM RNA-class probability 0.542369
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14827687 120 + 27905053
GACUCGACUUGAGACUCUUCCACGAAAUGGCGAAACCCGUUUUGGGUCUCAGCCUCUCGGGUCCAAGAGUGUCUUUCAAUUGUAUUCAAUGCUAACUCAAUUGCUCUGGCCGAGGGCUAC
..........(((((((......(((((((......))))))))))))))((((.(((((..(((.(((((..........((((...)))).........))))))))))))))))).. ( -36.01)
>DroSec_CAF1 5853 117 + 1
---UCGACUUGAGACUCUUCCACGAAAUGGCGAAACCCGUUUUGGGUCUCAGCCUCUCGGGUCCAAGAGUGUCUUUCAAUUGUAUUCAAUGCUAACUCAAUUGCUCUGGCCGAGGGCUAC
---.......(((((((......(((((((......))))))))))))))((((.(((((..(((.(((((..........((((...)))).........))))))))))))))))).. ( -36.01)
>DroSim_CAF1 6004 117 + 1
---UUGACUUGAGACUCUUCCACGAAAUGGCGAAACCCGUUUUGGGUCUCAGCCUCUCCGGUCCAAGAGUGUCUUUCAAUUGUAUUCAAUGCUAACUCAAUUGCUCUGGCCGAGGGCUAC
---.......(((((((......(((((((......))))))))))))))((((.(((.((.(((.(((((..........((((...)))).........))))))))))))))))).. ( -34.61)
>consensus
___UCGACUUGAGACUCUUCCACGAAAUGGCGAAACCCGUUUUGGGUCUCAGCCUCUCGGGUCCAAGAGUGUCUUUCAAUUGUAUUCAAUGCUAACUCAAUUGCUCUGGCCGAGGGCUAC
..........(((((((......(((((((......))))))))))))))((((.(((.((.(((.(((((..........((((...)))).........))))))))))))))))).. (-34.61 = -34.61 +  -0.00)

alignment

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secondary structure

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Window 4

Location 14,827,687 – 14,827,807
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.20
Mean single sequence MFE -39.50
Consensus MFE -36.00
Energy contribution -36.67
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.91
SVM decision value 0.75
SVM RNA-class probability 0.840722
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14827687 120 - 27905053
GUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACAAUUGAAAGACACUCUUGGACCCGAGAGGCUGAGACCCAAAACGGGUUUCGCCAUUUCGUGGAAGAGUCUCAAGUCGAGUC
......((((((..(((((((((.(((.......))).))))))......((((((...((((((((((.(((((((.....)))))))))).))))).)))))))))))..)))))).. ( -43.30)
>DroSec_CAF1 5853 117 - 1
GUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACAAUUGAAAGACACUCUUGGACCCGAGAGGCUGAGACCCAAAACGGGUUUCGCCAUUUCGUGGAAGAGUCUCAAGUCGA---
.......(((((..(((((((((.(((.......))).))))))......((((((...((((((((((.(((((((.....)))))))))).))))).)))))))))))..)))))--- ( -39.90)
>DroSim_CAF1 6004 117 - 1
GUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACAAUUGAAAGACACUCUUGGACCGGAGAGGCUGAGACCCAAAACGGGUUUCGCCAUUUCGUGGAAGAGUCUCAAGUCAA---
.........(((..(((((((((.(((.......))).))))))......((((((...((((((((((.(((((((.....)))))))))).)))).))))))))))))..)))..--- ( -35.30)
>consensus
GUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACAAUUGAAAGACACUCUUGGACCCGAGAGGCUGAGACCCAAAACGGGUUUCGCCAUUUCGUGGAAGAGUCUCAAGUCGA___
.......(((((..(((((((((.(((.......))).))))))......((((((...((((((((((.(((((((.....)))))))))).))))).)))))))))))..)))))... (-36.00 = -36.67 +   0.67)

alignment

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secondary structure

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Window 5

Location 14,827,727 – 14,827,847
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -35.24
Consensus MFE -29.74
Energy contribution -30.08
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.84
SVM decision value 0.03
SVM RNA-class probability 0.546800
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14827727 120 - 27905053
UCGGUUAGACAGCCAGCCAAAGCUAUGGCCAUAUAACCAUGUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACAAUUGAAAGACACUCUUGGACCCGAGAGGCUGAGACCCAAA
..(((((....((((((....))..))))....)))))...((((((((((((((((((((((.(((.......))).)))))).......))).)))..))))).)))))......... ( -35.91)
>DroSec_CAF1 5890 116 - 1
UCGGUUAGACAG----CCAAAGCUAUGGCCAUAUAACCAUGUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACAAUUGAAAGACACUCUUGGACCCGAGAGGCUGAGACCCAAA
..(((((....(----(((......))))....)))))...((((((((((((((((((((((.(((.......))).)))))).......))).)))..))))).)))))......... ( -35.31)
>DroSim_CAF1 6041 120 - 1
UCGGUUAGACAGCCAGCCAAAGCUAUGGCCAUAUAACCAUGUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACAAUUGAAAGACACUCUUGGACCGGAGAGGCUGAGACCCAAA
..(((((....((((((....))..))))....)))))...((((((((((((((((((((((.(((.......))).)))))).......))).))).)).))).)))))......... ( -34.51)
>consensus
UCGGUUAGACAGCCAGCCAAAGCUAUGGCCAUAUAACCAUGUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACAAUUGAAAGACACUCUUGGACCCGAGAGGCUGAGACCCAAA
..(((((........((((......))))....)))))...((((((((((((((((((((((.(((.......))).)))))).......))).))).)).))).)))))......... (-29.74 = -30.08 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,827,767 – 14,827,887
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -49.93
Consensus MFE -44.84
Energy contribution -45.73
Covariance contribution 0.89
Combinations/Pair 1.05
Mean z-score -4.65
Structure conservation index 0.90
SVM decision value 1.27
SVM RNA-class probability 0.938718
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14827767 120 + 27905053
UGUAUUCAAUGCUAACUCAAUUGCUCUGGCCGAGGGCUACAUGGUUAUAUGGCCAUAGCUUUGGCUGGCUGUCUAACCGAUUCCAUUUCGCUUUGGCAGGGGCAAUUGAGGCACACUCUA
.........(((...((((((((((((.(((((((.......(((((.(((((((..((....))))))))).)))))((.......)).))))))).)))))))))))))))....... ( -46.80)
>DroSec_CAF1 5930 116 + 1
UGUAUUCAAUGCUAACUCAAUUGCUCUGGCCGAGGGCUACAUGGUUAUAUGGCCAUAGCUUUGG----CUGUCUAACCGAUUCCAUUUCGCCCUGGCAGGGGCAAUUGAGGCACACUCGA
.........(((...((((((((((((.(((.(((((.....(((((.(((((((......)))----)))).)))))((.......)))))))))).)))))))))))))))....... ( -51.20)
>DroSim_CAF1 6081 120 + 1
UGUAUUCAAUGCUAACUCAAUUGCUCUGGCCGAGGGCUACAUGGUUAUAUGGCCAUAGCUUUGGCUGGCUGUCUAACCGAUUCCAUUUCGCCCUGGCAGGGGCAAUUGAGGCACACUCGA
.........(((...((((((((((((.(((.(((((.....(((((.(((((((..((....))))))))).)))))((.......)))))))))).)))))))))))))))....... ( -51.80)
>consensus
UGUAUUCAAUGCUAACUCAAUUGCUCUGGCCGAGGGCUACAUGGUUAUAUGGCCAUAGCUUUGGCUGGCUGUCUAACCGAUUCCAUUUCGCCCUGGCAGGGGCAAUUGAGGCACACUCGA
.........(((...((((((((((((.(((.(((((.....(((((.(((((((..((....))))))))).)))))((.......)))))))))).)))))))))))))))....... (-44.84 = -45.73 +   0.89)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,827,767 – 14,827,887
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -42.90
Consensus MFE -38.43
Energy contribution -39.43
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.38
Structure conservation index 0.90
SVM decision value 1.56
SVM RNA-class probability 0.963843
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14827767 120 - 27905053
UAGAGUGUGCCUCAAUUGCCCCUGCCAAAGCGAAAUGGAAUCGGUUAGACAGCCAGCCAAAGCUAUGGCCAUAUAACCAUGUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACA
...(((((..(((((((((..(((((...((...((((....((((....)))).((((......)))).......))))...))....)).))).)))))))))...)))))....... ( -37.20)
>DroSec_CAF1 5930 116 - 1
UCGAGUGUGCCUCAAUUGCCCCUGCCAGGGCGAAAUGGAAUCGGUUAGACAG----CCAAAGCUAUGGCCAUAUAACCAUGUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACA
((.(((((..(((((((((..((((((((((...((((....(((((...((----(....))).)))))......))))...))))).)).))).)))))))))...)))))))..... ( -44.20)
>DroSim_CAF1 6081 120 - 1
UCGAGUGUGCCUCAAUUGCCCCUGCCAGGGCGAAAUGGAAUCGGUUAGACAGCCAGCCAAAGCUAUGGCCAUAUAACCAUGUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACA
((.(((((..(((((((((..((((((((((...((((....((((....)))).((((......)))).......))))...))))).)).))).)))))))))...)))))))..... ( -47.30)
>consensus
UCGAGUGUGCCUCAAUUGCCCCUGCCAGGGCGAAAUGGAAUCGGUUAGACAGCCAGCCAAAGCUAUGGCCAUAUAACCAUGUAGCCCUCGGCCAGAGCAAUUGAGUUAGCAUUGAAUACA
...(((((..(((((((((..((((((((((...((((....(((((...(((........))).)))))......))))...))))).)).))).)))))))))...)))))....... (-38.43 = -39.43 +   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 12:00:02 2006