Locus 3727

Sequence ID 3R_DroMel_CAF1
Location 10,118,693 – 10,118,844
Length 151
Max. P 0.979152
window5972 window5973 window5974

overview

Window 2

Location 10,118,693 – 10,118,804
Length 111
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 80.30
Mean single sequence MFE -28.43
Consensus MFE -22.64
Energy contribution -23.87
Covariance contribution 1.23
Combinations/Pair 1.07
Mean z-score -2.32
Structure conservation index 0.80
SVM decision value 1.83
SVM RNA-class probability 0.979152
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10118693 111 + 27905053
CAGCAAAAAAAAAAAAAUAAGAGCCAUCCA---UCUUUGUCCUUCGU--UUGAAAUAGACAUGUGAUAGGCUAAACAUGUACAUGGCAUGUAUAUUUCACUACCGACUGGCCCACU
....................(.((((....---.....(((....((--.(((((((.((((((.((..((.......))..)).)))))).)))))))..)).))))))).)... ( -21.20)
>DroSec_CAF1 28026 98 + 1
CGGCCAA-----------AAGAGCCAUCCA---ACUUUGUCCUUCGCCAUUGAAAUAGACAUGCGAUAGGCCAAACA--UACAUGGCAUGU--AUUUCACUGGCGACUGGCCCACU
.(((((.-----------.((((.......---.)))).....((((((.((((((..((((((.((.(........--..))).))))))--)))))).)))))).))))).... ( -31.90)
>DroSim_CAF1 24465 101 + 1
CGGCCAA-----------AAGAGCCAUUUGUGUCCUGUGUCCUUCGCCAUUGAAAUAGACAUGCGAUAGGCCAAACA--UACAUGGCAUGU--AUUUCACUGGCGACUGGCCCACU
.(((((.-----------.((..((....).)..)).......((((((.((((((..((((((.((.(........--..))).))))))--)))))).)))))).))))).... ( -32.20)
>consensus
CGGCCAA___________AAGAGCCAUCCA___ACUUUGUCCUUCGCCAUUGAAAUAGACAUGCGAUAGGCCAAACA__UACAUGGCAUGU__AUUUCACUGGCGACUGGCCCACU
.(((((..............((....))...............((((((.((((((..((((((.((.(............))).))))))..)))))).)))))).))))).... (-22.64 = -23.87 +   1.23)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,118,693 – 10,118,804
Length 111
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 80.30
Mean single sequence MFE -29.80
Consensus MFE -24.46
Energy contribution -25.79
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -1.20
Structure conservation index 0.82
SVM decision value 0.03
SVM RNA-class probability 0.550004
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10118693 111 - 27905053
AGUGGGCCAGUCGGUAGUGAAAUAUACAUGCCAUGUACAUGUUUAGCCUAUCACAUGUCUAUUUCAA--ACGAAGGACAAAGA---UGGAUGGCUCUUAUUUUUUUUUUUUUGCUG
...((((((..((((((.(...((.(((((.......))))).)).))))))...(((((..(((..--..))))))))....---.)..)))))).................... ( -24.70)
>DroSec_CAF1 28026 98 - 1
AGUGGGCCAGUCGCCAGUGAAAU--ACAUGCCAUGUA--UGUUUGGCCUAUCGCAUGUCUAUUUCAAUGGCGAAGGACAAAGU---UGGAUGGCUCUU-----------UUGGCCG
....((((((((((((.((((((--((((((...(((--.(.....).))).))))))..)))))).)))))).......(((---(....))))...-----------)))))). ( -31.90)
>DroSim_CAF1 24465 101 - 1
AGUGGGCCAGUCGCCAGUGAAAU--ACAUGCCAUGUA--UGUUUGGCCUAUCGCAUGUCUAUUUCAAUGGCGAAGGACACAGGACACAAAUGGCUCUU-----------UUGGCCG
.(((..((..((((((.((((((--((((((...(((--.(.....).))).))))))..)))))).)))))).)).)))...........((((...-----------..)))). ( -32.80)
>consensus
AGUGGGCCAGUCGCCAGUGAAAU__ACAUGCCAUGUA__UGUUUGGCCUAUCGCAUGUCUAUUUCAAUGGCGAAGGACAAAGA___UGGAUGGCUCUU___________UUGGCCG
...((((((.((((((.((((((..((((((.(((.............))).))))))..)))))).)))))).................)))))).................... (-24.46 = -25.79 +   1.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,118,730 – 10,118,844
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.86
Mean single sequence MFE -32.07
Consensus MFE -18.50
Energy contribution -20.93
Covariance contribution 2.44
Combinations/Pair 1.07
Mean z-score -1.96
Structure conservation index 0.58
SVM decision value 0.16
SVM RNA-class probability 0.611835
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10118730 114 + 27905053
CCUUCGU--UUGAAAUAGACAUGUGAUAGGCUAAACAUGUACAUGGCAUGUA----UAUUUCACUACCGACUGGCCCACUUACGAGUACAUUUGAAUACAGGUGUAUCUUCGCCUGAUUG
..(((((--.(((((((.((((((.((..((.......))..)).)))))).----)))))))...((....)).......)))))............((((((......)))))).... ( -27.40)
>DroSec_CAF1 28052 112 + 1
CCUUCGCCAUUGAAAUAGACAUGCGAUAGGCCAAACA--UACAUGGCAUGU------AUUUCACUGGCGACUGGCCCACUUACGAGUACAUUUGAAUACAGGUGUAUCUUCGCCUGAUUG
((.((((((.((((((..((((((.((.(........--..))).))))))------)))))).))))))..))........................((((((......)))))).... ( -33.40)
>DroSim_CAF1 24494 112 + 1
CCUUCGCCAUUGAAAUAGACAUGCGAUAGGCCAAACA--UACAUGGCAUGU------AUUUCACUGGCGACUGGCCCACUUACGAGCACAUUUGAAUACAGGUGUAUCUUCGCCUGAUUG
((.((((((.((((((..((((((.((.(........--..))).))))))------)))))).))))))..))........................((((((......)))))).... ( -33.40)
>DroEre_CAF1 27926 102 + 1
CCCUCGGCUGAG--------UGGCUGUAGGCCAAACU--UACAUGGCAUGCACGAGUACUUCACU--CGACUGGCACACUUA------CAUUUAAAUACAGGUGUAUCUUCGGCUGAUCG
...(((((((((--------((((((((.((((....--....)))).))).(((((.....)))--))...))).))).((------(((((......)))))))...))))))))... ( -34.10)
>consensus
CCUUCGCCAUUGAAAUAGACAUGCGAUAGGCCAAACA__UACAUGGCAUGU______AUUUCACUGGCGACUGGCCCACUUACGAGUACAUUUGAAUACAGGUGUAUCUUCGCCUGAUUG
((.((((((.((((((.........(((.((((..........)))).)))......)))))).))))))..))........................((((((......)))))).... (-18.50 = -20.93 +   2.44)

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 11:08:33 2006