Locus 1397

Sequence ID 3R_DroMel_CAF1
Location 4,078,041 – 4,078,240
Length 199
Max. P 0.957113
window2300 window2301 window2302 window2303

overview

Window 0

Location 4,078,041 – 4,078,161
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -31.57
Consensus MFE -22.79
Energy contribution -23.23
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.72
SVM decision value 0.26
SVM RNA-class probability 0.658190
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4078041 120 + 27905053
UGUCGGAUAACAAUUAUUUAAUUCGGGUUGGCAGCAGGCUGAAAUUAAAAUAACUUAGGCGACGAACUUUUUUCGCUGCCGAGUUUGUGUCUUAAGUCUUUAGACUUAAGACAGCAGUUA
.......((((.....((((((((((.(((....))).))).)))))))..(((((.((((.((((.....)))).)))))))))(((((((((((((....))))))))))).)))))) ( -36.20)
>DroEre_CAF1 6593 116 + 1
UGUCGGAUAACAAUUAUUUAAUUCGGGUUGGCACCAGGCUGAAAUUCAAAC----GAGGCGACGAACUUUUCUCGAAUUCGAGUUCGUGUCUUAAGUCGUAAGACUCAAGACAGCAGUUA
.......((((..........(((((.(((....))).)))))........----...((.((((((((...........))))))))(((((.((((....)))).))))).)).)))) ( -32.80)
>DroYak_CAF1 3645 108 + 1
UGUCGGAUAACAAUUAUUUAAUUCGGGUUGGCAGCAGGCUGAAAUUCAAAUGACUGAGGCGACGAACUUUUCUUGAAUUCGAGUUUGUGUCUUAAGUCUUUAGACU------------UA
.(((.................(((((.(((....))).)))))........(((((((((.((((((((...........))))))))))))).))))....))).------------.. ( -25.70)
>consensus
UGUCGGAUAACAAUUAUUUAAUUCGGGUUGGCAGCAGGCUGAAAUUCAAAU_ACUGAGGCGACGAACUUUUCUCGAAUUCGAGUUUGUGUCUUAAGUCUUUAGACU_AAGACAGCAGUUA
.(((..(..((..........(((((.(((....))).)))))...........((((((.((((((((...........)))))))))))))).))..)..)))............... (-22.79 = -23.23 +   0.45)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,078,081 – 4,078,201
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.22
Mean single sequence MFE -29.73
Consensus MFE -15.45
Energy contribution -17.57
Covariance contribution 2.11
Combinations/Pair 1.05
Mean z-score -2.33
Structure conservation index 0.52
SVM decision value 1.47
SVM RNA-class probability 0.957113
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4078081 120 + 27905053
GAAAUUAAAAUAACUUAGGCGACGAACUUUUUUCGCUGCCGAGUUUGUGUCUUAAGUCUUUAGACUUAAGACAGCAGUUAUACUUUAUGGGGCGUCUUAUGACACAUGGAUAUGCUGUAA
...........(((((.((((.((((.....)))).)))))))))..(((((((((((....)))))))))))(((((.(((.((((((....(((....))).)))))))))))))).. ( -37.80)
>DroEre_CAF1 6633 97 + 1
GAAAUUCAAAC----GAGGCGACGAACUUUUCUCGAAUUCGAGUUCGUGUCUUAAGUCGUAAGACUCAAGACAGCAGUUAUAUUUUAUG-------------------GAUAUGCUGUAA
.........((----(((....)........((((....)))).))))(((((.((((....)))).))))).(((((.(((((.....-------------------)))))))))).. ( -27.30)
>DroYak_CAF1 3685 108 + 1
GAAAUUCAAAUGACUGAGGCGACGAACUUUUCUUGAAUUCGAGUUUGUGUCUUAAGUCUUUAGACU------------UAUAUUUUAUGGGGAGUCUUAUGACACCUGGAUAUGCUGUAA
...........(((((((((.((((((((...........))))))))))))).)))).....((.------------(((((((...(((..(((....))).))))))))))..)).. ( -24.10)
>consensus
GAAAUUCAAAU_ACUGAGGCGACGAACUUUUCUCGAAUUCGAGUUUGUGUCUUAAGUCUUUAGACU_AAGACAGCAGUUAUAUUUUAUGGGG_GUCUUAUGACAC_UGGAUAUGCUGUAA
.................((((((((((((...........))))))))(((((.((((....)))).)))))........................................)))).... (-15.45 = -17.57 +   2.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,078,081 – 4,078,201
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.22
Mean single sequence MFE -24.40
Consensus MFE -11.24
Energy contribution -13.80
Covariance contribution 2.56
Combinations/Pair 1.06
Mean z-score -2.58
Structure conservation index 0.46
SVM decision value 0.64
SVM RNA-class probability 0.807820
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4078081 120 - 27905053
UUACAGCAUAUCCAUGUGUCAUAAGACGCCCCAUAAAGUAUAACUGCUGUCUUAAGUCUAAAGACUUAAGACACAAACUCGGCAGCGAAAAAAGUUCGUCGCCUAAGUUAUUUUAAUUUC
...............(((((....)))))....(((((((....((.(((((((((((....))))))))))))).....(((.(((((.....))))).))).....)))))))..... ( -33.50)
>DroEre_CAF1 6633 97 - 1
UUACAGCAUAUC-------------------CAUAAAAUAUAACUGCUGUCUUGAGUCUUACGACUUAAGACACGAACUCGAAUUCGAGAAAAGUUCGUCGCCUC----GUUUGAAUUUC
.....((.....-------------------.................((((((((((....))))))))))(((((((((....))).....)))))).))...----........... ( -22.70)
>DroYak_CAF1 3685 108 - 1
UUACAGCAUAUCCAGGUGUCAUAAGACUCCCCAUAAAAUAUA------------AGUCUAAAGACUUAAGACACAAACUCGAAUUCAAGAAAAGUUCGUCGCCUCAGUCAUUUGAAUUUC
.....((........(((((....(......)........((------------((((....)))))).))))).....((((((.......))))))..)).((((....))))..... ( -17.00)
>consensus
UUACAGCAUAUCCA_GUGUCAUAAGAC_CCCCAUAAAAUAUAACUGCUGUCUU_AGUCUAAAGACUUAAGACACAAACUCGAAUUCGAGAAAAGUUCGUCGCCUCAGU_AUUUGAAUUUC
.....((.........................................((((((((((....)))))))))).....((((....))))...........)).................. (-11.24 = -13.80 +   2.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,078,121 – 4,078,240
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.06
Mean single sequence MFE -25.18
Consensus MFE -12.44
Energy contribution -13.11
Covariance contribution 0.67
Combinations/Pair 1.11
Mean z-score -2.55
Structure conservation index 0.49
SVM decision value 1.18
SVM RNA-class probability 0.926828
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4078121 119 - 27905053
GAGAAUCUCC-ACAACCAGUUAUGUGUCUGCAGUCUAGUAUUACAGCAUAUCCAUGUGUCAUAAGACGCCCCAUAAAGUAUAACUGCUGUCUUAAGUCUAAAGACUUAAGACACAAACUC
(((.......-.....((((((((((.(((.(((.....))).))))))......(((((....)))))..........))))))).(((((((((((....)))))))))))....))) ( -30.70)
>DroEre_CAF1 6669 101 - 1
AAGAACCACUGGUAACCUGUUUUGUAUCUGCAGCCUAGUAUUACAGCAUAUC-------------------CAUAAAAUAUAACUGCUGUCUUGAGUCUUACGACUUAAGACACGAACUC
.......(((((....((((.........)))).))))).....((((....-------------------.............))))((((((((((....))))))))))........ ( -21.13)
>DroYak_CAF1 3725 108 - 1
AAGAAUCUUCGGCAACCAGUUUUGUGUCUGCAGUCUAGUAUUACAGCAUAUCCAGGUGUCAUAAGACUCCCCAUAAAAUAUA------------AGUCUAAAGACUUAAGACACAAACUC
..........(....).(((((.((((((..(((((..(((.(((.(.......).))).))))))))............((------------((((....))))))))))))))))). ( -23.70)
>consensus
AAGAAUCUCCGGCAACCAGUUUUGUGUCUGCAGUCUAGUAUUACAGCAUAUCCA_GUGUCAUAAGAC_CCCCAUAAAAUAUAACUGCUGUCUU_AGUCUAAAGACUUAAGACACAAACUC
..................(((.(((((((((..............)).............................................((((((....)))))))))))))))).. (-12.44 = -13.11 +   0.67)

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 10:09:04 2006