Locus 7613

Sequence ID 3R_DroMel_CAF1
Location 20,415,435 – 20,415,672
Length 237
Max. P 0.799432
window12284 window12285 window12286

overview

Window 4

Location 20,415,435 – 20,415,539
Length 104
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -28.46
Consensus MFE -26.16
Energy contribution -27.00
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -1.26
Structure conservation index 0.92
SVM decision value 0.61
SVM RNA-class probability 0.799432
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20415435 104 + 27905053
UUUUCUAGCGGGUUAUAUCUAACCGAAAGGCUAGAAAAUUUGCCAAAGAGUUUUAUUUUUGCUACACAAGGGCAGGUGUACGGGGCGUACGUAGAAUUUUUACC
.......(((((((...((((.((....)).)))).)))))))..(((((((((((.((((((.......)))))).(((((...))))))))))))))))... ( -26.50)
>DroSec_CAF1 37703 102 + 1
U--UCUAGCGGGUUAUAUCCAUCCGAAAGGCUAGAAAUUUCGGCAAAGAGUUUUAUUUUUGCUCCACAAGGGCAGGUGUACGGGGCGUAUGUAGAAUUUUUACC
(--((((((((((...))))...(....)))))))).....((..(((((((((((...(((((((((........)))..))))))...))))))))))).)) ( -29.20)
>DroSim_CAF1 41251 104 + 1
UUUUCUAGCGGGUUAUAUCCAUCCGAAAGGCUAGAAAUUUCGCCAAAGAGUUUUAUUUUUGCUCCACAAGGGCAGGUGUACGGGGCGUAUGUAGAAUUUUUACC
.((((((((((((...))))...(....)))))))))........(((((((((((...(((((((((........)))..))))))...)))))))))))... ( -29.90)
>DroEre_CAF1 37315 104 + 1
UUUUCUAGCGGGUUAUAUCCAUCCGAAAGGCUAGAAAUUUCGCGACAGAGUUUUAUUUUUGCUCCACAAGGGCAGGUGUACGGGGCGUAUGUAGAAUUUUUACC
.((((((((((((...))))...(....))))))))).........((((((((((...(((((((((........)))..))))))...)))))))))).... ( -28.40)
>DroYak_CAF1 41768 104 + 1
UUUUCUAGCGGGUUAUAUCCAAGCGAAAGGCUAGAAAUUUCGCCACAGAGUUUUAUUUUUGCUCCACAAGGGCAGGUGUACGGGGCGUAUGUAGAAUUUUUACC
.((((((((((((...))))...(....))))))))).........((((((((((...(((((((((........)))..))))))...)))))))))).... ( -28.30)
>consensus
UUUUCUAGCGGGUUAUAUCCAUCCGAAAGGCUAGAAAUUUCGCCAAAGAGUUUUAUUUUUGCUCCACAAGGGCAGGUGUACGGGGCGUAUGUAGAAUUUUUACC
.((((((((((((...))))...(....)))))))))........(((((((((((...(((((((((........)))..))))))...)))))))))))... (-26.16 = -27.00 +   0.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,415,539 – 20,415,647
Length 108
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 89.17
Mean single sequence MFE -23.37
Consensus MFE -18.02
Energy contribution -18.46
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.51
Structure conservation index 0.77
SVM decision value 0.08
SVM RNA-class probability 0.574449
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20415539 108 + 27905053
GAAAACCGAAAGAAAAGCCGAAAAAUAA----AAUAUAAA-----ACGGAAGUGUGGGAAUACCUGUGU-CCAUAUACUUAUAGCUUUUCCAACACAUGAAAGUGUAGACUUUGGUCC
....((((((.(((((((((........----........-----.)).((((((((((.((....)))-)).)))))))...)))))))....((((....))))....)))))).. ( -21.93)
>DroSec_CAF1 37805 108 + 1
GAAAACCGAAAGAAAAGCCGAAAAUAAA----AAUAUAAA-----ACGGAAGUGUGGGAAUAGCUGUGU-CCAUAUACUUACAGAUUUUCCAACACAUGAAAGUGUAGACUUUGGUCC
......(....)....((((((......----........-----((....))((.((((...(((((.-.........)))))...)))).))((((....))))....)))))).. ( -21.90)
>DroSim_CAF1 41355 108 + 1
GAAAACCGAAAGAAAAGCCGAAAAUAAA----AAUAUAAA-----ACGGAAGUGUGGGAAUAGCUGUGU-CCAUAUACUUACAGCUUUUCCAACACAUGAAAGUGUAGACUUUGGUCC
......(....)....((((((......----........-----((....))((.((((.(((((((.-.........))))))).)))).))((((....))))....)))))).. ( -26.80)
>DroEre_CAF1 37419 114 + 1
GAAAACCGAAAGAAAAGCCGAAAAUAAAGCCGAAUAUAAAUA---ACGGAAGUGUGGGAAAAGUUGUGC-CCAUAUGCUUAUAGCUUUUGCAGCUCAUCAGUGUGUAGACUUUGGUCC
....((((((....((((...........(((..........---.)))..(((((((..........)-))))))))))......(((((((((....))).)))))).)))))).. ( -20.80)
>DroYak_CAF1 41872 114 + 1
GAAAACCGAAAGAAAAGCCGAAAAUAUA----AAUAUAAAUAACAACGGAAGUGUGGGAAAAGCGGUGCCCCAUAUGCUUAUAGCUUUUCCAACACAUGAGAGUGUAGACUUUGGUCC
......(....)....((((((......----.............((....))((.((((((((...((.......)).....)))))))).))((((....))))....)))))).. ( -25.40)
>consensus
GAAAACCGAAAGAAAAGCCGAAAAUAAA____AAUAUAAA_____ACGGAAGUGUGGGAAUAGCUGUGU_CCAUAUACUUAUAGCUUUUCCAACACAUGAAAGUGUAGACUUUGGUCC
......(....)....((((((.......................((....)).((((((.(((((((...........)))))))))))))((((......))))....)))))).. (-18.02 = -18.46 +   0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,415,573 – 20,415,672
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.52
Mean single sequence MFE -23.72
Consensus MFE -19.32
Energy contribution -19.72
Covariance contribution 0.40
Combinations/Pair 1.17
Mean z-score -1.61
Structure conservation index 0.81
SVM decision value 0.25
SVM RNA-class probability 0.653988
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20415573 99 + 27905053
AA-----ACGGAAGUGUGGGAAUACCUGUGU-CCAUAUACUUAUAGCUUUUCCAACACAUGAAAGUGUAGACUUUGGUCCGAAAACCGAAAU---------ACG------UAAAUAGAAA
..-----.((((.((((.((((...(((((.-.........)))))...)))).)))).(.(((((....))))).)))))...........---------...------.......... ( -19.60)
>DroSec_CAF1 37839 99 + 1
AA-----ACGGAAGUGUGGGAAUAGCUGUGU-CCAUAUACUUACAGAUUUUCCAACACAUGAAAGUGUAGACUUUGGUCCGAAACCCGAAAU---------ACG------UAAAUAGAAU
..-----.((((.((((.((((...(((((.-.........)))))...)))).)))).(.(((((....))))).)))))...........---------...------.......... ( -22.60)
>DroSim_CAF1 41389 99 + 1
AA-----ACGGAAGUGUGGGAAUAGCUGUGU-CCAUAUACUUACAGCUUUUCCAACACAUGAAAGUGUAGACUUUGGUCCGAAACCCGAAAU---------ACG------UAAAUAGAAU
..-----.((((.((((.((((.(((((((.-.........))))))).)))).)))).(.(((((....))))).)))))...........---------...------.......... ( -27.50)
>DroEre_CAF1 37457 105 + 1
AAUA---ACGGAAGUGUGGGAAAAGUUGUGC-CCAUAUGCUUAUAGCUUUUGCAGCUCAUCAGUGUGUAGACUUUGGUCCGAAAACCAAAAU---------ACGUA--CAUAAAUAGAAA
....---((....))((.(.((((((((((.-.(....)..)))))))))).).))......(((((((...((((((......)))))).)---------)))))--)........... ( -21.70)
>DroYak_CAF1 41906 120 + 1
AAUAACAACGGAAGUGUGGGAAAAGCGGUGCCCCAUAUGCUUAUAGCUUUUCCAACACAUGAGAGUGUAGACUUUGGUCCGAAAACCAAAAUACCGAAAAUACGUACACAUAAAUAGAAA
.............((((.((((((((...((.......)).....)))))))).))))......(((((...((((((......))))))....((......)))))))........... ( -27.20)
>consensus
AA_____ACGGAAGUGUGGGAAUAGCUGUGU_CCAUAUACUUAUAGCUUUUCCAACACAUGAAAGUGUAGACUUUGGUCCGAAAACCGAAAU_________ACG______UAAAUAGAAA
........((((.((((.((((.(((((((...........))))))).)))).))))...(((((....)))))..))))....................................... (-19.32 = -19.72 +   0.40)

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 12:50:12 2006