Locus 4508

Sequence ID 3R_DroMel_CAF1
Location 11,959,012 – 11,959,102
Length 90
Max. P 0.668098
window7365 window7366

overview

Window 5

Location 11,959,012 – 11,959,102
Length 90
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 74.11
Mean single sequence MFE -19.87
Consensus MFE -8.68
Energy contribution -10.04
Covariance contribution 1.36
Combinations/Pair 1.15
Mean z-score -1.92
Structure conservation index 0.44
SVM decision value 0.28
SVM RNA-class probability 0.668098
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11959012 90 + 27905053
--CCC-AAAUUAGUUUGCACCUUCGG---CAGGUGCAAUUUUCCC--------CACUAAUUUAAGUGUGCUGUUGGCCCCGC---UCAAUUCGCCCAGCCAUUCUAA
--...-((((((((((((((((....---.)))))))).......--------.)))))))).((((.((((..(((.....---.......))))))))))).... ( -24.00)
>DroSec_CAF1 63451 90 + 1
--CCC-AAAAUUGUUUACACCUUUGU---CAGGUGCAAUUUUCCC--------AACUAAUUUAGUUGUGCUGUUGGCCCCGC---UCAAUUCGCCCAGCCAUUCUAA
--...-(((((((....(((((....---.))))))))))))..(--------(((((...)))))).((((..(((.....---.......)))))))........ ( -17.10)
>DroSim_CAF1 63546 90 + 1
--CCC-AAAAUUGUUUACACCUUCGU---CAGGUGCAAUUUUCCC--------AACUAAUUUAGUUUUGCUGUUGGCCCCGC---UCAAUUCGCCCAGCCAUUCUAA
--...-(((((((....(((((....---.))))))))))))...--------.......((((..(.((((..(((.....---.......))))))).)..)))) ( -15.90)
>DroEre_CAF1 63881 76 + 1
--CCC---AAUAGUUGGCGCCUUUGG---CAGGUGCAAUAUACCC--------AACAAAUUAAAUUGUGCU---------------CAAUUCGCCCAGCCAUUCUAA
--...---..(((.(((((((...))---).((.((.........--------.((((......))))...---------------......)))).))))..))). ( -16.01)
>DroYak_CAF1 66718 99 + 1
--CCCCCAAACGGUUGGCACCUUUGG---CAGGUGCAAUUUACUCCAAUAGUUAACUAAUUAAAUUGUGCUGUUGGCCCCGC---ACAAUUUGCCCAGCCAUUCUAA
--.........(((((((((((....---.))))))........................((((((((((.(......).))---))))))))..)))))....... ( -26.80)
>DroAna_CAF1 84048 91 + 1
UCUUC-UAAAUUGUUGACACCUCUUGGAAGAGGUGUAAUCUUGCC--------GACUAAUUUGAUU-------UGGCCCCGCCAUUUAAUUUGCCCAGCCAUUCUAA
.....-((((((((((((((((((....))))))))........)--------))).))))))...-------((((...((.(......).))...))))...... ( -19.40)
>consensus
__CCC_AAAAUUGUUGACACCUUUGG___CAGGUGCAAUUUUCCC________AACUAAUUUAAUUGUGCUGUUGGCCCCGC___UCAAUUCGCCCAGCCAUUCUAA
................((((((........))))))................................((((..(((...............)))))))........ ( -8.68 = -10.04 +   1.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,959,012 – 11,959,102
Length 90
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 74.11
Mean single sequence MFE -24.40
Consensus MFE -12.40
Energy contribution -13.35
Covariance contribution 0.95
Combinations/Pair 1.15
Mean z-score -1.70
Structure conservation index 0.51
SVM decision value 0.24
SVM RNA-class probability 0.650771
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11959012 90 - 27905053
UUAGAAUGGCUGGGCGAAUUGA---GCGGGGCCAACAGCACACUUAAAUUAGUG--------GGGAAAAUUGCACCUG---CCGAAGGUGCAAACUAAUUU-GGG--
......(((((..((.......---))..)))))........(((((((((((.--------.......((((((((.---....))))))))))))))))-)))-- ( -29.80)
>DroSec_CAF1 63451 90 - 1
UUAGAAUGGCUGGGCGAAUUGA---GCGGGGCCAACAGCACAACUAAAUUAGUU--------GGGAAAAUUGCACCUG---ACAAAGGUGUAAACAAUUUU-GGG--
(((((((((((..((.......---))..)))).......((((((...)))))--------)......((((((((.---....))))))))...)))))-)).-- ( -25.00)
>DroSim_CAF1 63546 90 - 1
UUAGAAUGGCUGGGCGAAUUGA---GCGGGGCCAACAGCAAAACUAAAUUAGUU--------GGGAAAAUUGCACCUG---ACGAAGGUGUAAACAAUUUU-GGG--
......(((((..((.......---))..)))))....(((((((((.....))--------)).....((((((((.---....))))))))....))))-)..-- ( -23.10)
>DroEre_CAF1 63881 76 - 1
UUAGAAUGGCUGGGCGAAUUG---------------AGCACAAUUUAAUUUGUU--------GGGUAUAUUGCACCUG---CCAAAGGCGCCAACUAUU---GGG--
....(((((.(((((((((((---------------....))))))..((((..--------((((.......)))).---.)))).)).))).)))))---...-- ( -18.40)
>DroYak_CAF1 66718 99 - 1
UUAGAAUGGCUGGGCAAAUUGU---GCGGGGCCAACAGCACAAUUUAAUUAGUUAACUAUUGGAGUAAAUUGCACCUG---CCAAAGGUGCCAACCGUUUGGGGG--
...((((((.(((..(((((((---((.(......).)))))))))...(((((.(((.....))).)))))(((((.---....)))))))).)))))).....-- ( -28.10)
>DroAna_CAF1 84048 91 - 1
UUAGAAUGGCUGGGCAAAUUAAAUGGCGGGGCCA-------AAUCAAAUUAGUC--------GGCAAGAUUACACCUCUUCCAAGAGGUGUCAACAAUUUA-GAAGA
......(((((..((..........))..)))))-------..(((((((((((--------.....))))((((((((....))))))))....))))).-))... ( -22.00)
>consensus
UUAGAAUGGCUGGGCGAAUUGA___GCGGGGCCAACAGCACAAUUAAAUUAGUU________GGGAAAAUUGCACCUG___CCAAAGGUGCAAACAAUUUU_GGG__
......(((((..((..........))..))))).....................................((((((........))))))................ (-12.40 = -13.35 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:04 2006