Locus 6806

Sequence ID 3R_DroMel_CAF1
Location 17,978,209 – 17,978,302
Length 93
Max. P 0.824342
window11049 window11050

overview

Window 9

Location 17,978,209 – 17,978,302
Length 93
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 80.41
Mean single sequence MFE -24.95
Consensus MFE -14.74
Energy contribution -15.72
Covariance contribution 0.97
Combinations/Pair 1.10
Mean z-score -1.77
Structure conservation index 0.59
SVM decision value 0.14
SVM RNA-class probability 0.602594
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17978209 93 + 27905053
AGCACCCAUCAAACCCAUGGAACCCAUGGAGGG-----UUGUCA------------GAGGUCUGGCAUUCAAAAAUUGAAAAACCAAAAUUUAAGCUGGGCCAGCUUUUU
(((.((((.(....((((((...))))))..((-----((((((------------(....))))).((((.....)))).)))).........).))))...))).... ( -26.00)
>DroSim_CAF1 22794 93 + 1
AGCACCCAUGAAACCCAUGGAACCCAUGGAGGG-----UUGUCA------------GAGGUCUGGCAUUCAAAAAUUGAAAAACCAAAAUUUAAGCUGGGCCAGCUUUUU
.....(((((.....)))))(((((.....)))-----))...(------------((((.(((((.((((.....))))...(((..........))))))))))))). ( -26.10)
>DroEre_CAF1 22114 93 + 1
AGCACCCAUGGAACCCAUGGAACCCAUGGAGGG-----UUGUCA------------GAGGUCUGGCAUUCAAAAAUUGAAAAACCAAAAUUUAAGCUGGGCCAGCUUUUU
.....((((((...))))))(((((.....)))-----))...(------------((((.(((((.((((.....))))...(((..........))))))))))))). ( -27.80)
>DroWil_CAF1 22434 106 + 1
AACAACGAUGAAUCCUCUCCAGCA---AGAGGGCAAGUGUGUAAGAGAGAGAGAAUAAGGUCUGGCAUUCAAAAAUUGAAAAACCAAAAUUUAAGCUGGG-CAGCUUUUU
.(((.((.....((((((......---))))))....))))).....((((((......(((..((.((((.....))))(((......)))..))..))-)..)))))) ( -17.90)
>DroYak_CAF1 22577 91 + 1
AGCACCGA--GCACCCAUGGAACCCAUGGAGGG-----UUGUCA------------GAGGUCUGGCAUUCAAAAAUUGAAAAACCAAAAUUUAAGCUGGGCCAGCUUUUU
(((.((.(--((..((((((...))))))..((-----((((((------------(....))))).((((.....)))).)))).........))).))...))).... ( -28.20)
>DroAna_CAF1 19955 84 + 1
GGGCUUGG--G---CCACGAUUC----CGAGGG-----UUGUCA------------GAGGUCUGGCAUUCAAAAAUUGAAAAACCAAAAUUUAAGCUGGGCCAGCUUUUU
(((((.((--.---((((.....----....((-----((((((------------(....))))).((((.....)))).)))).........).))).)))))))... ( -23.67)
>consensus
AGCACCCAUGAAACCCAUGGAACCCAUGGAGGG_____UUGUCA____________GAGGUCUGGCAUUCAAAAAUUGAAAAACCAAAAUUUAAGCUGGGCCAGCUUUUU
..............(((((.....)))))...........................((((.(((((.((((.....))))...(((..........)))))))))))).. (-14.74 = -15.72 +   0.97)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,978,209 – 17,978,302
Length 93
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 80.41
Mean single sequence MFE -25.48
Consensus MFE -15.53
Energy contribution -16.58
Covariance contribution 1.06
Combinations/Pair 1.09
Mean z-score -2.15
Structure conservation index 0.61
SVM decision value 0.69
SVM RNA-class probability 0.824342
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17978209 93 - 27905053
AAAAAGCUGGCCCAGCUUAAAUUUUGGUUUUUCAAUUUUUGAAUGCCAGACCUC------------UGACAA-----CCCUCCAUGGGUUCCAUGGGUUUGAUGGGUGCU
....(((..((((((((((((..((((....))))..)))))..))(((((((.------------((..((-----(((.....))))).)).))))))).)))))))) ( -30.30)
>DroSim_CAF1 22794 93 - 1
AAAAAGCUGGCCCAGCUUAAAUUUUGGUUUUUCAAUUUUUGAAUGCCAGACCUC------------UGACAA-----CCCUCCAUGGGUUCCAUGGGUUUCAUGGGUGCU
....(((..(((((..........((((..((((.....)))).))))(((((.------------((..((-----(((.....))))).)).)))))...)))))))) ( -27.30)
>DroEre_CAF1 22114 93 - 1
AAAAAGCUGGCCCAGCUUAAAUUUUGGUUUUUCAAUUUUUGAAUGCCAGACCUC------------UGACAA-----CCCUCCAUGGGUUCCAUGGGUUCCAUGGGUGCU
....(((..(((((..........((((..((((.....)))).))))(((((.------------((..((-----(((.....))))).)).)))))...)))))))) ( -27.30)
>DroWil_CAF1 22434 106 - 1
AAAAAGCUG-CCCAGCUUAAAUUUUGGUUUUUCAAUUUUUGAAUGCCAGACCUUAUUCUCUCUCUCUUACACACUUGCCCUCU---UGCUGGAGAGGAUUCAUCGUUGUU
...(((((.-...)))))....((((((..((((.....)))).))))))....(((((((((..(.................---.)..)))))))))........... ( -20.07)
>DroYak_CAF1 22577 91 - 1
AAAAAGCUGGCCCAGCUUAAAUUUUGGUUUUUCAAUUUUUGAAUGCCAGACCUC------------UGACAA-----CCCUCCAUGGGUUCCAUGGGUGC--UCGGUGCU
....(((..(((.(((.......(((((..((((.....)))).)))))((((.------------((..((-----(((.....))))).)).))))))--).)))))) ( -26.90)
>DroAna_CAF1 19955 84 - 1
AAAAAGCUGGCCCAGCUUAAAUUUUGGUUUUUCAAUUUUUGAAUGCCAGACCUC------------UGACAA-----CCCUCG----GAAUCGUGG---C--CCAAGCCC
.....((((((((.........((((((..((((.....)))).))))))..((------------(((...-----...)))----))...).))---)--)..))).. ( -21.00)
>consensus
AAAAAGCUGGCCCAGCUUAAAUUUUGGUUUUUCAAUUUUUGAAUGCCAGACCUC____________UGACAA_____CCCUCCAUGGGUUCCAUGGGUUCCAUCGGUGCU
...((((((...))))))....((((((..((((.....)))).))))))..............................(((((((...)))))))............. (-15.53 = -16.58 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:25 2006