Locus 6222

Sequence ID 2R_DroMel_CAF1
Location 19,562,754 – 19,562,849
Length 95
Max. P 0.939534
window9969 window9970

overview

Window 9

Location 19,562,754 – 19,562,849
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.32
Mean single sequence MFE -27.17
Consensus MFE -14.20
Energy contribution -14.64
Covariance contribution 0.45
Combinations/Pair 1.17
Mean z-score -1.82
Structure conservation index 0.52
SVM decision value 0.04
SVM RNA-class probability 0.551641
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19562754 95 + 20766785
AUAUAGAUGCAACAAUUAU------AACUGAAGAUGGGCUUGUCCAAGCGUUGCGUUUUAUGCUCCAUAGCACACACGCCAC-------------------CAUUUGGAUGCAGCAUCUG
...(((((((.........------..((......))((..(((((((.((.((((....((((....))))...)))).))-------------------..))))))))).))))))) ( -24.90)
>DroSec_CAF1 2139 95 + 1
AUAUAGAUGCAACAAUUAU------AGCCGAAGAUGGGCUUGUCCAAGCGUUGCGUUUUAUGCUCCAUAGCACACACGCCAC-------------------CAUUUGGAUGCAGCAUCUG
...(((((((.........------((((.......)))).(((((((.((.((((....((((....))))...)))).))-------------------..)))))))...))))))) ( -28.60)
>DroSim_CAF1 2107 95 + 1
AUAUAGAUGCAACAAUUAU------UGCCGAAGAUGGGCUUGUCCAAGCGUUGCGUUUUAUGCUCCAUAGCACACACGCCAC-------------------CAUUUGGAUGCAGCAUCUG
...(((((((.........------.(((.......)))..(((((((.((.((((....((((....))))...)))).))-------------------..)))))))...))))))) ( -27.90)
>DroEre_CAF1 2076 95 + 1
AUUUAGAUGCAACAAUUAU------AACAGAAGAUGAGCUUGUCCAAGCGUUGAGUUUUAUGCUCCAUAGCACACACGCCAA-------------------CAUUUGGAUGCAGCAUCUG
...(((((((.........------..((.....)).((..(((((((.((((.((....((((....)))).....)))))-------------------).))))))))).))))))) ( -24.80)
>DroWil_CAF1 2584 119 + 1
CUGUAAGUGCUUAAAAUAUUUGCGAAUCUGGAGAGGAGCUAG-CCAAGCGUGCAUCUUUAUGCUCUACAGCGCGAAUGCUGUACUCUGUUUGCACAAAGUGCAUUUAGUUGCAGACUCCA
((((((((((......((((((((...(((.(((((......-))..(((((......)))))))).)))))))))))..)))).(((..(((((...)))))..)))))))))...... ( -31.90)
>DroYak_CAF1 2241 95 + 1
AUAUAGAUGCAACAAUUAU------AACAGAAGAUGAGCUUGUCCAAGCGUUGAGUUUUAUGCUCCAUAGCACACACGCCAA-------------------CAUUUGGAUGCAGCAUCUG
...(((((((.........------..((.....)).((..(((((((.((((.((....((((....)))).....)))))-------------------).))))))))).))))))) ( -24.90)
>consensus
AUAUAGAUGCAACAAUUAU______AACAGAAGAUGAGCUUGUCCAAGCGUUGAGUUUUAUGCUCCAUAGCACACACGCCAC___________________CAUUUGGAUGCAGCAUCUG
...(((((((...........................((((....))))...........(((((((......................................)))).)))))))))) (-14.20 = -14.64 +   0.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,562,754 – 19,562,849
Length 95
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.32
Mean single sequence MFE -30.17
Consensus MFE -15.98
Energy contribution -16.82
Covariance contribution 0.84
Combinations/Pair 1.17
Mean z-score -2.49
Structure conservation index 0.53
SVM decision value 1.28
SVM RNA-class probability 0.939534
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19562754 95 - 20766785
CAGAUGCUGCAUCCAAAUG-------------------GUGGCGUGUGUGCUAUGGAGCAUAAAACGCAACGCUUGGACAAGCCCAUCUUCAGUU------AUAAUUGUUGCAUCUAUAU
.((((((.((((((((.((-------------------...((((.((((((....))))))..))))..)).)))))..(((.........)))------.....))).)))))).... ( -27.40)
>DroSec_CAF1 2139 95 - 1
CAGAUGCUGCAUCCAAAUG-------------------GUGGCGUGUGUGCUAUGGAGCAUAAAACGCAACGCUUGGACAAGCCCAUCUUCGGCU------AUAAUUGUUGCAUCUAUAU
.((((((.((((((((.((-------------------...((((.((((((....))))))..))))..)).)))))..((((.......))))------.....))).)))))).... ( -33.50)
>DroSim_CAF1 2107 95 - 1
CAGAUGCUGCAUCCAAAUG-------------------GUGGCGUGUGUGCUAUGGAGCAUAAAACGCAACGCUUGGACAAGCCCAUCUUCGGCA------AUAAUUGUUGCAUCUAUAU
.((((((.((((((((.((-------------------...((((.((((((....))))))..))))..)).)))))...(((.......))).------.....))).)))))).... ( -32.80)
>DroEre_CAF1 2076 95 - 1
CAGAUGCUGCAUCCAAAUG-------------------UUGGCGUGUGUGCUAUGGAGCAUAAAACUCAACGCUUGGACAAGCUCAUCUUCUGUU------AUAAUUGUUGCAUCUAAAU
.((((((.((((((((.((-------------------((((....((((((....))))))....)))))).)))))..(((.........)))------.....))).)))))).... ( -27.80)
>DroWil_CAF1 2584 119 - 1
UGGAGUCUGCAACUAAAUGCACUUUGUGCAAACAGAGUACAGCAUUCGCGCUGUAGAGCAUAAAGAUGCACGCUUGG-CUAGCUCCUCUCCAGAUUCGCAAAUAUUUUAAGCACUUACAG
(((((..((((.((..(((((((((((....)))))))(((((......)))))...))))..)).)))).(((...-..)))....))))).....((...........))........ ( -31.70)
>DroYak_CAF1 2241 95 - 1
CAGAUGCUGCAUCCAAAUG-------------------UUGGCGUGUGUGCUAUGGAGCAUAAAACUCAACGCUUGGACAAGCUCAUCUUCUGUU------AUAAUUGUUGCAUCUAUAU
.((((((.((((((((.((-------------------((((....((((((....))))))....)))))).)))))..(((.........)))------.....))).)))))).... ( -27.80)
>consensus
CAGAUGCUGCAUCCAAAUG___________________GUGGCGUGUGUGCUAUGGAGCAUAAAACGCAACGCUUGGACAAGCCCAUCUUCAGUU______AUAAUUGUUGCAUCUAUAU
.((((((.(((.............................(((((.((((((....)))))).......)))))(((......)))....................))).)))))).... (-15.98 = -16.82 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:02 2006