Locus 5713

Sequence ID 2R_DroMel_CAF1
Location 18,100,604 – 18,100,709
Length 105
Max. P 0.712348
window9150 window9151

overview

Window 0

Location 18,100,604 – 18,100,709
Length 105
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 69.45
Mean single sequence MFE -23.60
Consensus MFE -4.31
Energy contribution -5.55
Covariance contribution 1.24
Combinations/Pair 1.18
Mean z-score -1.75
Structure conservation index 0.18
SVM decision value -0.05
SVM RNA-class probability 0.508704
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18100604 105 + 20766785
-UUGAACUCUCCCUUACGUGCCCAUCAAAGAGAGU-UAUAUUAAAAGAGAACCAAAUUCUCUUCUCUU-GAUUUGG---AUUUAAGAGGCUUUCUUUUGUAUUU-------UUAUAUU
-......................((.(((((((((-........(((((((.....)))))))(((((-((.....---..)))))))))))))))).))....-------....... ( -20.00)
>DroSec_CAF1 51841 109 + 1
-UUGAACUCUCCCUUACGUGCCCGUCAAUGAGAGU-UAUAUUGAAAGAGAACCAAAUUCUCUUCUCUU-GAUUUGG---ACUUAAGAGGCUUUAUUUUGAAUUUAGUA---UUUGAUU
-...(((((((....(((....)))....))))))-)((((((((((((((.....))))))((((((-((.....---..))))))))............)))))))---)...... ( -23.30)
>DroSim_CAF1 52595 109 + 1
-UUGAACUCUCCCUUACGUGCCCGUCAAUGAGAGU-UAUAUUGAAAGAGAACCAAAUUCUCUUCUCUU-GAUUUGG---ACUUAAGAGGCUUUAUUUUGAAUUUAGUA---UUUGAUU
-...(((((((....(((....)))....))))))-)((((((((((((((.....))))))((((((-((.....---..))))))))............)))))))---)...... ( -23.30)
>DroEre_CAF1 52529 100 + 1
CUUGAACCUACUCUUUGG-------------GAAU-UGCU----UAGAGAGCCCAAGUCUCCUCUCUUUUUGUCUCUUUAUUUAAGAGGCGUUCUUUUCAAUGUAGUUGAAUUUGAUU
.......((((...(((.-------------.((.-.((.----.((((((..........))))))....(((((((.....)))))))))..))..))).))))............ ( -23.20)
>DroYak_CAF1 54164 106 + 1
CUUAAGCUUUCUCUUGCGCACCAGUCAAA--GAGUCAGUU----CAGGGCACCAAAUUCUGCUCUCUUUGAAUAGG---CGUUAAGAGGCUUUCUUUGAAAUUUACUU---UUUGAGU
...((((...(((((((((.....(((((--(((.(((..----...(....).....)))..))))))))....)---)).))))))))))..((..(((......)---))..)). ( -28.20)
>consensus
_UUGAACUCUCCCUUACGUGCCCGUCAAAGAGAGU_UAUAUU_AAAGAGAACCAAAUUCUCUUCUCUU_GAUUUGG___ACUUAAGAGGCUUUCUUUUGAAUUUAGUA___UUUGAUU
.....((((((..................))))))...........(((((.....))))).((((((...............))))))............................. ( -4.31 =  -5.55 +   1.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,100,604 – 18,100,709
Length 105
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 69.45
Mean single sequence MFE -21.98
Consensus MFE -5.79
Energy contribution -7.15
Covariance contribution 1.36
Combinations/Pair 1.17
Mean z-score -1.87
Structure conservation index 0.26
SVM decision value 0.38
SVM RNA-class probability 0.712348
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18100604 105 - 20766785
AAUAUAA-------AAAUACAAAAGAAAGCCUCUUAAAU---CCAAAUC-AAGAGAAGAGAAUUUGGUUCUCUUUUAAUAUA-ACUCUCUUUGAUGGGCACGUAAGGGAGAGUUCAA-
.......-------......((((((.((((((((...(---(......-..))...))))....)))).)))))).....(-(((((((((.(((....))).))))))))))...- ( -22.60)
>DroSec_CAF1 51841 109 - 1
AAUCAAA---UACUAAAUUCAAAAUAAAGCCUCUUAAGU---CCAAAUC-AAGAGAAGAGAAUUUGGUUCUCUUUCAAUAUA-ACUCUCAUUGACGGGCACGUAAGGGAGAGUUCAA-
.......---....................(((((....---.......-)))))((((((((...)))))))).......(-((((((....(((....)))....)))))))...- ( -21.10)
>DroSim_CAF1 52595 109 - 1
AAUCAAA---UACUAAAUUCAAAAUAAAGCCUCUUAAGU---CCAAAUC-AAGAGAAGAGAAUUUGGUUCUCUUUCAAUAUA-ACUCUCAUUGACGGGCACGUAAGGGAGAGUUCAA-
.......---....................(((((....---.......-)))))((((((((...)))))))).......(-((((((....(((....)))....)))))))...- ( -21.10)
>DroEre_CAF1 52529 100 - 1
AAUCAAAUUCAACUACAUUGAAAAGAACGCCUCUUAAAUAAAGAGACAAAAAGAGAGGAGACUUGGGCUCUCUA----AGCA-AUUC-------------CCAAAGAGUAGGUUCAAG
.......(((((.....)))))..(((((((((((.....)))))......((((((..........)))))).----.)).-((((-------------.....))))..))))... ( -18.30)
>DroYak_CAF1 54164 106 - 1
ACUCAAA---AAGUAAAUUUCAAAGAAAGCCUCUUAACG---CCUAUUCAAAGAGAGCAGAAUUUGGUGCCCUG----AACUGACUC--UUUGACUGGUGCGCAAGAGAAAGCUUAAG
.......---................(((((((((..((---((((.((((((((..(((..((..(....)..----))))).)))--))))).))).))).)))))...))))... ( -26.80)
>consensus
AAUCAAA___AACUAAAUUCAAAAGAAAGCCUCUUAAAU___CCAAAUC_AAGAGAAGAGAAUUUGGUUCUCUUU_AAUAUA_ACUCUCAUUGACGGGCACGUAAGGGAGAGUUCAA_
..............................((((((...............((((((((((((...))))))))..........))))..............)))))).......... ( -5.79 =  -7.15 +   1.36)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:30 2006