Locus 9249

Sequence ID 3R_DroMel_CAF1
Location 24,670,983 – 24,671,143
Length 160
Max. P 0.999173
window14782 window14783 window14784

overview

Window 2

Location 24,670,983 – 24,671,103
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.33
Mean single sequence MFE -34.12
Consensus MFE -31.12
Energy contribution -32.40
Covariance contribution 1.28
Combinations/Pair 1.11
Mean z-score -2.26
Structure conservation index 0.91
SVM decision value 3.41
SVM RNA-class probability 0.999173
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24670983 120 + 27905053
UUUUGUUGUUGUUCUUCAAACAGCUGAGCGGCGGACGGAUAUUUGUUGUUGCUGCGCCCGGGAAGCUGCGCAGCGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCGAAAAUUAAA
(((((((((((((((((.........(((((((((......)))))))))(((((((..((....))))))))))))))))(((.............)))....))))))))))...... ( -39.32)
>DroSec_CAF1 12063 120 + 1
UUUUGUUGUUGUUCUUCAAACAGCUGAGCGGCGGACGGAUAUUUGUUGUUGAUGCGCCCGGGAAGCAGCGCAGCGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUUGCAAAAAUUAAA
((((((.((((((((((.....((((.((((((.(..((((.....))))..).))))..(....).)).)))))))))))(((.............)))....))).))))))...... ( -30.22)
>DroSim_CAF1 12054 120 + 1
UUUUGUUGUUGUUCUUCAAACAGCUGAGCGGCGGACGGAUAUUUGUUGUUGCUCCGCCCGGGAAGCUGCGCAACGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCCAAAAUUAAA
(((((((((((((((((...(((((..(.((((((..((((.....))))..)))))))....)))))......)))))))(((.............)))....))))).)))))..... ( -33.02)
>DroEre_CAF1 13559 120 + 1
UUUUGUUGUUGUUUUACAAACAGCUGAGCGGCGGACGGAUAUUUGUUGAUGCUGCGCCCGGGAAGCUGCGCAGUGAAUAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCAAAAAUUAAA
((((((((((..(((((..........(((((((((((....)))))..))))))((.(((....))).)).)))))....(((.............)))....))))))))))...... ( -28.12)
>DroYak_CAF1 12194 120 + 1
UUUUGUUGUUGUUUUCCAAACAGCUGAGCGGCGGACGGAUAUUUGUUGUUGCUGCGCCCGGGAAGCUGCGCAGCGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCAAAAAUUAAA
(((((((((((((((((.........(((((((((......)))))))))(((((((..((....))))))))))))))))(((.............)))....))))))))))...... ( -39.92)
>consensus
UUUUGUUGUUGUUCUUCAAACAGCUGAGCGGCGGACGGAUAUUUGUUGUUGCUGCGCCCGGGAAGCUGCGCAGCGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCAAAAAUUAAA
(((((((((((((((((.........(((((((((......)))))))))(((((((..((....))))))))))))))))(((.............)))....))))))))))...... (-31.12 = -32.40 +   1.28)

alignment

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secondary structure

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Window 3

Location 24,671,023 – 24,671,143
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.50
Mean single sequence MFE -30.93
Consensus MFE -20.38
Energy contribution -21.34
Covariance contribution 0.96
Combinations/Pair 1.17
Mean z-score -2.66
Structure conservation index 0.66
SVM decision value 0.13
SVM RNA-class probability 0.597771
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24671023 120 + 27905053
AUUUGUUGUUGCUGCGCCCGGGAAGCUGCGCAGCGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCGAAAAUUAAACGCGUUGCAAGUGCAGCAGAAAACAACGGUAAUAAUUCGC
..(((((((((((((((.......((.((((.(((.....)))..............(((........)))..........)))).))..))))))))....)))))))........... ( -32.90)
>DroSec_CAF1 12103 120 + 1
AUUUGUUGUUGAUGCGCCCGGGAAGCAGCGCAGCGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUUGCAAAAAUUAAACGUGUCGCGAGUGCAGCUGCAAACAACAGUAAUAAUUCGC
..(((((((((.(((((.((.((....(((..(((.....)))...............((((....))))..........))).)).)).)))))....).))))))))........... ( -29.70)
>DroSim_CAF1 12094 120 + 1
AUUUGUUGUUGCUCCGCCCGGGAAGCUGCGCAACGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCCAAAAUUAAAAUCGUCGCAAGUGCAGCUGCAAACAACAGUAAUAAUUCGC
..(((((((((((((.....)))((((((((...(.....)((((.............((........))..............))))..)))))))))).))))))))........... ( -31.13)
>DroEre_CAF1 13599 115 + 1
AUUUGUUGAUGCUGCGCCCGGGAAGCUGCGCAGUGAAUAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCAAAAAUUAAACG-----CAAGUGCAGCAGCAAAAAAAAAUAAUAUUUCGC
.(((((((..(((((((..((....))))))))).......((...............((........)).........((.-----...))))..)))))))................. ( -24.90)
>DroYak_CAF1 12234 120 + 1
AUUUGUUGUUGCUGCGCCCGGGAAGCUGCGCAGCGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCAAAAAUUAAACGCGUCGCGAGUGCAGCAGCAAGCAACCAUAAUAAUUUGC
..(((((((((((((((.((.((...((((..(((.....)))...............((........))..........)))))).)).)))))))))).))))).............. ( -36.00)
>consensus
AUUUGUUGUUGCUGCGCCCGGGAAGCUGCGCAGCGGAGAACGCGAAAAAUAAUAAAACGCAAAAAAUAGCAAAAAUUAAACGCGUCGCAAGUGCAGCAGCAAACAACAGUAAUAAUUCGC
..((((((((...((.(....)..(((((((.(((.....)))...............((........))....................))))))).)).))))))))........... (-20.38 = -21.34 +   0.96)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,671,023 – 24,671,143
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.50
Mean single sequence MFE -30.38
Consensus MFE -22.10
Energy contribution -23.46
Covariance contribution 1.36
Combinations/Pair 1.13
Mean z-score -2.12
Structure conservation index 0.73
SVM decision value 0.56
SVM RNA-class probability 0.781679
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24671023 120 - 27905053
GCGAAUUAUUACCGUUGUUUUCUGCUGCACUUGCAACGCGUUUAAUUUUCGCUAUUUUUUGCGUUUUAUUAUUUUUCGCGUUCUCCGCUGCGCAGCUUCCCGGGCGCAGCAACAACAAAU
.............(((((....((((((.((((.((((((..((((...(((........)))....)))).....))))))....(((....)))....)))).))))))))))).... ( -32.70)
>DroSec_CAF1 12103 120 - 1
GCGAAUUAUUACUGUUGUUUGCAGCUGCACUCGCGACACGUUUAAUUUUUGCAAUUUUUUGCGUUUUAUUAUUUUUCGCGUUCUCCGCUGCGCUGCUUCCCGGGCGCAUCAACAACAAAU
............(((((((.(((((.(....(((((......((((...(((((....)))))....))))....)))))....).)))))((.(((.....)))))...)))))))... ( -31.60)
>DroSim_CAF1 12094 120 - 1
GCGAAUUAUUACUGUUGUUUGCAGCUGCACUUGCGACGAUUUUAAUUUUGGCUAUUUUUUGCGUUUUAUUAUUUUUCGCGUUCUCCGUUGCGCAGCUUCCCGGGCGGAGCAACAACAAAU
............(((((((.((((((((....((((.((...((((....((........)).....)))).)).))))((........))))))))(((.....))))))))))))... ( -28.40)
>DroEre_CAF1 13599 115 - 1
GCGAAAUAUUAUUUUUUUUUGCUGCUGCACUUG-----CGUUUAAUUUUUGCUAUUUUUUGCGUUUUAUUAUUUUUCGCGUUAUUCACUGCGCAGCUUCCCGGGCGCAGCAUCAACAAAU
((((((..........))))))((((((.((((-----....((((...(((........)))....))))......((((........)))).......)))).))))))......... ( -25.10)
>DroYak_CAF1 12234 120 - 1
GCAAAUUAUUAUGGUUGCUUGCUGCUGCACUCGCGACGCGUUUAAUUUUUGCUAUUUUUUGCGUUUUAUUAUUUUUCGCGUUCUCCGCUGCGCAGCUUCCCGGGCGCAGCAACAACAAAU
.............((((.((((((((((.(..((((((((..((((...(((........)))....)))).....)))))....))).).)))(((.....)))))))))))))).... ( -34.10)
>consensus
GCGAAUUAUUACUGUUGUUUGCUGCUGCACUUGCGACGCGUUUAAUUUUUGCUAUUUUUUGCGUUUUAUUAUUUUUCGCGUUCUCCGCUGCGCAGCUUCCCGGGCGCAGCAACAACAAAU
((((((..........)))))).(((((.((((.((.((...((((...(((........)))....))))......((((........)))).)).)).)))).))))).......... (-22.10 = -23.46 +   1.36)

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 13:29:48 2006