Locus 7533

Sequence ID 3L_DroMel_CAF1
Location 20,234,467 – 20,234,584
Length 117
Max. P 0.905764
window12244 window12245

overview

Window 4

Location 20,234,467 – 20,234,584
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.25
Mean single sequence MFE -39.20
Consensus MFE -25.27
Energy contribution -25.00
Covariance contribution -0.27
Combinations/Pair 1.40
Mean z-score -1.20
Structure conservation index 0.64
SVM decision value -0.02
SVM RNA-class probability 0.521329
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20234467 117 + 23771897
CCGUAGAGCUGU---UGAGCACAGUUUCUAUAACUGCACACGUCUCUACCACACCCUUCUCCUUCUCCUUGGAGUACAAAUUGGAGAAGCUCUGGUGCUUUGAGCCUGGCGUUGAACUAC
..((((((((((---.....))))))....((((.((.((.(.(((.....(((((((((((..(((....)))........)))))))....))))....)))).))))))))..)))) ( -30.90)
>DroVir_CAF1 3623 114 + 1
------UGCUGUGCGUGGUAACGGUUUCGAUGACUGCACACGUUUCCACUACGCCCUUUUCCUUCUCCUUUGAGUAGAGAUUGGAGAAGCUUUGAUGCUUGGAGCCGGGCGUCGAGCUGC
------.(((..(((((....(((((.....)))))..))))).....(.((((((((((((.((((.........))))..))))))((((..(...)..)))).)))))).))))... ( -36.90)
>DroPse_CAF1 3819 117 + 1
CCGCGGAACUGU---GGAGCACCGUUUCGAUAACGGCGCACGUUUCAACGACGCCCUUCUCUUUCUCUUUGGAGUAGAGAUUGGAGAAGCUCUGGUGCUUGGACCCGGGCGUGGAGCUGC
(((((...(((.---((((((((...........((((..(((....))).))))(((((((.(((((.......)))))..)))))))....))))))....))))).)))))...... ( -42.80)
>DroWil_CAF1 3824 117 + 1
CACCGGGACUUG---GCAAUACCGUCUCAAUUACAGCGCAUGUUUCGACAACACCUUUCUCCUUCUCUUUGGAGUAGAGAUUGGAGAAACUCUGAUGUUUAGAGCCAGGUGUAGAACUAC
...((..((.((---((..................)).)).))..))...((((((((((((.(((((.......)))))..)))))).((((((...))))))..))))))........ ( -32.57)
>DroMoj_CAF1 8252 114 + 1
------UGCUGUGCGUGGUGACAGUCUCAAUGACUGCGCACGUUUCCACAACGCCCUUUUCCUUCUCUUUGGAAUAGAGAUUGGAAAAGCUUUGAUGCUUGGAGCCGGGCGUUGAGCUGC
------.((((((((((....)((((.....)))))))))).......((((((((((((((.(((((.......)))))..))))))((((..(...)..)))).)))))))))))... ( -49.20)
>DroPer_CAF1 3882 117 + 1
CCGCGGAACUGU---GGAGCACCGUUUCGAUAACGGCGCACGUUUCAACGACGCCCUUCUCUUUCUCUUUGGAGUAGAGAUUGGAGAAGCUCUGGUGCUUGGACCCGGGCGUGGAGCUGC
(((((...(((.---((((((((...........((((..(((....))).))))(((((((.(((((.......)))))..)))))))....))))))....))))).)))))...... ( -42.80)
>consensus
CCGCGGAACUGU___GGAGCACCGUUUCGAUAACUGCGCACGUUUCAACAACGCCCUUCUCCUUCUCUUUGGAGUAGAGAUUGGAGAAGCUCUGAUGCUUGGAGCCGGGCGUGGAGCUGC
.....................(((((.....)))))............(.((((((((((((.(((((.......)))))..))))))(((((((...))))))).)))))).)...... (-25.27 = -25.00 +  -0.27)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 20,234,467 – 20,234,584
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.25
Mean single sequence MFE -38.02
Consensus MFE -24.67
Energy contribution -23.57
Covariance contribution -1.11
Combinations/Pair 1.40
Mean z-score -1.78
Structure conservation index 0.65
SVM decision value 1.04
SVM RNA-class probability 0.905764
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20234467 117 - 23771897
GUAGUUCAACGCCAGGCUCAAAGCACCAGAGCUUCUCCAAUUUGUACUCCAAGGAGAAGGAGAAGGGUGUGGUAGAGACGUGUGCAGUUAUAGAAACUGUGCUCA---ACAGCUCUACGG
........(((((..((.....)).......(((((((........(((....)))..)))))))))))).((((((..(((..(((((.....)))))..)...---))..)))))).. ( -36.10)
>DroVir_CAF1 3623 114 - 1
GCAGCUCGACGCCCGGCUCCAAGCAUCAAAGCUUCUCCAAUCUCUACUCAAAGGAGAAGGAAAAGGGCGUAGUGGAAACGUGUGCAGUCAUCGAAACCGUUACCACGCACAGCA------
...(((.(((((((...(((..((......))((((((..............)))))))))...)))))).((((.((((.((...(....)...)))))).))))...)))).------ ( -37.34)
>DroPse_CAF1 3819 117 - 1
GCAGCUCCACGCCCGGGUCCAAGCACCAGAGCUUCUCCAAUCUCUACUCCAAAGAGAAAGAGAAGGGCGUCGUUGAAACGUGCGCCGUUAUCGAAACGGUGCUCC---ACAGUUCCGCGG
........((((((.((...((((......))))..))..(((((.(((....)))..))))).))))))(((.(((..((((((((((.....))))))))...---))..))).))). ( -40.20)
>DroWil_CAF1 3824 117 - 1
GUAGUUCUACACCUGGCUCUAAACAUCAGAGUUUCUCCAAUCUCUACUCCAAAGAGAAGGAGAAAGGUGUUGUCGAAACAUGCGCUGUAAUUGAGACGGUAUUGC---CAAGUCCCGGUG
(((.(((.((((((.(((((.......)))))((((((..(((((.......))))).))))))))))))....)))...)))(((((.......)))))...((---(.......))). ( -31.80)
>DroMoj_CAF1 8252 114 - 1
GCAGCUCAACGCCCGGCUCCAAGCAUCAAAGCUUUUCCAAUCUCUAUUCCAAAGAGAAGGAAAAGGGCGUUGUGGAAACGUGCGCAGUCAUUGAGACUGUCACCACGCACAGCA------
...(((((((((((...(((((((......))))......(((((.......))))).)))...)))))))).(....)((((((((((.....)))))......)))))))).------ ( -42.50)
>DroPer_CAF1 3882 117 - 1
GCAGCUCCACGCCCGGGUCCAAGCACCAGAGCUUCUCCAAUCUCUACUCCAAAGAGAAAGAGAAGGGCGUCGUUGAAACGUGCGCCGUUAUCGAAACGGUGCUCC---ACAGUUCCGCGG
........((((((.((...((((......))))..))..(((((.(((....)))..))))).))))))(((.(((..((((((((((.....))))))))...---))..))).))). ( -40.20)
>consensus
GCAGCUCAACGCCCGGCUCCAAGCACCAGAGCUUCUCCAAUCUCUACUCCAAAGAGAAGGAGAAGGGCGUCGUGGAAACGUGCGCAGUUAUCGAAACGGUGCUCA___ACAGCUCCGCGG
(((.....((((((........((......))((((((..(((((.......))))).)))))))))))).((....)).)))((((((.....)))))).................... (-24.67 = -23.57 +  -1.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:36 2006