Locus 5268

Sequence ID 3L_DroMel_CAF1
Location 14,549,237 – 14,549,387
Length 150
Max. P 0.851460
window8332 window8333 window8334

overview

Window 2

Location 14,549,237 – 14,549,357
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.94
Mean single sequence MFE -43.97
Consensus MFE -38.55
Energy contribution -38.05
Covariance contribution -0.50
Combinations/Pair 1.12
Mean z-score -1.65
Structure conservation index 0.88
SVM decision value 0.75
SVM RNA-class probability 0.840123
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14549237 120 - 23771897
GGUCUGGUUCCAGAAUCGUCGCACCAAAUGGCGCAAACGGCAUGCGGCGGAAAUGGCCACGGCCAAAAGGAAACAGGACGAUAUGGGCGGCGAUAACGAUGGCGAUUGCAGCGAGACCAU
(((((.((((((..((((((((.((....)).))....(((.((.(((.......))).)))))....(....)..)))))).)))...(((((..(....)..)))))))).))))).. ( -44.90)
>DroVir_CAF1 27231 120 - 1
GGUUUGGUUUCAGAAUCGUCGCACCAAAUGGCGCAAACGUCAUGCGGCGGAAAUGGCCACGGCCAAGCGGAAACAGGACGACAUGGGCGGCGACAACGAUGGAGACUGCAGCGAGACCAU
(((((.(((.(((..(((((((.(((.((((((....)))))).((((.....((((....)))).))(....)....))...))))))))))((....))....))).))).))))).. ( -43.60)
>DroGri_CAF1 27612 120 - 1
GGUUUGGUUUCAGAAUCGUCGCACCAAAUGGCGCAAACGUCAUGCGGCGGAAAUGGCAACGGCCAAGCGGAAACAGGAUGACAUGGGUGGCGACAACGAUGGCGACUGCAGCGAGACCAU
(((((.(((.(((..((((((((.....(((((....)))))))))))))...((((....)))).(((....).......(((.(.((....)).).)))))..))).))).))))).. ( -43.00)
>DroWil_CAF1 164250 120 - 1
GGUUUGGUUUCAGAAUCGUCGCACCAAAUGGCGCAAACGUCAUGCGGCCGAAAUGGCCACAGCGAAGCGGAAACAGGACGACAUGGGUGGCGAUAACGAUGGCGAUUGCAGCGAGACCAU
(((((.(((.((..((((((((.((....)).))...((((((.(((((.....))))..........(....)..........).))))))........)))))))).))).))))).. ( -41.60)
>DroMoj_CAF1 30297 120 - 1
GGUUUGGUUUCAGAAUCGUCGCACCAAAUGGCGCAAGCGUCAUGCGGCGGAAAUGGCAACGGCCAAGCGGAAACAGGACGACAUGGGUGGCGACAACGACGGCGACUGCAGCGAGACCAU
(((((.(((.(((....((((((((.....((....))..((((((((.....((((....)))).))(....)....)).))))))).)))))..((....)).))).))).))))).. ( -44.80)
>DroAna_CAF1 22759 120 - 1
GGUCUGGUUCCAGAACCGUCGCACCAAAUGGCGCAAACGGCAUGCGGCGGAAAUGGCCACGGCCAAGAGGAAACAGGACGACAUGGGCGGCGACAACGACGGGGACUGCAGCGAGGCCAU
(((((.(((.(((..(((((((.(((..(((((((.......)))(((.......)))...))))...(....).........)))))(....)...)))))...))).))).))))).. ( -45.90)
>consensus
GGUUUGGUUUCAGAAUCGUCGCACCAAAUGGCGCAAACGUCAUGCGGCGGAAAUGGCCACGGCCAAGCGGAAACAGGACGACAUGGGCGGCGACAACGAUGGCGACUGCAGCGAGACCAU
(((((.(((.(((..(((((((.(((...(.((((.......)))).).....((((....))))...(....).........))))))))))...(......).))).))).))))).. (-38.55 = -38.05 +  -0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,549,277 – 14,549,387
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.18
Mean single sequence MFE -31.92
Consensus MFE -22.08
Energy contribution -21.88
Covariance contribution -0.19
Combinations/Pair 1.11
Mean z-score -1.27
Structure conservation index 0.69
SVM decision value 0.23
SVM RNA-class probability 0.642344
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14549277 110 + 23771897
CGUCCUGUUUCCUUUUGGCCGUGGCCAUUUCCGCCGCAUGCCGUUUGCGCCAUUUGGUGCGACGAUUCUGGAACCAGACCUGCAACAAAA-------CCAAGAAAUAAC--UA-CGCUUU
(((...(((...((((((..(((((.......))))).(((((((.(((((....)))))))))..((((....))))...)))......-------))))))...)))--.)-)).... ( -32.90)
>DroPse_CAF1 25444 102 + 1
CGUCCUGUUUCCUCUUGGCCGUGGCCAUUUCCGCCGCAUGCCGCUUGCGCCAUUUGGUGCGGCGAUUCUGGAACCAAACCUGCA----------------AAACGUAAG--UAAAACUUU
..(((.(..((.....(((.(((((.......)))))..)))(((.(((((....))))))))))..).)))............----------------..((....)--)........ ( -29.70)
>DroGri_CAF1 27652 112 + 1
CAUCCUGUUUCCGCUUGGCCGUUGCCAUUUCCGCCGCAUGACGUUUGCGCCAUUUGGUGCGACGAUUCUGAAACCAAACCUGUAACAAUU-------CCAAAUUGAAAUGGCA-AACUUU
.....................((((((((((..........((((.(((((....)))))))))....((....))..............-------.......)))))))))-)..... ( -24.10)
>DroWil_CAF1 164290 105 + 1
CGUCCUGUUUCCGCUUCGCUGUGGCCAUUUCGGCCGCAUGACGUUUGCGCCAUUUGGUGCGACGAUUCUGAAACCAAACCUGUAAAAAAG-------GGGAAACAA--------AACUUU
.((..(((((((...(((.(((((((.....))))))))))((((.(((((....)))))))))..............(((.......))-------)))))))).--------.))... ( -38.10)
>DroAna_CAF1 22799 100 + 1
CGUCCUGUUUCCUCUUGGCCGUGGCCAUUUCCGCCGCAUGCCGUUUGCGCCAUUUGGUGCGACGGUUCUGGAACCAGACCUGCAAAAAAA-------CCAACAAGGA-------------
..(((((((......((((....))))........(((.((((((.(((((....)))))))))))((((....))))..))).......-------..))).))))------------- ( -33.70)
>DroPer_CAF1 28992 118 + 1
CGUCCUGUUUCCUCUUGGCCGUGGCCAUUUCCGCCGCAUGCCGCUUGCGCCAUUUGGUGCGACGAUUCUGGAACCAAACCUGCAACGGAAAAUGUAAGCGAAACGUAAG--UAAAACUUU
......(((((((..((((....))))((((((..(((...((.(((((((....)))))))))....((....))....)))..)))))).....)).))))).....--......... ( -33.00)
>consensus
CGUCCUGUUUCCUCUUGGCCGUGGCCAUUUCCGCCGCAUGCCGUUUGCGCCAUUUGGUGCGACGAUUCUGGAACCAAACCUGCAACAAAA_______CCAAAACGUAA___UA_AACUUU
......(((((.........(((((.......)))))....((.(((((((....))))))))).....))))).............................................. (-22.08 = -21.88 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 14,549,277 – 14,549,387
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.18
Mean single sequence MFE -35.92
Consensus MFE -26.88
Energy contribution -26.35
Covariance contribution -0.52
Combinations/Pair 1.21
Mean z-score -1.56
Structure conservation index 0.75
SVM decision value 0.79
SVM RNA-class probability 0.851460
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14549277 110 - 23771897
AAAGCG-UA--GUUAUUUCUUGG-------UUUUGUUGCAGGUCUGGUUCCAGAAUCGUCGCACCAAAUGGCGCAAACGGCAUGCGGCGGAAAUGGCCACGGCCAAAAGGAAACAGGACG
......-..--(((.((((((..-------((((((((((..((((....)))).((((.((.((....)).))..))))..)))))))))).((((....))))..))))))...))). ( -33.40)
>DroPse_CAF1 25444 102 - 1
AAAGUUUUA--CUUACGUUU----------------UGCAGGUUUGGUUCCAGAAUCGCCGCACCAAAUGGCGCAAGCGGCAUGCGGCGGAAAUGGCCACGGCCAAGAGGAAACAGGACG
...((...(--(....))..----------------.))..((((..((((....((((((((((.....((....))))..))))))))...((((....))))...))))...)))). ( -33.30)
>DroGri_CAF1 27652 112 - 1
AAAGUU-UGCCAUUUCAAUUUGG-------AAUUGUUACAGGUUUGGUUUCAGAAUCGUCGCACCAAAUGGCGCAAACGUCAUGCGGCGGAAAUGGCAACGGCCAAGCGGAAACAGGAUG
...(((-.((((((((..(((((-------(((((.........))))))))))..(((((((.....(((((....)))))))))))))))))))))))........(....)...... ( -35.60)
>DroWil_CAF1 164290 105 - 1
AAAGUU--------UUGUUUCCC-------CUUUUUUACAGGUUUGGUUUCAGAAUCGUCGCACCAAAUGGCGCAAACGUCAUGCGGCCGAAAUGGCCACAGCGAAGCGGAAACAGGACG
...(((--------((((((((.-------((........(((((.......))))).((((.....((((((....))))))(.((((.....)))).).)))))).))))))))))). ( -36.30)
>DroAna_CAF1 22799 100 - 1
-------------UCCUUGUUGG-------UUUUUUUGCAGGUCUGGUUCCAGAACCGUCGCACCAAAUGGCGCAAACGGCAUGCGGCGGAAAUGGCCACGGCCAAGAGGAAACAGGACG
-------------.....(((.(-------(((((((...(((((((..(((...((((((((((....)).((.....)).))))))))...)))))).))))..))))))))..))). ( -36.30)
>DroPer_CAF1 28992 118 - 1
AAAGUUUUA--CUUACGUUUCGCUUACAUUUUCCGUUGCAGGUUUGGUUCCAGAAUCGUCGCACCAAAUGGCGCAAGCGGCAUGCGGCGGAAAUGGCCACGGCCAAGAGGAAACAGGACG
.........--.....(((((.(((....(((((((((((.(((((((....((....))..))))))).((....))....)))))))))))((((....)))).))))))))...... ( -40.60)
>consensus
AAAGUU_UA___UUACGUUUUGG_______UUUUGUUGCAGGUUUGGUUCCAGAAUCGUCGCACCAAAUGGCGCAAACGGCAUGCGGCGGAAAUGGCCACGGCCAAGAGGAAACAGGACG
.........................................((((..((((....((((((((.....((.((....)).))))))))))...((((....))))...))))...)))). (-26.88 = -26.35 +  -0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:00 2006