Locus 3875

Sequence ID 3L_DroMel_CAF1
Location 11,220,317 – 11,220,413
Length 96
Max. P 0.927636
window6029 window6030

overview

Window 9

Location 11,220,317 – 11,220,413
Length 96
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 78.76
Mean single sequence MFE -32.83
Consensus MFE -19.81
Energy contribution -20.93
Covariance contribution 1.13
Combinations/Pair 1.04
Mean z-score -2.16
Structure conservation index 0.60
SVM decision value 1.06
SVM RNA-class probability 0.909420
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11220317 96 + 23771897
AAAUGAAACGUUGCCGUUGAGCAACUUGAUUCCAAUGGACUUGGCUCACUCAGUGAGUGAAAAACGGCAACGGCGCACGAGAGC-----CGUGUGUGCAGG
........((((((((((............(((...))).((.((((((...)))))).)).))))))))))(((((((.....-----)))))))..... ( -34.60)
>DroVir_CAF1 31378 81 + 1
GAGCGCGACGUUGCCGUUGUACAACUCGUUUGCAGGCGGCUCAGCUCACAAUGUGAGUGAAAAACGGCAACAAGGC--------------------GCAGG
..((((...(((((((((.....((((..(((..(((......)))..)))...))))....)))))))))...))--------------------))... ( -32.70)
>DroSec_CAF1 29081 96 + 1
AAAUGAAACGUUGCCGUUGAGCAACUUGAUUCCAAUGGACUUGGCUCACUCAGUGAGUGAAAAACGGCAACGGCGCACAAGAGC-----CGUGUGUGCAGG
........((((((((((............(((...))).((.((((((...)))))).)).))))))))))(((((((.....-----..)))))))... ( -34.80)
>DroSim_CAF1 29302 96 + 1
AAAUGAAACGUUGCCGUUGAGCAACUUGAUUCCAAUGGACUUGGCUCACUCAGUGAGUGAAAAUCGGCAACGGCGCACAAGAGC-----CGUGUGUGCAGG
........(((((((((..(((...(((....)))..).))..))((((((...)))))).....)))))))(((((((.....-----..)))))))... ( -34.80)
>DroYak_CAF1 31277 96 + 1
AAAUGAAACGUUGCCGUUGAGCAACUUGAUUCCAAUGGACGCGGCUCACUCAGUGAGUGAAAAUUGGCAACGGCGCACAAGAGC-----CGUGUGUGCAGG
........(((((((((((..(...(((....)))..)...))))((((((...)))))).....)))))))(((((((.....-----..)))))))... ( -31.70)
>DroAna_CAF1 30482 99 + 1
-GAUGAAACGUUGCCGUUGAGCAACUGGCUUCCAGGCCGCUUUUCUCACUCAGUAACUGAAAAUCGGCAACGCUGCCCCU-AGCCCCAUCGUGUGUGCAGG
-((((....(((((((.((((....(((((....))))).....)))).((((...))))....)))))))((((....)-)))..))))........... ( -28.40)
>consensus
AAAUGAAACGUUGCCGUUGAGCAACUUGAUUCCAAUGGACUUGGCUCACUCAGUGAGUGAAAAACGGCAACGGCGCACAAGAGC_____CGUGUGUGCAGG
........((((((((((....)))..................((((((...)))))).......)))))))..(((((...((......)).)))))... (-19.81 = -20.93 +   1.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,220,317 – 11,220,413
Length 96
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 78.76
Mean single sequence MFE -30.73
Consensus MFE -19.14
Energy contribution -19.64
Covariance contribution 0.50
Combinations/Pair 1.10
Mean z-score -2.19
Structure conservation index 0.62
SVM decision value 1.18
SVM RNA-class probability 0.927636
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11220317 96 - 23771897
CCUGCACACACG-----GCUCUCGUGCGCCGUUGCCGUUUUUCACUCACUGAGUGAGCCAAGUCCAUUGGAAUCAAGUUGCUCAACGGCAACGUUUCAUUU
...((((.....-----......))))..((((((((((.(((((((...)))))))((((.....)))).............))))))))))........ ( -29.70)
>DroVir_CAF1 31378 81 - 1
CCUGC--------------------GCCUUGUUGCCGUUUUUCACUCACAUUGUGAGCUGAGCCGCCUGCAAACGAGUUGUACAACGGCAACGUCGCGCUC
...((--------------------((..((((((((((...(((((...((((..((......))..))))..))).))...))))))))))..)))).. ( -32.60)
>DroSec_CAF1 29081 96 - 1
CCUGCACACACG-----GCUCUUGUGCGCCGUUGCCGUUUUUCACUCACUGAGUGAGCCAAGUCCAUUGGAAUCAAGUUGCUCAACGGCAACGUUUCAUUU
...(((((....-----.....)))))..((((((((((.(((((((...)))))))((((.....)))).............))))))))))........ ( -30.70)
>DroSim_CAF1 29302 96 - 1
CCUGCACACACG-----GCUCUUGUGCGCCGUUGCCGAUUUUCACUCACUGAGUGAGCCAAGUCCAUUGGAAUCAAGUUGCUCAACGGCAACGUUUCAUUU
...(((((....-----.....)))))..((((((((((((((((((...)))))))((((.....))))))))..(((....))))))))))........ ( -29.70)
>DroYak_CAF1 31277 96 - 1
CCUGCACACACG-----GCUCUUGUGCGCCGUUGCCAAUUUUCACUCACUGAGUGAGCCGCGUCCAUUGGAAUCAAGUUGCUCAACGGCAACGUUUCAUUU
...(((((....-----.....)))))..(((((((.......((((...))))((((.((.(((...))).....)).))))...)))))))........ ( -27.90)
>DroAna_CAF1 30482 99 - 1
CCUGCACACACGAUGGGGCU-AGGGGCAGCGUUGCCGAUUUUCAGUUACUGAGUGAGAAAAGCGGCCUGGAAGCCAGUUGCUCAACGGCAACGUUUCAUC-
(((((.((.....))..)).-)))((.((((((((((...(((((...)))))((((...((((((......))).))).)))).))))))))))))...- ( -33.80)
>consensus
CCUGCACACACG_____GCUCUUGUGCGCCGUUGCCGAUUUUCACUCACUGAGUGAGCCAAGUCCAUUGGAAUCAAGUUGCUCAACGGCAACGUUUCAUUU
...((((................))))..(((((((....(((((((...)))))))...................(((....))))))))))........ (-19.14 = -19.64 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:52 2006