Locus 3281

Sequence ID 3L_DroMel_CAF1
Location 9,624,130 – 9,624,224
Length 94
Max. P 0.844337
window5101 window5102

overview

Window 1

Location 9,624,130 – 9,624,224
Length 94
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 82.87
Mean single sequence MFE -26.57
Consensus MFE -20.61
Energy contribution -20.61
Covariance contribution 0.00
Combinations/Pair 1.28
Mean z-score -2.28
Structure conservation index 0.78
SVM decision value 0.76
SVM RNA-class probability 0.844337
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9624130 94 + 23771897
AAGGUCAAAUUACGUACCCGUGGCGUAUACU----CGAUUUAGUGUACGGUUUGCGUAUACGCCACGUUGGCCCAGCCACAAAAACCAAUCGAAUUGC
..(((.............((((((((((((.----(((....(....)...))).)))))))))))).((((...)))).....)))........... ( -28.20)
>DroSec_CAF1 19811 94 + 1
AAGGUCAAAUUACGUACCCGUGGCGUAUACU----CGAUUUAGUGUACGGUUUGCGUAUACGCCACGUUGGCUAAGCCACAAAAACCAAUCAAAUUGC
..(((.............((((((((((((.----(((....(....)...))).)))))))))))).((((...)))).....)))........... ( -28.20)
>DroSim_CAF1 22259 94 + 1
AAGGUCAAAUUACGUUCCCGUGGCGUAUACU----CGAUUUAGUGUACGAGUUGCGUAUACGCCACGUUGGCUAAGCCACAAAAACCAAUCGAAUUGC
..(((.............((((((((((((.----((((((.......)))))).)))))))))))).((((...)))).....)))........... ( -31.20)
>DroEre_CAF1 19242 94 + 1
AAGGCCAAAUUACGUACUCGUGGCGUAUACU----CAAUUUAGUGUACGGCUUGCGUAUACGCCACGUUGGCCCAGCCACAAAAACCAAUCGAAUUGC
..((((((..........((((((((((((.----(((....(....)...))).))))))))))))))))))......................... ( -29.50)
>DroYak_CAF1 20000 94 + 1
AAGGCCAAACUACGUACUCGUGGCGUAUACU----CAAUUUAGUGUACGGUUUGCGUAUACGCCACGUUGGCCCAGCCACAAAAACCAAUCGAAUUGC
..((((((..........((((((((((((.----(((....(....)...))).))))))))))))))))))......................... ( -30.20)
>DroAna_CAF1 32575 88 + 1
CAAACUAGAUUACGUAUACGCCGUGUAUGCAAGCACCAUCUGAU----AAAUUACGUAUACGCCACGUUCGCC-----GC-AAAACCAAUCGAAUUUC
.......((((..(((((((..((((......))))(....)..----......)))))))((..(....)..-----))-......))))....... ( -12.10)
>consensus
AAGGCCAAAUUACGUACCCGUGGCGUAUACU____CGAUUUAGUGUACGGUUUGCGUAUACGCCACGUUGGCCCAGCCACAAAAACCAAUCGAAUUGC
..((((((..........((((((((((((.........................))))))))))))))))))......................... (-20.61 = -20.61 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,624,130 – 9,624,224
Length 94
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 82.87
Mean single sequence MFE -27.89
Consensus MFE -20.80
Energy contribution -21.16
Covariance contribution 0.36
Combinations/Pair 1.25
Mean z-score -1.59
Structure conservation index 0.75
SVM decision value 0.14
SVM RNA-class probability 0.602652
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9624130 94 - 23771897
GCAAUUCGAUUGGUUUUUGUGGCUGGGCCAACGUGGCGUAUACGCAAACCGUACACUAAAUCG----AGUAUACGCCACGGGUACGUAAUUUGACCUU
.........(((((((........)))))))((((((((((((....................----.))))))))))))(((.((.....))))).. ( -28.10)
>DroSec_CAF1 19811 94 - 1
GCAAUUUGAUUGGUUUUUGUGGCUUAGCCAACGUGGCGUAUACGCAAACCGUACACUAAAUCG----AGUAUACGCCACGGGUACGUAAUUUGACCUU
...........((((....((((...)))).((((((((((((....................----.))))))))))))............)))).. ( -27.40)
>DroSim_CAF1 22259 94 - 1
GCAAUUCGAUUGGUUUUUGUGGCUUAGCCAACGUGGCGUAUACGCAACUCGUACACUAAAUCG----AGUAUACGCCACGGGAACGUAAUUUGACCUU
...........((((....((((...)))).((((((((((.....(((((..........))----)))))))))))))............)))).. ( -28.10)
>DroEre_CAF1 19242 94 - 1
GCAAUUCGAUUGGUUUUUGUGGCUGGGCCAACGUGGCGUAUACGCAAGCCGUACACUAAAUUG----AGUAUACGCCACGAGUACGUAAUUUGGCCUU
((....(((.......)))..)).(((((((((((((((((((.(((.............)))----.))))))))))))..........))))))). ( -32.12)
>DroYak_CAF1 20000 94 - 1
GCAAUUCGAUUGGUUUUUGUGGCUGGGCCAACGUGGCGUAUACGCAAACCGUACACUAAAUUG----AGUAUACGCCACGAGUACGUAGUUUGGCCUU
((....(((.......)))..)).(((((((((((((((((((.(((.............)))----.))))))))))))..........))))))). ( -31.32)
>DroAna_CAF1 32575 88 - 1
GAAAUUCGAUUGGUUUU-GC-----GGCGAACGUGGCGUAUACGUAAUUU----AUCAGAUGGUGCUUGCAUACACGGCGUAUACGUAAUCUAGUUUG
.(((((.(((((.....-((-----.((....)).))((((((((....(----(((((.......))).)))....)))))))).))))).))))). ( -20.30)
>consensus
GCAAUUCGAUUGGUUUUUGUGGCUGGGCCAACGUGGCGUAUACGCAAACCGUACACUAAAUCG____AGUAUACGCCACGGGUACGUAAUUUGACCUU
...........((((....((((...)))).((((((((((((.........................))))))))))))............)))).. (-20.80 = -21.16 +   0.36)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:47 2006