Locus 3661

Sequence ID X_DroMel_CAF1
Location 9,796,841 – 9,797,083
Length 242
Max. P 0.933928
window6000 window6001 window6002

overview

Window 0

Location 9,796,841 – 9,796,952
Length 111
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 90.27
Mean single sequence MFE -25.01
Consensus MFE -22.11
Energy contribution -21.67
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -1.78
Structure conservation index 0.88
SVM decision value 0.24
SVM RNA-class probability 0.646980
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9796841 111 + 22224390
ACACACUCACACACACACCACCC---CCCCUAUUUGACUCUACGCCCCUGUACUUUGGGGCCACCCUCUUUUAGCUGCCGUUUCAAUUUGGCCUUCUCAGAGGAACUGAGGUUG
.....((((..............---.................(((((........)))))...(((((.......((((........))))......)))))...)))).... ( -25.62)
>DroSec_CAF1 11542 104 + 1
ACAC----------ACACCACCCCCCCCCCUAUUUGACUCUACGCCCCUGUACUUUGGGGCCACCCUCUUUUAGCUGCCGUUUCAAUUUGGCCUUCUCAAGGGAACUGAGGUUG
....----------.......................(((...(((((........)))))..((((.....((..((((........)))))).....))))....))).... ( -23.70)
>DroSim_CAF1 12679 101 + 1
ACAC----------ACACCACCC---CUCCUAUUUGACUCUACGCCCCUGUACUUUGGGGCCACCCUCUUUUAGCUGCCGUUUCAAUUUGGCCUUCUCAAGGGAACUGAGGUUG
....----------........(---(((..............(((((........)))))..((((.....((..((((........)))))).....))))....))))... ( -25.70)
>consensus
ACAC__________ACACCACCC___CCCCUAUUUGACUCUACGCCCCUGUACUUUGGGGCCACCCUCUUUUAGCUGCCGUUUCAAUUUGGCCUUCUCAAGGGAACUGAGGUUG
.....................................(((...(((((........))))).....((((((((..((((........))))...)).))))))...))).... (-22.11 = -21.67 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,796,878 – 9,796,973
Length 95
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 70.23
Mean single sequence MFE -31.52
Consensus MFE -17.45
Energy contribution -17.32
Covariance contribution -0.13
Combinations/Pair 1.37
Mean z-score -1.69
Structure conservation index 0.55
SVM decision value 0.59
SVM RNA-class probability 0.792066
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9796878 95 - 22224390
AUGCUAAACAGCAAUGC--------C---AGC--------------CAACCUCAGUUCCUCUGAGAAGGCCAAAUUGAAACGGCAGCUAAAAGAGGGUGGCCCCAAAGUACAGGGGCGUA
.((((....))))....--------(---(.(--------------(...(((((.....)))))...(((..........)))..........)).))(((((........)))))... ( -28.50)
>DroPse_CAF1 22217 120 - 1
AUGCUAAACAGAGGAGGAGCUGGAGCUGGAGCUCUAGCUGGAGCAGGAGCAGGAGCACCCUCGAGCAGGCCAAAUUGAAACAGCAGCGUGGAGGGGGUGGUUGGGUGCUGGGUGGAGCCC
..(((..((........(((((((((....)))))))))....(((..((..((.(((((((.......(((..(((......)))..))).))))))).))..)).))).))..))).. ( -42.80)
>DroSec_CAF1 11572 95 - 1
AUGCUAAACAGCAAUGC--------C---AGC--------------CAACCUCAGUUCCCUUGAGAAGGCCAAAUUGAAACGGCAGCUAAAAGAGGGUGGCCCCAAAGUACAGGGGCGUA
.((((....))))((((--------(---.((--------------((.((((..(((......))).(((..........)))........)))).)))).((........))))))). ( -27.40)
>DroSim_CAF1 12706 95 - 1
AUGCUAAACAGCAAUGC--------C---AGC--------------CAACCUCAGUUCCCUUGAGAAGGCCAAAUUGAAACGGCAGCUAAAAGAGGGUGGCCCCAAAGUACAGGGGCGUA
.((((....))))((((--------(---.((--------------((.((((..(((......))).(((..........)))........)))).)))).((........))))))). ( -27.40)
>consensus
AUGCUAAACAGCAAUGC________C___AGC______________CAACCUCAGUUCCCUUGAGAAGGCCAAAUUGAAACGGCAGCUAAAAGAGGGUGGCCCCAAAGUACAGGGGCGUA
.((((....))))............................................(((((.((...(((..........)))..))....)))))..(((((........)))))... (-17.45 = -17.32 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,796,973 – 9,797,083
Length 110
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 86.97
Mean single sequence MFE -32.80
Consensus MFE -23.84
Energy contribution -24.40
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -3.39
Structure conservation index 0.73
SVM decision value 1.23
SVM RNA-class probability 0.933928
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9796973 110 - 22224390
CGGAAAGGGGGGCUGGAAUAGC---CCCGGAAGAGGGGUGGUCCCAAAAAAAAAAAAAAAAACGAGGG-GACCAAAACAGUUUUGAAAACUGUAAUUAUUUUAAGGGAUUCUUU
........(((((((...))))---))).((((((...(((((((.....................))-)))))..((((((.....))))))...............)))))) ( -31.00)
>DroSec_CAF1 11667 103 - 1
CGGAAAAGG-GGCCGGAAUAGCCGCCCCGAAAGAGGGGUGGUGCCAAAA----------AAUCGAGGGGGGCCAAAACAGUUUUGAAAACUGUAAUUAUUUUAAGGGAUUCUUU
.((((....-((((((....((((((((......)))))))).))....----------..((....))))))...((((((.....))))))...............)))).. ( -32.80)
>DroSim_CAF1 12801 102 - 1
CGGAAAGGG-GGCCGGAAUAGCCGCCCCGGAAGAGGGGUGGUGCCAAAA----------AACCGAGGG-GGCCAAAACAGUUUUGAAAACUGUAAUUAUUUUAAGGGAUUCUUU
...((((((-((((((....((((((((......)))))))).))....----------..((...))-))))...((((((.....))))))...............)))))) ( -34.60)
>consensus
CGGAAAGGG_GGCCGGAAUAGCCGCCCCGGAAGAGGGGUGGUGCCAAAA__________AAACGAGGG_GGCCAAAACAGUUUUGAAAACUGUAAUUAUUUUAAGGGAUUCUUU
....(((((...((((....((((((((......)))))))).))....................((....))...((((((.....))))))............))..))))) (-23.84 = -24.40 +   0.56)

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 11:05:05 2006