Locus 4271

Sequence ID X_DroMel_CAF1
Location 11,234,056 – 11,234,198
Length 142
Max. P 0.999937
window7020 window7021 window7022

overview

Window 0

Location 11,234,056 – 11,234,163
Length 107
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 93.62
Mean single sequence MFE -26.52
Consensus MFE -23.90
Energy contribution -24.10
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.15
Structure conservation index 0.90
SVM decision value 0.11
SVM RNA-class probability 0.590552
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11234056 107 + 22224390
------UUGCCCAUUUUCCUGGCUUUUUAACGAAUCGUUACUUACUUAAGACGCUUAAGGCGCUCGGCCUUCUCGCUUUUGUGGGCCAAGCGUCGCCCAUUUCCGUUUCCGGU
------..............(((....(((((...))))).........((((((((((((.....)))))(((((....)))))..)))))))))).....(((....))). ( -28.60)
>DroSec_CAF1 20988 107 + 1
------UUGCCCAUUUUCCUGCCUUUAUAACGAAUCGUUUCUUACUUAAGACGCUUAAGGCGCUCGGCCUUCUCGCUUUUGUGGGCCAAGCGUCGCCCAUUUCCGUUUCCGGU
------..............(((.....((((....((.((((....)))).))....((((((.(((((.(........).))))).)))))).........))))...))) ( -27.20)
>DroSim_CAF1 12803 107 + 1
------CUGCCCAUUUUCCUGCCUUUAUAACGAAUCGUUACUUACUUAAGACGCUUAAGGCGCUCGGCCUUCUCGCUUUUGUGGGCCAAGCGUCGCCCAUUUCCGUUUCCGGU
------..............((.....(((((...))))).........((((((((((((.....)))))(((((....)))))..)))))))))......(((....))). ( -25.00)
>DroEre_CAF1 20836 113 + 1
ACCAUUUUGCCCAUUUUCCUGCCUUUUUAACGAAUCGUUACUUACUUAAGACGCUUAAGGCGCUCGGCCUCCUCGCUUUUGUGGGCCAAGCGUCGCCCAUUUCCGUUUCCGGU
....................(((.....((((...((((..........)))).....((((((.((((..(........)..)))).)))))).........))))...))) ( -25.60)
>DroYak_CAF1 12858 112 + 1
GCAUUUUUACCCAUUUUCCUGCCUU-UUAACGAAUCGUUACUUACUUAAGACGCUUAAGGCGCUCGGCCUCCUCGCUUUUGUGGGCCAAGCGUCGCCCAUUUCCGUUUCCGGU
....................(((..-..((((...((((..........)))).....((((((.((((..(........)..)))).)))))).........))))...))) ( -26.20)
>consensus
______UUGCCCAUUUUCCUGCCUUUUUAACGAAUCGUUACUUACUUAAGACGCUUAAGGCGCUCGGCCUUCUCGCUUUUGUGGGCCAAGCGUCGCCCAUUUCCGUUUCCGGU
....................(((.....((((...((((..........)))).....((((((.((((..(........)..)))).)))))).........))))...))) (-23.90 = -24.10 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,234,056 – 11,234,163
Length 107
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 93.62
Mean single sequence MFE -33.71
Consensus MFE -32.18
Energy contribution -32.22
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.49
Structure conservation index 0.95
SVM decision value 4.67
SVM RNA-class probability 0.999937
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11234056 107 - 22224390
ACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGAAGGCCGAGCGCCUUAAGCGUCUUAAGUAAGUAACGAUUCGUUAAAAAGCCAGGAAAAUGGGCAA------
.(((....))).((((((((.(((((((((..(........)..))))))))).((((((...)))))).......)).)))))).....(((.........)))..------ ( -33.60)
>DroSec_CAF1 20988 107 - 1
ACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGAAGGCCGAGCGCCUUAAGCGUCUUAAGUAAGAAACGAUUCGUUAUAAAGGCAGGAAAAUGGGCAA------
.(((....)))......((...((((((((..(........)..))))))))(((((.....((((....))))((((...))))...)))))..........))..------ ( -32.80)
>DroSim_CAF1 12803 107 - 1
ACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGAAGGCCGAGCGCCUUAAGCGUCUUAAGUAAGUAACGAUUCGUUAUAAAGGCAGGAAAAUGGGCAG------
.(((....)))......((...((((((((..(........)..))))))))(((((..((.......))..((((((...)))))).)))))..........))..------ ( -34.00)
>DroEre_CAF1 20836 113 - 1
ACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGGAGGCCGAGCGCCUUAAGCGUCUUAAGUAAGUAACGAUUCGUUAAAAAGGCAGGAAAAUGGGCAAAAUGGU
.(((....)))...........((((((((..(........)..))))))))((((......((((.......(((((...))))).......))))....))))........ ( -34.64)
>DroYak_CAF1 12858 112 - 1
ACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGGAGGCCGAGCGCCUUAAGCGUCUUAAGUAAGUAACGAUUCGUUAA-AAGGCAGGAAAAUGGGUAAAAAUGC
.(((....)))......(((..((((((((..(........)..))))))))((((......((((..((...(((((...))))).-...))))))....)))).....))) ( -33.50)
>consensus
ACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGAAGGCCGAGCGCCUUAAGCGUCUUAAGUAAGUAACGAUUCGUUAAAAAGGCAGGAAAAUGGGCAA______
.(((....)))...........((((((((..(........)..))))))))((((......((((.......(((((...))))).......))))....))))........ (-32.18 = -32.22 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,234,090 – 11,234,198
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 96.84
Mean single sequence MFE -36.18
Consensus MFE -35.26
Energy contribution -35.10
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.51
Structure conservation index 0.97
SVM decision value 4.41
SVM RNA-class probability 0.999891
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11234090 108 - 22224390
GCCAGUUUAGCUACAACGAGCAACAACAACAGCGCACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGAAGGCCGAGCGCCUUAAGCGUCUUAAGUAAG
(((.((((.(((......)))...............(((....))))))).)))(((((((((((..(........)..))))))))((.....)))))......... ( -35.30)
>DroSec_CAF1 21022 108 - 1
GCCAGUUUAGCUACAACGAGCAACAACAACAGCGCACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGAAGGCCGAGCGCCUUAAGCGUCUUAAGUAAG
(((.((((.(((......)))...............(((....))))))).)))(((((((((((..(........)..))))))))((.....)))))......... ( -35.30)
>DroSim_CAF1 12837 108 - 1
GCCAGUUUAGCUACAACGAGCAACAACAACAGCGCACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGAAGGCCGAGCGCCUUAAGCGUCUUAAGUAAG
(((.((((.(((......)))...............(((....))))))).)))(((((((((((..(........)..))))))))((.....)))))......... ( -35.30)
>DroEre_CAF1 20876 105 - 1
GCCAGGUUAGCUACAACGGGCAACAACAACA---CACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGGAGGCCGAGCGCCUUAAGCGUCUUAAGUAAG
(((..(((.(((......)))))).......---..(((....))).....)))(((((((((((..(........)..))))))))((.....)))))......... ( -37.50)
>DroYak_CAF1 12897 105 - 1
GCCAGGUUAGCUACAACGAGCAACAACAACA---CACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGGAGGCCGAGCGCCUUAAGCGUCUUAAGUAAG
(((..(((.(((......)))))).......---..(((....))).....)))(((((((((((..(........)..))))))))((.....)))))......... ( -37.50)
>consensus
GCCAGUUUAGCUACAACGAGCAACAACAACAGCGCACCGGAAACGGAAAUGGGCGACGCUUGGCCCACAAAAGCGAGAAGGCCGAGCGCCUUAAGCGUCUUAAGUAAG
(((......(((......)))...............(((....))).....)))(((((((((((..(........)..))))))))((.....)))))......... (-35.26 = -35.10 +  -0.16)

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 11:20:52 2006