Locus 5105

Sequence ID 2R_DroMel_CAF1
Location 16,603,519 – 16,603,709
Length 190
Max. P 0.999974
window8161 window8162 window8163

overview

Window 1

Location 16,603,519 – 16,603,629
Length 110
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 95.35
Mean single sequence MFE -17.78
Consensus MFE -16.08
Energy contribution -16.08
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.90
SVM decision value 3.71
SVM RNA-class probability 0.999547
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16603519 110 - 20766785
CAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAAUCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUAAAUU-UCCUACAAAU-UUACAAACAUGAUAUAACUGAAAA
.........(((((((((((((((((((.(((....)))..))))))..))))).)))))))).......((((((-(.....))))-)))..................... ( -17.60)
>DroSec_CAF1 3511 108 - 1
CAAAACCUUAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUAAAUU-UCCUACAAAU-UUACA-UCAUG-UUUAACUGAAAA
..((((..((((((((((((((((((((.((......))..))))))..))))).)))))))))......((((((-(.....))))-)))..-....)-)))......... ( -18.50)
>DroSim_CAF1 3532 108 - 1
CAAAACCUUAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUAAAUU-UCCUACAAAU-UUACA-UCAUG-UUUAACUGAAAA
..((((..((((((((((((((((((((.((......))..))))))..))))).)))))))))......((((((-(.....))))-)))..-....)-)))......... ( -18.50)
>DroEre_CAF1 5256 108 - 1
CAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUAAAUU-UCCUAAAAAU-UUACA-UCAUG-UUUAACUGAAAA
..((((...(((((((((((((((((((.((......))..))))))..))))).)))))))).......((((((-(.....))))-)))..-....)-)))......... ( -17.60)
>DroYak_CAF1 3667 110 - 1
CAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCUUAAAUGAUACUAAAAUAAAUUUUCCUAAAAAUUUUACG-CCAUG-UUUAACUGAAAA
..((((...(((((((((((((((((((.((......))..))))))..))))).))))))))........(((((((....)))))))....-....)-)))......... ( -16.70)
>consensus
CAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUAAAUU_UCCUACAAAU_UUACA_UCAUG_UUUAACUGAAAA
.........(((((((((((((((((((.((......))..))))))..))))).))))))))................................................. (-16.08 = -16.08 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,603,557 – 16,603,669
Length 112
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 95.71
Mean single sequence MFE -23.64
Consensus MFE -23.08
Energy contribution -22.92
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.75
Structure conservation index 0.98
SVM decision value 5.11
SVM RNA-class probability 0.999974
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16603557 112 - 20766785
GUACAAUCCAAUUGUUGUACAUGUCCAAAUAGUUUCUAAGCAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAAUCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUA
(((((((......))))))).............................(((((((((((((((((((.(((....)))..))))))..))))).))))))))......... ( -23.20)
>DroSec_CAF1 3547 112 - 1
GUACAAUUCAAUUGUUGUACAUGUCCAAAUAGUUCUUAAGCAAAACCUUAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUA
(((((((......)))))))............................((((((((((((((((((((.((......))..))))))..))))).)))))))))........ ( -24.20)
>DroSim_CAF1 3568 112 - 1
GUACAAUUCAAUUAUUGUACAUGUCCAAAUAGUUUUUAAGCAAAACCUUAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUA
(((((((......)))))))...........(((((.....)))))..((((((((((((((((((((.((......))..))))))..))))).)))))))))........ ( -24.30)
>DroEre_CAF1 5292 112 - 1
GUACAAUGACAUUGUUGUACAUGUCCAAAUAGUUUUUAAGCAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUA
(((((((......)))))))...........(((((.....)))))...(((((((((((((((((((.((......))..))))))..))))).))))))))......... ( -23.50)
>DroYak_CAF1 3705 112 - 1
GUACAAUCAAAUAGUUGUACAUGUCCAAAUAGUUUUUAAGCAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCUUAAAUGAUACUAAAAUA
(((((((......)))))))...........(((((.....)))))...(((((((((((((((((((.((......))..))))))..))))).))))))))......... ( -23.00)
>consensus
GUACAAUCCAAUUGUUGUACAUGUCCAAAUAGUUUUUAAGCAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAACCAAUCGAAUAUUGUACCAUAAAUGAUACUAAAAUA
(((((((......))))))).............................(((((((((((((((((((.((......))..))))))..))))).))))))))......... (-23.08 = -22.92 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,603,589 – 16,603,709
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.82
Mean single sequence MFE -22.96
Consensus MFE -20.48
Energy contribution -20.76
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -1.75
Structure conservation index 0.89
SVM decision value 1.96
SVM RNA-class probability 0.983925
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16603589 120 - 20766785
GUUUUCAGUAUCAGAUCCUAAUCAAAACAUUUAAAGAAGUGUACAAUCCAAUUGUUGUACAUGUCCAAAUAGUUUCUAAGCAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAAUCAA
....(((((...(((..(((.((............)).(((((((((......))))))))).......)))..))).(((((.(((.((.....))))).))))).)))))........ ( -23.20)
>DroSec_CAF1 3579 120 - 1
GUUUUCAGUAUCAGAUCCUAAUCAAAACAUUUAAAGAAGUGUACAAUUCAAUUGUUGUACAUGUCCAAAUAGUUCUUAAGCAAAACCUUAUCAUUUGGGUAUUGUUCGCUGACCAACCAA
....(((((..........................((.(((((((((......))))))))).)).............(((((.((((........)))).))))).)))))........ ( -23.00)
>DroSim_CAF1 3600 120 - 1
GUUUUCUGUAUCAGAUCCUAAUCAAAACAUUUAAAGAAGUGUACAAUUCAAUUAUUGUACAUGUCCAAAUAGUUUUUAAGCAAAACCUUAUCAUUUGGGUAUUGUUCGCUGACCAACCAA
..........((((.........(((((((((...((.(((((((((......))))))))).)).)))).)))))..(((((.((((........)))).)))))..))))........ ( -22.70)
>DroEre_CAF1 5324 117 - 1
GUUUUCAGUAUCAGAUCCUUAUCAAAACAUUUAA---AGUGUACAAUGACAUUGUUGUACAUGUCCAAAUAGUUUUUAAGCAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAACCAA
....(((((..............(((((((((..---.(((((((((......)))))))))....)))).)))))..(((((.(((.((.....))))).))))).)))))........ ( -24.00)
>DroYak_CAF1 3737 117 - 1
GUUUUUAGUAUCAGAUCCUAAUCAAAACAUUUAA---AGUGUACAAUCAAAUAGUUGUACAUGUCCAAAUAGUUUUUAAGCAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAACCAA
..........((((.........(((((((((..---.(((((((((......)))))))))....)))).)))))..(((((.(((.((.....))))).)))))..))))........ ( -21.90)
>consensus
GUUUUCAGUAUCAGAUCCUAAUCAAAACAUUUAAAGAAGUGUACAAUCCAAUUGUUGUACAUGUCCAAAUAGUUUUUAAGCAAAACCUCAUCAUUUGGGUAUUGUUCGCUGACCAACCAA
....(((((..............(((((((((......(((((((((......)))))))))....)))).)))))..(((((.((((........)))).))))).)))))........ (-20.48 = -20.76 +   0.28)

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 11:36:40 2006