Locus 4606

Sequence ID 3R_DroMel_CAF1
Location 12,109,515 – 12,109,676
Length 161
Max. P 0.999889
window7569 window7570 window7571

overview

Window 9

Location 12,109,515 – 12,109,623
Length 108
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 72.73
Mean single sequence MFE -22.18
Consensus MFE -15.66
Energy contribution -16.11
Covariance contribution 0.45
Combinations/Pair 1.25
Mean z-score -1.63
Structure conservation index 0.71
SVM decision value 1.78
SVM RNA-class probability 0.976804
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12109515 108 + 27905053
AAAAUCAUAUGCGUUGCGUAUAUCG---GAAAGAGGAUCGCUUUAAGCCUUAAGCGAAA-UAAUUGGGGAACGCCAGUUUUUUAAGCCAGUUCAAUUGGGCGAUUAAUUUGA
..(((((((((((...))))))).(---(........((((((........))))))..-...(((((((((....))))))))).)).((((....))))))))....... ( -22.10)
>DroSec_CAF1 15592 95 + 1
AAAAGCAAAUGUAUUGCGUAUAUUG---GAAAGAGGAUCGCCUUAAGCCUUUGGCGAAAUUAAUUGGGGAA-------------AGCCAAUUCAUUGGGGCGAUUAAA-AAA
....((((.....))))........---.......((((((((((((((...)))......((((((....-------------..))))))..)))))))))))...-... ( -25.00)
>DroSim_CAF1 15535 94 + 1
AAAAGCAUAUACGC----AAUACAGGAAGAAAGAGAAUUGCCUUAAACCUUUGGCGAAAUUAAUUGGGGAA-------------AGCCAGUUCAUUGGGGCGAUUAAA-AAA
....((......))----.................(((((((((((....(((((................-------------.)))))....)))))))))))...-... ( -19.43)
>consensus
AAAAGCAUAUGCGUUGCGUAUAUAG___GAAAGAGGAUCGCCUUAAGCCUUUGGCGAAAUUAAUUGGGGAA_____________AGCCAGUUCAUUGGGGCGAUUAAA_AAA
...................................(((((((((((....(((((..............................)))))....)))))))))))....... (-15.66 = -16.11 +   0.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,109,545 – 12,109,652
Length 107
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 75.37
Mean single sequence MFE -26.89
Consensus MFE -18.89
Energy contribution -19.24
Covariance contribution 0.35
Combinations/Pair 1.24
Mean z-score -2.90
Structure conservation index 0.70
SVM decision value 4.40
SVM RNA-class probability 0.999889
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12109545 107 + 27905053
AGGAUCGCUUUAAGCCUUAAGCGAAA-UAAUUGGGGAACGCCAGUUUUUUAAGCCAGUUCAAUUGGGCGAUUAAUUUGAAUUUGUACAAAAAGCGGG---------GUGUAAAUUAA
....((((((........))))))..-..........(((((.(((((((..((.(((((((((((....)))).))))))).))..)))))))..)---------))))....... ( -25.10)
>DroSec_CAF1 15622 103 + 1
AGGAUCGCCUUAAGCCUUUGGCGAAAUUAAUUGGGGAA-------------AGCCAAUUCAUUGGGGCGAUUAAA-AAAAUUUGUACGAAAAGCGGGAAUAAAUGCGUACAAAUAAA
..((((((((((((((...)))......((((((....-------------..))))))..)))))))))))...-...(((((((((.................)))))))))... ( -29.83)
>DroSim_CAF1 15564 103 + 1
AGAAUUGCCUUAAACCUUUGGCGAAAUUAAUUGGGGAA-------------AGCCAGUUCAUUGGGGCGAUUAAA-AAAAUUUGUACGAAAAGUGGGAACAAAUGCGUGUAAAUAAA
..(((((((((((....(((((................-------------.)))))....)))))))))))...-...(((((((((.....((....))....)))))))))... ( -25.73)
>consensus
AGGAUCGCCUUAAGCCUUUGGCGAAAUUAAUUGGGGAA_____________AGCCAGUUCAUUGGGGCGAUUAAA_AAAAUUUGUACGAAAAGCGGGAA_AAAUGCGUGUAAAUAAA
..(((((((((((....(((((..............................)))))....))))))))))).......(((((((((.................)))))))))... (-18.89 = -19.24 +   0.35)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,109,583 – 12,109,676
Length 93
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 75.09
Mean single sequence MFE -18.88
Consensus MFE -12.32
Energy contribution -12.33
Covariance contribution 0.01
Combinations/Pair 1.15
Mean z-score -2.00
Structure conservation index 0.65
SVM decision value 1.88
SVM RNA-class probability 0.981119
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12109583 93 + 27905053
GCCAGUUUUUUAAGCCAGUUCAAUUGGGCGAUUAAUUUGAAUUUGUACAAAAAGCGGG---------GUGUAAAUUAAUCUCACAAGAGAUCAAUCGCAUAU
.((.(((((((..((.(((((((((((....)))).))))))).))..))))))).))---------((((..(((.(((((....))))).))).)))).. ( -20.00)
>DroSec_CAF1 15660 89 + 1
------------AGCCAAUUCAUUGGGGCGAUUAAA-AAAAUUUGUACGAAAAGCGGGAAUAAAUGCGUACAAAUAAAUUUCACAAGAAAUCAAUCGCAUAU
------------..((((....)))).((((((...-...(((((((((.................)))))))))..(((((....))))).)))))).... ( -19.23)
>DroSim_CAF1 15602 89 + 1
------------AGCCAGUUCAUUGGGGCGAUUAAA-AAAAUUUGUACGAAAAGUGGGAACAAAUGCGUGUAAAUAAAUCUCAGAAGAAAUCAAUCGCAUAU
------------..((((....)))).((((((...-...(((((((((.....((....))....)))))))))...(((....)))....)))))).... ( -17.40)
>consensus
____________AGCCAGUUCAUUGGGGCGAUUAAA_AAAAUUUGUACGAAAAGCGGGAA_AAAUGCGUGUAAAUAAAUCUCACAAGAAAUCAAUCGCAUAU
...........................((((((.......(((((((((.................)))))))))..(((((....))))).)))))).... (-12.32 = -12.33 +   0.01)

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 11:34:27 2006