Locus 2100

Sequence ID 3L_DroMel_CAF1
Location 5,762,166 – 5,762,333
Length 167
Max. P 0.880091
window3267 window3268 window3269

overview

Window 7

Location 5,762,166 – 5,762,264
Length 98
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 79.56
Mean single sequence MFE -30.15
Consensus MFE -17.74
Energy contribution -17.68
Covariance contribution -0.06
Combinations/Pair 1.24
Mean z-score -2.20
Structure conservation index 0.59
SVM decision value 0.81
SVM RNA-class probability 0.855758
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5762166 98 - 23771897
UAUCACUGGAAGCGGGGAAUAACCGAGUCGCAAGACUACAGGAGAUUAGCACACGGAAGUAUAC-CAAAGAAUGUAACCACUUUGGGUUACUACAAUUG-------
..((..(((..((....(((..((.((((....))))...))..))).))..((....))...)-))..))..((((((......))))))........------- ( -25.70)
>DroSec_CAF1 4768 106 - 1
UAUCGCUGCAAUCGGGGAAUAACCGAGUCGCAAGACUACAGGAGAUACCAACACGGAAGUCUCCAUAAAGGAUGUAACCACUUUGGGUUAUACUGAUUGAUUUAAA
........(((((((.......((.((((....))))...((((((.((.....))..)))))).....)).(((((((......))))))))))))))....... ( -33.50)
>DroSim_CAF1 4549 106 - 1
UAUCGCUGCAAUCGGGGAAUAACCGGGUCGUAAGACUACAGGAGAUACCAACACGGAAGUUUACAUAAAGGAUGUAACCACUUUGGGUUAAACUGAUUGAUUUAAG
........(((((((((.((..((.((((....))))...))..)).))(((.(.(((((((((((.....))))))..))))).))))...)))))))....... ( -29.20)
>DroEre_CAF1 4718 105 - 1
UACCGCUGCAAGCGGGG-AUAGCCGGGUCGUAAGACUCCAGGAGACCCCAACACGGAAGUCUCCGUAAGGGAUGAAACCACUUUCAGUUUAAAUUAUGGAUUUAGG
..((((((.(((.((..-....(((((((....))).)).((((((.((.....))..)))))).....))......)).))).)))).((((((...)))))))) ( -32.20)
>consensus
UAUCGCUGCAAGCGGGGAAUAACCGAGUCGCAAGACUACAGGAGAUACCAACACGGAAGUCUACAUAAAGGAUGUAACCACUUUGGGUUAAAAUGAUUGAUUUAAG
..((.(((....(((.......)))((((....)))).)))...........((....)).........)).(((((((......))))))).............. (-17.74 = -17.68 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,762,199 – 5,762,300
Length 101
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 86.44
Mean single sequence MFE -37.12
Consensus MFE -27.25
Energy contribution -27.12
Covariance contribution -0.12
Combinations/Pair 1.23
Mean z-score -2.15
Structure conservation index 0.73
SVM decision value 0.91
SVM RNA-class probability 0.880091
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5762199 101 - 23771897
GGUCAAUCCGUGCUGGUCAGGGACAAUGGCGAAGGUUAUCACUGGAAGCGGGGAAUAACCGAGUCGCAAGACUACAGGAGAUUAGCACACGGAAGUAUAC-C
((.....))(((((((((........((((....))))((.(((....(((.......)))((((....)))).))))))))))))))((....))....-. ( -34.80)
>DroSec_CAF1 4808 102 - 1
GGUCAAUCCGUGCUGGUCAGGGGCACCAGCGAAGGUUAUCGCUGCAAUCGGGGAAUAACCGAGUCGCAAGACUACAGGAGAUACCAACACGGAAGUCUCCAU
((....((((((((((((....).))))))...(((.(((.(((...((((.......))))(((....)))..)))..))))))...))))).....)).. ( -36.40)
>DroSim_CAF1 4589 102 - 1
GGUCAAUCCGUGCUGGUCAGGGGCACCAGCGAAGGUUAUCGCUGCAAUCGGGGAAUAACCGGGUCGUAAGACUACAGGAGAUACCAACACGGAAGUUUACAU
(((...(((.((((((((....).)))))))..(((((((.(((....))).).)))))).((((....))))...)))...)))...((....))...... ( -33.90)
>DroEre_CAF1 4758 101 - 1
GGUCAAUCCGCGCUGGUCAGGGACAAUGGCGAAGGUUACCGCUGCAAGCGGGG-AUAGCCGGGUCGUAAGACUCCAGGAGACCCCAACACGGAAGUCUCCGU
(((..((((.((((.(.(((((....((((....)))))).)))).)))).))-)).)))(((((....))).)).((((((.((.....))..)))))).. ( -43.40)
>consensus
GGUCAAUCCGUGCUGGUCAGGGACAACAGCGAAGGUUAUCGCUGCAAGCGGGGAAUAACCGAGUCGCAAGACUACAGGAGAUACCAACACGGAAGUCUACAU
((((..(((.(((((((.......)))))))..(((((((.(((....))).).)))))).((((....))))...))))))).....((....))...... (-27.25 = -27.12 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,762,229 – 5,762,333
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.54
Mean single sequence MFE -40.60
Consensus MFE -23.96
Energy contribution -24.48
Covariance contribution 0.52
Combinations/Pair 1.21
Mean z-score -1.71
Structure conservation index 0.59
SVM decision value 0.16
SVM RNA-class probability 0.611224
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5762229 104 - 23771897
AAGAUCGGCCUGUGCCGGUG-------GAGCGCUGGAGUAGGUCAAUCCGU----GCUGGUCAGGGACAAUGGCGAAGGUUAUCACUGGAAGCGGGGAAUAACCGAGUCGCAAGA-----
......((((((..((((((-------...))))))..))))))..(((.(----(.....)).))).....((((.(((((((.(((....))).).))))))...))))....----- ( -37.80)
>DroSec_CAF1 4839 104 - 1
AAGAUCUGCCUGCGCCGGCG-------GAGCGCUGGAGUAGGUCAAUCCGU----GCUGGUCAGGGGCACCAGCGAAGGUUAUCGCUGCAAUCGGGGAAUAACCGAGUCGCAAGA-----
..(((..((((((.((((((-------...)))))).))))))..))).((----(((.......)))))..((((.(((((((.(((....))).).))))))...))))....----- ( -42.60)
>DroSim_CAF1 4620 104 - 1
AAGAUCUGCCUGCGCCGGCG-------GAGCGCUGGAGUAGGUCAAUCCGU----GCUGGUCAGGGGCACCAGCGAAGGUUAUCGCUGCAAUCGGGGAAUAACCGGGUCGUAAGA-----
..(((((((((((.((((((-------...)))))).)))))).......(----(((((((....).)))))))..(((((((.(((....))).).)))))))))))......----- ( -41.80)
>DroEre_CAF1 4789 95 - 1
AAAAUGUGCCUGCUCCGGU---------------GGAGUAGGUCAAUCCGC----GCUGGUCAGGGACAAUGGCGAAGGUUACCGCUGCAAGCGGGG-AUAGCCGGGUCGUAAGA-----
....((.(((((((((...---------------)))))))))))(((((.----((((..(........((((....))))((((.....))))).-.))))))))).......----- ( -35.40)
>DroAna_CAF1 5460 120 - 1
AAAAUGUGGCUCCACCGGCCCGGCCCGGCCAGCUGGAGUAGGUCAGUCCAUUGUCUCUGGUCAGGGACAAUGGCGAAGGUUAGCAGUGCAAUCGGGGAAUAACCGGGUCACCAAAAAUUA
.....(((....))).((((((((((((((.((....)).)))).(.(((((((((((....))))))))))))...((((.((...)))))).))).....)))))))........... ( -45.40)
>consensus
AAGAUCUGCCUGCGCCGGCG_______GAGCGCUGGAGUAGGUCAAUCCGU____GCUGGUCAGGGACAAUGGCGAAGGUUAUCGCUGCAAUCGGGGAAUAACCGGGUCGCAAGA_____
.........((((.(((((............))))).))))(((...(((.......))).....)))....((((.(((((((.(((....))).).))))))...))))......... (-23.96 = -24.48 +   0.52)

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 10:24:22 2006