Locus 2978

Sequence ID 3L_DroMel_CAF1
Location 8,545,747 – 8,545,863
Length 116
Max. P 0.991299
window4654 window4655 window4656

overview

Window 4

Location 8,545,747 – 8,545,851
Length 104
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.58
Mean single sequence MFE -34.10
Consensus MFE -34.10
Energy contribution -33.35
Covariance contribution -0.75
Combinations/Pair 1.20
Mean z-score -5.47
Structure conservation index 1.00
SVM decision value 2.26
SVM RNA-class probability 0.991299
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8545747 104 + 23771897
AAC---------------U-AAUUGAUGGUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUUCAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGACCCUCGCCAAUCU
...---------------.-....((.(((..((((((((((((((((((..((((((.((...(........)..)).)))))))))))))))))).))))))..))).))........ ( -34.10)
>DroVir_CAF1 825 115 + 1
AACUACC----CCCCA-CUCAUCUAAUGAUUCCAGUAAGAUAUGUUUGAUAUUCUUGGUUGUUACAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUUGUUGAAACUCU
.......----.....-......(((..((..((((((((((((((((((..((((((.((..((........)).)).)))))))))))))))))).))))))..))..)))....... ( -32.50)
>DroPse_CAF1 926 104 + 1
AAC---------------U-AAUUGGGGAUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUACAUUCAAGAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUACCCGGAAAUCU
...---------------.-..((.(((((..((((((((((((((((((..((((((.((..((........)).)).)))))))))))))))))).))))))..)).))).))..... ( -35.90)
>DroGri_CAF1 912 115 + 1
ACCAACU----ACCCA-CUCAUCUAAUGAUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUACAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUUGUUGAAACUCU
.......----.....-......(((..((..((((((((((((((((((..((((((.((..((........)).)).)))))))))))))))))).))))))..))..)))....... ( -32.60)
>DroMoj_CAF1 851 120 + 1
AACUACCUAUCCACUACCUCAUCUAACGAUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUACAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUCGCUUAAACUCU
.......................(((((((..((((((((((((((((((..((((((.((..((........)).)).)))))))))))))))))).))))))..)))).)))...... ( -33.60)
>DroPer_CAF1 932 104 + 1
AAC---------------U-AAUUGGGGAUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUACAUUCAAGAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUACCCGGAAAUCU
...---------------.-..((.(((((..((((((((((((((((((..((((((.((..((........)).)).)))))))))))))))))).))))))..)).))).))..... ( -35.90)
>consensus
AAC_______________U_AACUAAUGAUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUACAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUACCCGAAAAUCU
.......................(((((((..((((((((((((((((((..((((((.((..((........)).)).)))))))))))))))))).))))))..)))))))....... (-34.10 = -33.35 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,545,747 – 8,545,851
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.58
Mean single sequence MFE -26.18
Consensus MFE -20.38
Energy contribution -19.30
Covariance contribution -1.08
Combinations/Pair 1.15
Mean z-score -2.17
Structure conservation index 0.78
SVM decision value 0.57
SVM RNA-class probability 0.785860
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8545747 104 - 23771897
AGAUUGGCGAGGGUCACAGUAAUAAUAUGUUUGAUUCCUGGGUGAACUUUUGAAUGAAACAACCAAGAAUAUCAAACAUAUCUCACUGGAACCAUCAAUU-A---------------GUU
.((((((....(((..((((....(((((((((((..((.(((....((((....))))..))).))...)))))))))))...))))..))).))))))-.---------------... ( -26.90)
>DroVir_CAF1 825 115 - 1
AGAGUUUCAACAAUCACAGUAAUAAUAUGUUUGAUUCCUGGGUGAACUUUUGAAUGUAACAACCAAGAAUAUCAAACAUAUCUUACUGGAAUCAUUAGAUGAG-UGGGG----GGUAGUU
.....(((..((.((.((((((..(((((((((((..((.(((..((........))....))).))...))))))))))).))))))..(((....))))).-))..)----))..... ( -24.80)
>DroPse_CAF1 926 104 - 1
AGAUUUCCGGGUAUCACAGUAAUAAUAUGUUUGAUUCCUGGGUGAACUCUUGAAUGUAACAACCAAGAAUAUCAAACAUAUCUCACUGGAAUCCCCAAUU-A---------------GUU
........(((.((..((((....(((((((((((..((.(((..((........))....))).))...)))))))))))...))))..)).)))....-.---------------... ( -25.90)
>DroGri_CAF1 912 115 - 1
AGAGUUUCAACAAUCACAGUAAUAAUAUGUUUGAUUCCUGGGUGAACUUUUGAAUGUAACAACCAAGAAUAUCAAACAUAUCUCACUGGAAUCAUUAGAUGAG-UGGGU----AGUUGGU
......(((((.............(((((((((((..((.(((..((........))....))).))...)))))))))))((((((...(((....))).))-)))).----.))))). ( -26.00)
>DroMoj_CAF1 851 120 - 1
AGAGUUUAAGCGAUCACAGUAAUAAUAUGUUUGAUUCCUGGGUGAACUUUUGAAUGUAACAACCAAGAAUAUCAAACAUAUCUCACUGGAAUCGUUAGAUGAGGUAGUGGAUAGGUAGUU
...((((((.((((..((((....(((((((((((..((.(((..((........))....))).))...)))))))))))...))))..)))))))))).................... ( -27.60)
>DroPer_CAF1 932 104 - 1
AGAUUUCCGGGUAUCACAGUAAUAAUAUGUUUGAUUCCUGGGUGAACUCUUGAAUGUAACAACCAAGAAUAUCAAACAUAUCUCACUGGAAUCCCCAAUU-A---------------GUU
........(((.((..((((....(((((((((((..((.(((..((........))....))).))...)))))))))))...))))..)).)))....-.---------------... ( -25.90)
>consensus
AGAGUUUCAACAAUCACAGUAAUAAUAUGUUUGAUUCCUGGGUGAACUUUUGAAUGUAACAACCAAGAAUAUCAAACAUAUCUCACUGGAAUCAUCAAAU_A_______________GUU
........((..((..((((....(((((((((((..((.(((..((........))....))).))...)))))))))))...))))..))..))........................ (-20.38 = -19.30 +  -1.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,545,771 – 8,545,863
Length 92
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 86.31
Mean single sequence MFE -18.66
Consensus MFE -16.88
Energy contribution -17.05
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.90
SVM decision value 2.09
SVM RNA-class probability 0.987663
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8545771 92 + 23771897
UAUGUUUGAUAUUCUUGGUUGUUUCAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGACCCUCGCCAAUCUACUAAAA-CACUC-------
((((((((((..((((((.((...(........)..)).))))))))))))))))........(((.....))).............-.....------- ( -18.10)
>DroVir_CAF1 860 99 + 1
UAUGUUUGAUAUUCUUGGUUGUUACAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUUGUUGAAACUCUACUAAA-CCAACCAAAACCA
((((((((((..((((((.((..((........)).)).))))))))))))))))........((....((((.............-.))))....)).. ( -18.94)
>DroPse_CAF1 950 97 + 1
UAUGUUUGAUAUUCUUGGUUGUUACAUUCAAGAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUACCCGGAAAUCUACUAAAC-CCCCA-AACCC-
((((((((((..((((((.((..((........)).)).))))))))))))))))......(((.(....)))).............-.....-.....- ( -18.50)
>DroWil_CAF1 905 94 + 1
UAUGUUUGAUAUUCUUGGUUGUUACAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUCGUCGG-AAUCUACUAAAA-ACCAA---UUC-
((((((((((..((((((.((..((........)).)).))))))))))))))))......(((.......)))-............-.....---...- ( -18.70)
>DroAna_CAF1 844 92 + 1
UAUGUUUGAUAUUCUUGGUUGUUACAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGACUCUCGCCAAUCUACUAAAA-UACAC-------
((((((((((..((((((.((..((........)).)).))))))))))))))))........(((.....))).............-.....------- ( -19.20)
>DroPer_CAF1 956 97 + 1
UAUGUUUGAUAUUCUUGGUUGUUACAUUCAAGAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUACCCGGAAAUCUACUAAAC-CCCCA-AACCC-
((((((((((..((((((.((..((........)).)).))))))))))))))))......(((.(....)))).............-.....-.....- ( -18.50)
>consensus
UAUGUUUGAUAUUCUUGGUUGUUACAUUCAAAAGUUCACCCAGGAAUCAAACAUAUUAUUACUGUGAUACUCGGAAAUCUACUAAAA_CACCA____CC_
((((((((((..((((((.((..((........)).)).))))))))))))))))............................................. (-16.88 = -17.05 +   0.17)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:38 2006