Locus 4518

Sequence ID 2R_DroMel_CAF1
Location 14,813,072 – 14,813,268
Length 196
Max. P 0.978021
window7242 window7243

overview

Window 2

Location 14,813,072 – 14,813,192
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.40
Mean single sequence MFE -29.92
Consensus MFE -19.98
Energy contribution -20.18
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -2.57
Structure conservation index 0.67
SVM decision value -0.01
SVM RNA-class probability 0.530331
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14813072 120 - 20766785
AACCUCACGAAGUUCGCGUUAGAAAAGUCUUUGCAAUUUCCGUUUGCUUCGAACGCGUUUGAACGCUUUAAAUGCCAGCGAAGAACUGAAGUACAAAUAUCGCACAUUUUGAGAACUAAA
..........((((((((..(((....))).))).(((((.((...(((((...((((((((.....))))))))...))))).)).)))))....................)))))... ( -25.90)
>DroSec_CAF1 14866 118 - 1
AACCUCACGAAGUUCGCGUUAGAAAA--CUUUGCGAUUUUCGUUUGCUUCGAACGCGUUUGAACGCUUUAAAUGCCAGCGAAGAACUGAAAUACAAAUAUCGCACAUUUUGAGAACUAAA
...((((.((((((..(....)..))--))))((((((((((.((.(((((...((((((((.....))))))))...))))))).))))).......)))))......))))....... ( -28.51)
>DroSim_CAF1 9128 118 - 1
AACCUCACGAAGUUCGCGUUAGAAAA--CUUUGCGAUUUUCGUGUGCUUCGAACGCGUUUGAACGCUUUAAAUGCCAGCGAAGAACUGAAAUACAAAUAUCGCACAUUUUGAGAACUAAA
...((((.((((((..(....)..))--))))((((((((((.((.(((((...((((((((.....))))))))...))))).))))))).......)))))......))))....... ( -30.11)
>DroEre_CAF1 7748 115 - 1
-----CCCGAAGUUCUCGGUACAAAAAUCAUUUGGAUUUCAGUUUACUUCGAACGCGUUUGAACGCUUUAAAUGCCAGCGAAGAACUGAAAUACAAAUAUCGCACAUUUUGAGAACUAAA
-----.....(((((((((..........(((((.(((((((((..(((((...((((((((.....))))))))...)))))))))))))).)))))..........)))))))))... ( -35.65)
>DroYak_CAF1 9012 120 - 1
AACCUCUCGAAGUUCUCGUUACAAAAAUCAUUUGGAUUUCAGUUUGCCUCGAACGCGUUUUAACGCUUUAAAUGCCAGCGAAGAACUGAAAUACAAAUAUCGCACAUUUUGAGAACCAAA
...........(((((((...........(((((.((((((((((...(((...((((((.........))))))...))).)))))))))).)))))...........))))))).... ( -29.45)
>consensus
AACCUCACGAAGUUCGCGUUAGAAAA_UCUUUGCGAUUUCCGUUUGCUUCGAACGCGUUUGAACGCUUUAAAUGCCAGCGAAGAACUGAAAUACAAAUAUCGCACAUUUUGAGAACUAAA
..........(((((....................(((((.((...(((((...((((((((.....))))))))...))))).)).))))).((((..........)))).)))))... (-19.98 = -20.18 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,813,152 – 14,813,268
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.01
Mean single sequence MFE -23.93
Consensus MFE -6.39
Energy contribution -8.07
Covariance contribution 1.68
Combinations/Pair 1.19
Mean z-score -2.22
Structure conservation index 0.27
SVM decision value 1.80
SVM RNA-class probability 0.978021
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14813152 116 + 20766785
GAAAUUGCAAAGACUUUUCUAACGCGAACUUCGUGAGGUUUUCGCACUUA---UGAUUAAAAGUUGCGUUGGAGGAAAAACAAUAUUAAACAAAACAAUUGUCAUUU-CUCCGAAACAAC
.......................(((((..((....))..))))).....---.........((((..(((((((((..(((((.............)))))..)))-))))))..)))) ( -27.52)
>DroSec_CAF1 14946 115 + 1
AAAAUCGCAAAG--UUUUCUAACGCGAACUUCGUGAGGUUU-CAAGUUUAAAGUAA-AAAAAGUUGCGUUGGAGGAAAAACAAAAUUAAACAAAACAAUUGACAUUU-CUCCGAAGCAAC
....((((.(((--(((.(....).)))))).)))).....-..............-.....(((((.(((((((((...(((...............)))...)))-)))))).))))) ( -25.46)
>DroSim_CAF1 9208 116 + 1
AAAAUCGCAAAG--UUUUCUAACGCGAACUUCGUGAGGUUU-CAAGUUUAAAGUGAUUAAAAGUUGCGUUGGAGGAAAAACAAAAUCAAGCAAAACAAUUGUCAUUU-CUCCGAAGCAAC
..((((((.(((--(((.(....).))))))(....)....-..........))))))....(((((.(((((((((..((((...............))))..)))-)))))).))))) ( -29.26)
>DroEre_CAF1 7828 97 + 1
GAAAUCCAAAUGAUUUUUGUACCGAGAACUUCGGG--------------------AUUAAAAGUUGUGUUUAAAGGAAAAC--AAUUACGCAAAACAAUUGAAAUUU-GUGCGACGGAAC
....(((..(..(((((((..(((((...))))).--------------------..)))))))..)((((......))))--.....(((...((((.......))-)))))..))).. ( -18.20)
>DroYak_CAF1 9092 115 + 1
GAAAUCCAAAUGAUUUUUGUAACGAGAACUUCGAGAGGUUUUCGAACUUA---UGAUUAAAAGUGGUGUAUACCGAACAAA--AAUUACGCAAAACAAUUUAAAUUAAAUACGACCAAAC
..........((((((((((..(((((((((....))))))))).((((.---.......))))(((....)))..)))))--)))))................................ ( -19.20)
>consensus
GAAAUCGCAAAGA_UUUUCUAACGCGAACUUCGUGAGGUUU_CAAACUUA___UGAUUAAAAGUUGCGUUGGAGGAAAAACAAAAUUAAGCAAAACAAUUGACAUUU_CUCCGAAGCAAC
..............(((((((((((.(((((.............................))))))))))))))))............................................ ( -6.39 =  -8.07 +   1.68)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:01 2006