Locus 1928

Sequence ID 3R_DroMel_CAF1
Location 5,448,767 – 5,448,921
Length 154
Max. P 0.884447
window3172 window3173

overview

Window 2

Location 5,448,767 – 5,448,881
Length 114
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 76.98
Mean single sequence MFE -29.38
Consensus MFE -12.98
Energy contribution -13.12
Covariance contribution 0.14
Combinations/Pair 1.13
Mean z-score -2.41
Structure conservation index 0.44
SVM decision value 0.93
SVM RNA-class probability 0.884447
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5448767 114 + 27905053
AUGCUCCUCUUCUUGCAGUGAUUACUAUUUAAAACAUGCUCAAUAUA----UUCAAAUAUAUAUUUUAUGUUGCAGGAAAACCUGGAGAGCGCUUUGCGCGAAUUUAAGCGCGAGAAA
..((((..(((((((((((....)))......((((((...((((((----(......))))))).))))))))))))).....)..))))..(((((((........)))))))... ( -30.00)
>DroSec_CAF1 2714 114 + 1
AUGCUCCUCUUCCUCCAGAGAUUAAUAUUUAAAUCAUAAUGGAUGUA----UUCAAAUAUAUAUUUUAUUUUCCAGGAAAACCUAGAGAGCGCUUUGCGCGAAUUUAAGCGCGAGAAA
..((((.(((...(((...((((........)))).....(((((((----(......)))))))).........)))......)))))))..(((((((........)))))))... ( -24.40)
>DroSim_CAF1 2661 114 + 1
AUGCUCCUCAUCCUGCAGAGAUUACUAUUUAAAUCAUAAUGGAUGUA----UUCAAAUAUAUAUUUUAUUUUGCAGGAAAACCUGGAGAGCGCUUUGCGCGAAUUUAAGCGCGAGAAA
..((((..(((((((((((((((........)))).....(((((((----(......))))))))...))))))))).....))..))))..(((((((........)))))))... ( -35.00)
>DroEre_CAF1 1383 113 + 1
AUGC-UCUAUUCCCGCAGAGAUUAUUAUUUAAAUCAGUUUGGAUAUA----UUCUAAAGUGUAUUCUGUUUUGCAGGAAAACCUGGAGAGCGCUUUGCGCGAAUUUAAGCGUGAGAAA
((((-(..((((.(((((((..............((.((((((....----.)))))).))......(((((.((((....)))).))))).))))))).))))...)))))...... ( -34.70)
>DroYak_CAF1 1218 114 + 1
AUCCAUCUGUUCCUGCAGAGAUUAUUAUUUUACUCAUUUUGGAUAUA----UUCUAAAGUACAUUGUAUUUUGCAGGAAAACCUGGAGAGCGCUUUGCGCGAAUUUAAGCGUGAGAAA
.((((....((((((((((((.((......)).))((((((((....----.)))))))).........))))))))))....))))......((..(((........)))..))... ( -32.10)
>DroAna_CAF1 1395 98 + 1
----------------AGGAUCUACUCCUU----GUUUUUGGAUCUAACAUUACUAAUGGAGCAAUCAUUUUCCAGGAGAACCUCGAGAGCGCUUUGCGUGAAUUUAAGCGCGAGAAA
----------------.(((((((......----.....))))))).......((..(((((........)))))..))...(((....((((((...........)))))))))... ( -20.10)
>consensus
AUGCUCCUCUUCCUGCAGAGAUUACUAUUUAAAUCAUUUUGGAUAUA____UUCAAAUAUAUAUUUUAUUUUGCAGGAAAACCUGGAGAGCGCUUUGCGCGAAUUUAAGCGCGAGAAA
....................................................................((((.((((....)))).))))...(((((((........)))))))... (-12.98 = -13.12 +   0.14)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,448,807 – 5,448,921
Length 114
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 73.88
Mean single sequence MFE -28.58
Consensus MFE -18.64
Energy contribution -19.00
Covariance contribution 0.36
Combinations/Pair 1.25
Mean z-score -1.43
Structure conservation index 0.65
SVM decision value 0.83
SVM RNA-class probability 0.861124
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5448807 114 - 27905053
CGGCGUUGGCCAAACUCAAGCGAGCGUUUUGCUUCAGAAUUUUCUCGCGCUUAAAUUCGCGCAAAGCGCUCUCCAGGUUUUCCUGCAACAUAAAAUA-UAUAUUUGAA----UAUAUUG
.(((....)))........(((((((((((((....((......))(((........))))))))))))))...(((....))))).......((((-(((......)----)))))). ( -32.50)
>DroVir_CAF1 11210 103 - 1
CGGCAUUUGCCAGGCUGAGACGCGCAUUUUGUUUCAGAAUUUUCUCACGCUUAAAUUCCCGCAAUGCGCUCUCCAAAUUAUCCUGCAAAUGAAUAAC---------------AACAGC-
...(((((((.(((..((((.((((((..(((....((((((..........))))))..)))))))))))))........))))))))))......---------------......- ( -25.20)
>DroPse_CAF1 19264 104 - 1
CAGCGUUGGCCAGGCUGAGACGAGCGUUUUGCUUAAGAAUUUUCUCUCGCUUAAAUUCACGCAAAGCGCUCUCCAGGUUCUCCUGCAAGAUUCGAAG---------------AAGGUCA
......(((((...((..((.(((((((((((....((((((..........))))))..)))))))))))..((((....))))......))..))---------------..))))) ( -31.80)
>DroWil_CAF1 858 104 - 1
CCGCGUUGGCUAAACUGAGACGAGCGUUUUGCUUUAGAAUUUUCUCACGUUUAAAUUCACGCAAAGCACUUUCAAGAUUCUCCUACAAAAAAAAAGAAGAUAUU---------------
....((.((..((.((..((.(((.(((((((....((((((..........))))))..))))))).))))).)).))..)).))..................--------------- ( -15.80)
>DroAna_CAF1 1415 118 - 1
CGGCAUUGGCCAGGCUGAGGCGAGCGUUUUGCUUCAGAAUUUUCUCGCGCUUAAAUUCACGCAAAGCGCUCUCGAGGUUCUCCUGGAAAAUGAUUGC-UCCAUUAGUAAUGUUAGAUCC
...((((..(((((..(((.((((((((((((....((((((..........))))))..)))))))))))....).))).)))))..))))(((((-(.....))))))......... ( -36.20)
>DroPer_CAF1 19465 104 - 1
CAGCGUUGGCCAGGCUGAGACGAGCGUUUUGCUUAAGAAUUUUCUCUCGCUUAAAUUCACGCAAAGCGCUCUCCAGGUUCUCCUGCAAGAUUCGAAG---------------AAGAUCA
....((.((..((.(((.((.(((((((((((....((((((..........))))))..)))))))))))))))).))..)).))..((((.....---------------..)))). ( -30.00)
>consensus
CGGCGUUGGCCAGGCUGAGACGAGCGUUUUGCUUCAGAAUUUUCUCACGCUUAAAUUCACGCAAAGCGCUCUCCAGGUUCUCCUGCAAAAUAAAAAA_______________AAGAUC_
..(((..((...((((..((.(((((((((((....((((((..........))))))..)))))))))))))..))))..)))))................................. (-18.64 = -19.00 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:07 2006