Locus 7972

Sequence ID 3R_DroMel_CAF1
Location 21,375,833 – 21,375,961
Length 128
Max. P 0.890660
window12834 window12835

overview

Window 4

Location 21,375,833 – 21,375,936
Length 103
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 93.07
Mean single sequence MFE -27.48
Consensus MFE -20.70
Energy contribution -21.14
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.46
Structure conservation index 0.75
SVM decision value 0.96
SVM RNA-class probability 0.890660
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21375833 103 + 27905053
GAGCCCAGCUCUGAUUGUUGUUAUGGAGUUGGCAUUUUGGACCAACAAAUUAUAUAUGCAUGCUUUGCAUAUAUCAAGUUAAUUGGGUUAAUUGACAACGCCA
..(((.(((((((((....)))..)))))))))....(((.((((..(((((((((((((.....)))))))))..))))..))))(((....)))....))) ( -26.30)
>DroSec_CAF1 70341 102 + 1
GAC-CCAGCUCUGAUUGUUGUUAUGGAGUUGCCAUUUUGGAACAACAAAUUAUAUAUGCAUGCUUUGCAUAUAUCAAGAUAAUUGGGUUAAUUGACAACGCCA
(((-((((.(((((((((((((((((.....)))).....))))))))....((((((((.....)))))))))).)))...))))))).............. ( -27.30)
>DroSim_CAF1 66717 102 + 1
GAG-CCGGCUCUGAUUGUUGUUAUGGAGUUGGCAUUUUGGAACAACAAAUUAUAUAUGCAUGCUUUGCAUAUAUCAAGUUAAUUGGGUUAAUUGACAACGCCA
..(-(((((((((((....)))..)))))))))....(((...........(((((((((.....)))))))))...((((((((...))))))))....))) ( -28.40)
>DroEre_CAF1 69783 100 + 1
GAG-CCAGCUCUGAUUCUUGUUAUGGAGUUGGCUU-UUGGAC-AAAAAAUUAUAUAUGCAUGCUAUACAUAUAUCAAGUUAAUUGGGUUAAUUGACAACGCCA
(((-(((((((((((....)))..)))))))))))-.(((.(-........(((((((.........)))))))...((((((((...))))))))...)))) ( -24.30)
>DroYak_CAF1 69280 102 + 1
GAG-CCAGCUCUGAUUCUUCUUAUGGAGUUGGCUUAUUGGACCAACAAAUUAUAUAUGCAUGUUAUGCAUAUAUCAAGUUAAUUGGGUUAAUUGACAACGCCA
(((-((((((((............)))))))))))..(((.((((..((((((((((((((...))))))))))..))))..))))(((....)))....))) ( -31.10)
>consensus
GAG_CCAGCUCUGAUUGUUGUUAUGGAGUUGGCAUUUUGGACCAACAAAUUAUAUAUGCAUGCUUUGCAUAUAUCAAGUUAAUUGGGUUAAUUGACAACGCCA
....((((((((............)))))))).....(((...........(((((((((.....)))))))))...((((((((...))))))))....))) (-20.70 = -21.14 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,375,867 – 21,375,961
Length 94
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 77.25
Mean single sequence MFE -22.67
Consensus MFE -9.94
Energy contribution -10.63
Covariance contribution 0.69
Combinations/Pair 1.06
Mean z-score -2.06
Structure conservation index 0.44
SVM decision value 0.04
SVM RNA-class probability 0.552052
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21375867 94 - 27905053
GAGAA-------AAAAUAACUUUG------GCUGCAUA------UGGCGUUGUCAAUUAACCCAAUUAACUUGAUAUAUGCAAAGCAUGCAUAUAUAAUUUGUUGGUCCAAAA
.....-------........((((------(.......------(((.((((.....)))))))((((((...(((((((((.....))))))))).....))))))))))). ( -20.50)
>DroPse_CAF1 85712 100 - 1
UGAAU-CUGCAGAGAUCUGCCUUG------GCCAGAUAGUGGUGCUGCGGCGUCAAUUAACCCAAUUAACCCGAUAUAUGCAUAACAUGAAUAUAUAAUAUCGG--GCC----
(((..-((((((..((((((....------).))))).......))))))..)))..............(((((((((((.((.......)).))).)))))))--)..---- ( -24.80)
>DroSec_CAF1 70374 100 - 1
GAGAA-AAAUGAAAAAUAACUUUG------GCUACAUA------UGGCGUUGUCAAUUAACCCAAUUAUCUUGAUAUAUGCAAAGCAUGCAUAUAUAAUUUGUUGUUCCAAAA
.....-..............((((------(..(((..------(((.((((.....))))))).........(((((((((.....))))))))).......))).))))). ( -19.40)
>DroSim_CAF1 66750 101 - 1
GAGAACAAAUGAAAAACAACUUUG------GCUGCAUA------UGGCGUUGUCAAUUAACCCAAUUAACUUGAUAUAUGCAAAGCAUGCAUAUAUAAUUUGUUGUUCCAAAA
....................((((------(..(((..------(((.((((.....))))))).........(((((((((.....))))))))).......))).))))). ( -19.70)
>DroEre_CAF1 69816 104 - 1
GAGAA-AAAUGAAAAAUAACUUUGGACAGGGCUCAAUA------UGGCGUUGUCAAUUAACCCAAUUAACUUGAUAUAUGUAUAGCAUGCAUAUAUAAUUUUUU-GUCCAA-A
.....-...............((((((((((.......------(((.((((.....))))))).........((((((((((...))))))))))....))))-))))))-. ( -22.80)
>DroYak_CAF1 69313 106 - 1
GGGAA-AAAUGGAAAAUAACUUCGGACAGGGCUGCAUA------UGGCGUUGUCAAUUAACCCAAUUAACUUGAUAUAUGCAUAACAUGCAUAUAUAAUUUGUUGGUCCAAUA
.....-...((((...........(((((.(((.....------.))).))))).......(((((.......((((((((((...)))))))))).....)))))))))... ( -28.80)
>consensus
GAGAA_AAAUGAAAAAUAACUUUG______GCUGCAUA______UGGCGUUGUCAAUUAACCCAAUUAACUUGAUAUAUGCAAAGCAUGCAUAUAUAAUUUGUUGGUCCAAAA
............................................(((.((((.....))))))).........(((((((((.....)))))))))................. ( -9.94 = -10.63 +   0.69)

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 12:59:17 2006