Locus 2677

Sequence ID 2R_DroMel_CAF1
Location 9,443,721 – 9,443,857
Length 136
Max. P 0.864074
window4402 window4403

overview

Window 2

Location 9,443,721 – 9,443,838
Length 117
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 88.97
Mean single sequence MFE -24.42
Consensus MFE -17.45
Energy contribution -17.73
Covariance contribution 0.28
Combinations/Pair 1.10
Mean z-score -1.83
Structure conservation index 0.71
SVM decision value 0.13
SVM RNA-class probability 0.598862
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9443721 117 - 20766785
GCCAGAAGGCAAUUCAA-AAUGCCAUAACAAUCAGUUGGCAAUUAAA-UGGCGCCCCUCUUCAAAACACCUCCACCUCGCAACACCCCCCAAUUGCCCAAUGCCAAUGGCCAUGGUAAU
((((...(((((((...-..(((((...........)))))......-..(((........................)))..........)))))))....(((...)))..))))... ( -20.46)
>DroSec_CAF1 30786 117 - 1
GCCAGAAGGCAAUUCAAAAAUGCCAUAACAAUCAGUUGGCAAUUAAA-UGGCGCUCCUCUUCAAAAAACCUCCGCCUCGCAACACCC-CCAAGUGCCCAAUGCCAAUGGCCCUGGUAAU
(((((..((((.........))))..........(((((((......-.((((...................))))..(((.(....-....))))....)))))))....)))))... ( -26.01)
>DroSim_CAF1 39027 109 - 1
GCCAGAAGGCAAUUCAA-AAUGCCAUAACAAUCAGUUGGCAAUUAAA-UGGCGCCCCUCUUCAAAAAACCUCCACCUCGCAACACCC-CCAAUU-------GAUAAUGGCCCUGGUAAU
(((((..((((......-..))))......(((((((((........-..(((........................))).......-))))))-------))).......)))))... ( -22.19)
>DroEre_CAF1 30846 110 - 1
GCCAGAAGGCAAUUCGA-AAUGCCAUAGCAAUCAGUUGGCAAUUAUAUUGGCGCCCCUCUUUAAA-AGCCUCCACCUCGCAACACCC-CCAA------AGUGCCAAUGGCCCUGGUAAU
(((((..(((.......-..(((((..((.....)))))))....(((((((((...........-.((.........)).......-....------.)))))))))))))))))... ( -28.05)
>DroYak_CAF1 30914 110 - 1
GCCAGAAGGCAAUUCAA-AGUGCCAUAACAAUCAGUUGGCAAUUAAAUUGGCGCCCCUCUUUAAA-AACCUCCACCUCGCUACACCC-CCAA------AGUGCCAAUGGCCCUGGUAAU
(((((..(((.......-..(((((...........))))).....((((((((...........-.....................-....------.)))))))).))))))))... ( -25.39)
>consensus
GCCAGAAGGCAAUUCAA_AAUGCCAUAACAAUCAGUUGGCAAUUAAA_UGGCGCCCCUCUUCAAAAAACCUCCACCUCGCAACACCC_CCAA_U____AAUGCCAAUGGCCCUGGUAAU
(((((..(((..........(((((..((.....))))))).......(((((...............................................)))))...))))))))... (-17.45 = -17.73 +   0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,443,761 – 9,443,857
Length 96
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 93.57
Mean single sequence MFE -19.65
Consensus MFE -19.28
Energy contribution -19.12
Covariance contribution -0.16
Combinations/Pair 1.06
Mean z-score -1.20
Structure conservation index 0.98
SVM decision value 0.84
SVM RNA-class probability 0.864074
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9443761 96 - 20766785
UGCCCCAACUCAAUGGCGUGCCAGAAGGCAAUUCAA-AAUGCCAUAACAAUCAGUUGGCAAUUAAA-UGGCGCCCCUCUUCAAAACACCUCCACCUCG
..............((.(((((((((.....)))..-..(((((...........)))))......-)))))).))...................... ( -19.40)
>DroSec_CAF1 30825 96 - 1
AGC-CCAACUCAAUGGCGUGCCAGAAGGCAAUUCAAAAAUGCCAUAACAAUCAGUUGGCAAUUAAA-UGGCGCUCCUCUUCAAAAAACCUCCGCCUCG
.((-(.........)))(((((((((.....))).....(((((...........)))))......-))))))......................... ( -19.90)
>DroSim_CAF1 39059 95 - 1
AGC-CCAACUCAAUGGCGUGCCAGAAGGCAAUUCAA-AAUGCCAUAACAAUCAGUUGGCAAUUAAA-UGGCGCCCCUCUUCAAAAAACCUCCACCUCG
.((-(.........)))(((((((((.....)))..-..(((((...........)))))......-))))))......................... ( -19.50)
>DroEre_CAF1 30879 95 - 1
AGC-CCAACUCAAUGGCGUGCCAGAAGGCAAUUCGA-AAUGCCAUAGCAAUCAGUUGGCAAUUAUAUUGGCGCCCCUCUUUAAA-AGCCUCCACCUCG
.((-(.(((((.(((((((....(((.....)))..-.))))))).).....))))))).........(((.............-.)))......... ( -20.04)
>DroYak_CAF1 30947 95 - 1
AGC-CCAACUCAAUGGCGUGCCAGAAGGCAAUUCAA-AGUGCCAUAACAAUCAGUUGGCAAUUAAAUUGGCGCCCCUCUUUAAA-AACCUCCACCUCG
.((-(.........)))(((((((..((((......-..)))).((((.....)))).........)))))))...........-............. ( -19.40)
>consensus
AGC_CCAACUCAAUGGCGUGCCAGAAGGCAAUUCAA_AAUGCCAUAACAAUCAGUUGGCAAUUAAA_UGGCGCCCCUCUUCAAAAAACCUCCACCUCG
..............((.(((((((((.....))).....(((((..((.....))))))).......)))))).))...................... (-19.28 = -19.12 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:04 2006