Locus 1212

Sequence ID 2L_DroMel_CAF1
Location 3,246,817 – 3,246,973
Length 156
Max. P 0.667291
window1983 window1984

overview

Window 3

Location 3,246,817 – 3,246,934
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.74
Mean single sequence MFE -34.38
Consensus MFE -23.58
Energy contribution -23.70
Covariance contribution 0.12
Combinations/Pair 1.18
Mean z-score -2.01
Structure conservation index 0.69
SVM decision value 0.18
SVM RNA-class probability 0.620277
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3246817 117 - 22407834
AACUUGGGUGCAUCUUAAAUUUGAUGCGACCGCAUUUCCGCAAUUCGCGGUAAGUAAUUCAAUGGCAUUGGCUUGAAAUAAAAUUUGAUGCCCCUCAUGUGGCAGGCAGUUGGUGGC---
.(((((((((((((........))))).)))......((((.....)))))))))........(.(((..(((..((......))..)((((((......))..))))))..))).)--- ( -32.40)
>DroSec_CAF1 80890 113 - 1
AACUGCGGUGCAUCUUAAAUUUGAUGCGACCGCAUUUCCGCAAUUCGCGGUAAGUAAUUCAAUGGCAUUGGCUUGAAAUAAAAUUUGAUGCCCCUCAUGUGGC----AGUUGGUGGC---
....((((((((((........))))).)))))((((((((.....)))).))))........(.(((..(((..((......))..)((((.(....).)))----)))..))).)--- ( -35.70)
>DroSim_CAF1 84030 113 - 1
AACUGCGGUGCAUCUUAAAUUUGAUGCGACCGCAUUUCCGCAAUUCGCGGUAAGUAAUUCAAUGGCAUUGGCUUGAAAUAAAUUUUGAUGCCCCUCAUGUGGC----AGUUGGUGGC---
....((((((((((........))))).)))))((((((((.....)))).))))........(.(((..(((..(((....)))..)((((.(....).)))----)))..))).)--- ( -36.40)
>DroEre_CAF1 77677 111 - 1
AACUUCAGAGCAUCUUAAAUUUGAUGCGACCGCGCAUCCGCAAUUCGCAGUAUGUAAUUCAAUGGCAGUGGCUUCAAAUAAAAUUUGAUGCCC--CCACUGGC----AGUUGGUGGA---
.........(((((........)))))..(((((((((.((.....)).).))))....(((((.(((((((.((((((...)))))).))).--..)))).)----).))))))).--- ( -32.30)
>DroYak_CAF1 76914 116 - 1
AACUUCGGAGCAUCUUAAAUUUGAUGCGACCGCAUAUCCGCAAUUCGCAGAAUGUAAUUCAAUUGCAGUGGCUUCAAAUAAAAUUUAAUGCCUCUCCACUGGC----AGUUGGCGGAUAU
.....(((.(((((........)))))..))).((((((((.((((...))))......((((((((((((......((........))......))))).))----))))))))))))) ( -35.10)
>consensus
AACUUCGGUGCAUCUUAAAUUUGAUGCGACCGCAUUUCCGCAAUUCGCGGUAAGUAAUUCAAUGGCAUUGGCUUGAAAUAAAAUUUGAUGCCCCUCAUGUGGC____AGUUGGUGGC___
.........(((((........)))))..((((((((((((.....)))).))))....((((((((((((.((.......)).))))))))((......))......)))))))).... (-23.58 = -23.70 +   0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,246,854 – 3,246,973
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.21
Mean single sequence MFE -29.84
Consensus MFE -21.56
Energy contribution -22.48
Covariance contribution 0.92
Combinations/Pair 1.12
Mean z-score -2.10
Structure conservation index 0.72
SVM decision value 0.28
SVM RNA-class probability 0.667291
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3246854 119 + 22407834
UAUUUCAAGCCAAUGCCAUUGAAUUACUUACCGCGAAUUGCGGAAAUGCGGUCGCAUCAAAUUUAAGAUGCACCCAAGUUCCUGAA-AAACACUUUUUGAAUGGCACAGUAAAAUUUUAU
.............((((((((((((.....((((.....))))...((.(((.(((((........)))))))))))))))..(((-((....))))).))))))).............. ( -27.60)
>DroSec_CAF1 80923 120 + 1
UAUUUCAAGCCAAUGCCAUUGAAUUACUUACCGCGAAUUGCGGAAAUGCGGUCGCAUCAAAUUUAAGAUGCACCGCAGUUCCUGAAAAAACACUUUUUGAAUGGUGCAGUAAAAUUUUAU
...(((((((....))..)))))(((((((((((.....))((((.((((((.(((((........))))))))))).))))....................)))).)))))........ ( -34.00)
>DroSim_CAF1 84063 119 + 1
UAUUUCAAGCCAAUGCCAUUGAAUUACUUACCGCGAAUUGCGGAAAUGCGGUCGCAUCAAAUUUAAGAUGCACCGCAGUUCCUGAA-AAACACUUUUUGAAUGGCGCAGUAAAAUUUUAU
..............((((((.((.........((.....))((((.((((((.(((((........))))))))))).))))....-.........)).))))))............... ( -33.40)
>DroEre_CAF1 77708 119 + 1
UAUUUGAAGCCACUGCCAUUGAAUUACAUACUGCGAAUUGCGGAUGCGCGGUCGCAUCAAAUUUAAGAUGCUCUGAAGUUCCUGGA-AAGCGCUUUUUGAAUGGCGCAAUAAAAUUUUAC
..............((((((.((.......((((.....))))..((((..(((((((........)))))...(.....)...))-..))))...)).))))))............... ( -27.30)
>DroYak_CAF1 76950 119 + 1
UAUUUGAAGCCACUGCAAUUGAAUUACAUUCUGCGAAUUGCGGAUAUGCGGUCGCAUCAAAUUUAAGAUGCUCCGAAGUUCCUGAA-AAACACUUUUCGAAUGGCGCACUAAAAUUUUAU
........((((..((((((((((...))))....))))))(((....(((..(((((........))))).)))....)))((((-((....))))))..))))............... ( -26.90)
>consensus
UAUUUCAAGCCAAUGCCAUUGAAUUACUUACCGCGAAUUGCGGAAAUGCGGUCGCAUCAAAUUUAAGAUGCACCGAAGUUCCUGAA_AAACACUUUUUGAAUGGCGCAGUAAAAUUUUAU
.............(((((((.((.........((.....))((((...((((.(((((........)))))))))...))))..............)).))))))).............. (-21.56 = -22.48 +   0.92)

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 09:56:44 2006