Locus 3002

Sequence ID 3R_DroMel_CAF1
Location 8,037,350 – 8,037,473
Length 123
Max. P 0.866039
window4831 window4832

overview

Window 1

Location 8,037,350 – 8,037,446
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.57
Mean single sequence MFE -34.56
Consensus MFE -21.54
Energy contribution -20.32
Covariance contribution -1.22
Combinations/Pair 1.22
Mean z-score -2.30
Structure conservation index 0.62
SVM decision value 0.85
SVM RNA-class probability 0.866039
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8037350 96 + 27905053
AGUAUGUUUACGAUAGUGUUG----------------------UGCCUG-GAACUAAGUCCACGACGCUCGCAGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGAUUUUGAUAAGGUUCC-
.(((....)))......((((----------------------.(((((-.(((((((((((((..(....)..))))))))))))).))..))).))))(((((((.....)))))))- ( -29.80)
>DroSec_CAF1 103393 115 + 1
AGUAUGUUUACGAUAGUGUUGUUUUGGGCAGUUAAGAUCGAAGUGCCUGGGAACUAAGUCCA---CGCUCGCGGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGAUUUCGAUAAGGUG-U-
....((((((.((((....)))).))))))......(((((((((((..(.(((((((((((---(((.....)))))))))))))).)...)))........))))))))......-.- ( -37.10)
>DroSim_CAF1 109658 116 + 1
ACUAUGUUUACGAUAGUGUUGUUUUGGGCAGUUAAGAUCGAAGUGCCUGGGAACUAAGUCCA---CGCUCGCGGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGAUUUCGAUAAGGUUCC-
(((((.......)))))((..(((..((((.((.......)).))))..).(((((((((((---(((.....))))))))))))))..))..)).....(((((((.....)))))))- ( -37.80)
>DroEre_CAF1 106467 117 + 1
AGUAUGCUUACGAUAAUGUUGUUUUGGGUAGUUAAAAUCGAAGUGCCUGGGAACUAAGUCCA---UACUUGCUGUGUGAGCUUAGUUGUAAUGGCCUAAUGGGGUUUUGAUAAGGUUCCU
....((((((.((((....)))).))))))(((((((((..((.(((..(.(((((((..((---(((.....)))))..))))))).)...))))).....)))))))))......... ( -31.90)
>DroYak_CAF1 108595 116 + 1
AGUAGGCUUACGAUAAUGUUGUUUUGGGUAGUUAAAAGCGAAGUGCCCGGGAACUAAGUCUA---UACUUGCUGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGGUUUUGAUAAGGUUCC-
..(((((((((((........(((((((((.((.......)).))))))))).(((((((((---(((.....)))))))))))))))))..))))))..((..(((.....)))..))- ( -36.20)
>consensus
AGUAUGUUUACGAUAGUGUUGUUUUGGGCAGUUAAAAUCGAAGUGCCUGGGAACUAAGUCCA___CGCUCGCGGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGAUUUUGAUAAGGUUCC_
......(((((((.(((.((.(((((..(......)..))))).(((..(.(((((((((((...(((.....)))))))))))))).)...))).....)).)))))).))))...... (-21.54 = -20.32 +  -1.22)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 8,037,371 – 8,037,473
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.61
Mean single sequence MFE -34.46
Consensus MFE -23.88
Energy contribution -23.52
Covariance contribution -0.36
Combinations/Pair 1.17
Mean z-score -1.68
Structure conservation index 0.69
SVM decision value 0.01
SVM RNA-class probability 0.538576
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8037371 102 + 27905053
---UGCCUG-GAACUAAGUCCACGACGCUCGCAGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGAUUUUGAUAAGGUUCC---------UCUGGUGGUUUAUGUACCCGACAUCAC-----
---.(((((-.(((((((((((((..(....)..))))))))))))).))..))).....(((((((.....)))))))---------((.((((.......)))).))......----- ( -31.70)
>DroSec_CAF1 103433 102 + 1
AAGUGCCUGGGAACUAAGUCCA---CGCUCGCGGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGAUUUCGAUAAGGUG-U---------ACUGGUGGUUUAUGUACCCGACAUCAC-----
....(((..(.(((((((((((---(((.....)))))))))))))).)...)))..................((((-(---------.(.((((.......)))).))))))..----- ( -36.50)
>DroSim_CAF1 109698 103 + 1
AAGUGCCUGGGAACUAAGUCCA---CGCUCGCGGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGAUUUCGAUAAGGUUCC---------UCUGGUGGUUUAUGUACCCGACAUCAC-----
..(((..(((((((((((((((---(((.....))))))))))))))..(((.(((....(((((((.....)))))))---------...))).)))......)))).)))...----- ( -36.00)
>DroEre_CAF1 106507 112 + 1
AAGUGCCUGGGAACUAAGUCCA---UACUUGCUGUGUGAGCUUAGUUGUAAUGGCCUAAUGGGGUUUUGAUAAGGUUCCUCUGGUUCCUCUGGUGGUUUGUGUACCCGACAUCAC-----
.((.(((..(.(((((((..((---(((.....)))))..))))))).)...)))))....((((....(((((...((.(..(.....)..).)))))))..))))........----- ( -33.30)
>DroYak_CAF1 108635 108 + 1
AAGUGCCCGGGAACUAAGUCUA---UACUUGCUGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGGUUUUGAUAAGGUUCC---------UCUGGUGGUUUAUGUACCCGACAUCACUCACC
.((((..(((((((((((((((---(((.....))))))))))))))..(((.(((....((..(((.....)))..))---------...))).)))......))))....)))).... ( -34.80)
>consensus
AAGUGCCUGGGAACUAAGUCCA___CGCUCGCGGUGUGGGCUUAGUUGUAAUGGCUUAAUGGGAUUUUGAUAAGGUUCC_________UCUGGUGGUUUAUGUACCCGACAUCAC_____
....(((..(.(((((((((((...(((.....)))))))))))))).)...)))....((((......(((((.(.((............)).).)))))...))))............ (-23.88 = -23.52 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:54 2006