Locus 1391

Sequence ID 3R_DroMel_CAF1
Location 4,063,602 – 4,063,705
Length 103
Max. P 0.782542
window2292 window2293

overview

Window 2

Location 4,063,602 – 4,063,705
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.68
Mean single sequence MFE -41.83
Consensus MFE -32.92
Energy contribution -33.14
Covariance contribution 0.23
Combinations/Pair 1.26
Mean z-score -1.26
Structure conservation index 0.79
SVM decision value 0.06
SVM RNA-class probability 0.562190
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4063602 103 + 27905053
--------UCGUCUGCAGCAU---------CGUAGCUGCCGACGAUCCCCGACAGCUAUCCAAGUAGUUUUUGCUGGGCAAUAAUGCGCCGGAGCAGGUCGGGUCGGCGAUGUGGAGCGU
--------(((((.(((((..---------....))))).)))))..((((((((((((....)))))).(((((.(((........))).).))))))))))...((........)).. ( -40.40)
>DroPse_CAF1 499 103 + 1
--------UUGUCGGCAGCGU---------CGUAGCUGCCGACGAUACCCGACAGUUAUCCAAGUAGUUUCUGCUGUGCGAUAAUCCGUCGGAGCAGGUCGGGUCGACGGUGUGGUGCGU
--------(((((((((((..---------....))))))))))).(((((((..((((....))))...(((((.((((......)).)).))))))))))))..(((........))) ( -43.10)
>DroSim_CAF1 438 100 + 1
--------UCGUUUGCAGCAU---------CGUAGCUGC-GACGAUCCCCGACAGCUAUC-AAGUAGUU-UUGCUGGGCAAUAAUGCGCCGGAGCAGGUCGGAUCGGCGAUGUGGAGCGU
--------(((((((((((..---------....)))))-))((((((..(((.(((..(-(((....)-)))(((((((....))).)))))))..))))))))))))).......... ( -35.30)
>DroWil_CAF1 1555 112 + 1
--------UUGUCGGCAGCAUCGUUGUUGUCGUAGCUGCCGACGAUCCCCGAUAGCUAUCCAAGUAGCUUCUGCUGGGCAAUAAUGCGCCGGAGCAAGUCGGGUCGACGAUGUGGUGCGU
--------(((((((((((..((.......))..))))))))))).(((.(..((((((....))))))....).))).....((((((((.(....((((...))))..).)))))))) ( -45.10)
>DroAna_CAF1 455 117 + 1
CAUCCCGAUCGUCGGCUGCAUCGUU---GUCGUAGCUGCCGACAAUGUCCGACAGCUAUCCGAGUAACUUCUGUUGGGCAAUGAUCCUCCGGAGCAGGUCGGGUCGGCGGUGUGGAGCAU
(..(((((((((((((.((..((..---..))..)).))))))..((((((((((...............)))))))))).((.(((...))).)))))))))..)((........)).. ( -43.96)
>DroPer_CAF1 499 103 + 1
--------UUGUCGGCAGCGU---------CGUAGCUGCCGACGAUACCCGACAGUUAUCCAAGUAGUUUCUGCUGUGCGAUAAUCCGUCGGAGCAGGUCGGGUCGACGGUGUGGUGCGU
--------(((((((((((..---------....))))))))))).(((((((..((((....))))...(((((.((((......)).)).))))))))))))..(((........))) ( -43.10)
>consensus
________UCGUCGGCAGCAU_________CGUAGCUGCCGACGAUCCCCGACAGCUAUCCAAGUAGUUUCUGCUGGGCAAUAAUCCGCCGGAGCAGGUCGGGUCGACGAUGUGGAGCGU
........(((((((((((...............)))))))))))..((((((.....(((...((((....))))(((........))))))....))))))................. (-32.92 = -33.14 +   0.23)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,063,602 – 4,063,705
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.68
Mean single sequence MFE -37.53
Consensus MFE -26.19
Energy contribution -27.50
Covariance contribution 1.31
Combinations/Pair 1.15
Mean z-score -1.98
Structure conservation index 0.70
SVM decision value 0.56
SVM RNA-class probability 0.782542
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4063602 103 - 27905053
ACGCUCCACAUCGCCGACCCGACCUGCUCCGGCGCAUUAUUGCCCAGCAAAAACUACUUGGAUAGCUGUCGGGGAUCGUCGGCAGCUACG---------AUGCUGCAGACGA--------
..((........))...((((((..(((((((.(((....)))))((......))....)))..)).))))))..(((((.(((((....---------..))))).)))))-------- ( -37.80)
>DroPse_CAF1 499 103 - 1
ACGCACCACACCGUCGACCCGACCUGCUCCGACGGAUUAUCGCACAGCAGAAACUACUUGGAUAACUGUCGGGUAUCGUCGGCAGCUACG---------ACGCUGCCGACAA--------
............((((...)))).(((.(((((((.(((((.((.((.((...)).)))))))))))))))))))..(((((((((....---------..)))))))))..-------- ( -38.90)
>DroSim_CAF1 438 100 - 1
ACGCUCCACAUCGCCGAUCCGACCUGCUCCGGCGCAUUAUUGCCCAGCAA-AACUACUU-GAUAGCUGUCGGGGAUCGUC-GCAGCUACG---------AUGCUGCAAACGA--------
.((.........(.((((((....((((..((.(((....))))))))).-......((-(((....))))))))))).)-(((((....---------..)))))...)).-------- ( -29.70)
>DroWil_CAF1 1555 112 - 1
ACGCACCACAUCGUCGACCCGACUUGCUCCGGCGCAUUAUUGCCCAGCAGAAGCUACUUGGAUAGCUAUCGGGGAUCGUCGGCAGCUACGACAACAACGAUGCUGCCGACAA--------
.((.((......)))).(((((.(((((..((.(((....)))))))))).(((((......))))).)))))....(((((((((..((.......))..)))))))))..-------- ( -41.90)
>DroAna_CAF1 455 117 - 1
AUGCUCCACACCGCCGACCCGACCUGCUCCGGAGGAUCAUUGCCCAACAGAAGUUACUCGGAUAGCUGUCGGACAUUGUCGGCAGCUACGAC---AACGAUGCAGCCGACGAUCGGGAUG
.............((((.(((((..(((((((..(((..(((.....)))..)))..)))))..)).)))))...((((((((.((..((..---..))..)).)))))))))))).... ( -38.00)
>DroPer_CAF1 499 103 - 1
ACGCACCACACCGUCGACCCGACCUGCUCCGACGGAUUAUCGCACAGCAGAAACUACUUGGAUAACUGUCGGGUAUCGUCGGCAGCUACG---------ACGCUGCCGACAA--------
............((((...)))).(((.(((((((.(((((.((.((.((...)).)))))))))))))))))))..(((((((((....---------..)))))))))..-------- ( -38.90)
>consensus
ACGCACCACACCGCCGACCCGACCUGCUCCGGCGCAUUAUUGCCCAGCAGAAACUACUUGGAUAGCUGUCGGGGAUCGUCGGCAGCUACG_________AUGCUGCCGACAA________
.................((((((..(((((((.......((((...)))).......)))))..)).))))))....(((((((((...............))))))))).......... (-26.19 = -27.50 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:54 2006