Locus 7727

Sequence ID 3R_DroMel_CAF1
Location 20,737,998 – 20,738,115
Length 117
Max. P 0.786838
window12460 window12461

overview

Window 0

Location 20,737,998 – 20,738,095
Length 97
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 81.18
Mean single sequence MFE -23.40
Consensus MFE -18.38
Energy contribution -18.30
Covariance contribution -0.08
Combinations/Pair 1.25
Mean z-score -1.34
Structure conservation index 0.79
SVM decision value 0.23
SVM RNA-class probability 0.646331
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20737998 97 - 27905053
-AA-AAAGCAGAUGGAGGGGCUGAGGGCGGAAGACCCUAAAA-AAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUGCGCAUUAAAAGUAAACAGUUA
-..-..............((((((((((....).))))....-..........((.((((....)))).))..(((((........)))))...))))). ( -24.50)
>DroSec_CAF1 34239 97 - 1
-AA-AAAGCGGAUGGAGGGGCUGAGGGCGGAAGACCCUAAAA-AAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUGCGCAUUAAAAGUAAACAGUUA
-..-...(((.(.((....(((.....(....).((((....-...)))))))((.((((....)))).))...)).).))).................. ( -24.50)
>DroSim_CAF1 35249 98 - 1
-AA-AAAGGGGAUGGAGGGGCUGAGGGCGGAAGACCCUAAAAAAAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUGCGCAUUAAAAGUAAACAGUUA
-..-..............((((((((((....).))))...............((.((((....)))).))..(((((........)))))...))))). ( -24.50)
>DroEre_CAF1 39505 96 - 1
-AAAAAAGCUGAUGGAGGGGCUGAGGGCGGAAGACCCUAAA---AAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUGCGCAUUAAAAGUAAACAGUUA
-.....(((((.....((.(((((((((....).)))....---......(((...)))....))))).))..(((((........)))))...))))). ( -26.70)
>DroYak_CAF1 36221 99 - 1
CAAAAAUACUGAUGAAGGGGCUGAGGGCGGAAGACUCUAAAA-AAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUGCGCAUUAAAAGUAAACAGUUA
.......((((.....((.(((((((((....).))).....-.......(((...)))....))))).))..(((((........)))))...)))).. ( -22.10)
>DroAna_CAF1 35193 76 - 1
---------------AGGGGCAGAGGGCGGGACUUGG-------CUGGGAGGAGAGGUCGAAGACGACGUCGG-C-UUCGGCGUUAAAAGUAAAUAGUUA
---------------....((.....))..((((..(-------((..((.(.((((((((........))))-)-)))..).))...)))....)))). ( -18.10)
>consensus
_AA_AAAGCGGAUGGAGGGGCUGAGGGCGGAAGACCCUAAAA_AAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUGCGCAUUAAAAGUAAACAGUUA
..................(((((...(((.(((.((((........))))...((.((((....)))).))....))).))).(((....))).))))). (-18.38 = -18.30 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,738,019 – 20,738,115
Length 96
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 79.62
Mean single sequence MFE -30.33
Consensus MFE -21.43
Energy contribution -21.05
Covariance contribution -0.38
Combinations/Pair 1.33
Mean z-score -1.54
Structure conservation index 0.71
SVM decision value 0.57
SVM RNA-class probability 0.786838
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20738019 96 - 27905053
UCAAUUGGCAAUGGG-CCCCC-AA-AAAGCAGAUGGAGGGGCUGAGGGCGGAAGACCCUAAAA-AAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUG
....(((((.....(-(((((-..-..(((..........))).(((((....).))))....-....))))))...((((....)))))))))...... ( -36.40)
>DroSec_CAF1 34260 96 - 1
UCAAUUGGUAAUGGG-CCCCC-AA-AAAGCGGAUGGAGGGGCUGAGGGCGGAAGACCCUAAAA-AAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUG
..............(-(((((-..-..(((..........))).(((((....).))))....-....))))))((.((((....)))).))........ ( -34.40)
>DroSim_CAF1 35270 97 - 1
UCAAUUGGUAAUGGG-CCCCC-AA-AAAGGGGAUGGAGGGGCUGAGGGCGGAAGACCCUAAAAAAAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUG
..............(-(((((-..-.........((.....)).(((((....).)))).........))))))((.((((....)))).))........ ( -31.50)
>DroEre_CAF1 39526 95 - 1
UCAAUUGGUAAUGGG-CCCCU-AAAAAAGCUGAUGGAGGGGCUGAGGGCGGAAGACCCUAAA---AAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUG
..............(-(((((-.....((((........)))).(((((....).))))...---...))))))((.((((....)))).))........ ( -33.50)
>DroYak_CAF1 36242 99 - 1
UCAAUUGGUAAUGGGGCCCCUCAAAAAUACUGAUGAAGGGGCUGAGGGCGGAAGACUCUAAAA-AAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUG
..............(((((((((..........)).))))))).(((((....).))))....-...((((...((.((((....)))).))...)))). ( -28.10)
>DroAna_CAF1 35214 74 - 1
UCAAUUGGUAAUAGG-CGUC----------------AGGGGCAGAGGGCGGGACUUGG-------CUGGGAGGAGAGGUCGAAGACGACGUCGG-C-UUC
......(((....((-((((----------------....((.....))..(((((..-------((....))..)))))......)))))).)-)-).. ( -18.10)
>consensus
UCAAUUGGUAAUGGG_CCCCC_AA_AAAGCGGAUGGAGGGGCUGAGGGCGGAAGACCCUAAAA_AAAAGGGGGCGGGGCCGGGGUCGGCGUCAAACUUUG
....((.((..(.((.((((.................)))))).)..)).))...((((........))))...((.((((....)))).))........ (-21.43 = -21.05 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:04 2006