Locus 2508

Sequence ID 2L_DroMel_CAF1
Location 6,913,648 – 6,913,756
Length 108
Max. P 0.798754
window4011 window4012

overview

Window 1

Location 6,913,648 – 6,913,756
Length 108
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 79.26
Mean single sequence MFE -37.62
Consensus MFE -23.92
Energy contribution -24.95
Covariance contribution 1.03
Combinations/Pair 1.30
Mean z-score -1.77
Structure conservation index 0.64
SVM decision value 0.61
SVM RNA-class probability 0.798754
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6913648 108 + 22407834
CACCUUUUGGCAUGGCGGCGACAUGGACACGUCCCCGUCGCCGCCUUCUUUGCCUAUCUUACUGUCCAGCUGCUGCUC-CUCACCGGAGGAUAGCUUCGGCCGCUGCUG
........((((.(((((((((..(((....)))..))))))))).....))))............((((.((...((-(((....)))))..((....)).)).)))) ( -47.00)
>DroSec_CAF1 1898 108 + 1
CACCUUUUGGCAUGGCGGCGACAUGGACACGUCUCCGUCGCCACCUUCUUCGCCUAACUUACUCCCCAGCUGCUGCUC-CUCGCCGGAGGAUAGCUUCGGCCGCUGCUG
........(((..((.((((((..(((....)))..)))))).))......)))............((((.((...((-(((....)))))..((....)).)).)))) ( -37.80)
>DroSim_CAF1 1914 108 + 1
CACCUUUUGGCAUGGCGGCGACAUGGACACGUCUCCGUCGCCACCUCCUUCGCCUAACUUACUCCCCAGCUGCUGCUC-CUCGCCGGAGGAUAGCUUCGGCCGCUGCUG
........(((..((.((((((..(((....)))..)))))).))......)))............((((.((...((-(((....)))))..((....)).)).)))) ( -37.80)
>DroEre_CAF1 1950 108 + 1
CACCUUUUGGCAUGGCGGCGACAUGGACACGUCCGCGUCGCCGCCUCCUUCGCCAAUCUUACUGUCCAGCUGCUGCUC-CUGGACGGAGGAUAGCUUCUGCCGUUGCUG
........((((.(((((((((.((((....)))).)))))))))......((..(((((.((((((((.........-))))))))))))).))...))))....... ( -48.70)
>DroYak_CAF1 1901 108 + 1
CACCUUCUGGCAUGGCGGCGACAUGGACACGUCCCCGUCGCCGACUCCUUCGCCCAUCUUACUGCCCAGCUGCUGCUC-CUCGACAAAGGAUAACUUCUGCCGCUGCUG
........((((.(((((((((..(((....)))..))))))((.....)))))........))))((((.((.((((-((......))))........)).)).)))) ( -33.50)
>DroAna_CAF1 1790 90 + 1
CACCUUCUGGCACGGCGGCGACAUGGAAACAUCCCCAUUCCCAG------------AGGUACU----AGUG---GCUCCCUGCUCAAUGGACAUCUUUUUCUUUGGUUG
.((((.((((...((.((....(((....)))))))....))))------------)))).((----(.((---((.....)).)).)))................... ( -20.90)
>consensus
CACCUUUUGGCAUGGCGGCGACAUGGACACGUCCCCGUCGCCACCUCCUUCGCCUAACUUACUGCCCAGCUGCUGCUC_CUCGCCGGAGGAUAGCUUCGGCCGCUGCUG
........((((((((((((((..(((....)))..))))))...(((((((...............(((....))).......)))))))........)))).)))). (-23.92 = -24.95 +   1.03)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,913,648 – 6,913,756
Length 108
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 79.26
Mean single sequence MFE -40.53
Consensus MFE -26.19
Energy contribution -27.80
Covariance contribution 1.61
Combinations/Pair 1.19
Mean z-score -1.30
Structure conservation index 0.65
SVM decision value 0.01
SVM RNA-class probability 0.537996
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6913648 108 - 22407834
CAGCAGCGGCCGAAGCUAUCCUCCGGUGAG-GAGCAGCAGCUGGACAGUAAGAUAGGCAAAGAAGGCGGCGACGGGGACGUGUCCAUGUCGCCGCCAUGCCAAAAGGUG
((((.(((((....))).(((((....)))-))...)).))))............((((.....((((((((((.(((....))).)))))))))).))))........ ( -46.60)
>DroSec_CAF1 1898 108 - 1
CAGCAGCGGCCGAAGCUAUCCUCCGGCGAG-GAGCAGCAGCUGGGGAGUAAGUUAGGCGAAGAAGGUGGCGACGGAGACGUGUCCAUGUCGCCGCCAUGCCAAAAGGUG
..(((...(((..((((.(((.(((((...-........))))))))...)))).)))......((((((((((..((....))..)))))))))).)))......... ( -44.10)
>DroSim_CAF1 1914 108 - 1
CAGCAGCGGCCGAAGCUAUCCUCCGGCGAG-GAGCAGCAGCUGGGGAGUAAGUUAGGCGAAGGAGGUGGCGACGGAGACGUGUCCAUGUCGCCGCCAUGCCAAAAGGUG
..(((...(((..((((.(((.(((((...-........))))))))...)))).)))......((((((((((..((....))..)))))))))).)))......... ( -44.10)
>DroEre_CAF1 1950 108 - 1
CAGCAACGGCAGAAGCUAUCCUCCGUCCAG-GAGCAGCAGCUGGACAGUAAGAUUGGCGAAGGAGGCGGCGACGCGGACGUGUCCAUGUCGCCGCCAUGCCAAAAGGUG
.......((((...((((((..(.((((((-.........)))))).)...)).))))......((((((((((.(((....))).)))))))))).))))........ ( -46.60)
>DroYak_CAF1 1901 108 - 1
CAGCAGCGGCAGAAGUUAUCCUUUGUCGAG-GAGCAGCAGCUGGGCAGUAAGAUGGGCGAAGGAGUCGGCGACGGGGACGUGUCCAUGUCGCCGCCAUGCCAGAAGGUG
..(((..(((.((.....(((((((((.(.-..((.((......)).))....).))))))))).))(((((((.(((....))).)))))))))).)))......... ( -42.10)
>DroAna_CAF1 1790 90 - 1
CAACCAAAGAAAAAGAUGUCCAUUGAGCAGGGAGC---CACU----AGUACCU------------CUGGGAAUGGGGAUGUUUCCAUGUCGCCGCCGUGCCAGAAGGUG
..(((...((........))..(((.(((.((...---..((----((.....------------))))....((.(((((....))))).)).)).))))))..))). ( -19.70)
>consensus
CAGCAGCGGCAGAAGCUAUCCUCCGGCGAG_GAGCAGCAGCUGGGCAGUAAGAUAGGCGAAGGAGGCGGCGACGGGGACGUGUCCAUGUCGCCGCCAUGCCAAAAGGUG
......((((.(..(((...(((....)))..)))..).)))).....................((((((((((.(((....))).))))))))))..(((....))). (-26.19 = -27.80 +   1.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:32 2006