Locus 6620

Sequence ID 3R_DroMel_CAF1
Location 17,422,350 – 17,422,454
Length 104
Max. P 0.999936
window10777 window10778

overview

Window 7

Location 17,422,350 – 17,422,454
Length 104
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 87.38
Mean single sequence MFE -23.06
Consensus MFE -22.38
Energy contribution -22.58
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.04
Structure conservation index 0.97
SVM decision value 4.67
SVM RNA-class probability 0.999936
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17422350 104 + 27905053
CCAGCAAAAGAAAAAUAUAAGAGAAAAACAAAAACAAUUUAUUCUAUAUGUACAACAUCUUGAGACGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUU
...............................................((((((((((......((.(((.((((((...)))))).))).)))))))))))).. ( -23.50)
>DroSec_CAF1 26300 91 + 1
CCGGCAAAAGAAAAA-------------AAAAAACAAUUUAUUCUAUAUGUACAACAUCUUGAGACGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUU
........((((.((-------------(........))).))))..((((((((((......((.(((.((((((...)))))).))).)))))))))))).. ( -24.20)
>DroSim_CAF1 23753 90 + 1
CCGGCAAAAGAAAAA--------------AAAAACAAUUUAUUCUAUAUGUACAACAUCUUGAGACGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUU
........((((.((--------------(.......))).))))..((((((((((......((.(((.((((((...)))))).))).)))))))))))).. ( -23.90)
>DroEre_CAF1 26049 87 + 1
CCACAAUAA-----------------AAAUAAAACAAUUUAUUCUAUAUGUACAACAUCUUGAGACGACCCCGCCGCUACGACGGCGUCAUCUGUUGUGCAUUU
.........-----------------.....................((((((((((...(((........(((((......))))))))..)))))))))).. ( -19.50)
>DroYak_CAF1 24062 94 + 1
CCAGCAAAAAAAAAA----------AGAAGAAAACAAUUUAUUCUAUAUGUACAACAUCUUGAGACGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUU
...............----------((((.(((....))).))))..((((((((((......((.(((.((((((...)))))).))).)))))))))))).. ( -24.20)
>consensus
CCAGCAAAAGAAAAA____________AAAAAAACAAUUUAUUCUAUAUGUACAACAUCUUGAGACGACCCCGUCGCUACGACGGCGUCAUCUGUUGUGCAUUU
...............................................((((((((((......((.(((.((((((...)))))).))).)))))))))))).. (-22.38 = -22.58 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,422,350 – 17,422,454
Length 104
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 87.38
Mean single sequence MFE -27.42
Consensus MFE -25.74
Energy contribution -25.58
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -2.60
Structure conservation index 0.94
SVM decision value 3.67
SVM RNA-class probability 0.999511
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17422350 104 - 27905053
AAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCGUCUCAAGAUGUUGUACAUAUAGAAUAAAUUGUUUUUGUUUUUCUCUUAUAUUUUUCUUUUGCUGG
....(((....(((((((.((((((...)))))).))))))).((((...((((.....((((((((.....)))))))).....))))....)))).)))... ( -28.40)
>DroSec_CAF1 26300 91 - 1
AAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCGUCUCAAGAUGUUGUACAUAUAGAAUAAAUUGUUUUUU-------------UUUUUCUUUUGCCGG
..(((.((((((((((((.((((((...)))))).))))))......)))))).)))..((((.(((........)-------------)).))))........ ( -26.70)
>DroSim_CAF1 23753 90 - 1
AAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCGUCUCAAGAUGUUGUACAUAUAGAAUAAAUUGUUUUU--------------UUUUUCUUUUGCCGG
..(((.((((((((((((.((((((...)))))).))))))......)))))).)))..((((.(((.......)--------------)).))))........ ( -26.40)
>DroEre_CAF1 26049 87 - 1
AAAUGCACAACAGAUGACGCCGUCGUAGCGGCGGGGUCGUCUCAAGAUGUUGUACAUAUAGAAUAAAUUGUUUUAUUU-----------------UUAUUGUGG
......((((((((((((.((((((...)))))).))))))......)))))).((((.((((((((....)))))))-----------------)...)))). ( -29.10)
>DroYak_CAF1 24062 94 - 1
AAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCGUCUCAAGAUGUUGUACAUAUAGAAUAAAUUGUUUUCUUCU----------UUUUUUUUUUGCUGG
..(((.((((((((((((.((((((...)))))).))))))......)))))).)))..((((.(((....))).))))----------............... ( -26.50)
>consensus
AAAUGCACAACAGAUGACGCCGUCGUAGCGACGGGGUCGUCUCAAGAUGUUGUACAUAUAGAAUAAAUUGUUUUUUU____________UUUUUCUUUUGCUGG
..(((.((((((((((((.((((((...)))))).))))))......)))))).)))............................................... (-25.74 = -25.58 +  -0.16)

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 12:26:05 2006