Locus 7765

Sequence ID 3R_DroMel_CAF1
Location 20,807,454 – 20,807,585
Length 131
Max. P 0.999736
window12525 window12526

overview

Window 5

Location 20,807,454 – 20,807,546
Length 92
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 81.54
Mean single sequence MFE -35.28
Consensus MFE -26.19
Energy contribution -27.08
Covariance contribution 0.89
Combinations/Pair 1.20
Mean z-score -1.61
Structure conservation index 0.74
SVM decision value 0.40
SVM RNA-class probability 0.721354
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20807454 92 - 27905053
CU-------GAGCACUGAGAACCGAGAACGGA-UAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUGAUGCUGGCGCGACUCC-GCGUCCUCCGACC
..-------.((((.......(((....))).-...((((((((((((((....))))))))))))))....))))((((((....)-)))))........ ( -38.50)
>DroPse_CAF1 17449 73 - 1
----------------------------CGGAUUCGCCGUCGUCGCCUUCCACCGAGGGUGAUGACUGAUGAUGCUGUCGCGUCUACAGUAUUUUCCGUCU
----------------------------((((......((((((((((((....))))))))))))....((((((((.......)))))))).))))... ( -29.50)
>DroSec_CAF1 23056 92 - 1
CU-------GAGCACUGAGAACCGAGAACGGA-UAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUGAUGCUGGCGCGUCUCC-GCGUCCUCCGACC
..-------.((((.......(((....))).-...((((((((((((((....))))))))))))))....))))((((((....)-)))))........ ( -38.00)
>DroSim_CAF1 23007 92 - 1
CU-------GAGCACUGAGAACCGAGAACGGA-UAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUGAUGCUGGCGCGUCUCC-GCGUCCUCCGACC
..-------.((((.......(((....))).-...((((((((((((((....))))))))))))))....))))((((((....)-)))))........ ( -38.00)
>DroEre_CAF1 20735 89 - 1
CU-------GAGAACUGAGAACCGAGAACGGA-UAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUGAUGCUGGCGCGACUCG-UCCUC---CGACC
..-------(((.((.(((..(((....))).-...((((((((((((((....))))))))))))))....(((....))).))))-).)))---..... ( -33.00)
>DroYak_CAF1 16146 99 - 1
CUGAACACUGAGCACUGAGAACCGAGAACGGA-UAGCAGUCGUCGCCUUUCAGCGAGGGUGAUGACUGAUGAUGCUGGCGCGACUCG-UCCUCCGCCGACC
..........((((.......(((....))).-...((((((((((((((....))))))))))))))....))))((((.((....-...)))))).... ( -34.70)
>consensus
CU_______GAGCACUGAGAACCGAGAACGGA_UAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUGAUGCUGGCGCGACUCC_GCGUCCUCCGACC
............................((((....((((((((((((((....))))))))))))))..(((((.((.......)).))))).))))... (-26.19 = -27.08 +   0.89)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,807,483 – 20,807,585
Length 102
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 94.75
Mean single sequence MFE -35.44
Consensus MFE -32.66
Energy contribution -32.50
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.42
Structure conservation index 0.92
SVM decision value 3.97
SVM RNA-class probability 0.999736
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20807483 102 - 27905053
AAUCCCGUUUGCAACCCUCGAAAAACCGAGAAUCGAGAACU-------GAGCACUGAGAACCGAGAACGGAUAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUG
....((((((......((((......))))..(((.(..((-------.(....).))..))))))))))....((((((((((((((....))))))))))))))... ( -36.20)
>DroSec_CAF1 23085 102 - 1
AAUCCCGUUUGCAACCCUCGAAAAACCGAGAAUCGAGAACU-------GAGCACUGAGAACCGAGAACGGAUAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUG
....((((((......((((......))))..(((.(..((-------.(....).))..))))))))))....((((((((((((((....))))))))))))))... ( -36.20)
>DroSim_CAF1 23036 102 - 1
AAUCCCGUUUGCAACCCUCGAAAUAGCGAGAAUCGAGAACU-------GAGCACUGAGAACCGAGAACGGAUAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUG
....((((((......((((......))))..(((.(..((-------.(....).))..))))))))))....((((((((((((((....))))))))))))))... ( -36.00)
>DroEre_CAF1 20761 101 - 1
AAUCCCGUUUGCAACCCUCGAAAAGC-GAGAAUCGAGAACU-------GAGAACUGAGAACCGAGAACGGAUAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUG
....((((((......((((.....)-)))..(((.(..((-------.(....).))..))))))))))....((((((((((((((....))))))))))))))... ( -35.80)
>DroYak_CAF1 16175 109 - 1
AAUCCCGUUUGCAACCCUCGAAAAACUGAGAAUCGAGAACUGAACACUGAGCACUGAGAACCGAGAACGGAUAGCAGUCGUCGCCUUUCAGCGAGGGUGAUGACUGAUG
....(((((..(....(((((...........))))).........((.(....).))....)..)))))....((((((((((((((....))))))))))))))... ( -33.00)
>consensus
AAUCCCGUUUGCAACCCUCGAAAAACCGAGAAUCGAGAACU_______GAGCACUGAGAACCGAGAACGGAUAGCAGUCGUCGCCUUCCAGCGAGGGUGAUGACUGAUG
....(((((..(....(((((...........)))))..((........))...........)..)))))....((((((((((((((....))))))))))))))... (-32.66 = -32.50 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:11 2006