Locus 8190

Sequence ID 3L_DroMel_CAF1
Location 21,539,816 – 21,539,938
Length 122
Max. P 0.992050
window13401 window13402 window13403

overview

Window 1

Location 21,539,816 – 21,539,908
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.99
Mean single sequence MFE -20.33
Consensus MFE -13.90
Energy contribution -14.10
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -1.41
Structure conservation index 0.68
SVM decision value 0.41
SVM RNA-class probability 0.727176
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21539816 92 - 23771897
---------CUCCAUUAUUAAUUGUGCGAUUGGAAACUCU-GGUUUUCAAUCACAUGAGUUUCAGAACCUUAGCCCAUUGUCUGCCAUUGCGA------------------GACAUGAAU
---------............(..((.((((((((((...-.)))))))))).))..).................(((.((((((....)).)------------------))))))... ( -21.60)
>DroPse_CAF1 40101 111 - 1
---------CUUUAUUAUUAAUUGUUCGAUUGGAAACUCUUAGUUUUCAAUCACAUGAAACUCAGAAUUAUACUCCAUUGUUUGCUAUUGCUAUUGCUAUUGCUUUUGCCCGACAUGAAU
---------..................((((((((((.....)))))))))).((((.....(((((....((......))..((....((....))....))))))).....))))... ( -18.40)
>DroEre_CAF1 29101 92 - 1
---------CUCCAUUAUUAAUUGUGCGAUUGGAAACUCU-GGUUUUCAAUCACAUGAGUUUCAGAACUUUAGCCCAUUGUCUGCCAUUGCGA------------------GACAUGAAU
---------............(..((.((((((((((...-.)))))))))).))..).................(((.((((((....)).)------------------))))))... ( -21.60)
>DroYak_CAF1 29439 92 - 1
---------CUCCAUUAUUAAUUGUGCGAUUGGAAACUCU-GGUUUUCAAUCACAUGAGUUUCAGAACUUUAGCCCAUUGUCUGCCAUUGCGA------------------GACAUGAAU
---------............(..((.((((((((((...-.)))))))))).))..).................(((.((((((....)).)------------------))))))... ( -21.60)
>DroAna_CAF1 12740 102 - 1
UGUAUUGCUGUCUAUUAUUAAUUGUGCGAUUGGAAACUCUUGGUUUUCAAUCACAUGAAAUUCAGAAUUUUACUCCAUUGUUUGUUAUUGCCA------------------GACAUGAAU
.(((...(((...(((.....(..((.((((((((((.....)))))))))).))..)))).))).....)))..(((.(((((.......))------------------))))))... ( -20.40)
>DroPer_CAF1 49209 111 - 1
---------CUUUAUUAUUAAUUGUUCGAUUGGAAACUCUUAGUUUUCAAUCACAUGAAACUCAGAAUUAUACUCCAUUGUUUGCUAUUGCUAUUGCUAUUGCUUUUGCCCGACAUGAAU
---------..................((((((((((.....)))))))))).((((.....(((((....((......))..((....((....))....))))))).....))))... ( -18.40)
>consensus
_________CUCCAUUAUUAAUUGUGCGAUUGGAAACUCU_GGUUUUCAAUCACAUGAAAUUCAGAACUUUACCCCAUUGUCUGCCAUUGCGA__________________GACAUGAAU
.....................(..((.((((((((((.....)))))))))).))..).........................((....))............................. (-13.90 = -14.10 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,539,838 – 21,539,938
Length 100
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 97.81
Mean single sequence MFE -18.86
Consensus MFE -16.33
Energy contribution -16.93
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.87
SVM decision value 2.30
SVM RNA-class probability 0.992050
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21539838 100 + 23771897
CAAUGGGCUAAGGUUCUGAAACUCAUGUGAUUGAAAACCAGAGUUUCCAAUCGCACAAUUAAUAAUGGAGAAAAAAG-CCAUGGCAAAAUAAAUAAAUAAA
......((((.((((......(((.((((((((.((((....)))).))))))))((........))))).....))-)).))))................ ( -21.00)
>DroSec_CAF1 11321 100 + 1
CAAUGGGCUAAGGUUCUGAAACUCAUGUGAUUGAAAACCAGAGUUUCCAAUCGCACAAUUAAUAAUGGAGAAAAAAC-CCAUGGCAAAAUAAAUAAAUAAA
......((((.((((......(((.((((((((.((((....)))).))))))))((........)))))....)))-)..))))................ ( -18.80)
>DroSim_CAF1 10446 99 + 1
CAAUG-GCUAAGGUUCUGAAACUCAUGUGAUUGAAAACCAGAGUUUCCAAUCGCACAAUUAAUAAUGGAGAAAAAAC-CCAUGGCAAAAUAAAUAAAUAAA
.....-((((.((((......(((.((((((((.((((....)))).))))))))((........)))))....)))-)..))))................ ( -18.80)
>DroEre_CAF1 29123 100 + 1
CAAUGGGCUAAAGUUCUGAAACUCAUGUGAUUGAAAACCAGAGUUUCCAAUCGCACAAUUAAUAAUGGAGAAAAAAC-CCAUGGCAAAAUAAAUAAAUAAA
..(((((......((((........((((((((.((((....)))).))))))))((........)).))))....)-))))................... ( -18.30)
>DroYak_CAF1 29461 101 + 1
CAAUGGGCUAAAGUUCUGAAACUCAUGUGAUUGAAAACCAGAGUUUCCAAUCGCACAAUUAAUAAUGGAGAAAAAACGCCACGGCAAAAUAAAUAAAUAAA
.....(((.....((((........((((((((.((((....)))).))))))))((........)).)))).....)))..................... ( -17.40)
>consensus
CAAUGGGCUAAGGUUCUGAAACUCAUGUGAUUGAAAACCAGAGUUUCCAAUCGCACAAUUAAUAAUGGAGAAAAAAC_CCAUGGCAAAAUAAAUAAAUAAA
......((((.((........(((.((((((((.((((....)))).))))))))((........)))))........)).))))................ (-16.33 = -16.93 +   0.60)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,539,838 – 21,539,938
Length 100
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 97.81
Mean single sequence MFE -21.82
Consensus MFE -17.54
Energy contribution -17.58
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.59
Structure conservation index 0.80
SVM decision value 1.14
SVM RNA-class probability 0.921027
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21539838 100 - 23771897
UUUAUUUAUUUAUUUUGCCAUGG-CUUUUUUCUCCAUUAUUAAUUGUGCGAUUGGAAACUCUGGUUUUCAAUCACAUGAGUUUCAGAACCUUAGCCCAUUG
.....................((-((...((((..........(..((.((((((((((....)))))))))).))..).....))))....))))..... ( -20.36)
>DroSec_CAF1 11321 100 - 1
UUUAUUUAUUUAUUUUGCCAUGG-GUUUUUUCUCCAUUAUUAAUUGUGCGAUUGGAAACUCUGGUUUUCAAUCACAUGAGUUUCAGAACCUUAGCCCAUUG
...................((((-(((..((((..........(..((.((((((((((....)))))))))).))..).....))))....))))))).. ( -23.26)
>DroSim_CAF1 10446 99 - 1
UUUAUUUAUUUAUUUUGCCAUGG-GUUUUUUCUCCAUUAUUAAUUGUGCGAUUGGAAACUCUGGUUUUCAAUCACAUGAGUUUCAGAACCUUAGC-CAUUG
................((...((-(((((..(((...........(((.((((((((((....)))))))))).))))))....)))))))..))-..... ( -21.70)
>DroEre_CAF1 29123 100 - 1
UUUAUUUAUUUAUUUUGCCAUGG-GUUUUUUCUCCAUUAUUAAUUGUGCGAUUGGAAACUCUGGUUUUCAAUCACAUGAGUUUCAGAACUUUAGCCCAUUG
...................((((-(((..((((..........(..((.((((((((((....)))))))))).))..).....))))....))))))).. ( -23.26)
>DroYak_CAF1 29461 101 - 1
UUUAUUUAUUUAUUUUGCCGUGGCGUUUUUUCUCCAUUAUUAAUUGUGCGAUUGGAAACUCUGGUUUUCAAUCACAUGAGUUUCAGAACUUUAGCCCAUUG
...................(.(((.....................(((.((((((((((....)))))))))).)))(((((....)))))..)))).... ( -20.50)
>consensus
UUUAUUUAUUUAUUUUGCCAUGG_GUUUUUUCUCCAUUAUUAAUUGUGCGAUUGGAAACUCUGGUUUUCAAUCACAUGAGUUUCAGAACCUUAGCCCAUUG
............(((((..((((.(......).))))......(..((.((((((((((....)))))))))).))..)....)))))............. (-17.54 = -17.58 +   0.04)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:01 2006