Locus 4818

Sequence ID 2L_DroMel_CAF1
Location 13,741,004 – 13,741,190
Length 186
Max. P 0.713854
window7626 window7627 window7628

overview

Window 6

Location 13,741,004 – 13,741,097
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.08
Mean single sequence MFE -26.90
Consensus MFE -21.15
Energy contribution -21.15
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -0.99
Structure conservation index 0.79
SVM decision value 0.10
SVM RNA-class probability 0.581316
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13741004 93 + 22407834
UCAAAGCGGCC---------------------------AACUCCACCCACUCCACCCACACAUUGGCGUGUGGUGAGGCGUGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUG
.......(((.---------------------------.....(((((((.(((.........))).))).))))((((((((.(((....)))..))))))))......)))....... ( -28.00)
>DroSec_CAF1 4785 84 + 1
UCAAAGCCACC---------------------------C---------ACUCCGCCCACACAUUGGCGUGUGGUGAGGCGUGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUG
.....((((((---------------------------.---------((..((((........)))).))))))((((((((.(((....)))..)))))))))).............. ( -24.50)
>DroAna_CAF1 17000 82 + 1
UCAAGGAC---------------------------------CUCG-----CCAGCUCACACUUUGGCGUGUGGUGAGGCGUGUUAUCGUCGGAUUUGCAUGCUUGCACAAGUCAUAAAUG
.....(((---------------------------------(.((-----((((........)))))).)..(((((((((((.(((....)))..)))))))).)))..)))....... ( -25.20)
>DroSim_CAF1 6443 93 + 1
UCAAAGCCACC---------------------------CACUCUACCCACUCCGCCCACACAUUGGCGUGUGGUGAGGCGUGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUG
.....((....---------------------------..(((...((((..((((........)))).)))).)))((((((.(((....)))..))))))..)).............. ( -24.80)
>DroEre_CAF1 6307 93 + 1
UCAAAACCGUC---------------------------CACUCCGCCCACUACGCCCACACAUUGGCGUGUGGUGAGGCGUGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUG
.((((.(((.(---------------------------....((((((((((((((((.....))).)))))))).)))).).....).))).))))...((((....))))........ ( -31.40)
>DroYak_CAF1 6533 120 + 1
UCAAAACCACCCACUCCGCCCACUCCGCCCACUCCGCCCACUCCGCCCACUUCGCCCACACAUUGGCGUGUGGUGAGGCGUGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUG
..........................((....(((((.....(((((((((.((((((.....))).))).)))).)))).).....).))))...))..((((....))))........ ( -27.50)
>consensus
UCAAAGCCACC___________________________CACUCCGCCCACUCCGCCCACACAUUGGCGUGUGGUGAGGCGUGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUG
........................................................(((((......)))))(((((((((((.(((....)))..)))))))).)))............ (-21.15 = -21.15 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,741,057 – 13,741,155
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.29
Mean single sequence MFE -36.18
Consensus MFE -23.09
Energy contribution -22.52
Covariance contribution -0.58
Combinations/Pair 1.29
Mean z-score -2.23
Structure conservation index 0.64
SVM decision value 0.38
SVM RNA-class probability 0.713854
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13741057 98 + 22407834
UGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUGUCAAUUGGCAUGGCA---------GGCGGAAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGU-------------
.....((.(((((......(((((((.((.((((...........)))).)))))---------))))....))))).))(((....)))(((....))).......------------- ( -34.80)
>DroSec_CAF1 4829 98 + 1
UGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUGUCAAUUGGCAUGGCA---------GGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGC-------------
.....((.(((((.((...(((((((.((.((((...........)))).)))))---------)))).)).))))).))(((....)))(((....))).......------------- ( -35.00)
>DroAna_CAF1 17042 115 + 1
UGUUAUCGUCGGAUUUGCAUGCUUGCACAAGUCAUAAAUGUCAAUUGGUGGGGCAACUCCAGCAGCCGG-----CGAAGGGGCAAGUGGUCGGCCAUCUACGUAAGUGGCAAGUAUGUGG
..............(..(((((((((....(((.....((((..(((.((((....).))).)))..))-----))....)))..((((....)))).(((....))))))))))))..) ( -35.60)
>DroSim_CAF1 6496 98 + 1
UGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUGUCAAUUGGCAUGGCA---------GGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGU-------------
.....((.(((((.((...(((((((.((.((((...........)))).)))))---------)))).)).))))).))(((....)))(((....))).......------------- ( -35.00)
>DroEre_CAF1 6360 111 + 1
UGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUGUCAAUUGGCAUGGCA---------AGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGUGCCGAGGAAAUGG
.....((.(((((((((...((((((.((.((((...........)))).)))))---------)))(...(((((...((((....)))).)))))...).))))).)))).))..... ( -38.50)
>DroYak_CAF1 6613 111 + 1
UGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUGUCAAUUGGCAUGGCA---------GGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGUGCCGAGGAAAUGG
.....((.(((((((((...((((((.((.((((...........)))).)))))---------)))(...(((((...((((....)))).)))))...).))))).)))).))..... ( -38.20)
>consensus
UGUUAUCGUCGGAUUUGCAUGCUUGCACAAGCCAUAAAUGUCAAUUGGCAUGGCA_________GGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGU_____________
......(.(((((..((((....))))...((((....((((....))))))))..................))))).)((((....))))((....))..................... (-23.09 = -22.52 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,741,097 – 13,741,190
Length 93
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 88.16
Mean single sequence MFE -31.02
Consensus MFE -26.34
Energy contribution -26.74
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.85
SVM decision value -0.00
SVM RNA-class probability 0.531410
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13741097 93 + 22407834
UCAAUUGGCAUGGCAGGCGGAAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGU------------------GCCCCAGCUGGUGUCAUAAUUACAGAUGACUAUCA
...((..((.(((..((((...........((((....))))((....)).......)------------------))))))))..))(((((........)))))..... ( -28.00)
>DroSec_CAF1 4869 93 + 1
UCAAUUGGCAUGGCAGGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGC------------------GCCCCAGCUGGUGUCAUAAUUACAGAUGACUAUCA
...((..((.(((..((((...........((((....))))((....)).......)------------------))))))))..))(((((........)))))..... ( -30.00)
>DroSim_CAF1 6536 93 + 1
UCAAUUGGCAUGGCAGGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGU------------------GCCCCAGCUGGUGUCAUAAUUACAGAUGACUAUCA
(((.(((..((((((((((((.(((((...((((....)))).)))))((((....))------------------))))).)))..)))))).....))).)))...... ( -29.70)
>DroEre_CAF1 6400 111 + 1
UCAAUUGGCAUGGCAAGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGUGCCGAGGAAAUGGAAGGCGCCCCAGCUGGCGUCAUAAUUACAGAUGACUAUCA
(((.(((.(((..(...(((.((((.....((((....))))((....))....)))).)))..)..)))...((((((......)))))).......))).)))...... ( -33.10)
>DroYak_CAF1 6653 111 + 1
UCAAUUGGCAUGGCAGGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGUGCCGAGGAAAUGGAAAGCGCCCCAGCUGGUGUCAUAAUUACAGAUGACUAUCA
...((..((.(((..((((...((((..(.((((....)))).)....((((....))))..........)))).)))))))))..))(((((........)))))..... ( -34.30)
>consensus
UCAAUUGGCAUGGCAGGCGGGAUUUCGAGGAGCCAAGUGGCUGCGAAAGCACAUAAGU__________________GCCCCAGCUGGUGUCAUAAUUACAGAUGACUAUCA
...((..((.(((..(((............((((....))))((....))..........................))))))))..))(((((........)))))..... (-26.34 = -26.74 +   0.40)

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 11:28:14 2006