Locus 6543

Sequence ID 3L_DroMel_CAF1
Location 17,291,883 – 17,292,117
Length 234
Max. P 0.984925
window10641 window10642 window10643

overview

Window 1

Location 17,291,883 – 17,291,997
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.82
Mean single sequence MFE -18.20
Consensus MFE -16.36
Energy contribution -16.37
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.90
SVM decision value 0.22
SVM RNA-class probability 0.639736
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17291883 114 + 23771897
CGACCCACCUUGCAACACCACCAUUUCCAUGCCACC------CCUUCCAUUGGCAGCACAAUGUGCGUAUAAAUAACGGAUUUCCUGUUAUAAAAUAUUUGUAACGACAUUUUCCCGAUU
.......(.((((((.(((((.(((....(((((..------........)))))....)))))).))....(((((((.....))))))).......)))))).).............. ( -17.70)
>DroSec_CAF1 175704 112 + 1
--ACCCACCUUGCAACACCACCAUCUCCAUGCCACC------CCAUCCACUGGCAGCACAAUGUGCGUAUAAAUAACGGAUUUCCUGUUAUAAAAUAUUUGUAACGACAUUUUCCCGAUU
--.....(.((((((..............(((((..------........)))))((((...))))......(((((((.....))))))).......)))))).).............. ( -17.60)
>DroSim_CAF1 171922 112 + 1
--ACCCACCUUGCAACGCCACCAUCUCCAUGCCACC------CCAUCCACUGGCAGCACAAUGUGCGUAUAAAUAACGGAUUUCCUGUUAUAAAAUAUUUGUAACGACAUUUUCCCGAUU
--.....(.(((((((((...(((.....(((((..------........))))).....))).))))....(((((((.....)))))))........))))).).............. ( -19.10)
>DroYak_CAF1 184437 118 + 1
--ACCCACCUUGCCACACCCCCAUUUCCAUGCCACCAUGCCACCAUCCACUGGCAGCACAAUGUGCGUAUAAAUAACGGAUUUCCUGUUAUAAAAUAUUUGUAACGACAUUUUCCCGAUU
--..........................((((.....(((((........)))))((((...)))))))).......(((.....((((((((.....))))))))......)))..... ( -18.40)
>consensus
__ACCCACCUUGCAACACCACCAUCUCCAUGCCACC______CCAUCCACUGGCAGCACAAUGUGCGUAUAAAUAACGGAUUUCCUGUUAUAAAAUAUUUGUAACGACAUUUUCCCGAUU
..........(((................(((((................)))))((((...)))))))........(((.....((((((((.....))))))))......)))..... (-16.36 = -16.37 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,291,997 – 17,292,117
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.42
Mean single sequence MFE -28.18
Consensus MFE -26.67
Energy contribution -26.18
Covariance contribution -0.50
Combinations/Pair 1.18
Mean z-score -2.17
Structure conservation index 0.95
SVM decision value 1.99
SVM RNA-class probability 0.984925
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17291997 120 + 23771897
UAUGUAUCCACACAUAUCCACACAGACGGAUUAUGCAUUCUGGCAUCAGUGCUCAAGAUACUAGCAUUUCUUCUUUGAAAAAUGUUUUGAAGUUUGUAGCGUAGGAUGUGGAAAAAUCUA
......((((((....((((((((((((.(((((((......)))).))).)((((((((......((((......))))..)))))))).))))))...)).)))))))))........ ( -26.10)
>DroSec_CAF1 175816 120 + 1
UAUGUAUCCACACAUAUCCACACAGACGGAUUAUGCAUGCUGGCAUCAGUGCUCAAAAUACUAGCACUUCUUCUUUAAAAAAUGUUUUGAAGUUUAUGGCCCAGCAUGUGGAAAAAUCGA
......(((((.(((((((........))).)))).((((((((...((((((.........))))))....((((((((....))))))))......).))))))))))))........ ( -32.10)
>DroSim_CAF1 172034 120 + 1
UAUGUAUCCACACAUAUCCACACAGACGGAUUAUGCAUGCUGGCAUCAGUGCUCAAAAUACUAGCACUUCUUCUUUAAAAAAUGUUUUGAAGUUUAUGGCCCAGCAUGUGGAAAAAUCUA
......(((((.(((((((........))).)))).((((((((...((((((.........))))))....((((((((....))))))))......).))))))))))))........ ( -32.10)
>DroYak_CAF1 184555 120 + 1
UAUGUAUCCACACAUAUCCACACAAACGGAUUAUGCAUGCUGGCAUCCGUGCUCAAAAUACUAGCACUUUUCCUUUAAAAAAUGUUUUCAAGUGUACUGUAAGGCAUUUGGAAAAACCUA
.((((...((..(((((((........))).))))..))...))))..(((((.........))))).................(((((((((((........)))))))))))...... ( -22.40)
>consensus
UAUGUAUCCACACAUAUCCACACAGACGGAUUAUGCAUGCUGGCAUCAGUGCUCAAAAUACUAGCACUUCUUCUUUAAAAAAUGUUUUGAAGUUUAUGGCCCAGCAUGUGGAAAAAUCUA
......(((((.(((((((........))).)))).((((((((....(((((.........))))).....((((((((....))))))))......)).)))))))))))........ (-26.67 = -26.18 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,291,997 – 17,292,117
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.42
Mean single sequence MFE -30.28
Consensus MFE -22.36
Energy contribution -22.55
Covariance contribution 0.19
Combinations/Pair 1.23
Mean z-score -1.84
Structure conservation index 0.74
SVM decision value 0.24
SVM RNA-class probability 0.649399
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17291997 120 - 23771897
UAGAUUUUUCCACAUCCUACGCUACAAACUUCAAAACAUUUUUCAAAGAAGAAAUGCUAGUAUCUUGAGCACUGAUGCCAGAAUGCAUAAUCCGUCUGUGUGGAUAUGUGUGGAUACAUA
........(((((((.((((((.((...........(((((((......)))))))...((((..((.(((....)))))..)))).......))..))))))....)))))))...... ( -26.30)
>DroSec_CAF1 175816 120 - 1
UCGAUUUUUCCACAUGCUGGGCCAUAAACUUCAAAACAUUUUUUAAAGAAGAAGUGCUAGUAUUUUGAGCACUGAUGCCAGCAUGCAUAAUCCGUCUGUGUGGAUAUGUGUGGAUACAUA
........((((((((((((........((((...............)))).((((((.........))))))....)))))))(((((.((((......))))))))))))))...... ( -33.86)
>DroSim_CAF1 172034 120 - 1
UAGAUUUUUCCACAUGCUGGGCCAUAAACUUCAAAACAUUUUUUAAAGAAGAAGUGCUAGUAUUUUGAGCACUGAUGCCAGCAUGCAUAAUCCGUCUGUGUGGAUAUGUGUGGAUACAUA
........((((((((((((........((((...............)))).((((((.........))))))....)))))))(((((.((((......))))))))))))))...... ( -33.86)
>DroYak_CAF1 184555 120 - 1
UAGGUUUUUCCAAAUGCCUUACAGUACACUUGAAAACAUUUUUUAAAGGAAAAGUGCUAGUAUUUUGAGCACGGAUGCCAGCAUGCAUAAUCCGUUUGUGUGGAUAUGUGUGGAUACAUA
..(((...(((...(((.(((.(((((...(....)((((((((....))))))))...))))).)))))).))).)))..((((((((.((((......))))))))))))........ ( -27.10)
>consensus
UAGAUUUUUCCACAUGCUGGGCCAUAAACUUCAAAACAUUUUUUAAAGAAGAAGUGCUAGUAUUUUGAGCACUGAUGCCAGCAUGCAUAAUCCGUCUGUGUGGAUAUGUGUGGAUACAUA
........(((((((.((((((..............((((((((....))))))))...((((.(((.(((....)))))).))))...........))))))....)))))))...... (-22.36 = -22.55 +   0.19)

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 12:23:47 2006