Locus 3175

Sequence ID 3L_DroMel_CAF1
Location 9,254,456 – 9,254,627
Length 171
Max. P 0.907843
window4950 window4951 window4952

overview

Window 0

Location 9,254,456 – 9,254,568
Length 112
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 77.78
Mean single sequence MFE -30.64
Consensus MFE -16.67
Energy contribution -17.12
Covariance contribution 0.45
Combinations/Pair 1.22
Mean z-score -2.00
Structure conservation index 0.54
SVM decision value 0.66
SVM RNA-class probability 0.814474
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9254456 112 + 23771897
CUACGAGUAUUA-----U-UAUGCAACCAA-UUUUUUUUUCUCCGUCCUGUUGCUGCAACACCAACGGUGGCAAAUGUUGCCGUAGAGUCGACAUCAGCUUUUCUGCUCUUGUCGAUGU
(((((.((((..-----.-.))))...(((-(...(((.((.((((..(((((...)))))...)))).)).))).)))).))))).(((((((..(((......)))..))))))).. ( -31.50)
>DroSec_CAF1 101271 111 + 1
CUACGAGUACUA-----U-UUUGCAACC-A-UUUUUUUUUCUCCGUCCUGUUGCUGCAACACCAACGGUGGCAAAUGUUGCCGUAGAGUCGACAGCAGCUUUUCUGCUCUUGUCGAUGU
(((((.(((.((-----(-((.((....-.-...........((((..(((((...)))))...))))..))))))).)))))))).((((((((.(((......))).)))))))).. ( -31.87)
>DroSim_CAF1 101646 113 + 1
CUACGAGUACUA-----U-UUUGCAACCCAUUUUUUUUUUCUCCGUUCUGUUGCUGCAACACCAACGGUGGCAAAUGUUGCCGUAGAGUCGACAGCAGCUUUUCUGCUCUUGUCGAUGU
(((((.(((.((-----(-((.((..................(((((.(((((...)))))..)))))..))))))).)))))))).((((((((.(((......))).)))))))).. ( -32.35)
>DroEre_CAF1 124047 106 + 1
CCACGAGUAAUC-----U-GCUACAACCUA-----UUUUUCUCCGUGC--UUGCUGCAACACCAACGGUAGCAAAUGUUGCAGGAGAGUCGACAGCAGAUUCUCCGCUCUUGUCGAUGU
.((.((((((((-----(-(((........-----....(((((.(((--(((((((..........))))))).....))))))))(....)))))))))....)))).))....... ( -29.40)
>DroYak_CAF1 118927 108 + 1
CUAUGAGUAAUC-----U-UUUGCCACCAA-----UUUUUCUCCGUCCAGUUGCUGCAACAACAGCGGUGGCAAAUGUUGCAAGCGAGUCGACAGCAGAUUUUCUGCUCUUGUCGAUGU
......(((((.-----.-(((((((((..-----........(.....)..((((......))))))))))))).)))))......(((((((((((.....))))...))))))).. ( -36.80)
>DroAna_CAF1 101990 108 + 1
UUGGGAAUAAACAGCAAUUUUUAC-AUAUA---UUUUUUUGCCUGUUC-CUUGAAGCAAUAAAAACAGUGGCAACUGUUGCCAGACAGCCGACGGCAGACUU------CCUGUCGAUGU
..(((((((....((((.......-.....---.....)))).)))))-))....(((..........(((((.....))))).........((((((....------.)))))).))) ( -21.93)
>consensus
CUACGAGUAAUA_____U_UUUGCAACCAA___UUUUUUUCUCCGUCCUGUUGCUGCAACACCAACGGUGGCAAAUGUUGCCGGAGAGUCGACAGCAGAUUUUCUGCUCUUGUCGAUGU
..........................................((((...((((...))))....))))(((((.....)))))....((((((((.((........)).)))))))).. (-16.67 = -17.12 +   0.45)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,254,456 – 9,254,568
Length 112
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 77.78
Mean single sequence MFE -31.81
Consensus MFE -17.80
Energy contribution -19.25
Covariance contribution 1.45
Combinations/Pair 1.21
Mean z-score -2.16
Structure conservation index 0.56
SVM decision value 1.06
SVM RNA-class probability 0.907843
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9254456 112 - 23771897
ACAUCGACAAGAGCAGAAAAGCUGAUGUCGACUCUACGGCAACAUUUGCCACCGUUGGUGUUGCAGCAACAGGACGGAGAAAAAAAAA-UUGGUUGCAUA-A-----UAAUACUCGUAG
...((((((..(((......)))..))))))..((((((((((((..((....))..))))))).(((((..................-...)))))...-.-----.......))))) ( -31.50)
>DroSec_CAF1 101271 111 - 1
ACAUCGACAAGAGCAGAAAAGCUGCUGUCGACUCUACGGCAACAUUUGCCACCGUUGGUGUUGCAGCAACAGGACGGAGAAAAAAAAA-U-GGUUGCAAA-A-----UAGUACUCGUAG
...((((((..(((......)))..))))))..((((((((((((..((....))..))))))).(((((..................-.-.)))))...-.-----.......))))) ( -31.65)
>DroSim_CAF1 101646 113 - 1
ACAUCGACAAGAGCAGAAAAGCUGCUGUCGACUCUACGGCAACAUUUGCCACCGUUGGUGUUGCAGCAACAGAACGGAGAAAAAAAAAAUGGGUUGCAAA-A-----UAGUACUCGUAG
...((((((..(((......)))..))))))..((((((((((((..((....))..))))))).(((((....((.............)).)))))...-.-----.......))))) ( -31.92)
>DroEre_CAF1 124047 106 - 1
ACAUCGACAAGAGCGGAGAAUCUGCUGUCGACUCUCCUGCAACAUUUGCUACCGUUGGUGUUGCAGCAA--GCACGGAGAAAAA-----UAGGUUGUAGC-A-----GAUUACUCGUGG
............((((..(((((((((.(((((((((((((((((..((....))..))))))))(...--.)..)))))....-----...))))))))-)-----))))..)))).. ( -36.71)
>DroYak_CAF1 118927 108 - 1
ACAUCGACAAGAGCAGAAAAUCUGCUGUCGACUCGCUUGCAACAUUUGCCACCGCUGUUGUUGCAGCAACUGGACGGAGAAAAA-----UUGGUGGCAAA-A-----GAUUACUCAUAG
...((((((...((((.....)))))))))).............((((((((((((((....)))))..((....)).......-----..)))))))))-.-----............ ( -34.70)
>DroAna_CAF1 101990 108 - 1
ACAUCGACAGG------AAGUCUGCCGUCGGCUGUCUGGCAACAGUUGCCACUGUUUUUAUUGCUUCAAG-GAACAGGCAAAAAAA---UAUAU-GUAAAAAUUGCUGUUUAUUCCCAA
.....(((((.------((...(((....(((...(((....)))..)))..(((((((.((((((....-....)))))))))))---))...-)))....)).)))))......... ( -24.40)
>consensus
ACAUCGACAAGAGCAGAAAAGCUGCUGUCGACUCUACGGCAACAUUUGCCACCGUUGGUGUUGCAGCAACAGGACGGAGAAAAAAA___UAGGUUGCAAA_A_____GAUUACUCGUAG
...((((((...((((.....)))))))))).......(((((((..((....))..))))))).(((((......................)))))...................... (-17.80 = -19.25 +   1.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,254,529 – 9,254,627
Length 98
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 80.95
Mean single sequence MFE -31.77
Consensus MFE -19.77
Energy contribution -21.72
Covariance contribution 1.95
Combinations/Pair 1.13
Mean z-score -1.72
Structure conservation index 0.62
SVM decision value 0.18
SVM RNA-class probability 0.619918
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9254529 98 + 23771897
CCGUAGAGUCGACAUCAGCUUUUCUGCUCUUGUCGAUGUCCUUGGGUGCUAUUGUCUGGCUCUUCCUGCCGCGAAAGCGCCUGCCACCCC--GCGCCAUC--
.((..(.(((((((..(((......)))..)))))))......(((((((.((((..(((.......))))))).)))))))......).--.)).....-- ( -33.80)
>DroSec_CAF1 101343 96 + 1
CCGUAGAGUCGACAGCAGCUUUUCUGCUCUUGUCGAUGUCCUUGGGUGCUAUUGUCUGGCUCGUCCUGCCGCGAAAGCGCCUGCU-C-CC--GCGCCAUC--
.(((.((((((((((.(((......))).))))))........(((((((.((((..(((.......))))))).))))))))))-)-..--))).....-- ( -34.80)
>DroSim_CAF1 101720 97 + 1
CCGUAGAGUCGACAGCAGCUUUUCUGCUCUUGUCGAUGUCCUUGGGUGCUAUUGUCUGGCUCUUCCCGCCGCGAAAGCGCCUGCC-CCCC--UCGCCAUC--
.....((((((((((.(((......))).))))))).......(((((((.((((..(((.......))))))).)))))))...-...)--))......-- ( -33.10)
>DroEre_CAF1 124114 97 + 1
CAGGAGAGUCGACAGCAGAUUCUCCGCUCUUGUCGAUGUCCUUGGGUGCUAUUGUCUGGCUCUUCCUGCCUCGCAAGCGCCUGCC-CCCC--GCACCAUC--
.((((..((((((((.((........)).)))))))).)))).(((((((..(((..(((.......)))..))))))))))((.-....--))......-- ( -33.00)
>DroYak_CAF1 118996 99 + 1
CAAGCGAGUCGACAGCAGAUUUUCUGCUCUUGUCGAUGUCCUUGGGUGCUAUUGUCUGGCUCUUCCUGCCUCGAAAGCGCCUGCU-CCCCGCGCACCAUC--
...(((.(((((((((((.....))))...)))))))......(((((((.(((...(((.......))).))).)))))))...-...)))........-- ( -36.00)
>DroAna_CAF1 102065 81 + 1
CCAGACAGCCGACGGCAGACUU------CCUGUCGAUGUCCUUGGCUGCCAUUGUCUCGCCCCUC-------G-----ACCUGCC-CCAC--ACACCAGCCU
...((((..((((((.......------.)))))).))))...(((((....(((...((.....-------.-----....)).-..))--)...))))). ( -19.90)
>consensus
CCGGAGAGUCGACAGCAGAUUUUCUGCUCUUGUCGAUGUCCUUGGGUGCUAUUGUCUGGCUCUUCCUGCCGCGAAAGCGCCUGCC_CCCC__GCACCAUC__
.......((((((((.((........)).))))))))......(((((((.(((...(((.......))).))).))))))).................... (-19.77 = -21.72 +   1.95)

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 10:51:23 2006