Locus 7687

Sequence ID 3R_DroMel_CAF1
Location 20,617,571 – 20,617,707
Length 136
Max. P 0.997043
window12399 window12400 window12401

overview

Window 9

Location 20,617,571 – 20,617,673
Length 102
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 81.71
Mean single sequence MFE -22.45
Consensus MFE -16.40
Energy contribution -16.02
Covariance contribution -0.37
Combinations/Pair 1.21
Mean z-score -1.70
Structure conservation index 0.73
SVM decision value 0.37
SVM RNA-class probability 0.706987
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20617571 102 + 27905053
CUAAAGCAAUCACUUGAAGAUCGACCUACAUUCAAAAGUAGGUUGGGAAAUCGAUGGGUGUUUGAAUUUGUUUGGAUUUCAAUAUGAUAUAUUACU-UAGUUU
........((((........(((((((((........)))))))))(((((((((..((......))..)))..))))))....))))........-...... ( -21.40)
>DroSec_CAF1 3549 93 + 1
UUAAAGUAAUCACUUGGAGAUCGACCUACAUUUAAAAGUAGGUUGGGAAAUCGAAGGGUGCUUGAAUUUAU----------AUAUGAUAUAUUACUUUACUUA
.((((((((((.(((.((..(((((((((........)))))))))....)).)))))).........(((----------((...))))).))))))).... ( -22.00)
>DroSim_CAF1 3528 93 + 1
UUAAAGUAAUCACUUGGAGAUCGACCUACAUUUAAAAGUAGGUUGGGAAAUCGAUGGGUGCUUGAAUUUAU----------AUAUGAUAUAUUACUUUACUUA
.((((((((.((((((..(((((((((((........))))))))....)))..))))))........(((----------((...))))))))))))).... ( -20.90)
>DroYak_CAF1 3820 102 + 1
UUAAAGUAAUCACCUGGCGAUUGGCCUACAUUGCAAAGUAGGUUGGGAAAUCGAUGGGUGUUGGAAUUGGUUUGGAUUUUAAUGUCAUAUAUUACU-CAGGUU
...........((((((((((..((((((........))))))..)....)))...((..((((((((......))))))))..)).........)-))))). ( -25.50)
>consensus
UUAAAGUAAUCACUUGGAGAUCGACCUACAUUUAAAAGUAGGUUGGGAAAUCGAUGGGUGCUUGAAUUUAU__________AUAUGAUAUAUUACU_UACUUA
.((((((((((((((...(((((((((((........))))))))....)))...))))).......((((............))))...))))))))).... (-16.40 = -16.02 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,617,571 – 20,617,673
Length 102
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 81.71
Mean single sequence MFE -15.76
Consensus MFE -11.41
Energy contribution -12.47
Covariance contribution 1.06
Combinations/Pair 1.12
Mean z-score -2.14
Structure conservation index 0.72
SVM decision value 1.22
SVM RNA-class probability 0.932465
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20617571 102 - 27905053
AAACUA-AGUAAUAUAUCAUAUUGAAAUCCAAACAAAUUCAAACACCCAUCGAUUUCCCAACCUACUUUUGAAUGUAGGUCGAUCUUCAAGUGAUUGCUUUAG
...(((-((((((........(((((...........))))).(((.....((((.....((((((........)))))).)))).....)))))))).)))) ( -15.50)
>DroSec_CAF1 3549 93 - 1
UAAGUAAAGUAAUAUAUCAUAU----------AUAAAUUCAAGCACCCUUCGAUUUCCCAACCUACUUUUAAAUGUAGGUCGAUCUCCAAGUGAUUACUUUAA
....(((((((....(((((..----------..(((((.(((....))).)))))..(.((((((........)))))).)........)))))))))))). ( -15.70)
>DroSim_CAF1 3528 93 - 1
UAAGUAAAGUAAUAUAUCAUAU----------AUAAAUUCAAGCACCCAUCGAUUUCCCAACCUACUUUUAAAUGUAGGUCGAUCUCCAAGUGAUUACUUUAA
....(((((((((((((...))----------)))...(((.......(((((........(((((........)))))))))).......))))))))))). ( -15.14)
>DroYak_CAF1 3820 102 - 1
AACCUG-AGUAAUAUAUGACAUUAAAAUCCAAACCAAUUCCAACACCCAUCGAUUUCCCAACCUACUUUGCAAUGUAGGCCAAUCGCCAGGUGAUUACUUUAA
.....(-((((((....((........))..............((((...(((((......(((((........)))))..)))))...)))))))))))... ( -16.70)
>consensus
AAACUA_AGUAAUAUAUCAUAU__________ACAAAUUCAAACACCCAUCGAUUUCCCAACCUACUUUUAAAUGUAGGUCGAUCUCCAAGUGAUUACUUUAA
....(((((((((......((((........))))........(((.....((((.....((((((........)))))).)))).....)))))))))))). (-11.41 = -12.47 +   1.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,617,594 – 20,617,707
Length 113
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 76.28
Mean single sequence MFE -17.88
Consensus MFE -10.24
Energy contribution -12.55
Covariance contribution 2.31
Combinations/Pair 1.10
Mean z-score -2.83
Structure conservation index 0.57
SVM decision value 2.79
SVM RNA-class probability 0.997043
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20617594 113 - 27905053
CAAUGGAA--UGUCUAUCUUACUUAACUUGCACUAGAAACUA-AGUAAUAUAUCAUAUUGAAAUCCAAACAAAUUCAAACACCCAUCGAUUUCCCAACCUACUUUUGAAUGUAGGU
...(((((--(((.(((.(((((((...............))-))))).)))..)))))((((((......................)))))))))((((((........)))))) ( -16.71)
>DroSec_CAF1 3572 106 - 1
CGAUAGACAUUCCCUAUCUUACUUAACUUGCACUAGUAAGUAAAGUAAUAUAUCAUAU----------AUAAAUUCAAGCACCCUUCGAUUUCCCAACCUACUUUUAAAUGUAGGU
.(((((.......)))))((((((.((((((....)))))).))))))..........----------..(((((.(((....))).)))))....((((((........)))))) ( -22.20)
>DroSim_CAF1 3551 106 - 1
CGAUAGACAUUCCCUAUCUUACUUAACUUGCACUAGUAAGUAAAGUAAUAUAUCAUAU----------AUAAAUUCAAGCACCCAUCGAUUUCCCAACCUACUUUUAAAUGUAGGU
.(((((.......)))))((((((.((((((....)))))).))))))..........----------............................((((((........)))))) ( -21.80)
>DroYak_CAF1 3843 105 - 1
CCCUU----------AUCGAACUUAUCUUUUACAAGAACCUG-AGUAAUAUAUGACAUUAAAAUCCAAACCAAUUCCAACACCCAUCGAUUUCCCAACCUACUUUGCAAUGUAGGC
.....----------((((((((((((((....))))...))-))).......((........))....................))))).......(((((........))))). ( -10.80)
>consensus
CGAUAGAC__UCCCUAUCUUACUUAACUUGCACUAGAAACUA_AGUAAUAUAUCAUAU__________ACAAAUUCAAACACCCAUCGAUUUCCCAACCUACUUUUAAAUGUAGGU
..............(((.((((((.((((((....)))))).)))))).)))............................................((((((........)))))) (-10.24 = -12.55 +   2.31)

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 12:52:01 2006