Locus 4910

Sequence ID 2R_DroMel_CAF1
Location 16,040,596 – 16,040,735
Length 139
Max. P 0.996800
window7864 window7865 window7866

overview

Window 4

Location 16,040,596 – 16,040,698
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 96.15
Mean single sequence MFE -22.82
Consensus MFE -21.92
Energy contribution -21.36
Covariance contribution -0.56
Combinations/Pair 1.11
Mean z-score -1.05
Structure conservation index 0.96
SVM decision value 0.01
SVM RNA-class probability 0.537074
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16040596 102 - 20766785
UUGACCGCGUGCGCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAGUGCUUUAAUCUACAAACCUCGC
(..(((.(((...(((...(((((((.........))))))).......(((....)))))).))))))..)(((((.....)))))............... ( -20.50)
>DroSec_CAF1 95491 100 - 1
UCGACCGCGUGCGCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAGUGCUUUAAUCUGCAA--UUCGC
((((((.(((...(((...(((((((.........))))))).......(((....)))))).)))))))))....(((.(((........))).--))).. ( -26.60)
>DroSim_CAF1 98867 101 - 1
UCGACCGCGUGCGCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAGUGCUUUAAUCUUCAA-CCUCGC
......(((.((.(((...(((((((.........))))))).......(((....)))))).))((((((((((((.....)))))....))))-)))))) ( -23.90)
>DroEre_CAF1 102159 101 - 1
UCGGCCGCGUGCCCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAGUGCUUUAAUCUACAA-CCUCGC
..(((.....)))(((...(((((((.........))))))).......(((....)))))).((((((((.(((((.....))))).....)))-)).))) ( -21.90)
>DroYak_CAF1 105699 101 - 1
UCGGCCGCGUGCCCCGAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAGUGCUUUAAUCUACAA-CCUCGC
..(((.....)))(((...(((((((.........))))))).......(((....)))))).((((((((.(((((.....))))).....)))-)).))) ( -21.20)
>consensus
UCGACCGCGUGCGCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAGUGCUUUAAUCUACAA_CCUCGC
((((((.(((...(((...(((((((.........))))))).......(((....)))))).)))))))))(((((.....)))))............... (-21.92 = -21.36 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,040,618 – 16,040,735
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 94.87
Mean single sequence MFE -34.06
Consensus MFE -29.83
Energy contribution -30.67
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -1.60
Structure conservation index 0.88
SVM decision value 1.24
SVM RNA-class probability 0.934811
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16040618 117 + 20766785
CUUCUUUAUCAACCCGCUCCAUUCUUGAGAAAUAUUGCUAUGCAAAUAUUUGUAUUGCAUAUUUUGGCGCACGCGGUCAAAUUCGCGAAUUGCAGGGGUAGAUAGCAAAGUGGUUUG
(((..(((((.(((((((.((....)).(((((((.((.((((((....)))))).))))))))))))((((((((......)))))...)))..)))).)))))..)))....... ( -32.70)
>DroSec_CAF1 95511 117 + 1
CUUCUUUAUCAACCCGCUCCAUUCUUGAGAAAUAUUGCUAUGCAAAUAUUUGUAUUGCAUAUUUUGGCGCACGCGGUCGAAUUCGCGGAUUGCAGGGGUGGAUAGCAAAGUGGUCUG
.........((..((((((((((((((.(((((((.((.((((((....)))))).)))))))))......(((((......))))).....)))))))))).......))))..)) ( -33.51)
>DroSim_CAF1 98888 117 + 1
CUUCUUUAUCAACCCGCUCCAUUCUUGAGAAAUAUUGCUAUGCAAAUAUUUGUAUUGCAUAUUUUGGCGCACGCGGUCGAAUUCGCGGAUUGCAGGGGUGGAUAGCAAAAUGGUUUG
.............(((((((........(((((((.((.((((((....)))))).))))))))).(((..(((((......)))))...))).)))))))................ ( -32.80)
>DroEre_CAF1 102180 117 + 1
CUUCUUUAUCAACCCGCUCCAUUCUUGAGAAAUAUUGCUAUGCAAAUAUUUGUAUUGCAUAUUUUGGGGCACGCGGCCGAAUUCGCGGAUUGCAGGGUUGGAUAACAAAGUGGUUUG
(((..(((((((((((((((((((....)))....(((.((((((....)))))).))).....))))))..(((((((......))).)))).))))).)))))..)))....... ( -37.30)
>DroYak_CAF1 105720 117 + 1
CUUCUUUAUCAACCCGCUCCAUUCUUGAGAAAUAUUGCUAUGCAAAUAUUUGUAUUGCAUAUUUCGGGGCACGCGGCCGAAUUCGCGAAUGGCUGGGGUGGCUAACAAAGUGGUUUG
(((..((((((.((((..((((((.((((((((((.((.((((((....)))))).)))))))))..(((.....)))....))).)))))).)))).))).)))..)))....... ( -34.00)
>consensus
CUUCUUUAUCAACCCGCUCCAUUCUUGAGAAAUAUUGCUAUGCAAAUAUUUGUAUUGCAUAUUUUGGCGCACGCGGUCGAAUUCGCGGAUUGCAGGGGUGGAUAGCAAAGUGGUUUG
.........(((.((((((((((((((.(((((((.((.((((((....)))))).)))))))))......(((((......))))).....))))))))).......))))).))) (-29.83 = -30.67 +   0.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,040,618 – 16,040,735
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 94.87
Mean single sequence MFE -30.22
Consensus MFE -26.84
Energy contribution -26.92
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.11
Structure conservation index 0.89
SVM decision value 2.75
SVM RNA-class probability 0.996800
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16040618 117 - 20766785
CAAACCACUUUGCUAUCUACCCCUGCAAUUCGCGAAUUUGACCGCGUGCGCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAG
.......((((..((((.(((((((((...((((........))))))).(((...(((((((.........))))))).......(((....)))))))).)))).))))..)))) ( -29.50)
>DroSec_CAF1 95511 117 - 1
CAGACCACUUUGCUAUCCACCCCUGCAAUCCGCGAAUUCGACCGCGUGCGCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAG
.......((((..((((.((((........((((........)))).((.(((...(((((((.........))))))).......(((....)))))).)))))).))))..)))) ( -29.70)
>DroSim_CAF1 98888 117 - 1
CAAACCAUUUUGCUAUCCACCCCUGCAAUCCGCGAAUUCGACCGCGUGCGCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAG
.......((((..((((.((((........((((........)))).((.(((...(((((((.........))))))).......(((....)))))).)))))).)))).)))). ( -27.80)
>DroEre_CAF1 102180 117 - 1
CAAACCACUUUGUUAUCCAACCCUGCAAUCCGCGAAUUCGGCCGCGUGCCCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAG
.......((((.(((((.(((((.......((((........)))).((.(((...(((((((.........))))))).......(((....)))))).)))))))))))).)))) ( -30.80)
>DroYak_CAF1 105720 117 - 1
CAAACCACUUUGUUAGCCACCCCAGCCAUUCGCGAAUUCGGCCGCGUGCCCCGAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAG
.......(((((((((((..(....(((((((((........))).......(((((((((.((.(((....))).)).)).)))))))....)))))).)..)))))))))))... ( -33.30)
>consensus
CAAACCACUUUGCUAUCCACCCCUGCAAUCCGCGAAUUCGACCGCGUGCGCCAAAAUAUGCAAUACAAAUAUUUGCAUAGCAAUAUUUCUCAAGAAUGGAGCGGGUUGAUAAAGAAG
.......((((..((((.((((........((((........)))).((.(((...(((((((.........))))))).......(((....)))))).)))))).))))..)))) (-26.84 = -26.92 +   0.08)

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 11:31:58 2006