Locus 4162

Sequence ID 2R_DroMel_CAF1
Location 13,687,014 – 13,687,143
Length 129
Max. P 0.999865
window6694 window6695 window6696

overview

Window 4

Location 13,687,014 – 13,687,114
Length 100
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 75.68
Mean single sequence MFE -24.02
Consensus MFE -12.22
Energy contribution -13.62
Covariance contribution 1.40
Combinations/Pair 1.21
Mean z-score -2.94
Structure conservation index 0.51
SVM decision value 3.37
SVM RNA-class probability 0.999089
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13687014 100 + 20766785
UGUGCCAAACAUAGA------UAUGUACUAUGUACUUGCGUACAUAUGUAUGUAUUGUUUGUAUUUUGGCAAACCAAAACAAACAGAAAAUUUGCAUAUUAUGCGC
(((((...(((((.(------(((((((((......)).)))))))).))))).((((((((..(((((....))))))))))))).......)))))........ ( -28.60)
>DroSec_CAF1 2885 91 + 1
UGUGCCAAACAUAUA------UAUGUACUAUGUACUUGCGUACAUAUG---------UUUGUAUUUUGGCAAACCAAAACAAACAGAAAAUUUGCAUAUUAUGCGC
.........((((.(------((((((.(((((((....)))))))((---------(((((..(((((....)))))))))))).......)))))))))))... ( -23.30)
>DroSim_CAF1 2934 100 + 1
UGUGCCAAACAUACA------UAUGUACUAUGUACUUUCGAACAUAUGUAUGUCUUGUUUGUAUUUUGGCAAACCAAAACAAACAGAAAAUUUGCAUAUUAUGCGC
(((((...(((((((------(((((.(...........).)))))))))))).((((((((..(((((....))))))))))))).......)))))........ ( -26.90)
>DroYak_CAF1 2919 106 + 1
UGUGCCAAACACACAUAUACGUAUGUACCAUGUAAUUGCUUACGUAUGUAUGUAUUGUUUGUAUCUUGGCGAACCAAAACAAACAGAAAAUUUGCAUAUUAUGUGC
(((((.........(((((((((((((.((......))..))))))))))))).((((((((...((((....)))).)))))))).......)))))........ ( -26.20)
>DroAna_CAF1 2800 89 + 1
UUUGGCAAACAUA-----------------UGUACGCAGGUACAUAUAUACUUCUUAUAUGUAUGCAGGCAAACCAAAACAAAUACGAAAGCUUUAUUUCAGGUGG
((((.(....(((-----------------(((((....))))))))((((.........))))...).))))(((....((((((....)...)))))....))) ( -15.10)
>consensus
UGUGCCAAACAUACA______UAUGUACUAUGUACUUGCGUACAUAUGUAUGUAUUGUUUGUAUUUUGGCAAACCAAAACAAACAGAAAAUUUGCAUAUUAUGCGC
(((((.......................(((((((....))))))).........(((((((..(((((....))))))))))))........)))))........ (-12.22 = -13.62 +   1.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,687,014 – 13,687,114
Length 100
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 75.68
Mean single sequence MFE -26.40
Consensus MFE -16.32
Energy contribution -16.80
Covariance contribution 0.48
Combinations/Pair 1.33
Mean z-score -3.64
Structure conservation index 0.62
SVM decision value 4.30
SVM RNA-class probability 0.999865
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13687014 100 - 20766785
GCGCAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUUGCCAAAAUACAAACAAUACAUACAUAUGUACGCAAGUACAUAGUACAUA------UCUAUGUUUGGCACA
((((((((((((.........((((((((((((....)))))..))))))).....(((.(((((((....))))))))))))))------).)))))...))... ( -30.10)
>DroSec_CAF1 2885 91 - 1
GCGCAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUUGCCAAAAUACAAA---------CAUAUGUACGCAAGUACAUAGUACAUA------UAUAUGUUUGGCACA
((((((((((((.........((((((((((((....)))))..)))))---------))(((((((....)))))))...))))------).)))))...))... ( -28.40)
>DroSim_CAF1 2934 100 - 1
GCGCAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUUGCCAAAAUACAAACAAGACAUACAUAUGUUCGAAAGUACAUAGUACAUA------UGUAUGUUUGGCACA
((((((...))))........((((((((((((....)))))..)))))))((((((((((((((.(....)........)))))------))))))))).))... ( -31.10)
>DroYak_CAF1 2919 106 - 1
GCACAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUCGCCAAGAUACAAACAAUACAUACAUACGUAAGCAAUUACAUGGUACAUACGUAUAUGUGUGUUUGGCACA
..........(((........((((((((((((....)))))..)))))))...((.((((((((((....))))...((((....))))..)))))).))))).. ( -26.60)
>DroAna_CAF1 2800 89 - 1
CCACCUGAAAUAAAGCUUUCGUAUUUGUUUUGGUUUGCCUGCAUACAUAUAAGAAGUAUAUAUGUACCUGCGUACA-----------------UAUGUUUGCCAAA
....(..(((((((((....)).)))))))..).......(((.((((((.....))))((((((((....)))))-----------------))))).))).... ( -15.80)
>consensus
GCGCAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUUGCCAAAAUACAAACAAGACAUACAUAUGUACGCAAGUACAUAGUACAUA______UGUAUGUUUGGCACA
..(((((..............((((((((((((....)))))..))))))).........(((((((....)))))))...............)))))........ (-16.32 = -16.80 +   0.48)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,687,038 – 13,687,143
Length 105
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 71.91
Mean single sequence MFE -22.55
Consensus MFE -7.91
Energy contribution -7.75
Covariance contribution -0.16
Combinations/Pair 1.31
Mean z-score -2.18
Structure conservation index 0.35
SVM decision value 0.81
SVM RNA-class probability 0.856588
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13687038 105 - 20766785
C-CGCCACU---------CCA-AUGGAAACAAGUUAAUGUGCGCAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUUGCCAAAAUACAAACAAUACAUACAUAUGUACGCAAGUACA
.-.(((((.---------...-.((....)).......))).))...(((((.........((((((((((((....)))))..))))))).......)))))((((....)))). ( -26.19)
>DroPse_CAF1 2596 101 - 1
C-CGUCCGUUCGCAAUUUGCA-AGCAAAACAAA-AAAUG-GCGCAAGACA-ACAAAUGUUGUGUUUGUUUC-GUUUGUCAAGUUU---AU----CAUAUGUAUGUA--CAUGUACA
.-...........((((((((-(((.(((((((-.....-.(....)(((-((....))))).))))))).-))))).)))))).---..----.((((((....)--)))))... ( -22.50)
>DroSec_CAF1 2909 96 - 1
C-CGCCACU---------CCA-AUGAAAACAAGUUAAUGUGCGCAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUUGCCAAAAUACAAA---------CAUAUGUACGCAAGUACA
.-.(((((.---------..(-((........)))...))).)).................((((((((((((....)))))..)))))---------))..(((((....))))) ( -22.50)
>DroSim_CAF1 2958 106 - 1
CCCGCCACU---------CCA-AUGGAAACAAGUUAAUGUGCGCAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUUGCCAAAAUACAAACAAGACAUACAUAUGUUCGAAAGUACA
.........---------...-.((....))......(((((((((...))))....((((((((((((((((....)))))..))))))).(((((....))))).))))))))) ( -23.70)
>DroYak_CAF1 2949 105 - 1
C-CGCCACU---------UCA-AUAGAAUCAAGGAAAUAUGCACAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUCGCCAAGAUACAAACAAUACAUACAUACGUAAGCAAUUACA
.-.......---------...-.........(((((((.((((.......)))).)))))))(((((((((((....)))))..)))))).............((((....)))). ( -21.50)
>DroPer_CAF1 2584 102 - 1
C-CGUCCGUUCGCAAUUUGCAAAGCAAAACAAA-AAAUG-GCGCAAGACA-ACAAAUGUUGUGUUUGUUUC-GUUUGUCAAGUUU---AU----CAUAUGUAUGUA--CAUGUACA
.-...........((((((..((((.(((((((-.....-.(....)(((-((....))))).))))))).-))))..)))))).---..----.((((((....)--)))))... ( -18.90)
>consensus
C_CGCCACU_________CCA_AUGAAAACAAGUAAAUGUGCGCAUAAUAUGCAAAUUUUCUGUUUGUUUUGGUUUGCCAAAAUACAAAC____CAUACAUAUGUACGCAAGUACA
..........................................(((.(((..((((((.....))))))....)))))).........................((((....)))). ( -7.91 =  -7.75 +  -0.16)

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 11:13:16 2006