Locus 1595

Sequence ID 3R_DroMel_CAF1
Location 4,575,771 – 4,575,931
Length 160
Max. P 0.799513
window2634 window2635 window2636

overview

Window 4

Location 4,575,771 – 4,575,862
Length 91
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 90.43
Mean single sequence MFE -20.55
Consensus MFE -15.88
Energy contribution -15.75
Covariance contribution -0.13
Combinations/Pair 1.11
Mean z-score -2.00
Structure conservation index 0.77
SVM decision value 0.61
SVM RNA-class probability 0.799513
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4575771 91 + 27905053
GAG-GUUAACUUAUGGUCUUGGUAUUGAUUUGCCAAAGUAUUAUAAUAUAGCAAAAAUGAACCU----AAGGCGAAUUUAGCCAAAAGUUGUACAA
...-((((((((......(((((...((((((((..((..((((............))))..))----..))))))))..))))))))))).)).. ( -17.40)
>DroSec_CAF1 32561 95 + 1
GAG-UUCAACUUAUGGUCUUGGUAUUGAUUUGCCAAAGUAGUAUAAUAUAGCAAAAAUGAACCUUAAUAAGGCGAAUUUAGCCAAAAGUUGUACAA
..(-(.((((((.((((.((((((......))))))..................((((...(((.....)))...)))).)))).)))))).)).. ( -20.50)
>DroEre_CAF1 33441 96 + 1
AAGGUUCAACUUAUGGUCUUGGUAUUGAUUUGCCAAAGUAGUAUAAUAUAGCCAAAAGGAACCUUAAUAAGGCGAAUUUAGCCAAAAGUUGUAGAA
(((((((..(((.((((.((((((......)))))).(((......))).)))).)))))))))).....(((.......)))............. ( -23.40)
>DroYak_CAF1 33143 96 + 1
GAGGUUCAACUUAUGGUUUUGGUAUUGAUUUGCCAAAGUAGUAUAAUAUAGCCAAAAUGAACCUUAACAAGGUGAAAUUACUCAAAAGUUGUACAA
((((((((..((.(((((((((((......)))))))(((......))).)))).)))))))))).((((..(((......)))....)))).... ( -20.90)
>consensus
GAG_UUCAACUUAUGGUCUUGGUAUUGAUUUGCCAAAGUAGUAUAAUAUAGCAAAAAUGAACCUUAAUAAGGCGAAUUUAGCCAAAAGUUGUACAA
......((((((.((((.((((((......)))))).........................(((.....)))........)))).))))))..... (-15.88 = -15.75 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,575,771 – 4,575,862
Length 91
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 90.43
Mean single sequence MFE -16.36
Consensus MFE -12.86
Energy contribution -13.92
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -1.84
Structure conservation index 0.79
SVM decision value 0.51
SVM RNA-class probability 0.762291
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4575771 91 - 27905053
UUGUACAACUUUUGGCUAAAUUCGCCUU----AGGUUCAUUUUUGCUAUAUUAUAAUACUUUGGCAAAUCAAUACCAAGACCAUAAGUUAAC-CUC
......(((((..(((.......)))..----.(((.....(((((((.............))))))).....)))........)))))...-... ( -14.82)
>DroSec_CAF1 32561 95 - 1
UUGUACAACUUUUGGCUAAAUUCGCCUUAUUAAGGUUCAUUUUUGCUAUAUUAUACUACUUUGGCAAAUCAAUACCAAGACCAUAAGUUGAA-CUC
..((.((((((.(((((......((((.....)))).....(((((((.............))))))).........)).))).)))))).)-).. ( -19.52)
>DroEre_CAF1 33441 96 - 1
UUCUACAACUUUUGGCUAAAUUCGCCUUAUUAAGGUUCCUUUUGGCUAUAUUAUACUACUUUGGCAAAUCAAUACCAAGACCAUAAGUUGAACCUU
.....((((((.((((((((...((((.....))))....)))))).............(((((..........)))))..)).))))))...... ( -18.00)
>DroYak_CAF1 33143 96 - 1
UUGUACAACUUUUGAGUAAUUUCACCUUGUUAAGGUUCAUUUUGGCUAUAUUAUACUACUUUGGCAAAUCAAUACCAAAACCAUAAGUUGAACCUC
..((.((((((.((..((((........)))).(((........((((.............))))........))).....)).)))))).))... ( -13.11)
>consensus
UUGUACAACUUUUGGCUAAAUUCGCCUUAUUAAGGUUCAUUUUGGCUAUAUUAUACUACUUUGGCAAAUCAAUACCAAGACCAUAAGUUGAA_CUC
.....((((((.(((((......((((.....)))).....(((((((.............))))))).........)).))).))))))...... (-12.86 = -13.92 +   1.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,575,826 – 4,575,931
Length 105
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 85.93
Mean single sequence MFE -26.32
Consensus MFE -19.30
Energy contribution -20.46
Covariance contribution 1.16
Combinations/Pair 1.14
Mean z-score -1.71
Structure conservation index 0.73
SVM decision value 0.20
SVM RNA-class probability 0.629702
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4575826 105 - 27905053
GAACCGGA----UAUUGACCCUUACCCAACUUAUUUGGGAUAGAGGCUUUCGAGGGUUUUACAAAUACAGUACUUGUACAACUUUUGGCUAAAUUCGCCUU----AGGUUCAU
(((((((.----.......))...(((((.....)))))...(((((..(((((((((.(((((.........))))).)))))))))........)))))----.))))).. ( -27.70)
>DroSec_CAF1 32616 113 - 1
AAACCGGAUGGAUAUUGACCCUUACCCAACUUAUUUGGGAUAGAGGCUUCCGAGGGUUUUACAAAUACAGUACUUGUACAACUUUUGGCUAAAUUCGCCUUAUUAAGGUUCAU
...((....))....(((.((((((((((.....)))))...(((((..(((((((((.(((((.........))))).)))))))))........)))))..))))).))). ( -29.40)
>DroSim_CAF1 33155 113 - 1
AAACCGGAUGAAUAUUGACCCUUACCCAACUUAUUUGGGAUAGAGGCUUCCGAGGGUUUUACAAAUACAGUACUUGUACAACUUUUGGCUAAAUUCGCCUUAUUAAGGUUCAU
...............(((.((((((((((.....)))))...(((((..(((((((((.(((((.........))))).)))))))))........)))))..))))).))). ( -29.00)
>DroEre_CAF1 33497 107 - 1
GAACCGGA----UACAAGCCCUUACUCAACUUAUUUGGUAC--AGGCUUCCGAGGGUUUUAUAAUUAUAAUACUUCUACAACUUUUGGCUAAAUUCGCCUUAUUAAGGUUCCU
((((((((----....((((..(((.(((.....)))))).--.)))))))((((...((((....))))..))))..........(((.......))).......))))).. ( -24.40)
>DroYak_CAF1 33199 107 - 1
GAUCCGGA----UAGUAGCCCUUACUCAACUUAUUUGGGAU--AGGCUUCCGAGGGUUUUAUGAUUAUAGUACUUGUACAACUUUUGAGUAAUUUCACCUUGUUAAGGUUCAU
((.(((((----....((((..(.(((((.....)))))).--.)))))))((((..............(((....)))......((((....)))))))).....)).)).. ( -21.10)
>consensus
GAACCGGA____UAUUGACCCUUACCCAACUUAUUUGGGAUAGAGGCUUCCGAGGGUUUUACAAAUACAGUACUUGUACAACUUUUGGCUAAAUUCGCCUUAUUAAGGUUCAU
(((((...................(((((.....)))))...(((((..(((((((((.(((((.........))))).)))))))))........))))).....))))).. (-19.30 = -20.46 +   1.16)

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 10:14:30 2006