Locus 7192

Sequence ID 3R_DroMel_CAF1
Location 18,960,364 – 18,960,532
Length 168
Max. P 0.952735
window11638 window11639 window11640 window11641

overview

Window 8

Location 18,960,364 – 18,960,470
Length 106
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 87.13
Mean single sequence MFE -33.40
Consensus MFE -24.56
Energy contribution -25.10
Covariance contribution 0.54
Combinations/Pair 1.03
Mean z-score -1.87
Structure conservation index 0.74
SVM decision value 0.43
SVM RNA-class probability 0.731840
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18960364 106 + 27905053
CGAUGUUUACCCAACAUGCUAAUGCAUUGAGCUCGAAUUCGAAUCGAUGC--GCUGGACGCGCAAUGAACAAACAACGGCCCGUCUCAGAUCUCGGA----UCUGAG-------AUCUG
..(((((.....)))))......(((((((..(((....))).)))))))--...(((((.((..((......))...)).)))))(((((((((..----..))))-------))))) ( -33.30)
>DroSec_CAF1 71778 106 + 1
CGAUGUUUACCCAACAUGCUAAUGCAUUGAGCUCGAAUUCGAAUCGAUGC--GCUGGACGCGCAAUGUACAAACAACGGCCCGUCUCAGAUCUCGGA----UCUGGG-------AACUG
((.(((((.....((((((....(((((((..(((....))).)))))))--((.....)))).))))..))))).)).....(((((((((...))----))))))-------).... ( -32.30)
>DroSim_CAF1 73381 113 + 1
CGAUGUUUACCCAACAUGCUAAUGCAUUGAGCUCGAAUUCGAAUCGAUGC--GCUGGACGCGCAAUGUACAAACAACGGCCCGUCUCAGAUCUCGGA----UCUGGGAUCUGGGAUCUG
..(((((.....)))))......(((((((..(((....))).)))))))--...(((((.((..(((....)))...)).)))))(((((((((((----((...))))))))))))) ( -40.60)
>DroEre_CAF1 71949 91 + 1
CGAUGUUUACCCAACAUGCUAAUGCAUUGAGCUCGAAUUCGAAUCGAUGC--GCUGGACGCGCAAUGAACAAACAACGGC-CGUCUCAGAU-------------------------CUC
..(((((.....)))))......(((((((..(((....))).)))))))--.(((((((.((..((......))...))-)))).)))..-------------------------... ( -24.80)
>DroYak_CAF1 74172 111 + 1
CGAUGUUUACCCAACAUGCUAAUGCAUUGAGCUCGAAUUCGAAUCGAUGCGCGCUGGACGCGCAAUGUACAAACAACGGG-CGUCUCAGAUCUCAGAGAUCUCAGAG-------AUCUC
.((((....(((...........(((((((..(((....))).)))))))((((.....))))..............)))-))))..(((((((.((....)).)))-------)))). ( -36.00)
>consensus
CGAUGUUUACCCAACAUGCUAAUGCAUUGAGCUCGAAUUCGAAUCGAUGC__GCUGGACGCGCAAUGUACAAACAACGGCCCGUCUCAGAUCUCGGA____UCUGAG_______AUCUG
..(((((.....)))))......(((((((..(((....))).)))))))...(((((((.((..((......))...)).)))).)))..((((((....))))))............ (-24.56 = -25.10 +   0.54)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,960,404 – 18,960,510
Length 106
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 82.77
Mean single sequence MFE -42.84
Consensus MFE -25.00
Energy contribution -27.93
Covariance contribution 2.93
Combinations/Pair 1.03
Mean z-score -2.87
Structure conservation index 0.58
SVM decision value 1.43
SVM RNA-class probability 0.952735
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18960404 106 + 27905053
GAAUCGAUGC--GCUGGACGCGCAAUGAACAAACAACGGCCCGUCUCAGAUCUCGGA----UCUGAG-------AUCUGGGAUCUGAGUUCUUUGGGAUCUCUCGAGACUGGGAUCUCU
((((((.(((--((.....))))).)))................(((((((((((((----((...)-------)))))))))))))))))...((((((((........)))))))). ( -43.30)
>DroSec_CAF1 71818 104 + 1
GAAUCGAUGC--GCUGGACGCGCAAUGUACAAACAACGGCCCGUCUCAGAUCUCGGA----UCUGGG-------AACUGGGAACUGGGUUC--GGGGAUCUCUCGAGACUGGGAUCUCG
(((((..(((--((.....)))))............((((((.(((((((((...))----))))))-------)...)))..))))))))--.((((((((........)))))))). ( -41.10)
>DroSim_CAF1 73421 111 + 1
GAAUCGAUGC--GCUGGACGCGCAAUGUACAAACAACGGCCCGUCUCAGAUCUCGGA----UCUGGGAUCUGGGAUCUGGGAACUGGGUUC--GGGGAUCUCUCGAGACUGGGAUCUCG
.......(((--((.....)))))............((((((.((((((((((((((----((...))))))))))))))))...))).))--)((((((((........)))))))). ( -51.00)
>DroEre_CAF1 71989 87 + 1
GAAUCGAUGC--GCUGGACGCGCAAUGAACAAACAACGGC-CGUCUCAGAU-------------------------CUCGGAUCUGGGUUC--GGGGAUC--UCGAAACUGGGAUCUCU
...(((.(((--((.....))))).)))...........(-((.(((((((-------------------------(...))))))))..)--))(((((--(((....)))))))).. ( -31.70)
>DroYak_CAF1 74212 107 + 1
GAAUCGAUGCGCGCUGGACGCGCAAUGUACAAACAACGGG-CGUCUCAGAUCUCAGAGAUCUCAGAG-------AUCUCGGAUCUGGGUUC--GGGGAUC--UCGAAACUGGGAUCUCU
((((((((((((((.....))))..(((....)))....)-)))).(((((((..((((((.....)-------)))))))))))))))))--(((((((--(((....)))))))))) ( -47.10)
>consensus
GAAUCGAUGC__GCUGGACGCGCAAUGUACAAACAACGGCCCGUCUCAGAUCUCGGA____UCUGAG_______AUCUGGGAUCUGGGUUC__GGGGAUCUCUCGAGACUGGGAUCUCU
(((((..........(((((.((..((......))...)).)))))(((((((((((..................))))))))))))))))...((((((((........)))))))). (-25.00 = -27.93 +   2.93)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,960,441 – 18,960,532
Length 91
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 89.47
Mean single sequence MFE -41.07
Consensus MFE -31.54
Energy contribution -31.10
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -4.15
Structure conservation index 0.77
SVM decision value 1.17
SVM RNA-class probability 0.925041
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18960441 91 + 27905053
CCCGUCUCAGAUCUCGGAUCUGAG-------AUCUGGGAUCUGAGUUCUUUGGGAUCUCUCGAGACUGGGAUCUCUCCUCGCAGAUCCCAUAUUCCAC
.....(((((((((((((((...)-------)))))))))))))).....((((((((..((((...(((....))))))).))))))))........ ( -40.40)
>DroSec_CAF1 71855 89 + 1
CCCGUCUCAGAUCUCGGAUCUGGG-------AACUGGGAACUGGGUUC--GGGGAUCUCUCGAGACUGGGAUCUCGCCUCGCAGAUCCCAUAUUCCAC
(((.(((((((((...))))))))-------)...)))...(((((((--(((.....))))))..((((((((.((...))))))))))...)))). ( -36.50)
>DroSim_CAF1 73458 96 + 1
CCCGUCUCAGAUCUCGGAUCUGGGAUCUGGGAUCUGGGAACUGGGUUC--GGGGAUCUCUCGAGACUGGGAUCUCGCCUCGCAGAUCCCAUAUUCCAC
(((.((((((((((((((((...))))))))))))))))...)))(((--(((.....))))))..((((((((.((...))))))))))........ ( -46.30)
>consensus
CCCGUCUCAGAUCUCGGAUCUGGG_______AUCUGGGAACUGGGUUC__GGGGAUCUCUCGAGACUGGGAUCUCGCCUCGCAGAUCCCAUAUUCCAC
...(((((.((.(((((.(((.((.........)).))).))))).))...(((....))))))))(((((((((.....).))))))))........ (-31.54 = -31.10 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,960,441 – 18,960,532
Length 91
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 89.47
Mean single sequence MFE -34.80
Consensus MFE -26.63
Energy contribution -27.30
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.77
SVM decision value 0.19
SVM RNA-class probability 0.626752
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18960441 91 - 27905053
GUGGAAUAUGGGAUCUGCGAGGAGAGAUCCCAGUCUCGAGAGAUCCCAAAGAACUCAGAUCCCAGAU-------CUCAGAUCCGAGAUCUGAGACGGG
........((((((((.(((((...(....)..)))))..)))))))).....((((((((.(.(((-------(...)))).).))))))))..... ( -33.80)
>DroSec_CAF1 71855 89 - 1
GUGGAAUAUGGGAUCUGCGAGGCGAGAUCCCAGUCUCGAGAGAUCCCC--GAACCCAGUUCCCAGUU-------CCCAGAUCCGAGAUCUGAGACGGG
.(((.....(((((((.((((((.........))))))..))))))).--....)))...(((.(((-------..((((((...)))))).)))))) ( -33.80)
>DroSim_CAF1 73458 96 - 1
GUGGAAUAUGGGAUCUGCGAGGCGAGAUCCCAGUCUCGAGAGAUCCCC--GAACCCAGUUCCCAGAUCCCAGAUCCCAGAUCCGAGAUCUGAGACGGG
.........(((((((.((((((.........))))))..))))))).--...(((.(((..((((((.(.((((...)))).).)))))).)))))) ( -36.80)
>consensus
GUGGAAUAUGGGAUCUGCGAGGCGAGAUCCCAGUCUCGAGAGAUCCCC__GAACCCAGUUCCCAGAU_______CCCAGAUCCGAGAUCUGAGACGGG
.(((.....(((((((.((((((.........))))))..)))))))...((((...)))))))............((((((...))))))....... (-26.63 = -27.30 +   0.67)

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 12:39:48 2006