Locus 4358

Sequence ID 3R_DroMel_CAF1
Location 11,482,760 – 11,482,890
Length 130
Max. P 0.880487
window7125 window7126 window7127

overview

Window 5

Location 11,482,760 – 11,482,862
Length 102
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 81.61
Mean single sequence MFE -23.32
Consensus MFE -20.03
Energy contribution -19.70
Covariance contribution -0.33
Combinations/Pair 1.09
Mean z-score -1.69
Structure conservation index 0.86
SVM decision value 0.91
SVM RNA-class probability 0.880487
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11482760 102 + 27905053
GAGCAAAAUGGGGUGAAAGUGAUUGGAUUAAAGGGAAAUCCUGGCUGAUAUCGGUGGAUAUUUCACAGGAAUUCCACGAUUACAUAAGAAGAAGGUGAUGCA
..(((..((.........(((((((........((((.(((((...((((((....))))))...))))).)))).)))))))...........))..))). ( -24.35)
>DroEre_CAF1 20470 90 + 1
GAGCAAAAUGG-GUGAGAGCGAUUGGAUGAAUGGGAAAUCCUGGGUGUUAUCGCUGGAUAUUUCACAGGAAUUCCACGAUUACGCAGGCAG-----------
..((....((.-((((...(((((.....))).((((.(((((((...((((....))))..)).))))).)))).)).)))).)).))..----------- ( -23.70)
>DroYak_CAF1 14342 95 + 1
GAGCGAAAUGGAGUGAAAGUGAUUGGAUGAAUGGGAAAUCCUGGGUGUUAACGCUAGAUAUUUCACAGGAAUUCCACGAUUAUGUAAGCAGAAGG-------
............((....(((((((........((((.(((((((((....)))).((....)).))))).)))).)))))))....))......------- ( -21.90)
>consensus
GAGCAAAAUGG_GUGAAAGUGAUUGGAUGAAUGGGAAAUCCUGGGUGUUAUCGCUGGAUAUUUCACAGGAAUUCCACGAUUACGUAAGCAGAAGG_______
..................(((((((........((((.(((((((((....)))).((....)).))))).)))).)))))))................... (-20.03 = -19.70 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,482,760 – 11,482,862
Length 102
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 81.61
Mean single sequence MFE -14.67
Consensus MFE -12.20
Energy contribution -12.53
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.83
SVM decision value 0.41
SVM RNA-class probability 0.724127
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11482760 102 - 27905053
UGCAUCACCUUCUUCUUAUGUAAUCGUGGAAUUCCUGUGAAAUAUCCACCGAUAUCAGCCAGGAUUUCCCUUUAAUCCAAUCACUUUCACCCCAUUUUGCUC
.(((.............(((....)))((((.(((((.(..(((((....)))))...)))))).))))............................))).. ( -16.40)
>DroEre_CAF1 20470 90 - 1
-----------CUGCCUGCGUAAUCGUGGAAUUCCUGUGAAAUAUCCAGCGAUAACACCCAGGAUUUCCCAUUCAUCCAAUCGCUCUCAC-CCAUUUUGCUC
-----------..((..(((....)))((((.(((((.(...((((....))))...).))))).)))).............))......-........... ( -15.30)
>DroYak_CAF1 14342 95 - 1
-------CCUUCUGCUUACAUAAUCGUGGAAUUCCUGUGAAAUAUCUAGCGUUAACACCCAGGAUUUCCCAUUCAUCCAAUCACUUUCACUCCAUUUCGCUC
-------..................(((((((....((((((........(....).....((((.........))))......))))))...))))))).. ( -12.30)
>consensus
_______CCUUCUGCUUACGUAAUCGUGGAAUUCCUGUGAAAUAUCCAGCGAUAACACCCAGGAUUUCCCAUUCAUCCAAUCACUUUCAC_CCAUUUUGCUC
.........................(.((((.(((((.....((((....)))).....))))).)))))................................ (-12.20 = -12.53 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,482,790 – 11,482,890
Length 100
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 72.07
Mean single sequence MFE -14.90
Consensus MFE -9.77
Energy contribution -10.53
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.66
SVM decision value 0.29
SVM RNA-class probability 0.669658
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11482790 100 - 27905053
UUA------------CUUACAAUACUAUUCAUGUUUCUACUGCAUCACCUUCUUCUUAUGUAAUCGUGGAAUUCCUGUGAAAUAUCCACCGAUAUCAGCCAGGAUUUCCCUU
(((------------(..............((((.......))))..............))))..(.((((.(((((.(..(((((....)))))...)))))).))))).. ( -16.59)
>DroSec_CAF1 17034 100 - 1
UUA------------CUUACAAUACUAUCCAGUUUUCUACUGCAUCACCUUCUUCUUACGUAAUCGUGGAAUUCCUGUGAAAUAUCCACCUAUAACUGCCAUGAUUUCCCUU
...------------..............((((.....)))).................(.((((((((.......(((.......))).........)))))))).).... ( -11.89)
>DroEre_CAF1 20499 100 - 1
UCAGCCCCCAUUAUGCAUACAAUAAUAUCCAGACUUCUA------------CUGCCUGCGUAAUCGUGGAAUUCCUGUGAAAUAUCCAGCGAUAACACCCAGGAUUUCCCAU
.........((((((((..((.((.............))------------.))..)))))))).(.((((.(((((.(...((((....))))...).))))).))))).. ( -19.02)
>DroYak_CAF1 14372 99 - 1
CCA--CCCUAUUAUACAUACAAU---AGCCAGCUUUCCA--------CCUUCUGCUUACAUAAUCGUGGAAUUCCUGUGAAAUAUCUAGCGUUAACACCCAGGAUUUCCCAU
...--..(((((........)))---))..(((......--------......))).........(.((((.(((((.(...................)))))).))))).. ( -12.11)
>consensus
UCA____________CAUACAAUACUAUCCAGAUUUCUA________CCUUCUGCUUACGUAAUCGUGGAAUUCCUGUGAAAUAUCCACCGAUAACACCCAGGAUUUCCCAU
.................................................................(.((((.(((((.....((((....)))).....))))).))))).. ( -9.77 = -10.53 +   0.75)

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 11:27:12 2006