Locus 835

Sequence ID 3R_DroMel_CAF1
Location 2,870,446 – 2,870,641
Length 195
Max. P 0.996456
window1324 window1325 window1326

overview

Window 4

Location 2,870,446 – 2,870,561
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.59
Mean single sequence MFE -41.77
Consensus MFE -40.39
Energy contribution -40.57
Covariance contribution 0.19
Combinations/Pair 1.09
Mean z-score -2.67
Structure conservation index 0.97
SVM decision value 2.70
SVM RNA-class probability 0.996456
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2870446 115 - 27905053
UGUUCCACCGCACACACU-----CGAGACCUUCUCUCCGCCCGGAUACGCACCUUUCCGUAUCCGUGUGUGGGUGCUCCUGGGAGUGGGCACCACAUAAUGGUUUCUAAUCCGGCACUUU
.......((((((((...-----.((((.....)))).....(((((((........)))))))))))))))(((((....(((.((((.((((.....)))).)))).))))))))... ( -43.30)
>DroSec_CAF1 1418 120 - 1
UGUUCCACCGCACACACUCGACUCGAGACCUUCUCUCCGCCCGGAUACGCACCUUUCCGUAUCCGUGUGUGGGUGCUCCUGGGAGUGGGCACCACAUAAUGGCUUCUAAUCCGGCACUUU
.......((((((((.((((...))))...............(((((((........)))))))))))))))(((((....(((.((((..(((.....)))..)))).))))))))... ( -41.40)
>DroSim_CAF1 1787 120 - 1
UGUUCCACCGCACACACUCGACUCGAGACCUUCUCUCCGCCCGGAUACGCACCUUUCCGUAUCCGUGUGCGGGUGCUCCAGGGAGUGGGCACCACAUAAUGGUUUCUAAUCCGGCACUUU
.......((((((((.((((...))))...............(((((((........)))))))))))))))(((((....(((.((((.((((.....)))).)))).))))))))... ( -45.40)
>DroEre_CAF1 2340 115 - 1
UGUUCCACCGCACACACU-----CGAGGCCUUCUCUCCGCCUGGAUACGCACCUUUCCGUAUCCCUGUGUGGGUGCCUCUGGGAAUGGGUAGCACAUAAUGGUUUCUAAUCCGGCACUUU
.......(((((((....-----..((((.........))))(((((((........))))))).)))))))(((((....(((.((((.(((........))))))).))))))))... ( -37.00)
>consensus
UGUUCCACCGCACACACU_____CGAGACCUUCUCUCCGCCCGGAUACGCACCUUUCCGUAUCCGUGUGUGGGUGCUCCUGGGAGUGGGCACCACAUAAUGGUUUCUAAUCCGGCACUUU
.......((((((((.........((((.....)))).....(((((((........)))))))))))))))(((((....(((.((((.((((.....)))).)))).))))))))... (-40.39 = -40.57 +   0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,870,486 – 2,870,601
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.27
Mean single sequence MFE -38.90
Consensus MFE -35.56
Energy contribution -35.50
Covariance contribution -0.06
Combinations/Pair 1.09
Mean z-score -2.27
Structure conservation index 0.91
SVM decision value 1.61
SVM RNA-class probability 0.967420
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2870486 115 - 27905053
CCAAGGAUGAAUGAGGAUACCCGAACAUGACACUUAUGGAUGUUCCACCGCACACACU-----CGAGACCUUCUCUCCGCCCGGAUACGCACCUUUCCGUAUCCGUGUGUGGGUGCUCCU
...((((.......((....))((((((..((....)).))))))((((.(((((((.-----.((((.....)))).....(((((((........)))))))))))))))))).)))) ( -38.70)
>DroSec_CAF1 1458 120 - 1
CCAAGGAUGAAUGAGGAUACCCGAACAUGACACUUAUGGAUGUUCCACCGCACACACUCGACUCGAGACCUUCUCUCCGCCCGGAUACGCACCUUUCCGUAUCCGUGUGUGGGUGCUCCU
...((((.......((....))((((((..((....)).))))))((((.(((((((.......((((.....)))).....(((((((........)))))))))))))))))).)))) ( -38.70)
>DroSim_CAF1 1827 120 - 1
CCAAGGAUGAAUGAGGAUACCCGAACAUGACACUUAUGGAUGUUCCACCGCACACACUCGACUCGAGACCUUCUCUCCGCCCGGAUACGCACCUUUCCGUAUCCGUGUGCGGGUGCUCCA
..............((((((((((((((..((....)).))))))....((((((.((((...))))...............(((((((........)))))))))))))))))).))). ( -41.20)
>DroEre_CAF1 2380 115 - 1
CCAAGGAUGAAUGAGGAUACCCGAACAUGACACUUAUGGAUGUUCCACCGCACACACU-----CGAGGCCUUCUCUCCGCCUGGAUACGCACCUUUCCGUAUCCCUGUGUGGGUGCCUCU
............((((......((((((..((....)).))))))((((.((((((..-----..((((.........))))(((((((........))))))).)))))))))))))). ( -37.00)
>consensus
CCAAGGAUGAAUGAGGAUACCCGAACAUGACACUUAUGGAUGUUCCACCGCACACACU_____CGAGACCUUCUCUCCGCCCGGAUACGCACCUUUCCGUAUCCGUGUGUGGGUGCUCCU
..............((((((((((((((..((....)).))))))....((((((.........((((.....)))).....(((((((........)))))))))))))))))).))). (-35.56 = -35.50 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,870,526 – 2,870,641
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.36
Mean single sequence MFE -43.55
Consensus MFE -39.82
Energy contribution -41.82
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.51
Structure conservation index 0.91
SVM decision value 1.45
SVM RNA-class probability 0.955151
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2870526 115 + 27905053
GCGGAGAGAAGGUCUCG-----AGUGUGUGCGGUGGAACAUCCAUAAGUGUCAUGUUCGGGUAUCCUCAUUCAUCCUUGGCAUGCACGCACGUUUUUUCGAUCCGGUUCCUUUCUUUCCC
..((((((((((..(((-----((..(((((.((((.....))))..(((.(((((..(((.............)))..)))))))))))))....))))).))(....).)))))))). ( -38.72)
>DroSec_CAF1 1498 120 + 1
GCGGAGAGAAGGUCUCGAGUCGAGUGUGUGCGGUGGAACAUCCAUAAGUGUCAUGUUCGGGUAUCCUCAUUCAUCCUUGGCAUGCACGCACGUUUUUUCGAUCCGGCUCCUUUCUUUCCC
..((((((((((..(((..(((((..(((((.((((.....))))..(((.(((((..(((.............)))..)))))))))))))....)))))..)))..)).)))))))). ( -46.62)
>DroSim_CAF1 1867 120 + 1
GCGGAGAGAAGGUCUCGAGUCGAGUGUGUGCGGUGGAACAUCCAUAAGUGUCAUGUUCGGGUAUCCUCAUUCAUCCUUGGCAUGCACGCACGUUUUUUCGAUCCGGCUCCUUUCUUUCCC
..((((((((((..(((..(((((..(((((.((((.....))))..(((.(((((..(((.............)))..)))))))))))))....)))))..)))..)).)))))))). ( -46.62)
>DroEre_CAF1 2420 115 + 1
GCGGAGAGAAGGCCUCG-----AGUGUGUGCGGUGGAACAUCCAUAAGUGUCAUGUUCGGGUAUCCUCAUUCAUCCUUGGCAUGCACGCACGUUUUUUCGAUCCGGCUCCUUUCUUUCCC
..(((((((((((((((-----((..(((((.((((.....))))..(((.(((((..(((.............)))..)))))))))))))....)))))...))))...)))))))). ( -42.22)
>consensus
GCGGAGAGAAGGUCUCG_____AGUGUGUGCGGUGGAACAUCCAUAAGUGUCAUGUUCGGGUAUCCUCAUUCAUCCUUGGCAUGCACGCACGUUUUUUCGAUCCGGCUCCUUUCUUUCCC
..((((((((((..(((.((((((..(((((.((((.....))))..(((.(((((..(((.............)))..)))))))))))))....)))))).)))..)).)))))))). (-39.82 = -41.82 +   2.00)

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 09:53:16 2006