Locus 4920

Sequence ID 3R_DroMel_CAF1
Location 12,911,196 – 12,911,353
Length 157
Max. P 0.772462
window8053 window8054 window8055

overview

Window 3

Location 12,911,196 – 12,911,313
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.22
Mean single sequence MFE -32.53
Consensus MFE -23.16
Energy contribution -23.17
Covariance contribution 0.01
Combinations/Pair 1.11
Mean z-score -2.56
Structure conservation index 0.71
SVM decision value 0.10
SVM RNA-class probability 0.584866
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12911196 117 + 27905053
UGGCGGCUCUAAUCAACAGCUGGAAAGAUAUCGAUAUCGACAGGA-GAAUAUCGAUAUUCAAUCGGUAUUCGAUACUGCUGCGAUACAGCAAAA--AAAAGAGAGAUUUCUCGGAUUAGA
.......(((((((....((((((......))..(((((.(((..-((((((((((.....))))))))))....)))...)))))))))....--....(((......))).))))))) ( -34.40)
>DroEre_CAF1 28693 120 + 1
UGGCGGCUCCAAUAAACAGCUGGAAAGUUAUCGAUAUCCUCAGGGCAUAUAUUAAUAUCGAAUCGGUAUUCGAUAGUGCUGCAAUACAGCAAAAAAAAAAGAGAGAUUUCUCGGAUUAGA
.......(((.......((((....))))...((.((((((..............((((((((....)))))))).(((((.....))))).........))).))).))..)))..... ( -25.80)
>DroYak_CAF1 29527 118 + 1
UGGCGGCUCCAAUAAACAGCUGGAAAGAUAUCGAUAUCGGCAGGGCGAAUAUCGAUAUCGAAUCGGUAUUCGAUACUGCUGCGAUACAGCAAAA--AAAAGAGAGAUUUCUCGGAUUAGA
.......(((........((((......(((((....((((((..(((((((((((.....)))))))))))...)))))))))))))))....--....(((......))))))..... ( -37.40)
>consensus
UGGCGGCUCCAAUAAACAGCUGGAAAGAUAUCGAUAUCGACAGGGCGAAUAUCGAUAUCGAAUCGGUAUUCGAUACUGCUGCGAUACAGCAAAA__AAAAGAGAGAUUUCUCGGAUUAGA
.......(((........(((((...(((((((((((...........)))))))))))...))))).........(((((.....))))).........(((......))))))..... (-23.16 = -23.17 +   0.01)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,911,196 – 12,911,313
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.22
Mean single sequence MFE -29.23
Consensus MFE -23.77
Energy contribution -24.67
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -2.40
Structure conservation index 0.81
SVM decision value 0.53
SVM RNA-class probability 0.772462
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12911196 117 - 27905053
UCUAAUCCGAGAAAUCUCUCUUUU--UUUUGCUGUAUCGCAGCAGUAUCGAAUACCGAUUGAAUAUCGAUAUUC-UCCUGUCGAUAUCGAUAUCUUUCCAGCUGUUGAUUAGAGCCGCCA
........((((....))))....--....(((.((...(((((((...(((.....(((((.((((((((...-...)))))))))))))....)))..)))))))..)).)))..... ( -30.20)
>DroEre_CAF1 28693 120 - 1
UCUAAUCCGAGAAAUCUCUCUUUUUUUUUUGCUGUAUUGCAGCACUAUCGAAUACCGAUUCGAUAUUAAUAUAUGCCCUGAGGAUAUCGAUAACUUUCCAGCUGUUUAUUGGAGCCGCCA
.....(((((((.(((.(((.........(((((.....))))).((((((((....))))))))..............)))))).))((......))..........)))))....... ( -24.20)
>DroYak_CAF1 29527 118 - 1
UCUAAUCCGAGAAAUCUCUCUUUU--UUUUGCUGUAUCGCAGCAGUAUCGAAUACCGAUUCGAUAUCGAUAUUCGCCCUGCCGAUAUCGAUAUCUUUCCAGCUGUUUAUUGGAGCCGCCA
........((((....))))....--....(((.((..(((((.(.((((.....)))).)((((((((((((.((...)).))))))))))))......)))))....)).)))..... ( -33.30)
>consensus
UCUAAUCCGAGAAAUCUCUCUUUU__UUUUGCUGUAUCGCAGCAGUAUCGAAUACCGAUUCGAUAUCGAUAUUCGCCCUGACGAUAUCGAUAUCUUUCCAGCUGUUUAUUGGAGCCGCCA
........((((....))))..........(((.((..(((((...((((.....))))..((((((((((((.........))))))))))))......)))))....)).)))..... (-23.77 = -24.67 +   0.89)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,911,236 – 12,911,353
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.30
Mean single sequence MFE -28.64
Consensus MFE -25.09
Energy contribution -25.10
Covariance contribution 0.01
Combinations/Pair 1.10
Mean z-score -1.80
Structure conservation index 0.88
SVM decision value 0.04
SVM RNA-class probability 0.552624
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12911236 117 - 27905053
GCGGGGGCACUUGACUAAUAAUUUUUUCGUUGGUAUCUCAUCUAAUCCGAGAAAUCUCUCUUUU--UUUUGCUGUAUCGCAGCAGUAUCGAAUACCGAUUGAAUAUCGAUAUUC-UCCUG
.((((((...((((...........(((((((((((.((.........((((....))))....--..((((((.....))))))....))))))))).))))..))))....)-))))) ( -26.12)
>DroEre_CAF1 28733 120 - 1
GCGGGGGCACUUGACUAAUAAUUUUUUCGUUGGUAUCUCAUCUAAUCCGAGAAAUCUCUCUUUUUUUUUUGCUGUAUUGCAGCACUAUCGAAUACCGAUUCGAUAUUAAUAUAUGCCCUG
...((((((.............(((((((((((........))))..)))))))...............(((((.....))))).((((((((....))))))))........)))))). ( -28.80)
>DroYak_CAF1 29567 118 - 1
GCGGGGGCACUUGACUAAUAAUUUUUUCGUUGGUAUCUCAUCUAAUCCGAGAAAUCUCUCUUUU--UUUUGCUGUAUCGCAGCAGUAUCGAAUACCGAUUCGAUAUCGAUAUUCGCCCUG
...(((((.....(((((..(.....)..))))).....(((......((((....))))....--...(((((.....)))))(((((((((....))))))))).)))....))))). ( -31.00)
>consensus
GCGGGGGCACUUGACUAAUAAUUUUUUCGUUGGUAUCUCAUCUAAUCCGAGAAAUCUCUCUUUU__UUUUGCUGUAUCGCAGCAGUAUCGAAUACCGAUUCGAUAUCGAUAUUCGCCCUG
...(((((....((..((....))..))(((((((((..(((......((((....)))).........(((((.....)))))............)))..)))))))))....))))). (-25.09 = -25.10 +   0.01)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:05 2006