Locus 9825

Sequence ID 3R_DroMel_CAF1
Location 26,132,828 – 26,132,961
Length 133
Max. P 0.870244
window15691 window15692

overview

Window 1

Location 26,132,828 – 26,132,931
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.18
Mean single sequence MFE -34.77
Consensus MFE -18.20
Energy contribution -19.09
Covariance contribution 0.89
Combinations/Pair 1.22
Mean z-score -2.63
Structure conservation index 0.52
SVM decision value 0.87
SVM RNA-class probability 0.870244
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26132828 103 - 27905053
UCCUGUCAGCUCCAGCUAUAU--------------AGCUUAUAGCAUAUAGCUGUCAUUGGAACAAUCAAUGGGCAUUGGAUUUUGG-GGGCUGGCCG--GUUCUUCCUGUCUGAAAUUU
.((.(((((((((((((((((--------------.((.....)))))))))).(((((((.....))))))).............)-)))))))).)--)................... ( -33.80)
>DroSec_CAF1 123400 100 - 1
UCCUGUCAGCUCCAGCUAUAU--------------AGCUUAUAGCAUAUAGCUGUCAUUGGAACAAUCAAUGGGCAUUGGAUUU-CU-GGGCUGGCCG--GUUCUUCCUGUCUGGAAU--
.((.(((((((((((((((((--------------.((.....)))))))))))(((((((.....)))))))...........-..-)))))))).)--)...((((.....)))).-- ( -35.30)
>DroSim_CAF1 129297 99 - 1
UCCUGUCAGCUCCAGCUAUAU--------------AGCUUAUAGCAUAUAGCUGUCAUUGGAACAAUCAAUGGGCAUUGGAUU--GG-GGGCUGGCCG--GUUCUUCCUGUCUGGAAU--
.((.(((((((((((((((((--------------.((.....))))))))))..........((((((((....))).))))--))-)))))))).)--)...((((.....)))).-- ( -37.30)
>DroEre_CAF1 132089 115 - 1
UCCUGUCAGCUCCAGCUAUAUUGCUUAUAGCUUAUAGCUUAUAGCAUAUAGCUGUCAUUGGAACAAUCAAUGGGCAUUGGAUUU-GG-GGGCUGGCCG--GUUCUUCCUGUCUGGAAUU-
.((.(((((((((((((((((.(((...(((.....)))...))))))))))).(((((((.....)))))))...........-.)-)))))))).)--)...((((.....))))..- ( -42.60)
>DroYak_CAF1 130853 111 - 1
UCCUGUCAGCUUCAGCUAUAUAGCUUAU-----AUAGCUUAUAGCAUAUAGCUGUCAUUGGAACAAUCAAGGGGCAUUCGAUUU-GGGGGGCUGGCCG--GUUCUUCCUGUCUGGAAUU-
.((.(((((((((((((((((.(((.((-----(.....))))))))))))))(((.((((.....))))..))).........-..))))))))).)--)...((((.....))))..- ( -34.90)
>DroPer_CAF1 133585 108 - 1
UCCUGUCAAUCCC--CUAGACCGCCC----CCCACCCCCUUUGGCCGAUAGCUGUCAUUGGAACAAUCAGUCAGCAUUCGAUU--GG-UCCGUGGUCAGUGUUCUUCCUGUCCGAC-U--
....(((......--...(((((((.----............)))(((..((((..(((((.....)))))))))..)))...--))-))...((.(((........))).)))))-.-- ( -24.72)
>consensus
UCCUGUCAGCUCCAGCUAUAU______________AGCUUAUAGCAUAUAGCUGUCAUUGGAACAAUCAAUGGGCAUUGGAUUU_GG_GGGCUGGCCG__GUUCUUCCUGUCUGGAAU__
....((((((((..((((((...................)))))).....(((..((((((.....))))))))).............))))))))........((((.....))))... (-18.20 = -19.09 +   0.89)

alignment

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secondary structure

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dotplot

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Window 2

Location 26,132,865 – 26,132,961
Length 96
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 79.80
Mean single sequence MFE -29.68
Consensus MFE -16.07
Energy contribution -16.24
Covariance contribution 0.17
Combinations/Pair 1.29
Mean z-score -2.23
Structure conservation index 0.54
SVM decision value 0.56
SVM RNA-class probability 0.782886
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26132865 96 + 27905053
CCAAUGCCCAUUGAUUGUUCCAAUGACAGCUAUAUGCUAUAAGCU--------------AUAUAGCUGGAGCUGACAGGAGGCGGAUCU--GACUCAUGUAGAUCUCGAAAU---
.....(((..(((...((((((......(((((((((.....)).--------------)))))))))))))...)))..)))((((((--(.(....))))))))......--- ( -29.30)
>DroSec_CAF1 123434 94 + 1
CCAAUGCCCAUUGAUUGUUCCAAUGACAGCUAUAUGCUAUAAGCU--------------AUAUAGCUGGAGCUGACAGGAGGCGGAUCU--GACUCAU--AUAUUUCGAAAU---
....((((..(((...((((((......(((((((((.....)).--------------)))))))))))))...)))..)))).....--.......--............--- ( -23.50)
>DroSim_CAF1 129330 94 + 1
CCAAUGCCCAUUGAUUGUUCCAAUGACAGCUAUAUGCUAUAAGCU--------------AUAUAGCUGGAGCUGACAGGAGGCGGAUCU--GACUCAU--AGAUUUCGAAAU---
.....(((..(((...((((((......(((((((((.....)).--------------)))))))))))))...)))..)))((((((--(.....)--))))))......--- ( -25.70)
>DroEre_CAF1 132124 108 + 1
CCAAUGCCCAUUGAUUGUUCCAAUGACAGCUAUAUGCUAUAAGCUAUAAGCUAUAAGCAAUAUAGCUGGAGCUGACAGGAGGCGGAUCU--GACUCAU--AGAUCUCGAAAC---
.....(((..(((...((((((......((((((((((...(((.....)))...))).)))))))))))))...)))..)))((((((--(.....)--))))))......--- ( -32.60)
>DroYak_CAF1 130889 103 + 1
CGAAUGCCCCUUGAUUGUUCCAAUGACAGCUAUAUGCUAUAAGCUAU-----AUAAGCUAUAUAGCUGAAGCUGACAGGAGGCGGAUCU--GACUCAU--AGAUCUCGAAAC---
(((.((((.((((((((...))))..(((((.((.((((((((((..-----...)))).)))))))).))))).)))).))))(((((--(.....)--))))))))....--- ( -33.00)
>DroPer_CAF1 133619 105 + 1
CGAAUGCUGACUGAUUGUUCCAAUGACAGCUAUCGGCCAAAGGGGGUGGG----GGGCGGUCUAG--GGGAUUGACAGGAGGCGGAUGUGUGACUCGC--GAAUC--GAAAAAGC
(((.((((..(((...(((((...(((.(((..(.(((......))).).----.))).)))...--)))))...)))..))))..((((.....)))--)..))--)....... ( -34.00)
>consensus
CCAAUGCCCAUUGAUUGUUCCAAUGACAGCUAUAUGCUAUAAGCU______________AUAUAGCUGGAGCUGACAGGAGGCGGAUCU__GACUCAU__AGAUCUCGAAAU___
....((((..(((...(((((......(((((((((((...)))...............)))))))))))))...)))..))))(((((...........))))).......... (-16.07 = -16.24 +   0.17)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:43:03 2006