Locus 3328

Sequence ID 3R_DroMel_CAF1
Location 8,943,693 – 8,943,872
Length 179
Max. P 0.894014
window5363 window5364

overview

Window 3

Location 8,943,693 – 8,943,808
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 72.60
Mean single sequence MFE -19.98
Consensus MFE -6.18
Energy contribution -6.86
Covariance contribution 0.68
Combinations/Pair 1.17
Mean z-score -1.96
Structure conservation index 0.31
SVM decision value 0.98
SVM RNA-class probability 0.894014
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8943693 115 - 27905053
AAUAUACUGCUAAAAGGGGGUAGGAAUCUUACACCAAAAGAAAAUGGUAAUAAUCCCAUCUUUAGCAAAAACUUAGCAGAAGCGAUCGAAAAUAGUCGAAUGAUAGAAUCAACUA
.......(((((((..((((((((...)))))((((........))))......)))...)))))))........((....))..((((......))))................ ( -21.50)
>DroSec_CAF1 65324 94 - 1
AAUAUACUGCUAAAAGGGGAUAGGAAUCUUACACCCAAAGAAAUUGGUAAUAAUUCCAUCUUUU-------CUUAGCAUAAGCGAUUGAAAAUAGUCGAA--------------A
.......((((((.(((((((.(((((.......((((.....)))).....))))))))))))-------.))))))....((((((....))))))..--------------. ( -21.40)
>DroSim_CAF1 66721 108 - 1
AAUAUACUGCUAAAAGGGGAUAGGAAUCUUACACCCAAAGAAAUUGGUAACAAUCCAAUCUUUU-------UUUAGCAAAAGCGAUCAAAAAUAGUCGAGUGAUAGAAACAACUA
....(((((((((((((((((.(((.(.((((.....((....)).)))).).))).)))))))-------)))))).....((((........))))))))............. ( -23.90)
>DroEre_CAF1 71146 106 - 1
AAUAUACUGCUAAAAGGGGGUAGGAGUCUUACACCCAAAGAAAUUGCUAUUAACCCCGACUCUU-------CUUAGCAAAAGUGAUGAAAAAUCAACGAG--AUAGAAUCAGCUA
........(((....((((((((.(.((((.......))))...).))))...))))((.((((-------(((.((....))(((.....)))...)))--).))).))))).. ( -19.40)
>DroYak_CAF1 72040 88 - 1
AAUAUACUGCUAAAAGGGGGUAGGAAUCUUACACCCAAAGAAAACACUAUUAU-------------------------GAAGCGAUAAAAUUUCGACGGA--AUAGACUCAACUA
...............(((.(((((...))))).)))..........(((((.(-------------------------(...(((.......))).)).)--))))......... ( -13.70)
>consensus
AAUAUACUGCUAAAAGGGGGUAGGAAUCUUACACCCAAAGAAAUUGGUAAUAAUCCCAUCUUUU_______CUUAGCAAAAGCGAUCAAAAAUAGUCGAA__AUAGAAUCAACUA
...............(((.(((((...))))).)))..............................................((((........))))................. ( -6.18 =  -6.86 +   0.68)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,943,773 – 8,943,872
Length 99
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 79.29
Mean single sequence MFE -29.95
Consensus MFE -22.06
Energy contribution -22.83
Covariance contribution 0.78
Combinations/Pair 1.20
Mean z-score -1.68
Structure conservation index 0.74
SVM decision value 0.88
SVM RNA-class probability 0.874046
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8943773 99 - 27905053
AUCGCACUCCUUGUGGCAGUGGAUUUAGAAAACGGGGACAGCAGACAC-GACACGUCAACUUGCAAAUAUACUGCUAAAAGGGGG-----UAGGAAUCUUACACC
......((((((.((((((((.((((.......(....).((((((..-.....)))....))))))).)))))))).))))))(-----((((...)))))... ( -28.50)
>DroPse_CAF1 70537 97 - 1
GGCGCACUCG-CAUGGCAGUGGAUUUGGAAAAUGGGGACAGCAGAC------ACGUCAACUUGCAAAUAUACUGCUGCGAGGAGGAGAGGGAGGAGCC-UGCGCC
(((((.((((-((..((((((.(((((.((..((....))...((.------...))...)).))))).))))))))))))......(((......))-)))))) ( -37.00)
>DroSim_CAF1 66794 99 - 1
AUCGCACUCCUUGUGGCAGUGGAUUUGGAAAACGGGGACACCAGACAC-GACACGUCAACUUGCAAAUAUACUGCUAAAAGGGGA-----UAGGAAUCUUACACC
......((((((.((((((((.(((((.((...((.....)).(((..-.....)))...)).))))).)))))))).)))))).-----............... ( -28.90)
>DroEre_CAF1 71217 99 - 1
AUCGCACUCCUUGUGGCAGUGGAUUUGGAAAACGGGGACAGCAGACAC-GACACGUCAACUUGCAAAUAUACUGCUAAAAGGGGG-----UAGGAGUCUUACACC
......((((((.((((((((.(((((.((...(....)....(((..-.....)))...)).))))).)))))))).))))))(-----((((...)))))... ( -31.00)
>DroAna_CAF1 71881 91 - 1
AUCGCACUCUUUGGUCCACUGGAUUUGGAAAACGGGGACAGCAGACACCGACACGUCAAGUUGCAAAUAUACUGCCAAGAGGUGA-----AA---------CACU
.((((.(((((.(((((.(((...........))))))).((((....((((.......))))........))))))))))))))-----..---------.... ( -22.00)
>DroPer_CAF1 72178 97 - 1
GGCGCACUCG-CAUGGCAGUGGAUUUGGAAAAUGGGGACAGCAGAC------ACGUCAACUUGCAAAUAUACUGCUGAGAGGAGGAGAGGGAGGAGCC-UGCGCC
(((((.(((.-(.((((((((.(((((.((..((....))...((.------...))...)).))))).)))))))).)..)))...(((......))-)))))) ( -32.30)
>consensus
AUCGCACUCCUUGUGGCAGUGGAUUUGGAAAACGGGGACAGCAGACAC_GACACGUCAACUUGCAAAUAUACUGCUAAAAGGGGG_____UAGGAGUC_UACACC
......((((((.((((((((.(((((.((...(....)....(((........)))...)).))))).)))))))).))))))..................... (-22.06 = -22.83 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:31 2006