Locus 2008

Sequence ID 3L_DroMel_CAF1
Location 5,517,432 – 5,517,539
Length 107
Max. P 0.984044
window3143 window3144

overview

Window 3

Location 5,517,432 – 5,517,539
Length 107
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 80.84
Mean single sequence MFE -31.81
Consensus MFE -16.07
Energy contribution -16.91
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -1.95
Structure conservation index 0.51
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5517432 107 + 23771897
CAUCGGAUUAGAAGGGGUCCUUGAGGCG--UUUCUACGCAUUUCCAAGAAUCUUCAUUAA--ACAAACAGCCCUACGGUGGGUUGAAUUCUAAGAAAUGAGCAGAAACCGC
....(((((......))))).....(((--(((((.(.((((((..(((((.........--.....((((((......)))))).)))))..)))))).).))))).))) ( -27.56)
>DroSec_CAF1 79154 106 + 1
CAUCGGAUUAGAAGGGGUCCUUCAGGGG--UUUCUACGCAUUUCCAAGAAUCUU-GUUAA--CCAAACAGCUCUACGGUGGGUGGAAUUCUAGGAAAUGAGCAGAAGCCGC
..........(((((...))))).(.((--(((((.(.(((((((.(((((.(.-.(..(--((............)))..)..).))))).))))))).).))))))).) ( -34.10)
>DroSim_CAF1 80653 106 + 1
CAUCGGAUUAGAAGGGGUCCUUCAGGGG--UUUCCACGCAUUUCCAAGAAUCUU-GUUAA--CCAAACAGCACUACGGUGGUUUGAAUUCUAGGAAAUGAGCAGAAACCGC
..........(((((...))))).(.((--((((..(.(((((((.(((((.((-(((..--...)))))(((....)))......))))).))))))).)..)))))).) ( -32.30)
>DroEre_CAF1 79903 95 + 1
CGUCGGAUUAGAGGCGGUCCUACUGGCG--UUUCCACGCAUUUCCACGAAUGUC-AUCAA--CCAAACG----------G-UUGGAAUUCUAGGAAAUGCGCAGAAACCGC
.(((((.....(((....))).)))))(--((((..(((((((((..((((...-.((((--((....)----------)-)))).))))..)))))))))..)))))... ( -34.00)
>DroYak_CAF1 68045 100 + 1
CGUCGGAUUAGCAAGGCUCCUACUGGCGCAUUUCUACGCAUUUCCAAGAAUGCC-AUUAAACCCAAACG----------GGGUUGAAUUCUAGGAAAUGAGCAGAAACCGC
...(((.........((.((....)).)).(((((.(.(((((((.(((((...-....(((((.....----------)))))..))))).))))))).).)))))))). ( -31.10)
>consensus
CAUCGGAUUAGAAGGGGUCCUUCAGGCG__UUUCUACGCAUUUCCAAGAAUCUU_AUUAA__CCAAACAGC_CUACGGUGGGUUGAAUUCUAGGAAAUGAGCAGAAACCGC
....(((((......)))))....((....(((((.(.(((((((.(((((...................................))))).))))))).).))))))).. (-16.07 = -16.91 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,517,432 – 5,517,539
Length 107
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 80.84
Mean single sequence MFE -34.14
Consensus MFE -21.03
Energy contribution -21.43
Covariance contribution 0.40
Combinations/Pair 1.15
Mean z-score -2.76
Structure conservation index 0.62
SVM decision value 1.96
SVM RNA-class probability 0.984044
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5517432 107 - 23771897
GCGGUUUCUGCUCAUUUCUUAGAAUUCAACCCACCGUAGGGCUGUUUGU--UUAAUGAAGAUUCUUGGAAAUGCGUAGAAA--CGCCUCAAGGACCCCUUCUAAUCCGAUG
(((.(((((((.(((((((.((((((((.(((......))).)).....--........)))))).))))))).)))))))--))).....(((..........))).... ( -29.61)
>DroSec_CAF1 79154 106 - 1
GCGGCUUCUGCUCAUUUCCUAGAAUUCCACCCACCGUAGAGCUGUUUGG--UUAAC-AAGAUUCUUGGAAAUGCGUAGAAA--CCCCUGAAGGACCCCUUCUAAUCCGAUG
..((.((((((.(((((((.((((((......((((..........)))--)....-..)))))).))))))).)))))).--))...(((((...))))).......... ( -31.20)
>DroSim_CAF1 80653 106 - 1
GCGGUUUCUGCUCAUUUCCUAGAAUUCAAACCACCGUAGUGCUGUUUGG--UUAAC-AAGAUUCUUGGAAAUGCGUGGAAA--CCCCUGAAGGACCCCUUCUAAUCCGAUG
..((((((..(.(((((((.((((((((((((((....)))..))))).--.....-..)))))).))))))).)..))))--))...(((((...))))).......... ( -34.60)
>DroEre_CAF1 79903 95 - 1
GCGGUUUCUGCGCAUUUCCUAGAAUUCCAA-C----------CGUUUGG--UUGAU-GACAUUCGUGGAAAUGCGUGGAAA--CGCCAGUAGGACCGCCUCUAAUCCGACG
((((((.((((((((((((..(((((((((-(----------(....))--)))..-)).))))..))))))))(((....--)))..))))))))))............. ( -38.70)
>DroYak_CAF1 68045 100 - 1
GCGGUUUCUGCUCAUUUCCUAGAAUUCAACCC----------CGUUUGGGUUUAAU-GGCAUUCUUGGAAAUGCGUAGAAAUGCGCCAGUAGGAGCCUUGCUAAUCCGACG
((((((((((((.((((((.((((((((((((----------.....))))....)-)).))))).))))))(((((....))))).))))))))))..)).......... ( -36.60)
>consensus
GCGGUUUCUGCUCAUUUCCUAGAAUUCAACCCACCGUAG_GCUGUUUGG__UUAAU_AAGAUUCUUGGAAAUGCGUAGAAA__CGCCUGAAGGACCCCUUCUAAUCCGAUG
.(((.((((((.(((((((.((((((.................................)))))).))))))).))))))........((((.....))))....)))... (-21.03 = -21.43 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:21 2006