Locus 3782

Sequence ID 3R_DroMel_CAF1
Location 10,250,999 – 10,251,091
Length 92
Max. P 0.880568
window6064 window6065

overview

Window 4

Location 10,250,999 – 10,251,091
Length 92
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.78
Mean single sequence MFE -24.07
Consensus MFE -20.31
Energy contribution -19.87
Covariance contribution -0.44
Combinations/Pair 1.18
Mean z-score -1.96
Structure conservation index 0.84
SVM decision value 0.91
SVM RNA-class probability 0.880568
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10250999 92 + 27905053
GUGGGCAGCG-CUGUGACACAUUUUGUCAUCAUUAGGCACAGUUGCCGGCUAAUAAUUUUAAUUUAGCCA----AAA----------------------AAUUAGUUGUAUUCGUUGGU
...(((((((-((((((((.....)))))).....)))...))))))((((((..........)))))).----...----------------------.................... ( -23.30)
>DroVir_CAF1 125999 90 + 1
GUGGGCAGCA-CUGUGACACAUUUUGUCAUCAUUAGCCACAGUUACCGGCUAAUAAUUUCAAUUUAGCCA----AAA----------------------AAUUAGCUGCAUUC--AGCU
....((((((-(((((.....................))))))....((((((..........)))))).----...----------------------.....)))))....--.... ( -22.40)
>DroGri_CAF1 114311 112 + 1
GUGGGCAGCA-GUGUGACACAUUUUGUCAUCAUUAGCCACAGUUGCCGGCUAAUAAUUUCAAUUUAGCCA----AAAAAAAAAAAAAAGAAGAAAAUAAAAUUAGCCGCAUUG--AGCU
(((((((((.-((((((((.....)))))........))).))))))((((((..........)))))).----................................)))....--.... ( -25.20)
>DroWil_CAF1 122268 94 + 1
GUGGGCAGCGGCUGUGACACAUUUUGUCAUCAUUAGCCACAGUUGCCGGCUAAUAAUUUCAAUUUGGCCAACAAAAA----------------------AAUUAGUUGCAUAUAUU---
(((((((((((((((((((.....))))))....))))...))))))((((((..........))))))........----------------------.........))).....--- ( -27.30)
>DroMoj_CAF1 119515 90 + 1
GUGGGCAGCA-CUGUGACACAUUUUGUCAUCAUUAGCCACAGUUGCCGGCUAAUAAUUUCAAUUUAGCCA----AAA----------------------AAUUAGCUGCAUUG--AGCU
....((((((-(((((.....................))))))....((((((..........)))))).----...----------------------.....)))))....--.... ( -22.40)
>DroAna_CAF1 98179 92 + 1
GUGGGCAGCG-CUGUGACACAUUUUGUCAUCAUUAGGCACAGUCGCCGGCUAAUAAUUUCAAUUUGGCCA----AAA----------------------AAUUAGUUGCAUUUCGGAGU
....(((((.-..((((((.....)))))).....(((......)))((((((..........)))))).----...----------------------.....))))).......... ( -23.80)
>consensus
GUGGGCAGCA_CUGUGACACAUUUUGUCAUCAUUAGCCACAGUUGCCGGCUAAUAAUUUCAAUUUAGCCA____AAA______________________AAUUAGCUGCAUUC__AGCU
....(((((....((((((.....)))))).................((((((..........))))))...................................))))).......... (-20.31 = -19.87 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,250,999 – 10,251,091
Length 92
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 81.78
Mean single sequence MFE -23.21
Consensus MFE -16.52
Energy contribution -17.55
Covariance contribution 1.03
Combinations/Pair 1.11
Mean z-score -1.95
Structure conservation index 0.71
SVM decision value 0.56
SVM RNA-class probability 0.782003
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10250999 92 - 27905053
ACCAACGAAUACAACUAAUU----------------------UUU----UGGCUAAAUUAAAAUUAUUAGCCGGCAACUGUGCCUAAUGAUGACAAAAUGUGUCACAG-CGCUGCCCAC
....................----------------------...----.((((((..........))))))((((...((((....((.(((((.....))))))))-)))))))... ( -19.90)
>DroVir_CAF1 125999 90 - 1
AGCU--GAAUGCAGCUAAUU----------------------UUU----UGGCUAAAUUGAAAUUAUUAGCCGGUAACUGUGGCUAAUGAUGACAAAAUGUGUCACAG-UGCUGCCCAC
((((--(....)))))....----------------------...----.(((...((((..(((((((((((.......)))))))))))((((.....)))).)))-)...)))... ( -28.20)
>DroGri_CAF1 114311 112 - 1
AGCU--CAAUGCGGCUAAUUUUAUUUUCUUCUUUUUUUUUUUUUU----UGGCUAAAUUGAAAUUAUUAGCCGGCAACUGUGGCUAAUGAUGACAAAAUGUGUCACAC-UGCUGCCCAC
((((--((((..((((((..........................)----)))))..))))).(((((((((((.(....))))))))))))((((.....))))....-.)))...... ( -25.57)
>DroWil_CAF1 122268 94 - 1
---AAUAUAUGCAACUAAUU----------------------UUUUUGUUGGCCAAAUUGAAAUUAUUAGCCGGCAACUGUGGCUAAUGAUGACAAAAUGUGUCACAGCCGCUGCCCAC
---.......(((.......----------------------...((((((((..(((.......))).))))))))..((((((...(.(((((.....))))))))))))))).... ( -22.50)
>DroMoj_CAF1 119515 90 - 1
AGCU--CAAUGCAGCUAAUU----------------------UUU----UGGCUAAAUUGAAAUUAUUAGCCGGCAACUGUGGCUAAUGAUGACAAAAUGUGUCACAG-UGCUGCCCAC
((((--((((..((((((..----------------------..)----)))))..))))).(((((((((((.(....))))))))))))((((.....))))....-.)))...... ( -27.50)
>DroAna_CAF1 98179 92 - 1
ACUCCGAAAUGCAACUAAUU----------------------UUU----UGGCCAAAUUGAAAUUAUUAGCCGGCGACUGUGCCUAAUGAUGACAAAAUGUGUCACAG-CGCUGCCCAC
...((((((...........----------------------)))----)))...................(((((.((((..(....)..((((.....))))))))-)))))..... ( -15.60)
>consensus
AGCU__AAAUGCAACUAAUU______________________UUU____UGGCUAAAUUGAAAUUAUUAGCCGGCAACUGUGGCUAAUGAUGACAAAAUGUGUCACAG_CGCUGCCCAC
..........((......................................((((((..........))))))((((.(((((((.................))))))).)))))).... (-16.52 = -17.55 +   1.03)

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 11:09:59 2006