Locus 8056

Sequence ID 3R_DroMel_CAF1
Location 21,640,221 – 21,640,330
Length 109
Max. P 0.948426
window12969 window12970

overview

Window 9

Location 21,640,221 – 21,640,330
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.78
Mean single sequence MFE -27.54
Consensus MFE -19.30
Energy contribution -19.67
Covariance contribution 0.37
Combinations/Pair 1.38
Mean z-score -1.96
Structure conservation index 0.70
SVM decision value 1.38
SVM RNA-class probability 0.948426
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21640221 109 + 27905053
AAUUUUUUUUUAAGUGUAUGGCAAAAAGAAAGCAUUCUGCUGGC---------AUGCAUAUGAAUUUCUUCUAGGAUACUUUUUUUAUGCGGUU--UGCCGCCCACGUUCCGCACUUGGA
........(((((((((..(((..((((((((.(((((((....---------..))....(((....))).))))).))))))))..((((..--..))))....)))..))))))))) ( -26.40)
>DroSec_CAF1 129569 108 + 1
AAAUUU-UCUCAAGUGUAUGGAAAAAAGAAAGCAUUCUGCUGGC---------AUGCACAUGAAUUUCUUUUAGGAUACUUUUUUUAUGCGGUU--UGCCGCCCACGUUCCUCACUUGGA
......-..(((((((...((((.((((((((.((((((..(((---------((....))).....))..)))))).))))))))..((((..--..)))).....)))).))))))). ( -28.30)
>DroSim_CAF1 126169 108 + 1
AAAUUU-UCUCAAGUGUAUGGAAAAAAGAAAGCAUUCUGCUGGC---------AUGCACAUGAAUUUCUUCUAGGAUACUUUUUUUAUGCGGUU--UGCCGCCCACGUUCCGCACUUGGA
......-..((((((((..((((.((((((((.(((((((....---------..))....(((....))).))))).))))))))..((((..--..)))).....)))))))))))). ( -29.20)
>DroEre_CAF1 122109 107 + 1
AACUUU-UUCCAAGUGUAUGGAAAAAAGAAUGCAUUCUGCUGGC---------AUGCACAUGAAUUUCUUCUAGGAUACUUUUUU-AUGCGGCU--UGCCGCCCACGUUCCGCACUUGGA
......-.(((((((((..((((...((((....))))((.(((---------(.((.((((((..(((....)))......)))-)))..)).--)))))).....))))))))))))) ( -31.00)
>DroYak_CAF1 126785 96 + 1
AACUUU-UUCCAAGUGUAUGCGAAAAAGAAAGCAUUCUGC-----------------------AUUUCUUCCAGGAUACUUUUUUCAUGCGGUUCAUGCCGCCCAUGUUCCUCACUUGGA
......-.((((((((...(((...(((((((.((((((.-----------------------(.....).)))))).)))))))...(((((....)))))...)))....)))))))) ( -28.30)
>DroAna_CAF1 109201 112 + 1
UCAUUU-UGUUGAGUGUGUCCAAAA---AAAUCAUUUAGCUGGCCAAAUUUUCAUGCACUUCGAACUCUUUUAGGAGAUGCUUUU--UGCGGUU--UACCGCCCUCGUUUCGUGCUCAGA
......-.((((((((.........---....))))))))...............((((..(((.((((....))))........--.((((..--..))))..)))....))))..... ( -22.02)
>consensus
AAAUUU_UUUCAAGUGUAUGGAAAAAAGAAAGCAUUCUGCUGGC_________AUGCACAUGAAUUUCUUCUAGGAUACUUUUUUUAUGCGGUU__UGCCGCCCACGUUCCGCACUUGGA
.........(((((((...((((..(((((((.((((((................................)))))).)))))))...(((((....))))).....)))).))))))). (-19.30 = -19.67 +   0.37)

alignment

Postscript

secondary structure

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dotplot

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Window 0

Location 21,640,221 – 21,640,330
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.78
Mean single sequence MFE -26.45
Consensus MFE -13.66
Energy contribution -14.66
Covariance contribution 1.00
Combinations/Pair 1.24
Mean z-score -1.90
Structure conservation index 0.52
SVM decision value 0.24
SVM RNA-class probability 0.650726
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21640221 109 - 27905053
UCCAAGUGCGGAACGUGGGCGGCA--AACCGCAUAAAAAAAGUAUCCUAGAAGAAAUUCAUAUGCAU---------GCCAGCAGAAUGCUUUCUUUUUGCCAUACACUUAAAAAAAAAUU
(((......)))..((((((((..--..))(((((.....((....)).(((....))).)))))..---------))).((((((........))))))....)))............. ( -22.80)
>DroSec_CAF1 129569 108 - 1
UCCAAGUGAGGAACGUGGGCGGCA--AACCGCAUAAAAAAAGUAUCCUAAAAGAAAUUCAUGUGCAU---------GCCAGCAGAAUGCUUUCUUUUUUCCAUACACUUGAGA-AAAUUU
((((((((((((((....((((..--..)))).........)).))))((((((((..(((.(((..---------....)))..))).)))))))).......)))))).))-...... ( -26.12)
>DroSim_CAF1 126169 108 - 1
UCCAAGUGCGGAACGUGGGCGGCA--AACCGCAUAAAAAAAGUAUCCUAGAAGAAAUUCAUGUGCAU---------GCCAGCAGAAUGCUUUCUUUUUUCCAUACACUUGAGA-AAAUUU
((((((((.((((...((((((..--..))))......(((((((.((.(((....)))....((..---------....)))).)))))))))...))))...)))))).))-...... ( -27.20)
>DroEre_CAF1 122109 107 - 1
UCCAAGUGCGGAACGUGGGCGGCA--AGCCGCAU-AAAAAAGUAUCCUAGAAGAAAUUCAUGUGCAU---------GCCAGCAGAAUGCAUUCUUUUUUCCAUACACUUGGAA-AAAGUU
((((((((......((((((((..--..))))..-(((((((.......(((....)))..((((((---------.........)))))).))))))))))).)))))))).-...... ( -31.30)
>DroYak_CAF1 126785 96 - 1
UCCAAGUGAGGAACAUGGGCGGCAUGAACCGCAUGAAAAAAGUAUCCUGGAAGAAAU-----------------------GCAGAAUGCUUUCUUUUUCGCAUACACUUGGAA-AAAGUU
((((((((.((..((((.....))))..))((..(((((((((((.(((..(....)-----------------------.))).))))))).))))..))...)))))))).-...... ( -28.80)
>DroAna_CAF1 109201 112 - 1
UCUGAGCACGAAACGAGGGCGGUA--AACCGCA--AAAAGCAUCUCCUAAAAGAGUUCGAAGUGCAUGAAAAUUUGGCCAGCUAAAUGAUUU---UUUUGGACACACUCAACA-AAAUGA
.....((((....((((.((((..--..)))).--........(((......)))))))..))))......((((((....)))))).((((---(.((((......)))).)-)))).. ( -22.50)
>consensus
UCCAAGUGCGGAACGUGGGCGGCA__AACCGCAUAAAAAAAGUAUCCUAGAAGAAAUUCAUGUGCAU_________GCCAGCAGAAUGCUUUCUUUUUUCCAUACACUUGAAA_AAAUUU
..((((((..........((((......))))................((((((((......(((...............)))......)))))))).......)))))).......... (-13.66 = -14.66 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:31 2006