Locus 8657

Sequence ID 3R_DroMel_CAF1
Location 23,149,395 – 23,149,575
Length 180
Max. P 0.815884
window13902 window13903

overview

Window 2

Location 23,149,395 – 23,149,498
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.49
Mean single sequence MFE -23.70
Consensus MFE -14.64
Energy contribution -14.45
Covariance contribution -0.19
Combinations/Pair 1.19
Mean z-score -1.43
Structure conservation index 0.62
SVM decision value 0.66
SVM RNA-class probability 0.815884
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23149395 103 - 27905053
CUGGGGCAAGAGUGAAUUUUAAGCUGCGCGCAAACAGCUUGAGCAAAUUCAUUAACAACAGAGCCAGAAC------------CGACGCCC-CCGAUCCAAAU----CCAAAUCCAAAAUC
..(((((...((((((((((((((((........))))))))...)))))))).............(...------------...)))))-)..........----.............. ( -23.30)
>DroPse_CAF1 4267 112 - 1
AAGGGGGAAGGGUAAGUUUUAAGCUGAGGGCAAACAGCUUGUGCAAAUUCAUUAACAACAGAGCCCGUCCU--CAUUCGAAAAGACCCAU-U-----CCAUUCCAUCCCAGCACAGAUUU
..(((((((((((...(((..((.(((((((.....((((.((............))...))))..)))))--))))..)))..)))).)-)-----)).......)))........... ( -28.21)
>DroSec_CAF1 320 94 - 1
CUGGGGCAAGAGUGAAUUUUAAGCUG---------AGCUUGAGCAAAUUCAUUAACAACAGAACCAGAGC------------CGACGCCC-CCGAUCCAAAU----CCAAAUCCAAAAUC
..(((((...((((((((((((((..---------.))))))...)))))))).............(...------------...)))))-)..........----.............. ( -17.90)
>DroSim_CAF1 4692 103 - 1
CUGGGGCAAGAGUGAAUUUUAAGCUGCGCGCAAACAGCUUGAGCAAAUUCAUUAACAACAGAACCAGAAC------------CGACGCCC-CCGAUCCAAAU----CCAAAUCCAAAAUC
..(((((...((((((((((((((((........))))))))...)))))))).............(...------------...)))))-)..........----.............. ( -23.30)
>DroYak_CAF1 4733 120 - 1
CCGGGGCAAGAGUGAAUUUUAAGCUGUGCGCAAACAGCUUGAGCAAAUUCAUUAACAACAGAACCAGAACCAGAACCAGAAACGACGCCCCCCAAUCCAAAUCCAUCCAAAUCCAAAAUC
..(((((...(((((((((((((((((......)))))))))...)))))))).........................(......))))))............................. ( -26.30)
>DroPer_CAF1 4260 107 - 1
AAGGGGGAAGAGUAAGUUUUAAGCUGAGGGCAAACAGCUUGUGCAAAUUCAUUAACAACAGAGCCCGUCCU--CAUUCGAAAAGACCCAU-U----------CCAUCCCAGCACAGAUUU
..(((((((..((...(((..((.(((((((.....((((.((............))...))))..)))))--))))..)))..))...)-)----------))..)))........... ( -23.20)
>consensus
CUGGGGCAAGAGUGAAUUUUAAGCUGAGCGCAAACAGCUUGAGCAAAUUCAUUAACAACAGAACCAGAAC____________CGACGCCC_CCGAUCCAAAU____CCAAAUCCAAAAUC
...((((...((((((((((((((((........)))))))...)))))))))..(....).........................)))).............................. (-14.64 = -14.45 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 23,149,458 – 23,149,575
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 89.03
Mean single sequence MFE -29.27
Consensus MFE -22.60
Energy contribution -23.73
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -1.84
Structure conservation index 0.77
SVM decision value 0.54
SVM RNA-class probability 0.774099
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23149458 117 + 27905053
AAGCUGUUUGCGCGCAGCUUAAAAUUCACUCUUGCCCCAGGCUGGUGGUAGCUAGGAAACUGAACCACACAAUAAGAAAUAAAGGCAGCCAUUAUGCUGAAUUAUGCAUUAUUGAAU
(((((((......))))))).............(((...)))..(((((...(((....))).))))).((((((...((((...((((......))))..))))...))))))... ( -31.60)
>DroSec_CAF1 383 108 + 1
AAGCU---------CAGCUUAAAAUUCACUCUUGCCCCAGGCUGGUGGUAGCUAGGAAACUGAACCACACAAUAAGAAAUAAAGGCAGCCAUUAUGCUGAAUUAUGCCUUAUUGAAU
.....---------((((((..................))))))(((((...(((....))).))))).(((((((..((((...((((......))))..))))..)))))))... ( -28.77)
>DroSim_CAF1 4755 117 + 1
AAGCUGUUUGCGCGCAGCUUAAAAUUCACUCUUGCCCCAGGCUGGUGGUAGCUAGGAAACUGAACCACACAAUAAGAAAUAAAGGCAGCCAUUAUGCUGAAUUAUGCUUUAUUGAAU
(((((((......))))))).............(((...)))..(((((...(((....))).))))).(((((((..((((...((((......))))..))))..)))))))... ( -31.80)
>DroYak_CAF1 4813 114 + 1
AAGCUGUUUGCGCACAGCUUAAAAUUCACUCUUGCCCCGGGCUG---GUAGCUAGGAAACUGAACUGCACAAUGAGAAAUAAGGGAAAUCAUUAUACUGAAUUAUGAGUUAUUAAAU
(((((((......)))))))..((((((((((((((...)))((---((((.(((....)))..)))).)).........)))))...(((......)))....))))))....... ( -24.90)
>consensus
AAGCUGUUUGCGCGCAGCUUAAAAUUCACUCUUGCCCCAGGCUGGUGGUAGCUAGGAAACUGAACCACACAAUAAGAAAUAAAGGCAGCCAUUAUGCUGAAUUAUGCAUUAUUGAAU
(((((((......))))))).............(((...)))..(((((...(((....))).))))).((((((...((((...((((......))))..))))...))))))... (-22.60 = -23.73 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:16:29 2006