Locus 722

Sequence ID 3L_DroMel_CAF1
Location 2,197,348 – 2,197,476
Length 128
Max. P 0.969970
window1107 window1108 window1109

overview

Window 7

Location 2,197,348 – 2,197,448
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 82.54
Mean single sequence MFE -38.88
Consensus MFE -26.80
Energy contribution -28.88
Covariance contribution 2.08
Combinations/Pair 1.12
Mean z-score -2.43
Structure conservation index 0.69
SVM decision value 1.38
SVM RNA-class probability 0.948420
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2197348 100 + 23771897
GCAGGCAAACACGGCAGACGACGUCAUGCCGAUGUAUCCAAUGGAUCCUAUGGAAACGAUGGCUCCGAUGGAGCCGGCAUUCCAUGGGUGUCCUCUUCGA
...((...(((((((((((...))).))))).)))..))...(((((((((((((....(((((((...)))))))...))))))))).))))....... ( -42.70)
>DroSec_CAF1 249353 100 + 1
GCAGGCAAACACGGCAGACGACGUCAUGCCGAUGUAUCCAGUGGAUCCUAUGGAUACGAUGGCUCCGAUGGAGCCAGCAUUCCAUGGGUGUCCUCUUCGG
...((...(((((((((((...))).))))).)))..))((.((((((((((((.....(((((((...)))))))....)))))))).)))).)).... ( -44.10)
>DroSim_CAF1 249826 100 + 1
GCAGGCAAACACGGCAGACGACGUCAUGCCGAUGUAUCCAGUGGAUCCUAUGGAUACGAUGGCUCCGAUGGAGCCAGCAUUCCAUGGGUGUCCUCUUCGG
...((...(((((((((((...))).))))).)))..))((.((((((((((((.....(((((((...)))))))....)))))))).)))).)).... ( -44.10)
>DroEre_CAF1 254696 91 + 1
GCAGGCAAACACGGCAGACGACGGCAUGCCAAU---------GGAUCCGAUGAAUCCGACGGCUCCGAUGGAGCCGUCAUUCCAUGAGUGUUCUGUUCGG
.(..((((((((((((..(....)..)))).((---------(((((....))....(((((((((...)))))))))..)))))..))))).)))..). ( -35.60)
>DroYak_CAF1 248334 82 + 1
GCAGGCAAACACGGCAGACGACGGCUUGCC------------------GAUGAAUCCGAUGGCUCCAAUGGAGCCGGCAUUCCAUGGGUGUUCCGUUCCG
...........(((.....(((((..((((------------------.((((((((...((((((...)))))))).))).))).))))..)))))))) ( -27.90)
>consensus
GCAGGCAAACACGGCAGACGACGUCAUGCCGAUGUAUCCA_UGGAUCCUAUGGAUACGAUGGCUCCGAUGGAGCCGGCAUUCCAUGGGUGUCCUCUUCGG
...((((...(((........)))..))))............((((((((((((.....(((((((...)))))))....)))))))).))))....... (-26.80 = -28.88 +   2.08) 

alignment

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secondary structure

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dotplot

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Window 8

Location 2,197,348 – 2,197,448
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 82.54
Mean single sequence MFE -36.58
Consensus MFE -27.62
Energy contribution -28.46
Covariance contribution 0.84
Combinations/Pair 1.13
Mean z-score -2.10
Structure conservation index 0.76
SVM decision value 1.09
SVM RNA-class probability 0.912931
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2197348 100 - 23771897
UCGAAGAGGACACCCAUGGAAUGCCGGCUCCAUCGGAGCCAUCGUUUCCAUAGGAUCCAUUGGAUACAUCGGCAUGACGUCGUCUGCCGUGUUUGCCUGC
.......(((..((.((((((((..((((((...))))))..)).)))))).)).)))...((..(((.(((((.(((...)))))))))))...))... ( -37.40)
>DroSec_CAF1 249353 100 - 1
CCGAAGAGGACACCCAUGGAAUGCUGGCUCCAUCGGAGCCAUCGUAUCCAUAGGAUCCACUGGAUACAUCGGCAUGACGUCGUCUGCCGUGUUUGCCUGC
....((.(((..((.((((((((.(((((((...))))))).))).))))).)).))).))((..(((.(((((.(((...)))))))))))...))... ( -40.20)
>DroSim_CAF1 249826 100 - 1
CCGAAGAGGACACCCAUGGAAUGCUGGCUCCAUCGGAGCCAUCGUAUCCAUAGGAUCCACUGGAUACAUCGGCAUGACGUCGUCUGCCGUGUUUGCCUGC
....((.(((..((.((((((((.(((((((...))))))).))).))))).)).))).))((..(((.(((((.(((...)))))))))))...))... ( -40.20)
>DroEre_CAF1 254696 91 - 1
CCGAACAGAACACUCAUGGAAUGACGGCUCCAUCGGAGCCGUCGGAUUCAUCGGAUCC---------AUUGGCAUGCCGUCGUCUGCCGUGUUUGCCUGC
.....(((..((..(((((.(((((((((((...)))((((..(((((.....)))))---------..))))..))))))))...)))))..)).))). ( -36.40)
>DroYak_CAF1 248334 82 - 1
CGGAACGGAACACCCAUGGAAUGCCGGCUCCAUUGGAGCCAUCGGAUUCAUC------------------GGCAAGCCGUCGUCUGCCGUGUUUGCCUGC
.((.((((...((..((((..((((((((((...))))))....((....))------------------))))..)))).))...)))).....))... ( -28.70)
>consensus
CCGAAGAGGACACCCAUGGAAUGCCGGCUCCAUCGGAGCCAUCGUAUCCAUAGGAUCCA_UGGAUACAUCGGCAUGACGUCGUCUGCCGUGUUUGCCUGC
.......((((((((((((((((.(((((((...))))))).))).))))).))................((((.(((...)))))))))))))...... (-27.62 = -28.46 +   0.84) 

alignment

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secondary structure

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dotplot

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Window 9

Location 2,197,384 – 2,197,476
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 83.59
Mean single sequence MFE -36.08
Consensus MFE -26.30
Energy contribution -28.82
Covariance contribution 2.52
Combinations/Pair 1.13
Mean z-score -2.56
Structure conservation index 0.73
SVM decision value 1.65
SVM RNA-class probability 0.969970
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2197384 92 + 23771897
UCCAAUGGAUCCUAUGGAAACGAUGGCUCCGAUGGAGCCGGCAUUCCAUGGGUGUCCUCUUCGAAUGGCUGAAAGCGGAGAGUAUCUGCUGC
......(((((((((((((....(((((((...)))))))...))))))))).))))..((((......))))((((((.....)))))).. ( -37.00)
>DroSec_CAF1 249389 92 + 1
UCCAGUGGAUCCUAUGGAUACGAUGGCUCCGAUGGAGCCAGCAUUCCAUGGGUGUCCUCUUCGGAUGGCUGAAAGCGGAGAGUAUCUGCUGC
..((((((((((((((((.....(((((((...)))))))....)))))))).))))((....))..))))..((((((.....)))))).. ( -43.00)
>DroSim_CAF1 249862 92 + 1
UCCAGUGGAUCCUAUGGAUACGAUGGCUCCGAUGGAGCCAGCAUUCCAUGGGUGUCCUCUUCGGAUGGCUGAAAGCGGAGAGUAUCUGCUGC
..((((((((((((((((.....(((((((...)))))))....)))))))).))))((....))..))))..((((((.....)))))).. ( -43.00)
>DroEre_CAF1 254729 86 + 1
------GGAUCCGAUGAAUCCGACGGCUCCGAUGGAGCCGUCAUUCCAUGAGUGUUCUGUUCGGAUGGCUAAGAGCGGAGAGUAGAUGCUGC
------((((.......))))(((((((((...)))))))))....(((.....((((((((..........)))))))).....))).... ( -29.40)
>DroYak_CAF1 248364 80 + 1
------------GAUGAAUCCGAUGGCUCCAAUGGAGCCGGCAUUCCAUGGGUGUUCCGUUCCGAUGGCUGAAAGCGGAGAGCAUCUGCUGC
------------((((..((((.(((((((...))))))).....((((.((.........)).)))).......))))...))))...... ( -28.00)
>consensus
UCCA_UGGAUCCUAUGGAUACGAUGGCUCCGAUGGAGCCGGCAUUCCAUGGGUGUCCUCUUCGGAUGGCUGAAAGCGGAGAGUAUCUGCUGC
......((((((((((((.....(((((((...)))))))....)))))))).))))..(((((....)))))((((((.....)))))).. (-26.30 = -28.82 +   2.52) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:29 2006