Locus 253

Sequence ID 2R_DroMel_CAF1
Location 1,636,388 – 1,636,557
Length 169
Max. P 0.972362
window540 window541 window542 window543

overview

Window 0

Location 1,636,388 – 1,636,482
Length 94
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 85.59
Mean single sequence MFE -28.27
Consensus MFE -20.74
Energy contribution -20.55
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.98
Structure conservation index 0.73
SVM decision value 0.74
SVM RNA-class probability 0.838261
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1636388 94 - 20766785
GGAACGGGAA---------UGGCAGAAAUGGCAAACAGGUGCCAUUGUAUGUGCUCUUGUAUCAAUUGCAUUGAGUGCCUUAUCUUGUCAGCCUUUUCUAGCU
((((.(((..---------((((((((((((((......)))))))....(..(((.((((.....))))..)))..)....)).))))).))).)))).... ( -29.30)
>DroSec_CAF1 22185 93 - 1
GGAACGGG-A---------UGGCAGAAAUGGCAAACAGGUGCCAUUGUAUGUGCUCUUGUAUCAAUUGCAUUGAGUGCCUUAUCUUGUCAGCCUUUUCUAGAU
((((.(((-.---------((((((((((((((......)))))))....(..(((.((((.....))))..)))..)....)).))))).))).)))).... ( -30.70)
>DroSim_CAF1 20614 93 - 1
GGAACGGG-A---------UGGCAGAAAUGGCAAACAGGUGCCAUUGUAUGUGCUCUUGUAUCAAUUGCAUUGAGUGCCUUAUCUUGUCAGCCUUUUCUAGAU
((((.(((-.---------((((((((((((((......)))))))....(..(((.((((.....))))..)))..)....)).))))).))).)))).... ( -30.70)
>DroEre_CAF1 24712 91 - 1
GGAGCGGGAACGGCAAAAGCGGCAAAAAUGGCAAACAGGUGCCAUUG------------UAUCAAAUGCAUUGAGUGCCUUAUCUAGUCAGCCUUUUCUAGAU
((((.(((.((.((....))((((..(((((((......))))))).------------..((((.....)))).)))).......))...))).)))).... ( -22.40)
>consensus
GGAACGGG_A_________UGGCAGAAAUGGCAAACAGGUGCCAUUGUAUGUGCUCUUGUAUCAAUUGCAUUGAGUGCCUUAUCUUGUCAGCCUUUUCUAGAU
((((.(((............((((..(((((((......)))))))...............((((.....)))).))))............))).)))).... (-20.74 = -20.55 +  -0.19) 

alignment

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secondary structure

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dotplot

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Window 1

Location 1,636,414 – 1,636,518
Length 104
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 83.54
Mean single sequence MFE -32.10
Consensus MFE -19.79
Energy contribution -20.35
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.66
Structure conservation index 0.62
SVM decision value 1.14
SVM RNA-class probability 0.921873
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1636414 104 + 20766785
CACUCAAUGCAAUUGAUACAAGAGCACAUACAAUGGCACCUGUUUGCCAUUUCUGCCA---------UUCCCGUUCCCCAUUUCCAUCCAGGGGAUGAAGAACGGAG--UGGUGU
.......(((..(((...)))..))).....(((((((......)))))))...((((---------((((.((((..(((..((.....))..)))..))))))))--)))).. ( -34.90)
>DroSec_CAF1 22211 103 + 1
CACUCAAUGCAAUUGAUACAAGAGCACAUACAAUGGCACCUGUUUGCCAUUUCUGCCA---------U-CCCGUUCCCCAUUUCCAUCCAAGGGAUGAAGAACGGGG--UGGUGC
.......(((..(((...)))..))).....(((((((......)))))))...((((---------(-(((((((..(((..(.......)..)))..))))))))--)))).. ( -36.40)
>DroSim_CAF1 20640 103 + 1
CACUCAAUGCAAUUGAUACAAGAGCACAUACAAUGGCACCUGUUUGCCAUUUCUGCCA---------U-CCCGUUCCCCAUUUCCACCCAAGGGAUGAAGAACGGAG--UGGUGC
.......(((..(((...)))..))).....(((((((......)))))))...((((---------.-.((((((..(((..(.......)..)))..))))))..--)))).. ( -30.80)
>DroEre_CAF1 24738 102 + 1
CACUCAAUGCAUUUGAUA------------CAAUGGCACCUGUUUGCCAUUUUUGCCGCUUUUGCCGUUCCCGCUCCCCAUUUUCAUCCA-GGGUUGAAAAACGGAGUGUGGUGC
...((((.....))))..------------.(((((((......)))))))......((....)).((.((((((((...((((((.(..-..).))))))..)))))).)).)) ( -26.30)
>consensus
CACUCAAUGCAAUUGAUACAAGAGCACAUACAAUGGCACCUGUUUGCCAUUUCUGCCA_________U_CCCGUUCCCCAUUUCCAUCCAAGGGAUGAAGAACGGAG__UGGUGC
(((.((.........................(((((((......)))))))...................((((((..((((((.......))))))..))))))....))))). (-19.79 = -20.35 +   0.56) 

alignment

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secondary structure

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dotplot

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Window 2

Location 1,636,414 – 1,636,518
Length 104
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 83.54
Mean single sequence MFE -35.65
Consensus MFE -27.08
Energy contribution -27.82
Covariance contribution 0.75
Combinations/Pair 1.10
Mean z-score -2.45
Structure conservation index 0.76
SVM decision value 1.69
SVM RNA-class probability 0.972362
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1636414 104 - 20766785
ACACCA--CUCCGUUCUUCAUCCCCUGGAUGGAAAUGGGGAACGGGAA---------UGGCAGAAAUGGCAAACAGGUGCCAUUGUAUGUGCUCUUGUAUCAAUUGCAUUGAGUG
......--.((((((((((((..((.....))..))))))))))))..---------..(((..(((((((......)))))))...)))((((.((((.....))))..)))). ( -36.70)
>DroSec_CAF1 22211 103 - 1
GCACCA--CCCCGUUCUUCAUCCCUUGGAUGGAAAUGGGGAACGGG-A---------UGGCAGAAAUGGCAAACAGGUGCCAUUGUAUGUGCUCUUGUAUCAAUUGCAUUGAGUG
(((((.--.((((((((((((.((......))..))))))))))))-.---------((.((....)).))....)))))..........((((.((((.....))))..)))). ( -40.00)
>DroSim_CAF1 20640 103 - 1
GCACCA--CUCCGUUCUUCAUCCCUUGGGUGGAAAUGGGGAACGGG-A---------UGGCAGAAAUGGCAAACAGGUGCCAUUGUAUGUGCUCUUGUAUCAAUUGCAUUGAGUG
...(((--..(((((((((((.((......))..))))))))))).-.---------)))((..(((((((......)))))))...)).((((.((((.....))))..)))). ( -38.20)
>DroEre_CAF1 24738 102 - 1
GCACCACACUCCGUUUUUCAACCC-UGGAUGAAAAUGGGGAGCGGGAACGGCAAAAGCGGCAAAAAUGGCAAACAGGUGCCAUUG------------UAUCAAAUGCAUUGAGUG
......(((((((((((((..(((-((........)))))..((....))).)))))))(((..(((((((......))))))).------------.......)))...))))) ( -27.70)
>consensus
GCACCA__CUCCGUUCUUCAUCCCUUGGAUGGAAAUGGGGAACGGG_A_________UGGCAGAAAUGGCAAACAGGUGCCAUUGUAUGUGCUCUUGUAUCAAUUGCAUUGAGUG
(((((...(((((((.(((((((...))))))))))))))...))..............(((..(((((((......)))))))...)))..............)))........ (-27.08 = -27.82 +   0.75) 

alignment

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secondary structure

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dotplot

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Window 3

Location 1,636,451 – 1,636,557
Length 106
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 87.43
Mean single sequence MFE -36.15
Consensus MFE -27.66
Energy contribution -27.48
Covariance contribution -0.19
Combinations/Pair 1.13
Mean z-score -1.79
Structure conservation index 0.77
SVM decision value 0.52
SVM RNA-class probability 0.767086
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1636451 106 - 20766785
CGAUACUAAUGGGUGCAGACCAGUGGGUCACGAGACAGAACACCA--CUCCGUUCUUCAUCCCCUGGAUGGAAAUGGGGAACGGGAA---------UGGCAGAAAUGGCAAACAGGU
.........((..(((...(((((((.((........))...)))--)((((((((((((..((.....))..))))))))))))..---------)))((....)))))..))... ( -34.60)
>DroSec_CAF1 22248 105 - 1
CGAUACUGAUGGGUGCAGACCAGUGGGUCACGAGACAGAGCACCA--CCCCGUUCUUCAUCCCUUGGAUGGAAAUGGGGAACGGG-A---------UGGCAGAAAUGGCAAACAGGU
.....(((...(((((.((((....)))).(......).))))).--.((((((((((((.((......))..))))))))))))-.---------((.((....)).))..))).. ( -41.00)
>DroSim_CAF1 20677 105 - 1
CGAUACUGAUGGGUGCAGACCAGUGGGUCACGAGACAGAGCACCA--CUCCGUUCUUCAUCCCUUGGGUGGAAAUGGGGAACGGG-A---------UGGCAGAAAUGGCAAACAGGU
.....(((...(((((.((((....)))).(......).))))).--.((((((((((((.((......))..))))))))))))-.---------((.((....)).))..))).. ( -38.20)
>DroEre_CAF1 24763 116 - 1
CCAUACUGAUGGGUACAAACCAGUGGGUCAGGAGACAGAGCACCACACUCCGUUUUUCAACCC-UGGAUGAAAAUGGGGAGCGGGAACGGCAAAAGCGGCAAAAAUGGCAAACAGGU
((((....))))......(((.((..(((((....)...((.((.(.(((((((((.((.(..-..).))))))))))).).)).....((....)).)).....))))..)).))) ( -30.80)
>consensus
CGAUACUGAUGGGUGCAGACCAGUGGGUCACGAGACAGAGCACCA__CUCCGUUCUUCAUCCCUUGGAUGGAAAUGGGGAACGGG_A_________UGGCAGAAAUGGCAAACAGGU
.........((..(((...((.((..(((....)))...)).((...(((((((.(((((((...))))))))))))))...)).............))((....)))))..))... (-27.66 = -27.48 +  -0.19) 

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 09:33:40 2006