Locus 4951

Sequence ID 3L_DroMel_CAF1
Location 13,704,963 – 13,705,099
Length 136
Max. P 0.775669
window7815 window7816 window7817

overview

Window 5

Location 13,704,963 – 13,705,060
Length 97
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 62.57
Mean single sequence MFE -32.58
Consensus MFE -14.75
Energy contribution -14.72
Covariance contribution -0.03
Combinations/Pair 1.34
Mean z-score -1.58
Structure conservation index 0.45
SVM decision value 0.05
SVM RNA-class probability 0.557072
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13704963 97 - 23771897
UGCACGGAAUGCCAUGGCGAACUUGCCAA----ACCCACUUGGCAUGUCACUGCCAGGAGCAGGGAAUUCGGCAAGGGAUUGUCUGGCUGGCUGGCUACAU-------
.((.(((...((((.(((((.((((((..----.(((.(((((((......)))))))....))).....))))))...)))))))))...))))).....------- ( -39.20)
>DroSec_CAF1 112185 101 - 1
UGCACGGAAUGCCAUGGCAAACUUGCCAAACUUACCCACUUGGCAUGUCACUGCCAGGAGCAGGGAAUUCGGCAAGGGAUUGUCUGGCUGGCUGGCUACAU-------
.((.(((...((((.(((((.((((((.((.((.(((.(((((((......)))))))....))))))).))))))...)))))))))...))))).....------- ( -39.40)
>DroSim_CAF1 122990 100 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNUGCCAGGAGCAGGGAAUUCGGCAAGGGA-UGUCUGGCUGGCUGGCUACAU-------
....................................................(((((.(((.((..((((......)))-)..)).)))..))))).....------- ( -15.60)
>DroYak_CAF1 121980 97 - 1
UGCACGGAAUGCCAUGGCAAACUUGCCAA----ACCCACUUGGCAUGUCACUGCCAGGAGCAGGGAAUUCGGCAAGGGAUUGUCUGGCUGGCUGGCUACAU-------
.((.(((...((((.(((((.((((((..----.(((.(((((((......)))))))....))).....))))))...)))))))))...))))).....------- ( -39.50)
>DroAna_CAF1 169358 99 - 1
UGGAAAGAAACCUCUGCCAAACUUGCCAG----ACCCACUUGGUAUGUCUCUGCCGGUUAGAGCGAGUUAU-----GGGUUAGAUGGUUAGACGUCUCUAUGCGAGGG
..........((((..(((((((((((.(----(((.....((((......)))))))).).))))))).)-----))((.(((((......)))))....)))))). ( -29.20)
>consensus
UGCACGGAAUGCCAUGGCAAACUUGCCAA____ACCCACUUGGCAUGUCACUGCCAGGAGCAGGGAAUUCGGCAAGGGAUUGUCUGGCUGGCUGGCUACAU_______
(((..((....))...))).((.((((((..........)))))).))....(((((.((((((.(((((......))))).))).)))..)))))............ (-14.75 = -14.72 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,704,984 – 13,705,099
Length 115
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 79.41
Mean single sequence MFE -34.53
Consensus MFE -21.87
Energy contribution -24.40
Covariance contribution 2.53
Combinations/Pair 1.08
Mean z-score -1.74
Structure conservation index 0.63
SVM decision value 0.54
SVM RNA-class probability 0.775669
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13704984 115 + 23771897
AUCCCUUGCCGAAUUCCCUGCUCCUGGCAGUGACAUGCCAAGUGGGU----UUGGCAAGUUCGCCAUGGCAUUCCGUGCACUUCCCGCCACCCGCACACGCACUUGGCAUGUAAAAUAG
...(.((((((.............)))))).)(((((((((((((((----.(((.((((..((.((((....)))))))))).)))..))))((....)))))))))))))....... ( -39.12)
>DroPse_CAF1 102846 89 + 1
-----UUGC------CUCUGCUGCUGGCAGUGACACGACAAGUGGGU----UUGGCAACUUUGCCAUAGCAUACUCUUCAG----CG----CCUCACAU-------GCAUGCAAAAUAG
-----((((------...(((((..(((..((((((.....))).((----((((((....))))).))).......))).----.)----))...)).-------))).))))..... ( -22.90)
>DroSec_CAF1 112206 119 + 1
AUCCCUUGCCGAAUUCCCUGCUCCUGGCAGUGACAUGCCAAGUGGGUAAGUUUGGCAAGUUUGCCAUGGCAUUCCGUGCACUUCCCGCCACCCGCACACGCACUUGGCAUGCAAAAUAG
....(((((((((((.((..((..(((((......)))))))..))..)))))))))))((((((((((....)))))........((((...((....))...))))..))))).... ( -42.80)
>DroEre_CAF1 118445 115 + 1
AUCCCUUGCCGAAUUCCCUGCUCCUGGCAGUGACAUGCCAAGUGGGU----UUGGCAAGUUUGCCAUGGCAUUCCGUGCACUUCCCGCCACCCGCACACGCACUUGGCAUGUAAAAUAG
...(.((((((.............)))))).)(((((((((((((((----.(((.((((..((.((((....)))))))))).)))..))))((....)))))))))))))....... ( -39.12)
>DroYak_CAF1 122001 115 + 1
AUCCCUUGCCGAAUUCCCUGCUCCUGGCAGUGACAUGCCAAGUGGGU----UUGGCAAGUUUGCCAUGGCAUUCCGUGCACUUCCCAUCACCCGCACACGCACUUGGCAUGUAAAAUAG
...(.((((((.............)))))).)(((((((((((((((----.(((.((((..((.((((....)))))))))).)))..))))((....)))))))))))))....... ( -40.32)
>DroPer_CAF1 104264 89 + 1
-----UUGC------CUCUGCUGCUGGCAGUGACACGACAAGUGGGU----UUGGCAACUUUGCCAUAGCAUACUCUUCAG----CG----CCUCACAU-------GCAUGCAAAAUAG
-----((((------...(((((..(((..((((((.....))).((----((((((....))))).))).......))).----.)----))...)).-------))).))))..... ( -22.90)
>consensus
AUCCCUUGCCGAAUUCCCUGCUCCUGGCAGUGACAUGCCAAGUGGGU____UUGGCAAGUUUGCCAUGGCAUUCCGUGCACUUCCCGCCACCCGCACACGCACUUGGCAUGCAAAAUAG
.................((((.....))))((.(((((((((((.((.....((((......))))..(((.....)))..................)).)))))))))))))...... (-21.87 = -24.40 +   2.53)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,704,984 – 13,705,099
Length 115
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.41
Mean single sequence MFE -37.70
Consensus MFE -24.61
Energy contribution -27.67
Covariance contribution 3.06
Combinations/Pair 1.11
Mean z-score -1.43
Structure conservation index 0.65
SVM decision value 0.22
SVM RNA-class probability 0.638136
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13704984 115 - 23771897
CUAUUUUACAUGCCAAGUGCGUGUGCGGGUGGCGGGAAGUGCACGGAAUGCCAUGGCGAACUUGCCAA----ACCCACUUGGCAUGUCACUGCCAGGAGCAGGGAAUUCGGCAAGGGAU
.......(((((((((((((....))((((((((((...(((..((....))...)))..))))))..----)))))))))))))))(..((((.(((........)))))))..)... ( -42.90)
>DroPse_CAF1 102846 89 - 1
CUAUUUUGCAUGC-------AUGUGAGG----CG----CUGAAGAGUAUGCUAUGGCAAAGUUGCCAA----ACCCACUUGUCGUGUCACUGCCAGCAGCAGAG------GCAA-----
.....((((.(((-------.(((..((----((----.(((...........(((((....))))).----...(((.....)))))).)))).))))))...------))))----- ( -25.50)
>DroSec_CAF1 112206 119 - 1
CUAUUUUGCAUGCCAAGUGCGUGUGCGGGUGGCGGGAAGUGCACGGAAUGCCAUGGCAAACUUGCCAAACUUACCCACUUGGCAUGUCACUGCCAGGAGCAGGGAAUUCGGCAAGGGAU
...((((((((((((((((.(.(((.(..(((((((...(((..((....))...)))..)))))))..).)))))))))))))).((.((((.....)))).)).....))))))... ( -46.90)
>DroEre_CAF1 118445 115 - 1
CUAUUUUACAUGCCAAGUGCGUGUGCGGGUGGCGGGAAGUGCACGGAAUGCCAUGGCAAACUUGCCAA----ACCCACUUGGCAUGUCACUGCCAGGAGCAGGGAAUUCGGCAAGGGAU
.......(((((((((((((....))((((((((((...(((..((....))...)))..))))))..----)))))))))))))))(..((((.(((........)))))))..)... ( -43.60)
>DroYak_CAF1 122001 115 - 1
CUAUUUUACAUGCCAAGUGCGUGUGCGGGUGAUGGGAAGUGCACGGAAUGCCAUGGCAAACUUGCCAA----ACCCACUUGGCAUGUCACUGCCAGGAGCAGGGAAUUCGGCAAGGGAU
.......(((((((((((((....))((((..(((.((((((..((....))...))..)))).))).----)))))))))))))))(..((((.(((........)))))))..)... ( -41.80)
>DroPer_CAF1 104264 89 - 1
CUAUUUUGCAUGC-------AUGUGAGG----CG----CUGAAGAGUAUGCUAUGGCAAAGUUGCCAA----ACCCACUUGUCGUGUCACUGCCAGCAGCAGAG------GCAA-----
.....((((.(((-------.(((..((----((----.(((...........(((((....))))).----...(((.....)))))).)))).))))))...------))))----- ( -25.50)
>consensus
CUAUUUUACAUGCCAAGUGCGUGUGCGGGUGGCGGGAAGUGCACGGAAUGCCAUGGCAAACUUGCCAA____ACCCACUUGGCAUGUCACUGCCAGGAGCAGGGAAUUCGGCAAGGGAU
.......(((((((((((((((((((............)))))))........(((((....)))))........))))))))))))..((((.....))))................. (-24.61 = -27.67 +   3.06)

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 11:37:48 2006