Locus 6563

Sequence ID X_DroMel_CAF1
Location 16,415,354 – 16,415,562
Length 208
Max. P 0.986187
window10720 window10721 window10722 window10723

overview

Window 0

Location 16,415,354 – 16,415,465
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 88.89
Mean single sequence MFE -23.59
Consensus MFE -20.36
Energy contribution -20.93
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.04
Structure conservation index 0.86
SVM decision value 1.25
SVM RNA-class probability 0.935645
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16415354 111 + 22224390
AAAAUUUGAAUUGCUACCCGAAAGUUGAAUUUUAAUUUGGGCACUUCAUAAAGGCCAACGUGAGUUUCCUUUUAUGUUUAUUUUGGUUAGUGCCUUUUCCUCUUCCGACUU
.....................((((((...........(((((((.((((((((..(((....)))..))))))))............)))))))..........)))))) ( -23.82)
>DroSec_CAF1 35978 111 + 1
AAAAUUCGAAUUGCUACCCGAAAGUUGAAUUUUAAUUUAGGCACUUCAUAAAGGCCAACGUGAGUUUCCUUUUAUGUUUAUUUUGGUUAGUGCCUUUUCCUCUUCCGACUU
(((((((((....(.....)....))))))))).....(((((((.((((((((..(((....)))..))))))))............)))))))................ ( -24.72)
>DroSim_CAF1 32282 111 + 1
AAAAUUUGAAUUGCUACCCGAAAGUUGAAUUUUAAUUUGGGCACUUCAUAAAGGCCAACGUGAGUUCCCUUUUAUGUUUAUUUUGGUUAGUGCCUUUUCCUCUUCCGACUU
.....................((((((...........(((((((.((((((((..(((....)))..))))))))............)))))))..........)))))) ( -23.82)
>DroYak_CAF1 33893 97 + 1
--------------UACCCAAAUUUUUCAUUUUAACUUGGGCACUUCAUAAAGGCCAACGUGAGUUUCCUUUUAUGUUUAUUUUGGUUAGUGCCUUUUCCUGUGCCGACUU
--------------.........................(((((..((((((((..(((....)))..))))))))........(((....))).......)))))..... ( -22.00)
>consensus
AAAAUUUGAAUUGCUACCCGAAAGUUGAAUUUUAAUUUGGGCACUUCAUAAAGGCCAACGUGAGUUUCCUUUUAUGUUUAUUUUGGUUAGUGCCUUUUCCUCUUCCGACUU
.....................((((((...........(((((((...(((((...((((((((......))))))))..)))))...)))))))..........)))))) (-20.36 = -20.93 +   0.56)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,415,425 – 16,415,543
Length 118
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 96.15
Mean single sequence MFE -35.38
Consensus MFE -27.48
Energy contribution -27.35
Covariance contribution -0.13
Combinations/Pair 1.07
Mean z-score -2.73
Structure conservation index 0.78
SVM decision value 0.01
SVM RNA-class probability 0.537335
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16415425 118 - 22224390
UUUCUGCGCUUCAUCCUUCGCAUCCUCUUCUGCUGCAGAUGACGUUUCGGGCCCAAGAAAAAGGAUGCGUGCUGAUGAAAGUCGGAAGAGGAAAAGGCACUAACCAAAAUAAACAUAA
.......((((..(((((((((((((.((((...((.((.......))..))...))))..))))))))..(((((....)))))..)))))..)))).................... ( -34.10)
>DroSec_CAF1 36049 115 - 1
UUUCUG--UUUCAUCCUUCGCAUCCUCUUCUGCUGCAGAUGACGUUUCG-GCCCAAGAAAAAGGAUGCGUGCUGAUGAAAGUCGGAAGAGGAAAAGGCACUAACCAAAAUAAACAUAA
....((--(((..(((((((((((((.((((...((.((.......)).-))...))))..))))))))..(((((....)))))..)))))..)))))................... ( -31.80)
>DroSim_CAF1 32353 116 - 1
UUUCUG--CUUCAUCCUUCGCAUCCUCUUCUGCUGCAGAUGACGUUUCGGGUCCAAGAAAAAGGAUGCGUGCUGAUGAAAGUCGGAAGAGGAAAAGGCACUAACCAAAAUAAACAUAA
....((--(((..(((((((((((((.((((...((.((.......))..))...))))..))))))))..(((((....)))))..)))))..)))))................... ( -32.70)
>DroYak_CAF1 33950 116 - 1
UUUCUG--CUUCAUCCUUCGCAUCCUUUUUUGCUGCAGAUGACGUUUCGGGCCCAAGAAAAAGGAUGCGUGCUGAUGAAAGUCGGCACAGGAAAAGGCACUAACCAAAAUAAACAUAA
....((--(((..((((..((((((((((((...((.((.......))..))....))))))))))))((((((((....))))))))))))..)))))................... ( -42.90)
>consensus
UUUCUG__CUUCAUCCUUCGCAUCCUCUUCUGCUGCAGAUGACGUUUCGGGCCCAAGAAAAAGGAUGCGUGCUGAUGAAAGUCGGAAGAGGAAAAGGCACUAACCAAAAUAAACAUAA
.............(((((((((((((.((((...((...(((....))).))...))))..))))))))..(((((....)))))..)))))...((......))............. (-27.48 = -27.35 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,415,465 – 16,415,562
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 95.31
Mean single sequence MFE -29.30
Consensus MFE -27.94
Energy contribution -27.38
Covariance contribution -0.56
Combinations/Pair 1.11
Mean z-score -2.53
Structure conservation index 0.95
SVM decision value 2.03
SVM RNA-class probability 0.986187
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16415465 97 + 22224390
UCAUCAGCACGCAUCCUUUUUCUUGGGCCCGAAACGUCAUCUGCAGCAGAAGAGGAUGCGAAGGAUGAAGCGCAGAAACGGCAACGAAUGCCAAGUA
(((((....(((((((((((.((...((..((.......)).))...)))))))))))))...))))).(.(((....((....))..))))..... ( -29.40)
>DroSec_CAF1 36089 94 + 1
UCAUCAGCACGCAUCCUUUUUCUUGGGC-CGAAACGUCAUCUGCAGCAGAAGAGGAUGCGAAGGAUGAAA--CAGAAACGGCAAAGAAUGCCAAGUA
(((((....(((((((((((.((...((-.((.......)).))...)))))))))))))...)))))..--.......((((.....))))..... ( -30.70)
>DroSim_CAF1 32393 95 + 1
UCAUCAGCACGCAUCCUUUUUCUUGGACCCGAAACGUCAUCUGCAGCAGAAGAGGAUGCGAAGGAUGAAG--CAGAAACGGCAAAGAAUGCCAAGUA
(((((....((((((((((......(((.......))).((((...))))))))))))))...)))))..--.......((((.....))))..... ( -29.00)
>DroYak_CAF1 33990 95 + 1
UCAUCAGCACGCAUCCUUUUUCUUGGGCCCGAAACGUCAUCUGCAGCAAAAAAGGAUGCGAAGGAUGAAG--CAGAAACGGCAAAAAAUGCCAAGUA
(((((....((((((((((((..((.((..((.......)).))..))))))))))))))...)))))..--.......((((.....))))..... ( -28.10)
>consensus
UCAUCAGCACGCAUCCUUUUUCUUGGGCCCGAAACGUCAUCUGCAGCAGAAGAGGAUGCGAAGGAUGAAG__CAGAAACGGCAAAGAAUGCCAAGUA
(((((....((((((((((((.(((.(...((....))...).)))..))))))))))))...)))))...........((((.....))))..... (-27.94 = -27.38 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,415,465 – 16,415,562
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 95.31
Mean single sequence MFE -29.35
Consensus MFE -27.62
Energy contribution -27.25
Covariance contribution -0.38
Combinations/Pair 1.08
Mean z-score -2.07
Structure conservation index 0.94
SVM decision value 1.33
SVM RNA-class probability 0.943307
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16415465 97 - 22224390
UACUUGGCAUUCGUUGCCGUUUCUGCGCUUCAUCCUUCGCAUCCUCUUCUGCUGCAGAUGACGUUUCGGGCCCAAGAAAAAGGAUGCGUGCUGAUGA
.....((((.....))))...........(((((...((((((((.((((...((.((.......))..))...))))..))))))))....))))) ( -29.10)
>DroSec_CAF1 36089 94 - 1
UACUUGGCAUUCUUUGCCGUUUCUG--UUUCAUCCUUCGCAUCCUCUUCUGCUGCAGAUGACGUUUCG-GCCCAAGAAAAAGGAUGCGUGCUGAUGA
.....((((.....)))).......--..(((((...((((((((.((((...((.((.......)).-))...))))..))))))))....))))) ( -29.10)
>DroSim_CAF1 32393 95 - 1
UACUUGGCAUUCUUUGCCGUUUCUG--CUUCAUCCUUCGCAUCCUCUUCUGCUGCAGAUGACGUUUCGGGUCCAAGAAAAAGGAUGCGUGCUGAUGA
.....((((.....)))).......--..(((((...((((((((.((((...((.((.......))..))...))))..))))))))....))))) ( -27.50)
>DroYak_CAF1 33990 95 - 1
UACUUGGCAUUUUUUGCCGUUUCUG--CUUCAUCCUUCGCAUCCUUUUUUGCUGCAGAUGACGUUUCGGGCCCAAGAAAAAGGAUGCGUGCUGAUGA
.....((((.....)))).......--..(((((...(((((((((((((...((.((.......))..))....)))))))))))))....))))) ( -31.70)
>consensus
UACUUGGCAUUCUUUGCCGUUUCUG__CUUCAUCCUUCGCAUCCUCUUCUGCUGCAGAUGACGUUUCGGGCCCAAGAAAAAGGAUGCGUGCUGAUGA
.....((((.....))))...........(((((...((((((((.((((...((...(((....))).))...))))..))))))))....))))) (-27.62 = -27.25 +  -0.38)

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 12:17:02 2006