Locus 3231

Sequence ID 3R_DroMel_CAF1
Location 8,621,706 – 8,621,870
Length 164
Max. P 0.991481
window5224 window5225 window5226 window5227 window5228

overview

Window 4

Location 8,621,706 – 8,621,804
Length 98
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 91.50
Mean single sequence MFE -35.00
Consensus MFE -30.69
Energy contribution -31.17
Covariance contribution 0.47
Combinations/Pair 1.13
Mean z-score -1.98
Structure conservation index 0.88
SVM decision value 1.27
SVM RNA-class probability 0.938347
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8621706 98 + 27905053
UGGCUUUUGCGGCGUUGUCACAGCCGAUGUGUCGUGCUGCAUGUUGCACACUGCGUUGCCACAUGUGUAGCACACUCGCAUUAACCAUGGAAAAGCGA
..((((((.((((.........)))((((((..(((((((((((.(((........))).))))))..)))))...))))))......).)))))).. ( -34.80)
>DroSec_CAF1 49034 98 + 1
UGGCUUUUGCGGCGUUGUCACAGCCGAUGUGUCGUGCUGCAUGUUGCACACUGCGUUGCCACAUGUGUAGCACGCUCGCAUUAACCAAGGAAAAGCGA
..((((((.((((.........)))((((((.((((((((((((.(((........))).))))))..))))))..))))))......).)))))).. ( -37.70)
>DroSim_CAF1 63346 98 + 1
UGGCUUUUGCGGCGUUGUCACAGCCGAUGUGUCGUGCUGCAUGUUGCACACUGCGUUGCCACAUGUGUAGCACACUCGCAUUAACCAAGGAAAAGCGA
..((((((.((((.........)))((((((..(((((((((((.(((........))).))))))..)))))...))))))......).)))))).. ( -35.00)
>DroEre_CAF1 61148 98 + 1
UGGCUUUUGCGGCGUUGUCACAGCCGAUGUGUCGUGCUGCAUGUUGCACACUGCGUUGCCACAUGUGUAGCACACUCGCAUUAACCAAGGAGAAGCGA
..((((((.((((.........)))((((((..(((((((((((.(((........))).))))))..)))))...))))))......).)))))).. ( -35.10)
>DroYak_CAF1 53411 98 + 1
UGGCUUUUGCGGCGUUGUCACAGCCGAUGUGUCGUGCUGCAUGUUGCACACUGCGUUGCCACAUGUGUAGCACACUCGCAUUAACCAAGGAAAAGCGA
..((((((.((((.........)))((((((..(((((((((((.(((........))).))))))..)))))...))))))......).)))))).. ( -35.00)
>DroAna_CAF1 44954 96 + 1
CGGCUUUUGCGGCGUUGUCACAGCCGAUGUCUCGUGUUGCAUGUUGCACAUCCAUGUGCCACAUGUGCAA--CACUCACACAAGCAAAAAAAAAGAGG
....(((((((((((((.......)))))))..(((((((((((.(((((....))))).)))..)))))--)))........))))))......... ( -32.40)
>consensus
UGGCUUUUGCGGCGUUGUCACAGCCGAUGUGUCGUGCUGCAUGUUGCACACUGCGUUGCCACAUGUGUAGCACACUCGCAUUAACCAAGGAAAAGCGA
..((((((.((((.........)))((((((..(((((((((((.(((........))).)))..))))))))...))))))......).)))))).. (-30.69 = -31.17 +   0.47)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,621,706 – 8,621,804
Length 98
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 91.50
Mean single sequence MFE -37.38
Consensus MFE -31.78
Energy contribution -32.15
Covariance contribution 0.37
Combinations/Pair 1.23
Mean z-score -3.14
Structure conservation index 0.85
SVM decision value 2.27
SVM RNA-class probability 0.991481
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8621706 98 - 27905053
UCGCUUUUCCAUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUGCAGCACGACACAUCGGCUGUGACAACGCCGCAAAAGCCA
...........(((((..((((.((((((.((((.((((....)))))))))).....(((((.(((....))))))))....))))))))..))))) ( -37.70)
>DroSec_CAF1 49034 98 - 1
UCGCUUUUCCUUGGUUAAUGCGAGCGUGCUACACAUGUGGCAACGCAGUGUGCAACAUGCAGCACGACACAUCGGCUGUGACAACGCCGCAAAAGCCA
...........(((((..((((.((((((.((((.((((....)))))))))).....(((((.(((....))))))))....))))))))..))))) ( -39.50)
>DroSim_CAF1 63346 98 - 1
UCGCUUUUCCUUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUGCAGCACGACACAUCGGCUGUGACAACGCCGCAAAAGCCA
...........(((((..((((.((((((.((((.((((....)))))))))).....(((((.(((....))))))))....))))))))..))))) ( -37.60)
>DroEre_CAF1 61148 98 - 1
UCGCUUCUCCUUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUGCAGCACGACACAUCGGCUGUGACAACGCCGCAAAAGCCA
...........(((((..((((.((((((.((((.((((....)))))))))).....(((((.(((....))))))))....))))))))..))))) ( -37.60)
>DroYak_CAF1 53411 98 - 1
UCGCUUUUCCUUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUGCAGCACGACACAUCGGCUGUGACAACGCCGCAAAAGCCA
...........(((((..((((.((((((.((((.((((....)))))))))).....(((((.(((....))))))))....))))))))..))))) ( -37.60)
>DroAna_CAF1 44954 96 - 1
CCUCUUUUUUUUUGCUUGUGUGAGUG--UUGCACAUGUGGCACAUGGAUGUGCAACAUGCAACACGAGACAUCGGCUGUGACAACGCCGCAAAAGCCG
........(((((((((((((..(((--((((((((.((.....)).)))))))))))...))))))......(((.((....))))))))))))... ( -34.30)
>consensus
UCGCUUUUCCUUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUGCAGCACGACACAUCGGCUGUGACAACGCCGCAAAAGCCA
...........(((((..((((.((((((.((((.((((....)))))))))).....(((((.(((....))))))))....))))))))..))))) (-31.78 = -32.15 +   0.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,621,745 – 8,621,843
Length 98
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 95.51
Mean single sequence MFE -30.95
Consensus MFE -29.40
Energy contribution -29.52
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -1.51
Structure conservation index 0.95
SVM decision value 1.73
SVM RNA-class probability 0.974666
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8621745 98 - 27905053
ACAGCAUCCUGAGUUUUCCUGGGCUUUCCCGGGCCUUUCUCGCUUUUCCAUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUG
...(((..(((.(((..((((((....)))))).....(((((((..(....)..)).)))))...(((((....)))))))).)))..)))...... ( -32.80)
>DroSec_CAF1 49073 98 - 1
ACAGCAUCCUGAGUUUUCCUGGGCUUUCCCGGGCCUUUCUCGCUUUUCCUUGGUUAAUGCGAGCGUGCUACACAUGUGGCAACGCAGUGUGCAACAUG
...(((..(((((....((((((....))))))...)))((((((..(....)..)).))))(((((((((....))))).))))))..)))...... ( -33.20)
>DroSim_CAF1 63385 98 - 1
ACAGCAUCCUGAGUUUUCCUGGGCUUUCCCGGGCCUUUCUCGCUUUUCCUUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUG
...(((..(((.(((..((((((....)))))).....(((((((..(....)..)).)))))...(((((....)))))))).)))..)))...... ( -32.80)
>DroEre_CAF1 61187 98 - 1
ACAGCAUCCUGAGUUUCCCUGAGUUUUCCCAAGCCUUUCUCGCUUCUCCUUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUG
...((((.(..((......((((...............))))......))..)...))))..((((((.((((.((((....)))))))))).)))). ( -24.06)
>DroYak_CAF1 53450 98 - 1
ACAGCAUCCUGAGUUUUUCCCGGCUUUCCCGGGCCUUUCUCGCUUUUCCUUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUG
...(((..(((.(((...(((((.....))))).....(((((((..(....)..)).)))))...(((((....)))))))).)))..)))...... ( -31.90)
>consensus
ACAGCAUCCUGAGUUUUCCUGGGCUUUCCCGGGCCUUUCUCGCUUUUCCUUGGUUAAUGCGAGUGUGCUACACAUGUGGCAACGCAGUGUGCAACAUG
...(((..(((.(((..((((((....)))))).....(((((((..(....)..)).)))))...(((((....)))))))).)))..)))...... (-29.40 = -29.52 +   0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,621,765 – 8,621,870
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 93.14
Mean single sequence MFE -29.12
Consensus MFE -24.56
Energy contribution -24.68
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -1.45
Structure conservation index 0.84
SVM decision value 0.55
SVM RNA-class probability 0.776893
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8621765 105 + 27905053
CACAUGUGUAGCACACUCGCAUUAACCAUGGAAAAGCGAGAAAGGCCCGGGAAAGCCCAGGAAAACUCAGGAUGCUGUGAAUGGAGUGUGAAUGCGCGAAGCUGA
....((((((.(((((((.((((...(((((......(((.....((.(((....))).))....)))......))))))))))))))))..))))))....... ( -31.50)
>DroSec_CAF1 49093 105 + 1
CACAUGUGUAGCACGCUCGCAUUAACCAAGGAAAAGCGAGAAAGGCCCGGGAAAGCCCAGGAAAACUCAGGAUGCUGUGAAUGGAGUGUGAAUGCGCGAAGCUGA
....((((((.(((((((.((((......((......(((.....((.(((....))).))....)))......))...)))))))))))..))))))....... ( -28.50)
>DroSim_CAF1 63405 105 + 1
CACAUGUGUAGCACACUCGCAUUAACCAAGGAAAAGCGAGAAAGGCCCGGGAAAGCCCAGGAAAACUCAGGAUGCUGUGAAUGGAGUGUGAAUGCGCGAAGCUGA
....((((((.(((((((.((((......((......(((.....((.(((....))).))....)))......))...)))))))))))..))))))....... ( -28.90)
>DroEre_CAF1 61207 99 + 1
CACAUGUGUAGCACACUCGCAUUAACCAAGGAGAAGCGAGAAAGGCUUGGGAAAACUCAGGGAAACUCAGGAUGCUGUGAAUGAAGUGUGAAUGCGCGA------
....((((((.((((((((((.((.((...(((...(......).((((((....))))))....))).)).)).))))).....)))))..)))))).------ ( -24.50)
>DroYak_CAF1 53470 105 + 1
CACAUGUGUAGCACACUCGCAUUAACCAAGGAAAAGCGAGAAAGGCCCGGGAAAGCCGGGAAAAACUCAGGAUGCUGUGAAUGGAGUGUGAAUGCGCGAAGCUGA
....((((((.(((((((.((((......((......(((.....(((((.....))))).....)))......))...)))))))))))..))))))....... ( -32.20)
>consensus
CACAUGUGUAGCACACUCGCAUUAACCAAGGAAAAGCGAGAAAGGCCCGGGAAAGCCCAGGAAAACUCAGGAUGCUGUGAAUGGAGUGUGAAUGCGCGAAGCUGA
....((((((.(((((((.((((...((..(......(((.....((.(((....))).))....)))......)..)))))))))))))..))))))....... (-24.56 = -24.68 +   0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,621,765 – 8,621,870
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 93.14
Mean single sequence MFE -25.78
Consensus MFE -23.74
Energy contribution -23.90
Covariance contribution 0.16
Combinations/Pair 1.16
Mean z-score -1.35
Structure conservation index 0.92
SVM decision value 0.97
SVM RNA-class probability 0.893071
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8621765 105 - 27905053
UCAGCUUCGCGCAUUCACACUCCAUUCACAGCAUCCUGAGUUUUCCUGGGCUUUCCCGGGCCUUUCUCGCUUUUCCAUGGUUAAUGCGAGUGUGCUACACAUGUG
........((((((((.((..((((....(((.....(((....((((((....)))))).....)))))).....))))....)).)))))))).......... ( -29.10)
>DroSec_CAF1 49093 105 - 1
UCAGCUUCGCGCAUUCACACUCCAUUCACAGCAUCCUGAGUUUUCCUGGGCUUUCCCGGGCCUUUCUCGCUUUUCCUUGGUUAAUGCGAGCGUGCUACACAUGUG
..(((..((((((((......(((.....(((.....(((....((((((....)))))).....))))))......)))..)))))..))).)))......... ( -24.70)
>DroSim_CAF1 63405 105 - 1
UCAGCUUCGCGCAUUCACACUCCAUUCACAGCAUCCUGAGUUUUCCUGGGCUUUCCCGGGCCUUUCUCGCUUUUCCUUGGUUAAUGCGAGUGUGCUACACAUGUG
........((((((((.((..(((.....(((.....(((....((((((....)))))).....))))))......)))....)).)))))))).......... ( -28.50)
>DroEre_CAF1 61207 99 - 1
------UCGCGCAUUCACACUUCAUUCACAGCAUCCUGAGUUUCCCUGAGUUUUCCCAAGCCUUUCUCGCUUCUCCUUGGUUAAUGCGAGUGUGCUACACAUGUG
------..((((((((.(..........(((....))).(((..((.(((.......((((.......)))))))...))..)))).)))))))).......... ( -18.61)
>DroYak_CAF1 53470 105 - 1
UCAGCUUCGCGCAUUCACACUCCAUUCACAGCAUCCUGAGUUUUUCCCGGCUUUCCCGGGCCUUUCUCGCUUUUCCUUGGUUAAUGCGAGUGUGCUACACAUGUG
........((((((((.((..(((.....(((.....(((.....(((((.....))))).....))))))......)))....)).)))))))).......... ( -28.00)
>consensus
UCAGCUUCGCGCAUUCACACUCCAUUCACAGCAUCCUGAGUUUUCCUGGGCUUUCCCGGGCCUUUCUCGCUUUUCCUUGGUUAAUGCGAGUGUGCUACACAUGUG
........((((((((.((..(((.....(((.....(((....((((((....)))))).....))))))......)))....)).)))))))).......... (-23.74 = -23.90 +   0.16)

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 10:56:15 2006