Locus 3924

Sequence ID 3R_DroMel_CAF1
Location 10,664,236 – 10,664,472
Length 236
Max. P 0.998467
window6284 window6285 window6286 window6287 window6288

overview

Window 4

Location 10,664,236 – 10,664,340
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.90
Mean single sequence MFE -26.68
Consensus MFE -22.08
Energy contribution -22.64
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -1.88
Structure conservation index 0.83
SVM decision value 1.03
SVM RNA-class probability 0.902994
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10664236 104 - 27905053
CUCUUUUAAUGUUUUCAUAACUUUCAGCGCGUCUGUCAAUAAGUCGAAUUCUUGGAAACAA-GCUCGAAACUUAAGUCACGUUACGUGACUGCCAUGUCAAUGGC---------------
.................(((.(((((((.((.((.......)).)).....(((....)))-))).)))).)))(((((((...)))))))(((((....)))))--------------- ( -25.50)
>DroSec_CAF1 5892 102 - 1
C--UUUUAAUGUUUUCAUAACUUUCGGCGCGUCUGUCAAUAAGUCGAAUUCUUGGAAACAA-GCUCGAAACUUAAGUCACGUUACGUGACUGCCAUGUCAAUGGC---------------
.--......((((((((.....((((((..............))))))....)))))))).-............(((((((...)))))))(((((....)))))--------------- ( -27.64)
>DroSim_CAF1 5952 102 - 1
C--UUUUAAUGUUUUCAUAACUUUCGACGCGUCUGUCAAUAAGUCGAAUUCUUGGAAACAA-GCUCGAAACUUAAGUCACGUUACGUGACUGCCAUGUCAAUGGC---------------
.--......((((((((.....((((((..............))))))....)))))))).-............(((((((...)))))))(((((....)))))--------------- ( -28.24)
>DroEre_CAF1 2379 102 - 1
C--UUUUAAUGUUUUCAUAACUUUCGGCGCGUCUGUCAAUAAGUCGAAUUCUUGGAAACAG-GCUCGAAACUUAAGUCACGUUACGUGACUCCCAUGCCAAUGGC---------------
.--......((((((((.....((((((..............))))))....))))))))(-((..........(((((((...))))))).....)))......--------------- ( -24.60)
>DroWil_CAF1 11858 116 - 1
----GCUAAUGUUUUCAUAACUUUUGGCGCGUCUGUCAAUAAGUUGAAUUCUUGGAAACAAAAUUCUAAACUUAAGUCAAGUUACGUGACUUUCAUGUCAAUGCCCUAGGCAGGGACCUG
----(((((.(((.....)))..)))))...........(((((((((((.(((....))))))))..))))))(((((.......)))))..((.(((..((((...))))..))).)) ( -27.40)
>consensus
C__UUUUAAUGUUUUCAUAACUUUCGGCGCGUCUGUCAAUAAGUCGAAUUCUUGGAAACAA_GCUCGAAACUUAAGUCACGUUACGUGACUGCCAUGUCAAUGGC_______________
.........((((((((.....((((((..............))))))....))))))))..............(((((((...)))))))(((((....)))))............... (-22.08 = -22.64 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,664,340 – 10,664,447
Length 107
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 87.50
Mean single sequence MFE -32.26
Consensus MFE -22.65
Energy contribution -23.65
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.70
SVM decision value 0.57
SVM RNA-class probability 0.785301
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10664340 107 + 27905053
GAACGCCCACCCCCCAAAUGCCUGGCAAGCUUUGGGGUUUUUUCUCCUUUU--GGUAUGGCCAAAA-----AAAAAAAAGGUUCACUGCCUGGGCAAAAAUUAUGGUGCCCAGC
((((.......(((((((.((.......)))))))))((((((....((((--((.....))))))-----..)))))).)))).....(((((((..(....)..))))))). ( -32.30)
>DroSec_CAF1 5994 112 + 1
GAACGGCCUCCCCCCAAAUGCCUGGCAAGCUUUGGGGUUUUUUCUCCUUUU--GGUAUGGCCAAAAAAAGAAAAAAAAAGGUUCACUGCCUGGGCAAAAAUUAUGGUACCCAGC
((((.......(((((((.((.......)))))))))((((((((..((((--((.....))))))..))))))))....)))).....(((((..............))))). ( -33.54)
>DroSim_CAF1 6054 111 + 1
GAACGCCCUCCCCCCAAAUGCCUGGCAAGCUUUGGGGUUUUUUCUCCUUUU--GGUAUGGCCAAA-AAAGAAAAAAAAAGGUUCACUGCCUGGGCAAAAAUUAUGGUGCCCAGC
((((.......(((((((.((.......)))))))))((((((((..((((--((.....)))))-).))))))))....)))).....(((((((..(....)..))))))). ( -38.00)
>DroEre_CAF1 2481 103 + 1
GAACGCCCUCUCCCCAAAUGCCUGGCAAGCUUUGG-GUUUUUUCUCCAUACCAAAUAUGACCA----------AAAAAAGGUUCACAGCCUGGGCAAAAAUGAUGGUGCCCAGU
((((........((((((.((.......)))))))-)((((((...((((.....))))...)----------)))))..)))).....(((((((..(....)..))))))). ( -25.20)
>consensus
GAACGCCCUCCCCCCAAAUGCCUGGCAAGCUUUGGGGUUUUUUCUCCUUUU__GGUAUGGCCAAA______AAAAAAAAGGUUCACUGCCUGGGCAAAAAUUAUGGUGCCCAGC
((((.......(((((((.((.......)))))))))................((.....))..................)))).....(((((((..(....)..))))))). (-22.65 = -23.65 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,664,340 – 10,664,447
Length 107
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -39.45
Consensus MFE -27.34
Energy contribution -30.53
Covariance contribution 3.19
Combinations/Pair 1.08
Mean z-score -3.14
Structure conservation index 0.69
SVM decision value 1.27
SVM RNA-class probability 0.939021
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10664340 107 - 27905053
GCUGGGCACCAUAAUUUUUGCCCAGGCAGUGAACCUUUUUUUU-----UUUUGGCCAUACC--AAAAGGAGAAAAAACCCCAAAGCUUGCCAGGCAUUUGGGGGGUGGGCGUUC
.(((((((..........)))))))...((..(((((((((((-----((((((.....))--))))))))))))..((((((((((.....))).))))))))))..)).... ( -42.30)
>DroSec_CAF1 5994 112 - 1
GCUGGGUACCAUAAUUUUUGCCCAGGCAGUGAACCUUUUUUUUUCUUUUUUUGGCCAUACC--AAAAGGAGAAAAAACCCCAAAGCUUGCCAGGCAUUUGGGGGGAGGCCGUUC
.(((((((..........)))))))........(((((((((((((((((((((.....))--))))))))))))))((((((((((.....))).))))))))))))...... ( -42.60)
>DroSim_CAF1 6054 111 - 1
GCUGGGCACCAUAAUUUUUGCCCAGGCAGUGAACCUUUUUUUUUCUUU-UUUGGCCAUACC--AAAAGGAGAAAAAACCCCAAAGCUUGCCAGGCAUUUGGGGGGAGGGCGUUC
.(((((((..........)))))))........(((((((((((((((-(((((.....))--)))).)))))))))((((((((((.....))).))))))))))))...... ( -41.20)
>DroEre_CAF1 2481 103 - 1
ACUGGGCACCAUCAUUUUUGCCCAGGCUGUGAACCUUUUUU----------UGGUCAUAUUUGGUAUGGAGAAAAAAC-CCAAAGCUUGCCAGGCAUUUGGGGAGAGGGCGUUC
.(((((((..........)))))))(((.(.....((((((----------(..((((((...)))))).)))))))(-((((((((.....))).))))))...).))).... ( -31.70)
>consensus
GCUGGGCACCAUAAUUUUUGCCCAGGCAGUGAACCUUUUUUUU______UUUGGCCAUACC__AAAAGGAGAAAAAACCCCAAAGCUUGCCAGGCAUUUGGGGGGAGGGCGUUC
.(((((((..........))))))).....((((.((((((((((((((...((.....))..))))))))))))))((((((((((.....))).))))))).......)))) (-27.34 = -30.53 +   3.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,664,380 – 10,664,472
Length 92
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 82.42
Mean single sequence MFE -25.31
Consensus MFE -18.38
Energy contribution -19.50
Covariance contribution 1.12
Combinations/Pair 1.04
Mean z-score -3.13
Structure conservation index 0.73
SVM decision value 2.73
SVM RNA-class probability 0.996687
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10664380 92 + 27905053
UUUCUCCUUUU--GGUAUGGCCAAAA-----AAAAAAAAGGUUCACUGCCUGGGCAAAAAUUAUGGUGCCCAGCAAAAGGGAGAGAAGAA-------GAAAUGUGA
(((((((((((--(((((((((....-----........)).))).))))((((((..(....)..))))))...)))))))))))....-------......... ( -27.30)
>DroSec_CAF1 6034 97 + 1
UUUCUCCUUUU--GGUAUGGCCAAAAAAAGAAAAAAAAAGGUUCACUGCCUGGGCAAAAAUUAUGGUACCCAGCAAAAGGGAAAGAAGGA-------GAAAUGUGA
(((((((((((--......(((................((((.....)))).))).............(((.......)))..)))))))-------))))..... ( -23.63)
>DroSim_CAF1 6094 96 + 1
UUUCUCCUUUU--GGUAUGGCCAAA-AAAGAAAAAAAAAGGUUCACUGCCUGGGCAAAAAUUAUGGUGCCCAGCAAAAGGGAAAGAUGGA-------GAAAUGUGA
(((((((((((--((.....)))))-)..............(((.((..(((((((..(....)..)))))))....)).)))....)))-------))))..... ( -27.20)
>DroEre_CAF1 2520 96 + 1
UUUCUCCAUACCAAAUAUGACCA----------AAAAAAGGUUCACAGCCUGGGCAAAAAUGAUGGUGCCCAGUAAAAGGGAGAGAAGGCGGAAUGUGAAAUGUGA
(((((((...........((((.----------......))))......(((((((..(....)..)))))))......))))))).................... ( -23.10)
>consensus
UUUCUCCUUUU__GGUAUGGCCAAA______AAAAAAAAGGUUCACUGCCUGGGCAAAAAUUAUGGUGCCCAGCAAAAGGGAAAGAAGGA_______GAAAUGUGA
(((((((((((...((......................((((.....))))(((((..(....)..))))).)).))))))))))).................... (-18.38 = -19.50 +   1.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,664,380 – 10,664,472
Length 92
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 82.42
Mean single sequence MFE -24.10
Consensus MFE -16.64
Energy contribution -16.20
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -3.85
Structure conservation index 0.69
SVM decision value 3.11
SVM RNA-class probability 0.998467
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10664380 92 - 27905053
UCACAUUUC-------UUCUUCUCUCCCUUUUGCUGGGCACCAUAAUUUUUGCCCAGGCAGUGAACCUUUUUUUU-----UUUUGGCCAUACC--AAAAGGAGAAA
.........-------......(((((...((((((((((..........)))))).))))..............-----((((((.....))--))))))))).. ( -23.70)
>DroSec_CAF1 6034 97 - 1
UCACAUUUC-------UCCUUCUUUCCCUUUUGCUGGGUACCAUAAUUUUUGCCCAGGCAGUGAACCUUUUUUUUUCUUUUUUUGGCCAUACC--AAAAGGAGAAA
.....((((-------(((...........((((((((((..........)))))).))))...................((((((.....))--))))))))))) ( -23.30)
>DroSim_CAF1 6094 96 - 1
UCACAUUUC-------UCCAUCUUUCCCUUUUGCUGGGCACCAUAAUUUUUGCCCAGGCAGUGAACCUUUUUUUUUCUUU-UUUGGCCAUACC--AAAAGGAGAAA
.....((((-------(((...........((((((((((..........)))))).))))..................(-(((((.....))--))))))))))) ( -25.80)
>DroEre_CAF1 2520 96 - 1
UCACAUUUCACAUUCCGCCUUCUCUCCCUUUUACUGGGCACCAUCAUUUUUGCCCAGGCUGUGAACCUUUUUU----------UGGUCAUAUUUGGUAUGGAGAAA
.....((((.(((.((.................(((((((..........)))))))..(((((.((......----------.)))))))...)).))))))).. ( -23.60)
>consensus
UCACAUUUC_______UCCUUCUCUCCCUUUUGCUGGGCACCAUAAUUUUUGCCCAGGCAGUGAACCUUUUUUUU______UUUGGCCAUACC__AAAAGGAGAAA
......................(((((......(((((((..........)))))))...(((..((.................)).))).........))))).. (-16.64 = -16.20 +  -0.44)

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 11:13:33 2006