Locus 1602

Sequence ID 3L_DroMel_CAF1
Location 4,700,098 – 4,700,316
Length 218
Max. P 0.698053
window2480 window2481 window2482

overview

Window 0

Location 4,700,098 – 4,700,206
Length 108
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 80.49
Mean single sequence MFE -22.77
Consensus MFE -14.53
Energy contribution -14.87
Covariance contribution 0.34
Combinations/Pair 1.13
Mean z-score -1.71
Structure conservation index 0.64
SVM decision value 0.01
SVM RNA-class probability 0.536509
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4700098 108 + 23771897
AAACUCAUAAUUAUUUUU--GAAAUUGAACAUGGCAUUUUGAGUUGUCAUUAUCGACUGCAAUUCAGUGCGGUAUGAAUUCAGUAAAGUGAGAACCGAAAAGCAAUAACU
..................--.............((.(((((.(((.(((((....((((.((((((........))))))))))..))))).)))))))).))....... ( -22.60)
>DroEre_CAF1 76263 109 + 1
CAAUA-AAAGUUGAAUUUCCGAAAUUGAAAAAGGCGUCUUGAGUUGUCAUUACCGACUGCAAUUCAAUGCGAUAUGAAUUGCAUAUAGUGAGAACCGAGAAGCCAUAACU
.....-..(((((..((((.......))))..(((.(((((.(((.((((((.....(((((((((........)))))))))..)))))).)))))))).))).))))) ( -31.80)
>DroYak_CAF1 79395 107 + 1
AAAUUUAUACUUAUAUUU--GAAAUUGAAAAAGGCAU-UUGAGCUGUCAUUACCAACUGCAAUUCAAUGCGAUAUAAGCUUAAUAAAAUGAGAACCGAGAAGCCAUAACU
....(((..((((((((.--...((((((....(((.-(((............))).)))..))))))..))))))))..)))........................... ( -13.90)
>consensus
AAAUU_AUAAUUAUAUUU__GAAAUUGAAAAAGGCAU_UUGAGUUGUCAUUACCGACUGCAAUUCAAUGCGAUAUGAAUUCAAUAAAGUGAGAACCGAGAAGCCAUAACU
................................(((.(((((.(((.(((((......((((......)))).(((.......))).))))).)))))))).)))...... (-14.53 = -14.87 +   0.34)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,700,126 – 4,700,245
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.87
Mean single sequence MFE -28.47
Consensus MFE -21.12
Energy contribution -21.75
Covariance contribution 0.62
Combinations/Pair 1.12
Mean z-score -1.72
Structure conservation index 0.74
SVM decision value 0.34
SVM RNA-class probability 0.698053
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4700126 119 + 23771897
AUGGCAUUUUGAGUUGUCAUUAUCGACUGCAAUUCAGUGCGGUAUGAAUUCAGUAAAGUGAGAACCGAAAAGCAAUAACUUA-AAACCGCUUAUGGUGUUAUUAAAAAUAGCUUGCGGUU
...((.(((((.(((.(((((....((((.((((((........))))))))))..))))).)))))))).)).........-.((((((....(.((((......)))).)..)))))) ( -32.40)
>DroSec_CAF1 73953 120 + 1
CAGCCAUUUUGAGUUUUCAUUAUCGACAGCAUUUCAGUGCGAUAUGAAUUCAAUAAAGUGAGAACCGAGAAGCCUUAACAUAAAAACCGCUUAUGGUGUUAUUAAAAAUAGCUUGCGGUU
..((..(((((.(((((((((.......((((....))))((.......)).....)))))))))))))).))...........((((((....(.((((......)))).)..)))))) ( -26.20)
>DroEre_CAF1 76292 119 + 1
AAGGCGUCUUGAGUUGUCAUUACCGACUGCAAUUCAAUGCGAUAUGAAUUGCAUAUAGUGAGAACCGAGAAGCCAUAACUUA-AAACCACUUAUGGUGUUAUUAAAAAUAGCUUGCGGUU
..(((.(((((.(((.((((((.....(((((((((........)))))))))..)))))).)))))))).)))........-.((((.(....(.((((......)))).)..).)))) ( -34.50)
>DroYak_CAF1 79423 118 + 1
AAGGCAU-UUGAGCUGUCAUUACCAACUGCAAUUCAAUGCGAUAUAAGCUUAAUAAAAUGAGAACCGAGAAGCCAUAACUUA-AAACCGCUUAUGGUGUUAUUAAAAAUAGCUUGCGGUU
..(((..-(((((((((........))((((......)))).....))))))).....((.....))....)))........-.((((((....(.((((......)))).)..)))))) ( -20.80)
>consensus
AAGGCAUUUUGAGUUGUCAUUACCGACUGCAAUUCAAUGCGAUAUGAAUUCAAUAAAGUGAGAACCGAGAAGCCAUAACUUA_AAACCGCUUAUGGUGUUAUUAAAAAUAGCUUGCGGUU
..(((.(((((.(((.(((((.......(((......)))..(((.......))).))))).)))))))).)))..........((((((....(.((((......)))).)..)))))) (-21.12 = -21.75 +   0.62)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,700,206 – 4,700,316
Length 110
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 93.55
Mean single sequence MFE -19.08
Consensus MFE -19.24
Energy contribution -19.08
Covariance contribution -0.16
Combinations/Pair 1.07
Mean z-score -1.05
Structure conservation index 1.01
SVM decision value 0.33
SVM RNA-class probability 0.692321
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4700206 110 - 23771897
CGAAACUUCCGUCAAGUUGUUGCAGUCUUUUUAACUGGUUGUGGCAACAAAAAAAAAAUAAAAAAUUCCCCAACCGCAAGCUAUUUUUAAUAACACCAUAAGCGGUUU-UA
...............(((((..((..(.........)..))..))))).......................((((((........................)))))).-.. ( -19.46)
>DroSec_CAF1 74033 107 - 1
CGAAACUUCCGUCAAGUUGUUGCAGUCUUUUUAACUGGUUGUGGCAACAACAAAAA----AAAAAUUCCCCAACCGCAAGCUAUUUUUAAUAACACCAUAAGCGGUUUUUA
...............(((((..((..(.........)..))..)))))........----...........((((((........................)))))).... ( -19.46)
>DroSim_CAF1 75358 102 - 1
CGAAACUUCCGUCAAGUUGUUGCAGUCUUUUUAACUGGUUGUGGCAACA----AAA----AAAUAUUCCCCAACCGCAAGCUAUUUUUAAUAACACCAUAAGCGGUUU-UA
...............(((((..((..(.........)..))..))))).----...----...........((((((........................)))))).-.. ( -19.46)
>DroEre_CAF1 76372 101 - 1
CGAAACUUCCGUCAAGUUGUUGCAGUCUUUUUAACUGGUUGUGGCAACAA-----A----AAAUAUUCUCCAACCGCAAGCUAUUUUUAAUAACACCAUAAGUGGUUU-UA
...............(((((..((..(.........)..))..)))))..-----.----...........((((((........................)))))).-.. ( -17.56)
>DroYak_CAF1 79502 101 - 1
CGAAACUUCCGUCAAGUUGUUGCAGUCUUUUUAACUGGUUGUGGCAACAA-----A----AAAUAUUCCCCAACCGCAAGCUAUUUUUAAUAACACCAUAAGCGGUUU-UA
...............(((((..((..(.........)..))..)))))..-----.----...........((((((........................)))))).-.. ( -19.46)
>consensus
CGAAACUUCCGUCAAGUUGUUGCAGUCUUUUUAACUGGUUGUGGCAACAA___AAA____AAAUAUUCCCCAACCGCAAGCUAUUUUUAAUAACACCAUAAGCGGUUU_UA
...............(((((..((..(.........)..))..))))).......................((((((........................)))))).... (-19.24 = -19.08 +  -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 10:11:41 2006