Locus 5279

Sequence ID 3R_DroMel_CAF1
Location 13,771,200 – 13,771,322
Length 122
Max. P 0.930583
window8614 window8615 window8616 window8617

overview

Window 4

Location 13,771,200 – 13,771,292
Length 92
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 78.40
Mean single sequence MFE -21.36
Consensus MFE -15.11
Energy contribution -14.62
Covariance contribution -0.50
Combinations/Pair 1.18
Mean z-score -1.89
Structure conservation index 0.71
SVM decision value 1.21
SVM RNA-class probability 0.930583
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13771200 92 + 27905053
UCCCCGCUCUCCAUUUCCCCCCCGUU-UUAGUCGCAA---ACAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACG
.........(((((((......((..-.....))...---..))))-----)))....(((((((((((((.....))))))))..))))).......... ( -22.20)
>DroSec_CAF1 43751 93 + 1
UCCCGGCUCUCCAUUUCCCCCCGUUUUUCAGACCCAA---CCAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACG
....(((..(((((((......(((.....)))....---..))))-----)))....((..(((((((((.....)))))))))..)))))......... ( -24.00)
>DroSim_CAF1 42641 93 + 1
UCCCGGCUCUCCAUUUCCCCCCGUUUUUCAGACCCAA---CCAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACG
....(((..(((((((......(((.....)))....---..))))-----)))....((..(((((((((.....)))))))))..)))))......... ( -24.00)
>DroEre_CAF1 42458 85 + 1
-----GCUCUCCAUUUGCCCCC---UUGCAGCCCCAA---CCAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACG
-----....((((((((.....---(((......)))---.)))))-----)))....(((((((((((((.....))))))))..))))).......... ( -23.70)
>DroYak_CAF1 50134 90 + 1
UCCCGGCUCUCCAUUUCCCCCC---UUUCAGCAUCAA---CCAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACG
....(((..(((((((......---............---..))))-----)))....((..(((((((((.....)))))))))..)))))......... ( -21.75)
>DroAna_CAF1 45198 87 + 1
UCUCUACUCUAC-------UCC---UUUCUCGCCCAAUGUCUAGCUUCUUUUUUUUUUUCAAUGAAAUUGCGUGAUGCAAUUGCAAUGUGGCAAGAU----
............-------...---..(((.(((((.(((...((.((......((((.....))))......)).))....))).)).))).))).---- ( -12.50)
>consensus
UCCCGGCUCUCCAUUUCCCCCC___UUUCAGACCCAA___CCAGAU_____GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACG
....................................................((((..(((((((((((((.....)))))))))..)))).))))..... (-15.11 = -14.62 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,771,200 – 13,771,292
Length 92
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 78.40
Mean single sequence MFE -25.37
Consensus MFE -15.88
Energy contribution -16.38
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.63
SVM decision value 0.22
SVM RNA-class probability 0.638296
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13771200 92 - 27905053
CGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGU---UUGCGACUAA-AACGGGGGGGAAAUGGAGAGCGGGGA
(((....((.(((((..((((((((.....))))))))))))).)).(((-----.(((((---((.......)-))))))..)))........))).... ( -30.50)
>DroSec_CAF1 43751 93 - 1
CGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGG---UUGGGUCUGAAAAACGGGGGGAAAUGGAGAGCCGGGA
.......(((((.((((((((((((.....)))))))).........(((-----.(((.(---((..........))).))))))...)))).))))).. ( -27.20)
>DroSim_CAF1 42641 93 - 1
CGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGG---UUGGGUCUGAAAAACGGGGGGAAAUGGAGAGCCGGGA
.......(((((.((((((((((((.....)))))))).........(((-----.(((.(---((..........))).))))))...)))).))))).. ( -27.20)
>DroEre_CAF1 42458 85 - 1
CGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGG---UUGGGGCUGCAA---GGGGGCAAAUGGAGAGC-----
...........((.(((((..(((((((.((((.......))))...(((-----(.....---.)))))))))))---....)))))))......----- ( -24.90)
>DroYak_CAF1 50134 90 - 1
CGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGG---UUGAUGCUGAAA---GGGGGGAAAUGGAGAGCCGGGA
.......(((((.((((((((((((.....)))))))).........(((-----..((..---((......))..---))..)))...)))).))))).. ( -25.10)
>DroAna_CAF1 45198 87 - 1
----AUCUUGCCACAUUGCAAUUGCAUCACGCAAUUUCAUUGAAAAAAAAAAAGAAGCUAGACAUUGGGCGAGAAA---GGA-------GUAGAGUAGAGA
----.(((((((.((.((.((((((.....)))))).)).))...............(........))))))))..---...-------............ ( -17.30)
>consensus
CGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC_____AUCUGG___UUGGGGCUGAAA___GGGGGGAAAUGGAGAGCCGGGA
.......((.((((..(((((((((.....))))))))))))).))....................................................... (-15.88 = -16.38 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,771,226 – 13,771,322
Length 96
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 80.61
Mean single sequence MFE -25.95
Consensus MFE -17.40
Energy contribution -18.35
Covariance contribution 0.95
Combinations/Pair 1.10
Mean z-score -1.89
Structure conservation index 0.67
SVM decision value 0.64
SVM RNA-class probability 0.809442
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13771226 96 + 27905053
UUAGUCGCAA---ACAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACGAGAAGAGGAAUUUCUUUCCAUUUUCGAGUU
.........(---((...(-----(((.((.(((((((((((((.....))))))))..))))).)).))))((((((..((((.....)))).)))))).))) ( -27.30)
>DroSec_CAF1 43778 96 + 1
UCAGACCCAA---CCAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACGAGCAGAGGAAUUUCUUUCCAUUUCCGAGUU
..........---.....(-----(((....(((((((((((((.....))))))))..)))))................((((.....))))...)))).... ( -24.40)
>DroSim_CAF1 42668 96 + 1
UCAGACCCAA---CCAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACGAGUAGAGGAAUUUCUUUCCAUUUCCGAGUU
..........---.....(-----(((....(((((((((((((.....))))))))..)))))................((((.....))))...)))).... ( -24.40)
>DroEre_CAF1 42477 96 + 1
GCAGCCCCAA---CCAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACGGGUAGAGGAAUUCCUUUCCAUUUCCCAGAU
...((((...---((....-----)).....(((((((((((((.....))))))))..))))).........))))...((((.....))))........... ( -28.20)
>DroYak_CAF1 50158 96 + 1
UCAGCAUCAA---CCAGAU-----GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACGGGCAGAGGAAUUUCUUUCCAUUUCCCAGAU
....((((..---...)))-----)......(((((((((((((.....))))))))..))))).........(((.(((((((.....)))).)))))).... ( -29.50)
>DroAna_CAF1 45215 94 + 1
UCUCGCCCAAUGUCUAGCUUCUUUUUUUUUUUCAAUGAAAUUGCGUGAUGCAAUUGCAAUGUGGCAAGAU----------GGAAUUUCUGCCAUCUUCCGGCUU
....(((.........................((.((.((((((.....)))))).)).)).((.(((((----------((........)))))))))))).. ( -21.90)
>consensus
UCAGACCCAA___CCAGAU_____GGAUUUCGCACUGCAAUUGCGUGCUGCAAUUGCAAAGUGCCAAUUUUACGAGCAGAGGAAUUUCUUUCCAUUUCCGAGUU
........................(((....(((((((((((((.....)))))))))..))))................((((.....))))...)))..... (-17.40 = -18.35 +   0.95)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,771,226 – 13,771,322
Length 96
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 80.61
Mean single sequence MFE -28.20
Consensus MFE -17.00
Energy contribution -17.70
Covariance contribution 0.70
Combinations/Pair 1.05
Mean z-score -2.48
Structure conservation index 0.60
SVM decision value 0.93
SVM RNA-class probability 0.884288
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13771226 96 - 27905053
AACUCGAAAAUGGAAAGAAAUUCCUCUUCUCGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGU---UUGCGACUAA
.....(((...((((.....))))..)))(((((((....(((((..((((((((.....)))))))))))))((.....-----.))..)---)))))).... ( -26.70)
>DroSec_CAF1 43778 96 - 1
AACUCGGAAAUGGAAAGAAAUUCCUCUGCUCGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGG---UUGGGUCUGA
.((((((..(((((.(((......)))..........((.(((((..((((((((.....))))))))))))).)).)))-----))....---)))))).... ( -28.10)
>DroSim_CAF1 42668 96 - 1
AACUCGGAAAUGGAAAGAAAUUCCUCUACUCGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGG---UUGGGUCUGA
.((((((..(((((.(((......)))..........((.(((((..((((((((.....))))))))))))).)).)))-----))....---)))))).... ( -28.10)
>DroEre_CAF1 42477 96 - 1
AUCUGGGAAAUGGAAAGGAAUUCCUCUACCCGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGG---UUGGGGCUGC
....(((....((((.....))))....)))......((.(((((..((((((((.....))))))))))))).)).(((-----(.....---.))))..... ( -30.00)
>DroYak_CAF1 50158 96 - 1
AUCUGGGAAAUGGAAAGAAAUUCCUCUGCCCGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC-----AUCUGG---UUGAUGCUGA
....(((....((((.....))))....)))......((.(((((..((((((((.....))))))))))))).))...(-----(((...---..)))).... ( -30.60)
>DroAna_CAF1 45215 94 - 1
AAGCCGGAAGAUGGCAGAAAUUCC----------AUCUUGCCACAUUGCAAUUGCAUCACGCAAUUUCAUUGAAAAAAAAAAAGAAGCUAGACAUUGGGCGAGA
..((((((((((((.(....).))----------))))).)).((.((.((((((.....)))))).)).)).........................))).... ( -25.70)
>consensus
AACUCGGAAAUGGAAAGAAAUUCCUCUACUCGUAAAAUUGGCACUUUGCAAUUGCAGCACGCAAUUGCAGUGCGAAAUCC_____AUCUGG___UUGGGGCUGA
...........((((.....)))).............((.((((..(((((((((.....))))))))))))).))............................ (-17.00 = -17.70 +   0.70)

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 11:50:58 2006