Locus 1448

Sequence ID 2R_DroMel_CAF1
Location 5,527,534 – 5,527,644
Length 110
Max. P 0.973680
window2475 window2476

overview

Window 5

Location 5,527,534 – 5,527,644
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.30
Mean single sequence MFE -30.50
Consensus MFE -25.08
Energy contribution -24.52
Covariance contribution -0.56
Combinations/Pair 1.21
Mean z-score -1.91
Structure conservation index 0.82
SVM decision value 1.72
SVM RNA-class probability 0.973680
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5527534 110 + 20766785
------AGAAUGACAUU-UGCU--UUAUUAUGCCAGCCAACAGUGUCCAACUUACGGAACCCAACCUAUACUUCCAAGUGGCAGGAAGUGAGGUUGACAAGGCGAACAAGGCUGUU-GUA
------......(((..-.(((--((.((.((((..((...(((.....)))...))....((((((.(((((((........)))))))))))))....)))))).)))))...)-)). ( -32.00)
>DroSec_CAF1 50822 118 + 1
AACUCAAGAAUGGCAUUUUUCC--UUAUUAUGCCAGCAAACAGUUUCCAUCUUACGGAACUCAACCUGUACUUCCAAGUGGCAGGAAGUGAGGUUGACAAGGCGAACAAGGCUGUUGGUA
..........((((((..(...--..)..))))))((.((((((((((.......)))).(((((((.(((((((........)))))))))))))).............)))))).)). ( -34.90)
>DroSim_CAF1 28130 112 + 1
------AGAAUGGCAUUUUUCC--UUAUUAUGCCAGCAAACAGUUUCCAUCUUACGGAACUCAACCUGUACUUCCAAGUGGCAGGAAGUGAGGUUGACAAGGCGAACAAGGCUGUUGGUA
------....((((((..(...--..)..))))))((.((((((((((.......)))).(((((((.(((((((........)))))))))))))).............)))))).)). ( -34.90)
>DroEre_CAF1 27908 112 + 1
AACCAA------GCAUUUACCCAAUUUUUUUUUCAACAAACAGUAUCCAACUUAUGGAACGCAGCCUGUACUUCCAAGUGGCAGGAAGUGAGGUUGACAA-GCGAACAAGGCUGUU-AUA
......------..........................((((((.((((.....))))..(((((((.(((((((........))))))))))))).)..-.........))))))-... ( -26.90)
>DroYak_CAF1 28968 97 + 1
AACUAA------AAAAU----------------AUAGAAAUGGUAUCCAACUUAUGGAACUCGGCCUGUACUUCCAAGUGGCAGGAAGUGAGGUUGACAAGGCGAACAAGGCUGUU-AUA
......------.....----------------.....((((((.((((.....))))..(((((((.(((((((........)))))))))))))).............))))))-... ( -23.80)
>consensus
AAC__AAGAAUGGCAUUUUUCC__UUAUUAUGCCAGCAAACAGUAUCCAACUUACGGAACUCAACCUGUACUUCCAAGUGGCAGGAAGUGAGGUUGACAAGGCGAACAAGGCUGUU_GUA
...................................((.((((((.(((.......)))...((((((.(((((((........)))))))))))))..............)))))).)). (-25.08 = -24.52 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,527,534 – 5,527,644
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.30
Mean single sequence MFE -28.28
Consensus MFE -19.78
Energy contribution -20.58
Covariance contribution 0.80
Combinations/Pair 1.13
Mean z-score -1.44
Structure conservation index 0.70
SVM decision value 0.21
SVM RNA-class probability 0.636959
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5527534 110 - 20766785
UAC-AACAGCCUUGUUCGCCUUGUCAACCUCACUUCCUGCCACUUGGAAGUAUAGGUUGGGUUCCGUAAGUUGGACACUGUUGGCUGGCAUAAUAA--AGCA-AAUGUCAUUCU------
..(-(((((...((((((.(((((((((((.((((((........))))))..)))))))......)))).))))))))))))..((((((.....--....-.))))))....------ ( -32.70)
>DroSec_CAF1 50822 118 - 1
UACCAACAGCCUUGUUCGCCUUGUCAACCUCACUUCCUGCCACUUGGAAGUACAGGUUGAGUUCCGUAAGAUGGAAACUGUUUGCUGGCAUAAUAA--GGAAAAAUGCCAUUCUUGAGUU
.........(((((((.(((...(((((((.((((((........))))))..))))))).....(((((..(....)..))))).)))..)))))--)).................... ( -32.80)
>DroSim_CAF1 28130 112 - 1
UACCAACAGCCUUGUUCGCCUUGUCAACCUCACUUCCUGCCACUUGGAAGUACAGGUUGAGUUCCGUAAGAUGGAAACUGUUUGCUGGCAUAAUAA--GGAAAAAUGCCAUUCU------
.........(((((((.(((...(((((((.((((((........))))))..))))))).....(((((..(....)..))))).)))..)))))--))..............------ ( -32.80)
>DroEre_CAF1 27908 112 - 1
UAU-AACAGCCUUGUUCGC-UUGUCAACCUCACUUCCUGCCACUUGGAAGUACAGGCUGCGUUCCAUAAGUUGGAUACUGUUUGUUGAAAAAAAAAUUGGGUAAAUGC------UUGGUU
...-..((((...((..((-((((.......((((((........)))))))))))).))((((((.....)))).)).....)))).......(((..(((....))------)..))) ( -25.41)
>DroYak_CAF1 28968 97 - 1
UAU-AACAGCCUUGUUCGCCUUGUCAACCUCACUUCCUGCCACUUGGAAGUACAGGCCGAGUUCCAUAAGUUGGAUACCAUUUCUAU----------------AUUUU------UUAGUU
...-(((.......((((.(((((.......((((((........))))))))))).)))).((((.....))))............----------------.....------...))) ( -17.71)
>consensus
UAC_AACAGCCUUGUUCGCCUUGUCAACCUCACUUCCUGCCACUUGGAAGUACAGGUUGAGUUCCGUAAGUUGGAAACUGUUUGCUGGCAUAAUAA__GGAAAAAUGCCAUUCUU__GUU
......((((.............(((((((.((((((........))))))..)))))))((((((.....)))).)).....))))................................. (-19.78 = -20.58 +   0.80)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:09 2006