Locus 4769

Sequence ID 3L_DroMel_CAF1
Location 13,386,981 – 13,387,141
Length 160
Max. P 0.985791
window7505 window7506 window7507

overview

Window 5

Location 13,386,981 – 13,387,101
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -35.99
Consensus MFE -34.15
Energy contribution -34.93
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -3.08
Structure conservation index 0.95
SVM decision value 2.02
SVM RNA-class probability 0.985791
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13386981 120 + 23771897
GAUACGUAGAGAGGGGGAUGAGUCAACAGGCGAAAAACGGUAAAAGCAGAAAGCAAUCGCCGGAAGCACCGUGAUUAUGCCCAUAAAUGGGCAUAGAUGCAUAUGAAAGACCUUUUUAAG
......((((((((.((.((..((....(((((......((....)).........))))).))..))))(((.(((((((((....))))))))).)))..........)))))))).. ( -34.76)
>DroSim_CAF1 58543 120 + 1
GAUACGUAGAGAGGGGGAUGAGUCAACAGGCGAAAAACGGUAAAAGCAGAAAGCAAUCGCCGGAAGCGCCGUGAUUAUGCCCAUAAAAGGGCAUAGCUGCAUAUGAAAGACCUUUUUAAG
.........(((((((..(...(((...((((.....((((....((.....))....))))....))))((..((((((((......))))))))..))...))).)..)))))))... ( -38.20)
>DroYak_CAF1 61095 120 + 1
GACUCGUAGAGAAGGGGAUGAGUCAACAGGCGAAAAACGGUAAAAGCAGAAAGCAAUCGCCGGAAGCGCCGUGAUUAUGCCCAUAAAUGGGCAUUGCUGCAUAUGAAAGACCUUUGUAAG
(((((((..........))))))).(((((((.....((((....((.....))....))))....))))((..(.(((((((....))))))).)..))..............)))... ( -35.00)
>consensus
GAUACGUAGAGAGGGGGAUGAGUCAACAGGCGAAAAACGGUAAAAGCAGAAAGCAAUCGCCGGAAGCGCCGUGAUUAUGCCCAUAAAUGGGCAUAGCUGCAUAUGAAAGACCUUUUUAAG
.........(((((((..(...(((...((((.....((((....((.....))....))))....))))((..((((((((......))))))))..))...))).)..)))))))... (-34.15 = -34.93 +   0.78)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,386,981 – 13,387,101
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -29.08
Consensus MFE -27.29
Energy contribution -27.40
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.39
Structure conservation index 0.94
SVM decision value 1.27
SVM RNA-class probability 0.938827
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13386981 120 - 23771897
CUUAAAAAGGUCUUUCAUAUGCAUCUAUGCCCAUUUAUGGGCAUAAUCACGGUGCUUCCGGCGAUUGCUUUCUGCUUUUACCGUUUUUCGCCUGUUGACUCAUCCCCCUCUCUACGUAUC
........((((...((...(((((((((((((....)))))))).....)))))....(((((..((..............))...)))))))..)))).................... ( -27.54)
>DroSim_CAF1 58543 120 - 1
CUUAAAAAGGUCUUUCAUAUGCAGCUAUGCCCUUUUAUGGGCAUAAUCACGGCGCUUCCGGCGAUUGCUUUCUGCUUUUACCGUUUUUCGCCUGUUGACUCAUCCCCCUCUCUACGUAUC
.......(((...........(((((((((((......))))))).....((((....(((..(..((.....))..)..))).....)))).)))).........)))........... ( -29.45)
>DroYak_CAF1 61095 120 - 1
CUUACAAAGGUCUUUCAUAUGCAGCAAUGCCCAUUUAUGGGCAUAAUCACGGCGCUUCCGGCGAUUGCUUUCUGCUUUUACCGUUUUUCGCCUGUUGACUCAUCCCCUUCUCUACGAGUC
.....................((((((((((((....)))))))......((((....(((..(..((.....))..)..))).....)))))))))((((..............)))). ( -30.24)
>consensus
CUUAAAAAGGUCUUUCAUAUGCAGCUAUGCCCAUUUAUGGGCAUAAUCACGGCGCUUCCGGCGAUUGCUUUCUGCUUUUACCGUUUUUCGCCUGUUGACUCAUCCCCCUCUCUACGUAUC
........((((...((........(((((((......))))))).....((((....(((..(..((.....))..)..))).....))))))..)))).................... (-27.29 = -27.40 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,387,021 – 13,387,141
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.76
Mean single sequence MFE -33.97
Consensus MFE -29.26
Energy contribution -30.04
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.86
SVM decision value 0.06
SVM RNA-class probability 0.564567
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13387021 120 - 23771897
GGGGUCGCUCCAACGGCUCCACACGCGCCUCCUCUUACUGCUUAAAAAGGUCUUUCAUAUGCAUCUAUGCCCAUUUAUGGGCAUAAUCACGGUGCUUCCGGCGAUUGCUUUCUGCUUUUA
(((((((......))))))).....((((.(((.((........)).)))..........(((((((((((((....)))))))).....)))))....))))...((.....))..... ( -35.60)
>DroSim_CAF1 58583 119 - 1
GGGGUCGCUCCAACGGCUCCUCCCCCGCCCCCUC-AACUGCUUAAAAAGGUCUUUCAUAUGCAGCUAUGCCCUUUUAUGGGCAUAAUCACGGCGCUUCCGGCGAUUGCUUUCUGCUUUUA
(((((((......)))))))......(((.....-..((((...................)))).(((((((......))))))).....)))((....(((....)))....))..... ( -33.81)
>DroYak_CAF1 61135 118 - 1
GGGGUCGCUCCAACUGCUCCACC-CCGCCCCCUC-AACUGCUUACAAAGGUCUUUCAUAUGCAGCAAUGCCCAUUUAUGGGCAUAAUCACGGCGCUUCCGGCGAUUGCUUUCUGCUUUUA
(((((.((.......))...)))-))(((.....-..((((...................))))..(((((((....)))))))......)))((....(((....)))....))..... ( -32.51)
>consensus
GGGGUCGCUCCAACGGCUCCACCCCCGCCCCCUC_AACUGCUUAAAAAGGUCUUUCAUAUGCAGCUAUGCCCAUUUAUGGGCAUAAUCACGGCGCUUCCGGCGAUUGCUUUCUGCUUUUA
(((((((......)))))))......(((........((((...................)))).(((((((......))))))).....)))((....(((....)))....))..... (-29.26 = -30.04 +   0.78)

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 11:32:43 2006