Locus 571

Sequence ID 3R_DroMel_CAF1
Location 2,132,685 – 2,132,878
Length 193
Max. P 0.997927
window908 window909 window910 window911

overview

Window 8

Location 2,132,685 – 2,132,801
Length 116
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 82.39
Mean single sequence MFE -30.50
Consensus MFE -22.44
Energy contribution -23.28
Covariance contribution 0.84
Combinations/Pair 1.23
Mean z-score -2.45
Structure conservation index 0.74
SVM decision value 1.65
SVM RNA-class probability 0.970009
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2132685 116 + 27905053
AAAUCCU-UUUUUUCAGAAAGUGCCGUGAUAGUCUGCAUAUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACUAAAACACUGAUAGUUGGUUCCAGUAACCAAUUAUC
.....((-(((.....)))))(((.(((((.((((((....((((((......))))))..))))))....))))))))...........(((((((((((.....))))))))))) ( -32.90)
>DroSec_CAF1 276041 117 + 1
AAAUCUUAUUUUUUCAGCAAGUGCCGUGGUAGUCUGCCUCUUAGGAAUACAUUUUUCUACGGCGGUCAUCGACCACGCAACAAAACCACUGAUAGUUGGAUCCAGUGACCAAUUAUC
....................((..((((((.(.(((((...((((((......)))))).))))).)....))))))..)).........(((((((((.((....))))))))))) ( -31.00)
>DroSim_CAF1 295476 117 + 1
AAAUCAUAUUUUUUCAGCAAGUGCCGUGGUAGUCUGCCUCUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACAAAACCACUGAUAGUUGGUUCCAGUGACCAAUUAUC
....................((..((((((.(((((((...((((((......)))))).)))))))....))))))..)).........(((((((((((.....))))))))))) ( -34.20)
>DroEre_CAF1 280221 117 + 1
AAAUUCUAUUUGUAUAGCAAGUGCAAUAAUAGUCUGCAUAUUUAAAGUACAUUUUUGUACGGCGGAGACUGAUCACGUAUUAAAGCCACAGAUAGUUGGUGCUAAAAGCCAACUAUC
.....((((((((((.....)))))..)))))..............(((((....)))))((((....)((((.....))))..)))...((((((((((.......)))))))))) ( -27.90)
>DroYak_CAF1 280865 117 + 1
AAAUUCUUUUUGUUUAGCAAGUGCAAUGAUAGUCUUCAUAUUAAGAAUACAUUUUUGUACGGCGGAGGCUGAUCACGUAAUAAAACCACAGAUAGUUGGUGCCAGUAGCCAACUAUC
..........((.(((((..((((((.(((.((.(((.......))).))))).)))))).......))))).))...............((((((((((.......)))))))))) ( -26.50)
>consensus
AAAUCCUAUUUUUUCAGCAAGUGCCGUGAUAGUCUGCAUAUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACAAAACCACUGAUAGUUGGUUCCAGUAACCAAUUAUC
.....................(((.(((((.((((((....((((((......))))))..))))))....))))))))...........((((((((((.......)))))))))) (-22.44 = -23.28 +   0.84) 

alignment

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secondary structure

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dotplot

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Window 9

Location 2,132,723 – 2,132,841
Length 118
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 83.64
Mean single sequence MFE -32.76
Consensus MFE -21.73
Energy contribution -21.77
Covariance contribution 0.04
Combinations/Pair 1.25
Mean z-score -3.36
Structure conservation index 0.66
SVM decision value 2.26
SVM RNA-class probability 0.991260
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2132723 118 + 27905053
AUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACUAAAACACUGAUAGUUGGUUCCAGUAACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUC
....((((((..(((((((...(((((......)).)))..........(((((((((((((.....))))))))))))))))))))..))))))....(((((.....))))).... ( -36.40)
>DroSec_CAF1 276080 109 + 1
CUUAGGAAUACAUUUUUCUACGGCGGUCAUCGACCACGCAACAAAACCACUGAUAGUUGGAUCCAGUGACCAAUUAUCAAAGAAAGAA---------UCGGAAUUGCCCAUUCCCAUC
....(((((...(((((((.((..((((...)))).))............((((((((((.((....)))))))))))).))))))).---------..((......))))))).... ( -27.20)
>DroSim_CAF1 295515 118 + 1
CUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACAAAACCACUGAUAGUUGGUUCCAGUGACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUC
....((((((..(((((((...(((((......)).)))..........(((((((((((((.....))))))))))))))))))))..))))))....(((((.....))))).... ( -36.80)
>DroEre_CAF1 280260 118 + 1
AUUUAAAGUACAUUUUUGUACGGCGGAGACUGAUCACGUAUUAAAGCCACAGAUAGUUGGUGCUAAAAGCCAACUAUCAGAGAAUGAAAUAUUCCGGUCGGAAUUGCCCAUUCCCAUC
.......(((((....)))))((((....)((((.....))))..)))...((((((((((.......)))))))))).(.(((((....(((((....)))))....))))).)... ( -35.30)
>DroYak_CAF1 280904 118 + 1
AUUAAGAAUACAUUUUUGUACGGCGGAGGCUGAUCACGUAAUAAAACCACAGAUAGUUGGUGCCAGUAGCCAACUAUCAGAGAAAGAAAUAUUCCGUUCAGAAUUGCCUAUUCCCAUU
.....(((((((.(((((...(((((((.((..((..((......))....((((((((((.......)))))))))).))...)).....)))))))))))).))..)))))..... ( -28.10)
>consensus
AUUAGGAAUACAUUUUUCUACGGCGGACAUCGAUCACGCAACAAAACCACUGAUAGUUGGUUCCAGUAACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUC
..((((((......)))))).(((((...((((..............(.((((((((((((.......)))))))))))).)...............))))..))))).......... (-21.73 = -21.77 +   0.04) 

alignment

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secondary structure

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dotplot

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Window 0

Location 2,132,763 – 2,132,878
Length 115
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 82.75
Mean single sequence MFE -26.16
Consensus MFE -17.46
Energy contribution -18.46
Covariance contribution 1.00
Combinations/Pair 1.15
Mean z-score -3.91
Structure conservation index 0.67
SVM decision value 2.96
SVM RNA-class probability 0.997927
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2132763 115 + 27905053
ACUAAAACACUGAUAGUUGGUUCCAGUAACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUGGGAAUCAACAAAUUUA---UAAAAAUG
.........(((((((((((((.....)))))))))))))...........((((....))))(((...((((((((...........))))))))...))).....---........ ( -28.30)
>DroSec_CAF1 276120 109 + 1
ACAAAACCACUGAUAGUUGGAUCCAGUGACCAAUUAUCAAAGAAAGAA---------UCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUGGGAAUCAACAAUUUCCUAUUAAAAAUG
..........((((((((((.((....)))))))))))).........---------..(((((((...((((((((...........))))))))...)))))))............ ( -25.40)
>DroSim_CAF1 295555 118 + 1
ACAAAACCACUGAUAGUUGGUUCCAGUGACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUAGGAAUCAACAAUUUCCUAUUAAAAAUG
.........(((((((((((((.....))))))))))))).(((.(....(((((....)))))....).)))...............(((((((........)))))))........ ( -28.20)
>DroEre_CAF1 280300 115 + 1
UUAAAGCCACAGAUAGUUGGUGCUAAAAGCCAACUAUCAGAGAAUGAAAUAUUCCGGUCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUGGUAAUCAGCCAAUUUA---UAAUAAUA
.....((((..((((((((((.......)))))))))).(.(((((....(((((....)))))....))))).)..............))))..............---........ ( -28.70)
>DroYak_CAF1 280944 115 + 1
AUAAAACCACAGAUAGUUGGUGCCAGUAGCCAACUAUCAGAGAAAGAAAUAUUCCGUUCAGAAUUGCCUAUUCCCAUUAAACUGAACUAUGACAAUCAACAAAUUUA---UAAUAAUA
(((((......((((((((((.......)))))))))).................((((((...((........)).....))))))................))))---)....... ( -20.20)
>consensus
ACAAAACCACUGAUAGUUGGUUCCAGUAACCAAUUAUCAGAGAAAGAAAUAUUCCGUUCGGAAUUGCCCAUUCCCAUCAAACUAAACUAUGGGAAUCAACAAAUUUA___UAAAAAUG
.........((((((((((((.......))))))))))))...................(((.(((...((((((((...........))))))))...))).)))............ (-17.46 = -18.46 +   1.00) 

alignment

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secondary structure

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dotplot

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Window 1

Location 2,132,763 – 2,132,878
Length 115
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 82.75
Mean single sequence MFE -29.24
Consensus MFE -19.36
Energy contribution -20.40
Covariance contribution 1.04
Combinations/Pair 1.18
Mean z-score -2.36
Structure conservation index 0.66
SVM decision value 1.10
SVM RNA-class probability 0.915900
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2132763 115 - 27905053
CAUUUUUA---UAAAUUUGUUGAUUCCCAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGAACGGAAUAUUUCUUUCUCUGAUAAUUGGUUACUGGAACCAACUAUCAGUGUUUUAGU
........---......((((.((((((((...........)))))))).))))(((((....)))))........(.((((((.((((((.....)))))).)))))).)....... ( -31.50)
>DroSec_CAF1 276120 109 - 1
CAUUUUUAAUAGGAAAUUGUUGAUUCCCAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGA---------UUCUUUCUUUGAUAAUUGGUCACUGGAUCCAACUAUCAGUGGUUUUGU
...........((((.(((((.((((((((...........)))))))).)))))))))..---------.....((.((((((.((((((....)).)))).)))))).))...... ( -29.80)
>DroSim_CAF1 295555 118 - 1
CAUUUUUAAUAGGAAAUUGUUGAUUCCUAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGAACGGAAUAUUUCUUUCUCUGAUAAUUGGUCACUGGAACCAACUAUCAGUGGUUUUGU
..........(((((((((((.((((((((...........)))))))).))))(((((....))))))))))))((.((((((.((((((....).))))).)))))).))...... ( -31.80)
>DroEre_CAF1 280300 115 - 1
UAUUAUUA---UAAAUUGGCUGAUUACCAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGACCGGAAUAUUUCAUUCUCUGAUAGUUGGCUUUUAGCACCAACUAUCUGUGGCUUUAA
........---...............(((((............(((((((((..(((((....)))))..))))))))).(((((((((.........))))))))))))))...... ( -30.10)
>DroYak_CAF1 280944 115 - 1
UAUUAUUA---UAAAUUUGUUGAUUGUCAUAGUUCAGUUUAAUGGGAAUAGGCAAUUCUGAACGGAAUAUUUCUUUCUCUGAUAGUUGGCUACUGGCACCAACUAUCUGUGGUUUUAU
((..((((---((..(((((((((((((....((((......))))....)))))))...))))))..............(((((((((.........)))))))))))))))..)). ( -23.00)
>consensus
CAUUUUUA___UAAAUUUGUUGAUUCCCAUAGUUUAGUUUGAUGGGAAUGGGCAAUUCCGAACGGAAUAUUUCUUUCUCUGAUAAUUGGUUACUGGAACCAACUAUCAGUGGUUUUGU
................(((((.((((((((...........)))))))).)))))((((....)))).........(.((((((.((((.........)))).)))))).)....... (-19.36 = -20.40 +   1.04) 

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 09:46:24 2006