Locus 7208

Sequence ID 2L_DroMel_CAF1
Location 20,247,538 – 20,247,770
Length 232
Max. P 0.969115
window11515 window11516 window11517 window11518

overview

Window 5

Location 20,247,538 – 20,247,650
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.76
Mean single sequence MFE -27.77
Consensus MFE -23.43
Energy contribution -24.10
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.84
SVM decision value 0.18
SVM RNA-class probability 0.622916
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20247538 112 + 22407834
AAAAAGAGAUGAAAAUAUGAUGUGUCCCGGUCCAUAAACCAUUUGAGAAGAAUCAACAAAAAGCAAGC-----CAAGCUUCCGUUCCGAGGACAAUCAUAUUCUCCCACCGGUU---CGG
.....((((.....(((((((.((((((((..(.........((((......))))....((((....-----...))))..)..))).))))))))))))))))...(((...---))) ( -26.10)
>DroSec_CAF1 6072 112 + 1
AAAAAGAGAUGAAAAUAUGAUGUGUCCCGGUCCAUAAACCAUUUGAGAAGAAUCAACAAAAAGCAAGCCAAGCCAAGCUUCCGUCCCGAGGACAUUCAUAUUCGCCCAC--------CGG
..........(..(((((((.(((((((((..(.........((((......))))......(.((((........)))).))..))).)))))))))))))..)....--------... ( -25.10)
>DroSim_CAF1 6503 120 + 1
AAAAAGAGAUGAAAAUAUGAUGUGUCCCGGUCCAUAAACCAUUUGAGAAGAAUCAACAAAAAGCAAGCCAAGCCAAGCUUCCGUUCCGAGGACAUUCAUAUUCUCCCACCGGUGCACCGG
.....((((.....((((((.(((((((((..(.........((((......))))......(.((((........)))).))..))).))))))))))))))))...((((....)))) ( -32.10)
>consensus
AAAAAGAGAUGAAAAUAUGAUGUGUCCCGGUCCAUAAACCAUUUGAGAAGAAUCAACAAAAAGCAAGCCAAGCCAAGCUUCCGUUCCGAGGACAUUCAUAUUCUCCCACCGGU____CGG
..........((.(((((((.(((((((((..(.........((((......))))......(.((((........)))).))..))).))))))))))))).))............... (-23.43 = -24.10 +   0.67)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,247,538 – 20,247,650
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.76
Mean single sequence MFE -34.57
Consensus MFE -29.63
Energy contribution -30.30
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.86
SVM decision value 0.25
SVM RNA-class probability 0.651307
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20247538 112 - 22407834
CCG---AACCGGUGGGAGAAUAUGAUUGUCCUCGGAACGGAAGCUUG-----GCUUGCUUUUUGUUGAUUCUUCUCAAAUGGUUUAUGGACCGGGACACAUCAUAUUUUCAUCUCUUUUU
(((---......)))((((((((((((((((.(((..(((((((...-----....))))))..((((......)))).........)..)))))))).))))))))))).......... ( -31.80)
>DroSec_CAF1 6072 112 - 1
CCG--------GUGGGCGAAUAUGAAUGUCCUCGGGACGGAAGCUUGGCUUGGCUUGCUUUUUGUUGAUUCUUCUCAAAUGGUUUAUGGACCGGGACACAUCAUAUUUUCAUCUCUUUUU
..(--------((((..((((((((.(((((.(((..((.(((((......)))))(((.((((..((....)).)))).)))...))..))))))))..)))))))))))))....... ( -33.80)
>DroSim_CAF1 6503 120 - 1
CCGGUGCACCGGUGGGAGAAUAUGAAUGUCCUCGGAACGGAAGCUUGGCUUGGCUUGCUUUUUGUUGAUUCUUCUCAAAUGGUUUAUGGACCGGGACACAUCAUAUUUUCAUCUCUUUUU
((((....))))...((((((((((.(((((.(((..((.(((((......)))))(((.((((..((....)).)))).)))...))..))))))))..)))))))))).......... ( -38.10)
>consensus
CCG____ACCGGUGGGAGAAUAUGAAUGUCCUCGGAACGGAAGCUUGGCUUGGCUUGCUUUUUGUUGAUUCUUCUCAAAUGGUUUAUGGACCGGGACACAUCAUAUUUUCAUCUCUUUUU
...............((((((((((.(((((.(((..((.(((((......)))))(((.((((..((....)).)))).)))...))..))))))))..)))))))))).......... (-29.63 = -30.30 +   0.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,247,650 – 20,247,770
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -33.45
Consensus MFE -30.64
Energy contribution -30.75
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -3.25
Structure conservation index 0.92
SVM decision value 1.64
SVM RNA-class probability 0.969115
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20247650 120 + 22407834
UUCGGGGGUCCAUAAAACUCCUGGCGGGAGUGCGACCAUUUCUGGUUAAGGCUCCCACAUAUGAGCCAUAAAAGAGUAACAACAAAUACCGAAAUUGUUAUUAAAUAACAACAUAACAAU
(((((.((((......(((((.....)))))..))))..((((..(((.(((((........))))).))).))))............)))))((((((((...........)))))))) ( -32.30)
>DroSec_CAF1 6184 117 + 1
UUCGGGGGUCCAUAAAACUCCUGGCGGGAGUGCGACCAUUUCUGGUUAGGGCCCCCACAUAUGAGCCAUAAAAGAGUAACAACAAAUACCGAAAUUGUUAUUAAAUAA---CAUAACAAU
(((((((((((.....(((((.....)))))..(((((....))))).)))))))).................(.(((........)))))))((((((((.......---.)))))))) ( -35.10)
>DroSim_CAF1 6623 120 + 1
UUCGGGGGUCCAUAAAACUCCUGGCGGGAGUGCGACCAUUUCUGGUUAGGGCUCCCACAUAUGAGCCAUAAAAGAGUAACAACAAAUACCGAAAUUGUUAUUAAAUAACAACAUAACAAU
(((((...........((((.((((((((((.((((((....))))).).)))))).(....).)))).....))))...........)))))((((((((...........)))))))) ( -32.95)
>consensus
UUCGGGGGUCCAUAAAACUCCUGGCGGGAGUGCGACCAUUUCUGGUUAGGGCUCCCACAUAUGAGCCAUAAAAGAGUAACAACAAAUACCGAAAUUGUUAUUAAAUAACAACAUAACAAU
...((((((((.....(((((.....)))))..(((((....))))).))))))))...((((...........((((((((............)))))))).........))))..... (-30.64 = -30.75 +   0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,247,650 – 20,247,770
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -32.60
Consensus MFE -31.92
Energy contribution -31.70
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.97
Structure conservation index 0.98
SVM decision value 0.94
SVM RNA-class probability 0.885884
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20247650 120 - 22407834
AUUGUUAUGUUGUUAUUUAAUAACAAUUUCGGUAUUUGUUGUUACUCUUUUAUGGCUCAUAUGUGGGAGCCUUAACCAGAAAUGGUCGCACUCCCGCCAGGAGUUUUAUGGACCCCCGAA
.......(((((((....)))))))..(((((.....((....))(((..((..((((....(((((((.....((((....))))....)))))))...))))..)).)))...))))) ( -32.00)
>DroSec_CAF1 6184 117 - 1
AUUGUUAUG---UUAUUUAAUAACAAUUUCGGUAUUUGUUGUUACUCUUUUAUGGCUCAUAUGUGGGGGCCCUAACCAGAAAUGGUCGCACUCCCGCCAGGAGUUUUAUGGACCCCCGAA
...((((((---.....(((((((((.........)))))))))......)))))).......((((((.((..((((....))))...(((((.....))))).....)).)))))).. ( -33.80)
>DroSim_CAF1 6623 120 - 1
AUUGUUAUGUUGUUAUUUAAUAACAAUUUCGGUAUUUGUUGUUACUCUUUUAUGGCUCAUAUGUGGGAGCCCUAACCAGAAAUGGUCGCACUCCCGCCAGGAGUUUUAUGGACCCCCGAA
.......(((((((....)))))))..(((((.....((....))(((..((..((((....(((((((.....((((....))))....)))))))...))))..)).)))...))))) ( -32.00)
>consensus
AUUGUUAUGUUGUUAUUUAAUAACAAUUUCGGUAUUUGUUGUUACUCUUUUAUGGCUCAUAUGUGGGAGCCCUAACCAGAAAUGGUCGCACUCCCGCCAGGAGUUUUAUGGACCCCCGAA
((((((((...........))))))))(((((.....((....))(((..((..((((....(((((((.....((((....))))....)))))))...))))..)).)))...))))) (-31.92 = -31.70 +  -0.22)

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 12:30:13 2006