Locus 2504

Sequence ID 3R_DroMel_CAF1
Location 6,835,985 – 6,836,243
Length 258
Max. P 0.999138
window4104 window4105 window4106

overview

Window 4

Location 6,835,985 – 6,836,098
Length 113
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 98.59
Mean single sequence MFE -25.85
Consensus MFE -24.21
Energy contribution -23.96
Covariance contribution -0.25
Combinations/Pair 1.03
Mean z-score -2.32
Structure conservation index 0.94
SVM decision value 3.39
SVM RNA-class probability 0.999138
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6835985 113 - 27905053
CCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUUGUUAGCCAGGCCAG--CAAAACAACAAAGCAAGCG
(((((((((.............)))))))))...((((((......))))))....((((....))))(((...(((((((((.((.......)--)..)))))))))..))).. ( -25.92)
>DroSec_CAF1 94860 113 - 1
CCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUUGUUAGCCAAGCCAG--CAAAACAACAAAGCAAGCG
(((((((((.............)))))))))...((((((......))))))....((((....))))(((...(((((((((.((.......)--)..)))))))))..))).. ( -25.92)
>DroSim_CAF1 101218 113 - 1
CCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUUGUUAGCCAGGCCAG--CAAAACAACAAAGCAAGCG
(((((((((.............)))))))))...((((((......))))))....((((....))))(((...(((((((((.((.......)--)..)))))))))..))).. ( -25.92)
>DroEre_CAF1 80118 113 - 1
CCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUUGUUAGCCAGGCCAG--CAAAACAACAAAGCAGGCG
(((((((((.............)))))))))...((((((......))))))....((((....))))(((...(((((((((.((.......)--)..)))))))))..))).. ( -25.62)
>DroYak_CAF1 93693 115 - 1
CCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUUGUUAGCCAGGCCAGCGCAAAACAACAAAGCAGGCG
(((((((((.............)))))))))...((((((......))))))....((((....))))(((...(((((((((.(((......).))..)))))))))..))).. ( -26.12)
>DroAna_CAF1 50950 113 - 1
CCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUUGUUAGCCAGGCCAG--CAAAACAACAAAGCAGGCG
(((((((((.............)))))))))...((((((......))))))....((((....))))(((...(((((((((.((.......)--)..)))))))))..))).. ( -25.62)
>consensus
CCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUUGUUAGCCAGGCCAG__CAAAACAACAAAGCAAGCG
(((((((((.............)))))))))...((((((......))))))....((((....))))(((...(((((((((................)))))))))..))).. (-24.21 = -23.96 +  -0.25)

alignment

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secondary structure

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Window 5

Location 6,836,018 – 6,836,136
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 98.43
Mean single sequence MFE -24.17
Consensus MFE -22.70
Energy contribution -22.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.94
SVM decision value 2.31
SVM RNA-class probability 0.992210
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6836018 118 - 27905053
CACUUCACUUUGUCCACACAG--AGCACACCCGUAGCGGACCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUU
.......((((((....))))--)).....(((...))).(((((((((.............)))))))))...((((((......))))))....((((....))))............ ( -22.92)
>DroSec_CAF1 94893 118 - 1
CACUUCACUUUGUCCACACAG--AGCACACCCGUAGCGGACCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUU
.......((((((....))))--)).....(((...))).(((((((((.............)))))))))...((((((......))))))....((((....))))............ ( -22.92)
>DroSim_CAF1 101251 118 - 1
CACUUCACUUUGUCCACACAG--AGCACACCCGUAGCGGACCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUU
.......((((((....))))--)).....(((...))).(((((((((.............)))))))))...((((((......))))))....((((....))))............ ( -22.92)
>DroEre_CAF1 80151 118 - 1
CACUUCACUUUGUCCACACAG--AGCACACCCGUAGCAGACCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUU
.......((((((....))))--)).........(((((((((((((((.............)))))))))...((((((......))))))....((((....))))......)))))) ( -23.62)
>DroYak_CAF1 93728 120 - 1
CACUUCACUUUGUCCACACAGAGAGCACACCCGUAGCGGACCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUU
...(((.((((((....)))))).((((....)).)))))(((((((((.............)))))))))...((((((......))))))....((((....))))............ ( -24.22)
>DroAna_CAF1 50983 118 - 1
CACUUUGCUUUGUCCACACAG--AGCACACCCGUAGCAGACCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUU
.....((((((((....))))--)))).......(((((((((((((((.............)))))))))...((((((......))))))....((((....))))......)))))) ( -28.42)
>consensus
CACUUCACUUUGUCCACACAG__AGCACACCCGUAGCGGACCACAUGAUAAAUAAUCGAUAAAUUAUGUGGACACAUGUUUAAUCUAGCAUGAAAUGGAAUCAUUUCCCUUCAAUUUGUU
..........((((((((......((((....)).))........((((.....))))........))))))))((((((......))))))....((((....))))............ (-22.70 = -22.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,836,136 – 6,836,243
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.33
Mean single sequence MFE -40.06
Consensus MFE -28.62
Energy contribution -28.34
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -2.37
Structure conservation index 0.71
SVM decision value 1.44
SVM RNA-class probability 0.953669
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6836136 107 + 27905053
AAGCCAGAGGCCCCAGGCCACGGACAUGGCUCCUCGUUUGCGGAUGGAA---GUGGGCGGGGA-AAGUGGACGGAGAAAGUGGGGUGG-UCAAAGUGGGCGUAGUG-----GGCGAA---
..(((....((((((..(..((..(((...((((((((..(........---)..))))))))-..)))..))..)....)))))).(-((......)))......-----)))...--- ( -41.70)
>DroSec_CAF1 95011 108 + 1
AAGCCAGAGGCCCCAGGCCACGGACAUGGCUCCUCGUUUGCGGCUGGAA---GUGGGCGGGGA-AAGUGGACGGAGAAAGUGGGGUUGGGCGGAGUGGGAGGAGGG-----AGCGAA---
..(((...(((((((..(..((..(((...((((((((..(........---)..))))))))-..)))..))..)....))))))).)))...............-----......--- ( -41.60)
>DroSim_CAF1 101369 112 + 1
AAGCCAGAGGCCCCAGGCCACGGACAUGGCUCCUCGUUUGCGGCUGGAA---GUGGGCGGGGA-AAGUGGACGGAGAAAGUGGGGUUU-GCUGAGUGGGCGGAGGGGCGAGGGCGAA---
..(((....(((((.(.(((((..(((...((((((((..(........---)..))))))))-..)))..)......((..(...).-.))..)))).)...)))))...)))...--- ( -46.70)
>DroEre_CAF1 80269 97 + 1
AAGCCAGAGGCCCCAGGCCACGGACAUGGCUCCUCGUUUGCGGCUGGUA---GUGGAUGGGGA-AAGCGGACGGAGAAAGUGGG-----GCAGAGUGG--------------GCGAAUGA
..(((....((((((.((((......))))((((((((..(........---)..))))))))-................))))-----))......)--------------))...... ( -37.60)
>DroYak_CAF1 93848 97 + 1
AAGCCAGAGGCCCCAGGCCACGGACAUGGCUCCUCGUUUGCGGCUGGAAUGGGGGGAUGGGGAAAAGUGGACGGAGAAAGUGG------GCAUAGUGG--------------GCGCA---
..(((....(((((...(..((..(((...(((((((((.(...........).)))))))))...)))..))..)...).))------))......)--------------))...--- ( -32.70)
>consensus
AAGCCAGAGGCCCCAGGCCACGGACAUGGCUCCUCGUUUGCGGCUGGAA___GUGGGCGGGGA_AAGUGGACGGAGAAAGUGGGGU___GCAGAGUGGG_G_AG_G______GCGAA___
...(((..((((...)))).((..(((...((((((((..(...........)..))))))))...)))..)).......)))..................................... (-28.62 = -28.34 +  -0.28)

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 10:38:08 2006