Locus 4631

Sequence ID 3R_DroMel_CAF1
Location 12,180,345 – 12,180,467
Length 122
Max. P 0.961480
window7611 window7612 window7613

overview

Window 1

Location 12,180,345 – 12,180,438
Length 93
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 80.99
Mean single sequence MFE -28.50
Consensus MFE -20.38
Energy contribution -21.75
Covariance contribution 1.37
Combinations/Pair 1.40
Mean z-score -2.76
Structure conservation index 0.72
SVM decision value 1.26
SVM RNA-class probability 0.937485
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12180345 93 + 27905053
AUACUUUUUUGUGUGCGGCUAUUAUCUGUUGUCGUGG---GCCGCAAAACGGAGCCAAAGCCAAUUAUUCUCGGCUUUGGCUGUUGUCGACUUUAU
((((......))))((((((.....(....).....)---)))))...((((((((((((((..........)))))))))).))))......... ( -30.70)
>DroPse_CAF1 6586 94 + 1
AUACAUGAUUGUUUUUGGCAUUUAUCUGGUAUCUGGUACUGCCGCC-AGCGAAGCCGACGCCAAUUAUUUUCAACUCUU-UUGUUGUUCACUUUGU
....(((((((...(((((.(((..(((((....((.....)))))-)).))))))))...)))))))...((((....-..)))).......... ( -19.90)
>DroSec_CAF1 5024 93 + 1
AUACUUUUUUGUUUGCGGCUAUCAUCUGUUGUCGUGG---GCCGCAAAACGAAGCCAAAGCCAAUUAUUCUCGGCUUUGGCUGUUGUCGACUUUAU
...........(((((((((..((.....)).....)---))))))))((((((((((((((..........)))))))))).))))......... ( -32.40)
>DroSim_CAF1 5095 93 + 1
AUACUUUUUUGUUUGCGGCUAUCAUCUGUUGUCGUGG---GCCGCAAAACGAAGCCAAAGCCAAUUAUUCUCGGCUUUGGCUGUUGUUGACUUUAU
............((((((((..((.....)).....)---)))))))(((((((((((((((..........)))))))))).)))))........ ( -33.00)
>DroEre_CAF1 4313 93 + 1
GUACUAUAUUGUUUGCGGCUAUCAUCUGCUGUCAUGG---GCCACAAAACAGAGCCAAAGCCAAUUAUACUCGGCUUUGGCUUUAGUCGACUUAAU
(.((((...((((((.((((.....(....).....)---))).).)))))(((((((((((..........))))))))))))))))........ ( -28.40)
>DroYak_CAF1 4929 93 + 1
AAACUAUACGGUUUGCGGCUAUCAACUGCUGUCGUGG---GCCACAAAGCGGACCCAAAGUCAAUUAUUCUCGGCUUUGGCUGUUGUCGACUUUAU
.........((((..((((...........))))..)---)))....(((((..((((((((..........)))))))))))))........... ( -26.60)
>consensus
AUACUUUAUUGUUUGCGGCUAUCAUCUGUUGUCGUGG___GCCGCAAAACGAAGCCAAAGCCAAUUAUUCUCGGCUUUGGCUGUUGUCGACUUUAU
........(((((((((((..((((........))))...))))).))))))((((((((((..........)))))))))).............. (-20.38 = -21.75 +   1.37)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,180,345 – 12,180,438
Length 93
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 80.99
Mean single sequence MFE -28.34
Consensus MFE -19.87
Energy contribution -21.32
Covariance contribution 1.45
Combinations/Pair 1.19
Mean z-score -3.50
Structure conservation index 0.70
SVM decision value 1.53
SVM RNA-class probability 0.961480
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12180345 93 - 27905053
AUAAAGUCGACAACAGCCAAAGCCGAGAAUAAUUGGCUUUGGCUCCGUUUUGCGGC---CCACGACAACAGAUAAUAGCCGCACACAAAAAAGUAU
........(((...((((((((((((......))))))))))))..))).((((((---..................))))))............. ( -28.97)
>DroPse_CAF1 6586 94 - 1
ACAAAGUGAACAACAA-AAGAGUUGAAAAUAAUUGGCGUCGGCUUCGCU-GGCGGCAGUACCAGAUACCAGAUAAAUGCCAAAAACAAUCAUGUAU
.....((((.((((..-....)))).......(((((((((((...)))-)))((.....))...............)))))......)))).... ( -20.70)
>DroSec_CAF1 5024 93 - 1
AUAAAGUCGACAACAGCCAAAGCCGAGAAUAAUUGGCUUUGGCUUCGUUUUGCGGC---CCACGACAACAGAUGAUAGCCGCAAACAAAAAAGUAU
.......(((....((((((((((((......))))))))))))))).((((((((---...((.(....).))...))))))))........... ( -31.60)
>DroSim_CAF1 5095 93 - 1
AUAAAGUCAACAACAGCCAAAGCCGAGAAUAAUUGGCUUUGGCUUCGUUUUGCGGC---CCACGACAACAGAUGAUAGCCGCAAACAAAAAAGUAU
..............((((((((((((......))))))))))))..((((.(((((---...((.(....).))...))))))))).......... ( -30.80)
>DroEre_CAF1 4313 93 - 1
AUUAAGUCGACUAAAGCCAAAGCCGAGUAUAAUUGGCUUUGGCUCUGUUUUGUGGC---CCAUGACAGCAGAUGAUAGCCGCAAACAAUAUAGUAC
.........((((.((((((((((((......)))))))))))).(((((.(((((---.(((........)))...))))))))))...)))).. ( -33.00)
>DroYak_CAF1 4929 93 - 1
AUAAAGUCGACAACAGCCAAAGCCGAGAAUAAUUGACUUUGGGUCCGCUUUGUGGC---CCACGACAGCAGUUGAUAGCCGCAAACCGUAUAGUUU
........(((.....((((((.(((......))).))))))...((.((((((((---...((((....))))...)))))))).))....))). ( -25.00)
>consensus
AUAAAGUCGACAACAGCCAAAGCCGAGAAUAAUUGGCUUUGGCUCCGUUUUGCGGC___CCACGACAACAGAUGAUAGCCGCAAACAAAAAAGUAU
..............((((((((((((......))))))))))))..(.((((((((.....................))))))))).......... (-19.87 = -21.32 +   1.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,180,365 – 12,180,467
Length 102
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 82.43
Mean single sequence MFE -35.88
Consensus MFE -19.24
Energy contribution -19.85
Covariance contribution 0.61
Combinations/Pair 1.32
Mean z-score -3.19
Structure conservation index 0.54
SVM decision value 0.66
SVM RNA-class probability 0.813454
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12180365 102 - 27905053
-GCAGCA-GGGUCACAAAAGUUCGAA--UGGCGAUAAAGUCGACAACAGCCAAAGCCGAGAAUAAUUGGCUUUGGCUCCGUUUUGCGGC---CCACGACAACAGAUAAU
-......-(((((.(((((.......--((((......)))).....((((((((((((......))))))))))))...))))).)))---))............... ( -36.20)
>DroPse_CAF1 6606 107 - 1
CGUAGAAGGGGUCGCAAAAGUUCGCCCCCCGCGACAAAGUGAACAACAA-AAGAGUUGAAAAUAAUUGGCGUCGGCUUCGCU-GGCGGCAGUACCAGAUACCAGAUAAA
.......(((((.((....))..))))).(((......)))..((((..-....))))......((((.(((((((...)))-)))).))))................. ( -27.70)
>DroSec_CAF1 5044 102 - 1
-GCAGCG-GGGUCACAAAAGUUCGAA--UGGCGAUAAAGUCGACAACAGCCAAAGCCGAGAAUAAUUGGCUUUGGCUUCGUUUUGCGGC---CCACGACAACAGAUGAU
-...(((-(((((.(((((...((((--((((......))))......(((((((((((......)))))))))))))))))))).)))---)).)).).......... ( -38.80)
>DroSim_CAF1 5115 102 - 1
-GCAGCA-GGGUCACAAAAGUUCGAA--UGGCGAUAAAGUCAACAACAGCCAAAGCCGAGAAUAAUUGGCUUUGGCUUCGUUUUGCGGC---CCACGACAACAGAUGAU
-......-(((((.(((((...((((--((((......))))......(((((((((((......)))))))))))))))))))).)))---))............... ( -38.00)
>DroEre_CAF1 4333 102 - 1
-GCAGCA-GGGUCACAAAAGUUCGAG--UAGCGAUUAAGUCGACUAAAGCCAAAGCCGAGUAUAAUUGGCUUUGGCUCUGUUUUGUGGC---CCAUGACAGCAGAUGAU
-((..((-(((((((((((.......--(((((((...)))).))).((((((((((((......))))))))))))...)))))))))---)).))...))....... ( -43.20)
>DroYak_CAF1 4949 102 - 1
-GCAGCA-GGGUCACAAAAGUUCGAA--CUGCGAUAAAGUCGACAACAGCCAAAGCCGAGAAUAAUUGACUUUGGGUCCGCUUUGUGGC---CCACGACAGCAGUUGAU
-......-((((((((((.((((((.--((.......))))))......((((((.(((......))).))))))....))))))))))---)).((((....)))).. ( -31.40)
>consensus
_GCAGCA_GGGUCACAAAAGUUCGAA__UGGCGAUAAAGUCGACAACAGCCAAAGCCGAGAAUAAUUGGCUUUGGCUCCGUUUUGCGGC___CCACGACAACAGAUGAU
..........(((........(((.......)))....((((.....((((((((((((......))))))))))))(((.....))).......))))....)))... (-19.24 = -19.85 +   0.61)

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 11:35:08 2006