Locus 3588

Sequence ID X_DroMel_CAF1
Location 9,618,108 – 9,618,287
Length 179
Max. P 0.973362
window5873 window5874 window5875

overview

Window 3

Location 9,618,108 – 9,618,226
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.63
Mean single sequence MFE -43.15
Consensus MFE -41.92
Energy contribution -42.18
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.97
SVM decision value 0.03
SVM RNA-class probability 0.548379
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9618108 118 + 22224390
--UACAGAUACCCAAUCUGUCUAUCGGAUCCACGUGGUUCCGUUGGACAAUUGAAUCAGAUGACGUGGCCCAGUUGGCGGCGGAAACGCGGCGGAAAGUCGCAGAAAUUGCUACGGGCAG
--....(((...((((.((((((.((((.((....)).)))).)))))))))).)))..........((((..((.((.(((....))).)).))..((.((((...)))).)))))).. ( -43.80)
>DroSec_CAF1 77451 118 + 1
--UACAGAUACCCAAUCUGUCUAUCGGAUCCACGUGGUUCCGUUGGACAAUUGAAUCCGAUGACGUGGCCCAGUUGGCGGCGGAAACGCGGCGGAAAGUCUCAGAAAUUGCUACGGGCAG
--(((((((.....))))(((.(((((((.((....((((....))))...)).)))))))))))))((((.((.(((((((....)))(((.....)))........)))))))))).. ( -40.00)
>DroEre_CAF1 83024 120 + 1
GAUACAGAUACCCAAUCUGUCUAUCGGAUCCACGUGGUUCCGUUGGACAAUUGAAUCCGAUGACGUGGCCCAGUUGGCGGCGGAAACGCGGCGGAAAGUCGCAGAAAUUGCUACGGGCAG
..(((((((.....))))(((.(((((((.((....((((....))))...)).)))))))))))))((((..((.((.(((....))).)).))..((.((((...)))).)))))).. ( -43.60)
>DroYak_CAF1 82499 120 + 1
GAUACAGAUACCCAAUCUGUCUAUCGGAUCCACGUGGUUCCGCUGGACAAUUGAAUCCGAUGACGUGGCCCAGUUGGCGGCGGAAACGCGGCGGAAAGUCGCAGAAAUUGCUACGGGCAG
..(((((((.....))))(((.((((((((((.(((....)))))))........))))))))))))((((..((.((.(((....))).)).))..((.((((...)))).)))))).. ( -45.20)
>consensus
__UACAGAUACCCAAUCUGUCUAUCGGAUCCACGUGGUUCCGUUGGACAAUUGAAUCCGAUGACGUGGCCCAGUUGGCGGCGGAAACGCGGCGGAAAGUCGCAGAAAUUGCUACGGGCAG
............((((.((((((.((((.((....)).)))).))))))))))..............((((..((.((.(((....))).)).))..((.((((...)))).)))))).. (-41.92 = -42.18 +   0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,618,186 – 9,618,287
Length 101
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 90.02
Mean single sequence MFE -31.15
Consensus MFE -27.83
Energy contribution -27.45
Covariance contribution -0.38
Combinations/Pair 1.04
Mean z-score -2.22
Structure conservation index 0.89
SVM decision value 1.71
SVM RNA-class probability 0.973362
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9618186 101 + 22224390
CGGAAACGCGGCGGAAAGUCGCAGAAAUUGCUACGGGCAGCUGGCGCUUUCCGCUCAGCCAUUUUCCUAUUUCCCCUUUCCAUUUCCCCAGUCCAUUUCCC---------------
.(((((.(((((((((((.(((...(.((((.....)))).).))))))))))))..))...)))))..................................--------------- ( -28.00)
>DroSec_CAF1 77529 101 + 1
CGGAAACGCGGCGGAAAGUCUCAGAAAUUGCUACGGGCAGCUGGGGCUUUCCGCUCAGCCAUUUUCCUAUUUCCCCUUUCCAUUUCCCCAGUCCAUUUCCC---------------
.(((((.(((((((((((((((((....(((.....))).)))))))))))))))..))...)))))..................................--------------- ( -33.80)
>DroEre_CAF1 83104 101 + 1
CGGAAACGCGGCGGAAAGUCGCAGAAAUUGCUACGGGCAGCUGGCGCUUUCCGCUCAGCCAUUUUCCUAUUUCCCCUGUCCAUUUCCCCAGCCCAUUUCCC---------------
.(((((.(.((((((((...((((....(((.....)))(((((((.....))).))))................))))...)))))...)))).))))).--------------- ( -30.40)
>DroYak_CAF1 82579 116 + 1
CGGAAACGCGGCGGAAAGUCGCAGAAAUUGCUACGGGCAGCUGGCGCUUUCCGCUCAGCCAUUUUCCUAUUUCCCCUGUCCAUUUCCCCAGCCCACUGCCCAUUUCCCAUUUUUUC
.(((((.(.(((((...((.((((...)))).))((((.(((((((.....))).)))).................((..........)))))).)))))).)))))......... ( -32.40)
>consensus
CGGAAACGCGGCGGAAAGUCGCAGAAAUUGCUACGGGCAGCUGGCGCUUUCCGCUCAGCCAUUUUCCUAUUUCCCCUGUCCAUUUCCCCAGCCCAUUUCCC_______________
.(((((.(((((((((((.(((...(.((((.....)))).).))))))))))))..))...)))))................................................. (-27.83 = -27.45 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,618,186 – 9,618,287
Length 101
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 90.02
Mean single sequence MFE -35.16
Consensus MFE -31.40
Energy contribution -31.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.30
Structure conservation index 0.89
SVM decision value -0.03
SVM RNA-class probability 0.516847
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9618186 101 - 22224390
---------------GGGAAAUGGACUGGGGAAAUGGAAAGGGGAAAUAGGAAAAUGGCUGAGCGGAAAGCGCCAGCUGCCCGUAGCAAUUUCUGCGACUUUCCGCCGCGUUUCCG
---------------.(((((((...((((((((.(....(.((((((........(((((.(((.....))))))))((.....)).)))))).)..)))))).)))))))))). ( -33.50)
>DroSec_CAF1 77529 101 - 1
---------------GGGAAAUGGACUGGGGAAAUGGAAAGGGGAAAUAGGAAAAUGGCUGAGCGGAAAGCCCCAGCUGCCCGUAGCAAUUUCUGAGACUUUCCGCCGCGUUUCCG
---------------.(((((((...(((.....(((((((........(((((...(((..((((..(((....)))..)))))))..)))))....))))))))))))))))). ( -30.70)
>DroEre_CAF1 83104 101 - 1
---------------GGGAAAUGGGCUGGGGAAAUGGACAGGGGAAAUAGGAAAAUGGCUGAGCGGAAAGCGCCAGCUGCCCGUAGCAAUUUCUGCGACUUUCCGCCGCGUUUCCG
---------------.((((((((((..(((((.(.(.(((..(............(((((.(((.....))))))))((.....))..)..)))).).)))))))).))))))). ( -36.70)
>DroYak_CAF1 82579 116 - 1
GAAAAAAUGGGAAAUGGGCAGUGGGCUGGGGAAAUGGACAGGGGAAAUAGGAAAAUGGCUGAGCGGAAAGCGCCAGCUGCCCGUAGCAAUUUCUGCGACUUUCCGCCGCGUUUCCG
.........((((((((((.(..((.((.((((((.(..(.(((............(((((.(((.....)))))))).))).)..).)))))).)).))..).))).))))))). ( -39.72)
>consensus
_______________GGGAAAUGGACUGGGGAAAUGGAAAGGGGAAAUAGGAAAAUGGCUGAGCGGAAAGCGCCAGCUGCCCGUAGCAAUUUCUGCGACUUUCCGCCGCGUUUCCG
.............................(((((((....(((((((..(((((...(((..((((..(((....)))..)))))))..))))).....))))).)).))))))). (-31.40 = -31.40 +   0.00)

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 11:03:10 2006