Locus 5338

Sequence ID X_DroMel_CAF1
Location 13,925,423 – 13,925,583
Length 160
Max. P 0.972360
window8645 window8646 window8647

overview

Window 5

Location 13,925,423 – 13,925,543
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -32.36
Consensus MFE -31.36
Energy contribution -31.96
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.97
SVM decision value 1.67
SVM RNA-class probability 0.970873
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13925423 120 + 22224390
AAUUUCCGUGAAAUCUCCAAAUCAAACAAGACACAUGCGUUGCGCAUGCGCAUUGUCCACUGGCAUCUGCACCACGGCAACACUGCCACGCAAGUCCUGCCGCUACACUGAGCGAAAAGC
...(((.(((...................((((.((((((.......))))))))))....((((..........((((....))))((....))..))))....))).)))........ ( -28.80)
>DroSec_CAF1 5594 120 + 1
AAUUUCCGUGAAAUCUCCAAAUCAAACAAGACACAUGCGUUGCGCAUGCGCAUUGUCCACUGGCAUCUGCACCACGGCAACACUGCCACGCAAGUCCUGCCGCUACACGGAGCGAAAAGC
...(((((((...................((((.((((((.......))))))))))....((((..........((((....))))((....))..))))....)))))))........ ( -34.90)
>DroSim_CAF1 7538 120 + 1
AAUUUCCGUGAAAUCUCCAAAUCAAACAAGACACAUGCGUUGCGCAUGCGCAUUGUCCACUGGCAUCUGCACCACGGCAACACUGCCACGCAAGUCCUGCCGCUACACGGAGCGAAAAGC
...(((((((...................((((.((((((.......))))))))))....((((..........((((....))))((....))..))))....)))))))........ ( -34.90)
>DroEre_CAF1 7474 120 + 1
AAUUUCCGUGAAAUCUUCAAAUCAAACAAGACACAUGCGUUGCGCAUGCGCAUUGUCCACUGGCAUCUGCAGCAUGGCAACACUGCCACGCAAGUCCUGCCGCUACACUGAGCGAAAAGC
...(((.(((...................((((.((((((.......))))))))))....((((.((...((.(((((....))))).)).))...))))....))).)))........ ( -31.00)
>DroYak_CAF1 7066 120 + 1
AAUUUCCGUGAAAUCUCCAAAUCAAACAAGACACAUGCGUUGCGCAUGCGCAUUGUCCACUGGCAUCUGCACCACGGCAACACUGCCACGCAAGUCCUGCCGCUACACGGCGCGAAAAGU
.....(((((...................((((.((((((.......))))))))))....((((..........((((....))))((....))..))))....))))).......... ( -32.20)
>consensus
AAUUUCCGUGAAAUCUCCAAAUCAAACAAGACACAUGCGUUGCGCAUGCGCAUUGUCCACUGGCAUCUGCACCACGGCAACACUGCCACGCAAGUCCUGCCGCUACACGGAGCGAAAAGC
...(((((((...................((((.((((((.......))))))))))....((((..........((((....))))((....))..))))....)))))))........ (-31.36 = -31.96 +   0.60)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,925,423 – 13,925,543
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.83
Mean single sequence MFE -44.90
Consensus MFE -40.26
Energy contribution -40.66
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.90
SVM decision value 1.69
SVM RNA-class probability 0.972360
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13925423 120 - 22224390
GCUUUUCGCUCAGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCAACGCAUGUGUCUUGUUUGAUUUGGAGAUUUCACGGAAAUU
..((((((....(..(.(((((((.(((.((...))))).))))))).)..).((..((((.((((((.(((((((((...))))))))).))))))...)))).....)).)))))).. ( -43.60)
>DroSec_CAF1 5594 120 - 1
GCUUUUCGCUCCGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCAACGCAUGUGUCUUGUUUGAUUUGGAGAUUUCACGGAAAUU
((.....))((((((..(((((((.(((.((...))))).)))))))..........((((.((((((.(((((((((...))))))))).))))))...))))......)))))).... ( -45.80)
>DroSim_CAF1 7538 120 - 1
GCUUUUCGCUCCGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCAACGCAUGUGUCUUGUUUGAUUUGGAGAUUUCACGGAAAUU
((.....))((((((..(((((((.(((.((...))))).)))))))..........((((.((((((.(((((((((...))))))))).))))))...))))......)))))).... ( -45.80)
>DroEre_CAF1 7474 120 - 1
GCUUUUCGCUCAGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCAUGCUGCAGAUGCCAGUGGACAAUGCGCAUGCGCAACGCAUGUGUCUUGUUUGAUUUGAAGAUUUCACGGAAAUU
..((((((((......)))((((......(((((((......)))))))......)))).((((((((.(((((((((...))))))))).))))).((((....)))).)))))))).. ( -42.60)
>DroYak_CAF1 7066 120 - 1
ACUUUUCGCGCCGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCAACGCAUGUGUCUUGUUUGAUUUGGAGAUUUCACGGAAAUU
..((((((((((.....(((((((.(((.((...))))).)))))))))))).((..((((.((((((.(((((((((...))))))))).))))))...)))).....))..))))).. ( -46.70)
>consensus
GCUUUUCGCUCCGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCAACGCAUGUGUCUUGUUUGAUUUGGAGAUUUCACGGAAAUU
..((((((....(((..(((((((.(((.((...))))).)))))))..))).((..((((.((((((.(((((((((...))))))))).))))))...)))).....)).)))))).. (-40.26 = -40.66 +   0.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,925,463 – 13,925,583
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.98
Mean single sequence MFE -41.18
Consensus MFE -35.50
Energy contribution -36.30
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.86
SVM decision value 0.81
SVM RNA-class probability 0.855279
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13925463 120 - 22224390
UAUACUUAUAAAUAUACCUAUCAAAGCGAGAAGAUGCCAAGCUUUUCGCUCAGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCA
........................(((((((((........)))))))))..((((((((((((.(((.((...))))).))))))).(((((..((((...)).)).))))).))))). ( -39.50)
>DroSec_CAF1 5634 120 - 1
UAUACUCAUAAAUAUACCUGUCAAAGCGAGAAGAUGCCAAGCUUUUCGCUCCGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCA
................((((((..(((((((((........)))))))))..(.....)))))))...((((((((.(((((((((((((......)))).))).)))))))).)))))) ( -41.70)
>DroSim_CAF1 7578 120 - 1
UAUACUCAUAAAUAUUCCUGUCAAAGCGAGAAGAUGCCAAGCUUUUCGCUCCGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCA
...............(((((((..(((((((((........)))))))))..(.....))))))))..((((((((.(((((((((((((......)))).))).)))))))).)))))) ( -42.70)
>DroEre_CAF1 7514 108 - 1
UAUACC------------AUUCAUGGCGACAAGAUGCCAAGCUUUUCGCUCAGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCAUGCUGCAGAUGCCAGUGGACAAUGCGCAUGCGCA
....((------------(((((((((((((...((((((((((.(((((......))))).))).))....))))).))))))))))..((....)).)))))....((((....)))) ( -39.80)
>DroYak_CAF1 7106 118 - 1
UCUACUUAUAAAU--GCUUAUCAAAGCGACAAGAUGCCAAACUUUUCGCGCCGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCA
((((((..((..(--((..((((..((((((...(((((..(..(((..((((.....)))).)))...)..))))).))))))..)))))))..))..))))))...((((....)))) ( -42.20)
>consensus
UAUACUCAUAAAUAUACCUAUCAAAGCGAGAAGAUGCCAAGCUUUUCGCUCCGUGUAGCGGCAGGACUUGCGUGGCAGUGUUGCCGUGGUGCAGAUGCCAGUGGACAAUGCGCAUGCGCA
.........................((((((((........))))))))...((((((((((((.(((.((...))))).))))))).(((((..((((...)).)).))))).))))). (-35.50 = -36.30 +   0.80)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:21 2006