Locus 5051

Sequence ID 2R_DroMel_CAF1
Location 16,414,234 – 16,414,382
Length 148
Max. P 0.998243
window8070 window8071 window8072

overview

Window 0

Location 16,414,234 – 16,414,342
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 80.82
Mean single sequence MFE -36.28
Consensus MFE -22.50
Energy contribution -23.30
Covariance contribution 0.80
Combinations/Pair 1.40
Mean z-score -1.84
Structure conservation index 0.62
SVM decision value 0.27
SVM RNA-class probability 0.661269
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16414234 108 - 20766785
CGCCAUCUACCGUUGGUAACGAUGAGCCCGGCCGUUCCUGGAAACACAGGCAGAUCUCGUUUUGACGAUAGAUGUCGCUGCAAUGUGUUCAAAAGCGUGUCAUUUAGA
(((((((((.(((..(.(((((.((.....(((.....((....))..)))...))))))))..))).)))))).(((......))).......)))........... ( -29.90)
>DroSec_CAF1 90155 108 - 1
CGCCAUCUACAGUUGGUAACGAUGAGCCCGGACGUUCCUGGAAACACAGGUAGAUGUCGUUUUAACGAUAGAUGGCGCUGCAAUUCGUUCAAAAAUGUGUCAUGUAGA
(((((((((..(((((.(((((((.(((.((.....))((....))..)))...))))))))))))..)))))))))(((((...((((....)))).....))))). ( -34.20)
>DroSim_CAF1 85878 108 - 1
CGCCAUCUACCGUUGGUAACGAUGAGCGCGGUCGUUUCUGGAAACACAAACAGAUGUCGUUUUGACGACAGAUGGCGCUGCAAUGCGUUCAAAAAUGUGUCAUGUAGA
((((((((..(((..(.((((((.......(((((((.((....)).)))).))))))))))..)))..))))))))((((((((((((....)))))))..))))). ( -37.81)
>DroEre_CAF1 89610 107 - 1
CGCCAUCUGUCGUCCGUAGAG-UGGUCCCCGCGGUUUCUACAAACACGGAUAGGUGUCGCCUUGCCGAUAGAUGGCGCUGCAGUGCGUUCAAAAGUGUGUCAUGUAGA
(((((((((((((((((...(-(((...)))).((((....)))))))))).((((......)))))))))))))))(((((..(((..(....)..)))..))))). ( -40.30)
>DroYak_CAF1 89872 105 - 1
CGCCAUCUACCGUCGGUAGAG---GAAGCCGUGGUUACUGGAAACACAUACAGGUGUCGUUCUCACGAUAGAUGGCGCUGCAGCGCGUUUAAAAAUGUGUCAUGUAGA
((((((((...((((..((((---((.(((...((...((....))...)).))).)).))))..))))))))))))((((((((((((....)))))))..))))). ( -39.20)
>consensus
CGCCAUCUACCGUUGGUAACGAUGAGCCCGGCCGUUCCUGGAAACACAGACAGAUGUCGUUUUGACGAUAGAUGGCGCUGCAAUGCGUUCAAAAAUGUGUCAUGUAGA
(((((((((.((((((.((((((((((......))))(((..........)))..)))))))))))).)))))))))((((((((((((....)))))))..))))). (-22.50 = -23.30 +   0.80)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,414,262 – 16,414,382
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 73.51
Mean single sequence MFE -34.35
Consensus MFE -24.99
Energy contribution -27.42
Covariance contribution 2.44
Combinations/Pair 1.14
Mean z-score -2.29
Structure conservation index 0.73
SVM decision value 3.04
SVM RNA-class probability 0.998243
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16414262 120 + 20766785
CAGCGACAUCUAUCGUCAAAACGAGAUCUGCCUGUGUUUCCAGGAACGGCCGGGCUCAUCGUUACCAACGGUAGAUGGCGCCAGUGCAACAUUAAGGACCUUUUCCAAUUUCAAAUCAUA
..(((.((((((((((...(((((.....((((((((((....)))))..)))))...)))))....)))))))))).)))..............(((.....))).............. ( -35.50)
>DroSec_CAF1 90183 99 + 1
CAGCGCCAUCUAUCGUUAAAACGACAUCUACCUGUGUUUCCAGGAACGUCCGGGCUCAUCGUUACCAACUGUAGAUGGCGCCAGUGCGACAUCA-------UCUCA--------------
..(((((((((((.(((..(((((......(((((((((....)))))..))))....)))))...))).))))))))))).............-------.....-------------- ( -31.30)
>DroSim_CAF1 85906 106 + 1
CAGCGCCAUCUGUCGUCAAAACGACAUCUGUUUGUGUUUCCAGAAACGACCGCGCUCAUCGUUACCAACGGUAGAUGGCGCCAGUGCAUCAUUAAGGUCCUUUUCC--------------
..(((((((((..(((...(((((....(((...(((((....)))))...)))....)))))....)))..))))))))).........................-------------- ( -30.70)
>DroYak_CAF1 89900 117 + 1
CAGCGCCAUCUAUCGUGAGAACGACACCUGUAUGUGUUUCCAGUAACCACGGCUUC---CUCUACCGACGGUAGAUGGCGCCAGUGCAUAAUUAGGGUCCUUUUCUAAUUUCAAUGCAGA
..((((((((((((((......(((((......)))))...........(((....---.....)))))))))))))))))...(((((((((((((.....))))))))...))))).. ( -39.90)
>consensus
CAGCGCCAUCUAUCGUCAAAACGACAUCUGCCUGUGUUUCCAGGAACGACCGCGCUCAUCGUUACCAACGGUAGAUGGCGCCAGUGCAACAUUAAGGUCCUUUUCC______________
..((((((((((((((...(((((.....((((((((((....)))))..)))))...)))))....))))))))))))))....................................... (-24.99 = -27.42 +   2.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,414,262 – 16,414,382
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 73.51
Mean single sequence MFE -36.78
Consensus MFE -26.98
Energy contribution -28.47
Covariance contribution 1.50
Combinations/Pair 1.21
Mean z-score -1.73
Structure conservation index 0.73
SVM decision value 1.45
SVM RNA-class probability 0.954901
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16414262 120 - 20766785
UAUGAUUUGAAAUUGGAAAAGGUCCUUAAUGUUGCACUGGCGCCAUCUACCGUUGGUAACGAUGAGCCCGGCCGUUCCUGGAAACACAGGCAGAUCUCGUUUUGACGAUAGAUGUCGCUG
..............(((.....))).............((((.((((((.(((..(.(((((.((.....(((.....((....))..)))...))))))))..))).)))))).)))). ( -34.50)
>DroSec_CAF1 90183 99 - 1
--------------UGAGA-------UGAUGUCGCACUGGCGCCAUCUACAGUUGGUAACGAUGAGCCCGGACGUUCCUGGAAACACAGGUAGAUGUCGUUUUAACGAUAGAUGGCGCUG
--------------.....-------............(((((((((((..(((((.(((((((.(((.((.....))((....))..)))...))))))))))))..))))))))))). ( -35.70)
>DroSim_CAF1 85906 106 - 1
--------------GGAAAAGGACCUUAAUGAUGCACUGGCGCCAUCUACCGUUGGUAACGAUGAGCGCGGUCGUUUCUGGAAACACAAACAGAUGUCGUUUUGACGACAGAUGGCGCUG
--------------........................((((((((((..(((..(.((((((.......(((((((.((....)).)))).))))))))))..)))..)))))))))). ( -36.21)
>DroYak_CAF1 89900 117 - 1
UCUGCAUUGAAAUUAGAAAAGGACCCUAAUUAUGCACUGGCGCCAUCUACCGUCGGUAGAG---GAAGCCGUGGUUACUGGAAACACAUACAGGUGUCGUUCUCACGAUAGAUGGCGCUG
..(((((...((((((.........)))))))))))..((((((((((...((((..((((---((.(((...((...((....))...)).))).)).))))..)))))))))))))). ( -40.70)
>consensus
______________GGAAAAGGACCUUAAUGAUGCACUGGCGCCAUCUACCGUUGGUAACGAUGAGCCCGGUCGUUCCUGGAAACACAGACAGAUGUCGUUUUGACGAUAGAUGGCGCUG
......................................(((((((((((.((((((.((((((((((......)))).((....)).........)))))))))))).))))))))))). (-26.98 = -28.47 +   1.50)

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 11:35:14 2006