Locus 5262

Sequence ID 2R_DroMel_CAF1
Location 17,127,625 – 17,127,825
Length 200
Max. P 0.890147
window8404 window8405 window8406

overview

Window 4

Location 17,127,625 – 17,127,745
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.00
Mean single sequence MFE -42.33
Consensus MFE -39.24
Energy contribution -39.52
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -1.26
Structure conservation index 0.93
SVM decision value 0.58
SVM RNA-class probability 0.787652
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17127625 120 - 20766785
GUUUGCAAUCUUCGCCUGCAGCGGGGCGGGAUGGUCCAGAACUCGGAGCAGUAUGAGCUCAUCCAUCGGGCCAUUUGCCUCUACCUGAAACGCACACUGGCGUUGAGGCGAUUUUAAAAG
...........((((((.(((.(((((((.(((((((.((.....((((.......)))).....))))))))))))))))...))).(((((......))))).))))))......... ( -44.00)
>DroSec_CAF1 63518 120 - 1
GUUUGUAAUCUUCGCCUGCAGCGGGGCGGGAUGGUCCAGAACUCGGAGCAGUAUGAGCUCAUCCAUCGGGCCAUUUGCCUCUAUCUGAAACGCACACUGGCGUUGAGGCGAUUUUAAAAG
.....(((...((((((.(((.(((((((.(((((((.((.....((((.......)))).....))))))))))))))))...))).(((((......))))).))))))..))).... ( -44.10)
>DroSim_CAF1 54363 120 - 1
GUUUGUAAUCUUCGCCUGCAGCGGGGCGGGAUGGUCCAAAACUCGGAGCAGUAUGAGCUCAUCCAUCGGGCCAUUUGCCUCUAUCUGAAACGCACACUGGCGUUGAGGCGAUUUUAAAAG
.....(((...((((((.(((.(((((((.(((((((........((((.......)))).......))))))))))))))...))).(((((......))))).))))))..))).... ( -42.86)
>DroEre_CAF1 69046 120 - 1
GUUUGCAAUCUUCGCUUGCAGCGGGGCGGGAUGGUCCAGAACUCGGAGCAGUAUGAGCUAAUCCAUCGGGCCAUUUGCCUCUAUCUGAAACGGACACUGGCGUUGAGGCGAUUUUAAAAG
...........((((((.(((((((((((.(((((((.(....)(((..(((....)))..)))...))))))))))))))..((((...)))).......))))))))))......... ( -39.40)
>DroYak_CAF1 70940 120 - 1
GUUUGCAAUCUUCGCCUGCAGCGGGGCGGUAUGGUCCAGAACUCGGAGCAGUAUGAGCUAAUACACCGGGCCAUUUGCCUCUAUCUGAAGCGCACACUCGCGUUGAGGCGAUUUUAAAAG
...........((((((.(((((((((((.(((((((.(....)((....((((......)))).))))))))))))))))........(((......)))))))))))))......... ( -41.30)
>consensus
GUUUGCAAUCUUCGCCUGCAGCGGGGCGGGAUGGUCCAGAACUCGGAGCAGUAUGAGCUCAUCCAUCGGGCCAUUUGCCUCUAUCUGAAACGCACACUGGCGUUGAGGCGAUUUUAAAAG
...........((((((.(((.(((((((.(((((((........((((.......)))).......))))))))))))))...))).(((((......))))).))))))......... (-39.24 = -39.52 +   0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,127,705 – 17,127,825
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.50
Mean single sequence MFE -46.30
Consensus MFE -37.54
Energy contribution -38.18
Covariance contribution 0.64
Combinations/Pair 1.09
Mean z-score -1.64
Structure conservation index 0.81
SVM decision value 0.66
SVM RNA-class probability 0.813521
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17127705 120 + 20766785
UCUGGACCAUCCCGCCCCGCUGCAGGCGAAGAUUGCAAACGAUGCCCAGGACGUCCACGAAAAUGUCCGGCAUCUUGGGCAGACGGUCAAAGGAUGGCGGCGUCUUAACCGCCUCCGCAU
....((((.((..((((...(((((.......)))))...((((((..((((((........))))))))))))..)))).)).))))...(((.(((((........)))))))).... ( -49.10)
>DroSec_CAF1 63598 120 + 1
UCUGGACCAUCCCGCCCCGCUGCAGGCGAAGAUUACAAACGAUGCCCAGGACGUCCACGAAAAUGUCCGGCAUCUUGGGCAGACGGUCAAAGGAUGGCGGCGUCUUAACCGCCCCUGCCU
....((((.((..(((((((.....)))............((((((..((((((........))))))))))))..)))).)).))))..(((..(((((........)))))....))) ( -46.30)
>DroSim_CAF1 54443 120 + 1
UUUGGACCAUCCCGCCCCGCUGCAGGCGAAGAUUACAAACGAUGCCCAGGACGUCCACGAAAAUGUCCGGCAUCUUGGGCAGACGGUCAAAGGAUGGCGGCGUCUUAACCGCCCCUGCCU
....((((.((..(((((((.....)))............((((((..((((((........))))))))))))..)))).)).))))..(((..(((((........)))))....))) ( -46.30)
>DroEre_CAF1 69126 120 + 1
UCUGGACCAUCCCGCCCCGCUGCAAGCGAAGAUUGCAAACGAUGCCCAAGACGUCCACGAAAAUGUCCGGCAUCUUAGGCAGACGGUCGAAGGAUGCGGGCGCCUUAGCCGCCUCCGUCU
....((((.((..(((....(((((.......)))))...((((((...(((((........))))).))))))...))).)).))))((.(((.((((.(......))))).))).)). ( -42.40)
>DroYak_CAF1 71020 120 + 1
UCUGGACCAUACCGCCCCGCUGCAGGCGAAGAUUGCAAACGAUGCCCAGGACGUCCACGAAAAUGUCCGGCAUCUUAGGCAGACGGUCGAAUGAGGGGGGCGUCGUAACUGCCUCCGUCU
....((((....((((........))))..(.((((....((((((..((((((........))))))))))))....)))).)))))....((.(((((((.......))))))).)). ( -47.40)
>consensus
UCUGGACCAUCCCGCCCCGCUGCAGGCGAAGAUUGCAAACGAUGCCCAGGACGUCCACGAAAAUGUCCGGCAUCUUGGGCAGACGGUCAAAGGAUGGCGGCGUCUUAACCGCCUCCGCCU
(((.((((.((..(((((((.....)))............((((((..((((((........))))))))))))..)))).)).))))...))).((.((((.......)))).)).... (-37.54 = -38.18 +   0.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,127,705 – 17,127,825
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.50
Mean single sequence MFE -50.54
Consensus MFE -45.30
Energy contribution -45.54
Covariance contribution 0.24
Combinations/Pair 1.09
Mean z-score -1.42
Structure conservation index 0.90
SVM decision value 0.96
SVM RNA-class probability 0.890147
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17127705 120 - 20766785
AUGCGGAGGCGGUUAAGACGCCGCCAUCCUUUGACCGUCUGCCCAAGAUGCCGGACAUUUUCGUGGACGUCCUGGGCAUCGUUUGCAAUCUUCGCCUGCAGCGGGGCGGGAUGGUCCAGA
....(((((((((......)))))).)))...((((((((((((..((((((((((.(((....))).))))..))))))(((.(((.........)))))).)))).)))))))).... ( -54.00)
>DroSec_CAF1 63598 120 - 1
AGGCAGGGGCGGUUAAGACGCCGCCAUCCUUUGACCGUCUGCCCAAGAUGCCGGACAUUUUCGUGGACGUCCUGGGCAUCGUUUGUAAUCUUCGCCUGCAGCGGGGCGGGAUGGUCCAGA
(((....((((((......))))))..)))..((((((((((((..((((((((((.(((....))).))))..))))))............(((.....))))))).)))))))).... ( -51.20)
>DroSim_CAF1 54443 120 - 1
AGGCAGGGGCGGUUAAGACGCCGCCAUCCUUUGACCGUCUGCCCAAGAUGCCGGACAUUUUCGUGGACGUCCUGGGCAUCGUUUGUAAUCUUCGCCUGCAGCGGGGCGGGAUGGUCCAAA
(((....((((((......))))))..)))..((((((((((((..((((((((((.(((....))).))))..))))))............(((.....))))))).)))))))).... ( -51.20)
>DroEre_CAF1 69126 120 - 1
AGACGGAGGCGGCUAAGGCGCCCGCAUCCUUCGACCGUCUGCCUAAGAUGCCGGACAUUUUCGUGGACGUCUUGGGCAUCGUUUGCAAUCUUCGCUUGCAGCGGGGCGGGAUGGUCCAGA
.((.(((.(((((......).)))).))).))(((((((((((((((((((((((.....)).))).)))))))))).(((((.((((.......)))))))))....)))))))).... ( -50.80)
>DroYak_CAF1 71020 120 - 1
AGACGGAGGCAGUUACGACGCCCCCCUCAUUCGACCGUCUGCCUAAGAUGCCGGACAUUUUCGUGGACGUCCUGGGCAUCGUUUGCAAUCUUCGCCUGCAGCGGGGCGGUAUGGUCCAGA
.((.((.(((.((....))))).)).))....((((((((((((..((((((((((.(((....))).))))..))))))(((.(((.........)))))).)))))).)))))).... ( -45.50)
>consensus
AGGCGGAGGCGGUUAAGACGCCGCCAUCCUUUGACCGUCUGCCCAAGAUGCCGGACAUUUUCGUGGACGUCCUGGGCAUCGUUUGCAAUCUUCGCCUGCAGCGGGGCGGGAUGGUCCAGA
.......((((((......)))))).......((((((((((((..((((((((((.(((....))).))))..))))))............(((.....))))))))).)))))).... (-45.30 = -45.54 +   0.24)

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 11:40:29 2006