Locus 5118

Sequence ID 3L_DroMel_CAF1
Location 14,060,023 – 14,060,169
Length 146
Max. P 0.774495
window8106 window8107 window8108

overview

Window 6

Location 14,060,023 – 14,060,129
Length 106
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 79.39
Mean single sequence MFE -29.77
Consensus MFE -19.94
Energy contribution -20.67
Covariance contribution 0.72
Combinations/Pair 1.15
Mean z-score -1.21
Structure conservation index 0.67
SVM decision value 0.01
SVM RNA-class probability 0.536902
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14060023 106 - 23771897
GGAGCUCCUGCAGUUGACCAAUGUCCUGCUUCAGGAUGUGGUCAUCAUUCAGGAGAACUAAGUUCCCAAUACGA-AGUUCCAAAUAUGUUAAACCGAUCGUCUGGCC
((((((((((....((((((.(((((((...))))))))))))).....)))))((((...)))).........-.)))))............(((......))).. ( -31.20)
>DroPse_CAF1 62675 93 - 1
GGAGCUGCUCCAGCUGCCGAAUGUCCACCUGCAGGAUGUGGUUAUCGUCCAGGAGAACUAAGCUUGAA--------------CGGAUUACCAACCGACCGACCGACC
(((((((...))))).))....(((..((((.(.((((....)))).).))))........(.(((..--------------(((........)))..))).)))). ( -22.00)
>DroSec_CAF1 58563 107 - 1
GGAGCUCCUGCAGUUGACCAAUGUCCUCCUUCAGGAUGUUGUCAUCAUUCAGGAGAACUAAGUUCCCAUUAGGAAAGUUCCAAAGAUGUAAAACCGAUCGUCCGGCC
((((((((((....((((.((((((((.....)))))))))))).....)))))........((((.....)))).)))))............(((......))).. ( -30.60)
>DroSim_CAF1 59559 106 - 1
GGAGCUCCUGCAGUUGACCAAUGUCCUCCUGCAGGAUGUGGUCAUCAUUCAGGAGAACUAAGUUCCCAUUAGGA-AGUUCCAAAGAUGUAAAACCGAUCGUCCGGCC
((((((((((..(.((((((.((((((.....)))))))))))).).....((.((((...))))))..)))).-))))))............(((......))).. ( -34.40)
>DroEre_CAF1 56490 106 - 1
GGAGCUCCUGCAGUUGACCAAUGUCCUUCUUAAGGAUGUGGUCAUCACUCAGGAGAACUAAGUUCCCAAUAGAA-AGUUAUAAGCAAGAAAAUCCGAUCGUCCGACC
(((.((((((.(((((((((.((((((.....))))))))))))..)))))))))((((...(((......)))-)))).............)))............ ( -29.60)
>DroYak_CAF1 60049 93 - 1
GGAGCUCCUGCAGUUGACCAAUGUCCUGCUCCAGGAUGUGGUCAUCAUUCAGGAGAACUAAGUUCCCC--------------AGGAAGAAAACCCGAUCGUCUGGCC
((((((((((....((((((.(((((((...))))))))))))).....))))).......)))))((--------------(((..((........)).))))).. ( -30.81)
>consensus
GGAGCUCCUGCAGUUGACCAAUGUCCUCCUUCAGGAUGUGGUCAUCAUUCAGGAGAACUAAGUUCCCA_UAGGA_AGUUCCAAAGAUGAAAAACCGAUCGUCCGGCC
((..((((((.(((((((((.((((((.....))))))))))))..)))))))))..))..................................(((......))).. (-19.94 = -20.67 +   0.72)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,060,050 – 14,060,169
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.16
Mean single sequence MFE -43.73
Consensus MFE -24.33
Energy contribution -25.92
Covariance contribution 1.59
Combinations/Pair 1.18
Mean z-score -2.14
Structure conservation index 0.56
SVM decision value 0.19
SVM RNA-class probability 0.624195
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14060050 119 + 23771897
GAACU-UCGUAUUGGGAACUUAGUUCUCCUGAAUGAUGACCACAUCCUGAAGCAGGACAUUGGUCAACUGCAGGAGCUCCUGCUCGUUAUGGAUGGGCCGGUCCAGAGGAUAACCCAAUG
.....-...(((((((......(((((((..(((((((((((..(((((...)))))...))))))...(((((....))))))))))..))).))))..((((...))))..))))))) ( -41.50)
>DroPse_CAF1 62700 108 + 1
------------UUCAAGCUUAGUUCUCCUGGACGAUAACCACAUCCUGCAGGUGGACAUUCGGCAGCUGGAGCAGCUCCUGCUCGUUAGUGAUGGGACGAUCCAGGGGGUAGCCGAGGG
------------.....(((....(((((((((((....((.((((((((((.((..(....).)).)))((((((...))))))..))).)))))).)).))))))))).)))...... ( -37.60)
>DroSec_CAF1 58590 120 + 1
GAACUUUCCUAAUGGGAACUUAGUUCUCCUGAAUGAUGACAACAUCCUGAAGGAGGACAUUGGUCAACUGCAGGAGCUCCUGCUCGUUAUGGAUGGGACGGUCCAGAGGAUAGCCCAAUG
......(((((((((((.((..((((((((..(.((((....)))).)..))))))))...))))....(((((....))))))))))).)))((((...((((...))))..))))... ( -41.60)
>DroSim_CAF1 59586 119 + 1
GAACU-UCCUAAUGGGAACUUAGUUCUCCUGAAUGAUGACCACAUCCUGCAGGAGGACAUUGGUCAACUGCAGGAGCUCCUGCUCGUUAUGGAUGGGACGGUCCAGAGGAUAACCCAAUG
.....-(((((((((((.((..(((((((((...((((....))))...)))))))))...))))....(((((....))))))))))).)))((((...((((...))))..))))... ( -43.50)
>DroYak_CAF1 60074 108 + 1
------------GGGGAACUUAGUUCUCCUGAAUGAUGACCACAUCCUGGAGCAGGACAUUGGUCAACUGCAGGAGCUCCUGCUCGUUGCGGAUGGGCCGGUCCAGGGGAUAGCCCAAUG
------------(((((((...))))))).......((((((..(((((...)))))...)))))).((((((((((....)))).)))))).(((((..((((...)))).)))))... ( -46.60)
>DroAna_CAF1 59184 107 + 1
-------------UGGGGCUUAGUUCUCCUGGACGAUGACCACAUCCUGGAGCUGGACAUUGGGCAGCUGCAGCAGGGCCUGCUCGUUGUCGAUGCGACGGUCCAGGGGAUAGCCCAGUG
-------------..(((((....((((((((((((((....)))).((..(((.((((.(((((((..((......))))))))).)))).).))..)))))))))))).))))).... ( -51.60)
>consensus
____________UGGGAACUUAGUUCUCCUGAAUGAUGACCACAUCCUGAAGCAGGACAUUGGUCAACUGCAGGAGCUCCUGCUCGUUAUGGAUGGGACGGUCCAGAGGAUAGCCCAAUG
.............((((((...))))))...(((((((((((..((((.....))))...))))))...(((((....)))))))))).....((((...((((...))))..))))... (-24.33 = -25.92 +   1.59)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,060,050 – 14,060,169
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.16
Mean single sequence MFE -38.65
Consensus MFE -25.14
Energy contribution -25.78
Covariance contribution 0.64
Combinations/Pair 1.19
Mean z-score -2.00
Structure conservation index 0.65
SVM decision value 0.54
SVM RNA-class probability 0.774495
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14060050 119 - 23771897
CAUUGGGUUAUCCUCUGGACCGGCCCAUCCAUAACGAGCAGGAGCUCCUGCAGUUGACCAAUGUCCUGCUUCAGGAUGUGGUCAUCAUUCAGGAGAACUAAGUUCCCAAUACGA-AGUUC
...((((((.(((...)))..))))))(((.......(((((....))))).(.((((((.(((((((...))))))))))))).).....)))(((((..((.......))..-))))) ( -41.50)
>DroPse_CAF1 62700 108 - 1
CCCUCGGCUACCCCCUGGAUCGUCCCAUCACUAACGAGCAGGAGCUGCUCCAGCUGCCGAAUGUCCACCUGCAGGAUGUGGUUAUCGUCCAGGAGAACUAAGCUUGAA------------
...((((((...(((((((.((.((((((.(....).((((((((((...)))))...(......).)))))..)))).))....)))))))).).....))).))).------------ ( -33.00)
>DroSec_CAF1 58590 120 - 1
CAUUGGGCUAUCCUCUGGACCGUCCCAUCCAUAACGAGCAGGAGCUCCUGCAGUUGACCAAUGUCCUCCUUCAGGAUGUUGUCAUCAUUCAGGAGAACUAAGUUCCCAUUAGGAAAGUUC
...(((((..(((...)))..).))))(((.......(((((....))))).(.((((.((((((((.....)))))))))))).).....)))(((((...((((.....))))))))) ( -36.90)
>DroSim_CAF1 59586 119 - 1
CAUUGGGUUAUCCUCUGGACCGUCCCAUCCAUAACGAGCAGGAGCUCCUGCAGUUGACCAAUGUCCUCCUGCAGGAUGUGGUCAUCAUUCAGGAGAACUAAGUUCCCAUUAGGA-AGUUC
(((((((((((....(((......)))...)))))..(((((....)))))......))))))..((((((...((((....))))...))))))....((.((((.....)))-).)). ( -38.30)
>DroYak_CAF1 60074 108 - 1
CAUUGGGCUAUCCCCUGGACCGGCCCAUCCGCAACGAGCAGGAGCUCCUGCAGUUGACCAAUGUCCUGCUCCAGGAUGUGGUCAUCAUUCAGGAGAACUAAGUUCCCC------------
...((((((.(((...)))..))))))(((((.....)).))).((((((....((((((.(((((((...))))))))))))).....)))))).............------------ ( -40.90)
>DroAna_CAF1 59184 107 - 1
CACUGGGCUAUCCCCUGGACCGUCGCAUCGACAACGAGCAGGCCCUGCUGCAGCUGCCCAAUGUCCAGCUCCAGGAUGUGGUCAUCGUCCAGGAGAACUAAGCCCCA-------------
....(((((.((.(((((((....((.(((....))))).((((((.(((.(((((.........))))).))).).).))))...))))))).))....)))))..------------- ( -41.30)
>consensus
CAUUGGGCUAUCCCCUGGACCGUCCCAUCCAUAACGAGCAGGAGCUCCUGCAGUUGACCAAUGUCCUCCUCCAGGAUGUGGUCAUCAUUCAGGAGAACUAAGUUCCCA____________
....(((((.((.((((((..................(((((....))))).(.((((((.((((((.....)))))))))))).).)))))).))....)))))............... (-25.14 = -25.78 +   0.64)

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 11:42:26 2006