Locus 4940

Sequence ID 3R_DroMel_CAF1
Location 12,995,615 – 12,995,747
Length 132
Max. P 0.717868
window8083 window8084 window8085

overview

Window 3

Location 12,995,615 – 12,995,707
Length 92
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 86.80
Mean single sequence MFE -23.57
Consensus MFE -21.95
Energy contribution -21.95
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 0.93
SVM decision value 0.36
SVM RNA-class probability 0.702421
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12995615 92 - 27905053
CGCCAUUUUCACAGCUCGACAAAAUGGCGACAAGGACAUCCACAUC------------------CACAUCCAGUUGGCUCUGCCGCCUGCUGCUAUUCGGCUUUUGCAUU
(((((((((...........)))))))))....(((........))------------------).....((((.(((......))).)))).......((....))... ( -22.20)
>DroSec_CAF1 15951 86 - 1
CGCCAUUUUCACAGCUCGACAAAAUGGCGACAAGGACAUCCA------------------------CAUCCAGUUGGCUCUGCCGCCUGCUGCUAUUCGGCUUUUGCAUU
(((((((((...........)))))))))....((....)).------------------------....((((.(((......))).)))).......((....))... ( -21.80)
>DroSim_CAF1 8121 86 - 1
CGCCAUUUUCACAGCUCGACAAAAUGGCGACAAGGACAUCCA------------------------CAUCCAGUUGGCUCUGCCGCCUGCUGCUAUUCGGCUUUUGCAUU
(((((((((...........)))))))))....((....)).------------------------....((((.(((......))).)))).......((....))... ( -21.80)
>DroEre_CAF1 16376 86 - 1
CGCCAUUUUCACAGCUCGACAAAAUGGCGACAAGGACAUCCA------------------------CAUCCAGUUGGCUCUGCCGCCUGCUGCUAUUCGGCUUUUGCAUU
(((((((((...........)))))))))....((....)).------------------------....((((.(((......))).)))).......((....))... ( -21.80)
>DroYak_CAF1 16788 110 - 1
CGCCAUUUUCACAGCUCGACAAAAUGGCGACAAGGACAUCCACAUCCACAUCCACAACCACAUCCACAUCCAGUUGGCUCUGCCGCCUGCUGCUAUUCGGCUUUUGCAUU
(((((((((...........)))))))))....(((........))).......................((((.(((......))).)))).......((....))... ( -22.20)
>DroAna_CAF1 16284 104 - 1
CGCCAUUUUCGCAGCUCGACAAAAUGGCGACAAGGACAUCCACAUCCGCAUCC------GCAUUCACAUCCAGUUGGCUCUGCCGCCUGCUGGUACUCGGCUUUUGCAUU
(((((((((((.....)))..))))))))....(((........)))(((...------((........(((((.(((......))).)))))......))...)))... ( -31.64)
>consensus
CGCCAUUUUCACAGCUCGACAAAAUGGCGACAAGGACAUCCA________________________CAUCCAGUUGGCUCUGCCGCCUGCUGCUAUUCGGCUUUUGCAUU
(((((((((...........)))))))))....((....)).............................((((.(((......))).)))).......((....))... (-21.95 = -21.95 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,995,651 – 12,995,747
Length 96
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 77.31
Mean single sequence MFE -30.60
Consensus MFE -20.60
Energy contribution -20.57
Covariance contribution -0.03
Combinations/Pair 1.14
Mean z-score -1.30
Structure conservation index 0.67
SVM decision value 0.39
SVM RNA-class probability 0.717868
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12995651 96 + 27905053
ACUGGAUGUG------------------GAUGUGGAUGUCCUUGUCGCCAUUUUGUCGAGCUGU---GAAAAUGGCGGCGUCUUUGGCGCCAUUGCGUUUCUGCUUUGCCAAAAAAA
..(((..(..------------------((.((((.((((..((((((((((((..........---.)))))))))))).....))))))))......))..)....)))...... ( -28.40)
>DroPse_CAF1 23950 83 + 1
ACUGG------------------------------AUGUCCUUGUCGCCAUUUUGUCGAGCUGC---GAGAAUGGCGGCAUCUUUGGCGCCAUUGCGUUU-UGCUUUGCCAAAAAAA
...((------------------------------....)).(((((((((((..(((.....)---)))))))))))))..(((((((.....((....-.))..))))))).... ( -26.20)
>DroWil_CAF1 17510 96 + 1
GGCGGAUGUG------------------UCAGUAGA-GUCUUUGUCGCCAUUUUGUCGAGCUGCUUGGAAAAUGGCGUCCUCUUUGGCGCCAUUGAGU-UCUAUGUUGCCAAA-AUA
(((((..(((------------------((((.(((-(.....(.(((((((((.(((((...)))))))))))))).))))))))))))(((.(...-.).))))))))...-... ( -31.00)
>DroYak_CAF1 16824 114 + 1
ACUGGAUGUGGAUGUGGUUGUGGAUGUGGAUGUGGAUGUCCUUGUCGCCAUUUUGUCGAGCUGU---GAAAAUGGCGGCGUCUUUGGCGCCAUUGCGUUUCUGCUUUGCCAAAAAAA
..(((..(..((((..((....((((.((((......)))).))))((((((((..........---.))))))))(((((.....)))))))..))..))..)....)))...... ( -34.10)
>DroAna_CAF1 16320 106 + 1
ACUGGAUGUGAAUGC------GGAUGCGGAUGUGGAUGUCCUUGUCGCCAUUUUGUCGAGCUGC---GAAAAUGGCGGCGUCUUUGGCGCCAUUGCGU-UCUGCUUUGCCAAA-AAA
..(((..((((((((------(((((.((((......)))).))))(((((((..(((.....)---)))))))))(((((.....)))))..)))))-)).))....)))..-... ( -37.70)
>DroPer_CAF1 89844 83 + 1
ACUGG------------------------------AUGUCCUUGUCGCCAUUUUGUCGAGCUGC---GAGAAUGGCGGCAUCUUUGGCGCCAUUGCGUUU-UGCUUUGCCAAAAAAA
...((------------------------------....)).(((((((((((..(((.....)---)))))))))))))..(((((((.....((....-.))..))))))).... ( -26.20)
>consensus
ACUGGAUGUG__________________GAUGUGGAUGUCCUUGUCGCCAUUUUGUCGAGCUGC___GAAAAUGGCGGCGUCUUUGGCGCCAUUGCGUUUCUGCUUUGCCAAAAAAA
..........................................((((((((((((..............))))))))))))..(((((((.....(((....)))..))))))).... (-20.60 = -20.57 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,995,651 – 12,995,747
Length 96
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 77.31
Mean single sequence MFE -21.97
Consensus MFE -14.88
Energy contribution -15.55
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.06
Structure conservation index 0.68
SVM decision value -0.03
SVM RNA-class probability 0.520778
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12995651 96 - 27905053
UUUUUUUGGCAAAGCAGAAACGCAAUGGCGCCAAAGACGCCGCCAUUUUC---ACAGCUCGACAAAAUGGCGACAAGGACAUCCACAUC------------------CACAUCCAGU
..((((((((...(......)((....)))))))))).(.(((((((((.---..........))))))))).)..(((........))------------------)......... ( -21.10)
>DroPse_CAF1 23950 83 - 1
UUUUUUUGGCAAAGCA-AAACGCAAUGGCGCCAAAGAUGCCGCCAUUCUC---GCAGCUCGACAAAAUGGCGACAAGGACAU------------------------------CCAGU
..((((((((...(..-...)((....))))))))))((.(((((((.((---(.....)))...))))))).)).((....------------------------------))... ( -21.60)
>DroWil_CAF1 17510 96 - 1
UAU-UUUGGCAACAUAGA-ACUCAAUGGCGCCAAAGAGGACGCCAUUUUCCAAGCAGCUCGACAAAAUGGCGACAAAGAC-UCUACUGA------------------CACAUCCGCC
..(-((((((..(((.(.-...).)))..))))))).((((((((((((..............)))))))))........-((....))------------------....)))... ( -22.34)
>DroYak_CAF1 16824 114 - 1
UUUUUUUGGCAAAGCAGAAACGCAAUGGCGCCAAAGACGCCGCCAUUUUC---ACAGCUCGACAAAAUGGCGACAAGGACAUCCACAUCCACAUCCACAACCACAUCCACAUCCAGU
..((((((((...(......)((....)))))))))).(.(((((((((.---..........))))))))).)..(((........)))........................... ( -21.10)
>DroAna_CAF1 16320 106 - 1
UUU-UUUGGCAAAGCAGA-ACGCAAUGGCGCCAAAGACGCCGCCAUUUUC---GCAGCUCGACAAAAUGGCGACAAGGACAUCCACAUCCGCAUCC------GCAUUCACAUCCAGU
.((-((((((...(....-.)((....)))))))))).((((((((((((---(.....)))..))))))))....(((........)))))....------............... ( -24.10)
>DroPer_CAF1 89844 83 - 1
UUUUUUUGGCAAAGCA-AAACGCAAUGGCGCCAAAGAUGCCGCCAUUCUC---GCAGCUCGACAAAAUGGCGACAAGGACAU------------------------------CCAGU
..((((((((...(..-...)((....))))))))))((.(((((((.((---(.....)))...))))))).)).((....------------------------------))... ( -21.60)
>consensus
UUUUUUUGGCAAAGCAGAAACGCAAUGGCGCCAAAGACGCCGCCAUUUUC___GCAGCUCGACAAAAUGGCGACAAGGACAUCCACAUC__________________CACAUCCAGU
..((((((((...................))))))))...(((((((((..............)))))))))............................................. (-14.88 = -15.55 +   0.67)

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 11:42:34 2006