Locus 7103

Sequence ID 3R_DroMel_CAF1
Location 18,731,723 – 18,731,872
Length 149
Max. P 0.972541
window11487 window11488 window11489

overview

Window 7

Location 18,731,723 – 18,731,813
Length 90
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 78.63
Mean single sequence MFE -29.66
Consensus MFE -18.71
Energy contribution -19.32
Covariance contribution 0.61
Combinations/Pair 1.13
Mean z-score -1.78
Structure conservation index 0.63
SVM decision value 0.44
SVM RNA-class probability 0.736804
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18731723 90 - 27905053
AAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUC----------------CAGUCCA--------CCCAGUCAUCUGAAAUGAAGGCUCUUUUGCCGGAGGCUGCAGUAAUUAC
...(((..(((((..(((((.....)))))...)----------------)..(((.--------..(((....))).......(((......))))))))).)))........ ( -29.10)
>DroSec_CAF1 165313 97 - 1
AAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUC----------------CUG-CCAUCCAGUCACCCAGUCAUCCGAAAUGAAGGCUCUUUCGCCGGAGGCUGCAGUAAUUAC
...(((..((((((((((((.....)))))....----------------.))-)).(((..........((((.....)))).(((......))))))))).)))........ ( -31.10)
>DroSim_CAF1 156994 89 - 1
AAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUC----------------CUG-CCAUCCA--------GUCAUCCGAAAUGAAGGCUCUUUCGCCGGAGGCUGCAGUAAUUAC
...(((..((((((((((((.....)))))....----------------.))-)).(((.--------.((((.....)))).(((......))))))))).)))........ ( -31.10)
>DroEre_CAF1 163047 85 - 1
------------GGAGCAGGAAUCUGCUGCCAUC----------------CAG-UCACCCAGUCAUCCAGUCGUCUGAAAUGAAGGCUCCUUCGCCGGAGGCUGCAGUAAUUAC
------------(((((((....))))).))...----------------(((-((.((...((((.(((....)))..)))).(((......))))).))))).......... ( -24.90)
>DroYak_CAF1 163950 113 - 1
AAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUCCUGCCAUACAGUCACCCAG-UCAACCAGUCAUCCAGUCAUCUGAAAUGAAGGCUCCUUCGCCGGAGGCUGCAGUAAUUAC
...(((..((((((((((((.....))))).....))))..............-....((..((((.(((....)))..)))).(((......))))).))).)))........ ( -32.10)
>consensus
AAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUC________________CAG_CCAUCCAGUCACCCAGUCAUCUGAAAUGAAGGCUCUUUCGCCGGAGGCUGCAGUAAUUAC
...((((....))))(((((.....))))).....................................(((((.((((...(((((....))))).))))))))).......... (-18.71 = -19.32 +   0.61)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,731,779 – 18,731,872
Length 93
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 87.17
Mean single sequence MFE -32.92
Consensus MFE -26.17
Energy contribution -26.55
Covariance contribution 0.38
Combinations/Pair 1.04
Mean z-score -1.81
Structure conservation index 0.79
SVM decision value 0.62
SVM RNA-class probability 0.802253
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18731779 93 + 27905053
------GAUGGCAGGAGAUUCCUGCUGCCGGCGAGCAUUUAACCUGCUCCUCUUCCUGUCGCCAGUAGAGUCC-UUGCCGCCAC-------UGUCUCCAUGCUGCUC
------...((((((((((....(.((.(((((((((.......)))))((((..(((....))).))))...-..)))).)))-------.)))))).)))).... ( -31.70)
>DroSec_CAF1 165376 90 + 1
------GAUGGCAGGAGAUUCCUGCUGCCGGCGAGCAUUUAACCUGCUCCUCUUCCUGUCGCCAGAAGAGUCC-UUGC---CAC-------UAUCUCCAUGCCGCUC
------...((((((((((..(....)..((((((((.......)))))((((((.((....))))))))...-..))---)..-------.)))))).)))).... ( -30.30)
>DroSim_CAF1 157049 93 + 1
------GAUGGCAGGAGAUUCCUGCUGCCGGCGAGCAUUUAACCUGCUCCUCUUCCUGUCGCCAGAAGAGUCC-UUGCCGCCAC-------UGUAUCCAUGCUGCUC
------...(((((.((....)).)))))((((((((.......)))))((((((.((....))))))))...-..)))((...-------.(((....))).)).. ( -30.00)
>DroYak_CAF1 164023 107 + 1
UGGCAGGAUGGCAGGAGAUUCCUGCUGCCGGCGAGCAUUUAACCUGCUCCUCUUCCUGUCGCCAGAAGAGUCCUUUGCUGCCUCUGUCCCCUGUCGCCGUUCUGCUC
.((((((((((((((.(((....((.((.((.(((((.......)))))((((((.((....)))))))).))...)).))....))).)))...))))))))))). ( -39.70)
>consensus
______GAUGGCAGGAGAUUCCUGCUGCCGGCGAGCAUUUAACCUGCUCCUCUUCCUGUCGCCAGAAGAGUCC_UUGCCGCCAC_______UGUCUCCAUGCUGCUC
.........(((((.((....)).)))))((((((((.......)))))((((((.((....))))))))......)))............................ (-26.17 = -26.55 +   0.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,731,779 – 18,731,872
Length 93
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 87.17
Mean single sequence MFE -38.75
Consensus MFE -30.58
Energy contribution -31.58
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.63
Structure conservation index 0.79
SVM decision value 1.69
SVM RNA-class probability 0.972541
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18731779 93 - 27905053
GAGCAGCAUGGAGACA-------GUGGCGGCAA-GGACUCUACUGGCGACAGGAAGAGGAGCAGGUUAAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUC------
..((.((.((....))-------...))(((..-...((((.(((....)))..))))(((((.......)))))))).)).(((((.....)))))....------ ( -38.90)
>DroSec_CAF1 165376 90 - 1
GAGCGGCAUGGAGAUA-------GUG---GCAA-GGACUCUUCUGGCGACAGGAAGAGGAGCAGGUUAAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUC------
....((((.((((((.-------...---((..-((.((((((((....)).))))))(((((.......))))).))....))....))))))))))...------ ( -37.30)
>DroSim_CAF1 157049 93 - 1
GAGCAGCAUGGAUACA-------GUGGCGGCAA-GGACUCUUCUGGCGACAGGAAGAGGAGCAGGUUAAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUC------
..((.((.((....))-------...))(((..-...((((((((....)).))))))(((((.......)))))))).)).(((((.....)))))....------ ( -37.20)
>DroYak_CAF1 164023 107 - 1
GAGCAGAACGGCGACAGGGGACAGAGGCAGCAAAGGACUCUUCUGGCGACAGGAAGAGGAGCAGGUUAAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUCCUGCCA
(.((((...(((...((((((.....((.((...((.((((((((....)).))))))(((((.......))))).)).)).)).....)))))))))...))))). ( -41.60)
>consensus
GAGCAGCAUGGAGACA_______GUGGCGGCAA_GGACUCUUCUGGCGACAGGAAGAGGAGCAGGUUAAAUGCUCGCCGGCAGCAGGAAUCUCCUGCCAUC______
.........................(.((((......((((((((....)).))))))(((((.......))))))))).).(((((.....))))).......... (-30.58 = -31.58 +   1.00)

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 12:37:26 2006