Locus 6648

Sequence ID 3R_DroMel_CAF1
Location 17,468,785 – 17,468,941
Length 156
Max. P 0.883557
window10820 window10821 window10822

overview

Window 0

Location 17,468,785 – 17,468,882
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 86.49
Mean single sequence MFE -27.62
Consensus MFE -19.78
Energy contribution -22.38
Covariance contribution 2.60
Combinations/Pair 1.12
Mean z-score -1.60
Structure conservation index 0.72
SVM decision value -0.03
SVM RNA-class probability 0.518954
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17468785 97 + 27905053
CUAGUAUUAGAAUGGACCGACUGUUUUCGGCUGCCUCAUUUCCCAGUCGAGUUUGUUGUUCUUUCAGGGCUUCCUGCAACUGCAACAGGAAGCGAAA
.........(((.(((.((((....((((((((..........))))))))...)))).))))))...((((((((.........)))))))).... ( -28.80)
>DroSec_CAF1 20869 97 + 1
CUAGUAUUAGAAUGGACCGACUGUUUUCGGCUGCCUCAUUUCCCAGUCGAAUUUGUUGUUCUUCCAGGGCUUCCUGCAACUGCAACAGGAAGCGAAA
............((((.((((....((((((((..........))))))))...))))....))))..((((((((.........)))))))).... ( -28.10)
>DroSim_CAF1 22092 97 + 1
CUAGUAUUAGAAUGGACCGACUGUUUUCGGCUGCCUCAUUUCCCAGUCGAGUUUGUUGUUCUUUCAGGGCUUCCUGCAACUGCAACAGGAAGCGAAA
.........(((.(((.((((....((((((((..........))))))))...)))).))))))...((((((((.........)))))))).... ( -28.80)
>DroEre_CAF1 21369 81 + 1
CUAGUAUUAGAAUGGACCUACUGUUUUCGGCUCUCUCUGU----------------UGUUCUUUCAGGGCUUCCUGCAACUGCAACAGGAAGCGGAA
.........((((((.....))))))((.(((.((.((((----------------(((..((.((((....)))).))..)))))))))))).)). ( -22.80)
>DroYak_CAF1 21513 97 + 1
CUAGUAUUAGAAUGGACUGACUGCUUUCGGCUCCCUCUGUUCCUGGUCGUGUUUUUUGUCCUUUCAGGGCUUCCUGCAACUGCAACAGGAAGCCGAA
.........(((.((((.((..((...(((((............))))).))..)).)))).)))..(((((((((.........)))))))))... ( -29.60)
>consensus
CUAGUAUUAGAAUGGACCGACUGUUUUCGGCUGCCUCAUUUCCCAGUCGAGUUUGUUGUUCUUUCAGGGCUUCCUGCAACUGCAACAGGAAGCGAAA
.........(((.((((.(((....((((((((..........))))))))...))))))).)))...((((((((.........)))))))).... (-19.78 = -22.38 +   2.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,468,849 – 17,468,941
Length 92
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 73.65
Mean single sequence MFE -26.78
Consensus MFE -15.95
Energy contribution -15.53
Covariance contribution -0.41
Combinations/Pair 1.31
Mean z-score -1.62
Structure conservation index 0.60
SVM decision value 0.82
SVM RNA-class probability 0.858997
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17468849 92 + 27905053
CAGGGCUUCCUGCAACUGCAACAGGAAGCGAAAAGUGGUUGCUGCUGCAAUAGCAGACGUGCAAUGGGGAACGUAGCU---GAAAAACCAGCACU
....((((((((.........))))))))......(.(((((((((((....)))).)).))))).).....((.(((---(......)))))). ( -29.90)
>DroSec_CAF1 20933 92 + 1
CAGGGCUUCCUGCAACUGCAACAGGAAGCGAAAAGUGGUUGCUGCUGCAAUAGCAGACGUACAAUGGGGAACGUACCU---CAGAGACCAGCACU
....((((((((.........))))))))..........(((((((((....))))..((....(((((......)))---))...))))))).. ( -29.60)
>DroSim_CAF1 22156 92 + 1
CAGGGCUUCCUGCAACUGCAACAGGAAGCGAAAAGUGGUUGCUGCUGCAAUAGCAGACGUACAAUGGGGAACGUAGCU---CAAAACGCAGCACU
....((((((((.........))))))))....((((.((((..((((....))))((((.(......).))))....---......)))))))) ( -27.70)
>DroEre_CAF1 21417 91 + 1
CAGGGCUUCCUGCAACUGCAACAGGAAGCGGAAAGUGGUUGCUGCUGCGA-AGCAGACGUACGAUGGGGAACUUGGCU---CAAAAGCCAGCAUG
....((((((((.........)))))))).....((.(((((((((....-))))).)).)).))((....))(((((---....)))))..... ( -28.00)
>DroYak_CAF1 21577 70 + 1
CAGGGCUUCCUGCAACUGCAACAGGAAGCCGAAAGUGGUUGCU----------------------GGGGAACGUAGCU---CAAAAACCAGCAUU
...(((((((((.........))))))))).....(((((..(----------------------(((........))---))..)))))..... ( -24.90)
>DroPer_CAF1 23477 79 + 1
------CCCUUGCAAUUCCAACAGGAAACGGAAAGUGGUUGCUGUUGCAGUUGUAAA-----AAUGGGGAAGCACGCUGCACCACACACU-----
------(((((((((((.((((((..(((........))).)))))).)))))))..-----...))))..((.....))..........----- ( -20.60)
>consensus
CAGGGCUUCCUGCAACUGCAACAGGAAGCGAAAAGUGGUUGCUGCUGCAAUAGCAGACGUACAAUGGGGAACGUAGCU___CAAAAACCAGCACU
......((((((((((..(....(....).....)..)))))..((((....)))).........)))))......................... (-15.95 = -15.53 +  -0.41)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,468,849 – 17,468,941
Length 92
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 73.65
Mean single sequence MFE -27.38
Consensus MFE -13.63
Energy contribution -14.80
Covariance contribution 1.17
Combinations/Pair 1.16
Mean z-score -1.95
Structure conservation index 0.50
SVM decision value 0.93
SVM RNA-class probability 0.883557
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17468849 92 - 27905053
AGUGCUGGUUUUUC---AGCUACGUUCCCCAUUGCACGUCUGCUAUUGCAGCAGCAACCACUUUUCGCUUCCUGUUGCAGUUGCAGGAAGCCCUG
.(((((((....))---))).))........((((..(.((((....))))).)))).........(((((((((.......))))))))).... ( -29.90)
>DroSec_CAF1 20933 92 - 1
AGUGCUGGUCUCUG---AGGUACGUUCCCCAUUGUACGUCUGCUAUUGCAGCAGCAACCACUUUUCGCUUCCUGUUGCAGUUGCAGGAAGCCCUG
..(((((......(---(.(((((........))))).))(((....))).)))))..........(((((((((.......))))))))).... ( -31.40)
>DroSim_CAF1 22156 92 - 1
AGUGCUGCGUUUUG---AGCUACGUUCCCCAUUGUACGUCUGCUAUUGCAGCAGCAACCACUUUUCGCUUCCUGUUGCAGUUGCAGGAAGCCCUG
..((((((((....---(((.((((..........))))..)))...)).))))))..........(((((((((.......))))))))).... ( -31.70)
>DroEre_CAF1 21417 91 - 1
CAUGCUGGCUUUUG---AGCCAAGUUCCCCAUCGUACGUCUGCU-UCGCAGCAGCAACCACUUUCCGCUUCCUGUUGCAGUUGCAGGAAGCCCUG
..((((((((....---))))................(.((((.-..)))))))))..........(((((((((.......))))))))).... ( -27.80)
>DroYak_CAF1 21577 70 - 1
AAUGCUGGUUUUUG---AGCUACGUUCCCC----------------------AGCAACCACUUUCGGCUUCCUGUUGCAGUUGCAGGAAGCCCUG
..((((((.....(---(((...)))).))----------------------)))).........((((((((((.......))))))))))... ( -27.50)
>DroPer_CAF1 23477 79 - 1
-----AGUGUGUGGUGCAGCGUGCUUCCCCAUU-----UUUACAACUGCAACAGCAACCACUUUCCGUUUCCUGUUGGAAUUGCAAGGG------
-----..((((((((...((.(((.........-----.........)))...)).))))).(((((........)))))..)))....------ ( -15.97)
>consensus
AGUGCUGGUUUUUG___AGCUACGUUCCCCAUUGUACGUCUGCUAUUGCAGCAGCAACCACUUUCCGCUUCCUGUUGCAGUUGCAGGAAGCCCUG
..(((((...........(........)...........((((....)))))))))..........(((((((((.......))))))))).... (-13.63 = -14.80 +   1.17)

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 12:26:47 2006