Locus 6138

Sequence ID 2R_DroMel_CAF1
Location 19,327,784 – 19,327,903
Length 119
Max. P 0.991107
window9825 window9826 window9827 window9828

overview

Window 5

Location 19,327,784 – 19,327,878
Length 94
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 88.51
Mean single sequence MFE -36.10
Consensus MFE -27.24
Energy contribution -27.92
Covariance contribution 0.68
Combinations/Pair 1.15
Mean z-score -2.65
Structure conservation index 0.75
SVM decision value 1.64
SVM RNA-class probability 0.969254
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19327784 94 + 20766785
AUAAACAUUUAUAGCAAGCGAGCGUGGGUGGAAAAGCUGCGGCGGCGGAGCUUUCCACGCUCCCGAAGCGAAAAGCGUUCGCUCUCGCUUUUCA
.............((..(.(((((((((.....(((((.((....)).)))))))))))))).)...))((((((((........)))))))). ( -36.60)
>DroSec_CAF1 5723 91 + 1
AUAAGCAUUUAUAGCAAGCGAGCGUGGGUGGAAAAGCUGCGGCGGCGGAGCUUUCCACGCUCCCGAAGCGAAAAGCGCUCGCUCUC---UUCCA
....((.......)).(((((((((..(((((((.(((.((....)).))))))))))(((.....))).....)))))))))...---..... ( -36.00)
>DroSim_CAF1 5754 94 + 1
AUAAACAUUUAUAGCAAGCGAGCGUGGGUGGGAAAGCUGCGGCGGCGGAGCUUUCCACGCUCCCGAAGCGAAAAGCGCUCGCUCUCGCUUUCCA
...............(((((((.(((((((((((((((.((....)).)))))))).((((.....)))).....))))))).))))))).... ( -41.60)
>DroEre_CAF1 5808 94 + 1
AUAAACAUUUAUGGCAAGCGAGCGUGGGUGGAAAAGCUUCCCGCGCGGAGCUUUCCACGCUCCCGCAAAGAAAAGCGUUCGCUCUCGCUUUCCA
...........(((.(((((((.(((((((((((.(((((......)))))))))))).....(((........))).)))).))))))).))) ( -36.90)
>DroYak_CAF1 5771 90 + 1
AUAAACUUUUAUGGCAAGCGAGCGUGGGUGGAAAAGCUGCUGCCGCUGAGCUUUCCACGCUCCCGAAAAGAAAAGCGUCUGCUCUCGCUU----
.....(((((.(((.....(((((((((.((...(((.......)))...)).)))))))))))))))))..(((((........)))))---- ( -29.40)
>consensus
AUAAACAUUUAUAGCAAGCGAGCGUGGGUGGAAAAGCUGCGGCGGCGGAGCUUUCCACGCUCCCGAAGCGAAAAGCGUUCGCUCUCGCUUUCCA
............(((.((((((((((.(((((((.(((.((....)).)))))))))).)...(.....)....)))))))))...)))..... (-27.24 = -27.92 +   0.68)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,327,784 – 19,327,878
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 88.51
Mean single sequence MFE -34.24
Consensus MFE -26.58
Energy contribution -27.86
Covariance contribution 1.28
Combinations/Pair 1.04
Mean z-score -2.11
Structure conservation index 0.78
SVM decision value 1.13
SVM RNA-class probability 0.919899
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19327784 94 - 20766785
UGAAAAGCGAGAGCGAACGCUUUUCGCUUCGGGAGCGUGGAAAGCUCCGCCGCCGCAGCUUUUCCACCCACGCUCGCUUGCUAUAAAUGUUUAU
.((((((((........))))))))((...(.((((((((((((((.((....)).)))))).....)))))))).)..))............. ( -34.40)
>DroSec_CAF1 5723 91 - 1
UGGAA---GAGAGCGAGCGCUUUUCGCUUCGGGAGCGUGGAAAGCUCCGCCGCCGCAGCUUUUCCACCCACGCUCGCUUGCUAUAAAUGCUUAU
....(---(..(((((((((((((......))))))((((((((((.((....)).))).)))))))....)))))))..))............ ( -33.70)
>DroSim_CAF1 5754 94 - 1
UGGAAAGCGAGAGCGAGCGCUUUUCGCUUCGGGAGCGUGGAAAGCUCCGCCGCCGCAGCUUUCCCACCCACGCUCGCUUGCUAUAAAUGUUUAU
....(((((..(((((((((.....)).....((((((((((((((.((....)).)))))))).....))))))))))))).....))))).. ( -34.90)
>DroEre_CAF1 5808 94 - 1
UGGAAAGCGAGAGCGAACGCUUUUCUUUGCGGGAGCGUGGAAAGCUCCGCGCGGGAAGCUUUUCCACCCACGCUCGCUUGCCAUAAAUGUUUAU
(((.(((((((.(((((........)))))(((.(((((((....)))))))((((.....)))).)))...))))))).)))........... ( -38.50)
>DroYak_CAF1 5771 90 - 1
----AAGCGAGAGCAGACGCUUUUCUUUUCGGGAGCGUGGAAAGCUCAGCGGCAGCAGCUUUUCCACCCACGCUCGCUUGCCAUAAAAGUUUAU
----((((((((((....))))))........((((((((((((((..((....)))))))).....))))))))))))............... ( -29.70)
>consensus
UGGAAAGCGAGAGCGAACGCUUUUCGCUUCGGGAGCGUGGAAAGCUCCGCCGCCGCAGCUUUUCCACCCACGCUCGCUUGCUAUAAAUGUUUAU
.((((((((........)))))))).....(.((((((((((((((..((....)))))))).....)))))))).)................. (-26.58 = -27.86 +   1.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,327,812 – 19,327,903
Length 91
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 86.02
Mean single sequence MFE -29.08
Consensus MFE -17.12
Energy contribution -20.32
Covariance contribution 3.20
Combinations/Pair 1.00
Mean z-score -2.42
Structure conservation index 0.59
SVM decision value 0.01
SVM RNA-class probability 0.536914
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19327812 91 + 20766785
UGGAAAAGCUGCGGCGGCGGAGCUUUCCACGCUCCCGAAGCGAAAAGCGUUCGCUCUCGCUUUUCACUUUUCACUUUUCUCGCCUCCGCCU-----
..........((((.((((((((.......))))).((((.((((((((........)))))))).))))...........))).))))..----- ( -35.30)
>DroSec_CAF1 5751 88 + 1
UGGAAAAGCUGCGGCGGCGGAGCUUUCCACGCUCCCGAAGCGAAAAGCGCUCGCUCUC---UUCCACUUUUCACUUUGCUCGCCUCCGCCU-----
..........((((.((((((((.......)))))(((((.((((((.(.........---...).)))))).)))))...))).))))..----- ( -30.20)
>DroSim_CAF1 5782 91 + 1
UGGGAAAGCUGCGGCGGCGGAGCUUUCCACGCUCCCGAAGCGAAAAGCGCUCGCUCUCGCUUUCCACUUUUCACUUUUCUCGCCUCCGCCU-----
..........((((.((((((((.......))))).(((((((..(((....))).)))))))..................))).))))..----- ( -32.30)
>DroEre_CAF1 5836 96 + 1
UGGAAAAGCUUCCCGCGCGGAGCUUUCCACGCUCCCGCAAAGAAAAGCGUUCGCUCUCGCUUUCCACUUUUCACUUUUCUCGCCUCCGCCUCCGCC
.(((((((......(((.(((((.......))))))))...(.((((((........)))))).)........)))))))................ ( -25.80)
>DroYak_CAF1 5799 84 + 1
UGGAAAAGCUGCUGCCGCUGAGCUUUCCACGCUCCCGAAAAGAAAAGCGUCUGCUCUCGCUU-------UUCACUUUUCUCGCCUCCGCCU-----
.(((...((....)).((.((((.......))))..(((((((((((((........)))))-------)))..)))))..)).)))....----- ( -21.80)
>consensus
UGGAAAAGCUGCGGCGGCGGAGCUUUCCACGCUCCCGAAGCGAAAAGCGUUCGCUCUCGCUUUCCACUUUUCACUUUUCUCGCCUCCGCCU_____
..........((((.((((((((.......))))).((((.((((((.(...((....))....).)))))).))))....))).))))....... (-17.12 = -20.32 +   3.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,327,812 – 19,327,903
Length 91
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 86.02
Mean single sequence MFE -37.86
Consensus MFE -27.18
Energy contribution -28.98
Covariance contribution 1.80
Combinations/Pair 1.07
Mean z-score -3.40
Structure conservation index 0.72
SVM decision value 2.25
SVM RNA-class probability 0.991107
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19327812 91 - 20766785
-----AGGCGGAGGCGAGAAAAGUGAAAAGUGAAAAGCGAGAGCGAACGCUUUUCGCUUCGGGAGCGUGGAAAGCUCCGCCGCCGCAGCUUUUCCA
-----..((((.(((.....((((((((((((....((....))...))))))))))))..(((((.......)))))))).)))).......... ( -42.50)
>DroSec_CAF1 5751 88 - 1
-----AGGCGGAGGCGAGCAAAGUGAAAAGUGGAA---GAGAGCGAGCGCUUUUCGCUUCGGGAGCGUGGAAAGCUCCGCCGCCGCAGCUUUUCCA
-----..((((.(((...(.((((((((((((...---(....)...)))))))))))).)(((((.......)))))))).)))).......... ( -37.40)
>DroSim_CAF1 5782 91 - 1
-----AGGCGGAGGCGAGAAAAGUGAAAAGUGGAAAGCGAGAGCGAGCGCUUUUCGCUUCGGGAGCGUGGAAAGCUCCGCCGCCGCAGCUUUCCCA
-----..((((.(((.....((((((((((((....((....))...))))))))))))..(((((.......)))))))).)))).......... ( -42.50)
>DroEre_CAF1 5836 96 - 1
GGCGGAGGCGGAGGCGAGAAAAGUGAAAAGUGGAAAGCGAGAGCGAACGCUUUUCUUUGCGGGAGCGUGGAAAGCUCCGCGCGGGAAGCUUUUCCA
.((....))......(.(((((((((((((((....((....))...))))))))(((((((((((.......))))).))))))..)))))))). ( -37.60)
>DroYak_CAF1 5799 84 - 1
-----AGGCGGAGGCGAGAAAAGUGAA-------AAGCGAGAGCAGACGCUUUUCUUUUCGGGAGCGUGGAAAGCUCAGCGGCAGCAGCUUUUCCA
-----.((.((((((((((((((((..-------..((....))...)))))))))).(((.((((.......))))..))).....)))))))). ( -29.30)
>consensus
_____AGGCGGAGGCGAGAAAAGUGAAAAGUGGAAAGCGAGAGCGAACGCUUUUCGCUUCGGGAGCGUGGAAAGCUCCGCCGCCGCAGCUUUUCCA
......((.((((((.....((((((((((((....((....))...))))))))))))..(((((.......))))).........)))))))). (-27.18 = -28.98 +   1.80)

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 12:03:42 2006