Locus 6183

Sequence ID 2R_DroMel_CAF1
Location 19,467,412 – 19,467,567
Length 155
Max. P 0.691114
window9899 window9900 window9901

overview

Window 9

Location 19,467,412 – 19,467,532
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.78
Mean single sequence MFE -45.90
Consensus MFE -31.08
Energy contribution -30.92
Covariance contribution -0.16
Combinations/Pair 1.34
Mean z-score -2.03
Structure conservation index 0.68
SVM decision value 0.26
SVM RNA-class probability 0.659548
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19467412 120 + 20766785
CAUCUGCAAGCUGCUGCAGCACAUUGCGCCCACGGAGCGGCUGCAGGUGCAGGCCAAGUGCCUGGCGAUCAACCUGCGGAUCUACGGGCCGCAGGUCUUCAUCGCGGCCAAAAUCCUGUG
.(((((((.((((((.(.((.....))(....)).)))))))))))))(((((......(((..(((((..((((((((.((....))))))))))....))))))))......))))). ( -55.40)
>DroSim_CAF1 2754 120 + 1
CAUCUGCAAGCUGCUGCAGCACAUCGCGCCGACGGAGAGGCUGCAGGUGCAGGCCAAGUGCCUGGCCAUCAACCUGCGUAUCUAUGGGCCGCAGGUCUUCAUCGCGGCCAAGAUCCUGUG
...(((((......)))))((((..(((((........))).((((((...(((((......)))))....))))))))((((...((((((.(((....))))))))).))))..)))) ( -47.30)
>DroPer_CAF1 3800 120 + 1
CAUUUGCAAGCUUUUGCAGCAUAUUGCACCUACAGAAAGACUGCAGGUUCAAGCUAAAUGCUUAGCUAUAAAUUUAAGAAUCUAUGGGCCGCAGGUGUUCAUUGCCGCCAAAAUUCNNNN
...((((((....))))))((((.((.((((.(((.....))).)))).))((((((....))))))...............))))(((.((((.......)))).)))........... ( -27.10)
>DroEre_CAF1 2074 120 + 1
CAUCUGCAAGCUGCUCCAGCACAUUGCGCCCACGGAGCGGCUGCAGGUGCAGGCCAAGUGCCUGGCGAUUAACCUGAGGAUCUACGGGCCGCAGGUCUUCAUCGCGGCCAAGAUCCUGUG
((((((((.((((((((.((.....))(....)))))))))))))))))(((((.....)))))............(((((((...((((((.(((....))))))))).)))))))... ( -59.00)
>DroWil_CAF1 1480 120 + 1
UAUCUGUAAACUAUUGCAGCACAUAGCACCAACUGAACGAUUGCAGGUGCAAGCCAAGUGUCUGGCCAUUAAUCUGCGUAUCUAUGGACCUCAAGUGUUUAUUGCUGCCAAAAUCUUAUG
...............((((((...(((((.........((((((((((....((((......)))).....))))))).)))..((.....)).)))))...))))))............ ( -29.10)
>DroYak_CAF1 2402 120 + 1
CAUCUGCAAGCUGCUGCAGCACAUUGCGCCCACGGAGCGGCUGCAGGUGCAGGCCAAGUGCCUGGCCAUCAACCUGAGGAUCUACGGGCCGCAGGUCUUCAUUGCGGCCAAGAUCCUGUG
((((((((.((((((.(.((.....))(....)).))))))))))))))..(((((......))))).........(((((((...((((((((.......)))))))).)))))))... ( -57.50)
>consensus
CAUCUGCAAGCUGCUGCAGCACAUUGCGCCCACGGAGCGGCUGCAGGUGCAGGCCAAGUGCCUGGCCAUCAACCUGAGGAUCUACGGGCCGCAGGUCUUCAUCGCGGCCAAAAUCCUGUG
((((((((.((((((...((.....))..(....)))))))))))))))(((((.....))))).............((((.....((((((.(((....)))))))))...)))).... (-31.08 = -30.92 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,467,412 – 19,467,532
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.78
Mean single sequence MFE -46.53
Consensus MFE -34.11
Energy contribution -33.48
Covariance contribution -0.63
Combinations/Pair 1.47
Mean z-score -1.85
Structure conservation index 0.73
SVM decision value 0.33
SVM RNA-class probability 0.691114
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19467412 120 - 20766785
CACAGGAUUUUGGCCGCGAUGAAGACCUGCGGCCCGUAGAUCCGCAGGUUGAUCGCCAGGCACUUGGCCUGCACCUGCAGCCGCUCCGUGGGCGCAAUGUGCUGCAGCAGCUUGCAGAUG
....((((((.(((((((.........)))))))...))))))((((((((...((.((((.....))))))..(((((((((((.....))))......)))))))))))))))..... ( -55.10)
>DroSim_CAF1 2754 120 - 1
CACAGGAUCUUGGCCGCGAUGAAGACCUGCGGCCCAUAGAUACGCAGGUUGAUGGCCAGGCACUUGGCCUGCACCUGCAGCCUCUCCGUCGGCGCGAUGUGCUGCAGCAGCUUGCAGAUG
....(.((((.(((((((.........)))))))...)))).)((((((((..((((((....)))))).....(((((((...((((....)).))...)))))))))))))))..... ( -50.60)
>DroPer_CAF1 3800 120 - 1
NNNNGAAUUUUGGCGGCAAUGAACACCUGCGGCCCAUAGAUUCUUAAAUUUAUAGCUAAGCAUUUAGCUUGAACCUGCAGUCUUUCUGUAGGUGCAAUAUGCUGCAAAAGCUUGCAAAUG
....((((((.(((.(((.........))).)))...))))))...........((.((((.(((((((((.((((((((.....)))))))).)))...))))..)).))))))..... ( -34.40)
>DroEre_CAF1 2074 120 - 1
CACAGGAUCUUGGCCGCGAUGAAGACCUGCGGCCCGUAGAUCCUCAGGUUAAUCGCCAGGCACUUGGCCUGCACCUGCAGCCGCUCCGUGGGCGCAAUGUGCUGGAGCAGCUUGCAGAUG
...(((((((.(((((((.........)))))))...)))))))((((((((..((...))..))))))))...(((((((.(((((...(((((...)))))))))).)).)))))... ( -54.00)
>DroWil_CAF1 1480 120 - 1
CAUAAGAUUUUGGCAGCAAUAAACACUUGAGGUCCAUAGAUACGCAGAUUAAUGGCCAGACACUUGGCUUGCACCUGCAAUCGUUCAGUUGGUGCUAUGUGCUGCAAUAGUUUACAGAUA
....(((((...((((((.....(((((((((((....)))..((((......((((((....)))))).....)))).....))))...)))).....))))))...)))))....... ( -30.40)
>DroYak_CAF1 2402 120 - 1
CACAGGAUCUUGGCCGCAAUGAAGACCUGCGGCCCGUAGAUCCUCAGGUUGAUGGCCAGGCACUUGGCCUGCACCUGCAGCCGCUCCGUGGGCGCAAUGUGCUGCAGCAGCUUGCAGAUG
...(((((((.(((((((.........)))))))...)))))))(((((((..((((((....)))))).....(((((((((((.....))))......))))))))))))))...... ( -54.70)
>consensus
CACAGGAUCUUGGCCGCAAUGAAGACCUGCGGCCCAUAGAUCCGCAGGUUGAUGGCCAGGCACUUGGCCUGCACCUGCAGCCGCUCCGUGGGCGCAAUGUGCUGCAGCAGCUUGCAGAUG
....((((((.(((((((.........)))))))...)))))).(((((((..((((((....)))))).((((.(((.(((........))))))..)))).....)))))))...... (-34.11 = -33.48 +  -0.63)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,467,452 – 19,467,567
Length 115
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 90.43
Mean single sequence MFE -44.93
Consensus MFE -35.71
Energy contribution -36.88
Covariance contribution 1.17
Combinations/Pair 1.12
Mean z-score -2.29
Structure conservation index 0.79
SVM decision value 0.08
SVM RNA-class probability 0.574485
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19467452 115 + 20766785
CUGCAGGUGCAGGCCAAGUGCCUGGCGAUCAACCUGCGGAUCUACGGGCCGCAGGUCUUCAUCGCGGCCAAAAUCCUGUGGAAGUACUCCAACAGCAGUGCGGCCAACGAGAACU
...((((..(.......)..))))(((((..((((((((.((....))))))))))....)))))((((......(((((((.....))).))))......)))).......... ( -48.40)
>DroSec_CAF1 2100 115 + 1
CUGCAGGUGCAGGCCAAGUGCCUGGCCAUCAACCUGCGGAUCUACGGGCCGCAGGUCUUCAUCGCGGCCAAGAUCCUGUGGAAGUACUCCAACAGCAGUGCGGCCAACGAGAACU
((((((((...(((((......)))))....)))))))).(((...(((((((((((........))))......(((((((.....))).))))...)))))))....)))... ( -51.30)
>DroSim_CAF1 2794 115 + 1
CUGCAGGUGCAGGCCAAGUGCCUGGCCAUCAACCUGCGUAUCUAUGGGCCGCAGGUCUUCAUCGCGGCCAAGAUCCUGUGGAAGUACUCCAACAGCAGUGCGGCCAACGAGAACU
..((((((...(((((......)))))....))))))((.(((...(((((((((((........))))......(((((((.....))).))))...)))))))....))))). ( -48.60)
>DroEre_CAF1 2114 115 + 1
CUGCAGGUGCAGGCCAAGUGCCUGGCGAUUAACCUGAGGAUCUACGGGCCGCAGGUCUUCAUCGCGGCCAAGAUCCUGUGGAAGUACUCCAACAGCAGUGCGGCCAACGAGAACU
...(((((....((((......)))).....)))))(((((((...((((((.(((....))))))))).))))))).(((..(((((.(....).)))))..)))......... ( -44.90)
>DroWil_CAF1 1520 115 + 1
UUGCAGGUGCAAGCCAAGUGUCUGGCCAUUAAUCUGCGUAUCUAUGGACCUCAAGUGUUUAUUGCUGCCAAAAUCUUAUGGAAAUAUUCAAAUAGCAGUGCAGCAAAUGAAAAUU
..((((((....((((......)))).....)))))).............(((..(((((((((((((((........)))...........)))))))).))))..)))..... ( -25.90)
>DroYak_CAF1 2442 115 + 1
CUGCAGGUGCAGGCCAAGUGCCUGGCCAUCAACCUGAGGAUCUACGGGCCGCAGGUCUUCAUUGCGGCCAAGAUCCUGUGGAAGUACUCGAACAGCAGUGCGGCCAACGAGAACU
...(((((...(((((......)))))....)))))(((((((...((((((((.......)))))))).))))))).(((..((((((.....).)))))..)))......... ( -50.50)
>consensus
CUGCAGGUGCAGGCCAAGUGCCUGGCCAUCAACCUGCGGAUCUACGGGCCGCAGGUCUUCAUCGCGGCCAAGAUCCUGUGGAAGUACUCCAACAGCAGUGCGGCCAACGAGAACU
((((((((....((((......)))).....)))))))).(((...(((((((((((........))))......(((((((.....))).))))...)))))))....)))... (-35.71 = -36.88 +   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 12:04:53 2006