Locus 890

Sequence ID 3R_DroMel_CAF1
Location 3,006,341 – 3,006,568
Length 227
Max. P 0.995275
window1410 window1411 window1412

overview

Window 0

Location 3,006,341 – 3,006,454
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 74.71
Mean single sequence MFE -29.07
Consensus MFE -19.82
Energy contribution -20.86
Covariance contribution 1.04
Combinations/Pair 1.18
Mean z-score -1.85
Structure conservation index 0.68
SVM decision value 1.47
SVM RNA-class probability 0.956535
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3006341 113 + 27905053
UGGGACCACAAGUUAGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGACCACCACCACCUCCGCCCCACCAGCAACACCAAUCCCUGACACCGCAGCUG
((((................((((((...((((((...))))))....))))))..(((((....)))))........)))).((((......................)))) ( -30.05)
>DroSec_CAF1 52695 104 + 1
UGGGACCGCAAGUUAGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGACCACCACCACCGCCGCCCCACCAGCAACACCAGUCACUGACA---------
((((.(.((...........((((((...((((((...))))))....))))))..(((((....)))))...)).).)))).(((..((....))..)))...--------- ( -33.50)
>DroSim_CAF1 53123 104 + 1
UGGGACCACAAGUUAGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGAC---------CGCCGCCCAACCAGCAACACCAGUCACUGACACCGCAGCAG
..((.((((..(.......)((((((...((((((...))))))....))))))...)))).)---------)((.((.....(((..((....))..))).....)).)).. ( -27.40)
>DroWil_CAF1 56504 92 + 1
UGCAGCCGCAUGUCAGGAUUGAGCAGAUUCUACAACAUUUGCAACAAAGUGUUCCAGGCGGACAGCCACCACCUCCGCCG--------ACA-------------UCACAACAG
.((....))(((((((((((.....))))))..(((((((......)))))))...((((((...........)))))))--------)))-------------)........ ( -23.00)
>DroYak_CAF1 61012 110 + 1
UGGGACCACAAGUUCGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGACCACC---ACCGCCGCCCCAUCAGCAGCACCAGUCUCUAACACCGCAGCAG
.(((((..............((((((...((((((...))))))....))))))..(((((....))---)))((.((.......)).))....))))).............. ( -31.40)
>consensus
UGGGACCACAAGUUAGAAUCGAACAGAUACUGCAGCACCUGCAGCAAACUGUUCCAGGUGGACCACCACCACCGCCGCCCCACCAGCAACACCAGUCACUGACACCGCAGCAG
...........(((((....((((((...((((((...))))))....))))))..(((((.............)))))...................))))).......... (-19.82 = -20.86 +   1.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,006,341 – 3,006,454
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 74.71
Mean single sequence MFE -43.22
Consensus MFE -28.78
Energy contribution -30.18
Covariance contribution 1.40
Combinations/Pair 1.34
Mean z-score -2.36
Structure conservation index 0.67
SVM decision value 2.56
SVM RNA-class probability 0.995275
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3006341 113 - 27905053
CAGCUGCGGUGUCAGGGAUUGGUGUUGCUGGUGGGGCGGAGGUGGUGGUGGUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCUAACUUGUGGUCCCA
..(((((((..((((...))))..)))).)))(((((.((((((((((....)))))..((((((..((((((((...)))))))).)))))).......)))).).))))). ( -46.70)
>DroSec_CAF1 52695 104 - 1
---------UGUCAGUGACUGGUGUUGCUGGUGGGGCGGCGGUGGUGGUGGUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCUAACUUGCGGUCCCA
---------..((((..((....))..))))((((((.((((((((((....)))))..((((((..((((((((...)))))))).)))))).......)).))).)))))) ( -50.50)
>DroSim_CAF1 53123 104 - 1
CUGCUGCGGUGUCAGUGACUGGUGUUGCUGGUUGGGCGGCG---------GUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCUAACUUGUGGUCCCA
..(((((....((((..((....))..))))....)))))(---------(.((((.(.((((((..((((((((...)))))))).)))))).).........)))).)).. ( -42.00)
>DroWil_CAF1 56504 92 - 1
CUGUUGUGA-------------UGU--------CGGCGGAGGUGGUGGCUGUCCGCCUGGAACACUUUGUUGCAAAUGUUGUAGAAUCUGCUCAAUCCUGACAUGCGGCUGCA
..(((((.(-------------(((--------((((((((((....))).)))))).(((.....(((..(((.((........)).))).)))))).)))))))))).... ( -27.00)
>DroYak_CAF1 61012 110 - 1
CUGCUGCGGUGUUAGAGACUGGUGCUGCUGAUGGGGCGGCGGU---GGUGGUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCGAACUUGUGGUCCCA
.....((((..((((...))))..))))...((((((.(((((---((....)))))..((((((..((((((((...)))))))).))))))...........)).)))))) ( -49.90)
>consensus
CUGCUGCGGUGUCAGUGACUGGUGUUGCUGGUGGGGCGGCGGUGGUGGUGGUCCACCUGGAACAGUUUGCUGCAGGUGCUGCAGUAUCUGUUCGAUUCUAACUUGUGGUCCCA
...........((((..((....))..)))).(((((.(((((((.......)))))..((((((..((((((((...)))))))).))))))...........)).))))). (-28.78 = -30.18 +   1.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,006,454 – 3,006,568
Length 114
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 76.62
Mean single sequence MFE -35.45
Consensus MFE -28.18
Energy contribution -28.93
Covariance contribution 0.75
Combinations/Pair 1.20
Mean z-score -1.12
Structure conservation index 0.79
SVM decision value 0.72
SVM RNA-class probability 0.833719
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3006454 114 + 27905053
CAUCCGC-AGCAGCAACAAAUUUCGCAGCAACAUCCUGGUCAUUAUGUGCCCAUCGUGCACAGUGGAGUGCCGCCACCGCCACCAGGACAUGGCAUUGCCAUUGUCGAUGGGCAA
.......-.((.((..........)).))..................(((((((((...((((((((((((((...((.......))...))))))).)))))))))))))))). ( -38.90)
>DroSec_CAF1 52799 114 + 1
CAUCCGC-AGCAGCAACCAACUCCGCAGCAACAUCCUGAUCAUUAUGUGCCCAUCGUGCACAGUGGAGUGCCGCCGCCGCCGCCAGGACAUGGCAUUGCCAUUGUCGAUGGGCAA
.......-.((.((..........)).))..................(((((((((...((((((((((((((...((.......))...))))))).)))))))))))))))). ( -40.00)
>DroSim_CAF1 53227 114 + 1
CAUCCGC-AGCAGCAACCAACUCCGCAGCAACAUCCUGGUCAUUAUGUGCCCAUCGUGCACAGUGGAGUGCCGCCGCCGCCGCCAGGACAUGGCAUUGCCGUUGUCGAUGGGCAA
((((.((-(((.((((...(((((((..((......)).......(((((.......))))))))))))...((((...((....))...)))).)))).))))).))))..... ( -39.30)
>DroYak_CAF1 61122 108 + 1
CAGCAGCA-------ACAAGCUCCGCAGCAACAUCCGGGUCAUUAUGUGCCCAUCGUACACAGUGGAGUGCCACCGCCGCCACCAGGACAUGGCAUUGCCAUUGUCGAUGGGCAA
..(((((.-------....)))..)).....................(((((((((...((((((((((((((...((.......))...))))))).)))))))))))))))). ( -41.50)
>DroMoj_CAF1 50951 101 + 1
----AGC----AACAACAAAGACCU------CUGCCUCCUCAUUAUGUGCCCAUAGUGCACAGUGGGGUGCCACCACCGCCGCCGCCCCAUGGCAUUGCUAUAGUCGAUGGCCAG
----...----..............------.((((.........(((((.......)))))((((((((.(.........).))))))))))))..(((((.....)))))... ( -26.80)
>DroAna_CAF1 45519 94 + 1
---------------------ACAGCCCCAGCAUCCAGGACACUAUGUGCCCAUUGUGCACAGUGGAGUCCCGCCACCCCCACCAGCUCAUGGCAUUGCCAUUGUGGAUGGACAG
---------------------...((....)).((((((((.((((((((.......))))).))).))))........((((......(((((...))))).)))).))))... ( -26.20)
>consensus
CAUCCGC____AGCAACAAACUCCGCAGCAACAUCCUGGUCAUUAUGUGCCCAUCGUGCACAGUGGAGUGCCGCCACCGCCACCAGGACAUGGCAUUGCCAUUGUCGAUGGGCAA
...............................................(((((((((...((((((((((((((...((.......))...))))))).)))))))))))))))). (-28.18 = -28.93 +   0.75)

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 09:54:41 2006