Locus 692

Sequence ID 3R_DroMel_CAF1
Location 2,469,274 – 2,469,416
Length 142
Max. P 0.929324
window1098 window1099 window1100

overview

Window 8

Location 2,469,274 – 2,469,389
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 66.39
Mean single sequence MFE -29.05
Consensus MFE -12.43
Energy contribution -11.68
Covariance contribution -0.75
Combinations/Pair 1.53
Mean z-score -2.10
Structure conservation index 0.43
SVM decision value 0.63
SVM RNA-class probability 0.804614
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2469274 115 + 27905053
UUUAAGCCGUAACUUGAAAUGGA---UUUGAUCAGCAUGUCGACGAACCGGUUCUUAAACCGGAACCUACUCGAUCGUUACGGUUUAAACCACAAACCAAAAGCUAAAAUUUUAUGCG--
(((((((((((((((((...((.---.(((((......)))))....((((((....))))))..))...))))..))))))))))))).............((...........)).-- ( -29.80)
>DroSim_CAF1 1701 117 + 1
UUUAGGUCGCGGCUUGAAAAGGAACAUUCAAUCAACAUGUCGACGAACCGGUUCUUAAACCGGAACCUUUUCUAUCGGUACGGCUCAAACACCGAACCAA-AGCAAAAAAA--AAGCGCC
....((.(((.(((((((((((.((((.........)))).......((((((....))))))..)))))))....(((.(((........))).))).)-))).......--..))))) ( -31.50)
>DroEre_CAF1 1001 117 + 1
UUUAAGCCGUGGUUUGAAAUGGAACCGCGGUGCAGUAUGUCCACGAACCGGUUCCCAAACCGGAACCUUAUCAUUUAAUACGGUACAAACCCCAAACAAAAAGCUAAAAUGAUAUGG---
.....((((((((((......))))))))))................((((((....))))))..((.((((((((.....(((....))).....(.....)...)))))))).))--- ( -30.20)
>DroYak_CAF1 1795 98 + 1
UUUAGUCCGUGGCUUGAAAUAAAAACUCGGCUCAGCAUGACGACGAACCGGUUCUCAAAACGGAGCCUUAUCAAUCAAUAUGGCUCGA--------------GCUACAUUGA--------
........(((((((((...........(((((....(((.(((......))).))).....)))))...(((.......))).))))--------------))))).....-------- ( -24.70)
>consensus
UUUAAGCCGUGGCUUGAAAUGGAACCUCGGAUCAGCAUGUCGACGAACCGGUUCUCAAACCGGAACCUUAUCAAUCAAUACGGCUCAAACCCCAAACCAA_AGCUAAAAUGA_AUGC___
....(((((((..((((....................((....))....((((((......)))))).......)))))))))))................................... (-12.43 = -11.68 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,469,311 – 2,469,416
Length 105
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 61.93
Mean single sequence MFE -23.50
Consensus MFE -9.20
Energy contribution -9.10
Covariance contribution -0.10
Combinations/Pair 1.38
Mean z-score -2.58
Structure conservation index 0.39
SVM decision value 1.20
SVM RNA-class probability 0.929324
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2469311 105 + 27905053
CGACGAACCGGUUCUUAAACCGGAACCUACUCGAUCGUUACGGUUUAAACCACAAACCAAAAGCUAAAAUUUUAUGCG--------UUCACGGCACUUCUUGUAGCAUUGAUU
.......((((((....)))))).......(((((.((((((((((.......)))))................(((.--------......)))......)))))))))).. ( -21.90)
>DroSim_CAF1 1741 110 + 1
CGACGAACCGGUUCUUAAACCGGAACCUUUUCUAUCGGUACGGCUCAAACACCGAACCAA-AGCAAAAAAA--AAGCGCCGUGAACUUCACGGCACUUCUUGUAACAUAGAUU
.......((((((....)))))).......(((((.(((.(((........))).)))..-.((((.....--(((.((((((.....)))))).))).))))...))))).. ( -32.30)
>DroEre_CAF1 1041 81 + 1
CCACGAACCGGUUCCCAAACCGGAACCUUAUCAUUUAAUACGGUACAAACCCCAAACAAAAAGCUAAAAUGAUAUGG---------------------------GCUC-----
.......((((((....))))))..((.((((((((.....(((....))).....(.....)...)))))))).))---------------------------....----- ( -16.30)
>consensus
CGACGAACCGGUUCUUAAACCGGAACCUUAUCAAUCGAUACGGUUCAAACCCCAAACCAAAAGCUAAAAUA_UAUGCG________UUCACGGCACUUCUUGUAGCAU_GAUU
....(((((((((((......)))))).((......))...)))))................................................................... ( -9.20 =  -9.10 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,469,311 – 2,469,416
Length 105
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 61.93
Mean single sequence MFE -31.17
Consensus MFE -12.26
Energy contribution -15.10
Covariance contribution 2.84
Combinations/Pair 1.14
Mean z-score -2.39
Structure conservation index 0.39
SVM decision value 0.75
SVM RNA-class probability 0.840975
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2469311 105 - 27905053
AAUCAAUGCUACAAGAAGUGCCGUGAA--------CGCAUAAAAUUUUAGCUUUUGGUUUGUGGUUUAAACCGUAACGAUCGAGUAGGUUCCGGUUUAAGAACCGGUUCGUCG
.......((((.((...((((.(....--------)))))....)).))))....((((((.....))))))....(((.((((..(((((........)))))..))))))) ( -25.90)
>DroSim_CAF1 1741 110 - 1
AAUCUAUGUUACAAGAAGUGCCGUGAAGUUCACGGCGCUU--UUUUUUUGCU-UUGGUUCGGUGUUUGAGCCGUACCGAUAGAAAAGGUUCCGGUUUAAGAACCGGUUCGUCG
..(((((((...(((((((((((((.....))))))))))--)))....)).-.((((.((((......)))).)))))))))....(..((((((....))))))..).... ( -42.50)
>DroEre_CAF1 1041 81 - 1
-----GAGC---------------------------CCAUAUCAUUUUAGCUUUUUGUUUGGGGUUUGUACCGUAUUAAAUGAUAAGGUUCCGGUUUGGGAACCGGUUCGUGG
-----((((---------------------------(..((((((((.(((.....)))((.(((....))).))..)))))))).((((((......))))))))))).... ( -25.10)
>consensus
AAUC_AUGCUACAAGAAGUGCCGUGAA________CGCAUA_AAUUUUAGCUUUUGGUUUGGGGUUUGAACCGUAACGAUAGAAAAGGUUCCGGUUUAAGAACCGGUUCGUCG
.................((((((((.....))))))))................(((((((.....)))))))..............(..((((((....))))))..).... (-12.26 = -15.10 +   2.84)

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 09:49:32 2006