Locus 6309

Sequence ID 3R_DroMel_CAF1
Location 16,485,086 – 16,485,222
Length 136
Max. P 0.998835
window10291 window10292 window10293 window10294

overview

Window 1

Location 16,485,086 – 16,485,200
Length 114
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 67.11
Mean single sequence MFE -24.18
Consensus MFE -6.50
Energy contribution -8.18
Covariance contribution 1.68
Combinations/Pair 1.12
Mean z-score -2.39
Structure conservation index 0.27
SVM decision value 1.24
SVM RNA-class probability 0.935474
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16485086 114 + 27905053
AUUACUUAUUCAAUUAUAUCACUUUUCCGCCUUCACCACACUUCACAAUAGGUCGAAUGCAGGUGGAUAAAGGUUCCACCUGGAUUGCUCUUUCGU-UGGAUAAGGCGGUCAAAA
..........................(((((((..((((((((......))))..(((.((((((((.......)))))))).)))........).-)))..)))))))...... ( -30.60)
>DroSec_CAF1 41061 95 + 1
ACUACAAAUUCAAUUAUAGCACUUUUCCGCCAUCUCAACACUUCACAAUAAGUCGAAAGCAGGUGGAAAAAGGUUCCACU-------CUCUUUC-------------GGUCAAAA
............................(((........((((......)))).(((((..(((((((.....)))))))-------..)))))-------------)))..... ( -17.30)
>DroSim_CAF1 42352 102 + 1
ACUACUUAUUCAAUUAUAGCACUUUGCCGCCUUCUCCACACUUCACAAUAAGUCGAAAGCAGGUGGAAAAAGGUUCCACCUGGAUUACUCUUUC-------------GGUCAAAA
......................((((((...........((((......)))).((((((((((((((.....))))))))).......)))))-------------)).)))). ( -21.11)
>DroEre_CAF1 43065 105 + 1
-UUACUUAUCCCAUAGAACCACUU---------CUCCACACUUUACGAUGAGUCGAGUGCAGGUGGAACAAGGAUCCACCUGGAUUGAGUUUUCGUUUGGAUAAGGCAGUCAAAA
-...(((((((....(((..((((---------.(((.(((((.((.....)).))))).(((((((.......))))))))))..)))).)))....))))))).......... ( -32.00)
>DroYak_CAF1 44017 94 + 1
--UACUUAUUCCAUUGACCCACUUUUCCUCCUUCCCCACACUUCACG-------------------AACAAGGAUCCACCUGGAUUUCCUUUUCGUUUGGAUAAGGCAGUCGAAA
--...........(((((...(((.(((................(((-------------------((.((((((((....)))..))))))))))..))).)))...))))).. ( -19.87)
>consensus
ACUACUUAUUCAAUUAUACCACUUUUCCGCCUUCUCCACACUUCACAAUAAGUCGAAAGCAGGUGGAAAAAGGUUCCACCUGGAUUGCUCUUUCGU_UGGAUAAGGCGGUCAAAA
...........................................................((((((((.......))))))))................................. ( -6.50 =  -8.18 +   1.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,485,086 – 16,485,200
Length 114
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 67.11
Mean single sequence MFE -28.74
Consensus MFE -5.44
Energy contribution -7.44
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.19
SVM decision value 0.06
SVM RNA-class probability 0.564422
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16485086 114 - 27905053
UUUUGACCGCCUUAUCCA-ACGAAAGAGCAAUCCAGGUGGAACCUUUAUCCACCUGCAUUCGACCUAUUGUGAAGUGUGGUGAAGGCGGAAAAGUGAUAUAAUUGAAUAAGUAAU
......(((((((.....-.((((.((....))((((((((.......))))))))..))))(((((((....)))).))).))))))).......................... ( -32.50)
>DroSec_CAF1 41061 95 - 1
UUUUGACC-------------GAAAGAG-------AGUGGAACCUUUUUCCACCUGCUUUCGACUUAUUGUGAAGUGUUGAGAUGGCGGAAAAGUGCUAUAAUUGAAUUUGUAGU
(((..(((-------------(((((((-------.((((((.....)))))))).))))))((((......))))))..)))............(((((((......))))))) ( -24.70)
>DroSim_CAF1 42352 102 - 1
UUUUGACC-------------GAAAGAGUAAUCCAGGUGGAACCUUUUUCCACCUGCUUUCGACUUAUUGUGAAGUGUGGAGAAGGCGGCAAAGUGCUAUAAUUGAAUAAGUAGU
(((((.((-------------....((....)).((((((((.....))))))))((((((..(.((((....)))).)..))))))))))))).(((((..........))))) ( -27.80)
>DroEre_CAF1 43065 105 - 1
UUUUGACUGCCUUAUCCAAACGAAAACUCAAUCCAGGUGGAUCCUUGUUCCACCUGCACUCGACUCAUCGUAAAGUGUGGAG---------AAGUGGUUCUAUGGGAUAAGUAA-
..........(((((((....(((.(((...((((((((((.......)))))))(((((..((.....))..)))))))).---------.)))..)))....)))))))...- ( -33.80)
>DroYak_CAF1 44017 94 - 1
UUUCGACUGCCUUAUCCAAACGAAAAGGAAAUCCAGGUGGAUCCUUGUU-------------------CGUGAAGUGUGGGGAAGGAGGAAAAGUGGGUCAAUGGAAUAAGUA--
..((.(((.((((.((((.((((((((((..(((....)))))))).))-------------------)))......))))....))))...))).))...............-- ( -24.90)
>consensus
UUUUGACCGCCUUAUCCA_ACGAAAGAGCAAUCCAGGUGGAACCUUUUUCCACCUGCAUUCGACUUAUUGUGAAGUGUGGAGAAGGCGGAAAAGUGCUAUAAUUGAAUAAGUAAU
.................................((((((((.......))))))))........................................................... ( -5.44 =  -7.44 +   2.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,485,121 – 16,485,222
Length 101
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 67.86
Mean single sequence MFE -30.48
Consensus MFE -12.14
Energy contribution -14.46
Covariance contribution 2.32
Combinations/Pair 1.33
Mean z-score -2.89
Structure conservation index 0.40
SVM decision value 3.25
SVM RNA-class probability 0.998835
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16485121 101 + 27905053
CCACACUUCACAAUAGGUCGAAUGCAGGUGGAUAAAGGUUCCACCUGGAUUGCUCUUUCGU-UGGAUAAGGCGGUCAAAAGGACUUGACUUGGGAGUGUCAU
..(((((((.(((((((((.....((((((((.......))))))))((((((.(((((..-..)).))))))))).....))))))..))))))))))... ( -38.40)
>DroSec_CAF1 41096 82 + 1
CAACACUUCACAAUAAGUCGAAAGCAGGUGGAAAAAGGUUCCACU-------CUCUUUC-------------GGUCAAAAGGACUUGACUUGGGAAUGUCGU
..(((.(((....(((((((((((..(((((((.....)))))))-------..)))))-------------((((.....)))).)))))).))))))... ( -25.60)
>DroSim_CAF1 42387 89 + 1
CCACACUUCACAAUAAGUCGAAAGCAGGUGGAAAAAGGUUCCACCUGGAUUACUCUUUC-------------GGUCAAAAGGACUUGACUUGGGAAUGUCGU
..(((.(((....((((((((((((((((((((.....))))))))).......)))))-------------((((.....)))).)))))).))))))... ( -27.91)
>DroEre_CAF1 43090 102 + 1
CCACACUUUACGAUGAGUCGAGUGCAGGUGGAACAAGGAUCCACCUGGAUUGAGUUUUCGUUUGGAUAAGGCAGUCAAAAGGACUGUGGUUUGGGAUGUUUG
(((..((..((((.((.((.(((.((((((((.......)))))))).))))).)).))))..)).....((((((.....))))))....)))........ ( -35.20)
>DroYak_CAF1 44050 81 + 1
CCACACUUCACG-------------------AACAAGGAUCCACCUGGAUUUCCUUUUCGUUUGGAUAAGGCAGUCGAAAGGACUUAAGCUAGGAGUGUC--
..((((((((((-------------------((.((((((((....)))..))))))))))........(((((((.....))))...))).))))))).-- ( -25.30)
>consensus
CCACACUUCACAAUAAGUCGAAAGCAGGUGGAAAAAGGUUCCACCUGGAUUGCUCUUUCGU_UGGAUAAGGCGGUCAAAAGGACUUGACUUGGGAAUGUCGU
..(((.(((....((((((.....((((((((.......)))))))).........................((((.....)))).)))))).))))))... (-12.14 = -14.46 +   2.32)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,485,121 – 16,485,222
Length 101
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 67.86
Mean single sequence MFE -25.34
Consensus MFE -9.24
Energy contribution -11.20
Covariance contribution 1.96
Combinations/Pair 1.06
Mean z-score -2.45
Structure conservation index 0.36
SVM decision value 2.12
SVM RNA-class probability 0.988464
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16485121 101 - 27905053
AUGACACUCCCAAGUCAAGUCCUUUUGACCGCCUUAUCCA-ACGAAAGAGCAAUCCAGGUGGAACCUUUAUCCACCUGCAUUCGACCUAUUGUGAAGUGUGG
...(((((.((((((((((....))))))...........-.((((.((....))((((((((.......))))))))..)))).....))).).))))).. ( -27.60)
>DroSec_CAF1 41096 82 - 1
ACGACAUUCCCAAGUCAAGUCCUUUUGACC-------------GAAAGAG-------AGUGGAACCUUUUUCCACCUGCUUUCGACUUAUUGUGAAGUGUUG
.(((((((.((((((((((....))))))(-------------(((((((-------.((((((.....)))))))).)))))).....))).).))))))) ( -27.40)
>DroSim_CAF1 42387 89 - 1
ACGACAUUCCCAAGUCAAGUCCUUUUGACC-------------GAAAGAGUAAUCCAGGUGGAACCUUUUUCCACCUGCUUUCGACUUAUUGUGAAGUGUGG
.(.(((((.((((((((((....))))))(-------------(((((.......(((((((((.....))))))))))))))).....))).).))))).) ( -28.41)
>DroEre_CAF1 43090 102 - 1
CAAACAUCCCAAACCACAGUCCUUUUGACUGCCUUAUCCAAACGAAAACUCAAUCCAGGUGGAUCCUUGUUCCACCUGCACUCGACUCAUCGUAAAGUGUGG
................(((((.....)))))......(((...............((((((((.......))))))))((((..((.....))..))))))) ( -23.60)
>DroYak_CAF1 44050 81 - 1
--GACACUCCUAGCUUAAGUCCUUUCGACUGCCUUAUCCAAACGAAAAGGAAAUCCAGGUGGAUCCUUGUU-------------------CGUGAAGUGUGG
--.(((((.(..((...((((.....)))))).........((((((((((..(((....)))))))).))-------------------)))).))))).. ( -19.70)
>consensus
ACGACAUUCCCAAGUCAAGUCCUUUUGACCGCCUUAUCCA_ACGAAAGAGCAAUCCAGGUGGAACCUUUUUCCACCUGCAUUCGACUUAUUGUGAAGUGUGG
...(((((..........(((.....)))..........................((((((((.......)))))))).................))))).. ( -9.24 = -11.20 +   1.96)

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 12:18:22 2006