Locus 6530

Sequence ID 3L_DroMel_CAF1
Location 17,278,790 – 17,279,110
Length 320
Max. P 0.999574
window10603 window10604 window10605 window10606 window10607 window10608

overview

Window 3

Location 17,278,790 – 17,278,910
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.17
Mean single sequence MFE -23.72
Consensus MFE -22.36
Energy contribution -23.16
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.94
SVM decision value 3.01
SVM RNA-class probability 0.998102
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17278790 120 + 23771897
GAGUGUAUAAAAAUGUCGCUCAAUUAAAGUGUAGACACUUAAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCUCAACAAAGUCU
(((((((..........((((.....((((((.((..........)).))))))......(.((((.......)))))))))(((((((...)))))))....))))))).......... ( -26.30)
>DroSec_CAF1 162488 120 + 1
GAGUGUAUAAAAAUGUCGCUCAAUUAAAGUGUAGACACUUAAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCUCAACAAAGUCU
(((((((..........((((.....((((((.((..........)).))))))......(.((((.......)))))))))(((((((...)))))))....))))))).......... ( -26.30)
>DroSim_CAF1 157547 120 + 1
GAGUGUAUAAAAAUGUCGCUCAAUUAAAGUGUAGACACUUAAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCUCAACAAAGUCU
(((((((..........((((.....((((((.((..........)).))))))......(.((((.......)))))))))(((((((...)))))))....))))))).......... ( -26.30)
>DroEre_CAF1 165541 120 + 1
CAGUGUAUAAAAAUGUCGCUCAAUUAAAGUGUAGACACUUAAAAUUCAACACUUAAUUUUGUGCGUCACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCCCAACAAAGUCU
..(((((..........((((.((((..((((.(((.(.(((((((........))))))).).)))))))))))...))))(((((((...)))))))....)))))............ ( -21.60)
>DroYak_CAF1 170444 120 + 1
GAGAGUAUAAAAAUGUCGCUCAAUUAAAGUGUAGACACUUAAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCCCAACAAAGUCU
....(((..........((((.....((((((.((..........)).))))))......(.((((.......)))))))))(((((((...)))))))....))).............. ( -18.10)
>consensus
GAGUGUAUAAAAAUGUCGCUCAAUUAAAGUGUAGACACUUAAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCUCAACAAAGUCU
(((((((..........((((.....((((((.((..........)).))))))......(.((((.......)))))))))(((((((...)))))))....))))))).......... (-22.36 = -23.16 +   0.80)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,278,790 – 17,278,910
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.17
Mean single sequence MFE -25.96
Consensus MFE -26.20
Energy contribution -25.80
Covariance contribution -0.40
Combinations/Pair 1.06
Mean z-score -1.51
Structure conservation index 1.01
SVM decision value 1.59
SVM RNA-class probability 0.965874
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17278790 120 - 23771897
AGACUUUGUUGAGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUUAAGUGUCUACACUUUAAUUGAGCGACAUUUUUAUACACUC
......((((((((((((((((......))))))))..))))))))..(((((..(((((........))))(.((((..(((((....))))).)))).))..)))))........... ( -26.30)
>DroSec_CAF1 162488 120 - 1
AGACUUUGUUGAGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUUAAGUGUCUACACUUUAAUUGAGCGACAUUUUUAUACACUC
......((((((((((((((((......))))))))..))))))))..(((((..(((((........))))(.((((..(((((....))))).)))).))..)))))........... ( -26.30)
>DroSim_CAF1 157547 120 - 1
AGACUUUGUUGAGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUUAAGUGUCUACACUUUAAUUGAGCGACAUUUUUAUACACUC
......((((((((((((((((......))))))))..))))))))..(((((..(((((........))))(.((((..(((((....))))).)))).))..)))))........... ( -26.30)
>DroEre_CAF1 165541 120 - 1
AGACUUUGUUGGGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUGACGCACAAAAUUAAGUGUUGAAUUUUAAGUGUCUACACUUUAAUUGAGCGACAUUUUUAUACACUG
......((((((((((((((((......))))))))..))))))))..(((((..(((.(((....((((((.((..........)).))))))...))).))))))))........... ( -25.50)
>DroYak_CAF1 170444 120 - 1
AGACUUUGUUGGGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUUAAGUGUCUACACUUUAAUUGAGCGACAUUUUUAUACUCUC
......((((((((((((((((......))))))))..))))))))..(((((..(((((........))))(.((((..(((((....))))).)))).))..)))))........... ( -25.40)
>consensus
AGACUUUGUUGAGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUUAAGUGUCUACACUUUAAUUGAGCGACAUUUUUAUACACUC
......((((((((((((((((......))))))))..))))))))..(((((..(((.(((....((((((.((..........)).))))))...))).))))))))........... (-26.20 = -25.80 +  -0.40)

alignment

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secondary structure

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Window 5

Location 17,278,830 – 17,278,950
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.00
Mean single sequence MFE -19.68
Consensus MFE -16.72
Energy contribution -16.76
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.43
Structure conservation index 0.85
SVM decision value 0.08
SVM RNA-class probability 0.573346
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17278830 120 + 23771897
AAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCUCAACAAAGUCUAUUAACAACACACUGCUAGAACGAGAUAGACAGCUGAAAU
...............((((((.((..............((((...(((((((......))))))).))))......(((((((.....................))))))).)))))))) ( -18.80)
>DroSec_CAF1 162528 120 + 1
AAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCUCAACAAAGUCUAUUAACAACACACUGCUAGAACGAGAUAGACAGCUGAAAU
...............((((((.((..............((((...(((((((......))))))).))))......(((((((.....................))))))).)))))))) ( -18.80)
>DroSim_CAF1 157587 120 + 1
AAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCUCAACAAAGUCUAUUAACAACACACUGCUAGAACGAGAUAGACAGCUGAAAU
...............((((((.((..............((((...(((((((......))))))).))))......(((((((.....................))))))).)))))))) ( -18.80)
>DroEre_CAF1 165581 120 + 1
AAAAUUCAACACUUAAUUUUGUGCGUCACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCCCAACAAAGUCUAUUAACAACACACUGCUAGAACGAGAUAGACAGUUGAAAU
....((((((..((((((.(((((.((.((....))..))))))).))))))........................(((((((.....................))))))).)))))).. ( -21.50)
>DroYak_CAF1 170484 120 + 1
AAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCCCAACAAAGUCUAUUAACAACACACUGCAGGAACGAGAUAGACAGUUGAGCU
....((((((..........(.((((((.......((...))(((((((...)))))))...)))))).)......(((((((.......(......)......))))))).)))))).. ( -20.52)
>consensus
AAAAUUCAACACUUAAUUUCGUGCGUAACAUUAAUGCCGAGCACAUAAUUAAAUUAUGUUAAUUACGCUCAACAAAGUCUAUUAACAACACACUGCUAGAACGAGAUAGACAGCUGAAAU
....((((.(..........(.((((((.......((...))(((((((...)))))))...)))))).)......(((((((.....................))))))).).)))).. (-16.72 = -16.76 +   0.04)

alignment

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secondary structure

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Window 6

Location 17,278,830 – 17,278,950
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.00
Mean single sequence MFE -30.16
Consensus MFE -28.44
Energy contribution -28.40
Covariance contribution -0.04
Combinations/Pair 1.07
Mean z-score -2.38
Structure conservation index 0.94
SVM decision value 3.74
SVM RNA-class probability 0.999574
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17278830 120 - 23771897
AUUUCAGCUGUCUAUCUCGUUCUAGCAGUGUGUUGUUAAUAGACUUUGUUGAGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUU
..(((((((((..((..(((((.(((((.((.(.......).)).))))))))))..))..)))..((((((((.(((((..((((....))))..))))).)))))))))))))).... ( -29.90)
>DroSec_CAF1 162528 120 - 1
AUUUCAGCUGUCUAUCUCGUUCUAGCAGUGUGUUGUUAAUAGACUUUGUUGAGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUU
..(((((((((..((..(((((.(((((.((.(.......).)).))))))))))..))..)))..((((((((.(((((..((((....))))..))))).)))))))))))))).... ( -29.90)
>DroSim_CAF1 157587 120 - 1
AUUUCAGCUGUCUAUCUCGUUCUAGCAGUGUGUUGUUAAUAGACUUUGUUGAGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUU
..(((((((((..((..(((((.(((((.((.(.......).)).))))))))))..))..)))..((((((((.(((((..((((....))))..))))).)))))))))))))).... ( -29.90)
>DroEre_CAF1 165581 120 - 1
AUUUCAACUGUCUAUCUCGUUCUAGCAGUGUGUUGUUAAUAGACUUUGUUGGGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUGACGCACAAAAUUAAGUGUUGAAUUUU
..(((((((((..((..(((.(((((((.((.(.......).)).))))))))))..))..)))..((((((((.((((((((.((....))))).))))).)))))))))))))).... ( -30.00)
>DroYak_CAF1 170484 120 - 1
AGCUCAACUGUCUAUCUCGUUCCUGCAGUGUGUUGUUAAUAGACUUUGUUGGGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUU
.(((((((.((((((..((...(......)...))...))))))...)))))))....(((((((...((((((.(((((..((((....))))..))))).)))))))))))))..... ( -31.10)
>consensus
AUUUCAGCUGUCUAUCUCGUUCUAGCAGUGUGUUGUUAAUAGACUUUGUUGAGCGUAAUUAACAUAAUUUAAUUAUGUGCUCGGCAUUAAUGUUACGCACGAAAUUAAGUGUUGAAUUUU
..(((((((((..((..(((((.(((((.((.(.......).)).))))))))))..))..)))..((((((((.(((((..((((....))))..))))).)))))))))))))).... (-28.44 = -28.40 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,278,950 – 17,279,070
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.17
Mean single sequence MFE -30.32
Consensus MFE -27.82
Energy contribution -27.46
Covariance contribution -0.36
Combinations/Pair 1.09
Mean z-score -1.70
Structure conservation index 0.92
SVM decision value 1.91
SVM RNA-class probability 0.982411
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17278950 120 + 23771897
GGCUGACAGAAGGAGACGGACACUGAGGCGAAAUCCCUUUUGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUC
(..((((((((((.((((..(.....).))...)))))))))((((.....))))................)))..)...(((((((..(((((.......))))).....))))))).. ( -29.40)
>DroSec_CAF1 162648 120 + 1
GGCUGACAGAAGGAGACGGACACCGGGGCCAAAUCCCUUUUGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUC
(..((((((((((.((.((.(......)))...)))))))))((((.....))))................)))..)...(((((((..(((((.......))))).....))))))).. ( -31.10)
>DroSim_CAF1 157707 120 + 1
GGCUGACAGAAGGAGACGGACACCGGGGCCAAAUCCCUUUUGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUC
(..((((((((((.((.((.(......)))...)))))))))((((.....))))................)))..)...(((((((..(((((.......))))).....))))))).. ( -31.10)
>DroEre_CAF1 165701 120 + 1
GCCUGAUAGAAGGAGACGGACACUGAGGCUAAAUCCCUUUUGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUC
...((((.(((((.......((..((((.......)))).))((((.....)))).............))))).))))..(((((((..(((((.......))))).....))))))).. ( -29.50)
>DroYak_CAF1 170604 120 + 1
GCCUGAUGGAAGGAGACGGACGCAGAAGCUAAAUCCCUUUUGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUC
...((((.(((((.........((((((........))))))((((.....)))).............))))).))))..(((((((..(((((.......))))).....))))))).. ( -30.50)
>consensus
GGCUGACAGAAGGAGACGGACACCGAGGCCAAAUCCCUUUUGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUC
(..((((((((((.((.((.(......)))...)))))))))((((.....))))................)))..)...(((((((..(((((.......))))).....))))))).. (-27.82 = -27.46 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,278,990 – 17,279,110
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -23.80
Consensus MFE -23.80
Energy contribution -23.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 1.00
SVM decision value 1.90
SVM RNA-class probability 0.981844
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17278990 120 + 23771897
UGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUCCAGAACGGAACGACAAUUUAAUUUCAAGUUUAAUGGCAAA
..((((.....)))).....(((...(((((.........(((((((..(((((.......))))).....)))))))(((.....)))................)))))...))).... ( -23.80)
>DroSec_CAF1 162688 120 + 1
UGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUCCAGAACGGAACGACAAUUUAAUUUCAAGUUUAAUGGCAAA
..((((.....)))).....(((...(((((.........(((((((..(((((.......))))).....)))))))(((.....)))................)))))...))).... ( -23.80)
>DroSim_CAF1 157747 120 + 1
UGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUCCAGAACGGAACGACAAUUUAAUUUCAAGUUUAAUGGCAAA
..((((.....)))).....(((...(((((.........(((((((..(((((.......))))).....)))))))(((.....)))................)))))...))).... ( -23.80)
>DroEre_CAF1 165741 120 + 1
UGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUCCAGAACGGAACGACAAUUUAAUUUCAAGUUUAAUGGCAAA
..((((.....)))).....(((...(((((.........(((((((..(((((.......))))).....)))))))(((.....)))................)))))...))).... ( -23.80)
>DroYak_CAF1 170644 120 + 1
UGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUCCAGAACGGAACGACAAUUUAAUUUCAAGUUUAAUGGCAAA
..((((.....)))).....(((...(((((.........(((((((..(((((.......))))).....)))))))(((.....)))................)))))...))).... ( -23.80)
>consensus
UGGGCCAAAAAGGCCAAACAUCAAAUAACUUUCAAUCAAUUCCAAUUAGGCCAGCUCCCUUUUGGCAUAAAAAUUGGAUCCAGAACGGAACGACAAUUUAAUUUCAAGUUUAAUGGCAAA
..((((.....)))).....(((...(((((.........(((((((..(((((.......))))).....)))))))(((.....)))................)))))...))).... (-23.80 = -23.80 +   0.00)

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 12:23:13 2006