Locus 5077

Sequence ID X_DroMel_CAF1
Location 13,273,146 – 13,273,306
Length 160
Max. P 0.986002
window8247 window8248 window8249 window8250 window8251

overview

Window 7

Location 13,273,146 – 13,273,249
Length 103
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 89.35
Mean single sequence MFE -28.98
Consensus MFE -22.36
Energy contribution -22.40
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.44
Structure conservation index 0.77
SVM decision value -0.05
SVM RNA-class probability 0.507685
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13273146 103 + 22224390
-------GUGUGUGUUUUGCAUCCUGUUCGUCCUUGCUGCUCGUUCGCAUUUCCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUUCGACAAUUCGUCAGACAUUGU
-------....((((((.((....(((.((........((((((((((.......)))).....))))))(((((.....)))))....)))))....)).))))))... ( -27.00)
>DroSec_CAF1 18592 100 + 1
-------GUGUGU---UGGCAUCCUGCUCGUCCGUGCUGCUCGUUCGCAUUUCCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUUCGACAAUUCGUCAGACAUUGU
-------((((.(---((((....((.(((........((((((((((.......)))).....))))))(((((.....)))))....)))))....)))))))))... ( -28.30)
>DroSim_CAF1 17980 100 + 1
-------GUGUGU---UUGCAUCCUGUUCGUCCUUGCUGCUCGUUCGCAUUUCCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUUCGACAAUUCGUCAGACAUUGU
-------..((((---(((.((...(((.(((......((((((((((.......)))).....))))))(((((.....))))).....))))))..)))))))))... ( -28.60)
>DroEre_CAF1 19345 107 + 1
UGCGCUUGUGUGC---UUGCAUCCUGUUCGUCCUUGCUGCUCGCUCACAUUUCCAGCGACAACAACGAGCACCGCAUUCUGCGGUUUUUCGACAAUUCGUCAGACAUUGU
.((((....))))---.........((((((...((.((.(((((.........))))))).))))))))(((((.....))))).....(((.....)))......... ( -27.90)
>DroYak_CAF1 18713 107 + 1
GGCACUUGUCUUU---GCACAUCCUGUUCGUCCUUGCUGCUCGUUCACAUUACCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUGCGACAAUUCGUCAGACAUUGU
.(((..(((((..---(((......((((((..(((.((((.((.......)).)))).)))..))))))(((((.....)))))..)))(((.....)))))))).))) ( -33.10)
>consensus
_______GUGUGU___UUGCAUCCUGUUCGUCCUUGCUGCUCGUUCGCAUUUCCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUUCGACAAUUCGUCAGACAUUGU
.........................((((((..(((.((((.(.........).)))).)))..))))))(((((.....))))).....(((.....)))......... (-22.36 = -22.40 +   0.04)

alignment

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secondary structure

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Window 8

Location 13,273,146 – 13,273,249
Length 103
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 89.35
Mean single sequence MFE -30.82
Consensus MFE -27.92
Energy contribution -27.52
Covariance contribution -0.40
Combinations/Pair 1.08
Mean z-score -1.70
Structure conservation index 0.91
SVM decision value 1.51
SVM RNA-class probability 0.960350
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13273146 103 - 22224390
ACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGCGAACGAGCAGCAAGGACGAACAGGAUGCAAAACACACAC-------
.....((((......(((((.....(((((.....)))))((((((.....((((.......))))))))))......)))))...)))).............------- ( -28.00)
>DroSec_CAF1 18592 100 - 1
ACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGCGAACGAGCAGCACGGACGAGCAGGAUGCCA---ACACAC-------
.....(((((.(((....)))....(((((.....)))))((((((.....((((.......))))))))))....)))))(.((.....))).---......------- ( -30.10)
>DroSim_CAF1 17980 100 - 1
ACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGCGAACGAGCAGCAAGGACGAACAGGAUGCAA---ACACAC-------
....(((.((.((..((((((....(((((.....)))))((((((.....((((.......))))))))))........)).))))..)))).---)))...------- ( -28.90)
>DroEre_CAF1 19345 107 - 1
ACAAUGUCUGACGAAUUGUCGAAAAACCGCAGAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGUGAGCGAGCAGCAAGGACGAACAGGAUGCAA---GCACACAAGCGCA
....((..((.((..((((((....(((((.....)))))..((.(((((((((((.(.....).))))).)))))).)))).))))..)))).---.)).......... ( -31.60)
>DroYak_CAF1 18713 107 - 1
ACAAUGUCUGACGAAUUGUCGCAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGUAAUGUGAACGAGCAGCAAGGACGAACAGGAUGUGC---AAAGACAAGUGCC
....((((((((.....)))(((..(((((.....)))))(.(((((.((((.(((.((.......)).))).)))).))))).)......)))---..)))))...... ( -35.50)
>consensus
ACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGCGAACGAGCAGCAAGGACGAACAGGAUGCAA___ACACAC_______
.....((((......(((((.....(((((.....)))))((((((.....((((.......))))))))))......)))))...)))).................... (-27.92 = -27.52 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,273,179 – 13,273,283
Length 104
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 95.58
Mean single sequence MFE -29.90
Consensus MFE -26.62
Energy contribution -26.90
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.81
Structure conservation index 0.89
SVM decision value 1.96
SVM RNA-class probability 0.983846
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13273179 104 + 22224390
UCGUUCGCAUUUCCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUUCGACAAUUCGUCAGACAUUGUUGACACUGUGUCUGAAGUCUGAUGUCUGAUGUCU
..((.(((.......))))).....((((.(((((.....)))))..))))......(((((((((((...(((............))).)))))))))))... ( -30.90)
>DroSec_CAF1 18622 104 + 1
UCGUUCGCAUUUCCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUUCGACAAUUCGUCAGACAUUGUUGACACCGUGUCUGAAGUCUAAUGUCUGAUGUCU
..((.(((.......))))).....((((.(((((.....)))))..))))......((((((((((((..(((..((....))..)))))))))))))))... ( -31.10)
>DroSim_CAF1 18010 104 + 1
UCGUUCGCAUUUCCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUUCGACAAUUCGUCAGACAUUGUUGACACUGUGUCUGAAGUCUGAUGUCUGAUGUCU
..((.(((.......))))).....((((.(((((.....)))))..))))......(((((((((((...(((............))).)))))))))))... ( -30.90)
>DroEre_CAF1 19382 104 + 1
UCGCUCACAUUUCCAGCGACAACAACGAGCACCGCAUUCUGCGGUUUUUCGACAAUUCGUCAGACAUUGUUGACACUGUGUCUGCAGUCUGAAGUCUGAAGUCU
..(((.........)))(((.....((((.(((((.....)))))..))))........(((((((((((.(((.....))).))))).....)))))).))). ( -28.90)
>DroYak_CAF1 18750 104 + 1
UCGUUCACAUUACCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUGCGACAAUUCGUCAGACAUUGUUGACACUGCGUCUGAAGUCUGAUGUCUGAUGUCU
(((((.........)))))......((((.(((((.....))))))))).((((...((((((((.((...(((.....))).)).)))))))).....)))). ( -27.70)
>consensus
UCGUUCGCAUUUCCAGCGACAACAACGAGCACCGCAUUUUGCGGUUUUUCGACAAUUCGUCAGACAUUGUUGACACUGUGUCUGAAGUCUGAUGUCUGAUGUCU
(((((.........)))))......((((.(((((.....)))))..))))......(((((((((((...(((............))).)))))))))))... (-26.62 = -26.90 +   0.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,273,179 – 13,273,283
Length 104
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 95.58
Mean single sequence MFE -30.50
Consensus MFE -27.50
Energy contribution -27.34
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -1.78
Structure conservation index 0.90
SVM decision value 2.03
SVM RNA-class probability 0.986002
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13273179 104 - 22224390
AGACAUCAGACAUCAGACUUCAGACACAGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGCGAACGA
.((((.(.((((.....(.(((((((..((....))..))))))).)...))))((...(((((.....)))))..))).)))).((((.......)))).... ( -30.30)
>DroSec_CAF1 18622 104 - 1
AGACAUCAGACAUUAGACUUCAGACACGGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGCGAACGA
.((((.(.((((.....(.(((((((..((....))..))))))).)...))))((...(((((.....)))))..))).)))).((((.......)))).... ( -31.30)
>DroSim_CAF1 18010 104 - 1
AGACAUCAGACAUCAGACUUCAGACACAGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGCGAACGA
.((((.(.((((.....(.(((((((..((....))..))))))).)...))))((...(((((.....)))))..))).)))).((((.......)))).... ( -30.30)
>DroEre_CAF1 19382 104 - 1
AGACUUCAGACUUCAGACUGCAGACACAGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAGAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGUGAGCGA
...............(..((((....(((((.((((((((..((((.....))))....(((((.....)))))...)))))))).)))))....))))..).. ( -30.60)
>DroYak_CAF1 18750 104 - 1
AGACAUCAGACAUCAGACUUCAGACGCAGUGUCAACAAUGUCUGACGAAUUGUCGCAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGUAAUGUGAACGA
..................((((.((.(((((.((((((((...(((.....)))((...(((((.....))))))).)))))))).)))))))....))))... ( -30.00)
>consensus
AGACAUCAGACAUCAGACUUCAGACACAGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCGGUGCUCGUUGUUGUCGCUGGAAAUGCGAACGA
..........................(((((.((((((((..((((.....))))....(((((.....)))))...)))))))).)))))............. (-27.50 = -27.34 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,273,211 – 13,273,306
Length 95
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 92.83
Mean single sequence MFE -22.10
Consensus MFE -18.78
Energy contribution -18.66
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -1.64
Structure conservation index 0.85
SVM decision value 1.12
SVM RNA-class probability 0.918411
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13273211 95 - 22224390
CGACAACG------ACAACGAACCUGCUCAGACAUCAGACAUCAGACUUCAGACACAGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCG
((((((((------....))....((.((((((((..(((((...............)))))....))))))))))..))))))......(((.....))) ( -20.86)
>DroSec_CAF1 18654 101 - 1
CGACAACGACAACGACAACGAACCUGCUCAGACAUCAGACAUUAGACUUCAGACACGGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCG
......((((((((.....((......)).....(((((((((.(((.((......)).)))...)))))))))))..))))))......(((.....))) ( -22.80)
>DroSim_CAF1 18042 101 - 1
CGACAACGACAACGACAACGAACCUGCUCAGACAUCAGACAUCAGACUUCAGACACAGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCG
......((((((((....))....((.((((((((..(((((...............)))))....))))))))))..))))))......(((.....))) ( -21.36)
>DroEre_CAF1 19414 95 - 1
CGACAACG------ACAACGAAGCUGCUCAGACUUCAGACUUCAGACUGCAGACACAGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAGAAUGCG
......((------((((.((((((....)).))))...(.((((((((..(((.....)))..))..)))))).)..))))))......(((.....))) ( -24.50)
>DroYak_CAF1 18782 101 - 1
CGACAACGACAACGACAACGAACCUGCUCAGACAUCAGACAUCAGACUUCAGACGCAGUGUCAACAAUGUCUGACGAAUUGUCGCAAAACCGCAAAAUGCG
......((((((((....))....((.((((((((..(((((..(........)...)))))....))))))))))..))))))......(((.....))) ( -21.00)
>consensus
CGACAACGACAACGACAACGAACCUGCUCAGACAUCAGACAUCAGACUUCAGACACAGUGUCAACAAUGUCUGACGAAUUGUCGAAAAACCGCAAAAUGCG
((((((.................(((.((........))...))).(.(((((((..((....))..))))))).)..))))))......(((.....))) (-18.78 = -18.66 +  -0.12)

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 11:39:29 2006