Locus 4125

Sequence ID 2R_DroMel_CAF1
Location 13,543,166 – 13,543,314
Length 148
Max. P 0.994619
window6642 window6643 window6644 window6645

overview

Window 2

Location 13,543,166 – 13,543,274
Length 108
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 90.48
Mean single sequence MFE -50.83
Consensus MFE -45.41
Energy contribution -45.30
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -3.07
Structure conservation index 0.89
SVM decision value 1.72
SVM RNA-class probability 0.974145
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13543166 108 + 20766785
ACCCAGGCGCGCCAAGGAGCUGGCAGGCAGGAUGGGUUU-----GGGAUGCGCUGAGGAGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCAGGAGCAAACGAG
.(((((((.((((.....(((....))).)).)).))))-----))).(((.((..((.(((((((.((((((..(((...))))))))).))))))))).)).)))...... ( -48.70)
>DroSec_CAF1 90852 110 + 1
ACCCAGGCGCGCCAAGGAGCAGGCAGGCAGGAUGGGUUGGUGGGGGGAUGUGAU---GGGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAG
(((((.((..(((........)))..))....)))))........(..(((..(---(((((((((.((((((..(((...))))))))).))))))))))...)))..)... ( -49.70)
>DroSim_CAF1 94808 110 + 1
ACCCAGGCGCGCCAAGGAGCAGGCAGGCAGGAUGGGUUGGUGGGGGGAUGUGCU---GGGGUCCUUGGGCUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAG
(((((.((..(((........)))..))....)))))........(..((((((---(((((((((.((((((..(((...))))))))).))))))))))))).))..)... ( -54.10)
>consensus
ACCCAGGCGCGCCAAGGAGCAGGCAGGCAGGAUGGGUUGGUGGGGGGAUGUGCU___GGGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAG
(((((.((..(((........)))..))....)))))........(..(((......(((((((((.((((((..(((...))))))))).)))))))))....)))..)... (-45.41 = -45.30 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,543,166 – 13,543,274
Length 108
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 90.48
Mean single sequence MFE -43.93
Consensus MFE -42.37
Energy contribution -42.60
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -3.65
Structure conservation index 0.96
SVM decision value 2.50
SVM RNA-class probability 0.994619
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13543166 108 - 20766785
CUCGUUUGCUCCUGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCUCCUCAGCGCAUCCC-----AAACCCAUCCUGCCUGCCAGCUCCUUGGCGCGCCUGGGU
.......(((...(((((((((.(((((((((...)))..)))))).)))))))))...))).......-----..(((((....((.((((((....)))))).)).))))) ( -44.10)
>DroSec_CAF1 90852 110 - 1
CUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCCC---AUCACAUCCCCCCACCAACCCAUCCUGCCUGCCUGCUCCUUGGCGCGCCUGGGU
...(..((.((..(((((((((.(((((((((...)))..)))))).)))))))))---..))))..)........(((((....((.((((........)))).)).))))) ( -44.10)
>DroSim_CAF1 94808 110 - 1
CUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGCCCAAGGACCCC---AGCACAUCCCCCCACCAACCCAUCCUGCCUGCCUGCUCCUUGGCGCGCCUGGGU
...(..((.(((.(((((((((.(.(((((((...)))..)))).).)))))))))---.)))))..)........(((((....((.((((........)))).)).))))) ( -43.60)
>consensus
CUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCCC___AGCACAUCCCCCCACCAACCCAUCCUGCCUGCCUGCUCCUUGGCGCGCCUGGGU
......((((...(((((((((.(((((((((...)))..)))))).)))))))))...)))).............(((((....((.((((........)))).)).))))) (-42.37 = -42.60 +   0.23)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,543,205 – 13,543,314
Length 109
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 89.68
Mean single sequence MFE -42.90
Consensus MFE -35.67
Energy contribution -36.23
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -3.67
Structure conservation index 0.83
SVM decision value 1.49
SVM RNA-class probability 0.958760
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13543205 109 + 20766785
-----GGGAUGCGCUGAGGAGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCAGGAGCAAACGAGUUAAGUGCGCUCUAAAAUAUGUAGGGACACUGAUGGAAAA
-----.(..(((.((..((.(((((((.((((((..(((...))))))))).))))))))).)).)))..)......((((..(((((.......))))).))))......... ( -40.70)
>DroSec_CAF1 90891 111 + 1
GUGGGGGGAUGUGAU---GGGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAGUUAAGUGCGCUCUAAUAUAUGUACGGACACUGAUAGAAAA
(((...(..(((..(---(((((((((.((((((..(((...))))))))).))))))))))...)))..)((((.......))))...............))).......... ( -41.80)
>DroSim_CAF1 94847 111 + 1
GUGGGGGGAUGUGCU---GGGGUCCUUGGGCUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAGUUAAGUGCGCUCUAAAAUAUGUAAGGACACUGAUAGAAAA
(((...(..((((((---(((((((((.((((((..(((...))))))))).))))))))))))).))..)((((.......))))...............))).......... ( -46.20)
>consensus
GUGGGGGGAUGUGCU___GGGGUCCUUGGACUGGGAUGGAUGCCACCAGUCGAAGGACCCCGGCAGCAAACGAGUUAAGUGCGCUCUAAAAUAUGUAAGGACACUGAUAGAAAA
....((((.((((((...(((((((((.((((((..(((...))))))))).)))))))))...(((......))).))))))))))........................... (-35.67 = -36.23 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,543,205 – 13,543,314
Length 109
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 89.68
Mean single sequence MFE -35.70
Consensus MFE -32.11
Energy contribution -32.33
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -4.06
Structure conservation index 0.90
SVM decision value 1.88
SVM RNA-class probability 0.981320
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13543205 109 - 20766785
UUUUCCAUCAGUGUCCCUACAUAUUUUAGAGCGCACUUAACUCGUUUGCUCCUGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCUCCUCAGCGCAUCCC-----
..........((((..............(((((.((.......)).)))))..(((((((((.(((((((((...)))..)))))).)))))))))....)))).....----- ( -35.90)
>DroSec_CAF1 90891 111 - 1
UUUUCUAUCAGUGUCCGUACAUAUAUUAGAGCGCACUUAACUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCCC---AUCACAUCCCCCCAC
..........(((................((((.((.......)).))))...(((((((((.(((((((((...)))..)))))).)))))))))---..))).......... ( -36.00)
>DroSim_CAF1 94847 111 - 1
UUUUCUAUCAGUGUCCUUACAUAUUUUAGAGCGCACUUAACUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGCCCAAGGACCCC---AGCACAUCCCCCCAC
.........(((((.(((..........))).)))))......(..((.(((.(((((((((.(.(((((((...)))..)))).).)))))))))---.)))))..)...... ( -35.20)
>consensus
UUUUCUAUCAGUGUCCCUACAUAUUUUAGAGCGCACUUAACUCGUUUGCUGCCGGGGUCCUUCGACUGGUGGCAUCCAUCCCAGUCCAAGGACCCC___AGCACAUCCCCCCAC
..........((((...............((((.((.......)).))))...(((((((((.(((((((((...)))..)))))).)))))))))....)))).......... (-32.11 = -32.33 +   0.23)

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 11:12:27 2006