Locus 4657

Sequence ID 3L_DroMel_CAF1
Location 13,191,107 – 13,191,375
Length 268
Max. P 0.987752
window7318 window7319 window7320 window7321

overview

Window 8

Location 13,191,107 – 13,191,227
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.19
Mean single sequence MFE -33.52
Consensus MFE -29.28
Energy contribution -29.64
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -1.76
Structure conservation index 0.87
SVM decision value 1.62
SVM RNA-class probability 0.968179
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13191107 120 + 23771897
CUCCAAUCCUCAAUCCUUGUCAGACUUUUCAGAGGAGGCGGCGAUGGGAAAGGCAUGCAAUUGGCAUGACAUUGCCAUGUUCCAGCUGGGACAAAGCCCGAAAACCGAAUUGAAAACCAA
.........(((((((((....((....)).)))))((((((((((.......(((((.....))))).))))))).((((((....))))))..)))...........))))....... ( -33.60)
>DroSec_CAF1 42404 113 + 1
CCCCAAU-------CCUCCUCAGACUUUUCAGAGAAGGCGGCGAUGGAAAAGGCAUGCAAUUGGCAUGACAUUGCCAUGUUCCAGCUGGGACAAAGCCCGAAAACCGAAUUGAAAACCAA
.......-------...........(((((((....((((((((((.......(((((.....))))).))))))).((((((....))))))..)))((.....))..))))))).... ( -31.80)
>DroSim_CAF1 40801 113 + 1
CCCCAAU-------CCUCGUCAGACUUUUCAGAGAAGGCGGCGAUGGGAAAGGCAUGCAAUUGGCAUGACAUUGCCAUGUUCCAGCUGGGACAAAGCCCGAAAACCGAAUUGAAAACCAA
.((((.(-------(.(((((...(((....)))..))))).))))))...(((.......(((((......)))))((((((....))))))..)))...................... ( -31.80)
>DroEre_CAF1 46051 112 + 1
-CCCAAU-------CCUCGAAAAACUUUUCAGGGCAGGCGGCGAUGGGAAAGGCAUGCAAUUGGCAUGACAUUGCCAUGUUCCAGCUGGGACAAAGCCCCAAAACCGAAUUGAAUGCCAA
-((((..-------(((.((((....)))))))((.....))..))))...(((((.(((((((((......)))).((((((....))))))..............))))).))))).. ( -35.80)
>DroYak_CAF1 42003 113 + 1
ACCCAAU-------CGUCGAAAAACUUUUCAGAGAAGGCGGCGAUGGGAAAGGCAUGCAAUUGGCAUGACAUUGCCAUGUUCCAGCUGUGACAAAGCCCGAAAACCGAAUUGAAAGCCAA
.((((.(-------(((((.....((((.....)))).))))))))))...(((...(((((((((......))))...(((..(((.......)))..))).....)))))...))).. ( -34.60)
>consensus
CCCCAAU_______CCUCGUCAGACUUUUCAGAGAAGGCGGCGAUGGGAAAGGCAUGCAAUUGGCAUGACAUUGCCAUGUUCCAGCUGGGACAAAGCCCGAAAACCGAAUUGAAAACCAA
.........................(((((((....((((((((((.......(((((.....))))).))))))).((((((....))))))..)))((.....))..))))))).... (-29.28 = -29.64 +   0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,191,227 – 13,191,335
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.88
Mean single sequence MFE -42.98
Consensus MFE -33.84
Energy contribution -35.84
Covariance contribution 2.00
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.79
SVM decision value 0.60
SVM RNA-class probability 0.795976
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13191227 108 + 23771897
GGAGUGGGACUGCAAGCUAGUGCUGAUGGAAUAGCUCAGCCAUGGCGUUGGGGUCUG------------AGUUGGAGUCGCCACCGGUGUGGCAUGUGGAUGCCAUGUUGAUGCCGGCAC
.((.(.(((((.(((((((..(((((.(......))))))..)))).))).))))).------------).))...((((.((.(((..((((((....))))))..))).)).)))).. ( -42.80)
>DroSec_CAF1 42517 97 + 1
GGAGUGGGACUGCAAGCUAGUGCUGAUGGAAUAGUUCAGCCAUGGCGUUGGGGUCUG------------AGUCGGAGUCGCCACCGGUGUGGCAUGUGGAU-----------GCCGGCAC
....(.(((((.(((((((..(((((.........)))))..)))).))).))))).------------)(((((.((((((((....))))).....)))-----------.))))).. ( -37.90)
>DroSim_CAF1 40914 108 + 1
GGAGUGGGACUGCAAGCUAGUGCUGAUGGAAUAGUUCAGCCAUGGCGUUGGGGUCUG------------AGUUGGAGUCGCCACCGGUGUGGCAUGUGGAUGCCAUGUUGAUGCCGGCAC
.((.(.(((((.(((((((..(((((.........)))))..)))).))).))))).------------).))...((((.((.(((..((((((....))))))..))).)).)))).. ( -43.20)
>DroEre_CAF1 46163 101 + 1
G-------GCUGCAAGCUAUUGCUGAUGGAAUAGUUCAGCCAUGGCGUUGGGGUCUG------------AGUCGGAGUCGCCACCGGUGUGGCAUGUGGAUGCCAUGUUGAUGCCGGCAC
(-------(((.((((((((.(((((.........))))).))))).))).))))..------------.(((((.((((((((....)))))((((((...)))))).))).))))).. ( -42.50)
>DroYak_CAF1 42116 120 + 1
GGAGUGGGGCUGCAAGCUAGUGCUGAUGGAAUAGUUCAGCCAUGGCGUUGGGAUCUGACUCGGAGUUGGAGUCGGAGUCGCCACCGGUGUGGCAUGUGGAUGCCAUGUUGAUGCCAGCAC
...(((.(((((..(((((.(.(....).).)))))))))).(((((((((((((((((((.......)))))))).)).))).(((..((((((....))))))..))))))))).))) ( -48.50)
>consensus
GGAGUGGGACUGCAAGCUAGUGCUGAUGGAAUAGUUCAGCCAUGGCGUUGGGGUCUG____________AGUCGGAGUCGCCACCGGUGUGGCAUGUGGAUGCCAUGUUGAUGCCGGCAC
......(((((.(((((((..(((((.........)))))..)))).))).)))))..............(((((.((((((((....)))))(((((.....))))).))).))))).. (-33.84 = -35.84 +   2.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,191,227 – 13,191,335
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.88
Mean single sequence MFE -32.56
Consensus MFE -26.36
Energy contribution -27.56
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.51
Structure conservation index 0.81
SVM decision value 2.09
SVM RNA-class probability 0.987752
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13191227 108 - 23771897
GUGCCGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCAACU------------CAGACCCCAACGCCAUGGCUGAGCUAUUCCAUCAGCACUAGCUUGCAGUCCCACUCC
.(((.(((.....((((((........(((((....)))))((.......)------------)..........))))))(((((.........)))))....))).))).......... ( -32.50)
>DroSec_CAF1 42517 97 - 1
GUGCCGGC-----------AUCCACAUGCCACACCGGUGGCGACUCCGACU------------CAGACCCCAACGCCAUGGCUGAACUAUUCCAUCAGCACUAGCUUGCAGUCCCACUCC
(((..(((-----------((....))))).))).(((((.((((.(((((------------.((....((......))(((((.........))))).)))).))).))))))))).. ( -26.50)
>DroSim_CAF1 40914 108 - 1
GUGCCGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCAACU------------CAGACCCCAACGCCAUGGCUGAACUAUUCCAUCAGCACUAGCUUGCAGUCCCACUCC
.(((.(((.....((((((........(((((....)))))((.......)------------)..........))))))(((((.........)))))....))).))).......... ( -31.70)
>DroEre_CAF1 46163 101 - 1
GUGCCGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCGACU------------CAGACCCCAACGCCAUGGCUGAACUAUUCCAUCAGCAAUAGCUUGCAGC-------C
.(((.(((.....((((((........(((((....)))))((.......)------------)..........))))))(((((.........)))))....))).)))..-------. ( -31.70)
>DroYak_CAF1 42116 120 - 1
GUGCUGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCGACUCCAACUCCGAGUCAGAUCCCAACGCCAUGGCUGAACUAUUCCAUCAGCACUAGCUUGCAGCCCCACUCC
.(((.(((.....((((((........(((((....)))))(((((.((.......)).)))))..........))))))(((((.........)))))....))).))).......... ( -40.40)
>consensus
GUGCCGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCGACU____________CAGACCCCAACGCCAUGGCUGAACUAUUCCAUCAGCACUAGCUUGCAGUCCCACUCC
.(((.(((.....((((((.......((((((....)))))).......................(....)...))))))(((((.........)))))....))).))).......... (-26.36 = -27.56 +   1.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,191,267 – 13,191,375
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.18
Mean single sequence MFE -35.28
Consensus MFE -26.84
Energy contribution -27.72
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -1.80
Structure conservation index 0.76
SVM decision value 0.47
SVM RNA-class probability 0.750041
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13191267 108 - 23771897
GUUCCCUCGACUGCCUCGAAGUGCGUAAUGCGCUCAUUACGUGCCGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCAACU------------CAGACCCCAACGCCAUG
........((.((((.....(..(((((((....)))))))..).))))))..((((((........(((((....)))))((.......)------------)..........)))))) ( -33.40)
>DroSec_CAF1 42557 97 - 1
GUCCCCUCGACUGCCUCGGAGUGCGUAAUGCGCUCAUUACGUGCCGGC-----------AUCCACAUGCCACACCGGUGGCGACUCCGACU------------CAGACCCCAACGCCAUG
..........(((..(((((((((((((((....))))))))((((((-----------((....)))))((....))))).)))))))..------------))).............. ( -33.20)
>DroSim_CAF1 40954 108 - 1
GUCCCCUCGACUGCCUCGAAGUGCGUAAUGCGCUCAUUACGUGCCGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCAACU------------CAGACCCCAACGCCAUG
........((.((((.....(..(((((((....)))))))..).))))))..((((((........(((((....)))))((.......)------------)..........)))))) ( -33.40)
>DroEre_CAF1 46196 108 - 1
GUCCCCUCGAAUGCCUCGAAGUGCGUAAUGCGCUCAUUACGUGCCGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCGACU------------CAGACCCCAACGCCAUG
........((.((((.....(..(((((((....)))))))..).))))))..((((((........(((((....)))))((.......)------------)..........)))))) ( -33.40)
>DroYak_CAF1 42156 120 - 1
GUCCCCUCGACCGCCUCGAAGUGCGUAAUGCGCUCAUUACGUGCUGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCGACUCCAACUCCGAGUCAGAUCCCAACGCCAUG
(((.....))).(((....((..(((((((....)))))))..))))).....((((((........(((((....)))))(((((.((.......)).)))))..........)))))) ( -43.00)
>consensus
GUCCCCUCGACUGCCUCGAAGUGCGUAAUGCGCUCAUUACGUGCCGGCAUCAACAUGGCAUCCACAUGCCACACCGGUGGCGACUCCGACU____________CAGACCCCAACGCCAUG
(((...((((.....)))).(..(((((((....)))))))..).))).....((((((.......((((((....)))))).......................(....)...)))))) (-26.84 = -27.72 +   0.88)

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 11:29:47 2006