Locus 2927

Sequence ID 2R_DroMel_CAF1
Location 10,151,126 – 10,151,256
Length 130
Max. P 0.827730
window4825 window4826 window4827

overview

Window 5

Location 10,151,126 – 10,151,224
Length 98
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 65.85
Mean single sequence MFE -25.89
Consensus MFE -11.36
Energy contribution -13.31
Covariance contribution 1.94
Combinations/Pair 1.11
Mean z-score -1.59
Structure conservation index 0.44
SVM decision value 0.32
SVM RNA-class probability 0.685093
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10151126 98 + 20766785
GUGAUAGUUUCUA------CCAAACACA--ACGUGAUUUUCUCACGACACCUGCGCUGGCCGAGAAAGUGGGA--------UCCAUCUUUCCAUUACGACUACCCUUGGCAGCC
(((...((((...------..))))...--.(((((.....))))).)))....((((.(((((..(((((((--------.......)))))))..(.....)))))))))). ( -24.00)
>DroSec_CAF1 11586 90 + 1
AUGAU--------------CCCAACACU--UCGUGACUUUCUCACGACACCUGCGCUGGCCGAGAAAGUGGGA--------UCCAUCUUUCCAUUACGGCUACCCUUGGCAGCC
..(((--------------(((..(((.--..)))((((((((......((......))..))))))))))))--------))..............((((.((...)).)))) ( -25.40)
>DroSim_CAF1 6567 98 + 1
UUGAUAGUUUCUU------CCAAGCAUU--UCGUGACUUUCUCACGACACCUGCGCUGGCCGAGAAAGUGGGA--------UCCAUCUUUCCAUUACGGCUACCCUUGGCAGCC
.............------....(((..--((((((.....))))))....)))((((.(((((..(((((((--------.......)))))))..((...))))))))))). ( -26.90)
>DroEre_CAF1 11882 97 + 1
GUGACAGCUCCGC------CCAAACUCUGCUCGUGACUCACUCACGACACCUGCGCUG-CCGAGAAAGUGGGA--------UCCAUCUUCA--CUAGAGCCACCCUUGGCAGCC
(((...((.....------.........))((((((.....)))))))))....((((-(((((...((((..--------....(((...--..))).)))).))))))))). ( -28.74)
>DroYak_CAF1 6635 106 + 1
GUAAUAGAUUUGC------CGAAACUCAGCUCGUGAUAUACUCACGACACCUGCGCUGGCCGAGAAAGUGGGAUCCAGGGAUCCAUCUUUC--CCAAAGCCACCCUUGGCAGCC
.........((((------(((..(.(((.((((((.....))))))...))).).((((.(.(((((..(((((....)))))..)))))--.)...))))...))))))).. ( -33.80)
>DroAna_CAF1 7556 91 + 1
UUUCUGGUUUCCUAUCUAUCCUCCUAUC--ACGCUGCUAUCUCUAGACCCCU---CU--------AGACGGAG--------UCCAUCUU--CAUGAUGUCCCCCGUGUAUCCCC
............................--((((.......((((((....)---))--------))).((.(--------..((((..--...))))..).))))))...... ( -16.50)
>consensus
GUGAUAGUUUCGC______CCAAACACU__UCGUGACUUUCUCACGACACCUGCGCUGGCCGAGAAAGUGGGA________UCCAUCUUUCCAUUACGGCCACCCUUGGCAGCC
...............................(((((.....)))))........((((.(((((...((((............................)))).))))))))). (-11.36 = -13.31 +   1.94)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,151,126 – 10,151,224
Length 98
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 65.85
Mean single sequence MFE -32.50
Consensus MFE -14.81
Energy contribution -16.25
Covariance contribution 1.44
Combinations/Pair 1.38
Mean z-score -1.69
Structure conservation index 0.46
SVM decision value 0.70
SVM RNA-class probability 0.827730
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10151126 98 - 20766785
GGCUGCCAAGGGUAGUCGUAAUGGAAAGAUGGA--------UCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGAAAAUCACGU--UGUGUUUGG------UAGAAACUAUCAC
(((((((...)))))))......(((((.(((.--------..))))))))((.(((((((((((((((....))....))).)--)))).))))------).))......... ( -30.50)
>DroSec_CAF1 11586 90 - 1
GGCUGCCAAGGGUAGCCGUAAUGGAAAGAUGGA--------UCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGAAAGUCACGA--AGUGUUGGG--------------AUCAU
(((((((...))))))).....((((((.(((.--------..)))))))))...(((((((.....((((((.....))))))--.))))))).--------------..... ( -34.30)
>DroSim_CAF1 6567 98 - 1
GGCUGCCAAGGGUAGCCGUAAUGGAAAGAUGGA--------UCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGAAAGUCACGA--AAUGCUUGG------AAGAAACUAUCAA
(((((((...)))))))......(((((.(((.--------..))))))))((..((((.(((....((((((.....))))))--..)))))))------..))......... ( -34.20)
>DroEre_CAF1 11882 97 - 1
GGCUGCCAAGGGUGGCUCUAG--UGAAGAUGGA--------UCCCACUUUCUCGG-CAGCGCAGGUGUCGUGAGUGAGUCACGAGCAGAGUUUGG------GCGGAGCUGUCAC
(((..((...))..)))....--....(((((.--------((((((((...(((-((.(...).))))).))))).(((.(((((...))))))------))))).))))).. ( -32.10)
>DroYak_CAF1 6635 106 - 1
GGCUGCCAAGGGUGGCUUUGG--GAAAGAUGGAUCCCUGGAUCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGUAUAUCACGAGCUGAGUUUCG------GCAAAUCUAUUAC
((((((((....))))...((--(((((..(((((....)))))..))))))))))).....((((.((((((.....))))))((((.....))------))..))))..... ( -41.40)
>DroAna_CAF1 7556 91 - 1
GGGGAUACACGGGGGACAUCAUG--AAGAUGGA--------CUCCGUCU--------AG---AGGGGUCUAGAGAUAGCAGCGU--GAUAGGAGGAUAGAUAGGAAACCAGAAA
.......(((((((..((((...--..))))..--------)))).(((--------((---(....)))))).........))--)...............(....)...... ( -22.50)
>consensus
GGCUGCCAAGGGUAGCCGUAAUGGAAAGAUGGA________UCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGAAAGUCACGA__AGUGUUUGG______AAGAAACUAUCAC
((((((.....))))))..........(((((............(((((.(.(.....).).)))))((((((.....)))))).......................))))).. (-14.81 = -16.25 +   1.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,151,152 – 10,151,256
Length 104
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 77.63
Mean single sequence MFE -37.45
Consensus MFE -21.65
Energy contribution -21.77
Covariance contribution 0.12
Combinations/Pair 1.38
Mean z-score -1.68
Structure conservation index 0.58
SVM decision value 0.32
SVM RNA-class probability 0.688195
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10151152 104 - 20766785
AGAGUCGACUAUUUGAUGGCUUUUGGGGGGCUGGCUGCCAAGGGUAGUCGUAAUGGAAAGAUGGA--------UCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGAAAAUC
...........(((.(((((.((((.(.(((((((((((...))))))).....((((((.(((.--------..))))))))).))))..).)))).))))).)))..... ( -32.60)
>DroSec_CAF1 11604 103 - 1
AGAGUCGACUAUUUGAUGGCUUUUGGG-GGCCGGCUGCCAAGGGUAGCCGUAAUGGAAAGAUGGA--------UCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGAAAGUC
......((((.(((.(((((.((((.(-(((((((((((...))))))).....((((((.(((.--------..))))))))).))))..).)))).))))).))).)))) ( -41.00)
>DroSim_CAF1 6593 103 - 1
AGAGUCGACUAUUUGAUGGCUUUUGGG-GGCUGGCUGCCAAGGGUAGCCGUAAUGGAAAGAUGGA--------UCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGAAAGUC
......((((.(((.(((((.((((.(-(((((((((((...))))))).....((((((.(((.--------..))))))))).))))..).)))).))))).))).)))) ( -38.00)
>DroEre_CAF1 11910 100 - 1
AGAGUCGACUAUUUGAUGGCUUUUGGG-GGCCGGCUGCCAAGGGUGGCUCUAG--UGAAGAUGGA--------UCCCACUUUCUCGG-CAGCGCAGGUGUCGUGAGUGAGUC
.....((((.(((((.((((((....)-)))))((((((.(((((((.((((.--......))))--------..)))))..)).))-)))).))))))))).......... ( -35.00)
>DroYak_CAF1 6663 109 - 1
AGAGUCGACUAUUUGAUGGCUUUUGUG-GGCUGGCUGCCAAGGGUGGCUUUGG--GAAAGAUGGAUCCCUGGAUCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGUAUAUC
(((((((.(.....).)))))))..((-.(((((((((((....))))...((--(((((..(((((....)))))..)))))))))))))).))((((((....).))))) ( -45.40)
>DroAna_CAF1 7588 89 - 1
CGAGUCGACUUCUUGAUGGCCUU-GGG-GUCUGGGGAUACACGGGGGACAUCAUG--AAGAUGGA--------CUCCGUCU--------AG---AGGGGUCUAGAGAUAGCA
.(((((.(((((.(((((.((((-(..-(((....)))...)))))..))))).)--))).).))--------)))..(((--------((---(....))))))....... ( -32.70)
>consensus
AGAGUCGACUAUUUGAUGGCUUUUGGG_GGCUGGCUGCCAAGGGUAGCCGUAAUGGAAAGAUGGA________UCCCACUUUCUCGGCCAGCGCAGGUGUCGUGAGAAAGUC
.....((((.(((((.(((((.......(((((.((.....)).)))))......(((((.(((...........))))))))..)))))...))))))))).......... (-21.65 = -21.77 +   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 10:42:57 2006