Locus 4639

Sequence ID 2R_DroMel_CAF1
Location 15,166,217 – 15,166,418
Length 201
Max. P 0.913759
window7457 window7458 window7459

overview

Window 7

Location 15,166,217 – 15,166,323
Length 106
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 93.39
Mean single sequence MFE -29.26
Consensus MFE -26.82
Energy contribution -26.94
Covariance contribution 0.12
Combinations/Pair 1.06
Mean z-score -1.40
Structure conservation index 0.92
SVM decision value 1.09
SVM RNA-class probability 0.913759
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15166217 106 + 20766785
UUCAUACGACAGUCAAAUAAACGCGGACUGCAGCCACAAAGAAAUGUGUGUGUAUCCUUAUCACACAGCACAUAAAUAAUAUUUAUUGUUCUUUAUGGGGCAG------------CGA
.....................((((((.((((..((((......))))..)))))))..........((.((((((.((((.....)))).))))))..)).)------------)). ( -23.60)
>DroSec_CAF1 4586 118 + 1
UUCAUACGACAGUCAAAUAAACGCGGACUGCAGCCACAAAGAAAUGUGUGUGUAUCCUUAUCACACAGCACAUAAAUAAUAUUUAUUGUUCUUUAUGGGGCAGCUCAAAGGGCCGCGA
.....................(((((.((((..(((.((((((((((((((((.........))))).))))).((((.....)))).)))))).))).))))((.....))))))). ( -30.50)
>DroSim_CAF1 6239 118 + 1
UUCAUACGACAGUCAAAUAAACGCGGACUGCAGCCACAAAGAAAUGUGUGUGUAUCCUUAUCACACAGCACAUAAAUAAUAUUUAUUGUUCUUUAUGGGGCAGCUCAAAGGGCCGCGA
.....................(((((.((((..(((.((((((((((((((((.........))))).))))).((((.....)))).)))))).))).))))((.....))))))). ( -30.50)
>DroEre_CAF1 6411 118 + 1
CUCAUACGGCAGUCAAAUAAGCGCGGACUGCAGCCGCAAAGGAAUGUGUGUGUAUCCUUAUCACACAGCACAUAAAUAAUAUUUAUUGUUCUUUAUGGGGCAGCACAAAGGGCCGCGA
......((((((((...........))))((.(((.(((((((((((((((((.........))))).)))((((((...)))))).))))))).)).))).)).......))))... ( -30.70)
>DroYak_CAF1 4604 118 + 1
UUCAUACGACAGUCAAAUAAACGCGGACUGCAGCCGCAAAGGAAUGUGUGUGUAUCCUUAUCACACAGCACAUAAAUAAUAUUUAUUGUUCUUUAUGGGGCAGCUCGAAGGGCCGCGA
.....................(((((...((.(((.(((((((((((((((((.........))))).)))((((((...)))))).))))))).)).))).))((....))))))). ( -31.00)
>consensus
UUCAUACGACAGUCAAAUAAACGCGGACUGCAGCCACAAAGAAAUGUGUGUGUAUCCUUAUCACACAGCACAUAAAUAAUAUUUAUUGUUCUUUAUGGGGCAGCUCAAAGGGCCGCGA
.....................(((((.((((..(((.((((((((((((((((.........))))).))))).((((.....)))).)))))).))).)))).........))))). (-26.82 = -26.94 +   0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,166,217 – 15,166,323
Length 106
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 93.39
Mean single sequence MFE -30.12
Consensus MFE -26.96
Energy contribution -28.24
Covariance contribution 1.28
Combinations/Pair 1.02
Mean z-score -1.30
Structure conservation index 0.90
SVM decision value 0.56
SVM RNA-class probability 0.781320
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15166217 106 - 20766785
UCG------------CUGCCCCAUAAAGAACAAUAAAUAUUAUUUAUGUGCUGUGUGAUAAGGAUACACACACAUUUCUUUGUGGCUGCAGUCCGCGUUUAUUUGACUGUCGUAUGAA
..(------------((((.((((((((((..((((((...))))))(((.((((((.......)))))))))..))))))))))..)))))....(((.....)))........... ( -26.10)
>DroSec_CAF1 4586 118 - 1
UCGCGGCCCUUUGAGCUGCCCCAUAAAGAACAAUAAAUAUUAUUUAUGUGCUGUGUGAUAAGGAUACACACACAUUUCUUUGUGGCUGCAGUCCGCGUUUAUUUGACUGUCGUAUGAA
.(((((........(((((.((((((((((..((((((...))))))(((.((((((.......)))))))))..))))))))))..))))))))))(((((.((.....)).))))) ( -33.20)
>DroSim_CAF1 6239 118 - 1
UCGCGGCCCUUUGAGCUGCCCCAUAAAGAACAAUAAAUAUUAUUUAUGUGCUGUGUGAUAAGGAUACACACACAUUUCUUUGUGGCUGCAGUCCGCGUUUAUUUGACUGUCGUAUGAA
.(((((........(((((.((((((((((..((((((...))))))(((.((((((.......)))))))))..))))))))))..))))))))))(((((.((.....)).))))) ( -33.20)
>DroEre_CAF1 6411 118 - 1
UCGCGGCCCUUUGUGCUGCCCCAUAAAGAACAAUAAAUAUUAUUUAUGUGCUGUGUGAUAAGGAUACACACACAUUCCUUUGCGGCUGCAGUCCGCGCUUAUUUGACUGCCGUAUGAG
..(((((.(((((((......))))))).....((((((......(((((.((((((.......)))))))))))......(((((....).))))...))))))...)))))..... ( -30.60)
>DroYak_CAF1 4604 118 - 1
UCGCGGCCCUUCGAGCUGCCCCAUAAAGAACAAUAAAUAUUAUUUAUGUGCUGUGUGAUAAGGAUACACACACAUUCCUUUGCGGCUGCAGUCCGCGUUUAUUUGACUGUCGUAUGAA
..(((((....((..((((.((.(((((....((((((...))))))(((.((((((.......)))))))))....))))).))..))))..)).(((.....))).)))))..... ( -27.50)
>consensus
UCGCGGCCCUUUGAGCUGCCCCAUAAAGAACAAUAAAUAUUAUUUAUGUGCUGUGUGAUAAGGAUACACACACAUUUCUUUGUGGCUGCAGUCCGCGUUUAUUUGACUGUCGUAUGAA
.(((((........(((((.((((((((((..((((((...))))))(((.((((((.......)))))))))..))))))))))..))))))))))(((((.((.....)).))))) (-26.96 = -28.24 +   1.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,166,323 – 15,166,418
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.14
Mean single sequence MFE -19.87
Consensus MFE -14.50
Energy contribution -14.67
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.73
SVM decision value 0.90
SVM RNA-class probability 0.877515
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15166323 95 + 20766785
AGAUGCCAACCCCACGGCCUAGUGUCAGUUGGGAAACAUUCAAGUGUUUCAAAUAUUUCUUAACAGCCCUCCCC--------------UGACACUU------GUUUACACACACA-----
....(((........)))..((((((((..(((((((((....)))))))...((.....)).....))....)--------------))))))).------.............----- ( -20.40)
>DroSec_CAF1 4704 84 + 1
AGAUGCCAACCCCACGGCCUAGUGUCAGUUGGGAAACAUUCAAGUGUUUCAAAUAUUUUUUAACAGCUUUCCCC--------------CGACACUU------GU----------------
....(((........)))..(((((((((((.(((((((....)))))))(((.....)))..)))))......--------------.)))))).------..---------------- ( -18.01)
>DroSim_CAF1 6357 84 + 1
AGAUGCCAACCCCACGGCCUAGUGUCAGUUGGGAAACAUUCAAGUGUUUCAAAUAUUUUUUAACAGCUUUCCCC--------------CGACACUU------GU----------------
....(((........)))..(((((((((((.(((((((....)))))))(((.....)))..)))))......--------------.)))))).------..---------------- ( -18.01)
>DroEre_CAF1 6529 75 + 1
AGAUGCCAACCCCACGGCCUAGUGUCAGUUGGGAAACAUUCAAGUGUUUCAAAUAUUUUUUAACAGCUUUCCCCC---------------------------------------------
.....(((((..(((......)))...)))))(((((((....))))))).........................--------------------------------------------- ( -15.40)
>DroYak_CAF1 4722 102 + 1
AGAUGCCAACCCCACGGCCUAGUGUCAGUUGGGAAACAUUCAAGUGUUUCAAAUAUUUUUUAACAGCUUUCCCCC-------------CGACACUUAUACGUGUAUACACACCCA-----
............((((....(((((((((((.(((((((....)))))))(((.....)))..))))).......-------------.))))))....))))............----- ( -21.10)
>DroAna_CAF1 4309 110 + 1
AGAUGCCAACCCCAAGGCCUAGUGUCAGUUGGGAAACAUUCAAGUGUUUCGAAUAUUUUUUAACAGCUUCCCCCCACGGUGGAAAGCCUGCCACUC------C----CACUCCCACUCCU
....(((........)))..((((..(((.(((((((((....))))))).............((((((((((....)).)).))).))).....)------)----.)))..))))... ( -26.30)
>consensus
AGAUGCCAACCCCACGGCCUAGUGUCAGUUGGGAAACAUUCAAGUGUUUCAAAUAUUUUUUAACAGCUUUCCCC______________CGACACUU______GU________________
.....(((((..(((......)))...)))))(((((((....)))))))...................................................................... (-14.50 = -14.67 +   0.17)

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 11:25:26 2006