Locus 3928

Sequence ID 2R_DroMel_CAF1
Location 12,951,523 – 12,951,650
Length 127
Max. P 0.972674
window6343 window6344 window6345

overview

Window 3

Location 12,951,523 – 12,951,615
Length 92
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 72.23
Mean single sequence MFE -27.92
Consensus MFE -12.65
Energy contribution -12.85
Covariance contribution 0.20
Combinations/Pair 1.31
Mean z-score -2.11
Structure conservation index 0.45
SVM decision value 1.26
SVM RNA-class probability 0.937582
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12951523 92 + 20766785
GC---------AAGUGCAAC-UGUAAGUGCAGCAGCGCUGCUUGAAAAACUGAGCGCCUGUUCCAAAGGCGCUGUAAAACUUAAAAACAACAAACAGACGC------G
((---------(..(((...-.)))..)))....((((((.(((........(((((((.......)))))))((...........))..))).))).)))------. ( -27.60)
>DroVir_CAF1 3621 93 + 1
---CAGCGA-GGCACACAGCAUGCAGUUGG-----CUGUGCUUUUUUCGCUGCGCGCCUGUUAAUAAGGCGCUGUAAAACUUAAAAACAACAAACAGACGC------G
---((((((-((((((((((.....)))).-----.))))))....)))))).((((((.......)))))).............................------. ( -29.50)
>DroGri_CAF1 3247 97 + 1
---CAGC-A-UGCAUGCAGC-UGUAGGGGA-----CUGAGCUUUUUUCGCUGUGCGCCUGUUAAUAAGGCGCUGUAAAACUUAAAAACAACAAACAGACGCGAGAGCG
---((((-.-((....))))-))(((....-----))).((((((..((((((((((((.......))))))(((...........)))....)))).)).)))))). ( -30.60)
>DroEre_CAF1 3426 92 + 1
GC---------AAGUGCAGC-UGUAAGUGCAGCAGCGCUGCUUGAAAAACUGCGCGCCUGUUCCAAAGGCGCUGUAAAACUUAAAAACAACAAACAGACGC------G
((---------(.((((.((-(((....))))).)))))))..........((((((((.......))))))(((...........)))..........))------. ( -28.90)
>DroMoj_CAF1 4742 93 + 1
GG-UAGCGA-GGC--ACAGCAUGCAGUUGG-----UUGUGCUGUUGGCGCUGUGCGCCUGUUAAUAAGGCGCUGUAAAACUUAAAAACAACAAACAGACGC------G
..-((((..-(((--(((((.........)-----)))))))))))(((((((((((((.......))))))(((...........)))....)))).)))------. ( -30.60)
>DroAna_CAF1 3222 94 + 1
GCG-AGCAAGUAAAUGCAAC-UGUAAAUGU-----CGCUGCUUGGAAAACUGCGCGCCUGUUCCAAAGGCGCUGUAAAACUUAAAAACAACAAACAGACCC-------
.((-((((.(..(.(((...-.)))....)-----..)))))))......(((((((((.......)))))).))).........................------- ( -20.30)
>consensus
GC__AGC_A__AAAUGCAGC_UGUAAGUGC_____CGCUGCUUGUAAAACUGCGCGCCUGUUAAAAAGGCGCUGUAAAACUUAAAAACAACAAACAGACGC______G
..............((((....(((.(((......))))))............((((((.......))))))))))................................ (-12.65 = -12.85 +   0.20)

alignment

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secondary structure

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Window 4

Location 12,951,523 – 12,951,615
Length 92
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 72.23
Mean single sequence MFE -28.59
Consensus MFE -16.13
Energy contribution -15.97
Covariance contribution -0.16
Combinations/Pair 1.20
Mean z-score -2.03
Structure conservation index 0.56
SVM decision value 1.70
SVM RNA-class probability 0.972674
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12951523 92 - 20766785
C------GCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUUGGAACAGGCGCUCAGUUUUUCAAGCAGCGCUGCUGCACUUACA-GUUGCACUU---------GC
.------(((.((((..((................(((((((.......)))))))...........(((((...)))))))..)))-).)))....---------.. ( -27.30)
>DroVir_CAF1 3621 93 - 1
C------GCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUAUUAACAGGCGCGCAGCGAAAAAAGCACAG-----CCAACUGCAUGCUGUGUGCC-UCGCUG---
(------(((((((((((((((...........)))))).......))))))))))((((((.....((((((-----(.........)))))))...-))))))--- ( -35.11)
>DroGri_CAF1 3247 97 - 1
CGCUCUCGCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUAUUAACAGGCGCACAGCGAAAAAAGCUCAG-----UCCCCUACA-GCUGCAUGCA-U-GCUG---
((((...(((((((((((((((...........)))))).......)))))))))..))))............-----.......((-((((....))-.-))))--- ( -25.81)
>DroEre_CAF1 3426 92 - 1
C------GCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUUGGAACAGGCGCGCAGUUUUUCAAGCAGCGCUGCUGCACUUACA-GCUGCACUU---------GC
.------(((((((((((((((...........))))).......))))))))))((((((......(((((...)))))......)-)))))....---------.. ( -31.51)
>DroMoj_CAF1 4742 93 - 1
C------GCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUAUUAACAGGCGCACAGCGCCAACAGCACAA-----CCAACUGCAUGCUGU--GCC-UCGCUA-CC
.------(((((((((((((((...........)))))).......)))))))))..((((...((((((((.-----.....))..))))))--...-.)))).-.. ( -28.41)
>DroAna_CAF1 3222 94 - 1
-------GGGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUUGGAACAGGCGCGCAGUUUUCCAAGCAGCG-----ACAUUUACA-GUUGCAUUUACUUGCU-CGC
-------((((.((((((.(((...........)))((((((.......)))))).........))))))(((-----((.......-)))))........)))-).. ( -23.40)
>consensus
C______GCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUAGGAACAGGCGCGCAGCGUUAAAAGCACAG_____CCACCUACA_GCUGCAUGC__U_GCU__GC
.......(((((((((((((((...........)))))).......)))))))))(((((............................)))))............... (-16.13 = -15.97 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,951,548 – 12,951,650
Length 102
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 79.62
Mean single sequence MFE -29.33
Consensus MFE -18.02
Energy contribution -19.14
Covariance contribution 1.11
Combinations/Pair 1.08
Mean z-score -1.85
Structure conservation index 0.61
SVM decision value 0.54
SVM RNA-class probability 0.775106
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12951548 102 - 20766785
CGC-AAACUAUUUUCCGCGCUGUAACUAAACGAGCGCGCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUUGGAACAGGCGCUCAGUUUUUCAAGCAGCG
(((-............(((((((......)).)))))(((((((((((((((...........))))).......))))))))))...............))) ( -28.41)
>DroVir_CAF1 3647 90 - 1
UGCAAAACUAUUUUG----CUUU---------CGCGCGCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUAUUAACAGGCGCGCAGCGAAAAAAGCACAG
.(((((.....))))----)(((---------((((((((((((((((((((...........)))))).......))))))))))).))))))......... ( -32.51)
>DroEre_CAF1 3451 102 - 1
CGC-AAACUAUUUUCCGCGCUGUAACUACACGAGCGCGCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUUGGAACAGGCGCGCAGUUUUUCAAGCAGCG
...-.............((((((........(((((((((((((((((((((...........))))).......)))))))))))).)))).....)))))) ( -30.73)
>DroYak_CAF1 3329 102 - 1
CGC-AAACUAUUUUCCGCGCUGUAACUACACGAGCGAGCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUUGGAACAGGCGCUCAGUUUUUCAAGCAGCG
...-.............((((((........(((((((((((((((((((((...........))))).......)))))))))))).)))).....)))))) ( -29.43)
>DroMoj_CAF1 4768 90 - 1
CUCAAAACUAUUUCG----CUUU---------CGCGCGCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUAUUAACAGGCGCACAGCGCCAACAGCACAA
..............(----((((---------.(((((((((((((((((((...........)))))).......)))))))))...)))).)).))).... ( -24.91)
>DroAna_CAF1 3250 99 - 1
GGC-AAACUAUC-CGCGCGCUGUAACUAUUCC-GCG-GGGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUUGGAACAGGCGCGCAGUUUUCCAAGCAGCG
(((-((((...(-(.((((..((....))..)-)))-.))...)))))))................((((((.......))))))((.(((.....))).)). ( -30.00)
>consensus
CGC_AAACUAUUUUCCGCGCUGUAACUA_ACGAGCGCGCGUCUGUUUGUUGUUUUUAAGUUUUACAGCGCCUUUGGAACAGGCGCGCAGUUUUUCAAGCAGCG
.................((((((.........(((..(((((((((((((((...........)))))).......)))))))))...)))......)))))) (-18.02 = -19.14 +   1.11)

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 11:07:35 2006