Locus 3749

Sequence ID 2L_DroMel_CAF1
Location 10,894,532 – 10,894,660
Length 128
Max. P 0.909598
window5903 window5904 window5905

overview

Window 3

Location 10,894,532 – 10,894,640
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.71
Mean single sequence MFE -33.10
Consensus MFE -21.49
Energy contribution -21.88
Covariance contribution 0.39
Combinations/Pair 1.21
Mean z-score -1.66
Structure conservation index 0.65
SVM decision value 0.11
SVM RNA-class probability 0.588186
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10894532 108 + 22407834
UUGCCAGUCAGUCGACAAGGC---AAGUUUAUUGUACUU--UGUACUU--GGUGGUU----AUGGCAUGAUGUAUUCGUGCCAUGGCAUGUAAUUCAUCAGCCGGCG-AGAUGAAUGAGU
(((((.(((....)))..(((---.........((((..--.)))).(--(((((((----(((((((((.....))))))))))))........))))))))))))-)........... ( -36.20)
>DroSec_CAF1 34083 104 + 1
UUGCCA----GUCGACAAGGC---AAGUUUAUUGUACUU--UGUACUU--GGGGGUU----AUGGCAUGAUGUAUUCGUGCCACGGCAUGUAAUUCAUCAGCCGGCG-AGAUGAAUGAGU
((((((----..(..((((((---((((.......)).)--))).)))--)..)..)----..(((.(((((.((((((((....))))).))).))))))))))))-)........... ( -33.80)
>DroSim_CAF1 34972 104 + 1
UUGCCA----GUCGACAAGGC---AAGUUUAUUGUACUU--UGUACUU--GGGGGUU----AUGGCAUGAUGUAUUCGUGCCACGGCAUGUAAUUCAUCAGCCGGCG-AGAUGAAUGAGU
((((((----..(..((((((---((((.......)).)--))).)))--)..)..)----..(((.(((((.((((((((....))))).))).))))))))))))-)........... ( -33.80)
>DroEre_CAF1 34280 103 + 1
GU---UGCCAGUCGACAAGGC---GAGUUUAUUGUACUG--UGUACUU---GGGGUU----AUGGCAAGAUGUAUUCGUGCCAGGGCAUGUAAUUUAUCA-CCGGGG-AGAUGAAUGAGU
.(---(((((..(..((((((---((((.......))).--))).)))---)..)..----.))))))........(((((....)))))..(((((((.-(....)-.))))))).... ( -26.90)
>DroYak_CAF1 35050 110 + 1
UUGCCAGCCAGCCGACAAGGC---AAGUUUAUUGUGCUU--UGUACUUUGGGGGGUU----AUGGCAUGAUGUAUUCGUGCCAGGGCAUGUAAUUCAUCAGCCAUGG-AGAUGAAUGAGU
..(((..((((...(((((((---(.........)))))--)))...))))..)))(----(((((.(((((.((((((((....))))).))).))))))))))).-............ ( -39.10)
>DroAna_CAF1 37553 113 + 1
UUGCCA-----CCGAGCAUGCAUGAAGUUUAUUGUCCUUUUUGUACAC--GGAAGACACAUGGGGUAUGAUGUAUUCGUGUCAGGGCAUGUAAUUCAUCUCGUGUCGCAAAUGAAUGAGC
((((.(-----(((((.....(((((......((((((....(.((((--(((..(((((((...)))).))).)))))))))))))).....))))))))).)).)))).......... ( -28.80)
>consensus
UUGCCA____GUCGACAAGGC___AAGUUUAUUGUACUU__UGUACUU__GGGGGUU____AUGGCAUGAUGUAUUCGUGCCAGGGCAUGUAAUUCAUCAGCCGGCG_AGAUGAAUGAGU
..........................(((((((((((.....))))................((((.(((((.((((((((....))))).))).))))))))).....))))))).... (-21.49 = -21.88 +   0.39)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,894,532 – 10,894,640
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.71
Mean single sequence MFE -24.08
Consensus MFE -14.72
Energy contribution -16.08
Covariance contribution 1.36
Combinations/Pair 1.05
Mean z-score -1.91
Structure conservation index 0.61
SVM decision value 0.14
SVM RNA-class probability 0.604246
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10894532 108 - 22407834
ACUCAUUCAUCU-CGCCGGCUGAUGAAUUACAUGCCAUGGCACGAAUACAUCAUGCCAU----AACCACC--AAGUACA--AAGUACAAUAAACUU---GCCUUGUCGACUGACUGGCAA
............-....((((((((.(((.(.(((....))).)))).))))).)))..----.......--..((((.--..))))........(---(((..(((....))).)))). ( -26.00)
>DroSec_CAF1 34083 104 - 1
ACUCAUUCAUCU-CGCCGGCUGAUGAAUUACAUGCCGUGGCACGAAUACAUCAUGCCAU----AACCCCC--AAGUACA--AAGUACAAUAAACUU---GCCUUGUCGAC----UGGCAA
............-.(((((((((((.(((.(.(((....))).)))).))))).)))..----...(..(--(((....--((((.......))))---..))))..)..----.))).. ( -25.10)
>DroSim_CAF1 34972 104 - 1
ACUCAUUCAUCU-CGCCGGCUGAUGAAUUACAUGCCGUGGCACGAAUACAUCAUGCCAU----AACCCCC--AAGUACA--AAGUACAAUAAACUU---GCCUUGUCGAC----UGGCAA
............-.(((((((((((.(((.(.(((....))).)))).))))).)))..----...(..(--(((....--((((.......))))---..))))..)..----.))).. ( -25.10)
>DroEre_CAF1 34280 103 - 1
ACUCAUUCAUCU-CCCCGG-UGAUAAAUUACAUGCCCUGGCACGAAUACAUCUUGCCAU----AACCCC---AAGUACA--CAGUACAAUAAACUC---GCCUUGUCGACUGGCA---AC
............-..((((-((((((...........(((((.((.....)).))))).----......---..((((.--..)))).........---...))))).)))))..---.. ( -18.50)
>DroYak_CAF1 35050 110 - 1
ACUCAUUCAUCU-CCAUGGCUGAUGAAUUACAUGCCCUGGCACGAAUACAUCAUGCCAU----AACCCCCCAAAGUACA--AAGCACAAUAAACUU---GCCUUGUCGGCUGGCUGGCAA
............-..((((((((((.(((.(.(((....))).)))).))))).)))))----..((..(((..(.(((--(.(((.........)---)).)))))...)))..))... ( -26.10)
>DroAna_CAF1 37553 113 - 1
GCUCAUUCAUUUGCGACACGAGAUGAAUUACAUGCCCUGACACGAAUACAUCAUACCCCAUGUGUCUUCC--GUGUACAAAAAGGACAAUAAACUUCAUGCAUGCUCGG-----UGGCAA
..........((((.((.(((((((((.....((.(((.(((((((.(((.(((.....)))))).)).)--))))......))).))......))))).....)))))-----).)))) ( -23.70)
>consensus
ACUCAUUCAUCU_CGCCGGCUGAUGAAUUACAUGCCCUGGCACGAAUACAUCAUGCCAU____AACCCCC__AAGUACA__AAGUACAAUAAACUU___GCCUUGUCGAC____UGGCAA
....(((((((..........)))))))....((((.(((((.((.....)).)))))................((((.....))))............................)))). (-14.72 = -16.08 +   1.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,894,568 – 10,894,660
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.78
Mean single sequence MFE -27.65
Consensus MFE -19.06
Energy contribution -18.87
Covariance contribution -0.19
Combinations/Pair 1.23
Mean z-score -1.62
Structure conservation index 0.69
SVM decision value 1.07
SVM RNA-class probability 0.909598
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10894568 92 + 22407834
-UGUACUU--GGUGGUU----AUGGCAUGAUGUAUUCGUGCCAUGGCAUGUAAUUCAUCAGCCGGCG-AGAUGAAUGAGUCGUAUUCAUAUA--------------UAU------AUUCA
-....(((--(.(((((----(((((((((.....))))))))).(.(((.....))))))))).))-))(((((((.....)))))))...--------------...------..... ( -27.50)
>DroSec_CAF1 34115 90 + 1
-UGUACUU--GGGGGUU----AUGGCAUGAUGUAUUCGUGCCACGGCAUGUAAUUCAUCAGCCGGCG-AGAUGAAUGAGUCGUAUUCAUAUA----------------U------AUUCA
-....(((--(......----.((((((((.....))))))))((((.((........)))))).))-))(((((((.....)))))))...----------------.------..... ( -26.30)
>DroSim_CAF1 35004 106 + 1
-UGUACUU--GGGGGUU----AUGGCAUGAUGUAUUCGUGCCACGGCAUGUAAUUCAUCAGCCGGCG-AGAUGAAUGAGUCGUAUUCAUAUAUAUUCACAUUCAUAUAU------AUUCA
-....(((--(......----.((((((((.....))))))))((((.((........)))))).))-))(((((((.(..((((......)))).).)))))))....------..... ( -29.00)
>DroEre_CAF1 34313 100 + 1
-UGUACUU---GGGGUU----AUGGCAAGAUGUAUUCGUGCCAGGGCAUGUAAUUUAUCA-CCGGGG-AGAUGAAUGAGUCGUAUUCAUA--UA--CACAUACUCGUAU------AUUCA
-(((((..---(((((.----.(((((.((.....)).)))))..))((((.(((((((.-(....)-.))))))).....((((....)--))--))))).)))))))------).... ( -24.20)
>DroYak_CAF1 35086 112 + 1
-UGUACUUUGGGGGGUU----AUGGCAUGAUGUAUUCGUGCCAGGGCAUGUAAUUCAUCAGCCAUGG-AGAUGAAUGAGUCGUAUUCAUAUAUA--CACAUACGAGUAUACUCGUAUUCA
-((((..........((----(((((.(((((.((((((((....))))).))).))))))))))))-..(((((((.....)))))))...))--)).(((((((....)))))))... ( -35.90)
>DroAna_CAF1 37588 101 + 1
UUGUACAC--GGAAGACACAUGGGGUAUGAUGUAUUCGUGUCAGGGCAUGUAAUUCAUCUCGUGUCGCAAAUGAAUGAGCCGUACACAUUUAUU--CA---------GU------AUUCA
((((((((--(((.((.(((((.(..((((.....))))..)....)))))...)).)).))))).)))).((((((((..(....).))))))--))---------..------..... ( -23.00)
>consensus
_UGUACUU__GGGGGUU____AUGGCAUGAUGUAUUCGUGCCAGGGCAUGUAAUUCAUCAGCCGGCG_AGAUGAAUGAGUCGUAUUCAUAUAUA__CA________UAU______AUUCA
..((((................((((((((.....)))))))).(((.....(((((((..........)))))))..)))))))................................... (-19.06 = -18.87 +  -0.19)

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 11:00:07 2006