Locus 4781

Sequence ID 3R_DroMel_CAF1
Location 12,512,973 – 12,513,102
Length 129
Max. P 0.984072
window7841 window7842 window7843

overview

Window 1

Location 12,512,973 – 12,513,066
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.47
Mean single sequence MFE -30.48
Consensus MFE -22.89
Energy contribution -21.83
Covariance contribution -1.05
Combinations/Pair 1.21
Mean z-score -2.10
Structure conservation index 0.75
SVM decision value 1.96
SVM RNA-class probability 0.984072
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12512973 93 + 27905053
UACCUUUUCUGUUGUUCCCGU----------UUUGGCCUUAACUCCAUCUU-----------------GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGGACUGC
..........((.((((((..----------(((((((............(-----------------((((...)))))(((((((.......)))))))...))))))))))))).)) ( -25.10)
>DroPse_CAF1 97 104 + 1
---GUUUUC---UGUUCCCAU----------UUUGGCUGUGUCUCCAUCUUGGCCAAUGCAUUGGUCGGCGACAUUUGCGAGCGAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGAGCUGC
---......---.((((((..----------((((((((((((.((.....((((((....)))))))).)))))..((.(((((((.......))))))))).)))))))))))))... ( -35.80)
>DroSec_CAF1 2069 93 + 1
UACCUUUUCUGUUGUUCCCGU----------UUUGGCCUUAACUCCAUCUU-----------------GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGGACUGC
..........((.((((((..----------(((((((............(-----------------((((...)))))(((((((.......)))))))...))))))))))))).)) ( -25.10)
>DroSim_CAF1 2134 93 + 1
UACCUUUUCUGUUGUUCCCGU----------UUUGGCCUUAACUCCAUCUU-----------------GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGGACUGC
..........((.((((((..----------(((((((............(-----------------((((...)))))(((((((.......)))))))...))))))))))))).)) ( -25.10)
>DroAna_CAF1 3625 93 + 1
---C--CGAUGUUGUUCCCGUUUUUGGCCGUUUUGGCCAUU-----GGCCG-----------------GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCGGAGGGAACUGC
---.--....((.((((((.....(((((.....)))))((-----(((((-----------------(((.(....)).(((((((.......)))))))))))))))).)))))).)) ( -36.00)
>DroPer_CAF1 3909 104 + 1
---GUUUUC---UGUUCCCAU----------UUUGGCUGUGUCUCCAUCUUGGCCAAUGCAUUGGUCGGCGACAUUUGCGAGCGAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGAGCUGC
---......---.((((((..----------((((((((((((.((.....((((((....)))))))).)))))..((.(((((((.......))))))))).)))))))))))))... ( -35.80)
>consensus
___CUUUUCUGUUGUUCCCGU__________UUUGGCCUUAACUCCAUCUU_________________GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGAACUGC
.............((((((............(((((((..............................((((...)))).(((((((.......)))))))...)))))))))))))... (-22.89 = -21.83 +  -1.05)

alignment

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secondary structure

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Window 2

Location 12,513,003 – 12,513,102
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.56
Mean single sequence MFE -33.37
Consensus MFE -27.53
Energy contribution -26.83
Covariance contribution -0.69
Combinations/Pair 1.10
Mean z-score -2.04
Structure conservation index 0.82
SVM decision value 0.60
SVM RNA-class probability 0.795738
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12513003 99 + 27905053
AACUCCAUCUU-----------------GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGGACUGCGACAGGUUUUUGUCGCAUUUAUCAUCGCAUCAGCAA----
..((((.(((.-----------------..(((....((.(((((((.......)))))))))..))))))))))..((((((((....)))))))).........((....))..---- ( -28.90)
>DroPse_CAF1 121 116 + 1
GUCUCCAUCUUGGCCAAUGCAUUGGUCGGCGACAUUUGCGAGCGAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGAGCUGCGACAGGUUUUUGUCGCAUUUAUCAUCGCAUCAGCGA----
(.((((.(((.(((((.((((...(((...)))...))))(((((((.......)))))))..)))))))).)))))((((((((....)))))))).......((((....))))---- ( -40.10)
>DroSec_CAF1 2099 99 + 1
AACUCCAUCUU-----------------GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGGACUGCGACAGGUUUUUGUCGCAUUUAUCAUCGCAUCAGCAA----
..((((.(((.-----------------..(((....((.(((((((.......)))))))))..))))))))))..((((((((....)))))))).........((....))..---- ( -28.90)
>DroSim_CAF1 2164 99 + 1
AACUCCAUCUU-----------------GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGGACUGCGACAGGUUUUUGUCGCAUUUAUCAUCGCAUCAGCAA----
..((((.(((.-----------------..(((....((.(((((((.......)))))))))..))))))))))..((((((((....)))))))).........((....))..---- ( -28.90)
>DroAna_CAF1 3660 98 + 1
U-----GGCCG-----------------GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCGGAGGGAACUGCGACAGGUUUUUGUCGCAUUUAUCAUCGCAUCAGCAAAGGC
.-----.(((.-----------------((((...)))).(((((((.......)))))))((((((((..(..((.((((((((....)))))))).))..)..)).))))))...))) ( -33.30)
>DroPer_CAF1 3933 116 + 1
GUCUCCAUCUUGGCCAAUGCAUUGGUCGGCGACAUUUGCGAGCGAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGAGCUGCGACAGGUUUUUGUCGCAUUUAUCAUCGCAUCAGCGA----
(.((((.(((.(((((.((((...(((...)))...))))(((((((.......)))))))..)))))))).)))))((((((((....)))))))).......((((....))))---- ( -40.10)
>consensus
AACUCCAUCUU_________________GCGACAUUUGCGAGCAAAUAAAUUCAAUUUGCUGCUGGUCAGAGGGAACUGCGACAGGUUUUUGUCGCAUUUAUCAUCGCAUCAGCAA____
............................((((...)))).(((((((.......)))))))((((((..(((..((.((((((((....)))))))).))..).))..))))))...... (-27.53 = -26.83 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,513,003 – 12,513,102
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.56
Mean single sequence MFE -31.02
Consensus MFE -24.02
Energy contribution -24.13
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.12
Structure conservation index 0.77
SVM decision value 0.34
SVM RNA-class probability 0.697684
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12513003 99 - 27905053
----UUGCUGAUGCGAUGAUAAAUGCGACAAAAACCUGUCGCAGUCCCCUCUGACCAGCAGCAAAUUGAAUUUAUUUGCUCGCAAAUGUCGC-----------------AAGAUGGAGUU
----((((....)))).......(((((((......))))))).....((((.....(((((((((.......))))))).))....(((..-----------------..))))))).. ( -29.00)
>DroPse_CAF1 121 116 - 1
----UCGCUGAUGCGAUGAUAAAUGCGACAAAAACCUGUCGCAGCUCCCUCUGACCAGCAGCAAAUUGAAUUUAUUCGCUCGCAAAUGUCGCCGACCAAUGCAUUGGCCAAGAUGGAGAC
----((((....)))).......(((((((......))))))).((((.((((((..(((((.(((.......))).))).))....)))(((((........)))))..))).)))).. ( -34.70)
>DroSec_CAF1 2099 99 - 1
----UUGCUGAUGCGAUGAUAAAUGCGACAAAAACCUGUCGCAGUCCCCUCUGACCAGCAGCAAAUUGAAUUUAUUUGCUCGCAAAUGUCGC-----------------AAGAUGGAGUU
----((((....)))).......(((((((......))))))).....((((.....(((((((((.......))))))).))....(((..-----------------..))))))).. ( -29.00)
>DroSim_CAF1 2164 99 - 1
----UUGCUGAUGCGAUGAUAAAUGCGACAAAAACCUGUCGCAGUCCCCUCUGACCAGCAGCAAAUUGAAUUUAUUUGCUCGCAAAUGUCGC-----------------AAGAUGGAGUU
----((((....)))).......(((((((......))))))).....((((.....(((((((((.......))))))).))....(((..-----------------..))))))).. ( -29.00)
>DroAna_CAF1 3660 98 - 1
GCCUUUGCUGAUGCGAUGAUAAAUGCGACAAAAACCUGUCGCAGUUCCCUCCGACCAGCAGCAAAUUGAAUUUAUUUGCUCGCAAAUGUCGC-----------------CGGCC-----A
(((.((((....))))........((((((.......((((.((....)).))))..(((((((((.......))))))).))...))))))-----------------.))).-----. ( -29.70)
>DroPer_CAF1 3933 116 - 1
----UCGCUGAUGCGAUGAUAAAUGCGACAAAAACCUGUCGCAGCUCCCUCUGACCAGCAGCAAAUUGAAUUUAUUCGCUCGCAAAUGUCGCCGACCAAUGCAUUGGCCAAGAUGGAGAC
----((((....)))).......(((((((......))))))).((((.((((((..(((((.(((.......))).))).))....)))(((((........)))))..))).)))).. ( -34.70)
>consensus
____UUGCUGAUGCGAUGAUAAAUGCGACAAAAACCUGUCGCAGUCCCCUCUGACCAGCAGCAAAUUGAAUUUAUUUGCUCGCAAAUGUCGC_________________AAGAUGGAGUU
....((((....)))).((((..(((((((......)))))))..............(((((((((.......))))))).))...)))).............................. (-24.02 = -24.13 +   0.11)

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 11:38:44 2006