Locus 5204

Sequence ID 3L_DroMel_CAF1
Location 14,354,808 – 14,354,940
Length 132
Max. P 0.671206
window8234 window8235

overview

Window 4

Location 14,354,808 – 14,354,908
Length 100
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 81.84
Mean single sequence MFE -22.35
Consensus MFE -16.84
Energy contribution -17.15
Covariance contribution 0.31
Combinations/Pair 1.12
Mean z-score -1.31
Structure conservation index 0.75
SVM decision value 0.06
SVM RNA-class probability 0.562771
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14354808 100 - 23771897
AGAAAAGUGCGCCAACUUUUCGCCUGAAUUGGCAACGCUUACU-----------CCACCCAACUUCCACUU-UCC--CCUAUUGGCUGCACUUUUG-CCAGGAGUCUUUUACACG
.(((((((......)))))))(((......))).......(((-----------((...............-...--((....))..(((....))-)..))))).......... ( -21.00)
>DroSec_CAF1 179325 100 - 1
AGAAAAGUGCGCCAACUUUUCGCCUGAAUUGGCAACGCUUACU-----------CCACCCAACUUCCACUU-UCC--CCUAUUGGCUGCACUUUUG-CCAGGAGUCUUUUACACG
.(((((((......)))))))(((......))).......(((-----------((...............-...--((....))..(((....))-)..))))).......... ( -21.00)
>DroEre_CAF1 177907 100 - 1
AGAAAAGUGCGCCAACUUUUCGCCUGAAUUGGCAACGCUUACU-----------CCACCCAACUUCCACUU-UCC--CCCAUUGGCUGCACUUUUG-CCAGGAGUAUUUUACACG
.(((((((......)))))))(((......)))......((((-----------((..((((.........-...--....))))..(((....))-)..))))))......... ( -22.49)
>DroYak_CAF1 185458 100 - 1
AGGAAAGUGCGCCAACUUUUCGCCUGAAUUGGCAACGCUUACU-----------CCACCCGACUUCCACUU-UCC--CCCAUUGGCUGCACUUUUG-CCAGGAGUCCUUUACACG
.((((((((.(((((.(((......))))))))..)))))..)-----------))....((((((.....-...--.....((((.........)-)))))))))......... ( -22.31)
>DroAna_CAF1 170953 93 - 1
AGAAAAGUGCGCCAACUUUUCGCUUGAAUUGGCAACGCUUACA-----------CC--------UCCACAUCGUC--CCCAUUGGCUGCACUUUUCCCCAGGAAACUUUUACAC-
.((((((((((((((...(((....))).(((..(((......-----------..--------.......))).--.)))))))).)))))))))...((....)).......- ( -23.26)
>DroPer_CAF1 189952 112 - 1
GGAAAAGUGCGCCAACUUUUCGCUCGAAUUGGCAACGCUUACACCUCGCUCCGUCCUCCCACCAUCCACCA-UCCACCGCAGUGGCUGCAAU-CUG-CCAGGAUCCGGACCCCCG
((..(((((.(((((...(((....))))))))..))))).........((((((((..((........((-.((((....)))).))....-.))-..))))..))))...)). ( -24.02)
>consensus
AGAAAAGUGCGCCAACUUUUCGCCUGAAUUGGCAACGCUUACU___________CCACCCAACUUCCACUU_UCC__CCCAUUGGCUGCACUUUUG_CCAGGAGUCUUUUACACG
..(((((((((((((......(((......)))...(....).......................................))))).)))))))).................... (-16.84 = -17.15 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 14,354,842 – 14,354,940
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.87
Mean single sequence MFE -22.07
Consensus MFE -16.00
Energy contribution -15.62
Covariance contribution -0.39
Combinations/Pair 1.19
Mean z-score -1.19
Structure conservation index 0.73
SVM decision value 0.29
SVM RNA-class probability 0.671206
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14354842 98 - 23771897
---GGCACGUCUUUUC-----CUCUUUUUUGGUCGGAAAUAGAAAAGUGCGCCAACUUUUCGCCUGAAUUGGCAACGCUUACU-----------CCACCCAACUUCCACUU-UCC--CCU
---.............-----.......((((..(((....(((((((......)))))))(((......))).........)-----------))..)))).........-...--... ( -20.10)
>DroPse_CAF1 175566 116 - 1
---GGCACGUCUUCCCUGUCUUUAUUUUUUGGUCGGAAAUGGAAAAGUGCGCCAACUUUUCGCUCGAAUUGGCAACGCUUACACCUCGCUCCGUCCUCCCACCAUCCACCA-UCCACCGC
---((((.(.....).)))).........((((.(((.(((((...((..(((((...(((....)))))))).))((.........)))))))..))).)))).......-........ ( -23.00)
>DroEre_CAF1 177941 97 - 1
----GCACGUCUUUUC-----CUCCUUUUUGGUCGGAAAUAGAAAAGUGCGCCAACUUUUCGCCUGAAUUGGCAACGCUUACU-----------CCACCCAACUUCCACUU-UCC--CCC
----((((.(((((((-----(.((.....))..))))).)))...))))(((((.(((......))))))))..........-----------.................-...--... ( -21.90)
>DroYak_CAF1 185492 101 - 1
GUGGGCACGUCUUUUC-----CUCUUUUUUGGUCGGAAAUAGGAAAGUGCGCCAACUUUUCGCCUGAAUUGGCAACGCUUACU-----------CCACCCGACUUCCACUU-UCC--CCC
(((((...........-----.........((((((.....(((((((......)))))))(((......)))..........-----------....)))))))))))..-...--... ( -24.95)
>DroAna_CAF1 170987 91 - 1
---GGCACGUCUUUUC-----CUCUUUUUUGGUCGGAAAUAGAAAAGUGCGCCAACUUUUCGCUUGAAUUGGCAACGCUUACA-----------CC--------UCCACAUCGUC--CCC
---.((((.(((((((-----(.((.....))..))))).)))...))))(((((.(((......))))))))..........-----------..--------...........--... ( -19.50)
>DroPer_CAF1 189985 116 - 1
---GGCACGUCUUCCCUGUCUUUAUUUUUUGGUCGGAAAUGGAAAAGUGCGCCAACUUUUCGCUCGAAUUGGCAACGCUUACACCUCGCUCCGUCCUCCCACCAUCCACCA-UCCACCGC
---((((.(.....).)))).........((((.(((.(((((...((..(((((...(((....)))))))).))((.........)))))))..))).)))).......-........ ( -23.00)
>consensus
___GGCACGUCUUUUC_____CUCUUUUUUGGUCGGAAAUAGAAAAGUGCGCCAACUUUUCGCCUGAAUUGGCAACGCUUACA___________CCACCCAACUUCCACUU_UCC__CCC
..............................(((.(((....(((((((......)))))))(((......)))...............................)))))).......... (-16.00 = -15.62 +  -0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:27 2006