Locus 6759

Sequence ID	3R_DroMel_CAF1
Location	17,823,757 – 17,823,849
Length	92
Max. P	0.904661

overview

Window 7

Location	17,823,757 – 17,823,849
Length	92
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	79.95
Mean single sequence MFE	-37.14
Consensus MFE	-26.43
Energy contribution	-25.88
Covariance contribution	-0.55
Combinations/Pair	1.20
Mean z-score	-2.04
Structure conservation index	0.71
SVM decision value	1.04
SVM RNA-class probability	0.904661
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17823757 92 + 27905053
GGCAACGAU-------------GGCGGCUGCCACUUGAGCCGCAA-AGCACGAGUCCUCGUCUAUUGUCUAAAGCAUGGCCAAGUGUUUGUUAGCAGCCGCCAUCG---
(....)(((-------------(((((((((((((((.(((((((-((.((((....)))))).)))).........))))))))).......)))))))))))).--- ( -43.61)
>DroVir_CAF1 120016 92 + 1
AGCGUUGAC---------GG-CUGUGGCUGCCACUUGAGCCGCAA-AACACGAGUCCUUGUCUAUUGUCUAAAGCAUGGCCAAGUGUUUGUUAGCAGUUGCUG------
(((...(((---------.(-((((((((........))))))..-...(((((..((((.((((.((.....)))))).))))..))))).))).)))))).------ ( -26.10)
>DroPse_CAF1 120139 109 + 1
GGCAACGACAACCGCGGCGGUCGGUGGCUGCCACUUGAGCCGCAACAGCGCCAGUCCUUGUCUAUUGUCUAAAGCAUGGCCAAGUGUUUGUUAGCAGCCGCCAUCGCCG
(....)........(((((((.(((((((((((((((.(((((((..((....))..))))....(((.....))).))))))))).......)))))))))))))))) ( -45.51)
>DroWil_CAF1 143410 86 + 1
GGCAACGAC-------------UGCGGCUGCCACUUGAGCCGCAA-A-CACGAGUCCUUGUCUAUUGUCUAAAGCAUGGCCAAGUGUUUGUUAGCAGCCGC--------
(....)...-------------.((((((((((((((.((((...-.-.((((....))))....(((.....))))))))))))).......))))))))-------- ( -29.11)
>DroMoj_CAF1 137925 91 + 1
------GGC---------UG-CUGUGGCUGCCACUUGAGCCGCAA-AACACGAGUCCUUGUCUAUUGUCUAAAGCAUGGCCAAGUGUUUGUUAGCAGCUGCUGCUGCC-
------(((---------.(-(.(..(((((((((((.(((((((-.(.((((....)))).).)))).........))))))))).......)))))..).)).)))- ( -33.01)
>DroPer_CAF1 119552 109 + 1
GGCAACGACAACCGCGGCGGUCGGUGGCUGCCACUUGAGCCGCAACAGCGCCAGUCCUUGUCUAUUGUCUAAAGCAUGGCCAAGUGUUUGUUAGCAGCCGCCAUCGCCG
(....)........(((((((.(((((((((((((((.(((((((..((....))..))))....(((.....))).))))))))).......)))))))))))))))) ( -45.51)
>consensus
GGCAACGAC_________GG_CGGUGGCUGCCACUUGAGCCGCAA_AGCACGAGUCCUUGUCUAUUGUCUAAAGCAUGGCCAAGUGUUUGUUAGCAGCCGCCAUCG___
.......................((((((((((((((.(((((((....((((....))))...)))).........))))))))).......))))))))........ (-26.43 = -25.88 +  -0.55)

alignment

secondary structure

dotplot

Window 8

Location	17,823,757 – 17,823,849
Length	92
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	79.95
Mean single sequence MFE	-36.32
Consensus MFE	-21.89
Energy contribution	-22.03
Covariance contribution	0.14
Combinations/Pair	1.09
Mean z-score	-2.01
Structure conservation index	0.60
SVM decision value	0.60
SVM RNA-class probability	0.795013
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17823757 92 - 27905053
---CGAUGGCGGCUGCUAACAAACACUUGGCCAUGCUUUAGACAAUAGACGAGGACUCGUGCU-UUGCGGCUCAAGUGGCAGCCGCC-------------AUCGUUGCC
---(((((((((((((.......(((((((((................((((....))))((.-..))))).)))))))))))))))-------------))))..... ( -43.01)
>DroVir_CAF1 120016 92 - 1
------CAGCAACUGCUAACAAACACUUGGCCAUGCUUUAGACAAUAGACAAGGACUCGUGUU-UUGCGGCUCAAGUGGCAGCCACAG-CC---------GUCAACGCU
------.(((..........((((((..(.((.((.((((.....)))))).)).)..)))))-).((((((...((((...))))))-))---------))....))) ( -23.10)
>DroPse_CAF1 120139 109 - 1
CGGCGAUGGCGGCUGCUAACAAACACUUGGCCAUGCUUUAGACAAUAGACAAGGACUGGCGCUGUUGCGGCUCAAGUGGCAGCCACCGACCGCCGCGGUUGUCGUUGCC
.(((((((((((((((.......(((((((((..((..(((....(((.......)))...)))..))))).))))))))))))...(((((...)))))))))))))) ( -45.61)
>DroWil_CAF1 143410 86 - 1
--------GCGGCUGCUAACAAACACUUGGCCAUGCUUUAGACAAUAGACAAGGACUCGUG-U-UUGCGGCUCAAGUGGCAGCCGCA-------------GUCGUUGCC
--------((((((((.......(((((((((..((...(((((...((.......)).))-)-))))))).)))))))))))))).-------------......... ( -31.41)
>DroMoj_CAF1 137925 91 - 1
-GGCAGCAGCAGCUGCUAACAAACACUUGGCCAUGCUUUAGACAAUAGACAAGGACUCGUGUU-UUGCGGCUCAAGUGGCAGCCACAG-CA---------GCC------
-(((.((.(..(((((.......(((((((((..((...(((((...((.......)).))))-).))))).)))))))))))..).)-).---------)))------ ( -29.21)
>DroPer_CAF1 119552 109 - 1
CGGCGAUGGCGGCUGCUAACAAACACUUGGCCAUGCUUUAGACAAUAGACAAGGACUGGCGCUGUUGCGGCUCAAGUGGCAGCCACCGACCGCCGCGGUUGUCGUUGCC
.(((((((((((((((.......(((((((((..((..(((....(((.......)))...)))..))))).))))))))))))...(((((...)))))))))))))) ( -45.61)
>consensus
___CGAUGGCGGCUGCUAACAAACACUUGGCCAUGCUUUAGACAAUAGACAAGGACUCGUGCU_UUGCGGCUCAAGUGGCAGCCACAG_CC_________GUCGUUGCC
..........((((((.......(((((((((.((.((((.....)))))).......((......))))).))))))))))))......................... (-21.89 = -22.03 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:16 2006