Locus 6498

Sequence ID	3R_DroMel_CAF1
Location	17,115,476 – 17,115,606
Length	130
Max. P	0.946998

overview

Window 9

Location	17,115,476 – 17,115,584
Length	108
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	89.10
Mean single sequence MFE	-26.80
Consensus MFE	-22.56
Energy contribution	-23.57
Covariance contribution	1.01
Combinations/Pair	1.08
Mean z-score	-3.03
Structure conservation index	0.84
SVM decision value	1.37
SVM RNA-class probability	0.946998
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17115476 108 - 27905053
GUACGCUGGCAAAAUAAGAGUUGUCAACAUACUCGUAAAACAAUAUGUUCGAUUAAUAGGAAAUAGUUUAACAAAUUGUGUUACUACAUUUCUUUGCCACAAGUAUAU
((((..(((((((....((((((....)).))))((((.(((((.((((.(((((........))))).)))).))))).))))........)))))))...)))).. ( -27.40)
>DroSec_CAF1 27769 105 - 1
GUACACUGGCAAA---AGAGUUGUCAACAUGCUCGUAAAACAACAUGUUGGAUUAUUAGGAAAUAAUUUAACAAAUUGUGUUGCUACCUUGUCUUGCCACAAGUAUAU
((((..((((((.---.((((((....)).))))((((.((((..((((((((((((....))))))))))))..)))).)))).........))))))...)))).. ( -28.90)
>DroSim_CAF1 26751 105 - 1
GUACACUGGCAAA---AGAGUUGUCAACAUGCUCGUAAAACAACAUGUUGGAUUAUUAGGAAAUAGUUUAACAAAUGGUGUUGAUACAUUCCCUUGACACAAGUAUAU
((((..((.(((.---.(((((((((((((....((......)).((((((((((((....))))))))))))....))))))))).))))..))).))...)))).. ( -24.10)
>consensus
GUACACUGGCAAA___AGAGUUGUCAACAUGCUCGUAAAACAACAUGUUGGAUUAUUAGGAAAUAGUUUAACAAAUUGUGUUGCUACAUUCCCUUGCCACAAGUAUAU
((((..((((((.....((((((....)).))))((((.((((..((((((((((((....))))))))))))..)))).)))).........))))))...)))).. (-22.56 = -23.57 +   1.01)

alignment

secondary structure

dotplot

Window 0

Location	17,115,511 – 17,115,606
Length	95
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	82.89
Mean single sequence MFE	-17.72
Consensus MFE	-11.96
Energy contribution	-13.02
Covariance contribution	1.06
Combinations/Pair	1.11
Mean z-score	-1.66
Structure conservation index	0.67
SVM decision value	0.15
SVM RNA-class probability	0.606756
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17115511 95 + 27905053
--UGUUAAACUAUUUCCUAUUAAUCGAACAUAUUGUUUUACGAGUAUGUUGACAACUCUUAUUUUGCCAGCGUACUCGCUGUAUAGCAACAAGAAAA
--(((((.((...............((((.....))))..(((((((((((.(((........))).)))))))))))..)).)))))......... ( -20.90)
>DroSec_CAF1 27804 92 + 1
--UGUUAAAUUAUUUCCUAAUAAUCCAACAUGUUGUUUUACGAGCAUGUUGACAACUCU---UUUGCCAGUGUACUCGCUGUAUAGCAACAAGAAAA
--.(((..((((((....)))))).(((((((((........)))))))))..)))(((---((((((((((....)))))....)))).))))... ( -20.40)
>DroSim_CAF1 26786 92 + 1
--UGUUAAACUAUUUCCUAAUAAUCCAACAUGUUGUUUUACGAGCAUGUUGACAACUCU---UUUGCCAGUGUACUCGCUGUAUAGCAACAAGAAAA
--.......................(((((((((........))))))))).....(((---((((((((((....)))))....)))).))))... ( -19.80)
>DroEre_CAF1 27938 81 + 1
UUUAUUCAACU-----CAAAUAAUUCAACAUUUUGUUUUGCG---CUAUUGAAA----U---UUUGCCAGUGUAC-CGCUGUAUAGCAACAAGAAAA
...........-----..............((((((..((((---(........----.---...))(((((...-)))))....)))))))))... (  -9.80)
>consensus
__UGUUAAACUAUUUCCUAAUAAUCCAACAUGUUGUUUUACGAGCAUGUUGACAACUCU___UUUGCCAGUGUACUCGCUGUAUAGCAACAAGAAAA
.........................(((((((((........)))))))))............(((((((((....)))))....))))........ (-11.96 = -13.02 +   1.06)

alignment

secondary structure

dotplot

Window 1

Location	17,115,511 – 17,115,606
Length	95
Sequences	4
Columns	97
Reading direction	reverse
Mean pairwise identity	82.89
Mean single sequence MFE	-19.78
Consensus MFE	-14.81
Energy contribution	-16.87
Covariance contribution	2.06
Combinations/Pair	1.20
Mean z-score	-1.79
Structure conservation index	0.75
SVM decision value	0.55
SVM RNA-class probability	0.777359
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17115511 95 - 27905053
UUUUCUUGUUGCUAUACAGCGAGUACGCUGGCAAAAUAAGAGUUGUCAACAUACUCGUAAAACAAUAUGUUCGAUUAAUAGGAAAUAGUUUAACA--
.((((((((((.......(((((((.(.((((((........)))))).).)))))))..(((.....)))....))))))))))..........-- ( -21.30)
>DroSec_CAF1 27804 92 - 1
UUUUCUUGUUGCUAUACAGCGAGUACACUGGCAAA---AGAGUUGUCAACAUGCUCGUAAAACAACAUGUUGGAUUAUUAGGAAAUAAUUUAACA--
......(((((.......(((((((...((((((.---....))))))...)))))))....)))))((((((((((((....))))))))))))-- ( -24.10)
>DroSim_CAF1 26786 92 - 1
UUUUCUUGUUGCUAUACAGCGAGUACACUGGCAAA---AGAGUUGUCAACAUGCUCGUAAAACAACAUGUUGGAUUAUUAGGAAAUAGUUUAACA--
......(((((.......(((((((...((((((.---....))))))...)))))))....)))))((((((((((((....))))))))))))-- ( -24.10)
>DroEre_CAF1 27938 81 - 1
UUUUCUUGUUGCUAUACAGCG-GUACACUGGCAAA---A----UUUCAAUAG---CGCAAAACAAAAUGUUGAAUUAUUUG-----AGUUGAAUAAA
........(((((((((....-)))...)))))).---.----.(((((((.---............)))))))((((((.-----....)))))). (  -9.62)
>consensus
UUUUCUUGUUGCUAUACAGCGAGUACACUGGCAAA___AGAGUUGUCAACAUGCUCGUAAAACAACAUGUUGGAUUAUUAGGAAAUAGUUUAACA__
......(((((.......(((((((...((((((........))))))...)))))))....)))))((((((((((((....)))))))))))).. (-14.81 = -16.87 +   2.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:49 2006