Locus 4613

Sequence ID	3R_DroMel_CAF1
Location	12,128,610 – 12,128,702
Length	92
Max. P	0.991500

overview

Window 3

Location	12,128,610 – 12,128,702
Length	92
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.64
Mean single sequence MFE	-25.00
Consensus MFE	-7.94
Energy contribution	-8.14
Covariance contribution	0.20
Combinations/Pair	1.15
Mean z-score	-2.60
Structure conservation index	0.32
SVM decision value	2.27
SVM RNA-class probability	0.991500
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12128610 92 + 27905053
UUGACUUUUGUUUG------------------------GGAGCCUAAAAAUUAAUAGUUUCAGAGAAAUCCUAAAUUUUCG--CUAGGGGAAAAAUAAAAAGCGAAAAUAUGGAAGUC--
..((((((..((((------------------------(((..((..((((.....))))...))...))))))(((((((--((...............))))))))))..))))))-- ( -20.76)
>DroSec_CAF1 34919 116 + 1
UUGACUUUUGUUUGAGAAUGUUGAGAAUAGAAUAGUCUGGAGACUAAAAAUUAAUAUUUUCAGAGAAAUCCAAAAUUUUCG--CUAGGGGAAAAAUAAAAAGCGAAAAUAUGGAAGUC--
..(((((((.((((((((((((((........(((((....)))))....)))))))))))))).)))((((..(((((((--((...............))))))))).))))))))-- ( -31.66)
>DroSim_CAF1 34667 113 + 1
UUGACUUUUGUUUGAGAAUA---GGACCAACACGACCUGGAGACUAAAAAUUAAUAUUUUCAGAGAAAUCCUAAAUUUUCG--CUAGGGGAAAAAUAAAGAGCGAAAAUAUGGAAGUC--
..(((((((.((((((((((---((.(......).)).(....)..........)))))))))).)))(((...(((((((--((...............)))))))))..)))))))-- ( -24.26)
>DroEre_CAF1 35021 113 + 1
UUGACUUUUAUUUGGGAGUA---UAACCAACGCAA-CUGGAUACUGAAAAUUAAUAUUUUCUGAGAAAUCCUAAAGUUUUACCCUAGGGGGAAAAUGA-AAGCGAAACUAUGGAAGUC--
..(((((((((((((.....---...))))(((..-..((((...((((((....))))))......))))....(((((.(((....))))))))..-..))).....)))))))))-- ( -26.20)
>DroYak_CAF1 39291 113 + 1
UUGACUUUUAUUUGGGUAUA---UAACCAACACAA-CUGGAUACUGAAA--UAAUAUUUUUAGAGAAAUCCUAAAGUUUCGCCCUAGGGGAAAUCUGA-AAGUGAAACUAUGGAAUUAUA
.......((((((.(((((.---...(((......-.)))))))).)))--)))((((((((((....(((((..(.....)..)))))....)))))-)))))................ ( -22.10)
>consensus
UUGACUUUUGUUUGAGAAUA___UAACCAACACAA_CUGGAGACUAAAAAUUAAUAUUUUCAGAGAAAUCCUAAAUUUUCG__CUAGGGGAAAAAUAAAAAGCGAAAAUAUGGAAGUC__
..(((((((((...........................(((..((.(((((....)))))...))...)))...(((((((.....................)))))))))))))))).. ( -7.94 =  -8.14 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	12,128,610 – 12,128,702
Length	92
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.64
Mean single sequence MFE	-19.66
Consensus MFE	-8.22
Energy contribution	-9.30
Covariance contribution	1.08
Combinations/Pair	1.14
Mean z-score	-2.41
Structure conservation index	0.42
SVM decision value	1.77
SVM RNA-class probability	0.976666
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12128610 92 - 27905053
--GACUUCCAUAUUUUCGCUUUUUAUUUUUCCCCUAG--CGAAAAUUUAGGAUUUCUCUGAAACUAUUAAUUUUUAGGCUCC------------------------CAAACAAAAGUCAA
--(((((((..(((((((((...............))--)))))))...)))....(((((((........)))))))....------------------------........)))).. ( -17.76)
>DroSec_CAF1 34919 116 - 1
--GACUUCCAUAUUUUCGCUUUUUAUUUUUCCCCUAG--CGAAAAUUUUGGAUUUCUCUGAAAAUAUUAAUUUUUAGUCUCCAGACUAUUCUAUUCUCAACAUUCUCAAACAAAAGUCAA
--((((((((.(((((((((...............))--)))))))..))))......(((.((((........(((((....)))))...)))).)))...............)))).. ( -21.86)
>DroSim_CAF1 34667 113 - 1
--GACUUCCAUAUUUUCGCUCUUUAUUUUUCCCCUAG--CGAAAAUUUAGGAUUUCUCUGAAAAUAUUAAUUUUUAGUCUCCAGGUCGUGUUGGUCC---UAUUCUCAAACAAAAGUCAA
--(((((....(((((((((...............))--))))))).(((((.....((((((((....))))))))...((((......)))))))---))...........))))).. ( -22.06)
>DroEre_CAF1 35021 113 - 1
--GACUUCCAUAGUUUCGCUU-UCAUUUUCCCCCUAGGGUAAAACUUUAGGAUUUCUCAGAAAAUAUUAAUUUUCAGUAUCCAG-UUGCGUUGGUUA---UACUCCCAAAUAAAAGUCAA
--(((((.........(((..-..........(((((((.....)))))))........((((((....)))))).........-..)))((((...---.....))))....))))).. ( -20.50)
>DroYak_CAF1 39291 113 - 1
UAUAAUUCCAUAGUUUCACUU-UCAGAUUUCCCCUAGGGCGAAACUUUAGGAUUUCUCUAAAAAUAUUA--UUUCAGUAUCCAG-UUGUGUUGGUUA---UAUACCCAAAUAAAAGUCAA
......(((..((((((.(((-(.((.......)))))).))))))...)))..............(((--(((..((((((((-.....))))...---.))))..))))))....... ( -16.10)
>consensus
__GACUUCCAUAUUUUCGCUUUUUAUUUUUCCCCUAG__CGAAAAUUUAGGAUUUCUCUGAAAAUAUUAAUUUUUAGUCUCCAG_UUGUGUUGGUCA___UAUUCCCAAACAAAAGUCAA
..(((((((..(((((((.....................)))))))...))).....((((((((....)))))))).....................................)))).. ( -8.22 =  -9.30 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:40 2006