Locus 2879

Sequence ID	X_DroMel_CAF1
Location	7,702,833 – 7,702,979
Length	146
Max. P	0.974068

overview

Window 9

Location	7,702,833 – 7,702,939
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.26
Mean single sequence MFE	-25.57
Consensus MFE	-16.72
Energy contribution	-17.41
Covariance contribution	0.69
Combinations/Pair	1.12
Mean z-score	-1.60
Structure conservation index	0.65
SVM decision value	0.01
SVM RNA-class probability	0.536988
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7702833 106 - 22224390
GACGCACUCAAGUGUCUAAAA----------ACGAGUAUGUCAUAAGCUCACAUUUGUACAGCUGAGGUCAAAAUGGUAGCAAUUAU----UUGCAAUUAUUUGAAAACAAUAUCAGUAG
(((((......))))).....----------..((((.........))))...........(((((.((..(((((((.((((....----)))).)))))))....))....))))).. ( -22.20)
>DroSec_CAF1 812 115 - 1
GACGCACUCAAGUGUCUAAAAAUUCCAAAGAACGAGUGUGUCAUAAGCUCACAGUUGCACAGCUGAGGUCAAAAUGGUAGCAAUUGU----UUGCAAUUAUUUGAAAACAAUAUCAG-AA
(((((((((.....(((...........)))..)))))))))....((..((((((((.((..((....))...))...))))))))----..)).....(((((........))))-). ( -29.10)
>DroSim_CAF1 8982 115 - 1
GACGCACUCAAGUGUCUAAAAAUUCCAAAGAACGAGUGUGUCAUAAGCUCACAGUUGCACAGCUGAGGUCAAAAUGGUAGCAAUUGU----UUGCAAUUAUUUGAAAACAAUAUUAG-AA
(((((((((.....(((...........)))..)))))))))....((..((((((((.((..((....))...))...))))))))----..))......................-.. ( -27.40)
>DroYak_CAF1 1626 119 - 1
GACGCACUCAAGUGUUUAAAAAUUCCACAGAACGAGUGUGUCAUAAGCUCGCAGUCGCACAGUUGCGGUCAAAAAAGUAGCAUACAUGGCAUUUUAUUUAUUUGAAAUCAAUAUCGG-AA
(((((((((..(((...........))).....)))))))))......((((((.(.....)))))))(((((.(((((((.......))....))))).)))))............-.. ( -23.60)
>consensus
GACGCACUCAAGUGUCUAAAAAUUCCAAAGAACGAGUGUGUCAUAAGCUCACAGUUGCACAGCUGAGGUCAAAAUGGUAGCAAUUAU____UUGCAAUUAUUUGAAAACAAUAUCAG_AA
(((((((((........................)))))))))....((........)).....((...(((((.((((.((((........)))).)))))))))...)).......... (-16.72 = -17.41 +   0.69)

alignment

secondary structure

dotplot

Window 0

Location	7,702,869 – 7,702,979
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.94
Mean single sequence MFE	-38.25
Consensus MFE	-30.27
Energy contribution	-30.90
Covariance contribution	0.63
Combinations/Pair	1.17
Mean z-score	-2.63
Structure conservation index	0.79
SVM decision value	1.72
SVM RNA-class probability	0.974068
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7702869 110 + 22224390
CUACCAUUUUGACCUCAGCUGUACAAAUGUGAGCUUAUGACAUACUCGU----------UUUUAGACACUUGAGUGCGUCAGGAGUUCAACGGGUGUGAUUCUAUGUGGCAAAGUGUAUU
....(((((((.((.((....((((..(((((((((.((((.((((((.----------...........)))))).)))).)))))).)))..))))......)).))))))))).... ( -34.70)
>DroSec_CAF1 847 120 + 1
CUACCAUUUUGACCUCAGCUGUGCAACUGUGAGCUUAUGACACACUCGUUCUUUGGAAUUUUUAGACACUUGAGUGCGUCAGGAGUUCAACGGGUGUGAUGCUAUGUGGCAAAGUGUAUU
....(((((((.((.((((...(((.((((((((((.((((.((((((...((((((...))))))....)))))).)))).)))))).)))).)))...))..)).))))))))).... ( -39.40)
>DroSim_CAF1 9017 120 + 1
CUACCAUUUUGACCUCAGCUGUGCAACUGUGAGCUUAUGACACACUCGUUCUUUGGAAUUUUUAGACACUUGAGUGCGUCAGGAGUUCAACGGGUGUGAUGCUAUGUGGCAAAGUGUAUU
....(((((((.((.((((...(((.((((((((((.((((.((((((...((((((...))))))....)))))).)))).)))))).)))).)))...))..)).))))))))).... ( -39.40)
>DroYak_CAF1 1665 120 + 1
CUACUUUUUUGACCGCAACUGUGCGACUGCGAGCUUAUGACACACUCGUUCUGUGGAAUUUUUAAACACUUGAGUGCGUCAGAAGUUCAUGGGGUGCCAUAGUUUGUGGAAAUGUGUAUU
............(((((((((((((.((..((((((.((((.((((((....(((...........))).)))))).)))).))))))..))..)).))))).))))))........... ( -39.50)
>consensus
CUACCAUUUUGACCUCAGCUGUGCAACUGUGAGCUUAUGACACACUCGUUCUUUGGAAUUUUUAGACACUUGAGUGCGUCAGGAGUUCAACGGGUGUGAUGCUAUGUGGCAAAGUGUAUU
....(((((((.((.((....((((.((((((((((.((((.((((((......................)))))).)))).)))))).)))).))))......)).))))))))).... (-30.27 = -30.90 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:41 2006